Benthic macroinvertebrate assemblages of a stream‐lake network in the upper zone of the trans‐Andean basin of the Valdivia River (Chile) - Jacqueline Salvo; Claudio Valdovinos; Pablo Fierro (New Zealand Journal of Marine and Freshwater Research, 2021)
Stream‐lake networks include multiple transition zones between lake‐like and river‐like conditions. This study analysed environmental features, macroinvertebrate assemblages (MIB) and functional feeding groups in outlet, inlet and tributary streams (i.e. streams other than the main stem) of a stream‐lake network in Chilean Andean lakes, to verify if lake outlets reflect an ecotone condition. Permutational analysis of variance and canonical analysis of principal coordinates based on environmental features and MIB revealed a significant difference between stream types. Higher taxa richness was found in tributaries, whereas population densities, equitability and diversity indices varied between stream types. Eighty‐five taxa were identified, with 7% of taxa found exclusively in outlets, 5% in inlets, and 22% in tributaries. Collector‐gatherers were dominant in all stream types and there was no statistical differences among feeding groups and stream types. The distance‐based linear model identified water temperature, % rock, % sand, and % FPOM coverage as having significant influence on richness and density of MIB in summer, while water temperature and %FPOM coverage were significant in spring. Our results suggest that lake outlets house MIB different than lake inlets and tributaries, as well as environmental variables, supporting the idea that Andean lake outlets reflect an ecotone condition.

The magnitude and frequency of storm surge in southern New Zealand - Ryan J. Adam; Michael J. Hilton; Tim Jowett; Wayne J. Stephenson (New Zealand Journal of Marine and Freshwater Research, 2021)
There is currently little understanding regarding storm surge in New Zealand, particularly in the southern region. To date, there has been no attempt to establish the frequency and magnitude of storm surge using observed sea level data on the open coast. The aim of this study is to examine the nature of storm surge in southern New Zealand and explore the influence of the Southern Annular Mode (SAM) and the El Nino Southern Oscillation (ENSO) on the frequency and magnitude of storm surge. Bayesian estimation is used through the ‘extRemes’ package in R to determine the return period for storm surge at three locations around southern New Zealand. The 100‐year return level varied between 0.91 and 1.31 m. In addition, a statistically significant increase (2.88%) in storm surge intensity (SSI) on the south‐east coastline was found. Applying cross‐correlation to assess the response of SSI to ENSO and SAM, returned no detectable relationship, except a weak relationship between SAM and SSI on the south‐east coast where a two‐three month lagged response was present.

New Zealand aquaculture industry: research, opportunities and constraints for integrative multitrophic farming - Jeanette M. E. Stenton‐Dozey; Philip Heath; Jeffrey S. Ren; Leonardo N. Zamora (New Zealand Journal of Marine and Freshwater Research, 2021)
The New Zealand aquaculture industry is based primarily on the production of Greenshell™ mussels, Chinook salmon and Pacific oysters. The industry is primed for development and is anticipating increasing its export earnings to NZ$3 billion by 2035. To achieve this target and retain its ‘clean and green’ image, the industry must be able to demonstrate that its practices are sustainable. Integrated multi‐trophic aquaculture (IMTA) systems provide an avenue to address this challenge, with most of the work in New Zealand focusing on the integration of low trophic level high‐value species such as sea cucumbers and seaweeds with mussels, providing environmental bioremediation and provision of valuable secondary products (nutraceuticals and pharmaceuticals). Ecophysiological, hydrodynamic and benthic diagenesis models have been developed to underpin this IMTA research into sustainable farming designs. However, many regulatory barriers are still in place, which together with the current lack of investment, market security for these new products and associated operational costs form the main constrains to development. Nevertheless, the recent emergence of aquaculture fora where industry, researchers, and regulators meet to discuss future research and development has invigorated interest in diversification of the sector, inclusive of IMTA within existing coastal areas and upcoming land‐based and open‐ocean operations.

Is existing legislation supporting socially acceptable aquaculture in the European Union? A transversal analysis of France, Italy and Spain - Marianna Cavallo; José A. Pérez Agúndez; Pascal Raux; Katia Frangoudes (Reviews in Aquaculture, 2021)
According to the European Commission, aquaculture is among those maritime sectors contributing to the blue economy due to its potential for generating jobs, business opportunities and, most importantly, for ensuring food security in Europe. In 2014, EU member states set new strategies to support sustainable aquaculture and ambitious targets of productions to be met by 2020 in the three segments, marine fish, freshwater fish and shellfish. A recent assessment made by the European Commission concludes that some countries might not be able to attain the established goals and this paper presents an in‐depth analysis of such strategies to identify the social constraints hampering aquaculture growth in France, Italy and Spain as well as the measures established to overcome them. Most of the identified issues are related to the social acceptability of local communities, local stakeholders and consumers, suggesting that this still represents an unsolved issue hampering aquaculture development in Europe. In fact, our results show that (a) the sector suffers from a bad image related to its environmental impacts; (b) a lack of integrated spatial planning is leading to increasing conflicts with other activities; and (c) there is predominance of top‐down consultation mechanisms. It is concluded that there is not a single solution to enhance social acceptability of aquaculture since this depends on a number of social, economic and environmental factors that may differ from site to site, and countries need to adopt a more integrated approach where concerns of local communities and stakeholders are understood and taken into account.

Freshwater pearl culture in Mexico: historic context, present status and future perspectives - Pedro E. Saucedo; Héctor Acosta‐Salmón; Douglas McLaurin‐Moreno; Alfonso Castillo‐Domínguez; Carolina E. Melgar‐Valdés; José M. Mazón‐Suástegui (Reviews in Aquaculture, 2021)
We revise the historic context of freshwater pearl culture in Asia, updating the present situation and perspectives of this activity in Mexico, and, possibly, in some Latin American countries. The review is based on the results of ten years of research conducted in southeast Mexico (state of Tabasco) to firstly determine the demography of freshwater mussel stocks and, based on this information, identify a target species with a higher potential for pearl farming: the fatmucket mussel Psoronaias crocodilorum . The main advances relative to the seeding technique for keshi pearl production and composite technique for half‐pearl (mabe) production are detailed and placed under perspective with China, as today's greatest producer of freshwater pearls. After ten years, several cohorts of keshi and mabe pearls have been produced, representing the first of their kind in Latin America. Although the yield and quality of these pearls has gradually been improved, some aspects of the keshi technique (preparation and seeding of the donor's mantle into the host's mantle) still require further optimisation. To promote social development, one of the goals of the project included the involvement of local communities in the manufacture and selling of handcrafts made from the shell. The other goal was to share the main outcomes derived from the keshi and mabe techniques with academics, producers, and government authorities through a series of training workshops aimed to create awareness in the local communities for the potential of freshwater pearl culture in Tabasco as an aquaculture‐based, environmentally friendly and viable model for socioeconomic development.

Organic aquaponics in the European Union: towards sustainable farming practices in the framework of the new EU regulation - Lorenzo Fruscella; Benz Kotzen; Sarah Milliken (Reviews in Aquaculture, 2021)
Under the new Commission Regulation (EU) 2018/848 which will enter into law in January 2022, aquaponic produce cannot be certified as organic in the European Union. Given the multiple components of an aquaponic system, which involve growing plants in hydroponic conditions, recycling of fish waste and raising fish in artificial conditions, the achievement of organic certification for aquaponic produce is a complex matter dictated by many parameters. Although in theory and in practice aquaponics fulfils nearly all organic farming principles, rules such as the need for crops to be cultivated in soil and the ban on using recirculating aquaculture systems currently prevent aquaponic produce from achieving organic certification. This review examines these rules in the new regulation on horticulture and aquaculture. The rules are evaluated, their foundations discussed, and suggestions are made on the type of system modifications that could potentially make it possible for aquaponic produce to be certified as organic. Suggested modifications include the use of soil in the hydroponic section and the implementation of environmental enrichment for improving the fish welfare in the aquaculture section. Several EU policies and strategies that support the development of aquaponics are also discussed, and potential policies for the development of organic aquaponics are formulated.

The redclaw crayfish: A prominent aquaculture species with invasive potential in tropical and subtropical biodiversity hotspots - Phillip J. Haubrock; Francisco J. Oficialdegui; Yiwen Zeng; Jiří Patoka; Darren C.J. Yeo; Antonín Kouba (Reviews in Aquaculture, 2021)
The redclaw crayfish ( Cherax quadricarinatus ; hereafter redclaw), native to northern Australia and southern New Guinea, is among the largest freshwater decapods. It matures early and is considered highly prolific as females may lay over one thousand eggs in a single clutch. Despite generally preferring slow‐moving streams in its native range, it has a wide environmental tolerance, making it capable of establishing populations when introduced to a wide range of other conditions and habitats. These biological and ecological features render it a highly suitable and popular species for aquaculture worldwide, being the second most important crayfish species economically (after the red swamp crayfish Procambarus clarkii ). Adding to that, its unique coloration fuels demand and value among aquarium enthusiasts, making it attractive for the aquarium pet trade. Today, redclaw is widely translocated (67 countries/territories) and various established wild populations (22 countries) have been reported on every continent except Antarctica. Information on its potential or observed impacts, however, is sparse and often anecdotal. To address this gap, this comprehensive review compiles all available information on this species, covering its taxonomy and description, biology and ecology, native and non‐native ranges accompanied with documented introduction pathways. Built upon these, we conducted biological and socio‐economic classification and species distribution modelling. We reveal a lack of thorough impact assessments for this species despite sufficient indications of major observable impacts at local scales. We call attention to the importance of managing the use of this prominent introduced species in aquaculture and aquarium pet trade.

Evolution of salmon lice in response to management strategies: a review - Andrew Coates; Ben L. Phillips; Samantha Bui; Frode Oppedal; Nick A. Robinson; Tim Dempster (Reviews in Aquaculture, 2021)
Ectoparasitic salmon lice ( Lepeophtheirus salmonis ) present a major challenge to Atlantic salmon ( Salmo salar ) aquaculture. The demand for effective louse control has produced diverse management strategies. These strategies essentially impose novel selection pressures on parasite populations, driving the evolution of resistance. Here we assess the potential for salmon lice to adapt to current prevention and control methods. Lice have evolved resistance to at least four of five chemical therapeutants, and use of these chemicals has declined significantly in recent years. The industry has shifted to alternative non‐chemical approaches, yet lice may adapt to these as well. Early research suggests that phenotypic variation exists in the louse population upon which non‐chemical selection pressures could act and that this variation may have a genetic basis. From the existing evidence, as well as an examination of evolutionary processes in other relevant parasite and pest systems, we conclude that the evolution of non‐chemical resistance is an emergent concern that must be considered by the industry. We recommend areas for focused research to better assess this risk. It is also important to determine whether phenotypic shifts in response to non‐chemical selection may shift the ecological niche of the parasite, as this may have cascading effects on wild salmon populations. We also recommend further research to identify strategy combinations that have antagonistic selective effects that slow louse evolution and those with synergistic effects that should be avoided. Greater understanding of evolutionary processes can inform aquaculture policies that counteract the rise of resistant parasite populations.

World aquaculture diversity: origins and perspectives - Benedetto Sicuro (Reviews in Aquaculture, 2021)
Aquaculture diversity is universally considered one of the main aspects that make aquaculture different from land animal farming. A retrospective analysis on 68 years of FAO data on world aquaculture production shows that this aquaculture diversity study is the most powerful and exhaustive theoretical tool to investigate aquaculture origin, evolution and connections with the surrounding world. Aquaculture diversity investigated with Shannon index and Pareto principle shows its thermodynamic nature and reveals an unexpectable regularity that sheds new light on aquaculture, thus putting aquaculture in a perfect theoretical context together with fisheries. Species dominance, vicariance and redundancy must be considered for a functional description of aquaculture diversity. Aquaculture diversity is not biological diversity as an aquaculture species is not necessarily a biological species. Aquaculture diversity shows that aquaculture is a modern colonization of aquatic domain and it has recently reached its maximum value that is 428 ± 11 species, of which 29 ± 1 will produce 80% of global annual production. A temporal and geographical analysis of global aquaculture diversity reveals an original and hopefully enlightening vision of modern aquaculture and its perspectives.

Tag use to monitor fish behaviour in aquaculture: a review of benefits, problems and solutions - Georgia Macaulay; Fletcher Warren‐Myers; Luke T. Barrett; Frode Oppedal; Martin Føre; Tim Dempster (Reviews in Aquaculture, 2021)
A variety of tagging techniques are now available to monitor fish behaviour, physiology and their environmental experience. Tagging is frequently used in aquaculture research to monitor free‐swimming individuals within farmed populations. However, for information gathered from tagged fish to be representative of farmed populations, tagging must not fundamentally affect fish behaviour, physiology or survival. Here, we systematically review studies that used tags to monitor farmed fish behaviour and test factors that affect tag retrieval and tag‐related mortality. Most studies using tags assessed movement and swimming behaviour in salmonids, predominantly in Europe and North America. Mortality of tagged fish was 10 times higher in sea‐cages (mean = 25%, range = 0–61.5%, n = 22 studies) than in tanks (mean = 2.5%, range = 0–17%, n = 23 studies), while mortality of tagged fish in sea‐cages was markedly higher in longer trials (from 4% in single day trials to 36% after 100 days). Higher‐than‐usual mortality rates among tagged fish, together with largely unknown sublethal effects on behaviour, should caution against using tagging studies to make decisions related to farm management. Moreover, key metrics such as mortality rates of tagged and untagged fish or evidence of sublethal effects are often unreported. We make several recommendations to improve future tagging studies and increase transparency in reporting. A greater insight into the causes of tagged fish mortality in sea‐cages is required to secure animal welfare and data validity in studies that use tags to assess fish behaviour in aquaculture.

MicroRNA regulation of viral replication in teleost fish: a review - Chi Zhang; Jiagang Tu; Yong‐An Zhang (Reviews in Aquaculture, 2021)
MicroRNAs (miRNAs) are single‐stranded non‐coding RNA molecules. In addition to participating in various biological processes of eukaryotes, such as cell proliferation, development, differentiation, metabolism, tumorigenesis, and apoptosis, miRNAs also play an important role in the regulation of virus replication. Here, we review the current knowledge on high‐throughput miRNA sequencing of teleost fish or fish cells in response to virus infection, the role of teleost fish miRNAs in regulating virus replication via targeting either fish or virus genes and the function of teleost fish virus‐encoded miRNAs during virus infection. Understanding the interaction between the miRNAs and the host or virus genes will lead to the identification of novel strategy to prevent virus infection in teleost fish.

Issue Information (Reviews in Aquaculture, 2021)

A comprehensive review on genetically modified fish: key techniques, applications and future prospects - Yan Wang; Naima Hamid; Pan‐Pan Jia; De‐Sheng Pei (Reviews in Aquaculture, 2021)
Genetically modified fish is a general term used for whole fish whose DNA has been artificially altered by directly integrating (or deleting) single or multiple genes to introduce or modify a targeted character. Different techniques have been performed to produce genetically modified fish. Importantly, the introduction of various types of fluorescent proteins has dramatically expanded the range of applications of genetically modified fish. Currently, genetically modified fish have been widely employed as experimental models for medical science, pharmacology and environmental toxicology. The commercial application of genetically modified fish in aquaculture is still up for debate, although the first commercialization of genetically modified fish, GloFish, was in 2003, and further, the United States and Canada approved the commercial production and sale of the AquAdvantage Salmon. In this review, we discuss the principles and developmental history of fish transgenesis via gene transfer and gene‐editing techniques, and their applications in diverse fields. Further, challenges and prospects associated with the genetically modified fish are discussed.

Kelp aquaculture in China: a retrospective and future prospects - Zi‐Min Hu; Ti‐Feng Shan; Jie Zhang; Quan‐Sheng Zhang; Alan T. Critchley; Han‐Gil Choi; Norishige Yotsukura; Fu‐Li Liu; De‐Lin Duan (Reviews in Aquaculture, 2021)
Globally, China has the largest scale of kelp cultivation and production operations. However, its kelp aquaculture industry is suffering from declining germplasm diversity, degradation of agronomic traits, the presence of polluted environments, changing ocean conditions and increasing anthropological interference. This review covers two of the most commercially important kelp species in China, viz. Saccharina japonica and Undaria pinnatifida . It summarizes the history of their cultivation, production, economic and ecological benefits, their breeding programmes (e.g. inter‐ and intra‐specific hybridization and marker‐assisted selection) and efforts towards population genetic diversity and conservation. The article focuses on three significant challenges, for example genetic cross‐contamination between the wild and farmed kelp populations, ocean warming and ocean acidification. Accordingly, we outline the steps required to provide several intervention measures, for example (i) collection and preservation of wild and cultivated kelp germplasm; (ii) selection of suitable cultivation sites under changing environmental conditions; (iii) developing stress‐resistant cultivars; and finally, (iv) adoption of innovative cultivation models. The review concludes with genome‐based, designs for molecular breeding and calls for the establishment of an East Asian Kelp Consortium (EAKC). Collectively, the Chinese kelp industry could provide beneficial goods and services, for example bioenergy to fine chemicals and environmental benefits, such as carbon capture, pH amelioration and provision of habitat for many other marine species of commercial value. The strategies proposed in this article thus have the potential to not only improve but also reinvigorate the kelp industry in China and nearby Japan and Korea, in the context of both environmental health and economic benefits.

A 12‐point checklist for surveillance of diseases of aquatic organisms: a novel approach to assist multidisciplinary teams in developing countries - Melba G. Bondad‐Reantaso; Nihad Fejzic; Brett MacKinnon; David Huchzermeyer; Sabina Seric‐Haracic; Fernando O. Mardones; Chadag Vishnumurthy Mohan; Nick Taylor; Mona Dverdal Jansen; Saraya Tavornpanich; Bin Hao; Jie Huang; et al. (Reviews in Aquaculture, 2021)
A 12‐point checklist in the design and practical application of active surveillance of diseases in aquatic organisms (farmed and wild) has been developed to serve as a methodological approach and guidance for a multidisciplinary team particularly in countries where surveillance expertise is limited. The checklist is based on a review of available main aquatic surveillance references and scientific literature and was further developed based on the outcomes of several aquaculture biosecurity project‐related workshops hosted by the Food and Agriculture Organization of the United Nations. The checklist includes the following: (1) scenario setting; (2) defining surveillance objective; (3) defining the populations; (4) disease clustering; (5) case definition; (6) diagnostic testing; (7) study design and sampling; (8) data collection and management; (9) data analysis; (10) validation and quality assurance; (11) human and financial resources and logistics requirements; and (12) surveillance in the bigger picture. For a multidisciplinary approach to disease control, knowledge of fish biology, aquaculture systems and many aspects of aquaculture health management are required. Surveillance needs significant financial investment and must be supported by adequate diagnostic capability, information system management, legal framework and communication networks, with transparent reporting mechanisms to allow rapid disease response for serious diseases of aquatic organisms. It is a stepwise and pragmatic approach that offers a good starting point for addressing disease issues especially in developing countries. It can be used as a model to build targeted surveillance competency and a basic reference when implementing a surveillance programme or improving existing programmes.

‘Aquafeed 3.0’: creating a more resilient aquaculture industry with a circular bioeconomy framework - Stefanie M. Colombo; Giovanni M. Turchini (Reviews in Aquaculture, 2021)

A multidisciplinary review of Tetradesmus obliquus : a microalga suitable for large‐scale biomass production and emerging environmental applications - Carlos Yure B. Oliveira; Cicero Diogo L. Oliveira; Ravindra Prasad; Hwai C. Ong; Evando S. Araujo; Nisha Shabnam; Alfredo O. Gálvez (Reviews in Aquaculture, 2021)
Microalgae biomass is among one of the most promising sustainable raw materials for many industrial sectors especially biodiesel production. Although a great diversity of microalgae species has been described and isolated, few have been used for large‐scale cultivation. This review presents a multidisciplinary overview of studies on Tetradesmus obliquus – a freshwater microalga suitable for large‐scale production and emerging environmental applications. It reviews the taxonomic history of T. obliquus and its potential commercial applications, including cultivations techniques and environmental parameters, production systems, harvesting and drying of biomass, and its biochemical composition. In addition, a model refinery for T. obliquus is proposed that combines the main productive bioprocesses. Finally, a bibliometric analysis is presented and opportunities for future research with T. obliquus are identified.

Sustainable large‐scale production of European flat oyster ( Ostrea edulis ) seed for ecological restoration and aquaculture: a review - Bérenger Colsoul; Pierre Boudry; María Luz Pérez‐Parallé; Ana Bratoš Cetinić; Tristan Hugh‐Jones; Isabelle Arzul; Nicolas Mérou; Karl Mathias Wegner; Corina Peter; Verena Merk; Bernadette Pogoda (Reviews in Aquaculture, 2021)
The conservation and active restoration of European flat oyster ( Ostrea edulis ) populations are a major focus of ecological restoration efforts to take advantage of the wide‐ranging ecosystem functions and services this species provides. Accordingly, additional and new demands for seed oysters have arisen. In commercial aquaculture (mariculture), the production of O. edulis is still largely based on natural seed collection. Considering the specific requirements, related to ecological restoration, such as the absence of pathogens and the preservation of high genetic diversity, the current supply is insufficient. Despite the development of breeding and controlled reproduction techniques for this species since the late 1930s, seed production today is mainly based on empirical concepts. Several of the issues that producers still face are already subjects of research; many others are still unanswered or even unaddressed. This review provides a summary of all available knowledge and technologies of O. edulis seed production. Furthermore, it provides a detailed reflection on implications for restoration, future challenges, open questions and it identifies relevant research topics for sustainable seed supply. The study covers the following aspects on (i) biology of the species, (ii) stressors – including pathogens and pollutants, (iii) genetics, (iv) history of production technologies, (v) seed production in polls, (vi) seed production in ponds and (vii) seed production in hatcheries. Future research needs on sex determinism, gametogenesis, cryopreservation, nutrition, selective breeding, pathogens and disease, and the development of reliable protocols for production are highlighted.

Time to rethink trophic levels in aquaculture policy - Richard S. Cottrell; Marc Metian; Halley E. Froehlich; Julia L. Blanchard; Nis Sand Jacobsen; Peter B. McIntyre; Kirsty L. Nash; David R. Williams; Lex Bouwman; Jessica A. Gephart; Caitlin D. Kuempel; Daniel D. Moran; et al. (Reviews in Aquaculture, 2021)
Aquaculture policy often promotes production of low‐trophic level species for sustainable industry growth. Yet, the application of the trophic level concept to aquaculture is complex, and its value for assessing sustainability is further complicated by continual reformulation of feeds. The majority of fed farmed fish and invertebrate species are produced using human‐made compound feeds that can differ markedly from the diet of the same species in the wild and continue to change in composition. Using data on aquaculture feeds, we show that technical advances have substantially decreased the mean effective trophic level of farmed species, such as salmon (mean TL = 3.48 to 2.42) and tilapia (2.32 to 2.06), from 1995 to 2015. As farmed species diverge in effective trophic level from their wild counterparts, they are coalescing at a similar effective trophic level due to standardisation of feeds. This pattern blurs the interpretation of trophic level in aquaculture because it can no longer be viewed as a trait of the farmed species, but rather is a dynamic feature of the production system. Guidance based on wild trophic position or historical resource use is therefore misleading. Effective aquaculture policy needs to avoid overly simplistic sustainability indicators such as trophic level. Instead, employing empirically derived metrics based on the specific farmed properties of species groups, management techniques and advances in feed formulation will be crucial for achieving truly sustainable options for farmed seafood.

The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome‐scale sturgeon genome - Christin Höhne; Dmitry Prokopov; Heiner Kuhl; Kang Du; Christophe Klopp; Sven Wuertz; Vladimir Trifonov; Matthias Stöck (Reviews in Aquaculture, 2021)
Sturgeon immunity is relevant for basic evolutionary and applied research, including caviar‐ and meat‐producing aquaculture, protection of wild sturgeons and their re‐introduction through conservation aquaculture. Starting from a comprehensive overview of immune organs, we discuss pathways of innate and adaptive immune systems in a vertebrate phylogenetic and genomic context. The thymus as a key organ of adaptive immunity in sturgeons requires future molecular studies. Likewise, data on immune functions of sturgeon‐specific pericardial and meningeal tissues are largely missing. Integrating immunological and endocrine functions, the sturgeon head kidney resembles that of teleosts. Recently identified pattern recognition receptors in sturgeon require research on downstream regulation. We review first acipenseriform data on Toll‐like receptors (TLRs), type I transmembrane glycoproteins expressed in membranes and endosomes, initiating inflammation and host defence by molecular pattern‐induced activation. Retinoic acid‐inducible gene‐I‐like (RIG‐like) receptors of sturgeons present RNA and key sensors of virus infections in most cell types. Sturgeons and teleosts share major components of the adaptive immune system, including B cells, immunoglobulins, major histocompatibility complex and the adaptive cellular response by T cells. The ontogeny of the sturgeon innate and onset of adaptive immune genes in different organs remain understudied. In a genomics perspective, our new data on 100 key immune genes exemplify a multitude of evolutionary trajectories after the sturgeon‐specific genome duplication, where some single‐copy genes contrast with many duplications, allowing tissue specialization, sub‐functionalization or both. Our preliminary conclusion should be tested by future evolutionary bioinformatics, involving all >1000 immunity genes. This knowledge update about the acipenseriform immune system identifies several important research gaps and presents a basis for future applications.

Bioeconomic modelling of hatchery, grow‐out and combined business of Australian black tiger shrimp Penaeus monodon farming - Maria C. Marín‐Riffo; Herman W. Raadsma; Dean R. Jerry; Greg J. Coman; Mehar S. Khatkar (Reviews in Aquaculture, 2021)
Penaeus monodon is the primary shrimp species farmed in Australia. Based on an extensive survey of the literature and industry information, we identified and compiled 318 different parameters related to shrimp aquaculture enterprises and production. Using these as input parameters, we performed detailed bioeconomic modelling for evaluating the economic viability of intensive culture scenarios and identified the major drivers of business profitability under Australian conditions. Three business types (hatchery, grow‐out and combined hatchery + grow‐out) were evaluated by simulating varying numbers of female broodstock and ponds in operation based on annual, six‐monthly, quarterly and monthly stocking events per year over a 10‐year period. Net present value was the main economic variable for comparison. The hatchery business was most profitable in scenario with 250 females being spawned monthly or 500 females at least quarterly, that is, >2000 females spawned per year. Feed, acquisition of broodstock and fixed labour were major costs for hatchery scenarios. For a grow‐out business, all scenarios were profitable even at the smallest scale modelled (50 ponds stocked annually). Feed, power and purchase of post‐larvae were major costs for grow‐out business. The combined business was the most profitable for a large enterprise and required at least 100 ponds stocked over the year. The three major costs in the combined business were feed, power and labour. Sensitivity analyses showed feed cost and survival parameters were critical for profitability.

A review of access and benefit‐sharing measures and literature in key aquaculture‐producing countries - Fran Humphries; John A.H. Benzie; Charles Lawson; Clare Morrison (Reviews in Aquaculture, 2021)
Countries increasingly use access and benefit‐sharing laws as a tool for the conservation and sustainable use of biological resources and associated traditional knowledge. These laws generally require the recipient of resources/knowledge to obtain the provider country’s prior informed consent before collection, use or transfer and to share the benefits from their use with the provider. The aim of this literature review is to comprehensively analyse access and benefit‐sharing laws and literature about the top five aquaculture‐producing countries – China, India, Indonesia, Viet Nam and Bangladesh – to identify research trends and gaps in relation to accessing and sharing the benefits of aquaculture genetic resources and associated traditional knowledge. Using a systematic quantitative literature review methodology, we found only 5% of the literature examined the implications of access and benefit‐sharing for aquaculture and these only related to publications about India’s arrangements. While the other countries had literature about their legal measures and literature about informal genetic resource sharing practices in aquaculture, none of them connected the two research topics. None of the countries had literature analysing the implications of access and benefit‐sharing in relation to traditional knowledge associated with aquaculture. We conclude that given these are the top global producers accounting for up to 80% of all aquaculture products, urgent research is needed to fill the literature gaps to assess whether access and benefit‐sharing as a legal/policy tool is achieving conservation and sustainable use goals for aquaculture genetic resources.

Chinese Abstracts (Reviews in Aquaculture, 2021)

A sex‐reversing factor: insulin‐like androgenic gland hormone in decapods - Rong Sun; Yanhe Li (Reviews in Aquaculture, 2021)
A large number of decapod crustaceans with sexual dimorphism in body size, most of which, are important economic animals. Besides, some of them such as the red swamp crayfish Procambarus clarkii possess strong invasive ability and would damage ecosystem environment. Thereby, monosex culture of decapods would contribute to not only increasing yield and profits, but also reducing the risks of biological invasion. Insulin‐like androgenic gland hormone was reported to be a key regulator in sex differentiation. All‐male populations in Macrobrachium rosenbergii were successfully produced through insulin‐like androgenic gland hormone manipulation. In addition to sex differentiation, insulin‐like androgenic gland hormone was reported to be involved in male secondary sex characteristics maintenance, growth, metabolism, morphology change, ovary development and other functions. Considering its important application value for decapods, insulin‐like androgenic gland hormone has attracted much attention in recent years. This hormone was reported to have the structure and function similar to androgenic gland hormone of isopods. In this study, the origin of name of androgenic gland hormone and insulin‐like androgenic gland hormone was investigated, and the recent research on structure, function, application and molecular regulation mechanism of insulin‐like androgenic gland hormone of decapods was reviewed.

Cover Image - Zi‐Min Hu; Ti‐Feng Shan; Jie Zhang; Quan‐Sheng Zhang; Alan T. Critchley; Han‐Gil Choi; Norishige Yotsukura; Fu‐Li Liu; De‐Lin Duan (Reviews in Aquaculture, 2021)
The cover image is based on the Review Article Kelp aquaculture in China: A retrospective and future prospects by Zi‐Min Hu et al., https://doi.org/10.1111/raq.12524 . image

Lytic regulated cell death in aquaculture fish - Xiaojing Xia; Bin He; Xiulin Zhang; Zhe Cheng; Mingcheng Liu; Xiaobing Wei; Jinqing Jiang; Jianhe Hu (Reviews in Aquaculture, 2021)
Cell death is an important physiological and pathological phenomenon in multicellular animals and occurs widely in various body’s systems. In recent years, researchers have gained a deeper understanding of the mechanisms of necrosis and apoptosis in mammals. In addition, many new forms of lytic regulated cell death (RCD), such as pyroptosis, necroptosis and ferroptosis, have been discovered, thus enhancing our understanding of the molecular mechanisms of programmed cell death (PCD) and the associated signalling pathways as well as their relationship with diseases. However, our understanding of lytic RCD in fish is limited. Recently, some progress has been made regarding the induction conditions, expression of related genes and regulation of lytic RCD in fish. Furthermore, research on the roles of lytic RCD in tissue development, against pathogenic microorganism, inflammatory disease and neurological disease, has also been advanced. Understanding lytic RCD in fish will enable the regulation of its occurrence through human intervention to inhibit disease processes, improve fish health and explore possible countermeasures based on these basic theoretical studies.

Supplemental carbon sources applied in biofloc technology aquaculture systems: types, effects and future research - Godwin Abakari; Guozhi Luo; Emmanuel O. Kombat; Elliot H. Alhassan (Reviews in Aquaculture, 2021)
Biofloc technology (BFT) systems have been driven towards increased sustainability in the last decade. BFT depends on maintenance of the optimal carbon‐to‐nitrogen (C/N) ratio through supplementation with organic carbon sources. The types of carbon sources and addition strategies are critical considerations in BFT systems. Thus for the purpose of this review, a thorough search of the literature was conducted to gather relevant information from reliable sources, ranging from reputable journals to books and useful reports in the field of BFT. Keywords used for the literature search include: ‘biofloc technology systems’, ‘carbon sources’, ‘solid carbon sources’, ‘effects of carbons sources’, ‘carbon source addition strategies’, ‘nutritional quality of bioflocs’, ‘carbon sources and water quality’, ‘C/N ratio in BFT’, and ‘carbon sources and bacterial community’. Among the several peer‐reviewed articles, books and technical reports consulted, 147 (dated from 1987 to 2020) were relevant for the preparation of this review. The current review thus examines the subject of supplemental carbon sources in BFT systems and discusses the various effects of their application with respect to the culture organism, microorganisms, water quality and the nutritional quality of flocs. The benefits and challenges associated with the types of carbon sources used in BFTs are also presented. Suggested organic carbon sources and their addition strategies are provided, and further research directions are proposed.

Respiratory quotient and the stoichiometric approach to investigating metabolic energy substrate use in aquatic ectotherms - Shuangyao Wang; Chris G. Carter; Quinn P. Fitzgibbon; Gregory G. Smith (Reviews in Aquaculture, 2021)
The respiratory quotient (RQ) has been used extensively as an index to evaluate metabolic energy expenditure in terrestrial animals including humans. In contrast, RQ use in understanding physiology and nutrition of aquatic ectotherms has been restricted due to technical challenges in measuring total CO 2 in water. With technical advances in measuring total CO 2 in water, RQ in aquatic ectotherms can be accurately determined and is potentially available as a valuable method. Here, we provide a comprehensive review of studies on RQ and metabolic energy substrate use in aquatic ectotherms. Metabolic energy substrate use is evaluated by a reliable stoichiometric bioenergetic approach, based on measuring RQ and nitrogen quotient (NQ) simultaneously. Stoichiometry provides a non‐destructive and unequivocal way to quantify the instantaneous oxidation of each major energy substrate (protein, lipid or carbohydrate). This review aims to refine knowledge about bioenergetics of aquatic ectotherms under different conditions including nutritional aspects of sustainable aquaculture. Notably, stoichiometry provides a promising approach to optimize feeds and feeding regimes to realize sustainable aquaculture under differing conditions and with differing feed ingredients. It also provides an approach to consider climate change impacts and physiological adaptation mechanisms for survival and development in farmed environments and natural ecosystems. Stoichiometric bioenergetics knowledge in aquatic ectotherms has relevance to commercial impacts in the face of overfishing and food security, and ecological significance in the face of environmental change scenarios. We suggest expanding the use of stoichiometry in future bioenergetic research in emerging aquaculture species.

The potential roles of sponges in integrated mariculture - Mert Gökalp; Daan Mes; Marit Nederlof; Hongwei Zhao; Jasper Merijn de Goeij; Ronald Osinga (Reviews in Aquaculture, 2021)
This mini‐review evaluates the use of marine sponges in integrated culture systems, two decades after the idea was first proposed. It was predicted that the concept would provide a double benefit: sponges would grow faster under higher organic loadings, and filtration by sponges would improve water quality. It is promising that the growth of some commercially interesting sponges is indeed faster in organically enriched areas. The applicability of sponges as filters for undesired microorganisms has been confirmed in laboratory studies. However, upscaled farming studies need to be done to demonstrate the value of sponges for in situ bioremediation of sewage discharge or waste produced by fish cages. In addition, a new idea is presented – the use of sponges as an engine to convert dissolved organic matter (DOM) into particulate organic matter (POM) that can be consumed by deposit feeders through a chain of processes termed the sponge loop. A theoretical design of an integrated culture with seaweeds ( Gracilaria sp.), sponges ( Halisarca caerulea ) and sea cucumbers ( Apostichopus japonica ) shows that 37% of the part of the primary production that is excreted by the seaweeds as DOM can be directly recovered in sponge biomass and a subsequent 12% in sea cucumber biomass after mediation (conversion of DOM to POM) by sponges. Hence, the total recovery of DOM into (sponge and sea cucumber) biomass within this IMTA is 49%.

Developing oral nanovaccines for fish: a modern trend to fight infectious diseases - Carlos Angulo; Marlene Tello‐Olea; Martha Reyes‐Becerril; Elizabeth Monreal‐Escalante; Luis Hernández‐Adame; Miriam Angulo; José M. Mazon‐Suastegui (Reviews in Aquaculture, 2021)
Nanovaccines constitute an innovative approach in vaccinology, enabled by the nanotechnology advances on the synthesis, functionalization and application of nanoparticles for immunization. Currently, several organic materials such as chitosan, poly(lactic‐co‐glycolic acid), nanopoliplexes and virus‐like particles (VLPs) have been used for nanovaccine development to fight against fish diseases. The oral route is the most practical and economical for fish vaccination; thus, several oral vaccine candidates have been developed by using NPs in which the antigen is encapsulated, surface exposed or recombinantly ensembled (VLPs), leading to promising results in terms of protection capacity against infectious diseases. In this review, the state of the art on oral nanovaccine prototypes developed for use in fish was analysed and discussed. Oral nanovaccines have showed remarkably possibilities for application in fish aquaculture, which surely will be adopted by the industry in the following years.

Compilation of antiviral treatments and strategies to fight fish viruses - Patricia Pereiro; Antonio Figueras; Beatriz Novoa (Reviews in Aquaculture, 2021)
The implementation of antiviral treatments and prophylaxis strategies in fish aquaculture needs to be established. The absence of commercial vaccines for most viral diseases affecting economically relevant fish species, and the total lack of treatments to fight these diseases once they have emerged in a fish farm remains one of the main bottlenecks in fish aquaculture production. However, although no antivirals are currently applied on farms, a great number of investigations have been conducted to assess the potential use of antiviral treatments against several fish viruses. Although most of these works were based on in vitro approaches, some included in vivo experiments to demonstrate the potential applicability of these treatments. This review summarizes the investigations conducted both in vitro and in vivo in the field of antiviral treatments against fish viruses. The highlighted works include those using piscine and non‐piscine proteins with antimicrobial functions, metabolites, chemical compounds (some of which are used in medicine to treat human viruses), bioactive compounds mainly isolated from plants and bacteria, and emerging DNA‐ and RNA‐based therapeutics. This information can be used for developing both specific and broad‐spectrum antiviral strategies to be further used in the aquaculture industry, and it may even provide interesting indications for biomedical research.

Best therapeutic practices for the use of antibacterial agents in finfish aquaculture: a particular view on European seabass ( Dicentrarchus labrax ) and gilthead seabream ( Sparus aurata ) in Mediterranean aquaculture - George Rigos; Dimitra Kogiannou; Francesc Padrós; Carles Cristòfol; Daniela Florio; Marialetizia Fioravanti; Carlos Zarza (Reviews in Aquaculture, 2021)
Antibacterial therapy is still in many cases the only way to control bacterial disease outbreaks, with relevant economic issues. Nevertheless, this necessity should also be well balanced with other relevant aspects such as suitability, efficacy and refinement of the treatments but also with consumer and environmental welfare. With this aim, the literature pertaining to the use of antibacterials (i.e. oxytetracycline, oxolinic acid, flumequine and potentiated sulphonamides) in Mediterranean farmed European seabass ( Dicentrarchus labrax ) and gilthead seabream ( Sparus aurata ) was reviewed and addressed. Knowledge of drug pharmacokinetics along with the related legislation is also presented. The main criteria, technical aspects and constraints affecting the design of an appropriate antibacterial therapy are also discussed. An evaluation of available bibliography revealed the existence of considerable information on several registered antibacterials, while it is limited for others. Typically, minimum inhibitory concentrations (MIC) have been used as a reference for antibacterial selection. However, the methodologies used for MIC assessment require refinement and more sophisticated data such as epidemiological cut‐off breakpoint values. Due to the characteristics of farming systems, antibacterials are mostly delivered through medicated feeds. The large number of production units and number of fish per unit, together with a limited timeframe margin for efficient therapy, makes Mediterranean gilthead seabream and European seabass, one of the best examples where the metaphylactic concept has to be considered in aquatic medicine. The information presented in this review should guide future action taken to fulfil research gaps and promote effective and prudent antibacterial practices.

Long‐term trends in the frequency and magnitude of upwelling along the West Coast of the South Island, New Zealand, and the impact on primary production - Stephen M. Chiswell; Joanne M. O’Callaghan (New Zealand Journal of Marine and Freshwater Research, 2021)
Satellite‐derived estimates of sea surface temperature (SST), chlorophyll (Chl), and fluorescence line height (FLH), from 22 sites ∼20 km offshore from the West Coast of the South Island, New Zealand (WCSI) are used to investigate long‐term trends in SST, the frequency and magnitude of cool and warm events, and their impacts on SSC and FLH. WCSI trends have been towards higher temperature and less chlorophyll, with a 0.83°C rise in mean along‐shore SST since 1982, and a 0.1 mg Chl m −3 drop in mean along‐shore SSC since 2002. With respect to the trend, there were 13 extreme cool and 14 extreme warm events between 1982 and 2019, with mean values of −2.55 and 2.62°C, respectively. There was no measurable change in the frequency of extreme events, but there is a suggestion that extreme events are becoming warmer. During extreme events, Chl and FLH show inverse relationships with SST, suggesting that there is an underlying response of increased primary production to lower temperatures. Likely mechanisms are that upwelling brings nutrients up from depth, or that Ekman flow forces freshwater farther offshore, simultaneously introducing nutrients into the offshore region and providing a more stable water column allowing production.

The physics of New Zealand’s shelf seas: introduction to the special issue - Craig L. Stevens; Joe O’Callaghan; Stephen M. Chiswell; Moninya Roughan (New Zealand Journal of Marine and Freshwater Research, 2021)

Frontal dynamics and water mass variability on the Campbell Plateau - Aitana Forcén‐Vázquez; Michael J. M. Williams; Melissa Bowen; Lionel Carter; Helen Bostock (New Zealand Journal of Marine and Freshwater Research, 2021)
The Campbell Plateau is a dominating bathymetric feature of New Zealand’s subantarctic region, strongly influencing the dynamics of both the Subtropical Front (STF) to the north and the Subantarctic Front (SAF) to the south. We present a consistent survey across New Zealand’s subantarctic of the relationships between front positions, bathymetry and water masses. The northwest side of the Campbell Plateau is comparatively warm due to a southward extension of the STF over the plateau. The SAF is steered south and east by the combined effect of the plateau and Macquarie Ridge, with waters originating in the SAF also found north of the plateau. Formation of Subantarctic Mode Water (SAMW) is confirmed, with a deep reservoir of SAMW persisting nearly a year after formation. Antarctic Intermediate Water (AAIW) is observed around the edges of the plateau, but not present on the plateau, confirming that the waters on the plateau are isolated from deeper Southern Ocean.

Sea temperature rise over the period 2002–2020 in Pelorus Sound, New Zealand – with possible implications for the aquaculture industry - Niall Broekhuizen; David R. Plew; Matt. H. Pinkerton; Mark. G. Gall (New Zealand Journal of Marine and Freshwater Research, 2021)
We assembled water‐temperature data (1.0–15 m depth horizon) from several field studies (spanning 2003–2020) within Pelorus Sound to generate composite time‐series of temperature at four locations. We also examined satellite‐sensed sea‐surface temperature records for the region (2002–2019). Time‐series were deseasoned and Sen‐slopes were calculated as measures of long‐term trend. All of the in‐situ slopes and most of the satellite slopes fell inside the range 0.2–0.4°C decade −1 . Within the in‐situ data, warming appears to have been less rapid during the spring (September‐November) quarter than in others. In the satellite data, warming was slower during both the winter and spring quarters. The satellite data indicate that warming has been less rapid inside the Sound than the nearby oceanic waters. Air temperatures inside the Sound have warmed at a rate similar to the nearby water (and a lesser rate than the oceanic ones) and riverine heat inputs have not changed appreciably. We infer that warming has been driven mainly by import of warming oceanic waters. We discuss the implications of future warming for the two marine crops grown in Pelorus Sound (Chinook salmon and Greenshell™ mussel) drawing upon literature concerning their responses to temperature.

Pūtahitanga: the intersection of western science and mātauranga Māori in the context of Aotearoa New Zealand’s physical oceanography - Craig L. Stevens; Kura Paul‐Burke (Ngāti Awa, Ngāti Whakahemo); Peter Russell (Ngāpuhi) (New Zealand Journal of Marine and Freshwater Research, 2021)
Aotearoa New Zealand is a land and cultures surrounded by one of the planet’s larger marine exclusive economic zones per capita. Understanding, living within and utilising this domain requires a well‐developed knowledge of the physical oceanography – fate, provenance and transfer of ocean‐water, material and energy. In the Aotearoa New Zealand context, understanding and utilising the environment through science also requires that Māori have a stake in the science and a pathway to connecting with their mātauranga. The pūtahitanga (intersection) of mātauranga Māori and western science perspectives brings challenges for implementation of the Vision Mātauranga framework for physical oceanographic science. Here we discuss the drivers and key themes for the pūtahitanga and propose a mahere kaupapa/plan bound by: (i) climate, (ii) decolonisation, (iii) shared language, (iv) data sovereignty, and (v) developing a cohort who can lead the field in the coming decades.

Evaluation of four global ocean reanalysis products for New Zealand waters–A guide for regional ocean modelling - Joao Marcos Azevedo Correia de Souza; Phellipe Couto; Rafael Soutelino; Moninya Roughan (New Zealand Journal of Marine and Freshwater Research, 2021)
A comparison between 4 (near) global ocean reanalysis products is presented for the waters around New Zealand. The objective is to provide information for an educated choice of ocean estate estimate. The simulations are compared to satellite and in situ observations, and vertical sections are extracted to evaluate the representation of the main regional boundary currents and their transport. Overall, the Copernicus GLORYS reanalysis exhibits the better performance, with more realistic ocean variability and smaller biases in the water column structure. However, the BlueLink Reanalysis (BRAN) provides more realistic transport estimates of the East Auckland Current, an important boundary current connecting New Zealand to the World Ocean. All simulations have important biases in both temperature and salinity, particularly in coastal regions. Moreover, they are not able to represent coastal currents and processes. Therefore, the present study results emphasise the need for a regional ocean reanalysis and a data assimilative operational forecast system.

A modelling synthesis of the volume flux through Cook Strait - Mark G. Hadfield; Craig L. Stevens (New Zealand Journal of Marine and Freshwater Research, 2021)
We present hindcasts of currents in Cook Strait from a baroclinic, tide‐resolving ocean model. Three hindcasts are run, forced respectively at the lateral boundaries with data from the Bluelink Reanalysis (BRAN), the global Hybrid Coordinate Ocean Model (HYCOM) and a New Zealand Shelf Seas baroclinic hindcast (NZROMS). The hindcast forced by BRAN is evaluated against measured currents at locations in the Cook Strait Narrows and South Taranaki Bight. The model reproduces the observed tidal, subtidal and mean currents well. The three hindcasts produce a 3‐year‐mean volume flux southward through the Narrows of 0.360, 0.734 and 0.230 Sv, respectively. When corrected for the observed discrepancies between model and measurements in the Narrows, the estimates are 0.430, 0.498 and 0.337 Sv. We conclude that true 3‐year mean volume flux through Cook Strait is 0.42 ± 0.08 Sv. The tidal volume flux amplitude is 4.68 Sv (M2). The subtidal fluctuations in volume flux have a standard deviation of 0.62 Sv. The effect of wind is investigated with a wind‐forced barotropic model, which produces volume flux fluctuations that are highly correlated ( r = 0.93) with the subtidal fluctuations from the baroclinic model, implying that the latter are largely wind‐generated.

Hydrodynamics and sediment transport on the North Canterbury Shelf, New Zealand - Cowan R. Nokes; Helen C. Bostock; Lorna J. Strachan; Mark G. Hadfield (New Zealand Journal of Marine and Freshwater Research, 2021)
This study uses a combination of regional ocean modelling systems (ROMS), a sediment transport model (sedtrans05) and detailed grainsize data with the aim of determining the hydrodynamics and primary sediment transport pathways on the North Canterbury Shelf (NCS), South Island of New Zealand. Combining the results from the hydrodynamic model, sediment grainsize data and sediment transport model in an unsupervised classification scheme, highlights 5 classes of sediment on the shelf. These classes include a high energy inner shelf with coarse sands and gravels (Class 1), a low to medium energy mid shelf allowing for the deposition of fine sediments in a large depocenter (Class 2 and 3), and an area on the mid to outer shelf of relict coarse sediments (Class 4). With the exception of Class 4, the sediment distribution is in equilibrium with the modern hydrodynamics and validates the ROMS and SedTrans05 models. This understanding of the NCS hydrodynamic and sedimentary system will help with the management of the marine environment, with the caveat that this is a highly dynamic environment which is influenced of earthquakes and large storms influencing erosion, transport and distribution of sediment in this region.

Variability of internal tide energy, mixing and nitrate fluxes in response to changes in stratification on the northeast New Zealand continental shelf - Jonathan Sharples; John R. Zeldis (New Zealand Journal of Marine and Freshwater Research, 2021)
A 4‐month time series of water column temperature structure on the shelf of North Island New Zealand is used to calculate the energy in the internal tide as stratification evolved between spring and summer. Average total energy in the internal tidal wave was 200 J m −2 , with peaks reaching 600 J m −2 . Wave energy was weakly correlated with stratification ( r = 0.2) and with the spring‐neap cycle of tidal currents ( r = 0.17). Overall there was little predictability in internal tide behaviour in response to the physical environment. Reduction in wave energy was associated with a downwelling‐favourable wind event which reduced stratification by mixing and by removing deeper water off the shelf. Vertical eddy diffusivity driven by internal wave dissipation ranged between 5.6 × 10 −5 and 3.2 × 10 −4 m 2 s −1 . Combined with nitrate data this diffusivity resulted in diapycnal nitrate fluxes towards the sea surface of 1.6–2.2 mmol m −2 day −1 . Strong stratification in summer reduced the eddy diffusivity but had little effect on nitrate flux as a strengthened vertical nitrate gradient compensated for the reduced diffusivity. This compensation will be important when predicting how stronger stratification in a warmer climate might alter diapycnal nutrient supplies to the upper ocean.

Physical oceanography of New Zealand/Aotearoa shelf seas – a review - Craig L. Stevens; Joanne M. O’Callaghan; Stephen M. Chiswell; Mark G. Hadfield (New Zealand Journal of Marine and Freshwater Research, 2021)
The shelf seas surrounding New Zealand/Aotearoa, a region nominally extending out to the 250 m depth contour, are complex and varied as they sit above the submerged continent of Zealandia. These seas surround the two main islands that span 1,500 km in latitude from 34°S to 47°S and include a series of plateaus that extend far beyond. This review summarises the present state of knowledge of the physical processes that control ocean transport and mixing in this domain. The focus is on documenting recent regional advances in understanding the balance between off‐shelf drivers, terrestrially sourced freshwater, winds, tides, stratification and the underlying topography. The review considers outstanding themes such as connectivity, climate and stratification and closes with an assessment of the potential future for understanding the physical marine environment of the shelf seas of the New Zealand region.

Circulation in Tasman‐Golden bays and Greater Cook Strait, New Zealand - Stephen M. Chiswell; Craig L. Stevens; Helen S. Macdonald; Brett S. Grant; Olivia Price (New Zealand Journal of Marine and Freshwater Research, 2021)
Analyses are presented of model simulations and Lagrangian drifter experiments designed to quantify circulation and dispersal in Tasman and Golden Bays, and their connection to Cook Strait, New Zealand. Observations made in autumn 2017 and summer 2018 are compared with numerical model results. The drifter experiments were focussed on three repeat experiments in each bay designed to measure the local horizontal eddy diffusivity. An additional experiment investigated the connection with, and flow through, Greater Cook Strait. Point by point velocities extracted from the model show low correlation with, but on average are in the same direction as observed velocities. Eddy diffusivities computed from the drifter experiments are highly variable, but the observations support the modelling. We find that the mean velocity in Tasman and Golden Bays is weak and the circulation is dominated by wind and tidal flows. The mean depth‐averaged velocity shows anticyclonic flows in the south of both Tasman and Golden Bays, with cyclonic flow in the north of Golden Bay. The mean near‐surface velocity is generally out of each bay and is compensated for by inward circulation at depth.

The Fiordland Current, southwest New Zealand: mean, variability, and trends - Mitchell Chandler; Melissa Bowen; Robert Owain Smith (New Zealand Journal of Marine and Freshwater Research, 2021)
The mean, interannual variability, decadal variability, and longer‐term trends in the across‐track geostrophic velocity of the poleward‐flowing boundary current along the Fiordland coast (the Fiordland Current, FC) are examined over the altimeter record (September 1992–May 2017). In the mean, the FC is southwestward, with stronger velocities in an inner current near the coast and weaker velocities in an outer current further offshore. Examination of the alongshore momentum balance suggests that the mean flow is driven by a poleward downsloping alongshore pressure gradient. At interannual time‐scales, variability in the FC was correlated with the alongshore wind stress, indicating that an equatorward (poleward) wind stress drives an equatorward (poleward) velocity anomaly. At decadal time‐scales, variability in the FC was correlated with the South Pacific wind stress curl, indicating that as the wind stress curl increases (decreases) the poleward flow in the FC weakens (strengthens), consistent with the response of a traditional eastern boundary current. Long‐term trends show a weakening outer current and strengthening inner current. Increasing flow in the inner current may result in increased transport of subtropical water around southern New Zealand.

Chinese Abstracts (Reviews in Aquaculture, 2021)

Issue Information (Reviews in Aquaculture, 2021)

Advancing the sustainability of aquaculture - Pin Nie; Eric Hallerman (Reviews in Aquaculture, 2021)

Discoloration in the marine red algae Pyropia : causative factors and exploiting the biotechnological potential of a waste resource - Kichul Cho; Jina Heo; Sang‐Moo Lee; Jinwook Han; Hyun Dae Hong; Hancheol Jeon; Hyun‐Ju Hwang; Kyunghwa Baek; Jong Won Han (Reviews in Aquaculture, 2021)
Pyropia ( Porphyra , referred to as ‘Gim’ in Korea or ‘Nori’ in Japan), an economically valuable alga, has long been consumed as seafood, especially in north‐east Asian countries. Its well‐established conventional mass cultivation and harvesting methods in coastal areas widen the industrial availability of edible Pyropia sp. However, the unexpected discoloration derived from causative factors during the cultivation process gives rise to serious economic losses in the aquaculture industry. For the industrial use of discoloured laver waste (DLW), recent articles have suggested that DLW biomass could be used as a source of agar polysaccharide, porphyran, γ‐aminobutyric acid and other value‐added bioactive compound productions. Although DLW biomass has economic potential, the lack of integrated information and relevant studies still limits its industrial availability. Therefore, we discussed recent research concerning the functional ingredients, causative factors and potential availability of DLW to provide integrated information. Furthermore, this review suggested the potential industrial application of DLW as a source for other value‐added material production.

An overview of cytokine used as adjuvants in fish: current state and future trends - Ming Guo; Chenghua Li (Reviews in Aquaculture, 2021)
Vaccination is the most appropriate way to control pathogens that threaten the global aquaculture industry. Unfortunately, vaccines generally do not provide satisfactory immune protection, especially those based on inactivated pathogens or recombinant antigens. Thus, it is necessary for adjuvants or immunostimulants to be used to improve the vaccine efficacy. Traditional adjuvants such as aluminium salts adjuvant and Freund’s adjuvant, are the most effective known adjuvants in aquaculture; however, due to their disadvantages, such as low adjuvanticity, short lasting time and serious side effects in vivo were also occurred. Searching for some combinations or alternative molecules of them as adjuvants is feasible to increase animal welfare without lowering the levels of immune protection. Recent advances in immunology confirmed that cytokines used as adjuvants have the advantages of eliciting the expression of costimulatory molecular and polarization of antigen‐presenting cells compared with aluminium slats adjuvant and oil adjuvant in fish farming. Moreover, the effects of most adjuvants are exerted mainly through the induction of cytokines production. Nowadays, cytokines have been evaluated for their abilities to offer effective adjuvant activities in both animal models and human studies. In this review, we summarized previous studies performed with different Th cytokines used as adjuvants on different types of fish vaccines, focusing on their protective efficacies and effects on the fish immune system as they delivered in vivo .

Ecological engineering in pond aquaculture: a review from the whole‐process perspective in China - XingGuo Liu; Zhengyi Shao; Guofeng Cheng; Shimin Lu; Zhaojun Gu; Hao Zhu; Hongye Shen; Jie Wang; Xiaolong Chen (Reviews in Aquaculture, 2021)
Pond aquaculture undeniably offers the potential for food production worldwide. In China, 45.83% of aquatic production is currently from pond aquaculture. However, with the continuous expansion of this practice, environmental problems such as a high level of water consumption, aquaculture water deterioration, pollution from effluent and aquatic product quality decline seriously restrict the sustainable development of pond aquaculture. In this review, we summarise the (i) the impacts of pond aquaculture on the environment, (ii) research progress in pond aquaculture ecological engineering, (iii) existing technologies regarding pond aquaculture ecological engineering systems, (iv) effects of applying pond aquaculture ecological engineering and (v) summary and prospects. Moreover, we discuss the merits and drawbacks of each method and technology, and future research priorities are reviewed. With this, an understanding of the role played by ecological engineering in pond aquaculture is provided, as well as guidance for precisely managing aquaculture water and effluent, aquaculture practices, and technological developments. In summary, the pond aquaculture ecological engineering can be managed so as to improve animal welfare and the stability of water treatment systems, reducing the adverse effects on the environment and public health, and enabling the sustainable development of pond aquaculture.

Yeast as major protein‐rich ingredient in aquafeeds: a review of the implications for aquaculture production - Jeleel Opeyemi Agboola; Margareth Øverland; Anders Skrede; Jon Øvrum Hansen (Reviews in Aquaculture, 2021)
Sustainability concerns associated with protein sources and currently used fishmeal and plant‐based meal have necessitated the quests for novel sustainable ingredients for use in aquafeeds. Yeasts have been proposed as sustainable ingredients particularly because of their potential to valorise non‐food lignocellulosic biomass into valuable protein resources. Prior to now, extensive studies exist on the role of yeast cell wall components in modulating health responses of fish. However, research on its use as a major protein source in fish diets is still in its infancy. The current review collates, synthesises and discusses the prospects of five major yeast species as future protein ingredients with respect to their nutritional adequacy in fish. Nutritional quality of Saccharomyces cerevisiae , Cyberlindnera jadinii , Kluyveromyces marxianus , Blastobotrys adeninivorans and Wickerhamomyces anomalus and their use as replacement for fishmeal and soy protein in the diets of Atlantic salmon and rainbow trout are discussed based on three protein quality indices: chemical score, essential amino acid index and ideal protein concept based on the first limiting amino acids, methionine. The crude protein contents of yeast (40–55%) are lower than that of fishmeal, but comparable with soya bean meal. Compared to fishmeal, the different yeast species have favourable amino acid profiles, except for methionine, lysine, arginine and phenylalanine which are the frequently limiting essential amino acids in Atlantic salmon and rainbow trout. This review also presents future area of research and emphasise the need for large‐scale production of yeast at competitive price to constitute a feasible replacement for fishmeal and soy protein in aquaculture.

Emergy synthesis for aquaculture: A review on its constraints and potentials - Luiz H. David; Sara M. Pinho; Feni Agostinho; Janaina Mitsue Kimpara; Karel J. Keesman; Fabiana Garcia (Reviews in Aquaculture, 2021)
The search for healthier protein sources and the growing demand for food by an increasing world population require aquaculture systems to not only be economically and technologically viable, but also sustainable. Among other methods, emergy synthesis is a powerful tool to assess the sustainability of production systems in a biophysical perspective. However, applications of emergy synthesis on aquaculture systems are seldomly found in the scientific literature. This work provides a literature review on emergy synthesis applied to aquaculture systems and discusses its constraints and potentials. The sixteen papers published between 2000‐2020 support the adoption of polycultures more than monocultures and highlight the importance of feed (4–70%) in the total emergy required by aquaculture systems, which require efforts for natural food. Methodological aspects of emergy synthesis applied in aquaculture systems that deserve attention by developers and analysts to avoid mistakes and erroneous conclusions were identified and discussed, and we propose some ways to solve them. These aspects are mainly related to inaccurate unit emergy values for water and feed, dubious procedures in quantifying and classifying water as renewable or non‐renewable resources, and the need to recognize the importance in accounting for ecosystem services and disservices. After overcoming these methodological inconsistencies, we foresee that emergy synthesis has potential political implications in supporting most sustainable aquaculture systems through economic (tax reduction and loans with reduced interests) and political (green labels) incentives. All these policies are important to achieve the ultimate goals of the United Nations’ Agenda 2030.

A global analysis on the systemic effects of antibiotics in cultured fish and their potential human health risk: a review - Samwel Mchele Limbu; Li‐Qiao Chen; Mei‐Ling Zhang; Zhen‐Yu Du (Reviews in Aquaculture, 2021)
The rearing of fish in intensive systems reduces their immunity leading to eruption of diseases, consequently prompting the use of antibiotics. Antibiotics are currently used in cultured fish globally to treat/prevent diseases. On the one hand, antibiotics used in aquaculture help to improve fish health by killing or inhibiting pathogenic bacteria proliferation. However, on the other hand, they cause multiple side effects. To date, information on systemic effects of antibiotics in cultured fish is scattered and their potential human health risk remains elusive. This review critically analyses and discusses the available information in the literature on the positive and negative effects of antibiotics in cultured fish and their potential human health risk via fish consumption. The review found 44 different antibiotics dominated by oxytetracycline were studied in various fish species worldwide. Antibiotics used in global aquaculture either decrease or increase fish growth and survival rates. They induce oxidative stress, which affect antioxidant and detoxification responses and cause host–microbiota dysbiosis. These changes compromise the fish immunity system, which ultimately lead to cellular damage. The toxicities generated inhibit the fish aerobic glycolysis, suppress lipogenesis and fatty acid β‐oxidation while increase energy demand by initiating gluconeogenesis and anaerobic glycolysis. Consumption of fish treated with antibiotics causes human health risk. Future studies are required on agents to restore dysfunctions induced by antibiotics in cultured fish, while attempts to limit their utilisation in aquaculture production are underway. [Correction added on 21 November 2020, after first online publication: The abstract has been amended to clarify the scope of the review.]

Towards cost‐effective biofouling management in salmon aquaculture: a strategic outlook - Nina Bloecher; Oliver Floerl (Reviews in Aquaculture, 2021)
Biofouling is an ongoing challenge for marine salmon aquaculture, impacting farming operations, fish health and welfare. Current mitigation strategies employed in Norway and Scotland rely mainly on the use of antifouling coatings and reactive removal of biofouling. These approaches are not only costly and of limited efficacy, but also pose active risks and likely contribute to mortality of fish during grow‐out at sea. Given the inefficiencies of current biofouling management approaches and the industry’s objectives for growth and sustainability, a strategic assessment of future avenues for biofouling management is needed. We here present such an assessment and outline three novel biofouling management strategies that, once implemented, could facilitate improved fish health and welfare, reduced environmental impacts and benefits to the public perception of fish farming. These strategies are based on: (i) efficient antifouling coatings; (ii) antifouling combined with intermittent cleaning; and (iii) grooming of nets. We discuss the advantages, challenges and research and development needs associated with the realisation of these strategies. Drawing on experiences from agricultural systems and invasive species management, we show how the costs involved in the implementation of new strategies will over time be offset by the direct and indirect benefits arising from a reduction in environmental and fish health impacts and an increase in the industry’s social licence to operate.

Integrated pest and disease management in aquaponics: A metadata‐based review - Ewumi Azeez Folorunso; Koushik Roy; Radek Gebauer; Andrea Bohatá; Jan Mraz (Reviews in Aquaculture, 2021)
Aquaponics has the potential to produce sustainable, high‐quality food through integration of hydroponics and aquaculture, but its commercialization is stalled by bottlenecks in pest and disease management. We reviewed integrated pest and disease management steps and techniques in hydroponics to qualify as suitable techniques for different aquaponic designs. Non‐chemical prophylactic measures are highly proficient for pest and disease prevention in all designs. Still, the use of chemical control methods remains highly complicated for all systems. We simulated 10–20% runoff concentrations of 9 pesticides in the common UVI design and compared them with NOEC, LC 50 of fish. Endosulfan seems most toxic with runoff AI (20.7 μg L −1 ) exceeding LC 50 (10.2 μg L −1 ) and NOEC (0.05 μg L −1 ). At 20% runoff, most chemical pesticides pose risks in aquaponic systems. Natural pesticides were also discussed as potential alternatives with low acute toxicity to fish, but little is known about their effects on water and bacteria. While insecticides and herbicides are replaceable by well‐established commercial biocontrol measures, fungicides and nematicides would still be relevant in aquaponics due to low efficiency of alternatives (e.g. natural enemies, entomopathogenic fungus). Monitoring and cultural control are the first approaches to contain pest population below the action threshold. Biological controls, in general, are adaptable to a larger extent. Further studies are required on how to utilize indigenous microbial community in aquaponics (dominated by Proteobacteria; effective at ~10 3 –10 9 CFU mL −1 ) as a frontline defence.

Challenges and benefits of applying fish behaviour to improve production and welfare in industrial aquaculture - Georgia Macaulay; Samantha Bui; Frode Oppedal; Tim Dempster (Reviews in Aquaculture, 2021)
An understanding of behaviour is used in zoos, laboratories and agriculture to reduce stressful aspects of the captive environment for animals. While fish are one of the most cultivated of all vertebrate groups, incorporating their behaviour into production management has proved elusive. Here, we evaluate the current evidence base relating to use of (i) innate behaviours of fish and (ii) their ability to learn new behaviours via human‐mediated training or through social learning, in fish farms. Studies that tested habituation and conditioning (training) as a tool to improve welfare demonstrate positive effects for improving fish welfare and coping capacity. However, methods solely reliant on innate behavioural responses to stimuli will always be imperfect, due to variation in individual responses which are often context dependent. To date, there has been no successful demonstration of social learning as a tool for aquaculture. While many experimental scale studies report promising results, few have translated to commercial scale, highlighting a mismatch between theoretical and practical use and cautions against extrapolation of results from small‐scale studies to commercial situations. While some promising evidence exists that fish behaviour can be integrated into farm management, logistical and scale‐related hurdles must be overcome before this can occur. We conclude that fish behaviour is an additional and currently under‐researched resource that could be integrated into farm practices to improve production and welfare in industrial aquaculture.

Use of glycerol in fish nutrition: a review - Marlise Teresinha Mauerwerk; Izabel Volkweis Zadinelo; Fábio Meurer (Reviews in Aquaculture, 2021)
Crude glycerol and its purified and synthesized forms derived from biodiesel production are non‐toxic, biodegradable, biocompatible and versatile, and can be converted into various chemicals or products for biological use. Among the possible uses, there is its use in fish feeding, due to the chemical and nutritional composition, for being classified as energetic food and has low cost. The possibility of using glycerol in fish diets has been motivated by increasing maize prices, the excessive amount of glycerol produced and its processing costs for other purposes. Glycerol use in fish diet formulations is feasible, provided that certain factors be evaluated, such as digestibility and inclusion levels. In this context, this review discussed the main aspects that must be taken into account regarding glycerol use in fish diets, such as the characteristics and chemical composition of its categories, their fish metabolism pathways and their influence on fish plasma glucose. Crude glycerol or glycerine displays good potential for use in fish feed, as it contains adequate energy concentrations and can replace part of fish feed maize. However, it is evident that assessments concerning specific physiological phases, such as fish in reproductive phases, as well glycerol stability in water, are required.

Microbiome diversity and dysbiosis in aquaculture - Sandra Infante‐Villamil; Roger Huerlimann; Dean R. Jerry (Reviews in Aquaculture, 2021)
With the continuous growth of the human population and associated need for high‐quality protein, the aquaculture sector will be required to increase significantly in productivity. This growth in productivity will be achieved through more efficient use of resources like feeds, genetic improvement and limiting the impacts of disease. One of the key links between animal productivity and disease is that of microbial diversity, with high‐throughput sequencing technologies increasing our understanding of the role microorganisms play in health, development and physiology of vertebrate and invertebrate hosts alike. Increasing our understanding of microbial–host interactions will help avoid or manage dysbiosis in aquaculture systems with the final aim of improving productivity. We review the current literature, which indicates that there is an association between productivity and microbial diversity in aquaculture systems, as changes in bacterial microbiomes are implicated in animal performance, in disease development associated with both bacterial and viral origin, and in dysbiosis triggered by environmental stressors or diet choice. Dysbiosis, whether in the form of the loss of beneficial bacteria, or the expansion of pathogens or potentially harmful microorganisms, can be used as an indicator tool for productivity monitoring purposes. Development of management strategies towards preserving the microbial balance, including maintaining or increasing diversity in the host, is critical for the health of cultured aquatic animals and will likely be critical for the expansion of aquaculture.

Multifaceted applications of probiotic Bacillus species in aquaculture with special reference to Bacillus subtilis - Sukanta K. Nayak (Reviews in Aquaculture, 2021)
Microorganisms play an important role in water quality maintenance, waste management, productivity enhancement, nutrient cycling, functional feed development, protection against infectious diseases, delivery of antigens and several other health benefits in aquaculture. The most significant use of microbes in aquaculture to minimize the antibiotics and drugs is through probiotics. The scope of probiotics in modern aquaculture has been enormous due to the detrimental consequences of routinely used antibiotics and chemotherapeutic agents and demand for safe aquatic products for human consumption. Since past few decades, both scientific and commercial interests are burgeoning in this field, and over the years, several probiotics are successfully used in aquaculture. Among various probiotics that are being used, Bacillus species are the common probiotics that are used in different aquatic animals. Several probiotics species belonging to Bacillus genus are currently been used, and Bacillus subtilis is one of such probiotics that is very well‐researched and most widely used probiotics in aquaculture. While its probiotic use has already been an important component in diverse aquaculture practices, its application in water quality improvement, utility in bioflocs/bioremediation and vehicle to express and delivery of heterologous antigen are noteworthy. It exerts innumerable beneficial effects such as improvement of growth, nutrition, immunity and disease resistance in aquatic species. This bacterium adopts a variety of disparate and overlapping mechanisms such as synergistic, antagonistic, competitive exclusion and immune‐stimulating effects. This review summarizes various applications of this bacterium as probiotics, bioremediating agent, bioflocing agent and possible live vaccine vehicle in aquaculture.

Fish welfare in offshore salmon aquaculture - Malthe Hvas; Ole Folkedal; Frode Oppedal (Reviews in Aquaculture, 2021)
To accommodate further growth in the Atlantic salmon aquaculture industry, new production sites may well be established at more exposed locations along the coast or even offshore. Here, fish will encounter strong currents and powerful waves, which are avoided at traditional sheltered locations. Exposed locations offer several advantages and necessitate new technological advancements. However, the most crucial question is whether Atlantic salmon are able to thrive in these more extreme environments. In this review, we describe how strong water currents affect the physiology, behaviour and ultimately the welfare of the fish. If ambient current speeds exceed swimming capacities, fish become fatigued and get stuck on the cage wall leading to unacceptable welfare. The swimming capacity will depend on both the magnitude and duration of the current speeds encountered. Moreover, several environmental and biological factors modulate swimming capabilities, where temperature, body size and health status are particularly important to consider. A series of empirical studies are subsequently used to formulate welfare guidelines with regard to biological limits in exposed aquaculture. In addition, owing to the growing popularity of cleaner fish in salmon aquaculture, we also evaluate their usefulness at exposed sites. Overall, Atlantic salmon is a powerful sustained swimmer, and based on available site surveys of ocean currents, we conclude that the prospects for responsible farming at exposed sites looks promising. However, cleaner fish species such as lumpfish and ballan wrasse are poor swimmers and are therefore not recommended for deployment at exposed sites.

Meta‐analysis of the use of seaweeds and their extracts as immunostimulants for fish: a systematic review - Valentin Thépot; Alexandra H. Campbell; Michael A Rimmer; Nicholas A Paul (Reviews in Aquaculture, 2021)
Disease is an enduring threat to aquaculture, with direct costs from outbreaks of more than US$6 billion a year. Efforts to reduce antibiotic use in aquaculture have resulted in a recent shift towards the use of immunostimulants that boost fish immune systems. Seaweeds are a potential source of unique immunostimulants because of their diverse taxonomy (11,353 species) and diverse bioactives, but there has been no synthesis of their effects on fish. A systematic review and meta‐analysis of 142 peer‐reviewed studies was conducted to evaluate the effects of seaweed on the innate immunity, resistance (to stress and pathogens) and growth of farmed fish. Overall, our review indicated that dietary supplementation with seaweeds or their extracts had substantial positive impacts on the health and growth of fish compared with control groups and were comparable to currently utilised immunostimulants. Dramatic effects on survival of fish during challenge experiments were detected, with an average of 33% higher survival of fish fed diets that included seaweeds or their extracts. This study provides broad evidence for the benefits of supplementing fish feed with the reviewed seaweeds or their bioactive extracts, including potential synergistic effects of supplements. However, the meta‐analysis also highlighted considerable variation among studies, and between fish and seaweed species, making it difficult to extrapolate results beyond individual experiments. Future studies should focus on developing synergistic combinations of ingredients and elucidating the mode of action through isolation of seaweed bioactives, together with standardisation of experimental conditions, to fast‐track the benefits of seaweed supplements for aquaculture.

Unveiling associations between ciliate parasites and bacterial microbiomes under warm‐water fish farm conditions – a review - Ladan Jahangiri; Andrew P. Shinn; Jarunan Pratoomyot; Giana Bastos Gomes (Reviews in Aquaculture, 2021)
Intensive fish production has arguably resulted in a consequential increase in the incidence of disease within the aquaculture industry. The frequency and the severity of disease events are in part affected by changing global climatic conditions. More importantly, these changes directly influence changes in water quality parameters and the dynamics of a microbiome, pathogenic or not, in aquatic farming. Changes in temperature, for example, have both direct and indirect effects on the health status of fish, potentially increasing their predisposition to infections. In general terms, fish infections are rarely caused by a single agent or factor – frequently, multiple pathogens, changes in water quality parameters, production factors (e.g. feed quality, stocking density) and host immunity are concomitantly responsible for the establishment of infections in fish farms. Ciliate protozoans represent an important microfauna in aquatic environments. Ciliated protozoans can proliferate quickly, debilitating the host, and, in the absence of an intervention, can lead to a significant loss of stock. Ciliate infections frequently facilitate the establishment of secondary microbial species, both of which are linked to environmental and culture conditions. In this review, economically important ciliated protozoans of warm‐water cultured fish and their potential interactions with their associated bacterial microbiomes (both on/in their hosts and their surrounding environment) are discussed. Also, potential environmental triggers behind ciliate outbreaks within warm‐water aquaculture are reviewed. With better knowledge about such interactions, it will be possible to highlight innovative strategies to control ciliate parasites and bacterial infections in aquaculture.

Cyprinid herpesvirus‐2 (CyHV‐2): a comprehensive review - Raja Swaminathan Thangaraj; Sundar Raj Nithianantham; Arathi Dharmaratnam; Raj Kumar; Pravata Kumar Pradhan; Sumithra Thangalazhy Gopakumar; Neeraj Sood (Reviews in Aquaculture, 2021)
Cyprinid herpesvirus‐2 (CyHV‐2) is a linear double‐stranded DNA virus in the genus Cyprinivirus of family Alloherpesviridae . The virus is known to be highly pathogenic to ornamental goldfish ( Carassius auratus ), crucian carp ( C. carassius ) and Gibel carp ( C. auratus gibelio ), and also to the hybrids of goldfish and other carps. Cyprinid herpesvirus‐2 , having the smallest genome (290.3 kb) among Cyprinivirus, causes herpesviral hematopoietic necrosis disease (HVHND) that results in huge economic losses in aquaculture industry as the disease can cause high mortality (50–100%) among the affected fish. The disease was initially reported as the cause of epizootics in juvenile goldfish of Japan during 1992 and 1993. To date, this disease has been reported around the world including Europe, North America, Oceania and Asia. Huge economic losses due to the CyHV‐2 infection among cultured gibel carp in China, during 2011–2012, mass mortality in crucian carp during 2012 in Italy, 95% mortality in goldfish during 2014 in France, 85% mortality in goldfish during 2016 in Poland had been reported. Strategies for controlling the spread of CyHV‐2 are thus urgently required to limit economic damage. Furthermore, the review will shed light on lacunae in current knowledge as well as on the perspectives that merits further investigations on CyHV‐2 research. The paper forms the first comprehensive overview of CyHV‐2 causing a serious economically significant fish disease and, will be helpful for the researchers to get all related information from a single manuscript.

Protein–protein interaction network: an emerging tool for understanding fish disease in aquaculture - Khor Waiho; Nor Afiqah‐Aleng; Mat Taib Mimi Iryani; Hanafiah Fazhan (Reviews in Aquaculture, 2021)
Protein–protein interactions (PPIs) play integral roles in a wide range of biological processes that regulate the overall growth, development, physiology and disease in living organisms. With the advancement of high‐throughput sequencing technologies, increasing numbers of PPI networks are being predicted and annotated, and these contribute greatly towards the understanding of pathogenesis and the discovery of novel drug targets for the treatment of diseases. The use of this tool is gaining popularity in the identification, understanding and treatment of diseases in humans and plants. Due to the importance of aquaculture in tackling the global food crisis by producing cheap and high‐quality protein source, the maintenance of the overall health status of aquaculture species is essential. With the increasing omics data on aquaculture species, the PPI network is an emerging tool for fish health maintenance. In this review, we first introduce the concept of PPI network, how they are discovered and their general application. Then, the current status of aquaculture and disease in aquaculture are discussed. The different applications of PPI network in aquaculture fish disease management such as biomarker identification, mechanism prediction, understanding of host–pathogen interaction, understanding of pathogen co‐infection interaction, and potential development of vaccines and treatments are subsequently highlighted. It is hoped that this emerging tool – PPI network – would deepen our understanding of the pathogenesis of various diseases and hasten the prevention and treatment processes in aquaculture species.

The decline of mussel aquaculture in the European Union: causes, economic impacts and opportunities - Lamprakis Avdelas; Edo Avdic‐Mravlje; Ana Cristina Borges Marques; Suzana Cano; Jacob J. Capelle; Natacha Carvalho; Maria Cozzolino; John Dennis; Tim Ellis; José M. Fernández Polanco; Jordi Guillen; Tobias Lasner; et al. (Reviews in Aquaculture, 2021)
In contrast to the increasing aquaculture production of mussels worldwide, production in the European Union (EU) has shown a decreasing trend over the last two decades. Aquaculture production of mussels in the EU peaked in the late 1990s at more than 600 000 tonnes; by 2016, production volume had dropped by 20% to 480 000 tonnes. As mussel production represents more than ⅓ of EU aquaculture production, this decrease is an important contributor to the stagnation of EU aquaculture. Previous studies have suggested diseases, lack of mussel seed (spat), and low profitability as the main causes of the EU mussel production decrease. In this study, we investigate how economic and environmental factors have contributed. Moreover, we examine if the different mussel production techniques (raft, longline, on‐bottom, and ‘bouchot’) have been differently affected, by analysing the economic performance and cost structure evolution for the period 2010–2016. We complement these results with a SWOT (strengths, weaknesses, opportunities, and threats) analysis of the EU mussel sector based on expert knowledge.

Nutritional immunity of fish intestines: important insights for sustainable aquaculture - Mahmoud A.O. Dawood (Reviews in Aquaculture, 2021)
Intensive culture systems are usually employed to increase the production, but we suspect that, in such systems, fish suffer infection and stress, which weakens their health. However, such systems may fail due to lack of resources or difficulty in controlling the rearing conditions’ optimization. When intensive culture systems fail, aquatic animals gradually stop feeding. Accordingly, their physiological status deteriorates, and their immunity is suppressed. Through some strategies, it is possible to protect fish from disease by providing balanced food that maintain intestinal health and improve digestion, thereby increasing immunity. Protecting the health of the intestinal barriers is the primary guarantee of fish health. The local immunity of the intestine is associated with the innate and adaptive immunity of the fish’s entire body. Thus, it is necessary to understand the interaction between the gut microbiota and the general immune system, as well as the most important reasons that can increase or suppress intestinal immunity. Many studies have confirmed that balanced diets containing basic nutritional requirements are the primary factor for maintaining intestinal health in aquatic animals. Another strategy for improving the intestine’s local immunity is to use some non‐nutritional food additives that increase the activity of beneficial bacteria and the secretion of digestive enzymes and decrease the harmful bacteria. This review article aimed to clarify the relationship between a balanced aquafeed and the intestinal health of aquatic animals by discussing the findings of related studies. Awareness of this correlation between diet and intestinal health is expected to aid the aquaculture industry to develop proper nutritional strategies that ensure the protection of fish health.

Enzymatic fish protein hydrolysates in finfish aquaculture: a review - Muhammad A.B. Siddik; Janet Howieson; Ravi Fotedar; Gavin J. Partridge (Reviews in Aquaculture, 2021)
In intensive farming systems, fish are held at high densities, which may increase stress, leading to susceptibility to diseases that result in economic losses. Therefore, effective feeding practices incorporating health‐promoting compounds such as proteins, hydrolysates and bioactive peptides that can stimulate the defence mechanisms of fish and achieve better growth are some of the priorities for sustainable aquaculture development. Globally, the fish processing industries generate and discard a large volume of waste every year, estimated at up to 60% of the harvested biomass. This waste can be converted to value‐added products such as fish protein hydrolysate (FPH) with the addition of various proteolytic enzymes. FPH from fish processing waste including skin, heads, muscle, viscera, liver and bones is a good source of protein, amino acids, peptides and antioxidants and has been found to possess desirable functional and bioactive peptides. A moderate inclusion of FPH in aquafeeds has the potential to improve growth, feed utilization, immune functions and disease resistance of fish. Production of FPH, targeted to more precise molecular weight ranges, has superior functionalities that are in high demand. With interest in FPH as an aquafeed supplement, this review aimed to summarize the source, production processes and functional properties of FPH and the reported impact of FPH in aquafeed supplement on fish growth, survival, feed utilization, immune response and disease resistance. Possible limitations of using FPH and future research potential as an opportunity for the use of processing fish waste are also discussed.

Advances of intra‐species molecular typing analysis of aquatic probiotics approved by the Chinese Ministry of Agriculture - Juan Hu; Yuanyuan Yao; Yalin Yang; Chenchen Gao; Fengli Zhang; Rui Xia; Chao Ran; Zhen Zhang; Jihong Liu Clarke; Zhigang Zhou (Reviews in Aquaculture, 2021)
Probiotics confer a health benefit on the host and could be used as a good alternative to antibiotics. Probiotics are strain‐specific when exerting their function, so it is necessary to identify them to strain level. In recent years, intra‐species molecular typing and identification methods have developed rapidly, which commonly are used for typing the main pathogenic bacteria and rare for studies on probiotic typing, whilst it is imperative. This article describes molecular typing methods including AFLP, RAPD, PFGE, ribotyping, MLST, rep‐PCR and whole‐genome sequencing to identity some aquatic probiotics approved by the Ministry of Agriculture of China, which are Bifidobacterium , Enterococcus , Lactobacillus , Pediococcus , Aspergillus , Bacillus , Rhodopseudomonas palustris and Streptococcus thermophilus . In addition, the principles, applications, advantages and disadvantages of these typing methods are also discussed.

Infectious diseases and treatment solutions of farmed greater amberjack Seriola dumerili with particular emphasis in Mediterranean region - George Rigos; Pantelis Katharios; Dimitra Kogiannou; Chiara M. Cascarano (Reviews in Aquaculture, 2021)
Greater amberjack ( Seriola dumerili ) is a very promising candidate for the diversification of the Mediterranean aquaculture due to its high demand, excellent flesh quality and high market prices. Its production expansion has, however, failed so far, due to several bottlenecks mainly related to pathology. This review addresses the major pathogens, which hinder the culture of greater amberjack with special focus in the Mediterranean region, and highlights possible treatment solutions. Among the important recorded pathogens of caged greater amberjack in the Mediterranean, the gill monogenean Zeuxapta seriolae seems to be the most problematic, causing significant losses. While formalin immersions are inefficient to combat this parasite, baths with hydrogen peroxide are extremely effective and praziquantel administration could be a more practical in‐feed treatment solution. The digenean blood flukes, Paradeontacylix spp., also account for important losses in greater amberjack farms in the same region. Dietary administration of praziquantel constitutes an effective therapeutic measure against those infections. Vibrio harveyi is also a bacterial pathogen severely affecting fish maintained both in land‐based facilities and in cages, whereas Epitheliocystis is a disease reported frequently that can be fatal when it occurs at early stages. Skin flukes such as Benedenia seriolae and Neobenedenia girellae as well as other parasites bacteria and viruses mentioned herein, which have caused substantial losses in Asian enterprises, but have not been identified yet in greater amberjack farmed in the Mediterranean, should be considered as potential threats.

Chinese Abstracts (Reviews in Aquaculture, 2021)

Moving towards more sustainable aquaculture practices: a meta‐analysis on the potential of plant‐enriched diets to improve fish growth, immunity and disease resistance - Miriam Reverter; Nathalie Tapissier‐Bontemps; Samira Sarter; Pierre Sasal; Domenico Caruso (Reviews in Aquaculture, 2021)
Aquatic animal diseases are one of the major limiting factors in aquaculture development, with disease emergence forecast to increase with global change. However, in order to treat increasing diseases in a context of global emergence of antimicrobial resistance and strengthening regulations on antimicrobial use, sustainable alternatives are urgently needed. The use of plant supplements to increase fish immunity and disease resistance has gained much popularity within the last decades. The use of functional supplements, such as plants, can also improve growth and feed assimilation, contributing to a better optimization of aquaculture resources (e.g. fish meal inclusion). We conducted a systematic review and meta‐analysis in order to identify the research gaps in the use of plant‐enriched diets in fish aquaculture and estimate, for the first time, the overall efficacy of plant‐enriched diets on fish growth, immunity and disease resistance as well as the effect of intrinsic parameters (fish trophic level, type of plant material, dosage, treatment duration and pathogen species) on the treatment efficacy. We found that plant‐enriched diets significantly enhanced growth, immunity and disease survival of treated fish, regardless of the fish trophic level, treatment duration and type of material used. We also show that plant supplements are a versatile alternative that can benefit different aquaculture sectors (from small‐scale fish farmers to intensive productions). Finally, we observed that studies need to improve the information reported about the plant material used (e.g. origin, identification, chemical composition), in order to allow the comparison of different experiments and improve their repeatability.

Effect of illumination on fish and amphibian: development, growth, physiological and biochemical processes - Alexander B. Ruchin (Reviews in Aquaculture, 2021)
Being one of the main environmental factors, the light factor influences many aspects of animal life. Photoperiod, light intensity (illumination) and wavelength are the primary periodic factors. There is a review that discusses the role of illumination on various life processes of aquatic anamnia vertebrates (fish and amphibians). The effect of light on the development, growth, respiration, consumption and efficiency of food conversion, hormone release, reproduction and behaviour of fish and amphibians has been studied. Illumination influences differently a significant number of physiological and biochemical processes and reactions of anamnia vertebrates at various development stages. The obtained results show that the nature of exposure to light is species‐specific and corresponds to the ecological niche of species. Illumination influences both positively and negatively the development, growth and other physiological processes of fish and amphibians. Illumination plays a special role during the first feeding of fish in the environment and aquaculture. There are positive and negative behavioural responses of fish to light. However, it is not always possible to distinguish fish species with only a negative or only a positive reaction to light. The quality of the reaction can be influenced by the stage of development of eggs or larvae, age characteristics, feeding status, season, time, the physiological state of fish, morbidity, etc. A promising area of research is the study of the influence of light on the hormonal status of the body and reproduction of fish. Also, the light pollution and its influence on the physiology of anamnia vertebrates are important.

Oxidative stress and use of antioxidants in fish semen cryopreservation - Leydy Sandoval‐Vargas; Mauricio Silva Jiménez; Jennie Risopatrón González; Elías Figueroa Villalobos; Elsa Cabrita; Iván Valdebenito Isler (Reviews in Aquaculture, 2021)
Reactive oxygen species (ROS) have been proposed as one of the main causes of the impairment of fish spermatozoa integrity and functionality during cryopreservation. The high content of unsaturated fatty acids in sperm cells and the low antioxidant capacity of diluted semen are key factors in making sperm cells susceptible to ROS attacks. For this reason, some recent studies have determined the antioxidant status of the seminal plasma and spermatozoa of fish species. Additionally, some studies have evaluated the effects of antioxidants on post‐thaw sperm quality. Although ROS are certainly involved in sperm damage, other factors, such as ice crystal formation, seem to play a crucial role in cryodamage. This challenge has not yet been resolved because both the endogenous antioxidant capacity of the semen and its response to different supplementation practices seem to present specific inter‐ and intraspecies characteristics and effects. This review summarises knowledge on antioxidant defence and oxidative stress in fish semen, as well as antioxidant supplementation in cryopreservation media, in order to establish perspectives for future studies.

Improving and standardizing protocols for alkaline protease quantification in fish - Héctor Nolasco‐Soria (Reviews in Aquaculture, 2021)
Assessing the activity of alkaline protease is a common procedure in many biological, physiological and nutritional studies, including the maturation and digestive capacity of the digestive tract, in gastric and non‐gastric fish species. After reviewing the available literature on fish digestive alkaline proteases published during a time span of ten years (2008–2018), it has been detected some possible methodological and/or interpretative inconsistencies in this kind of studies when quantifying alkaline protease activity and concluded that special attention should be paid on: (i) the proper preparation of intestine and pyloric caeca extracts, (ii) the use of the proper reaction conditions at the normal range of physiological pH values and temperature and (iii) the proper quantification of the number of peptide bonds hydrolysed for alkaline protease unit calculation. The implementation of these recommendations and the proposal of more suitable (previously tested) methodological steps will promote the standardization of feasible alkaline protease analytical procedures, as well as improve the reliability of comparative studies between different fish species of aquacultural importance, dealing with the alkaline proteolytic enzymes.

Use of biofloc technology in shrimp aquaculture: a comprehensive review, with emphasis on the last decade - Abdel‐Fattah M. El‐Sayed (Reviews in Aquaculture, 2021)
In face of the shortage of, and competition with, land and water, the sustainability of aquaculture will have to depend on vertical development, through improving production environments, increasing productivity and enhancing aquaculture technologies. Biofloc technology (BFT) has emerged as new alternative for sustainable aquaculture, which could contribute to FAO Sustainable Development Goals (SDGs) related to food security. Extensive research has been carried out on the development and application of BFT in aquaculture since early 1990s, with emphasis on shrimp culture. Over 40% of BFT publications in aquaculture were directed to shrimp farming. Therefore, I strongly believe that the accumulated knowledge on the applications of BFT in shrimp farming and the experience gained, especially during the last 10 years (2010–2020), are now more than worthy of critical review and analysis. This review summarizes the most update knowledge on the use of BFT in different marine shrimp and freshwater prawn aquaculture. Emphasis has been on factors affecting shrimp production in BFT systems, integration of biofloc‐based shrimp farming with other aquatic farmed species, nutritional value of bioflocs as a natural food or feed ingredient for farmed shrimp and prawn, the application of BFT in different rearing phases, the use of biofloc as a natural probiotics and their effects on shrimp health and physiological functions, economic considerations and commercial applications of BFT‐based shrimp aquaculture, and the major challenges facing shrimp farming in biofloc systems.

The relative importance of enhancement to the production of Salmon on Iturup Island (Kuril Islands, Russia) - Natalya Klovach; Vsevolod Leman; Ilya Gordeev (Reviews in Aquaculture, 2021)
A historical review of biological enhancement and fisheries for Iturup Island demonstrates that enhancement has significantly increased numbers of chum salmon while pink salmon are produced almost entirely naturally. Fourteen hatcheries currently produce and release chum salmon fry; four of these also generate pink salmon. Favourable natural conditions make the waters near Iturup Island one of the most productive marine areas in the Russian Far East. Efficient hatcheries combined with favourable conditions resulted in increases in chum salmon catches from less than 100 tonnes in the early 1990s to more than 20 000 tonnes in the late 2010s. Becoming better informed of factors controlling salmon production in the Kuril Islands should help scientists in other regions of the North Pacific understand what controls their own salmon populations.

Issue Information (Reviews in Aquaculture, 2021)

Granulomatosis in fish aquaculture: a mini review - Pablo Martínez‐Lara; Marcel Martínez‐Porchas; Teresa Gollas‐Galván; Jorge Hernández‐López; Glen R. Robles‐Porchas (Reviews in Aquaculture, 2021)
Bacterial infections represent the greatest threat for fish culture, especially those causing granulomatous processes. Although there are experimental models used to elucidate the mechanisms of pathogenicity in granulomatous processes, most of these aimed to understand the infection in superior vertebrates like humans; therefore, there is still an urgent need to expand the number of infection models focused on aquaculture. Granulomatous infections are difficult to detect in early stages due to the lack of clinical signs and because these clinical signs have a great similarity to those generated by other pathogenic bacteria. Besides, there is no evidence or reports of granulomatous co‐infections in aquaculture environments which is a plausible scenario either in culture systems or in the wild environment; co‐infections could interfere with a correct diagnosis of any granulomatous disease, as reported for granulomatous infections in terrestrial species. This revision aims to highlight the state of the art in the knowledge of pathogenic bacteria associated with granulomatosis in fish aquaculture as well as analysing this information.

Aerobic swimming in intensive finfish aquaculture: applications for production, mitigation and selection - David J. McKenzie; Arjan P. Palstra; Josep Planas; Simon MacKenzie; Marie‐Laure Bégout; Helgi Thorarensen; Marc Vandeputte; Daan Mes; Sonia Rey; Gudrun De Boeck; Paolo Domenici; Peter V. Skov (Reviews in Aquaculture, 2021)
We review knowledge on applications of sustained aerobic swimming as a tool to promote productivity and welfare of farmed fish species. There has been extensive interest in whether providing active species with a current to swim against can promote growth. The results are not conclusive but the studies have varied in species, life stage, swimming speed applied, feeding regime, stocking density and other factors. Therefore, much remains to be understood about mechanisms underlying findings of ‘swimming‐enhanced growth’, in particular to demonstrate that swimming can improve feed conversion ratio and dietary protein retention under true aquaculture conditions. There has also been research into whether swimming can alleviate chronic stress, once again on a range of species and life stages. The evidence is mixed but swimming does improve recovery from acute stresses such as handling or confinement. Research into issues such as whether swimming can improve immune function and promote cognitive function is still at an early stage and should be encouraged. There is promising evidence that swimming can inhibit precocious sexual maturation in some species, so studies should be broadened to other species where precocious maturation is a problem. Swimming performance is a heritable trait and may prove a useful selection tool, especially if it is related to overall robustness. More research is required to better understand the advantages that swimming may provide to the fish farmer, in terms of production, mitigation and selection.

How domestication alters fish phenotypes - Sylvain Milla; Alain Pasquet; Leila El Mohajer; Pascal Fontaine (Reviews in Aquaculture, 2021)
Domestication can be defined as the adaptation of an animal to the human environment and its constraints. Accumulating evidence strongly indicates that domestication plays essential roles in modulating the phenotypes of teleosts, despite the scattered information. Animal husbandry and molecular, physiological and behavioural studies have identified a high degree and complexity of biological changes induced by domestication. These phenotypic modifications during domestication vary greatly amongst species and physiological function (e.g. growth, reproduction, response to stress and immunity), probably due to a variety of intrinsic and extrinsic factors that can interfere with phenotypic changes. Indeed, much information about domestication is lacking, which impedes the generalisation of our understanding of the effects of domestication. This review gathers and clarifies the available information about the main effects of fish domestication. We use a broad physiological approach for understanding these biological consequences, from the genesis of domestication (e.g. netting from the wild) to the ultimate step (controlled artificial selection). We also suggest ways to predict the effects of domestication and to better understand the sources of the biological changes.

Insights into gene expression responses to infections in teleosts using microarray data: a systematic review - Mario Caruffo; Dinka Mandakovic; Pablo Cabrera; Igor Pacheco; Liliana Montt; Ignacio Chávez‐Báez; Madelaine Mejías; Francisca Vera‐Tamargo; Javiera Perez‐Valenzuela; Alonso Carrasco‐Labra; Rodrigo Pulgar (Reviews in Aquaculture, 2021)
The rapid growth of production in aquaculture in the last decades has brought unwanted consequences affecting fish health and increasing the susceptibility to different infections. This systematic review aimed to analyse and summarize the current knowledge of gene expression responses to infectious diseases in teleosts using viruses, bacteria, fungi and parasites as agents through published microarray data. We conducted searches in electronic databases, including PubMed, Web of Science and SCOPUS until 1 May 2019. We identified 862 citations across databases and manual searches. After removing duplicates, we screened 455 unique references using titles and abstracts, of which 262 proved potentially eligible and evaluated using full text. A total of 79 articles proved eligible for this review. From the articles retrieved, we examined 261 different experiments (or ‘studies’) and more than a hundred thousand differentially expressed genes (DEGs). This systematic review represents the first catalogue of genes (and their associated processes) that differentially transcribe in different teleost species (13 species) due to infections generated by a large variety of pathogens (38 types). Although the obtained gene expression results are in considerable measure associated with expected immune response, other genes showed surprising significant transcriptional outcomes that may unravel unknown functions related to fish infections. This type of investigations facilitates the visualization of existing gaps in researches that may inspire future analysis in non‐traditional but relevant host or pathogen species.

Healthy microbiome: a key to successful and sustainable shrimp aquaculture - Riya Rajeev; K.K. Adithya; G. Seghal Kiran; Joseph Selvin (Reviews in Aquaculture, 2021)
The microbiome of the host and its surroundings play a vital role in its health and well‐being. Unlike the terrestrial organisms that maternally acquire its microbiome, the aquatic species mainly get colonized by the microorganisms in its aquatic surrounding and are exposed to a wide variety of microbial community based on the type of aquatic environment the host inhabits. This review is focused on the aquaculture and shrimp microbiome and factors that influence its microbiome such as prebiotics, probiotics, synbiotics, diet, stress conditions, frequency and type of antibiotics used, host physiological conditions and developmental stages. This review also casts light on the role of the microbiome in enhancing the shrimp health, immune response, microbial colonization, and the effects of the biofloc system on shrimp and aquaculture microbiome. Moreover, beneficial microbes can be a safer alternative to harmful antibiotics used in aquaculture, which can thereby prevent the emergence of superbugs and also enhance the production rate. A proper understanding of the interactions between the host and its microbiome can help us to modulate and manipulate the aquaculture microbiome to enhance the health of aquatic organisms, which ensures the growth of the aquaculture industry. Therefore, the treatment strategies should be targeted towards the modulation of shrimp and aquaculture microbiome, which acts as beneficial partners to overcome the challenges confronted by the aquaculture sector.

Role of sex‐biased miRNAs in teleosts – a review - Rayees Ahmad Bhat; Manisha Priyam; Md Javed Foysal; Sanjay Kumar Gupta; Jitendra Kumar Sundaray (Reviews in Aquaculture, 2021)
MicroRNAs (miRNAs) are small non‐coding RNAs that control the expression of genes by targeting specific mRNAs. Data related to miRNAs are limited for fish species, with only 16 out of the 30 000 fish species enlisted in miRBase. In the present review, we have summarized the recent findings on the implication of miRNAs in the teleost reproduction with an emphasis on commercially important candidates. The information related to various miRNAs and their roles during different developmental stages of gonads in nine important species has been compiled. We have focused on the trend of sexual dimorphism in the gonadal miRNA repertoire of teleost species. Species‐specific variability is observed in the expression pattern of gonadal miRNAs in both male and female fish. It is noteworthy that our summarization of teleost miRNAs in reproduction has highlighted the gaps in functional information on the identified miRNAs (both conserved and novel). It is only after functional validation of the miRNA targets, one can use these findings to enhance reproductive health and production of the commercial teleost species to boost overall aquaculture sector.

A comparison of the bioremediation potential of five seaweed species in an integrated fish‐seaweed aquaculture system: implication for a multi‐species seaweed culture - Yun Hee Kang; Sangil Kim; Sun Kyeong Choi; Hyuk Je Lee; Ik Kyo Chung; Sang Rul Park (Reviews in Aquaculture, 2021)
We investigated the growth and bioremediation potential of five local seaweed species ( Codium fragile , Ulva pertusa , Ecklonia stolonifera , Saccharina japonica and Gracilariopsis chorda ), using an integrated fish‐seaweed culture system as a biofilter for effluents from black rockfish ( Sebastes schlegelii ) tanks. The specific growth rate, biomass and net yield values of green algae were higher than those of brown algae. The tissue N and P levels of all species increased at the end of the experiment, but N:P ratios varied among seaweed species. The uptake rate and efficiency of total ammonia nitrogen uptake were the highest in U . pertusa and lowest in S . japonica . The phosphate uptake efficiency among all species ranged from 43% for S . japonica to 30% for G. chorda . These results suggest that all species can efficiently remove enriched nitrogen and phosphorus from fish tank effluents and are suitable for integrated aquaculture and bioremediation. However, inter‐specific differences were observed among seaweeds with regard to the biofiltration performance for different forms of nitrogen. The highest total oxidized nitrogen (ToxN) uptake efficiency was observed in E . stolonifera and S . japonica , while the lowest was observed in U . pertusa . ToxN uptake rates of E . stolonifera and S . japonica was 1.8 times higher than that of U . pertusa . Thus, a seaweed polyculture that included species with varying nitrogen source‐specific biofiltration activities might allow us to remove nutrients from effluents more effectively. These results provide valuable information regarding the selection of optimal seaweed species in fish‐seaweed integrated systems.

Triploid induction in penaeid shrimps aquaculture: a review - Hidayah Manan; Mhd Ikhwanuddin (Reviews in Aquaculture, 2021)
The application of biotechnology in marine shrimp especially in penaeid shrimps aquaculture is increasing in demand. Researcher and scientist consents that application of biotechnology helps improve the shrimp quality and consequently increase the aquaculture shrimp productions. The monosex culture becomes one of the focuses nowadays as the techniques can help increasing the aquaculture yield and obviously increases the aquaculture production. The application of triploidy in penaeid shrimp helps to increase the shrimp size, faster the shrimp growth and also recognized as one of the successful techniques for monosex culture as well as induction of polyploidy, gynogenesis and hormones induces. Triploidy technique is also beneficial to be applied in the shrimp aquaculture for the production purposes. This review paper focuses on the triploid induction in penaeid shrimps, the suitable method to be applied, and also the overview of the triploidy induction from others previous study. Hopefully, this review paper can be the benchmark for the application of triploidy technique in shrimp aquaculture industry and help promoting the shrimp aquaculture shrimp productions in the future.

A review on the beneficial effect of thymol on health and production of fish - Mahmoud Alagawany; Mayada R. Farag; Sameh A. Abdelnour; Shaaban S. Elnesr (Reviews in Aquaculture, 2021)
The thymol molecule is a food additive, used to boost the growth, production and feed efficiency via improving the digestive secretion and activating the structure and function of digestive system. The major application of thymol essential oil is used in animal rations, particularly as a natural feed additive to decrease hazardous compounds in a wide range of animal species. Thymol essential oil plays an important role in improving the nutrient bioavailability, reproductive and productive performance, general health and immunity of livestock besides reducing problems of many animal diseases such as cancer and some other diseases. These roles may be attributed to the ability of thymol as anticancer, antimicrobial, antiviral, antioxidant, immunomodulators, anti‐inflammatory and antispasmodic factors through suppressing free radicals and harmful constituents from interacting with cellular biological components and its capability to manipulate the balance of the intestinal microbiota, increased digestion, metabolism and absorption of nutrients. This review elucidates the chemical structure and natural sources, physical proprieties and practical applications of thymol in fish nutrition.

Moulting in the grow‐out of farmed shrimp: a review - Daniel Lemos; Delphine Weissman (Reviews in Aquaculture, 2021)
The importance of moulting for growth in farmed shrimp is reviewed in relation to the physiological cycle, induction triggers, behavioural and compositional changes, elements for successful moulting and potential strategies for moulting management. Successful ecdysis is also dependent on pond water quality, health and nutritional status. The stages in the moulting cycle are as follows: premoult, the preparation period for moulting that comprises the longest period in the cycle and includes accumulation of nutrient reserves; post‐moult, short and crucial stage for shrimp recovery after moulting; and intermoult, when feeding is continuous and most of growth occurs. The ecdysis is very rapid and mainly dependent on suitable physiological status of individuals. Up to 10% of the whole shrimp moulting cycle may rely on body nutrient reserves, once feeding is decreased or ceased (premoult and post‐moult). Moulting is started by hormonal increments in haemolymph, 20‐hydroxyecdysone and methyl farnesoate, which are found similar in insects. Beyond health and nutrition, proper environmental conditions such as good water quality are essential for successful moulting, hardening of exoskeleton and rapid growth. Moulting prediction and management may result in significant feed savings in pond farming and potential effects of, for example, moon phases and stressors have to be further considered. The complex nature of moulting in shrimp, including different sorts of endocrine regulation and environmental stimuli, suggests it is difficult to be precisely controlled in farmed populations. Moulting physiology of shrimp is discussed in relation to some farming practices.

Immune responses and immunoprotection in crustaceans with special reference to shrimp - Amod Kulkarni; Sreedharan Krishnan; Deepika Anand; Shyam Kokkattunivarthil Uthaman; Subhendu Kumar Otta; Indrani Karunasagar; Rajendran Kooloth Valappil (Reviews in Aquaculture, 2021)
Crustacean aquaculture, dominated by shrimp, is a highly profitable food‐producing sector in the world. However, a variety of biotic and abiotic stressors can have adverse effect on the immune system of shrimp making them susceptible to diseases. Although a vertebrate‐like adaptive immune system is lacking in shrimp, an efficient innate immune system renders protection against invading pathogens. The innate immune system comprises two distinct but overlapping components, the cellular and humoral, and these are regulated through several signal transduction pathways. The signal pathways are initiated by the recognition of pathogen‐associated molecular patterns by germline‐encoded pattern recognition receptors leading to the production of different effector molecules that act against the pathogens. RNAi‐mediated post‐transcriptional gene silencing and microRNA regulation of immune response have also been found to be functional in shrimp. Similarly, apoptosis and apoptosis‐related genes are also reported, besides interferon (IFN) system‐like antiviral regulatory mechanism. Further, some form of immune memory, termed ‘immune priming’ or ‘innate immunity with specificity’ and ‘quasi‐immune response’ is recorded in shrimp and these abilities have been exploited in verifying the immunoprotection against different pathogens. Antigens developed either directly from the pathogens or through recombinant proteins have been tested for immune‐protective ability. RNAi‐mediated protection has also been demonstrated against different shrimp viruses. This review summarizes the available scientific information on immune responses and the immunoprotection trials carried out in crustaceans with a focus on shrimp. The available research evidences indicate the potential of developing effective immunoprophylactic measures in shrimp.

Perspectives on utilization of macrophytes as feed ingredient for fish in future aquaculture - Shahida Naseem; Sami Ullah Bhat; Adil Gani; Farooz Ahmad Bhat (Reviews in Aquaculture, 2021)
Aquaculture activity supplies high‐quality protein at affordable cost. A global call for foods of aquatic origin has heightened not only due to the zooming population growth, but also because of a choice of healthier foods for human beings. As the industry expands, it is facing the high cost of feeding because the key ingredients, that is fishmeal and fish oil, of aquadiet are very expensive. Identification of alternate foodstuffs that will remarkably minimize the expense of productivity of animal protein becomes a priority with due regard to environmental footprint. Alternative feed components are vital in partially or completely substituting unsustainable but high‐value components or constituents that will otherwise have direct competition with human use. Utilization of aquatic plants as a substitute for fish meal has the potential to revolutionize aquaculture in meeting global protein demand. A lot of money is spent on aquatic weed management, so this research idea tries to integrate both economic aspects and the environmental concerns. Macrophyte‐based feed ingredients have promising nutrient profile: crude protein ranges between 11% and 32%; lipid, 2.90% and 16.81%; and ash, 8% and 31%, a good array of amino acids; and a good amount of micro‐ and macronutrients that make them prosperous substituents for fish feed.

Effects of temperature on the rate of embryonic development of cephalopods in the light of thermal time applied to aquaculture - Lorenzo Márquez; Majorie Larson; Eduardo Almansa (Reviews in Aquaculture, 2021)
The temporal description of the embryonic development in ectothermic animals and the speed of development depends on environmental temperature. The concept of thermal time helps in solving this problem by making it possible to define a linear model of development linking developmental rate and temperature. The model has been scarcely applied to cephalopods in spite of being useful for programming embryonic development and hatching events. The potential application of the linear model of development would have particular interest in the case of emerging species for aquaculture such as Octopus vulgaris or Sepia officinalis . Therefore, the main goal of this work is to review the effect of temperature on the rate of embryonic development in cephalopods in relation to the linear model of development and to discuss its potential applications and limitations to cephalopod aquaculture. As a result, a good fitting of the model has been proven not only for the total time of development, but also for the time of the organogenesis phase, in nine species of cephalopods. Usually, threshold temperatures for different developmental phases, pre‐organogenesis, organogenesis and growth, are the same. In addition, the potential use of anisothermic protocols for egg incubation, as well as the problems connected with the asynchronicity of egg laying within a single spawning are also discussed. In consequence, the linear model of development seems to be useful for basic and applied research on cephalopod embryonic development and particularly for the advancement of cephalopod aquaculture.

Resilience of cold water aquaculture: a review of likely scenarios as climate changes in the Gulf of Maine - Ian R. Bricknell; Sean D. Birkel; Susan H. Brawley; Tyler Van Kirk; Heather J. Hamlin; Kyle Capistrant‐Fossa; Kimberly Huguenard; G. Peter Van Walsum; Zhilong L. Liu; Longhuan H. Zhu; Gretchen Grebe; Emma Taccardi; et al. (Reviews in Aquaculture, 2021)
Climate change is one of the biggest challenges facing development and continuation of sustainable aquaculture in temperate regions. We primarily consider the ecological and physical resilience of aquaculture in the Gulf of Maine (GoM), where a thriving industry includes marine algae, extensive and intensive shellfish aquaculture, and a well‐established Atlantic salmon industry, as well as the infrastructure required to support these economically important ventures. The historical record of sea surface temperature in the GoM, estimated from gridded, interpolated in situ measurements, shows considerable interannual and decade‐scale variability superimposed on an overall warming trend. Climate model projections of sea surface temperature indicate that the surface waters in the GoM could warm 0.5–3.5°C beyond recent values by the year 2100. This suggests that, while variability will continue, anomalous warmth of marine heatwaves that have been observed in the past decade could become the norm in the GoM ca . 2050, but with the most significant impacts to existing aquaculture along the southernmost region of the coast. We consider adaptations leading to aquacultural resilience despite the effects of warming, larger numbers of harmful nonindigenous species (including pathogens and parasites), acidification, sea‐level rise, and more frequent storms and storm surges. Some new species will be needed, but immediate attention to adapt existing species (e.g. preserve/define wild biodiversity, breed for temperature tolerance and incorporate greater husbandry) and aquaculture infrastructure can be successful. We predict that these measures and continued collaboration between industry, stakeholders, government and researchers will lead to sustaining a vibrant working waterfront in the GoM.

Mortality of marine mussels Mytilus edulis and M. galloprovincialis : systematic literature review of risk factors and recommendations for future research - Coralie Lupo; Stéphanie Bougeard; Véronique Le Bihan; Jean Louis Blin; Gwenhael Allain; Patrick Azéma; Fabienne Benoit; Christian Béchemin; Ismaël Bernard; Philippe Blachier; Léa Brieau; Morgane Danion; et al. (Reviews in Aquaculture, 2021)
The aim of this study was to summarise the literature reporting the risk factors for mortality in the mussel species Mytilus edulis and Mytilus galloprovincialis in order to identify potential science‐based solutions to prevent or mitigate mussel mortality outbreaks. We followed the PRISMA methodology: Preferred Reporting Items for Systematic Reviews and Meta‐Analyses. The studied corpus of 91 publications (114 studies) was highly heterogeneous with respect to the methodological approaches used to define or estimate mussel mortality and the related putative risk factors. Results showed that the mortality risk of both mussel species M. edulis and M. galloprovincialis varied across the seasons, increased with an elevated seawater temperature above a thermal threshold of 20 and 24°C, respectively, decreased by protecting mussels from predation, and was associated with the presence of pathogens in M. edulis . For M. galloprovincialis , using mussel spat from the same area where the farming is carried out and farming them together with another mussel species appears to reduce the mortality risk. However, for M. edulis , this could be achieved by using pure crosses and in particular mussel spat having a selected genotype. For wild bed conservation, sand accumulation and anthropogenic sedimentation should be minimised. Our analysis showed that current approaches to this research topic are limited and are unlikely to yield actionable evidence to identify mussel mortality prevention or mitigation strategies. Therefore, recommendations are offered to increase the ability of future eco‐epidemiological research to identify multiple exposures associated with mussel mortality, underpinned by standardised efforts and cooperative initiatives.

Microplastics and their potential effects on the aquaculture systems: a critical review - Aiguo Zhou; Yue Zhang; Shaolin Xie; Yuliang Chen; Xiang Li; Jun Wang; Jixing Zou (Reviews in Aquaculture, 2021)
According to the statistics, 8.3 billion metric tonnes of plastics have been produced since 1950s, which is far more than other synthetic materials and the annual production which are about 500 million tonnes per year at present. The production of plastics makes microplastics pollution extremely widespread distribution, which will have a lasting impact on the global environment, especially on the aquaculture systems. And the distribution of the microplastics is extremely imbalanced around the global waters. In the present review, we have summarized the development of aquaculture in the World and China based on the existing data sources. And the total aquaculture production of the World will over 90 million tonnes, which will exceed the capture production in 2020. Aquaculture products will become one of the most important sources of high‐quality protein. However, we found that many kinds of microplastics are detected and enriched in both farmed and captured species. Both endogenous and exogenous factors like the use of fishing plastic products, factory farming facility and equipment, natural and synthetic feed, animal health products, aquaculture fortifier and aquatic food additives make accumulation of microplastics easier. In addition, the safety of aquaculture products is closely related to human health because the residues of microplastics in fish leading to various potential hazards. In summary, this paper reviewed the relationship between microplastics and aquaculture, aimed at calling for the rational and restricted use of plastic products in the aquaculture ecosystems.

Challenges and prospects of Viral Envelope protein VP28‐based control strategies to combat white spot syndrome virus in penaeid shrimps: a review - Sivakumar Krishnankutty Chandrika; Sajeevan Thavarool Puthiyedathu (Reviews in Aquaculture, 2021)
VP28 is an essential WSSV envelope protein used to develop innate immune recognition in shrimp against WSSV, owing to its remarkable capability to localize on the surface of shrimp epithelial cells. Transgenically engineered viral VP28 protein from several expression systems was used to increase the survival chances of shrimp against WSSV pathogen, and their efficacy was found to last for 2–3 weeks following therapy. Though few reports have shown that DNA vaccination using the VP28 DNA construct is capable of protecting shrimp from WSSV, the exact mechanism behind the immunity is still unknown. Several research groups have provided insights into VP28‐driven dsRNA vaccination to protect shrimp against WSSV infection, but the stability attained by many of these vaccines turned out to be short‐lived. RNAi treatment with VP28dsRNA, shrimp showed better resistance to the WSSV challenge, although multiple doses of dsRNA are required to provide extended protection for up to 28 days. However, no foolproof protection was currently offered by VP28‐based recombinant protein or DNA vaccination against WSSV. In recent years, attention has been directed towards identifying small molecule inhibitors of VP28 through molecular docking and molecular dynamics simulation studies and is an emerging approach in drug development and design against WSSV. This review highlights the opportunities, limits and challenges of VP28‐based control strategies of White Spot Syndrome Virus, by emphasizing the status quo of current methodological approaches and suggesting future research directions of using it as a potential drug discovery target.

Probiotics and competitive exclusion of pathogens in shrimp aquaculture - Hazel Knipe; Ben Temperton; Anke Lange; David Bass; Charles R. Tyler (Reviews in Aquaculture, 2021)
Probiotics, live microorganisms that, when administered in adequate amounts, confer a health benefit on the host, offer an alternative to antibiotics and have become popular among shrimp farmers for use in the regulation of pond water quality, promotion of shrimp growth and the prevention of disease. Most shrimp probiotics are selected for testing based on their ability to competitively exclude pathogens through bacterial antagonism assays, although the mechanisms of pathogen exclusion are rarely investigated. In this review, we provide a comprehensive overview of the mechanisms of competitive exclusion (interference and exploitation competition) by species screened and subsequently identified as shrimp probiotics based on their ability to inhibit the growth of pathogenic bacteria in vitro . We show that the current methods used to identify potential probiotics preferentially select for interference‐based competitive mechanisms and may overlook the potential of many species to be considered a probiotic. Furthermore, we show that the efficiency of a probiotic in vivo may be improved by considering the suitability of competitive strategies to shrimp farming conditions. We highlight important limitations and future directions for the screening and identification of probiotics in shrimp aquaculture, to aid in the development of effective and sustainable microbial management strategies.

Deep learning for smart fish farming: applications, opportunities and challenges - Xinting Yang; Song Zhang; Jintao Liu; Qinfeng Gao; Shuanglin Dong; Chao Zhou (Reviews in Aquaculture, 2021)
The rapid emergence of deep learning (DL) technology has resulted in its successful use in various fields, including aquaculture. DL creates both new opportunities and a series of challenges for information and data processing in smart fish farming. This paper focuses on applications of DL in aquaculture, including live fish identification, species classification, behavioural analysis, feeding decisions, size or biomass estimation, and water quality prediction. The technical details of DL methods applied to smart fish farming are also analysed, including data, algorithms and performance. The review results show that the most significant contribution of DL is its ability to automatically extract features. However, challenges still exist; DL is still in a weak artificial intelligence stage and requires large amounts of labelled data for training, which has become a bottleneck that restricts further DL applications in aquaculture. Nevertheless, DL still offers breakthroughs for addressing complex data in aquaculture. In brief, our purpose is to provide researchers and practitioners with a better understanding of the current state of the art of DL in aquaculture, which can provide strong support for implementing smart fish farming applications.

Availability and usefulness of economic data on the effects of aquaculture: a North Atlantic comparative assessment - Eirik Mikkelsen; Lucia Fanning; Cornelia Kreiss; Suzannah‐Lynn Billing; John Dennis; Ramon Filgueira; Jon Grant; Gesche Krause; Doug Lipton; Molly Miller; José Perez; Selina Stead; et al. (Reviews in Aquaculture, 2021)
This paper focuses on the availability of economic indicators and metrics to assess effects of marine aquaculture production in the North Atlantic area (the EU, Norway, Canada and USA), including also social and environmental effects. We consider how aquaculture planning and management is organised in the different countries and the usefulness of economic information to address different aquaculture‐related policies. We find that the most relevant economic data for aquaculture management should be at the local and regional levels rather than nationally. The availability of such economic data is mapped for national, regional and local level. The focus is on data that are publicly available from authorities or research institutions. The availability of data is generally fairly good for national and regional data on the direct economic effects of aquaculture. Data on how aquaculture‐related products or input markets are affected are however poorly available, as are economic data on external effects from aquaculture. Countries with a larger aquaculture sector tend to have better availability of aquaculture‐related economic data than those with a smaller sector. An index is developed and calculated to show more specifically where the countries have relatively good or poor data availability compared to their needs. While it will not always be cost‐effective or meaningful to collect economic data on the effects of aquaculture, our study indicates that several countries could benefit from expanding such data collection. It can make trade‐off decisions more consistent and easier to perform, and aquaculture policies and measures can be better tailored to specific contexts.

Cleaner fish in aquaculture: review on diseases and vaccination - Toni Erkinharju; Roy A. Dalmo; Miroslava Hansen; Tore Seternes (Reviews in Aquaculture, 2021)
Combating and controlling sea lice causes large economic costs for the farmers, with estimated values of more than 305 million euros (€) per year. Increased resistance against traditional chemotherapeutants due to evolutionary drivers in the sea lice combined with the lack of an effective vaccine and few other chemical treatments available are expected to cause these costs to increase. Several possible methods for managing sea lice infestations have been investigated, but only cleaner fish has proven to have an effect on lice levels. Cleaning activity is well known in marine fish and has been observed in the wild as a form of symbiosis between two species: one species, the ‘client’ fish, seek out the other species, the ‘cleaner’ fish, to have ectoparasites and dead tissue cleared from its body. The Atlantic lumpfish is a relatively new aquaculture species, and wild‐caught mature fish are used as brood stock for farmed production. This poses a biosecurity risk, as wild fish can carry pathogens, and the use of quarantine and health screening is recommended. Vaccine development is unfortunately lagging far behind relatively to the wide spread and high utilisation of the fish. This review contains description of the main pathogens and diseases that affect cleaner fish.

Trends in aquaculture and conservation of sturgeons: a review of molecular and cytogenetic tools - Gyan Chandra; Dorota Fopp‐Bayat (Reviews in Aquaculture, 2021)
Sturgeons are the most primitive, endangered groups of vertebrates on the planet and often referred to as ‘living fossils’. Their natural populations are decreasing due to habitat destruction, blockage of spawning migration, pollution and overexploitation for their expensive black caviar and boneless meat. Currently, existing populations have little chance to survive without artificial breeding and sustainable ranching programmes. Convention on International Trade in Endangered Species (CITES) is regulating international trade of all Acipenseriformes and their products for effective conservation. The aim of this review paper was to describe the main innovative applications in sturgeon aquaculture and conservation, such as genome engineering techniques applied in sturgeon’s reproduction, molecular and ploidy analyses of embryo and larvae, sex determination, genome sequencing, gene expression analysis and genome transplantations. Further research is required to improve cryopreservation techniques, embryo banking and quick identification of disease in sturgeon aquaculture and conservation programme.

Decades‐long involvement of signalling pathways in cardiovascular research using zebrafish model and its global trends - Ambika Binesh (Reviews in Aquaculture, 2021)
Research on zebrafish as a model system began a few decades ago, and later, studies on zebrafish developmental biology and genetics resulted in the characterization of a large number of genes involved in vertebrate development and cell signalling pathways, thus establishing zebrafish as a relevant human disease model for research. Cardiovascular diseases (CVDs) are the first leading cause of death and are expected to rise over 23.6 million by 2030. Environmental toxicants such as drugs, alcohols and chemicals can activate/disrupt number of signalling pathways, led to the cardiovascular toxicity and perturb the development of myocardium, cardiomyocytes, cardiac valve formation and cardiac trabecular growth. Based on the total publication output, USA's contribution to cardiovascular research using zebrafish as a model organism was immense compared to that of other countries. Harvard University contributed comprehensive research on CVD using zebrafish model with a cumulative occurrence of keywords like zebrafish, angiogenesis, cardiovascular disease, pollutants and developmental process. Many pathways are redundant, and the activation of certain targets implicated in cardiovascular disease development is by inhibiting one particular pathway leading to activation of alternative signalling pathways. Targeting highly specific pathways by single compounds inhibiting only one protein generally leads to resistance to this therapeutic agent. It is understood from the publications and citations, that the use of zebrafish as a cardiovascular disease (CVD) model has been gradually expanded from 2000 to 2019, likely due to the recapitulated pathophysiology of the human heart.

The climate is still changing - Giovanni M. Turchini; Pin Nie (Reviews in Aquaculture, 2021)

Dynamics of phosphorus exchange between sediment and water in a gravel‐bed river - Robert J. Wilcock; Richard W. McDowell; John M. Quinn; J. Christopher Rutherford; Roger G. Young; Craig V. Depree (New Zealand Journal of Marine and Freshwater Research, 2020)
Phosphorus (P) stores in gravel‐bed rivers are released for uptake by periphyton when pH levels exceed 8.5. The Tukituki River has low alkalinity water and frequently experiences periphyton blooms, and daytime pH > 9 during summer low‐flows. We measured dissolved reactive P (DRP) and EPC 0 , the water concentration of DRP at which no net release or sorption from the river bed occurs, in sediment samples from the Tukituki River subject to controlled pH levels before (2014) and after (2017) changes to two wastewater discharges that reduced P release to the river by 95%. DRP released from 2014 sediments at pH 8.5–10 were 30 ± 10 mg/m 3 above background (pH 8) whereas those released from 2017 sediments were 5 ± 3 mg/m 3 above background. EPC 0 levels in 2014 and 2017 were 11 ± 6 and 7 ± 2 mg/m 3 , respectively. Field estimates of released DRP calculated from continuous pH and the Redfield equation suggested that most of the readily available DRP released from sediments at elevated pH is derived from material attached to recently deposited sediment. Subsequently, a reduction in wastewater inputs or agricultural runoff should reduce sediment DRP stores, and hence sediment fluxes, within a few years and mitigate periphyton blooms in addition to directly lowering water column concentrations.

Spatio‐temporal variation in species composition of New Zealand's whitebait fishery - Mark R. Yungnickel; Michael J. H. Hickford; David R. Schiel (New Zealand Journal of Marine and Freshwater Research, 2020)
Whitebait comprise a culturally, commercially and recreationally important fishery in New Zealand, where post‐larvae are netted while returning from their marine phase. In this study, we expanded an historical (1964) sampling programme to gain a contemporary understanding of the species composition of the whitebait fishery; 87 rivers were sampled over six months in 2015. Over the entire country, >12 species were found in samples and 87.6% of these were īnanga ( Galaxias maculatus ). Kōaro ( G. brevipinnis ) and banded kōkopu ( G. fasciatus ) were abundant in some rivers and regions at particular times of the year. Buller was the most variable region, spatially and temporally, for species composition; Canterbury was the least variable. Banded kōkopu whitebait migrated one month earlier north of Cook Strait than in the south. There was a positive association between the abundance of kōaro and banded kōkopu in samples and the level of indigenous forest cover in catchments. Compared to samples from 50 years ago, there was a greater proportion of kōaro and banded kōkopu whitebait throughout the country. This spatio‐temporal variability requires fishery regulations to be more tailored and flexible if they are to conserve the diversity of life‐histories present in the catch and sustain the whitebait fishery.

Relationships between long‐term ocean warming, marine heat waves and primary production in the New Zealand region - Stephen M. Chiswell; Philip J. H. Sutton (New Zealand Journal of Marine and Freshwater Research, 2020)
We test the paradigm that in a future warmer ocean, shallower winter mixing will lead to less net primary production (NPP), by investigating whether warming between 2002 and 2018 led to changes in NPP in the Tasman Sea/New Zealand region. The 2002–18 trend in sea surface temperature (SST) was positive over most of the region, and was driven by increasingly warmer summers and marine heat waves (MHWs) rather than year‐round warming. In contrast, the trends in sea surface chlorophyll (SSC) and NPP were generally positive over the Subtropical Front (STF) and in a subtropical band north‐east of New Zealand, but negative elsewhere. Regressions between SSC and SST, and between spring SSC and the coldest SST during the preceding winter, show similar spatial patterns to the SSC trend. We suggest these findings reflect different ecosystem functioning in the subtropical and subantarctic biomes that are separated by the STF. We conclude that any future warming is likely to lead to less production in the Tasman Sea, but more production over the STF. Three recent MHWs had different impacts on production, but generally led to less surface biomass north of the STF and more biomass south of the front.

Reference and current Trophic Level Index of New Zealand lakes: benchmarks to inform lake management and assessment - Jonathan M. Abell; Paul van Dam‐Bates; Deniz Özkundakci; David P. Hamilton (New Zealand Journal of Marine and Freshwater Research, 2020)
Knowledge of trophic status is fundamental to understanding the condition and function of lake ecosystems. We developed regression models to predict chlorophyll a concentrations (chl a ) in New Zealand lakes for reference and current states, based on an existing dataset of total nitrogen (TN) and total phosphorus (TP) concentrations for 1031 lakes. Models were then developed to predict Secchi depth based on chl a and a sediment resuspension term applicable to shallow lakes. Estimates of all four Trophic Level Index (TLI) variables (chl a , TN, TP and Secchi depth) were analysed to estimate reference and current state TLI for the nationally representative sample of 1031 lakes. There was a trend of eutrophication between reference and current states, with systematic differences among lake geomorphic types. Mean chl a increased 3.5‐fold (2.42 mg m −3 vs. 8.32 mg m −3 ) and mean Secchi depth decreased (indicating lower clarity) by approximately one‐third (9.62 m vs. 6.48 m) between reference and current states. On average, TLI increased by 0.67, with the TLI increase >1 in approximately one‐third (31%) of lakes. This study informs the status of lake ecosystems in NZ and provides benchmarks to guide management and assessment.

Reviewing the far‐reaching ecological impacts of human‐induced terrigenous sedimentation on shallow marine ecosystems in a northern‐New Zealand embayment - John D. Booth (New Zealand Journal of Marine and Freshwater Research, 2020)
Human settlement in Bay of Islands, New Zealand, beginning ∼1300 AD, wrought immense, conspicuous and enduring change to local shallow‐water marine ecologies, this review addressing those transformations attributable to increased rates of anthropogenically induced, land‐derived sedimentation. Elevated silt inflow, particularly after the late‐1800s, in course led to ∼130% expansion in mangrove ( Avicennia marina ) cover, with concomitant loss of saltmarsh, uppershore coarse‐shell beaches/cheniers, and (probably) intertidal seagrass ( Zostera muelleri ). Sedimentation also led to widespread loss of estuarine shellfish habitat, and, although not necessarily categorically causal, seems, at the same time to have contributed to such degradation among cockle ( Austrovenus stutchburyi ) populations that few individuals attain their potential size. Most changes, many seemingly irreversible, can be described as ecologically catastrophic, with ecosystems altered and destroyed, and uncommon habitats threatened. Sedimentation appears the single‐most important and enduring contributor to ecological degradation in shallow waters of this northern harbour, with time lags between stressor‐onset and realisation of impact (decades to centuries) that only now are becoming clear. Outstanding issues concern establishing the extent of relationship between levels of terrigenous sedimentation and cockles seldom attaining their previous maximum sizes, and origins of the possibly new, widespread phenomenon of living cockles accumulating and dying atop beach surfaces.

Biodiversity–Ecosystem Functioning (BEF) approach to further understanding aquaculture–environment interactions with application to bivalve culture and benthic ecosystems - Élise Lacoste; Christopher W. McKindsey; Philippe Archambault (Reviews in Aquaculture, 2020)
Coastal benthic ecosystems may be impacted by numerous human activities, including aquaculture, which continues to expand rapidly. Indeed, today aquaculture worldwide provides more biomass for human consumption than do wild fisheries. This rapid development raises questions about the interactions the practice has with the surrounding environment. In order to design strategies of sustainable ecosystem exploitation and marine spatial planning, a better understanding of coastal ecosystem functioning is needed so that tools to quantify impacts of human activities, including aquaculture, may be developed. To achieve this goal, some possible directions proposed are integrated studies leading to new concepts, model development based on these concepts and comparisons of various ecosystems on a global scale. This review draws on existing literature to (i) briefly summarize the major ecological interactions between off‐bottom shellfish aquaculture and the environment, (ii) introduce research on the influence of benthic diversity on ecosystem functioning (BEF relationships) and (iii) propose a holistic approach to conduct aquaculture–environment studies using a BEF approach, highlighting the need for integrated studies that could offer insights and perspectives to guide future research efforts and improve the environmental management of aquaculture.

Clostridium butyricum : a promising probiotic confers positive health benefits in aquatic animals - Ngoc Tuan Tran; Zhongzhen Li; Hongyu Ma; Yueling Zhang; Huaiping Zheng; Yi Gong; Shengkang Li (Reviews in Aquaculture, 2020)
Clostridium butyricum is a bacterium of rod shape, strictly anaerobic, Gram‐positive and form spores. Short‐chain fatty acids, biofuel compounds and precursors of biomaterials (H 2 , butanol and 1,3‐propanediol) are produced by C. butyricum during the fermentation of carbohydrates and sugars. In humans and animals, although C. butyricum has been found to be associated with botulism in infant and necrotising enterocolitis in preterm neonates, some strains have been demonstrated to be beneficial as probiotics. In aquatic animals, the application of C. butyricum as a probiotic has been commonly considered. In this review, we described and documented what we knew about the isolation, identification, phenotypic and biochemical characteristics, safety, pathogenicity and the mechanisms of action of C. butyricum in the gastrointestinal tract of aquatic animals. The evidence on the roles that C. butyricum plays in improving growth performance, digestibility, survival rate, immune response, disease resistance and the structure of intestinal tract, as well as the modulation of gut commensal microbiota and metabolic disorders in aquatic animals, is summarised. Albeit the probiotic C. butyricum has been applied in aquaculture, and further research, such as the inter‐relationships between the probiotic and the immune system of the host and the possible application of C. butyricum as an alternative to antibiotic substitution for the prevention and treatment of diseases, is required for future detailed studies.

Comparison of Norwegian health and welfare regulatory frameworks in salmon and chicken production - Kristine Gismervik; Brit Tørud; Tore S. Kristiansen; Tonje Osmundsen; Kristine Vedal Størkersen; Christian Medaas; Marianne Elisabeth Lien; Lars Helge Stien (Reviews in Aquaculture, 2020)
The health and welfare of farmed fish are often regarded with less concern than for other production animals. This review compares the Norwegian legal health and welfare frameworks for broiler chickens and farmed salmon, with the aim of improving regulations for salmon farming in Norway. Highlighting differences in laws, regulations and governmental organisation are also highly relevant in general, especially in developing welfare regulations for farmed fish in other countries. Norwegian chicken farmers must comply with two main laws, the Norwegian Animal Welfare Act and the Food Act, governed by the same ministry and governmental agency. The salmon farmers must in addition relate to the Aquaculture Act, different ministries and several agencies with different objectives. Compared to the regulation of chicken farming, the regulation of salmon farming is more complex, has potentially conflicting aims and uses less positive welfare phrasings. Thus, the regulation may be perceived as focusing on profitability over welfare. Despite having many similar paragraphs to regulation for chicken farming, salmon farming regulation is less strict in the daily securing of animals and recordings of mortality. There is no specified slaughterhouse control of high‐density productions, as there is for broiler chickens. There are also differences in the mandatory welfare courses, one being that infection prevention is a stated topic for chickens. The Norwegian Animal Welfare Act has no possibility of dispensation, meaning exceptions, and treats fish and other animals equally. Future regulatory frameworks for farmed fish production should avoid unintended downgrading of fish health and welfare.

A review on Spirulina: alternative media for cultivation and nutritive value as an aquafeed - Janice Alano Ragaza; Md. Sakhawat Hossain; Kristen A. Meiler; Stephanie F. Velasquez; Vikas Kumar (Reviews in Aquaculture, 2020)
The nutritional value of spirulina in aquafeeds has been studied extensively as a fishmeal replacer or as a functional feed additive to increase growth and health performance of fish in the last decade. Despite increased interest in spirulina research in aquaculture, its increased production cost still limits its use in commercial rations. Zarrouk’s medium is the standard substrate used for growing spirulina. Although this medium offers optimal biomass production, it incurs higher costs due to the expensive components needed for concocting the medium. In this regard, development of cost‐effective alternative culture medium or techniques is necessary for the industrial‐scale production of these microalgae. This paper reviews research on different alternative media for spirulina cultivation and its nutritive value as an aquafeed. Numerous alterations in the composition of Zarrouk’s medium with cheaper chemical ingredients have been explored as a potential substitute for cost‐effective microalgae cultivation. Industrial and processing wastes and by‐products with appropriate nutrient profiles for growing spirulina are also being considered as alternative culture media. The use of rice bran or other cheaper agricultural by‐products, as a cost‐effective growth medium for commercial‐scale spirulina production has yet to be explored extensively in agriculture‐based countries, especially in rice‐producing Asian countries.

Lycopene reduces the impacts of aquatic environmental pollutants and physical stressors in fish - Mahmoud A.O. Dawood; Mohsen Abdel‐Tawwab; Hany M.R. Abdel‐Latif (Reviews in Aquaculture, 2020)
Aquatic organisms are susceptible throughout their lives to chemical and physical stressors, which negatively affect their health. Various aquatic pollutants derived from industrial effluents, overuse of some agricultural pesticides, herbicides and insecticides may cause devastating toxicological aspects of aquatic organisms and deteriorate their health and growth. They also led to oxidative stress to fish due to the stimulation of the production of reactive oxygen species. Therefore, the need for using natural antioxidants to be used as feed additives is of great importance to counteract the hazardous oxidative stress responses. The use of phytochemicals, which characterized by substantial antioxidative effects, has been raised. Lycopene is the principal carotenoid pigment found in tomatoes and their products, vegetables and red fruits. Numerous studies have recommended the use of lycopene as a powerful antioxidant to attenuate the oxidative stress responses in several fish species exposed to various toxicants or any other stress conditions. Lycopene maintains the health condition of fish by enhancing the immune and antioxidative responses. This review article aimed to elucidate the current information about the potential use of dietary lycopene for several fish species and its capability to attenuate the oxidative stress and haemato‐immunological alterations resulted from aquatic environmental pollutants and other physical stressors. Additionally, the review discusses some aspects regarding the lycopene mode of action to assess the profits that would be of importance in the aquaculture industry.

The nitrification process for nitrogen removal in biofloc system aquaculture - Glen Ricardo Robles‐Porchas; Teresa Gollas‐Galván; Marcel Martínez‐Porchas; Luis Rafael Martínez‐Cordova; Anselmo Miranda‐Baeza; Francisco Vargas‐Albores (Reviews in Aquaculture, 2020)
Aquaculture is an economic activity that faces the unavoidable problem of water quality detriment, which is mainly generated by the improper management of production ponds, including inadequate water circulation and aeration, accumulation of undigested food residues, excretion of metabolic by‐products by the cultivated organisms and other. In addition, the increase in suspended organic matter together with the presence and generation of nitrogen compounds can severely affect the physiology of the animal, leading to significant losses in production. Ammonia (NH3), nitrite (NO2) and nitrate (NO3) are toxic in different scales and environmental conditions; therefore, reducing their concentrations in the culture units has paramount relevance. In this regard, bioflocs are an efficient alternative to transform nitrogen compounds into a non‐toxic form, taking advantage of the capabilities of the microbial communities conforming them. Also, nitrogen can be harnessed and incorporated as organic nitrogen, making the biofloc a source of useful natural food for the cultivated organism. The substantial reduction in the rate of water exchange favoured by the biofloc technology (BFT) is a beneficial advantage for both the production systems and the environment, diminishing the risk of introducing pathogens into the pond in parallel with the improvement in the water quality of effluents. Ammonia oxidation is an advantage adding value to the BFT systems and is discussed in this review.

Meta‐analysis of dietary supplementation effect of turmeric and curcumin on growth performance in fish - Mahougnon Siméon Fagnon; Chantal Thorin; Segolène Calvez (Reviews in Aquaculture, 2020)
Plant‐based additives are currently used in aquaculture for their various beneficial properties. Curcumin and turmeric are usually applied for their interesting results on growth performance of fish. In this paper, the effect of dietary inclusion of curcumin and turmeric powder on growth performance in fish was studied. Twenty data sets from 5 studies and 29 data sets from 8 publications were respectively computed for curcumin and turmeric in this analysis. Specific growth rate (SGR) was the quantitative criteria recorded for each data set. After, a brief systemic summary of each study, the quantitative analysis was performed. Results showed a significant increase in pooled standard mean difference (SMD) for both fixed and random model in curcumin and turmeric. Although fish species were categorized into family (subcategory), high heterogeneity (>96%) was found in all random and fixed model analysis. Contrary to turmeric, higher curcumin inclusion results in lower specific growth rate. The higher effect sizes observed when fed curcumin at lower inclusion levels suggests that feeding low levels of phytochemicals might be beneficial and its content in turmeric should be analysed for quite homogeneous feed. This study contributes to the analysis of overall growth performance properties of turmeric and curcumin incorporation in fish diet, irrespective to their strong antioxidant and anti‐inflammatory activities.

Acceptance of aquaculture as compared with traditional fishing in the province of Cadiz (Spain): an empirical study from the standpoint of social carrying capacity - Jose Ruiz‐Chico; José Maria Biedma‐Ferrer; Antonio Rafael Peña‐Sánchez; Mercedes Jiménez‐García (Reviews in Aquaculture, 2020)
This paper analyses the acceptance of aquaculture compared with fisheries in the province of Cadiz (Spain), in the context of social carrying capacity, the point at which its presence begins to be excessive and leads to significant problems for society. Researchers conducted 558 face‐to‐face surveys to study the societal acceptance of this sector in several dimensions (social, economy, quality, environment, etc.). We have also built an index to measure this acceptance, based on the variables studied to delve into this concept. For this purpose, we have followed a principal component analysis methodology with Varimax rotation, to which we have applied the Dalenius–Hodges stratification procedure. Analysis shows a high level of acceptance for aquaculture, indicating that it is far from its social saturation point. Rather, data indicate that even further development of this activity is advisable. In addition, respondents showed some indifference between socioeconomic and environmental objectives. We can conclude that the general perception of aquaculture is better among men than women, who have greater preferences for traditional fishing, and among higher‐income consumers. Informative campaigns should be organized to target the less convinced consumers, in the context of social carrying capacity. Production systems should be adjusted to improve the existing perception that aquaculture products are less natural; this perception arises from the misuse of chemicals and feeds, factors that are believed to have adverse effects on quality and flavour.

Beyond 2020 - Giovanni M. Turchini; Pin Nie (Reviews in Aquaculture, 2020)

Chinese Abstracts (Reviews in Aquaculture, 2020)

Incidence of antibiotic resistance in Vibrio spp - Ke‐Yan Loo; Vengadesh Letchumanan; Jodi Woan‐Fei Law; Priyia Pusparajah; Bey‐Hing Goh; Nurul‐Syakima Ab Mutalib; Ya‐Wen He; Learn‐Han Lee (Reviews in Aquaculture, 2020)
Vibrio species is a common natural inhabitant of brackish and saltwater. Vibrio sp. includes not only emerging pathogens but also well‐known and emerged pathogens, such as V. cholerae , V. parahaemolyticus and V. vulnificus . Although it is often harmless, pathogenic strains which could cause serious food‐borne illnesses/outbreaks in both humans and animals have been identified. Vibrio infection is usually self‐limiting and requires no clinical treatment. However, antibiotics are still required to treat severe cases of Vibrio infection. Recent reports have highlighted a rise in the presence of antibiotic‐resistant Vibrio in the environment. This hampers the clinical treatment of Vibrio infection and has been linked to the imprudent use of antibiotics in various fields such as human medicine, agriculture and animal husbandry. As a result, it has greatly jeopardized food security, threatened public health and impugned the growth of economy. Food is a potential vehicle of antibiotic‐resistant Vibrio where the resistant genes are transmitted to humans via ingestion of contaminated food. Hence, the surveillance, monitoring and management of antibiotic patterns of Vibrio are important for clinical treatment. This review focuses on different trends and global patterns of antibiotic resistance of Vibrio .

Trained immunity and perspectives for shrimp aquaculture - Suvra Roy; Peter Bossier; Parisa Norouzitallab; Daisy Vanrompay (Reviews in Aquaculture, 2020)
The global production of cultured crustaceans for 2018 is predicted to be ~8.63 million tonnes, and shrimp represents a significant portion of cultured crustaceans. Demands for shrimp are raising, also in developing countries as consumer preferences have evolved with rising incomes. Shrimp is mainly produced for consumption but during processing economically valuable products are being generated such as chitosan, which is used in cosmetics, food and beverages, agrochemicals and pharmaceuticals. However, the potential and sustainability of shrimp aquaculture production currently suffer from high mortality rates, losses due to especially bacterial and viral infections, and hence suboptimal yields. Vibrio parahaemolyticus acute hepatopancreatic necrosis and white spot syndrome virus (WSSV) disease outbreaks are examples of economically devastating disease outbreaks in shrimp. There is a need for prophylaxis of infectious diseases and for finding novel strategies for conditioning economically important shrimp broods so that they can produce more robust progenies and develop tolerance against biotic (pathogens) and abiotic stressors. Training the innate immune system of shrimp could be a possible avenue for improving animal’s health, and it might serve as potential unique strategy for conditioning the brood stock to have more robust progenies. The current review provides an overview on innate immune responses in shrimp after exposure to bacteria, viruses and abiotic stressors and on the possibilities to train the innate immune system of shrimp in order to improve health, not only of the animal itself but also of its progeny.

The role of oregano herb and its derivatives as immunomodulators in fish - Mahmoud Alagawany; Mayada R. Farag; Ayman S. Salah; Mohamed A. Mahmoud (Reviews in Aquaculture, 2020)
The motivation behind this article is to give point‐by‐point data about the beneficial applications of oregano feed supplement in fish diets as immunomodulators, antioxidant, antiviral, antifungal and antiparasitic. Use of this plant as feed additive plays an important role in the fish diet when compared to other synthetic feed additives. Oregano is rich in phytochemical compounds including carvacrol and thymol in addition to other phenolic compounds with antioxidant and immune‐enhancing activities. Origanum vulgare extract improved the immunological responses and enhanced non‐specific immunity. Also, non‐specific immunity and the lysosomal activity were significantly increased in rainbow trout fed diet enriched with 3.0 mL essential oil of Origanum onites L kg −1 diet for 60 days. Furthermore, non‐specific immune stimulant, antioxidant and nitric oxide activities were improved due to O. vulgare oil supplementation. In some recent studies, Origanum heracleoticum L essential oil as a growth enhancer increased the antioxidant status. In rainbow trout, the hepatic levels of antioxidant enzymes and the total antioxidant capacity increased by feeding diet enriched with 6 and 10 g kg −1 diet of O. vulgare extract. Therefore, the addition of oregano and/or derivatives as a dietary supplement in fish diet may promote growth and enhance the immunity and health of fish and this will be useful for nutritionists, physiologists and veterinarians.

Issue Information (Reviews in Aquaculture, 2020)

Modern ornamental aquaculture in Europe: early history of freshwater fish imports - Jindřich Novák; Lukáš Kalous; Jiří Patoka (Reviews in Aquaculture, 2020)
Modern ornamental fishkeeping is one of the most popular hobbies in the world, with various known positive and also negative aspects including the introduction of non‐native species. Despite this fact, the history of the first imports of freshwater tropical fish species for ornamental purposes has never been deeply studied and is usually simplified. Here, we present the first comprehensive review of reported imports in the period of the early history of this sector of aquaculture, ending with the end of the First World War. Moreover, the total number of kept species has been updated, with a forecast for the future. We present the summarised information in a wide context of both historical and current connections and viewpoints, highlighting the crucial role of German importers at this time. In this regard, the term ‘German aquarium phenomenon’ is proposed.

MicroRNA regulation of Toll‐like receptor, RIG‐I‐like receptor and Nod‐like receptor pathways in teleost fish - Qing Chu; Tianjun Xu (Reviews in Aquaculture, 2020)
The innate immune system is the first‐line defence against invading pathogens, and the main molecules involved in recognizing invading pathogens are the pattern recognition receptors. Accumulating evidences have demonstrated that activation and termination of the immune responses are regulated by various layers of regulators and mechanisms. MicroRNAs (miRNAs) are a group of small non‐coding RNAs that emerged as critical component of the complex regulatory networks in fish immune responses. In this review, we have summarized miRNA regulation in teleost fish, which can provide new insights into the regulation of innate immune receptor pathways in fish. Meanwhile, we comprehensively discuss the recent researches on how teleost miRNAs respond to the signalling pathways of innate immune receptors, including Toll‐like receptors, retinoic acid‐inducible gene‐I‐like receptors and Nod‐like receptors.

Mechanical induced wounds in fish – a review on models and healing mechanisms - Lene Sveen; Christian Karlsen; Elisabeth Ytteborg (Reviews in Aquaculture, 2020)
Skin wounds and injuries are frequently occurring in farmed fish, particularly in more intensive production systems. Any disruptions of the skin, such as mucus removal, scale loss or deeper incisions, are negatively correlated with barrier functions and disease resistance. In this review, the current knowledge on mechanically induced wounds in fish is dedicated to five areas of focus: (i) The anatomy and functions of fish skin, (ii) Techniques to inflict mechanical skin damage in farmed and laboratory fish for experimental purposes, (iii) Healing mechanisms of deep wounds, (iv) In vitro models for wound healing studies and (v) Wound care, with focus on factors that may enhance or delay skin regenerative processes. The aim of the review was to presents key points for a better understanding of skin resilience and fish robustness, with focus on Atlantic salmon, Salmo salar , in Norwegian coastal production environment.

Epidemiology of marine gill diseases in Atlantic salmon ( Salmo salar ) aquaculture: a review - Annette S. Boerlage; Angela Ashby; Ana Herrero; Aaron Reeves; George J. Gunn; Hamish D. Rodger (Reviews in Aquaculture, 2020)
Gill disease of farmed Atlantic salmon ( Salmo salar ) in the marine environment has emerged as a significant problem for the salmon aquaculture industry. Different types of marine salmon gill disease reported include amoebic gill disease (AGD), parasitic gill disease, viral gill disease, bacterial gill disease, zooplankton (cnidarian nematocyst)‐associated gill disease, harmful algal gill disease and chemical/toxin‐associated gill disease. The term ‘multifactorial gill disease’ is used when multiple distinguishable types of disease (as opposed to an obvious single primary type) are present. When gill disease is non‐specific, it is referred to as ‘complex gill disease’ (CGD) or ‘complex gill disorder’. These two terms are often used interchangeably and are overlapping. The significance of many infectious and non‐infectious agents that may be associated with CGD is often unclear. In this review, we summarise aspects of the different types of gill disease that are relevant to the epidemiology of gill disease and of CGD in particular. We also tabulate simultaneously occurring putative pathogens to explore the multifactorial nature of gill disease.

Development and current state of seawater shrimp farming, with an emphasis on integrated multi‐trophic pond aquaculture farms, in China – a review - Zhi‐Qiang Chang; Amir Neori; Yu‐Ying He; Ji‐Tao Li; Ling Qiao; Steven Ian Preston; Ping Liu; Jian Li (Reviews in Aquaculture, 2020)
Shrimp farming has been the fastest‐growing sector in seawater aquaculture and has contributed to improving the farmers income and the utilization efficiency of aquaculture resources in China. The shrimp industry has deployed ever‐improved and innovated methods, from extensive farming to semi‐intensive and intensive farming. Various high‐density intensive culture models, such as high‐land, greenhouse and indoor industrialized culture models, have been used for shrimp pond farming in the coastal area. However, efficiency, environmental and social considerations have led to an increasing adoption of the environmentally‐friendly culture model called integrated multi‐trophic aquaculture (IMTA). This has occurred most rapidly along the northern and central coasts of China. The deployed IMTA culture models reviewed here are shrimp + crab, shrimp + fish, shrimp + sea cucumber, shrimp + jellyfish + clam, shrimp + crab + clam, shrimp + crab + clam + fish and the ridgetail white shrimp polyculture in saline alkaline water, which have been tailored to local conditions and organisms' characteristics. Suitable organism varieties and the maintenance of suitable eco‐friendly water quality have been key to success. The eco‐friendly IMTA culture models described here fully exploit the pond culture resources, to increase production with minimal additional feed and labor inputs, while reducing effluent emissions and treatment cost. The performance of shrimp IMTA models is compared to shrimp monoculture models regarding the economics. An equally important outcome of this publication is making generally accessible the findings from a vast Chinese scientific literature on shrimp culture that has hitherto been unavailable in English.

Status of genetic and genomic approaches for delineating biological information and improving aquaculture production of farmed rohu, Labeo rohita (Ham, 1822) - Kiran D. Rasal; Jitendra Kumar Sundaray (Reviews in Aquaculture, 2020)
Farmed rohu, Labeo rohita , is an economically important freshwater aquaculture species in south Asia. Consumer preference for this species has driven researchers to develop genetically improved rohu (Jayanti) for important traits such as growth and disease resistance. The feeding and breeding biology of rohu is well‐studied, but the physiological responses to stress or climate change at the molecular level are less understood. We summarized the genetic and advanced molecular tools used for biological insights into farmed rohu. Recently, next‐generation sequencing technology (NGS) and genome informatics have helped to identify biological questions in fish using genome, transcriptome, metagenome, proteome and epigenome sequencing. We briefly reviewed past rohu research using traditional selective breeding methods for genetic improvement, as well as the other molecular tools that have been utilized to understand the fish’s physiology, health, nutrition, stress and reproduction. We discuss the molecular techniques used in rohu, such as gene cloning and expression profiling, DNA markers, NGS, metagenomics, epigenomics, proteomics, cell culture/cell line development and transgenics. Finally, we address the future perspectives of rohu research, which may be driven by NGS and other advanced techniques like genome editing to improve rohu aquaculture production. The comprehensive information presented here will provide insights for the carp aquaculture research community.

Application of meta‐analysis towards understanding the effect of adding a methionine hydroxy analogue in the diet on growth performance and feed utilization of fish and shrimp - Jingping Guo; Yida Bao; Robert Davis; Ash Abebe; Alan E. Wilson; Donald Allen Davis (Reviews in Aquaculture, 2020)
Methionine hydroxy analogue (MHA) has been widely used and shows positive effects on growth in poultry, swine, ruminant and aquatic animals. Nevertheless, the utilization efficiency of methionine hydroxy analogue remains controversial considering the wide variation in effects across studies, feeding parameters and environmental culture conditions. Meta‐analysis can quantify the effect of adding MHA on animal performance. Here, we analysed the effect of MHA‐supplemented diets on the final weight (FW), per cent weight gain (WG), protein efficiency ratio (PER), feed conversion ratio (FCR) and feed efficiency (FE) in common, diverse aquaculture taxa. To conduct the meta‐analyses, twenty‐three published studies were included that accounted for 249 effect sizes estimated across eight fish and one shrimp species. The effect size (measured as the standardized mean difference; Hedges’ g ) of response parameters between MHA level in a diet formulation and an MHA‐less control condition was calculated. Based on these results, adding MHA in the diet can significantly improve FW, WG, PER, and FE and decrease FCR for fish rather than shrimp. Using meta‐regression analysis, there was a significant quadratic linear relationship between MHA addition and effect size for FW ( P = 0.002 for MHA, P = 0.042 for MHA 2 ), and significant linear relationships between MHA addition and effect size for WG ( P = 0.0005) and FCR ( P = 0.002). There was no significant relationship, linear or non‐linear, between the MHA addition and effect size for FE ( P = 0.985) and PER ( P = 0.461). In all, when properly dosed in diets, MHA can significantly improve aquaculture production for fish.

Selective breeding of edible bivalves and its implication of global climate change - Karsoon Tan; Hongkuan Zhang; Huaiping Zheng (Reviews in Aquaculture, 2020)
Bivalve molluscs are very nutritious and are an important source of human animal protein. To date, bivalve farming has contributed to about 15% of the mean per capita animal protein intake of approximate 1.5 billion people around the world. Unfortunately, the effects of climate change, mainly global warming and ocean acidification, have had many deleterious effects on bivalve aquaculture, not only leading to mass mortalities of bivalves in farms and hatcheries, but also causing collapse of natural bivalve populations. In response to the recurrent mass mortalities of farmed bivalves, many selective breeding programmes have been launched with the breeding goal of reducing mortality rate caused by disease outbreaks and changing ocean conditions. This article reviews the progress and potential of selective breeding of edible bivalves in the context of global climate change. It is clear from the literature that in terms of environmental sensitivity, and disease resistance and tolerance, selective breeding has great potential for improving the robustness of edible bivalves with significant heritability and genetic gain. Because the robustness of edible bivalves to climate change is a complex trait affected by multiple genes, the application of modern genomic tools in selective breeding is expected to dramatically enhance the accuracy and efficacy of genetic improvements and produce bivalve strains that are robust to climate change. The information in this article is very useful for guidance on adaptation strategies for climate‐smart bivalve aquaculture solutions to be implemented in bivalve hatcheries and farms.

Prevention not cure: a review of methods to avoid sea lice infestations in salmon aquaculture - Luke T. Barrett; Frode Oppedal; Nick Robinson; Tim Dempster (Reviews in Aquaculture, 2020)
The Atlantic salmon aquaculture industry still struggles with ectoparasitic sea lice despite decades of research and development invested into louse removal methods. In contrast, methods to prevent infestations before they occur have received relatively little research effort, yet may offer key benefits over treatment‐focused methods. Here, we summarise the range of potential and existing preventative methods, conduct a meta‐analysis of studies trialling the efficacy of existing preventative methods and discuss the rationale for a shift to the prevention‐focused louse management paradigm. Barrier technologies that minimise host–parasite encounter rates provide the greatest protection against lice, with a weighted median 76% reduction in infestation density in cages with plankton mesh ‘snorkels’ or ‘skirts’, and up to a 100% reduction for fully enclosed cages. Other methods such as geographic spatiotemporal management, manipulation of swimming depth, functional feeds, repellents and host cue masking can drive smaller reductions that may be additive when used in combination with barrier technologies. Finally, ongoing development of louse‐resistant salmon lineages may lead to long‐term improvements if genetic gain is maintained, while the development of an effective vaccine remains a key target. Preventative methods emphasise host resistance traits while simultaneously reducing host–parasite encounters. Effective implementation has the potential to dramatically reduce the need for delousing and thus improve fish welfare, productivity and sustainability in louse‐prone salmon farming regions.

Unlocking the intraspecific aquaculture potential from the wild biodiversity to facilitate aquaculture development - Lola Toomey; Pascal Fontaine; Thomas Lecocq (Reviews in Aquaculture, 2020)
Domestication of new candidate species remains a long and difficult process often resulting in unfruitful attempts. Early steps in most domestication programmes often consider species as a unity, disregarding a part of the biodiversity: the wild intraspecific geographic differentiation. Yet, this differentiation can shape local specificities, which could lead to different domestication predisposition or socio‐economic attractiveness between populations. Therefore, considering this population‐specific potential could facilitate domestication and subsequent production of new candidate species. Here, we propose a three‐step integrative approach to standardise and facilitate new domestication attempts by taking advantage of wild geographic differentiation. Step 1 consists of classifying the wild biodiversity to identify prospective units (i.e. groups of differentiated allopatric populations). Step 2 allows comparing performances of these units in standardised conditions (i.e. rearing system) through a multifunction and multi‐trait assessment. Finally, step 3 highlights units with higher aquaculture potentials through the calculation of an aquaculture potential score. This approach, here applied to fish culture for human consumption, also aims at being extended to other taxa (e.g. crustaceans, molluscs) and other production goals.

Understanding and managing suspended solids in intensive salmonid aquaculture: a review - Mark Schumann; Alexander Brinker (Reviews in Aquaculture, 2020)
The intensive aquaculture of salmonids is a relatively young discipline within the animal husbandry sector. It differs to terrestrial livestock farming in one obvious and fundamental aspect – the aquatic environment. Besides great advantages such as buoyancy, the fluid medium also poses specific challenges for fish and fish farmers. One issue identified as a central problem in aquaculture is the presence of undissolved particulate matter in the water column. The ideal of fish living in pure, transparent water is seldom a reality as virtually every water body is subject to multiple inputs of solid matter, for example from the ground, the air and from the organisms living in it. In aquaculture, these solids are derived from both natural and anthropogenic sources, but by far the biggest input comprises excreted waste from the relatively high biomass of fish. The ratio of different inputs varies significantly between individual systems, dependent on factors such as the type of husbandry system, water exchange rate, the species being farmed, stocking density and the composition of the feed being supplied. This review aims to summarize potential sources of solid wastes in salmonid aquaculture, the properties of those solids and their implications for system stability, the quality of connected environments and the welfare of fish being reared. We will also review the expanding opportunities for solid management.

Global stakeholder vision for ecosystem‐based marine aquaculture expansion from coastal to offshore areas - Ibon Galparsoro; Arantza Murillas; Kemal Pinarbasi; Ana M.M. Sequeira; Vanessa Stelzenmüller; Ángel Borja; Anne Marie O´Hagan; Adele Boyd; Suzanne Bricker; Joxe Mikel Garmendia; Antje Gimpel; Aline Gangnery; et al. (Reviews in Aquaculture, 2020)
Marine aquaculture is the most promising industry for ensuring future provision of seafood. Yet, the worldwide growth and expansion of this industry have been slower than expected, calling for the identification of environmentally suitable sites while accounting for all factors that could constrain or benefit its establishment. Here, we determine the main obstacles and risks hindering the growth and expansion of marine aquaculture, as well as the needs and recommendations to overcome such constraints. Our analysis is based on results obtained from a consultation process held in 16 study sites located around the world with the participation of 614 stakeholders representing the research community, aquaculture industry, government, conservation groups, and education and fishermen associations. A high level of commonality exists in the main issues hindering aquaculture growth and expansion in coastal, off‐the‐coast and offshore aquaculture with most being attributed to interactions with other maritime activities, including conflicts with other users and administrative procedures, including licensing. Critical needs for improved management and expansion of the aquaculture industry are related to planning and management of developments and technological advances, with economic and market needs featuring to a lesser extent. Key procedures recommended to assist further aquaculture growth are the standardisation and simplification of regulatory frameworks, improvement of governance, and the adoption of participatory processes to facilitate meaningful and productive stakeholder engagement. We strongly recommend stakeholder participation to enhance insights on the full environmental and human dimensions of marine management and for implementation of ecosystem‐based marine spatial planning.

Climate change adaptation in aquaculture - Eranga K. Galappaththi; Stephanie T. Ichien; Amanda A. Hyman; Charlotte J. Aubrac; James D. Ford (Reviews in Aquaculture, 2020)
This study conducts the first systematic literature review of climate change adaptation in aquaculture. We address three specific questions: (i) What is aquaculture adapting to? (ii) How is aquaculture adapting? and (iii) What research gaps need to be addressed? We identify, characterise and examine case studies published between 1990 and 2018 that lie at the intersection of the domains of climate change, adaptation and aquaculture. The main areas of documented climate change impacts relate to extreme events and the general impacts of climate change on the aquaculture sector. Three categories of adaptation to climate change are identified: coping mechanisms at the local level (e.g. water quality management techniques), multilevel adaptive strategies (e.g. changing culture practices) and management approaches (e.g. adaptation planning, community‐based adaptation). We identify four potential areas for future research: research on inland aquaculture adaptation; studies at the household level; whether different groups of aquaculture farmers (e.g. indigenous people) face and adapt differently to climate change; and the use of GIS and remote sensing as cost‐effective tools for developing adaptation strategies and responses. The study brings essential practical and theoretical insights to the aquaculture industry as well as to climate change adaptation research across the globe.

Rickettsiales‐like organisms in bivalves and marine gastropods: a review - Roberto Cruz‐Flores; Jorge Cáceres‐Martínez (Reviews in Aquaculture, 2020)
Rickettsiales‐like organisms (RLOs) are intracellular bacteria that have been reported to be symbionts of over 60 species of bivalves and marine gastropod molluscs of aquaculture importance around the world. Morphologically, some of these prokaryotes are similar to bacteria from the order Rickettsiales, and in most cases, they form intracytoplasmic inclusions similar to those observed in bacteria of the family Anaplasmataceae . Genetically, only Candidatus Xenohaliotis californiensis ( C Xc), a parasite of several abalone species, has been classified as a member of the order Rickettsiales . The other two characterized RLOs are distantly related; one belongs to the same class (α‐proteobacteria), and the other belongs to the γ‐proteobacteria. Hyperparasitism of RLOs by bacteriophages has been reported in several species of mollusc and appears to have a negative effect on RLOs. The intracellular lifestyle of RLOs has been associated with cell alterations including hypertrophy and compression of the cytoplasmic organelles, and in most cases, no host reaction is observed by histology. In some cases, a high infection intensity of RLOs has been related to dysfunction of the affected organs that can result in disease, and in other cases, high burdens of RLOs have been associated with mortality, but most of these cases have yet to be confirmed. To date, only C Xc has been confirmed as the aetiological agent of a chronic and potentially lethal disease of several abalone species known as withering syndrome. This disease is listed by the World Organization of Animal Health. With the ever‐increasing interest in preserving fisheries and expanding the aquaculture production of mollusc species, more efforts should be focused on the characterization and study of RLOs to elucidate the type of symbiosis they maintain with their host and determine when they are acting as true pathogens that should be subjected to control in aquaculture. This review provides an overview of the literature on RLOs that infect bivalves and gastropods of aquaculture importance, and we discuss the most important aspects of these unique prokaryotes.

Aquaculture of green sea urchin in the Barents Sea: a brief review of Russian studies - Alexander G. Dvoretsky; Vladimir G. Dvoretsky (Reviews in Aquaculture, 2020)
Gonads of the green sea urchin ( Strongylocentrotus droebachiensis ) containing valuable carotenoids, polyunsaturated fatty acids, phospholipids and sulphated fucans are in great demand from the expanding market. In Russian waters of the Barents Sea, only a few sites are suitable for commercial harvesting and thus the development of green sea urchin farming in this region. Our review presents a short survey of Russian literature on biological aspects and rearing methods of green sea urchins in the Barents Sea. In the 1980s, spawning induction and larval culture experiments were undertaken to obtain larvae of S. droebachiensis . Later studies were undertaken to test optimal rations and conditions for gonad enhancement of adult sea urchins in sea cages and closed systems. Gonadal growth was higher and faster in sea urchins reared under controlled conditions in closed water circulation tanks compared with sea cages. Regular feeding of cultured animals provided them better gonadal growth than in wild sea urchins irrespective of food items. Algal diets showed a lower level of gonad yield compared with mixed diets (algae + squid, algae + fish), fish diets and prepared diets (artificial feed based on fish skin). The coast of the Kola Peninsula has a good potential for the development of the green sea urchin farming but several financial, socio‐economic, logistic and management problems must be solved before this process starts.

Surface display system for probiotics and its application in aquaculture - Yuan‐Yuan Yao; Ya‐Lin Yang; Chen‐Chen Gao; Feng‐Li Zhang; Rui Xia; Dong Li; Juan Hu; Chao Ran; Zhen Zhang; Jihong Liu‐Clarke; Zhi‐Gang Zhou (Reviews in Aquaculture, 2020)
Aquaculture is a fast‐growing and rapidly expanding industry in the world. Probiotics are widely used in aquaculture and have provided benefits to aquatic animal health, and it is also a promising alternative to antibiotics for control of fish diseases. With the development of biotechnology, new expression systems and novel techniques for the surface display of heterologous proteins in surface of probiotics cells have been developed. This review provides an overview of the systems and strategies for displaying functional proteins on the surface of probiotics commonly used in aquaculture, which are Bacillus subtilis , Bacillus thuringiensis , lactic acid bacteria represented by Lactococcus lactis and yeast. Their applications in aquaculture especially for oral vaccine development afforded by this technology and prospects and challenges associated with this technology are also highlighted.

Is biomass of filamentous green algae Cladophora spp. (Chlorophyta, Ulvophyceae) an unlimited cheap and valuable resource for medicine and pharmacology? A review - Alexander V. Prazukin; Elena V. Anufriieva; Nickolai V. Shadrin (Reviews in Aquaculture, 2020)
Filamentous green algae Cladophora spp. are cosmopolitans inhabiting waters with different salinity, from freshwater to hypersaline. Eutrophication of marine and inland waters results in the huge development of filamentous green algae, which reach high biomass and occupy large areas in different water bodies. This leads to the strong negative effect on the species richness of communities, significantly reduces the aesthetic value of coastal waters, hampers the recreational use of beaches and the coastline, and complicates industrial water intake and coastal fishing. Harvesting and the use of Cladophora biomass can be an effective tool to remediate eutrophic waters. Cladophor a spp. are also among the most promising subjects to use in the development of integrated multi‐trophic aquaculture; there is a big potential to use it. Aquaculture is one of the potential uses. To plan the use of a resource, business needs to know the availability and quantity of the resource, the price of the resource, as well as for what benefit and how it can be used. This review summarizes and analyses existing data to answer these questions. Cladophora biomass can be used for food for humans, livestock, cultivated fish and shrimps, as fertilizers, in the energy sector (biogas and biodiesel), and different industries. The use of Cladophora in medicine and pharmacology is one of the most profitable promising ways to utilize the biomass. This review shows that Cladophora biomass is an unlimited, low cost and valuable resource for medicine and pharmacology.

Parasites and coral‐associated invertebrates that impact coral health - Jonathan A. Barton; David G. Bourne; Craig Humphrey; Kate S. Hutson (Reviews in Aquaculture, 2020)
Globally coral reefs are in decline, largely driven by local anthropogenic pressures combined with broader cumulative impacts from climate change. Coral aquaculture will play an important role in active reef restoration and attempts to preserve some semblance of coral reefs in highly impacted areas. Achieving maximum growth and survivorship of cultured corals is necessary to achieve optimal results. This is not possible without the study of coral pests and diseases which can be detrimental to coral health. Here we review the complex relationships between corals and their associated symbiotic organisms, identify invertebrates that may harm the corals and suggest known management techniques in captivity. Groups considered included acoels (Xenacoelomorpha: Acoela), digeneans (Trematoda: Digenea), polyclads (Rhabditophora: Polycladida), gastropods (Mollusca: Gastropoda), decapods (Malacostraca: Decapoda), copepods (Hexanauplia: Copepoda) and pyrgomatids (Cirripedia: Pyrgomatidae). There are few empirically validated management techniques for coral pests, particularly in terms of large‐scale aquaculture, emphasizing the need for further directed research in this area. Information generated through the ornamental trade and hobbyists is valuable to inform future research direction targeted towards captive coral husbandry, reef ecosystem management and restoration strategies.

Roles of arginine in fish nutrition and health: insights for future researches - Seyyed Morteza Hoseini; Mukhtar Ahmad Khan; Morteza Yousefi; Benjamin Costas (Reviews in Aquaculture, 2020)
Amino acids are important molecules in fish nutrition with critical roles in protein synthesis, immune function and health. Among the essential amino acids, arginine is one of the functional amino acids in animals. Arginine requirement in fish ranges between 3.0 and 8.1% of dietary protein. The amino acid involves in ureagenesis, immune function, antioxidant defence, somatotropic axis, stress responses and ammonia detoxification in fish. To have an extended insight about the current knowledge of arginine effects in fish, this article reviewed available data on arginine effects in different fish species. It covers variations in arginine requirements of different fish species, interaction of arginine with lysine and glutamine, modulation of ureagenesis and ammonia detoxification, modulation of insulin and growth hormone responses, cortisol response, modulation of antioxidant system, immune responses and disease resistance. This review indicates that rearing conditions and dietary ingredients may affect fish arginine requirement. In addition, there is a need for further data about the antioxidant effects of arginine under oxidative condition, its immunostimulant effects under pathogenic challenge, mechanisms of ammonia detoxification and cortisol response by arginine in different fish species.

The new aspects of using some safe feed additives on alleviated imidacloprid toxicity in farmed fish: a review - Mohammed A. E. Naiel; Abdelrazeq M. Shehata; Samar S. Negm; Mohamed E. Abd El‐Hack; Mahmoud S. Amer; Asmaa F. Khafaga; May Bin‐Jumah; Ahmed A. Allam (Reviews in Aquaculture, 2020)
Intensive fish culturing systems depend on provides optimal water quality conditions. Hence, the most important aquaculture practices are the removal of contamination elements related not only to the water quality parameters unacceptable for aquatic species but also to the undesirable effect on the health of fish and consumers. During the last three decades, common applications and production of pesticides have amplified progressively. Due to the excessive use of imidacloprid as a highly effective insecticide, elevated accumulation is expected in an aquatic environment. A large part of applied pesticides emitted into the environment and only a small portion of them reach the final biological target, where it caused several hazards, such as accumulation and toxicity to non‐target creatures. Plant‐derived secondary metabolites are getting great attention due to their safety and therapeutic functions. Also, several feed additives in animal diets can act as chemopreventive agents, which have the potential to decrease the toxicity risk of many pollutants and detoxification of activated metabolites. Understanding the internal action mechanisms of various safe feed additives could lead to the novel therapeutic approaches for acute and chronic pesticide toxicity. This review intends to summarize how safe feed additives alter or mitigate the toxic effects of imidacloprid in farmed fish.

Effects of ammonia on shrimp physiology and immunity: a review - Mingming Zhao; Defu Yao; Shengkang Li; Yueling Zhang; Jude Juventus Aweya (Reviews in Aquaculture, 2020)
The rapid expansion in shrimp farming comes with problems such as inadequate culture technology, disease outbreak, water pollution and other environmental degradation‐related problems. Prominent among these is the level of ammonia, which has been rising steadily in the last couple of years, mainly due to farming practices and other anthropogenic activities, and therefore has had consequent effects on marine life, especially shrimp. While optimal ammonia levels are a good source of nitrogen for marine phytoplankton that increases the level of dissolved oxygen in water as well serves as food for shrimp, high levels of ammonia are harmful to shrimp. When shrimp pond ammonia levels go beyond the tolerance limits, it inhibits chitinase expression, moulting, growth, phenoloxidase and haemolymph antimicrobial activity, thereby attenuating shrimp innate immune response. In this review, we bring together recent information on the effects of ammonia stress on the growth, physiology, biochemistry, ammonia‐metabolizing enzymes and immunity of shrimp. We also propose areas of research that can be explored in the breeding of new ammonia‐tolerant and disease‐resistant shrimp with robust immune and/or physiological systems that could withstand environmental stress and pathogens.

Co‐culture of shrimp with commercially important plants: a review - Juan Francisco Fierro‐Sañudo; Gustavo Alejandro Rodríguez‐Montes de Oca; Federico Páez‐Osuna (Reviews in Aquaculture, 2020)
Shrimp farming is one of the most important worldwide developed sectors; however, this development has induced a series of negative environmental impacts. One strategy to reduce these impacts is the integration or co‐culture of shrimp farming with agriculture. The integration of shrimp farming with commercial plants has been carried out with the objective of minimizing the environmental impact through the use of biosolids and effluents enriched with nutrients, taking advantage of available resources and generating greater income for producers. The aim of this review was to present the state of the art of integrated shrimp–vascular plant culture, focus on those plants with commercial interest and describe the different forms of integration. We reviewed over 158 studies dealing with integrated shrimp–plant cultures at different salinities, as well as the influence of salinity in the performance of both biological components. Plants suitable for the integration with shrimp farming are also examined, including advantages and disadvantages. Finally, several features that require further research are identified.

A proposal of standardization for histopathological lesions to characterize fish diseases - Alba Lucía Rey; Javier Asín; Imanol Ruiz Zarzuela; Lluís Luján; Carlos A. Iregui; Ignacio de Blas (Reviews in Aquaculture, 2020)
The use of histopathology in fish sciences is broadly extended, although it is currently devoid of standardization across the literature. There have been initiatives to standardize every step of the histological evaluation, including description, diagnosis, interpretation, data recording and reporting, and statistical analysis, but, in general, the histopathological systems applied to date present a series of limitations that hamper the reproducibility of the derived data. On top of these limitations, an agreed, organ‐by‐organ list of lesions to be recorded is currently lacking. Therefore, this communication proposes a validated and comprehensive list of features to record in skin, head, eye, nervous system, gastrointestinal tract, gonads, kidney, and other organs of farmed red and Nile tilapias ( Oreochromis sp. and Oreochromis niloticus L., respectively), white cachama ( Piaractus brachypomus ), rainbow trout ( Oncorhynchus mykiss ) and other species. Once this list is agreed and accepted by fish pathologists and other fish scientists, it could be the cornerstone for the development of well‐established and reproducible histopathological scoring systems. This communication highlights the importance of standardization initiatives in fish histology to produce reliable and high‐quality data.

Current state of water quality indicators in urban streams in New Zealand - Jennifer Gadd; Ton Snelder; Caroline Fraser; Amy Whitehead (New Zealand Journal of Marine and Freshwater Research, 2020)
National assessments have highlighted that urban streams have some of the poorest water quality in New Zealand, yet there has been no analysis focussing on these streams. In this study we defined urban streams as >15% catchment urban land cover and used monitoring data to assess several indicators of water quality including dissolved metals, nutrients, bacteria and the macroinvertebrate community index. We investigated associations between the indicators and urban land cover, imperviousness and geographic location. Water quality was highly variable, within and between monitored sites; and invariably poor when compared to water quality criteria. Dissolved zinc was positively related to the proportion of urban land cover and imperviousness in the upstream catchment. There were significant differences in ammoniacal‐N, nitrate‐N, turbidity, MCI, dissolved zinc and E. coli between geographic locations. The analysis indicates that if urban development continues in its current form, increases in urban land cover around New Zealand can be expected to result in further declines in water quality and a reduced likelihood that water quality objectives will be achieved at impacted locations.

Nutrient attenuation in a shallow, gravel‐bed river. II. Spatial and temporal changes in nitrogen dynamics and community metabolism - J. Christopher Rutherford; Roger G. Young; John M. Quinn; Robert J. Wilcock (New Zealand Journal of Marine and Freshwater Research, 2020)
Instream processes alter the concentration and bioavailability of nutrients as they are transported downstream. By relating primary production and periphyton composition to changes in nutrient concentration in a gravel‐bed river this study made inferences about recycling and attenuation. Where dissolved inorganic nitrogen (DIN) was abundant, concentrations decreased linearly with distance but by less than required to meet the nitrogen demand of primary production. Where DIN was barely measurable photosynthesis was reduced but only by 50%. We infer that recycling sustained primary production even when DIN concentrations were negligibly small. One implication is that DIN removal underestimates attenuation. Further experimental research on recycling and improved modelling is required to better quantify the length of streams adversely affected by nutrients.

The stream hydrology response of converting a headwater pasture catchment to Pinus radiata plantation - Andrew O. Hughes; Rob Davies‐Colley; Margaret Bellingham; Gareth van Assema (New Zealand Journal of Marine and Freshwater Research, 2020)
The planting of degraded land with tree plantations may be effective at improving land use sustainability and profitability but it can also have significant effects on stream hydrology. In this paired catchment study, we report the stream hydrological response to partial (62%) afforestation of a steep pastoral catchment in the western Waikato Region, North Island, New Zealand. We comprehensively analyse the hydrological regime changes over a 23‐year period (including eight years before pine planting) with reference to a native‐forested ‘control’ catchment. Our results show that afforestation has markedly affected stream hydrology. Seven years after planting, the total annual runoff was 380 mm lower than predicted for the catchment in pasture. Two phases of plantation thinning resulted in the difference between measured and predicted runoff reducing to only 129 mm. Peak flows reduced by ∼50% while total stormflow reduced by ∼30% – which we attribute to canopy interception attenuating and delaying water yield. The impact of plantation establishment on low flows is not so clear, although afforestation appears to have reduced low flows by ∼25%. This study provides information on the hydrological impact of afforestation within a hitherto poorly‐represented New Zealand environment (i.e. high rainfall, sedimentary lithology‐based, North Island hill country).

Sediment‐related water quality of small hill‐country streams near Whatawhata, New Zealand. Response to integrated catchment management (ICM) - Rob Davies‐Colley; Andrew Hughes (New Zealand Journal of Marine and Freshwater Research, 2020)
Degradation of aquatic ecosystems by fine sediment is a global environmental problem, and damages reflect particle properties as well as mass concentration. We studied sediment‐related water quality (SRWQ) of small streams in hill‐country near Whatawhata, NZ, that have been monitored since 1995. In 2001, an integrated catchment management (ICM) plan was implemented in the Mangaotama (originally sheep‐beef) catchment – including conversion of steep headwaters to pine plantation, cattle exclusion, and native riparian plantings. The long‐term SRWQ within the Mangaotama catchment was examined with reference to a nearby native‐forested control catchment. Correlations between visual clarity, suspended particulate matter concentration and related variables were moderate to fairly strong. The ICM has not improved SRWQ as expected – plausibly because removal of cattle disturbance has been offset by decline in pasture ground cover under increasing shade of tree plantings. Worsening SRWQ is expected over the next several decades as channels widen towards a ‘forest’ morphology.

Nutrient attenuation in a shallow, gravel‐bed river. I. In‐situ chamber experiments - John M. Quinn; J. Christopher Rutherford; Sherry J. Schiff (New Zealand Journal of Marine and Freshwater Research, 2020)
Dissolved nutrient uptake and metabolism by periphyton in a central North Island gravel‐bed river were investigated using recirculating in‐situ chambers. Dissolved inorganic nitrogen (DIN) uptake was correlated with photosynthesis and chlorophyll but N uptake and carbon fixation were partly de‐coupled indicating storage. Dissolved reactive phosphorus (DRP) uptake was only weakly correlated with photosynthesis. Diatoms and green algae relied on DRP in the water, but Cyanobacteria met part of their P needs from storage. Dissolved organic nutrients were excreted in both light and dark incubations, with approximately 50% of DIN uptake during photosynthesis excreted as DON. To simulate diurnal variations in nutrients, oxygen and pH existing computer models need to de‐couple photosynthesis from nutrient uptake, allow for variable stoichiometry and better quantify recycling of organic nutrients.

Effects of agricultural and urban land cover on New Zealand’s estuarine water quality - Bruce D. Dudley; Olivia R. Burge; David Plew; John Zeldis (New Zealand Journal of Marine and Freshwater Research, 2020)
National‐scale analyses of land cover effects on water quality can aid in directing environmental policy. We compiled a coastal water quality database for New Zealand comprising 320 estuarine and coastal sites with records between 2013 and 2018. Previous literature had shown strong effects of agricultural and urban land cover on the quality of New Zealand’s rivers, so we examined their effects on estuaries, while controlling for marine dilution and freshwater flushing. Sites with greater freshwater influence had higher nutrient and faecal indicator bacteria concentrations, and turbidity, indicating that open coast and estuarine water quality is reduced predominantly via flows from the land. Nitrate, ammonium, total and dissolved reactive phosphorus, and water column chlorophyll‐ a concentrations were greater in estuaries with higher urban land cover and total phosphorus concentrations were greater with higher agricultural land cover. There was a marginally significant increase in turbidity as agricultural land cover increased. This is the first national‐scale compilation and analysis of New Zealand coastal water quality data, and the first national analysis of land cover effects on water quality in New Zealand estuaries.

Trialling tools using hand‐weeding, weed mat and artificial shading to control nuisance macrophyte growth at multiple scales in small agricultural waterways - Kathryn E. Collins; Catherine M. Febria; Hayley S. Devlin; Kristy L. Hogsden; Helen J. Warburton; Brandon C. Goeller; Angus R. McIntosh; Jon S. Harding (New Zealand Journal of Marine and Freshwater Research, 2020)
Introduced aquatic macrophytes can dominate small agricultural waterways in summer and autumn becoming a significant management problem. Excessive growth can clog waterways, causing drainage issues and reducing agricultural productivity while in‐stream velocities are reduced and sedimentation increased. Consequently, water managers remove them by mechanical clearance, chemical spray and cutting which can be costly and have negative impacts on in‐stream habitat and ecological health. We trialled three tools to reduce macrophytes: hand‐weeding, weed mat and artificial shading, at a reach‐scale (50 m) and larger‐scale (200–400 m). Hand‐weeding reduced cover in the short‐term, however macrophytes recovered to pre‐treatment levels within one season. Weed mat along the banks was effective at reducing emergent macrophytes, particularly Erythranthe guttata (monkey musk) and Nasturtium microphyllum (watercress). Weed mat lasted for several growing seasons and continued to be effective. Shading over the waterway using polythene markedly reduced submerged macrophytes indicating that heavy shading by riparian plantings could reduce submerged macrophytes in the longer‐term. These results indicate that in the short‐term, weed mat could be used to limit sprawling emergent macrophytes. In the longer‐term, weed mat used in conjunction with riparian planting could provide shading so that macrophyte cover in these small waterways could be reduced and controlled.

Preface: land‐use impacts on aquatic ecosystems ‐ tribute to John Quinn - Scott Larned; Kevin Collier; Clive Howard‐Williams (New Zealand Journal of Marine and Freshwater Research, 2020)

Nitrogen loads to New Zealand aquatic receiving environments: comparison with regulatory criteria - Ton H. Snelder; Amy L. Whitehead; Caroline Fraser; Scott T. Larned; Marc Schallenberg (New Zealand Journal of Marine and Freshwater Research, 2020)
There is concern about the deteriorating nutrient status of aquatic receiving environments in New Zealand. We estimated the amount by which current nitrogen (N) concentrations and loads exceed criteria in rivers, lakes and estuaries nationally. Criteria corresponded to national ‘bottom‐line’ (i.e. minimal) environmental objectives set by government policy. Three metrics were evaluated: (1) degree of compliance describes the current TN loads in receiving environments relative to criteria; (2) catchment N status describes the acceptability of catchment N loads compared to criteria; and (3) excess load indicates the amount by which the N load exceeds the maximum allowable load (kg yr −1 ). Non‐compliance with N criteria was broadly distributed nationally particularly in low‐elevation catchments. Catchments with unacceptable N status constituted at least 31% of New Zealand’s land area, which corresponds to at least 43% of the country’s agricultural land. The national excess load was estimated to be at least 19.1 Gg yr −1 . We are 97.5% confident that estimated excess loads exceed zero for nine of 15 regions and for the nation as a whole. The analyses provide a strategic assessment of where reductions in N emissions are required to achieve the minimal national objectives.

Modelling the effect of land management interventions and climate change on sediment loads in the Manawatū–Whanganui region - Les Basher; Raphael Spiekermann; John Dymond; Alex Herzig; Ella Hayman; Anne‐Gaelle Ausseil (New Zealand Journal of Marine and Freshwater Research, 2020)
SedNetNZ is used to model the effect of erosion control undertaken under the Sustainable Land Use Initiative (SLUI) and predict the effect of climate change on sediment load in the Manawatū–Whanganui region. Sediment load in 2004 is estimated at 13.4 Mt yr −1 ; by 2018, ≈5000 km 2 of land had farm plans implemented and annual sediment load reduced by 6.2% of the 2004 load. If SLUI stops at the 2018 level of implementation, by 2038 it is predicted to achieve a 15.7% reduction in annual sediment load. If SLUI continues to implement farm plans, 7949 km 2 of land will be treated by 2043 and annual sediment load could be reduced by a further 14.7%. Climate change is predicted to substantially increase sediment loads. By 2043 annual sediment load for the region is predicted to increase, compared to 2004, by between 8.3 and 23.7%. However, this can largely be offset by SLUI works. By 2090 an annual sediment load increase of between 53 and 224% due to climate change is predicted. The results suggest climate warming may dominate changes in sediment load in the future.

Incorporating Māori values into land management decision tools - Shannan K. Crow; Gail T. Tipa; Kyle D. Nelson; Amy L. Whitehead (New Zealand Journal of Marine and Freshwater Research, 2020)
Environmental sustainability and the long‐term wellbeing of Māori (the indigenous people of New Zealand) are interdependent and degradation of landscapes risks the progressive degradation of Māori wellbeing. The present study developed an analysis framework based on Ki Uta Ki Tai (holistic‐mountains to the sea‐ management philosophy advocated by Ngāi Tahu) for exploring relationships between landcover and Māori values to enable predictions of cultural values through space and time. We used this framework to predict how two Māori values (Overall Health and Cultural Land Use) have been altered as a result of landcover change between 2001–2012 in three Canterbury catchments. The area of native vegetation declined while exotic pasture increased between 2001–2012, and there were corresponding declines in both cultural health scores. These results suggest that the change in landcover has reduced the ability of the landscape to support Māori values. This framework for assessing changes in Māori values with respect to changing environmental conditions may identify opportunities for Māori to better engage in land use management decisions.

Microcoleus autumnalis and filamentous algae‐dominated mats and chlorophyll‐a increase with agricultural land use but respond differently to associated nutrient and sediment enrichment - Susanna A. Wood; Annika Wagenhoff; Logan Brown; Javier Atalah (New Zealand Journal of Marine and Freshwater Research, 2020)
This study investigated the impact of pastoral land use and nutrient and fine sediment inputs on Microcoleus autumnalis and filamentous algae‐dominated mats, and benthic chlorophyll‐ a in streams (lower North Island, New Zealand). Surveying and sampling was undertaken monthly at 61 sites spanning a wide gradient in catchment cover and environmental conditions. Two boosted regression tree models were built. The first models included pastoral land cover and five environmental variables as predictors. In the second model pastoral land cover was replaced by nutrient/sediment data. The abundance of the two mat types and chlorophyll‐ a increased when pastoral land cover was between 20% and 70% (model 1). Replacement of pastoral land cover by nutrient/sediment data (model 2) slightly improved the model fit for all three periphyton variables. Microcoleus autumnalis ‐dominant mats increased with dissolved inorganic nitrogen concentrations up to ca. 0.6 mg L −1 , and in streams with more frequent flushes. In contrast, filamentous algal‐dominated mats increased with turbidity, and in streams with less frequent flushes. Chlorophyll‐ a generally followed the response of the dominant periphyton type. Increased knowledge on responses of specific periphyton types, rather than total biomass, to environmental variables is essential to guide effective management strategies.

Community turnover provides insight into variable invertebrate recovery between restored streams with different integrated catchment management plans - Sharon Elizabeth Graham; John Martin Quinn (New Zealand Journal of Marine and Freshwater Research, 2020)
Understanding temporal patterns in restored environments is important for identifying potential barriers to recovery and improved management of degraded habitats. In this paper, we use temporal beta diversity analyses to compare invertebrate community recovery trajectories in three restored agricultural stream sites under different integrated catchment plans, a native forest reference site, and two unmodified pasture control stream sites over 24 years. The restored sites diverged from their initial community composition over time and became more similar to the reference site community, which was relatively stable over time. Variation partitioning showed that prior to restoration beta diversity was primarily associated with environmental and spatial drivers, whereas post‐restoration beta diversity was more influenced by temporal and environmental drivers, including changes in substrate size, fine sediments, water clarity, and nutrients, as well as temperature and flow regime. Species’ contributions to beta diversity varied between sites and years, with sensitive EPT taxa contributing more in reference and control sites. However, contributions of some EPT species, particularly mayflies, increased in restored sites post‐ICM. In summary, after nearly two decades of ICM, restored stream sites show recovery towards reference conditions, yet differences persist, indicating that rehabilitation may take longer, depending on the restoration goals.

Evidence for the effects of land use on freshwater ecosystems in New Zealand - Scott T. Larned; Jonathan Moores; Jenni Gadd; Brenda Baillie; Marc Schallenberg (New Zealand Journal of Marine and Freshwater Research, 2020)
To meet the challenges of preventing and reversing adverse effects of land use on ecosystems, management actions need to be founded on strong evidence. We used the pressure‐state‐impact (PSI) framework to assess evidence of land‐use effects on New Zealand freshwater ecosystems. The evidence consisted of published quantitative and categorical associations linking land‐use pressures to state changes and ecological impacts in rivers, lakes and aquifers. There was substantial evidence of land‐use effects, particularly where land use/land cover (LULC) classes were used as pressure variables. Proportions of catchment area in urban and pastoral LULC were consistently, positively correlated with contaminant levels in water bodies and negatively correlated with ecological‐health indicators. Other consistent PSI associations included positive correlations between cattle stocking rates and river contaminant levels, increased fine sediment and decreased ecological‐health scores in rivers following forest harvest, and increased river contaminant levels at sites with stock access. Despite these consistent associations, the evidence base has four general shortcomings that should be addressed: (1) inadequate integration of data and models that link land use and contaminant loss to state changes and impacts in freshwater ecosystems; (2) weak inferences based on LULC; (3) reliance on categorical PSI associations; (4) gaps in reported PSI associations.

Uncovering and defragmenting the role of the Toll pathway in the innate immune responses of cultured crustaceans against viral pathogens - Arturo Sánchez‐Paz; Adriana Muhlia‐Almazán (Reviews in Aquaculture, 2020)
Shrimp farming is considered the fastest growing aquaculture industry in the last decades, with an average growth in production of ~15% per year. Unfortunately, this industry has been affected by the emergence of viral diseases, and currently, there are no commercially available therapeutics against these pathogens. Therefore, a deeper understanding of the immune system components induced by viruses is imperative for the development of antiviral therapies in these species. It is well known that the Toll‐like receptor (TLR) signalling is involved in activating the innate immune responses in crustaceans. Although numerous research papers deal with the response of the individual components of this pathway involved in the antiviral response on different crustacean species, the information is highly fragmented. This review provides a detailed picture of the general structure and role of Spätzle, Toll receptors, MyD88, Tollip, Tube, Pelle, Pellino, Dorsal, Cactus and DIF, the elements constituting the Toll‐like receptor participating in the innate immune response against viral diseases in crustaceans. It summarizes the current knowledge progress about the influence of the Toll pathway components on the expression of antimicrobial peptides involved in the antiviral response of crustaceans. In addition, this review compares the structural and functional roles of the elements identified in crustaceans, with those of the popular model organism Drosophila . This systematic review may contribute to identify the existing gaps in the knowledge of the Toll pathway in crustaceans and help to carry out further studies that may be useful for the management of viral diseases.

Acute hepatopancreatic necrosis disease in penaeid shrimp - Ramya Kumar; Tze Hann Ng; Han‐Ching Wang (Reviews in Aquaculture, 2020)
Asian countries are the major producers of cultured Penaeid shrimps such as Penaeus monodon and Penaeus ( Litopenaeus ) vannamei . In recent years, shrimp production has declined due to the emergence of a bacterial disease called acute hepatopancreatic necrosis disease (AHPND). This disease is mainly caused by Vibrio parahaemolyticus , but other Vibrio species are also known to cause AHPND in shrimps. Here, in addition to reviewing recent developments in the field of AHPND diagnosis, host responses to AHPND, the role of microbiota during AHPND infection and the current treatment options for AHPND, we also describe a model of AHPND pathogenesis.

A review of inclusive business models and their application in aquaculture development - Alexander M. Kaminski; Froukje Kruijssen; Steven M. Cole; Malcolm C.M. Beveridge; Claire Dawson; Chadag V. Mohan; Sharon Suri; Manjurul Karim; Oai Li Chen; Michael J. Phillips; William Downing; Fred Weirowski; et al. (Reviews in Aquaculture, 2020)
For aquaculture to continue along its current growth trajectory and contribute towards achieving the Sustainable Development Goals, value chains must become more inclusive. Smallholders and other local value chain actors are often constrained by circumstances and market failures in the global aquaculture industry. Integrating these actors into aquaculture value chains through inclusive business models (IBMs) is often touted as a solution to sustainable and ethical trade and business that can generate development outcomes. We reviewed 36 papers under seven business models commonly used in agriculture development to assess their application in aquaculture value chains in lower‐income countries. A global value chain (GVC) analysis is used to unpack the economic and social upgrading objectives of the different IBMs, as well as the types of relational coordination used between actors in the chain to achieve development outcomes. The extent to which these IBMs helped poor actors overcome certain barriers is evaluated with a focus on how they may ensure or be a risk to inclusiveness through the relations and upgrading opportunities evident in their make‐up. The analysis found that the majority of the models focused on economic upgrading over social upgrading. Providing opportunities for the latter is key to achieving the inclusive objectives of IBMs. Greater horizontal coordination between actors can create further opportunities for economic upgrading established under vertical coordination with other nodes upstream and downstream in a value chain. There is a need to further contextualize these models to aquaculture systems and develop clear indicators of inclusiveness.

Biofloc technology: principles focused on potential species and the case study of Chilean river shrimp Cryphiops caementarius - David Antonio Ulloa Walker; María Cristina Morales Suazo; Maurício Gustavo Coelho Emerenciano (Reviews in Aquaculture, 2020)
The accelerated growth of aquaculture has caused environmental impacts in many countries. Examples include the use of large volumes of water, discharge of effluents with high nutrient content, the occupation of large areas, natural habitat alternation and the escape of exotic species. Biofloc technology (BFT) is an aquaculture tool that requires minimal water exchange, promotes the nutrient recycling optimizing resources and produces natural food in situ by forming suspended microbial aggregates in the water (bioflocs). These microorganisms provide multiple benefits such as water quality control, pathogen resistance and nutritional supplementation. Species such as Litopenaeus vannamei and tilapia have been successfully applied in BFT. In addition, there are also an increasing number of studies focused on alternative species with promising results. This paper describes essential aspects of biofloc technology, its application in aquaculture and the potential to extend its benefits to new aquaculture species such as Chilean river shrimp Cryphiops caementarius . This paper describes the future challenges of this technology as well as opportunities for its application.

Professor Sena S. De Silva (1946–2020) (Reviews in Aquaculture, 2020)

Carbohydrate utilisation by tilapia: a meta‐analytical approach - Roel M. Maas; Marc C.J. Verdegem; Geert F. Wiegertjes; Johan W. Schrama (Reviews in Aquaculture, 2020)
Currently, studies reporting the digestibility of carbohydrates, starch and especially non‐starch polysaccharides (NSP) in fish are scarce. Carbohydrate digestibility in the diet is largely dependent upon carbohydrate composition (starch vs. NSP). NSP are often considered to be indigestible and thus of no nutritional value. The present study reviews carbohydrates in fish feed, distinguishing between total carbohydrate, starch and NSP. Besides a qualitative approach, a meta‐analysis was performed, compiling available data from digestibility studies on tilapia. Our meta‐analysis confirms the negative effect of NSP on performance (FCR) and nutrient digestibility (crude protein, fat and energy). However, an average NSP digestibility of 24.3% was calculated in 95 cases. Out of these 95 cases, 88% of them showed a positive NSP digestibility. NSP digestibility was shown to contribute to energy digestibility. The digestion of NSP in fish is associated with fermentation in the gut, producing beneficial volatile fatty acids that are rapidly absorbed by the colonic lumen. Therefore, in diet formulation, digestibility and thus energy originating from NSP should be taken into consideration because NSP contribute to the energy needs of fish, here tilapia. Besides being an energy source, specific types of NSP may have immune‐modulating and prebiotic effects and may be increasingly added to fish feed as modulators of fish health. We suggest that NSP is potentially (partly) digested by a wide range of fish species, especially by warm‐water species with a long gut adapted to feeding on plant matter, as these factors favour gut fermentation.

Biofloc technology as a promising tool to improve aquaculture production - Mohammad Hossein Khanjani; Moslem Sharifinia (Reviews in Aquaculture, 2020)
Given that the expansion of the aquaculture industry is associated with increased environmental impact and its strong dependence on fishmeal in the diet, the use of biofloc technology can reduce these problems. This technology absorbs inorganic nitrogen from aquaculture wastewater and improves water quality as well as produces microbial protein that is directly used as a suitable feed supplement for aquatic animals. Furthermore, this technology reduces the feed conversion ratio and subsequent production cost. Biofloc is available to aquatic animals throughout the day and provides the necessary nutrients, fatty acids and minerals. Biofloc along with formulated diets provides a complete food chain for aquatic animals’ growth and thus improves growth performance. Since feed constitutes a major part of the aquaculture cost, having accurate information about biofloc system in aquatic animals’ nutrition can be beneficial and helpful. Compared to traditional aquaculture techniques, biofloc technology provides a more sustainable approach with minimal water exchange along with reduced feed intake and transforms it into a low‐cost sustainable technology for sustainable aquaculture development. Overall, this study highlights the significance of developing biofloc technology to improve aquaculture production and could be an alternative system for cultivation of important commercial species in aquaculture.

Issue Information (Reviews in Aquaculture, 2020)

The economics of Integrated Multi‐Trophic Aquaculture: where are we now and where do we need to go? - Duncan Knowler; Thierry Chopin; Rober Martínez‐Espiñeira; Amir Neori; Ana Nobre; Anthony Noce; Gregor Reid (Reviews in Aquaculture, 2020)
In integrated multi‐trophic aquaculture (IMTA), species from different trophic levels are raised in proximity to one another and the co‐products (organic and inorganic wastes) of one cultured species are recycled to serve as nutritional inputs for others. IMTA can reduce the ecological impacts near aquaculture operations, improve social perceptions of aquaculture and provide financial benefits for aquaculture producers via product diversification, faster production cycles and price premiums on IMTA products. We review aspects of IMTA’s economic potential and market acceptance and consider ways to address the current gaps in our understanding. We find that adopting IMTA raises the assimilative capacity of the farm and that IMTA substantively reduces the environmental cost of aquaculture. Moreover, integrating extractive species (e.g. invertebrates and/or seaweeds), with existing fed‐monoculture operations, can increase farm profits. The presence of positive public attitudes towards IMTA, as expressed by a willingness to pay a premium for its products, can further increase the profitability of adopting IMTA. Areas requiring more economic research include the development of comparative bioeconomic models of IMTA and the evaluation of competing production systems and their ability to internalize externalities to demonstrate the true value of IMTA to society. Further exploration of economic incentives, such as instruments needed to foster adoption of IMTA, and investigation of marketing opportunities, such as promoting the eco‐certification of IMTA products, are also needed. Our paper aimed to inform economists and non‐economists alike about the latest developments in IMTA economics, and spur further research on critical topics concerning this important subject.

Chinese Abstracts (Reviews in Aquaculture, 2020)

Lessons from Japan marine stock enhancement and sea ranching programmes over 100 years - Shuichi Kitada (Reviews in Aquaculture, 2020)
More than 26 billion juveniles of 180 marine species are released annually into the wild in over 20 countries, but the usefulness of this strategy remains unclear. Here, I analyse the effects of stocking by Japanese marine and salmon stock enhancement programmes and evaluate their efficacy through a Bayesian meta‐analysis of new and previously considered cases. The posterior mean recapture rate (±SD) was 8.3 ± 4.7%. Without considering personnel costs and negative impacts on wild populations, the mean economic efficiency was 2.8 ± 6.1, with many cases having values of 1 to 2. On the macro‐scale, the proportion of released seeds to total catch was 76 ± 20% for Japanese scallop, 28 ± 10% for abalone, 20 ± 5% for swimming crab, 13 ± 5% for kuruma prawn, 11 ± 4% for Japanese flounder and 7 ± 2% for red sea bream; according to these percentages, stocking effects were generally small, and population dynamics were unaffected by releases but dependent on the carrying capacity of the nursery habitat. All cases of Japanese releases, except for Japanese scallop, were probably economically unprofitable. Captive breeding reduces the fitness of hatchery fish in the wild. In addition, long‐term releases replace wild genes and may cause fitness decline in the recipient population when the proportion of hatchery fish is very high. Short‐term hatchery stocking can be useful, particularly for conservation purposes, but large‐scale programmes may harm the sustainability of populations. Nursery habitat recovery and fishing pressure reduction often outperform hatcheries in the long run.

Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish - Kumarasan Yukgehnaish; Praveen Kumar; Parimannan Sivachandran; Kasi Marimuthu; Aziz Arshad; Bilal Ahmad Paray; Jesu Arockiaraj (Reviews in Aquaculture, 2020)
Fish gut microbiome confers various effects to the host fish; this includes overall size, metabolism, feeding behaviour and immune response in the fish. The emergence of antimicrobial‐resistant (AMR) bacteria and hard to cure fish diseases warrant the possible utilization of gut microbes that exhibits a positive effect on the fish and thus lead to the usage of these microbes as probiotics. The widespread and systematic use of antibiotics has led to severe biological and ecological problems, especially the development of antibiotic resistance that affects the gut microbiota of aquatic organisms. Probiotics are proposed as an effective and environmentally friendly alternative to antibiotics, known as beneficial microbes. At the same time, prebiotics are considered beneficial to the host's health and growth by decreasing the prevalence of intestinal pathogens and/or changing the development of bacterial metabolites related to health. Uprise of sequencing technology and the development of intricate bioinformatics tools has provided a way to study these gut microbes through metagenomic analysis. From various metagenomic studies, ample of information was obtained; such information includes the effect of the gut microbiome on the physiology of fish, gut microbe composition of different fish, factors affecting the gut microbial composition of the fish and the immunological effect of gut microbes in fish; such this information related to the fish gut microbiome, their function and their importance in aquaculture is discussed in this review.

Assessment of carrying capacity for bivalve mariculture in subtropical and tropical regions: the need for tailored management tools and guidelines - Aubert Anaïs; Aschenbroich Adélaïde; Gaertner Jean‐Claude; Latchere Oihana; Archambault Philippe; Gaertner‐Mazouni Nabila (Reviews in Aquaculture, 2020)
In a context of increasing global food demand, the aquaculture sector, and more particularly bivalve mariculture, has expanded significantly. While the impact of bivalve mariculture was initially overlooked, it is now widely recognized that this industry can significantly impact the ecosystem and its services. Carrying capacity assessment tools have been developed accordingly and have proved to be a useful and efficient aid for mariculture management. However, carrying capacity assessment tools have been mostly designed and implemented in developed temperate countries, while bivalve mariculture is mainly expanding today in tropical and subtropical zones. To what extent the existing carrying capacity assessment tools are suited for use in tropical and subtropical regions has received little attention, and thus constitutes a major issue. The present review aims to fill this gap and highlights the key points to consider for the carrying capacity assessment of bivalve mariculture in tropical and subtropical regions. In line with the requirements for the sustainable development of human activities, and increasing recognition of the need for better integration of social aspects in the management processes, carrying capacity assessment should be undertaken in a more holistic way. Thus, the social, economic and environmental aspects are taken into account in our analysis. A step‐process plan for the sustainable management of bivalve mariculture in tropical and subtropical countries, through the assessment of carrying capacity, is proposed and discussed to offer guidance for managers.

Non‐invasive functional exploration techniques for bivalves with applications to pearl oyster Pinctada margaritifera - Gilles Le Moullac; Claude Soyez; Pierre Lyonnard; Sébastien Chabrier; Léo Milhade; Yannick Gueguen; Benoit Beliaeff (Reviews in Aquaculture, 2020)
Non‐invasive functional exploration techniques can provide information on different aspects of general organism functioning and, unlike lethal or invasive techniques, allow individual organisms to be monitored for as long as necessary. For bivalves, a fairly wide variety of methods and instrumental means exist allowing physiology to be assessed on‐line while keeping animals alive and intact. The current range of non‐invasive techniques for bivalves consists of systems for measuring metabolic flows and valve activity, which can be used on bivalve molluscs for as long as an individual animal's characteristics (e.g. size) make this technically feasible. In this paper, we present some of these non‐invasive techniques with applications for pearl oyster and list other potentially promising techniques. We also focus on a unique method we developed specifically for to record the pearl rotation characteristics within pearl oysters. This article presents the state of the art in non‐invasive functional exploration techniques. We hope that the information provided here will be useful to physiologists of bivalve marine molluscs through the tools and applications presented here or other future approaches based on them.

Bile acid metabolism in fish: disturbances caused by fishmeal alternatives and some mitigating effects from dietary bile inclusions - Nicholas Romano; Vikas Kumar; Gang Yang; Kimia Kajbaf; Marina B. Rubio; Ken Overturf; Andreas Brezas; Ronald Hardy (Reviews in Aquaculture, 2020)
Bile is a yellow‐green liquid produced in the liver from cholesterol and stored in the gallbladder of vertebrates. Bile improves the efficacy of lipid digestion by acting as an emulsifier and is essential in activating bile salt lipase, an enzyme that has broad substrate specificity. Bile improves the absorption of lipid soluble nutrients while also facilitating the excretion of cholesterol and toxic metabolites, particularly bilirubin. Dietary fishmeal alternatives often disturb bile acid status in fish resulting in either increased excretion/decreased intestinal reabsorption and/or decreased bile acid synthesis. Saponins and high molecular mass proteins are believed to contribute to altered bile acid status, which may reduce fish productivity. This situation can worsen with increased incorporations of plant‐based proteins in aquafeeds, but also may be mitigated by processing of fishmeal alternatives as well as the dietary inclusion of some bile acids/salts. This area of research will likely increase due to the roles dietary bile acids/salts can have on protecting digestive organs and improving nutrient utilization. This, however, depends on the bile type, level and fish species. This review discusses these aspects in regard to fish nutrition to help increase the inclusion of dietary fishmeal alternatives and thus enhance aquaculture sustainability.

The importance of pepsin‐like acid protease quantification in aquaculture studies: a revision of available procedures and presentation of a new protocol for its assessment - Héctor Nolasco‐Soria; Héctor‐Rodrigo Nolasco‐Alzaga; Enric Gisbert (Reviews in Aquaculture, 2020)
Assessing the activity of acid pepsin‐like protease is a common procedure in many biological, physiological and nutritional studies in gastric fish species. After reviewing the available literature on fish digestive acid proteases (stomach acid pepsin‐like proteases), especially those species of relevance for aquaculture purposes, published during a time span of ten years (2008–2018), authors detected some possible methodological and/or interpretative inconsistencies in this kind of studies when quantifying pepsin‐like enzymes. Thus, we concluded that special attention should be paid on the following issues when assessing digestive acid protease activity: (i) the proper preparation of stomach extracts, (ii) the use of the proper reaction conditions at the normal range of physiological pH and temperature values, and (iii) the proper quantification of the number of peptide bonds hydrolyzed for acid protease unit calculation. The implementation of these recommendations, and the proposal of more suitable (previously tested) methodological steps, will promote the standardization of acid pepsin‐like protease analytical procedures, as well as improve the reliability of comparative studies dealing with this proteolytic enzyme between different fish species of aquacultural importance.

Effects of short‐term storage on sperm function in fish semen: a review - Pablo Contreras; Kelly Dumorné; Patricio Ulloa‐Rodríguez; Osvaldo Merino; Elías Figueroa; Jorge G. Farías; Iván Valdebenito; Jennie Risopatrón (Reviews in Aquaculture, 2020)
Storage of refrigerated semen is a simple and inexpensive procedure that can facilitate the management and reproduction programmes in aquaculture and allows to store semen for in vitro reproduction, quality analyses, hatchery production support, selective in vitro breeding, disease diagnosis, transportation, cryopreservation and advanced molecular studies. Implementation of semen short‐term storage protocols for threatened or endangered fish represents a useful strategy for preservation of these species. Semen cold storage as technique is a useful strategy for the conservation of fish sperm. Analysing the male broodstock sperm quality during cold storage is a tool to identify the reproductive ability of cultivated fish. Thus, in this review we analysed the most relevant factors that affect sperm quality during cold storage of male broodstock semen as well as its effects on motility, viability, mitochondrial membrane potential, superoxide anion level and DNA fragmentation.

Recent advances of marine ornamental fish larviculture: broodstock reproduction, live prey and feeding regimes, and comparison between demersal and pelagic spawners - Jun Yu Chen; Chaoshu Zeng; Dean R. Jerry; Jennifer M. Cobcroft (Reviews in Aquaculture, 2020)
Marine ornamental fish are a key component of the multimillion‐dollar marine aquarium trade industry, a controversial industry due to current heavy reliance on wild‐collected specimens. Aquaculture of marine ornamental fish is considered as a sustainable alternative, but it is still in the early stage of development. This review focuses on the current state of marine ornamental fish aquaculture, by covering topics on reef fish reproductive biology in captivity, traditional and novel live feeds, feeding regimes and visual environment in larviculture. Where possible, major differences between demersal and pelagic spawners are compared and discussed. Overall, for many ornamental fish species, natural spawning can be achieved in a captive environment without the use of hormone induction; however, sex identification and successful pairing for reef fish species could be a challenge. With the use of both traditional (rotifers and Artemia ) and novel live feeds (e.g. marine copepods and ciliates), a range of breakthroughs in larval rearing of both demersal and pelagic spawning ornamental fish species have been achieved in recent years, although larval survival varies. To further improve the larval rearing success of marine ornamental fish, this review suggests that future research should focus on optimizing the use of live feed in terms of both quality and quantity, and establishment of well‐defined species‐specific larval feeding regime, as well as providing appropriate rearing condition through improved manipulation of light conditions and the ‘greenwater’ techniques in larval rearing.

Impact of environmental factors on the growth and maturation of farmed Arctic charr - Albert Kjartan Dagbjartarson Imsland; Snorri Gunnarsson; Helgi Thorarensen (Reviews in Aquaculture, 2020)
Farming of Arctic charr mainly takes place in land‐based farms applying intensive rearing methods with relatively high production costs. Depending on local conditions at each site, it is possible to regulate important environmental factors to improve productivity and well‐being of the fish. Knowledge about how these different environmental factors affect various farming traits is important to reduce production costs. This review shows how rearing temperature, photoperiod, salinity and feeding rate can affect farming traits such as growth rate, maturation and feed conversion efficiency of Arctic charr. High growth rate during juvenile phase when the fish are reared at higher temperatures can result in higher incidence of maturation during the on‐growing period. Overall, more moderate rearing temperature regimes seem to result in better long‐term growth rates. Photoperiod manipulation and feed ration can be used as tools to improve growth and reduce maturation. It is possible to rear Arctic charr successfully up to market size in salinities up to c. 27–28 ppt. However, extended rearing resulted in higher ratio of sexually mature fish at 29 than at 25 possibly linked to higher rearing temperatures in brackish water. Future studies should focus on better preserving the potential high growth rate of Arctic charr during juvenile phase into the on‐growing period and establish protocols to improve the seawater tolerance of Arctic charr.

Isogenic lines in fish – a critical review - Roman Franěk; Abdul Rasheed Baloch; Vojtěch Kašpar; Taiju Saito; Takafumi Fujimoto; Katsutoshi Arai; Martin Pšenička (Reviews in Aquaculture, 2020)
An isogenic line is a group of animals with an identical genotype, and its use is widely accepted for bioresearch standardization. Isogenic lines in fish can be generated within two generations via uniparental inheritance and can facilitate studies for which standardization and consistency are required. The availability and use of isogenic lines is limited, but isogenic lines in some fish species have been generated. Their power has been demonstrated in fields including human disease modelling, drug development, toxicology and also sequencing projects. The genetic basis of desired traits in aquaculture species can be identified using isogenic lines, which, in turn, will help to improve fish culture. This review summarized knowledge regarding the present status of isogenic lines in fish including approaches for their generation and verification, as well as challenges and potential applications for basic research and aquaculture.

Current approaches in decoding the molecular mechanisms of long‐term stress in adult farmed Atlantic salmon ( Salmo salar ) - Kine Samset Hoem; Ann‐Kristin Tveten (Reviews in Aquaculture, 2020)
Aquaculture sustainability and profit is highly dependent on good welfare for farmed fish including the economically important species Atlantic salmon ( Salmo salar ). Welfare is closely linked to stress, as prolonged stressful farming conditions can translate into reduced performance and health. Understanding how Atlantic salmon responds to aquaculture‐related stressors has for the past years been a key focus area of research. Present review evaluates the current state of the art by assessing a defined panel of 13 recent articles on the topic. Particular attention is paid to methodological approaches and challenges in investigating chronic stress effects. Stress experiments are performed in profoundly different ways based on scientific interest, and applied stressors range from environmental challenges, for example water quality, to management‐related practices and dietary stress. We show that majority of studies are limited to analysis at the transcriptional level. Quantitative reverse transcription PCR ( RT ‐ qPCR ) is the dominating technology, followed by microarray assays. Post‐translational studies are rare, and correlations between changes in transcript expressions and protein levels are generally not explored. We encourage future research to address this knowledge gap, as insight on proteome status may unravel more long‐standing physiological mechanisms towards stress, for example tertiary effects, that can only be postulated by transcriptional analyses. Attention should also be paid to regulatory mechanisms operating on pre‐ and post‐translational levels, for example micro RNA s, which may be affected by environmental challenges and play roles in modifying stress responses.

Overview and future perspectives of nitrifying bacteria on biofilters for recirculating aquaculture systems - Pamela Ruiz; José Miguel Vidal; Daniela Sepúlveda; Claudia Torres; Gabriela Villouta; Carlos Carrasco; Felipe Aguilera; Nathaly Ruiz‐Tagle; Homero Urrutia (Reviews in Aquaculture, 2020)
Intensive fish culture is a practice in aquaculture systems; however, it can produce negative environmental impacts due to the accumulation of organic nitrogen from feeding procedures, but also from fish wasting products. Recirculating aquaculture systems have emerged as one strategy to reduce these impacts, maintaining a healthy environment for fish. These reduce toxicity level through nitrifying biofilters, which use a microbial consortium to convert ammonia into nitrate. The main component of bacterial consortium is comprised by aerobic ammonia‐oxidizing bacteria and aerobic nitrite‐oxidizing bacteria, which are part of the whole nitrification process. These nitrifying bacteria grow in suspension or in fixed form, the latter characterized by a biofilm formation where bacteria adhere to a physical substrate in a self‐produced polymer matrix. The biofilm formation requires tight communication among bacteria to regulate the transcriptional circuits underlying the production of chemical signal molecules (e.g. N‐acetyl‐homoserine lactones) that control biofilm formation. This coordination is known as quorum sensing and can be considered as a mechanism that contributes to the coupling and maintenance of nitrification rate among bacteria by regulating expression levels of relevant genes associated with nitrification process. Therefore, the control of this process is crucial in recirculating aquaculture systems and its incorrect manipulation can produce a detriment of water quality. We here present an overview of the nitrification process in recirculating aquaculture systems. Subsequently, we describe nitrifying biofilters and nitrifying bacteria. Finally, we discuss how quorum sensing controls the efficiency of nitrifying bacteria and potential applications of nitrifying biofilters in intensive aquaculture systems.

Status and recommendations for sustainable freshwater aquaculture in Brazil - André B. Nobile; Almir M. Cunico; Jean R. S. Vitule; Jamile Queiroz; Ana P. Vidotto‐Magnoni; Diego A. Z. Garcia; Mário L. Orsi; Felipe P. Lima; Aline A. Acosta; Reinaldo J. da Silva; Fernanda D. do Prado; Fábio Porto‐Foresti; et al. (Reviews in Aquaculture, 2020)
Brazil is a megadiverse country and is participant of fundamental environmental agreements for biodiversity conservation. However, the internal politics and the cultures that affect negatively the ecological integrity in Brazilian freshwater need to be improved on the condition of sustainable management. Scientific community, the government and stakeholders are in constant conflicts of goals. Meanwhile, the current model for Brazilian aquaculture shows problems of ecological impact due to the lack of appropriated planning and legislation to the aquatic biota. The non‐recognition of sustainable census incorporated in its environmental politics reflects in an archaic and unsustainable management, with the following characters: a non‐specific approach for technical management, the indiscriminate use of interspecific hybrids and non‐native species and the lack of skilled labour. The potential impact on native species and the introduction of pathogens are the main negative effects on aquatic biota. This way, the aim of this article is to elucidate the conflicts of interests and ecological effects of fish aquaculture in Brazil, besides providing good practices and sustainable alternatives for management.

Assessing risks and mitigating impacts of harmful algal blooms on mariculture and marine fisheries - Andrew Ross Brown; Martin Lilley; Jamie Shutler; Chris Lowe; Yuri Artioli; Ricardo Torres; Elisa Berdalet; Charles R. Tyler (Reviews in Aquaculture, 2020)
Aquaculture is the fastest growing food sector globally and protein provisioning from aquaculture now exceeds that from wild capture fisheries. There is clear potential for the further expansion of marine aquaculture (mariculture), but there are associated risks. Some naturally occurring algae can proliferate under certain environmental conditions, causing deoxygenation of seawater, or releasing toxic compounds (phycotoxins), which can harm wild and cultured finfish and shellfish, and also human consumers. The impacts of these so‐called harmful algal blooms ( HAB s) amount to approximately 8 $billion/yr globally, due to mass mortalities in finfish, harvesting bans preventing the sale of shellfish that have accumulated unsafe levels of HAB phycotoxins and unavoided human health costs. Here, we provide a critical review and analysis of HAB impacts on mariculture (and wild capture fisheries) and recommend research to identify ways to minimise their impacts to the industry. We examine causal factors for HAB development in inshore versus offshore locations and consider how mariculture itself, in its various forms, may exacerbate or mitigate HAB risk. From a management perspective, there is considerable scope for strategic siting of offshore mariculture and holistic Environmental Approaches for Aquaculture, such as offsetting nutrient outputs from finfish farming, via the co‐location of extractive shellfish and macroalgae. Such pre‐emptive, ecosystem‐based approaches are preferable to reactive physical, chemical or microbiological control measures aiming to remove or neutralise HAB s and their phycotxins. To facilitate mariculture expansion and long‐term sustainability, it is also essential to evaluate HAB risk in conjunction with climate change.

Econometric models applied to aquaculture as tools for sustainable production - Daniel Peñalosa Martinell; Francisco Javier Vergara‐Solana; Luis César Almendarez‐Hernández; Marcelo Eduardo Araneda‐Padilla (Reviews in Aquaculture, 2020)
Aquaculture production must keep increasing if seafood demand is to be met. This increase in production has substantial impacts on the three pillars of sustainability (i.e. economy, society and environment). To fairly assess the effects that industry has, several tools have been used, mainly theoretical bioeconomic analysis. Even though theoretical models are essential for the assessment of sustainability, the application of econometric models that rely on empirical data to validate the theory proposed is a priority. The objective of this work was to analyse state of the art related to the use of econometric models in aquaculture industry and categorize findings according to their relationship with any of the three pillars of sustainability to promote the implementation of tools that allow balancing growth of the sector with rational use of resources. The study is divided into five sections. First, the introduction describes the current state of aquaculture, difficulties in management and use of econometric models as tools for improving it. Second, the methods used to develop the bibliometric and bibliographic review are described alongside the research questions. Third, the results of the literature review and categorization are proposed according to the sustainability pillars. Fourth, possible new applications of econometric models are discussed to assess sustainability challenges. Finally, a conclusion of the research is provided stating the benefits and challenges of the use of econometric models in aquaculture.

The use of carotenoid pigments as food additives for aquatic organisms and their functional roles - Daniel Pereira da Costa; Kleber Campos Miranda-Filho (Reviews in Aquaculture, 2020)
Aquatic organisms have various pigments contained in their body and may be an important characteristic for the consumer choice. Carotenoids are the main group of pigments present in aquatic organisms and play an important role not only in colouring but also in the growth, reproduction and maintenance of these animals. As aquatic animals do not have the ability to synthesize carotenoids, they must be ingested in the food, and in some cases, they are converted into forms that are possible to store or use in the animal metabolism. In this work, information was collected about the colour characteristics of aquatic organisms and their influence on aquaculture. Various dietary ingredients, such as vegetables and microorganisms, may be potential sources of pigments for aquaculture species, reducing production costs and dependence on synthetic sources of carotenoids. Some species with aquaculture potential may be better studied in terms of the ability to use carotenoid pigments and their function in the body.

The role of salinity in physiological responses of bivalves - Sajjad Pourmozaffar; Saeid Tamadoni Jahromi; Hossein Rameshi; Ali Sadeghi; Tahereh Bagheri; Siamak Behzadi; Mohsen Gozari; Mohammad Reza Zahedi; Shahrooz Abrari Lazarjani (Reviews in Aquaculture, 2020)
In recent years, financial losses due to salinity changes threat bivalve industry. In natural habitat, marine bivalves should be adapted to a series of environmental stressors, including biotic (virus, bacteria and protozoan) and abiotic (salinity, temperature and heavy metal) factors. It is known that salinity fluctuations able to change distribution and vital parameters of bivalves. Suboptimal salinity conditions resulted in changes in defense mechanism, growth, free amino acid, heart rate, oxygen consumption and filtration rate. However, it is necessary to determine the optimal salinity level of cultured bivalves to avoid the risk of mortality and improve growth rate. Therefore, this study aimed to review the findings from various reports in vitro and in vivo conditions which evaluated physiological and immunological responses of different bivalve species submitted to different salinity concentrations. The information of present study is very important in understanding the physiological responses of bivalves, which are living in highly changeable environment such as estuarine.

Factors influencing GH and IGF‐I gene expression on growth in teleost fish: how can aquaculture industry benefit? - Kostas A. Triantaphyllopoulos; Dimitris Cartas; Helen Miliou (Reviews in Aquaculture, 2020)
Growth is a polygenic and environmentally controlled trait with the most influential genes being those of growth hormone ( GH ) and insulin‐like growth factor‐I ( IGF‐I ), as they consist the core of the hypothalamic–pituitary–somatotropic (HPS) axis. As a result, the influence of environmental and dietary conditions on GH and IGF‐I gene expression has a great potential in planning to optimize fish health and production, as growth rate of fish is a key factor in aquaculture. In this review, we provide a molecular and physiological overview of GH and IGF‐I gene expression as well as all the participating factors regulating GH/IGF‐I axis in growth. We further discuss the genetic, dietary and environmental factors affecting growth rate. More importantly, how external factors in combination with diet such as temperature, photoperiod, salinity, pollutants and stocking density affect GH and IGF‐I expression and growth rate. In addition, there is evidence that photoperiod effect varies among species by altering the seasonal cycle of GH and IGF‐I gene expression and biological cycle of fish. Pollution has also a variable effect on GH, IGF‐I and fish growth rate, depending on the pollutant, species and sex. Finally, increased stocking density influences the HPS axis and growth, dependent on species, temperature and the stage of growth. Notably, interactions among these factors were observed by the reported importance, primarily feeding‐related stress one of the most important factors, while environmental would add or subtract on each other’s optimal or suboptimal conditions in a hierarchy of significance, as further discussed.

The evolution and application of carrying capacity in aquaculture: towards a research agenda - Jenny Weitzman; Ramón Filgueira (Reviews in Aquaculture, 2020)
Carrying capacity has become a fundamental concept within the context of environmental management. Carrying capacity for aquaculture has been studied since the 1960s and has attracted a dedicated literature focused on measuring the environmental and production limits of aquaculture developments. Nevertheless, management and policy face emerging challenges across environmental and social aspects and the growing need to manage multiple objectives in increasingly crowded aquatic ecosystems. Therefore, promoting more sustainable aquaculture development should consider how the tools, methods and research used to support management and decision‐making should advance to meet such challenges. Here, the conceptual and practical applications of carrying capacity are reviewed and future prospects discussed. Carrying capacity for aquaculture has developed a range of models, indicators and approaches to study the relationships between aquaculture and ecosystem components. Carrying capacity supports diverse management objectives to support physical, production, ecological and social goals, although greater emphasis has focused on ecological and production capacities. This review introduces research needs and strategies to advance methods and tools and improve carrying capacity utilization for more holistic, ecosystem‐based aquaculture decision‐making. This paper presents a five‐pillar research agenda for carrying capacity that (i) recognizes system complexity and is (ii) policy‐relevant, (iii) adaptive, (iv) interdisciplinary and (v) meaningful. By promoting knowledge uptake and addressing literature gaps, the proposed agenda could help operationalize a holistic approach to managing for aquaculture sustainability.

Success of fishmeal replacement through poultry by‐product meal in aquaculture feed formulations: a meta‐analysis - Harsha S.C. Galkanda‐Arachchige; Alan E. Wilson; Donald A. Davis (Reviews in Aquaculture, 2020)
Poultry by‐product meal ( PBM ) is a popular animal‐based protein source tested in aquaculture feed formulations for replacing fishmeal ( FM ), mainly due to its high protein content, relatively cheap price and broad availability. However, due to the well‐documented variability in success of PBM inclusions, a meta‐analysis approach was utilized to summarize the efficacy and success of PBM inclusion in aquaculture diet formulations substituting FM . Hedges’ g effect sizes were calculated by quantitatively comparing final weight and feed conversion ratio ( FCR ) between animals fed control (100% FM ) and PBM ‐supplemented FM diets using data from 47 published articles targeting 33 different species (141 and 96 effect size calculations for final weight and FCR , respectively). In addition, several analyses were performed to determine the effect of different moderators as well as variation across species. Meta‐regression was conducted to evaluate the effect of varying PBM proportions of the diet on the response variables. Overall, a non‐significant final weight but a significant higher FCR was detected with aquaculture species fed PBM diets. Similar trends in final weight were observed for subgroups. However, FCR for crustaceans and marine fish fed PBM diets was not significantly different than those fed control diets. In both freshwater and marine fish, ‘species’ was a significant moderator effect on responses, while the ‘level of FM replacement’ was significant only in marine fish. Higher between‐study heterogeneity was detected for fish, which may be due to the influence of certain factors, such as variability in nutritional quality and palatability and digestibility of PBM or due to variability on the fish meal used. In contrast, low between‐study variation was observed in crustaceans indicating consistent success in PBM ‐supplemented diets for shrimp compared with fish.

Feed‐based common carp farming and eutrophication: is there a reason for concern? - Koushik Roy; Jaroslav Vrba; Sadasivam J. Kaushik; Jan Mraz (Reviews in Aquaculture, 2020)
Metadata from 70 research articles on Cyprinus carpio digestibility published between 1973 and 2017, covering 71 feed ingredients, were analysed. Interquartile range (IR) of nitrogen (N) and phosphorus (P) content in feedstuffs was 5–8% and 0.7–1.2% of dry matter, respectively, with digestible N:P 7.2:1–44.1:1. IR of N digestibility (79–99%) was high, whereas IR of P digestibility (27–47%) was rather poor. Dietary energy digestibility (gross energy and non‐protein energy) was >76%. Higher P in feedstuffs caused significant negative interferences for N digestibility. IR of nutrient content in carp faeces was estimated at 0.5–1.7% N and 0.4–0.9% P. Considering the metabolic losses, the carp excreta have an ‘eutrophic’ N:P ratio (2.1:1–5.8:1). Eutrophication potential from feeding seems linked to P digestibility followed by bad protein profile of diets. While brewery wastes, microbial protein and natural prey offer high P digestibility (75–90%), large knowledge gaps still exist in P digestibility of various ingredients. Thermal processing does not always improve P digestibility; acidic pre‐incubation with phytases (optimum: 1500–2000 IU kg −1 feed) is worth exploring. Under semi‐intensive system, digestible ‘supplementary’ nutrients (N: 3.3–4.9%, P: 0.2–0.5%; even lower) can support at least 0.6–1.2 thermal growth coefficient (reasonable growth) and be ecologically relevant. We further considered validity of data within experimental conditions; effects on N/P utilization; non‐faecal losses (IRs 17–59% of N intake; 9–18% of P intake); and controversies over eutrophication. Recent eutrophication of carp fishponds might have been rather ‘management‐driven’ than carp's biological limitations. Ameliorative measures are outlined.

Nonintrusive methods for biomass estimation in aquaculture with emphasis on fish: a review - Daoliang Li; Yinfeng Hao; Yanqing Duan (Reviews in Aquaculture, 2020)
Fish biomass estimation is one of the most common and important practices in aquaculture. The regular acquisition of fish biomass information has been identified as an urgent need for managers to optimize daily feeding, control stocking densities and ultimately determine the optimal time for harvesting. However, it is difficult to estimate fish biomass without human intervention because fishes are sensitive and move freely in an environment where visibility, lighting and stability are uncontrollable. Until now, fish biomass estimation has been mostly based on manual sampling, which is usually invasive, time‐consuming and laborious. Therefore, it is imperative and highly desirable to develop a noninvasive, rapid and cost‐effective means. Machine vision, acoustics, environmental DNA and resistivity counter provide the possibility of developing nonintrusive, faster and cheaper methods for in situ estimation of fish biomass. This article summarizes the development of these nonintrusive methods for fish biomass estimation over the past three decades and presents their basic concepts and principles. The strengths and weaknesses of each method are analysed and future research directions are also presented. Studies show that the applications of information technology such as advanced sensors and communication technologies have great significance to accelerate the development of new means and techniques for more effective biomass estimation. However, the accuracy and intelligence still need to be improved to meet intensive aquaculture requirements. Through close cooperation between fisheries experts and engineers, the precision and the level of intelligence for fish biomass estimation will be further improved based on the above methods.

Methanogenic and fertilizing potential of aquaculture waste: towards freshwater farms energy self‐sufficiency in the framework of blue growth - Ndeye Aida Ndiaye; Halima Maiguizo-Diagne; Hamet Diaw Diadhiou; Waly Ndianco Ndiaye; Fulgence Diedhiou; Laurent Cournac; Mohamed Lamine Gaye; Saliou Fall; Patrice Brehmer (Reviews in Aquaculture, 2020)
The fisheries sector, particularly aquaculture, is a fundamental source of nutrition for humans, particularly in developing countries. The modern development of fish farming requires energy for production systems. This study investigates the potential of using organic wastes derived from fish fattening to produce on‐farm energy through the process of methanization. Oreochromis niloticus faeces methanogen potential was determined with (IFF) and without (UIFF) methanizer microbial inoculum. At the end of the manure methanation trials, the resulting digestates were tested as organic fertilizers for agriculture. The tests showed that inoculated fish faeces had faster biogas kinetics production compared with uninoculated fish faeces. In both cases, the produced biogas contained more than 60% methane (CH 4 ) from the second week of incubation, indicating that it was of good quality. Furthermore, the total CH 4 volume was twice as larger in IFF compared with UIFF. Biofertilizer tests showed no significant differences for most of the growth parameters in onion and tomato when compared to the unfertilized control, except in one case for tomato plants, which significantly increased its aboveground biomass. The results show that fish faeces are good methanogenic substrates conducive to energy recovery that could facilitate farm autonomy; however, valorization of the digestates as biofertilizer still requires extensive agronomic optimization. Based on our results, we estimate that equivalents of energy need of almost ten millions of people could be covered using the aquaculture potential in freshwater fish faeces biogas worldwide or that at least aquaculture farm energy self‐sufficiency could be fostered.

Dietary protein requirements of fish – a meta‐analysis - Aires Oliva Teles; Ana Couto; Paula Enes; Helena Peres (Reviews in Aquaculture, 2020)
There are hundreds of fish reared in aquaculture, but nutrient requirements of the different species are still scarcely studied. Dietary protein is usually one of the first nutrients to be evaluated when considering the nutritional requirements of a novel species for aquaculture. Data on dietary protein requirement are already available for a large number of species, and this study aims to review the available data, enhancing eventual differences due to species, feeding habits, fish size, rearing temperature and water salinity. Overall, dietary protein requirements in the different studies ranged between 24 and 70% of the diet, depending on species and life stanzas. Dietary protein requirements were directly related to fish trophic level and water salinity, and inversely related to rearing temperature. Dietary protein intake was linearly related to weight gain, while protein retention was not affected, averaging 187 g protein kg −1 weight gain. On average, fish require a protein intake of 624 g kg −1 weight gain and dietary protein retention efficiency is close to 32%.

Microalgal pigment induction and transfer in aquaculture - Ignacio Alejandro Pérez‐Legaspi; Veronica Valadez‐Rocha; Luis Alfredo Ortega‐Clemente; Maria Isabel Jiménez‐García (Reviews in Aquaculture, 2020)
Pigments are bioactive compounds produced by microalgae which have a very important role in the health and performance of aquaculture species, particularly in the early larval stages of marine fish and crustaceans. We review the production of specific pigments by microalgal species emphasizing on the specific culture and stress conditions to promote the accumulation of large amounts of pigments in microalgae such as Haematococcus pluvialis , and different genus of Dunaliella , Muriellopsis , Scenedesmus , Chlorella and Chlorococcum used for aquaculture. We also discuss the differences among different large‐scale production systems and review the dose–effect relation of pigments on the health and performance of different aquaculture species as well as discuss the feasibility of transferring the pigments by using zooplankton species to obtain the benefits of pigments and other compounds produced by microalgae. We conclude more research is needed on the specific dose effects of pigments in the health and performance of aquaculture species at specific developmental stages and that the transfer of these bioactive compounds using zooplankton species is worthy of consideration by the aquaculture industry.

Brood‐stock management and early hatchery rearing of Arctic charr ( Salvelinus alpinus (Linnaeus)) - Tom Robin Olk; Henrik Jeuthe; Helgi Thorarensen; Jens Wollebæk; Espen Lydersen (Reviews in Aquaculture, 2020)
Arctic charr ( Salvelinus alpinus (Linnaeus)) is a stenothermic cold‐water fish, which has been cultured in Northern Europe and North America since the 1980s. The industry has remained relatively small with an annual production between 6000 and 10 000 tonnes, and is still challenged by an unreliable offspring production. This review focuses on offspring production in Arctic charr aquaculture including holding conditions for brood‐stock, fertilisation and egg rearing until hatch. Brood‐stock requires low temperatures during summer (

Use and misuse of a common growth metric: guidance for appropriately calculating and reporting specific growth rate - Derek P. Crane; Derek H. Ogle; Daniel E. Shoup (Reviews in Aquaculture, 2020)
Growth is an important metric in fisheries and aquaculture. Growth of small fish over relatively short periods of time is commonly modelled with an exponential function using instantaneous growth rate ( g ). Instantaneous growth rates are logarithmic and inherently difficult to interpret, but specific growth rates ( SGR ) express growth as the intuitively understandable per cent change in size per unit of time. A simple metric of SGR ( G ) is easily computed by exponentiating g , subtracting 1 and multiplying by 100. However, several prominent fisheries publications suggest that SGR should be calculated by simply multiplying g by 100 (we call this G *). A search of the fisheries literature found that the number of papers that used SGR for fish increased significantly from 1830 papers in 2009 to 3170 papers in 2018. An extensive review of 300 papers from this search found that 92.6% were related to aquaculture and only 3.3% of all papers correctly used G to calculate SGR . We algebraically show that G * is fundamentally different than G and cannot be interpreted as a per cent change in weight per unit of time. Furthermore we demonstrate, with three examples from the literature, that using G * as if it were the same as G leads to biologically meaningful underestimates of true growth rates and estimated weights. Given these results and the simplicity with which G can be computed from g , we recommend that fisheries scientists abandon the pervasive practice of incorrectly measuring SGR as 100 times the instantaneous growth rate.

Challenges in the control of acanthocephalosis in aquaculture: special emphasis on Neoechinorhynchus buttnerae - Gustavo Moraes Ramos Valladão; Sílvia Umeda Gallani; Gabriela Tomas Jerônimo; Arthur Tavares de Seixas (Reviews in Aquaculture, 2020)
Acanthocephalans are endoparasites of several vertebrate species. These parasites are able to attach the host intestine, which culminates in low nutrient utilization and severe economic losses. This review discusses the impact of acanthocephalosis for aquaculture and demonstrates promising control and treatment measures against this parasitosis. Echinorhynchus truttae was considered one of the main parasites affecting salmonids; however, there are currently no scientific data on relevant outbreaks of this parasitosis. It is emphasized that, currently, the disease caused by Neoechinorhynchus buttnerae in tambaqui Colossoma macropomum is the fish acanthocephalosis with the strongest impact, besides being one of the most important acanthocephalosis affecting animal production worldwide. It has been noted that this disease has direct correlation with an environment replete with contaminated zooplankton and biosafety failures. Amongst revised synthetic chemotherapeutics, carbon tetrachloride and loperamide are described as being strongly efficient against E. truttae , and levamisole has been the most studied molecule for N. buttnerae . Considering the demand for alternative molecules, studies have shown that thyme, garlic and peppermint are promising against acanthocephalans. It must be emphasized a great need for standardization of in vitro and in vivo tests, as well as the need for studies on pharmacokinetics and pharmacodynamics. As prospects to control acanthocephalosis, we highlight the need for development of innovative aquaculture environments (biofloc and recirculation systems) that can prevent or extinguish the intermediate host, new methods of drug inclusion in the diet and genetic studies aiming improvement of resistant fish lineage and even the genome description of the parasite.

Fish trait preferences: a review of existing knowledge and implications for breeding programmes - Mamta Mehar; Wagdy Mekkawy; Cynthia McDougall; John A.H. Benzie (Reviews in Aquaculture, 2020)
Continued growth of the aquaculture sector will rely on the availability of fish with traits that respond to the needs and preferences of these users along the value chain. Such trait responsiveness requires that fish breeding programmes have reliable knowledge of these users’ trait preferences. The present study found from a non‐systematic literature review, that no fish breeding programme had reported user preference in their product‐profile design. A systematic literature review was then carried out to identify studies which have assessed fish trait preferences of different users, categorized by market segment and gender. This identified relatively few such studies ( n = 28 total), highlighting a lack of published information in this area. Some preferences were shared broadly among a range of users (e.g. size measures such as length or weight). A number of traits were of restricted preferences such as survival (important to farmers, hatchery and nursery operators) while appearance or taste dominated in the preferences for traders and consumers. Some of the preferred traits of users are not targets for selection in breeding programmes reported to date (e.g. body texture, nutritional value) The review also makes clear that there can be range of preferences that differ by gender and social or economic status of the user. Greater acceptance of more sustainable aquaculture products will require improved information on user preferences. This will need innovative tools to translate generally expressed preferences into well‐defined traits and to assess their trade‐offs for their incorporation in genetic improvement programmes that will better target benefits to users.

Species assemblage and recruitment patterns of echinoderms on shallow rocky reefs in central New Zealand - Andrea Glockner‐Fagetti; Nicole E. Phillips (New Zealand Journal of Marine and Freshwater Research, 2020)
Echinoderms play important ecological roles in the benthic community, but the processes that regulate their distribution are still poorly understood. The aim of this study was to describe the community structure in the shallow rocky reefs of the Wellington region of central New Zealand. Five sites from a harbour and an open coast were surveyed for adult echinoderm density and habitat composition. Additionally, artificial collectors were deployed to assess recruitment patterns. Five taxa were responsible for the assemblage variation within sites and their abundance was highly correlated with habitat composition. Patiriella regularis was highly abundant in all sites, while Coscinasterias muricata and Evechinus chloroticus were dominant in the Harbour. Echinoderm settlement showed interannual variations, as well as differences between locations. There was a significant pulse of C. muricata settlers, while ophiuroids were present in lower numbers but constantly during the studied period. E. chloroticus settlement was sporadic and the absence of a juvenile cohort in the open coast sites suggests that recruitment might not occur for up to 4 years. The present study provides insights on the echinoderm assemblage in the shallow rocky reefs of the Wellington region and contributes to a better understanding of recruitment patterns shaping population structure.

A genetic assessment of the taxonomic status of New Zealand mussels of the genus Xenostrobus Wilson, 1967 - Donald J. Colgan; Richard C. Willan; Lisa A. Kirkendale (New Zealand Journal of Marine and Freshwater Research, 2020)
The genus Xenostrobus consists of small, marine and estuarine mussels that all appear similar externally. One of its estuarine species, Xenostrobus securis, with a native range in New Zealand and Australia, has become invasive in the Northern Hemisphere. No genetic data are available to determine if X. securis populations from the two countries are conspecific. Additionally, marine Xenostrobus from New Zealand have often been regarded as a species, X. neozelanicus, distinct fromthe marine Australian species X. pulex . We combined new DNA sequences with published data to assess the taxonomic status of New Zealand Xenostrobus. The data comprised 658 aligned bases of mitochondrial cytochrome c oxidase subunit I (COI) gene and 331 bases of nuclear histone H3. There was no evidence that X. securis populations from Australia and New Zealand are specifically distinct. Northern Hemisphere specimens of X. securis belonged to Australian, not New Zealand, clades in phylogenetic analyses of COI data, suggesting the former country as their more likely original source. The results confirm that X. neozelanicus and X. pulex are distinct species and for nomenclatural completeness for this taxonomic decision a lectotype is designated for Mytilus ater Zelebor in Dunker and Zelebor, 1866 [ = Modiolus neozelanicus Iredale, 1915].

Genetic structure and recent population expansion in the commercially harvested deep‐sea decapod, Metanephrops challengeri (Crustacea: Decapoda) - Alexander J. F. Verry; Kerry Walton; Ian D. Tuck; Peter A. Ritchie (New Zealand Journal of Marine and Freshwater Research, 2020)
Determining the genetic structure and population dynamics of harvested species are key aspects of effective fisheries management. New Zealand scampi ( Metanephrops challengeri ) is a species of nethropid lobster that supports a commercial fishery on the continental shelf and slope around New Zealand. To determine the genetic structure and historical population demography of New Zealand scampi, we sequenced a 623 base‐pair fragment of the mitochondrial gene cytochrome c oxidase subunit one (CO1) from 321 individuals across six widely separated sites off the coast of mainland New Zealand and the subantarctic Auckland Islands, representing much of the species’ distribution. The Auckland Islands population was found to be genetically distinct from all other sampled populations, potentially resulting from an absence of continuous suitable habitat between the central‐eastern South Island and the Auckland Islands. An isolation‐by‐distance pattern of genetic structure was also detected. With the exception of the Mercury Islands, all sampled populations showed signs of recent population expansion, potentially linked to changes in habitat availability during the glacial‐interglacial cycles of the Pleistocene. We recommend that the current NZ scampi management areas and harvesting rates for each remain unchanged.

Evaluation of food competition and resource partitioning of recruiting fish with permanent residents in a seagrass habitat - Craig A. Meakin; Jian G. Qin (New Zealand Journal of Marine and Freshwater Research, 2020)
Recruiting King George whiting Sillaginodes punctatus were studied to assess the potential for food competition with permanent resident fish species in a nursery habitat. Marine migrant post larval S. punctatus ( 0.6) diet overlap with permanent resident fish species Favonigobius leteralis and Stigmatopora nigra . Food electivity index indicated that S. punctatus juveniles preferred harpacticoid copepods and amphipods, while juvenile Heteroclinus adelaide and Gymnapistes marmoratus migrating to the nursery habitat targeted larger prey such as amphipods. Preference for larger prey by H. adelaide and G. marmoratus species coupled with differences in prey composition in the stomach was due to mouth size and feeding habits, resulting in different food preferences to S. punctatus . The whiting showed an ontogenetic shift in diet with early settlers (>60 mm TL) consuming less copepods and more amphipods, while previous year recruits (>120 mm TL) consumed polychaete worms. This study indicates that competition for food resources between the new recruiting S. punctatus juveniles and permanent resident juveniles is reduced through differences in temporal and spatial feeding behaviours, mouth morphology, and ontogenetic shift in prey consumption.