Effects of biopedturbation by European badger Meles meles on the forest soil food web persist for years as revealed by nematode indicators - Paweł Kapusta; Olga Wiśniewska; Ewa Dmowska; Przemysław Kurek (Applied Soil Ecology, 2025)

Microbial dynamics and agroforestry impact on soil ecosystem multifunctionality following forest conversion to macadamia-based systems - Fandi Xu; Zhihong Guo; Yuchun Yang; Yanxuan Chen; Haidong Bai; Tongli Wang; Jiangchong Wu; Shuaifeng Li; Jianrong Su (Applied Soil Ecology, 2025)

Regulation of soil microbial nitrogen limitation by soybean rhizosphere diazotrophs under long-term no-till mulching - Jiajie Song; Shahzad Haider; Jianheng Song; Dingding Zhang; Sen Chang; Jinze Bai; Jiaqi Hao; Gaihe Yang; Guangxin Ren; Xinhui Han; Xiaojiao Wang; Chengjie Ren; et al. (Applied Soil Ecology, 2025)

The effects of a combination of maize/peanut intercropping and residue return on soil microbial nutrient limitation in maize fields - Fanyun Yao; Wei Qi; Yujun Cao; Jie Liang; Xiaodan Liu; Zhiming Liu; Yanjie Lv; Wenwen Wei; Wenhua Xu; Yang Yu; Xiang Li; Jian Feng; et al. (Applied Soil Ecology, 2025)

Effect of ivermectin and dung beetle communities on dung removal rate in cattle pastures - Lizbeth González-Gómez; Daniel González-Tokman; Juan H. García; Andrés Lira-Noriega; Federico Escobar (Applied Soil Ecology, 2025)

Earthworms multi-biomarker approach for ecotoxicological assessment of soils irrigated with reused treated wastewater - Antonio Calisi; Teodoro Semeraro; Maria Elena Giordano; Francesco Dondero; Maria Giulia Lionetto (Applied Soil Ecology, 2025)

Development and evaluation approach of soil quality in agricultural soils: Integrated system for a more reliable delineation of homogeneous management zones - Veljko Perović; Dragan Čakmak; Darko Jakšić; Miško Milanović; Marija Matić; Dragana Pavlović; Miroslava Mitrović; Pavle Pavlović (Applied Soil Ecology, 2025)

Distribution of plant-parasitic nematode communities across land-use types in the North of Portugal - Rui P. Carvalho; Carlos Guerra; Concha Cano-Díaz; Susana Mendes; Sofia R. Costa (Applied Soil Ecology, 2025)

Earthworm abundance and diversity in response to intensive crop management in organic field crop farms of southern Quebec, Canada - Stéphanie Lavergne; Caroline Halde; Derek H. Lynch (Applied Soil Ecology, 2025)

Impact of tillage practices and soil texture on soil health and earthworms in the Pannonian region: A comparative study from Austria and Hungary - Barbara Simon; Igor Dekemati; Hanaa T.M. Ibrahim; Maxwell M. Modiba; Márta Birkás; János Grósz; Martin Kulhanek; Reinhard W. Neugschwandtner; Anna Hofer; Viola Wagner; Marion Windisch; Karin Hage-Ahmed; et al. (Applied Soil Ecology, 2025)

Harnessing moringa seed extract for control of soil nitrate accumulation and nitrous oxide emissions on the Loess Plateau - Mingxia Yang; Chen Ban; Tianyi Zhao; Jia Zhao; Ningning Zhou; Lin Ma; Jianbin Zhou; Xiaofang Deng (Applied Soil Ecology, 2025)

The response mechanism of high-quality grass to typical poisonous weed root exudates and litter: Using Leymus chinensis and Stellera chamaejasme as examples - Ruohui Zhang; Shanmin Qu; Bin Zhang; Ying Gao; Fu Xing (Applied Soil Ecology, 2025)

Impacts of Spartina alterniflora invasion on soil carbon components of particulate and mineral-associated organic matter and soil organic matter mineralization in estuarine wetlands - Lin Wang; Yuan Li; Jie Hei; Weiqi Wang; Jordi Sardans; Zhihao Zhang; Fanjiang Zeng; Maoquan Ge; Yiyang Liao; Yunying Fang; Tony Vancov; Jiawei Gan; et al. (Applied Soil Ecology, 2025)

Latitudinal patterns and phosphorus-driven regulation of abundant and rare fungal communities in coastal wetlands - Shaokun Wang; Jing Li; Lijuan Cui; Rumiao Wang; Wei Li; Juntao Wang (Applied Soil Ecology, 2025)

12-year N addition enhances soil organic carbon decomposition by mediating microbial community composition in temperate plantations - Xinyi Wu; Yanyan Liu; Hongjin Zhang; Lizheng Dong; Yiping Zuo; Xiaoyue Li; Wei Wang (Applied Soil Ecology, 2025)

The dominance of K-strategy microbes enhances the potential of soil carbon decomposition under long-term warming - Yanli Gao; Jiacong Zhou; Teng-chiu Lin; Yiqing Li; Quanxin Zeng; Shidong Chen; Decheng Xiong; Qiufang Zhang; Zhijie Yang; Yusheng Yang (Applied Soil Ecology, 2025)

Toxicological effects of per- and polyfluoroalkyl substances (PFASs) on earthworms: Progress and prospects - Cheng Qin; Chenxi Lu; Chang Lu; Lixia Zhao; Xiaojing Li; Yang Sun; Liping Weng; Yongtao Li (Applied Soil Ecology, 2025)

Dynamics and resilience of earthworm fecal microbiomes under distinct feeding regimes - Ziyan Pan; Petr Heděnec; Qiang Lin; Lingjuan Li; Amirah Alias; Fang Deng; Jan Frouz (Applied Soil Ecology, 2025)

Origin and assembly characteristics of periphyton microbes in subtropical paddy fields: A case study in Tuojia catchment in Southern China - Zongming Li; Jie He; Jianlin Shen; Yanyan Li; Quan Yuan; Qihong Zhu; Jinshui Wu (Applied Soil Ecology, 2025)

Effect of grafted scion varieties on apple root growth, carbon and nitrogen metabolism and microbiome in roots and rhizosphere soil - Huanhuan Zhang; Dongdong Yao; Guangxin Zhang; Hossam Salah Mahmoud Ali; Xujiao Li; Yanshu Li; Tianqiang Liang; Fengyun Zhao; Songlin Yu; Kun Yu (Applied Soil Ecology, 2025)

Unraveling the role of pyrolysis temperature in biochar-mediated modulation of soil microbial communities and tobacco bacterial wilt disease - Shichen Li; Linyuan Yang; Tao Jiang; Waqar Ahmed; Fupeng Mei; Jinhao Zhang; Tao Zhang; Yingfen Yang; Xiaoci Peng; Qu Shan; Dexiang Luo; Zhengxiong Zhao (Applied Soil Ecology, 2025)

Does extending the incubation period really improve the accuracy of the Tea Bag Index as a measure of soil health? - Taiki Mori (Applied Soil Ecology, 2025)

The effects of biosolid microplastics on rhizosphere respiration of root exudates in Glycine max - Rebecca Lebel; Deqa Farow; Jill Crossman; Cameron Proctor (Applied Soil Ecology, 2025)

Decreased net N nitrification rate constrains soil N availability during long-term Camellia oleifera cultivation - Tinghao Zong; Jingwei Ma; Xinming Guan; Yusong Lin; Yuqi Chen; Meiqi Wang; Jiaze Lv; Yichao Rui; Yang Chen; Lichao Wu; Sheng Lu (Applied Soil Ecology, 2025)

Application of green manure combined with synthetic nitrogen fertilizer enhances soil aggregate stability in an arid wheat cropping system - Guocui Wang; Hanting Li; Falong Hu; Wen Yin; Zhilong Fan; Hong Fan; Yali Sun; Wei He; Qiang Chai (Applied Soil Ecology, 2025)

The role of rhizosphere microbial community structure in the growth and development of different tea cultivars - Xinyue Yin; Yujie Song; Jiazhi Shen; Litao Sun; Kai Fan; Hao Chen; Kangwei Sun; Zhaotang Ding; Yu Wang (Applied Soil Ecology, 2025)

Complementary nitrogen use by legume and grass enhances plant productivity irrespective of earthworm species - Linlin Zhong; Jing-Zhong Lu; Stefan Scheu; Melanie M. Pollierer (Applied Soil Ecology, 2025)

Prairie strips quickly alter soil bacterial and fungal communities in strips, but not in surrounding cropland - Corinn E. Rutkoski; Sarah E. Evans (Applied Soil Ecology, 2025)

Impact of land use changes on soil chemical properties, enzyme activities and microbial communities in two contrasting localities of the Argentinian Pampas - Florencia M. Barbero; María F. Dominchin; Romina A. Verdenelli; Ileana Frasier; Silvina B. Restovich; Ernesto J. Campilongo Mancilla; Estela C. Mlewski; Diana Labuckas; Silvina Vargas Gil; José M. Meriles (Applied Soil Ecology, 2025)

Soil microbes mediate the priming effect in response to 12 years of nitrogen management in different crop cultivation patterns - Kepan Yang; Yali Liu; Shiqiang Ge; Chaoqun Zou; Lei Liu; Xiting Zhang (Applied Soil Ecology, 2025)

Long-term belowground impacts of experimental fire and post-fire soil stabilization treatments in a gorse shrubland - Noela Carrera; Raquel Juan-Ovejero (Applied Soil Ecology, 2025)

Insect residual streams supplement improves chili pepper growth: Insights into the role of rhizosphere soil microbiome and metabolome - Hanghai Zhou; Xusong Zheng; Zhigang Zhu; Qi Shen; Chenghu Yang; Lijia Jiang; Hua Li; Yuxue Liu; Xiaohong Yao; Hong Sun; Xin Wang; Chunfang Zhang; et al. (Applied Soil Ecology, 2025)

Effects of long-term conservation tillage on soil aggregate carbon fractions and microbial characteristics under rice-oilseed rape rotation systems - Yanshi Li; Lijin Guo; Mengqin Wu; Chengfang Li (Applied Soil Ecology, 2025)

Dynamic relationships between microbial community, enzyme activity, and soil properties across global ecosystems - Grace Williams; Rita Miller; Shiping Deng (Applied Soil Ecology, 2025)

Unveiling halophilic microbial communities in calcite fossil sedimentary rocks and their implications for biomineralization - Balachandar Chinnappa; Balaji Thirupathi; Thanigaivel Sundaram; Yimtar L. Pongen; Saranya Vinayagam; Lalitha Gnanasekaran; Vishnu D. Rajput; Thirumurugan Durairaj (Applied Soil Ecology, 2025)

Soil microbes drive the negative effect of plant diversity on community stability in zokor-disturbed alpine grasslands - Chunping Zhang; Wenshuang Yao; Mengxuan He; Yunfeng Yang; Zhenhua Zhang; Jie Liu (Applied Soil Ecology, 2025)

Destabilized bacterial and fungal network weakens soil multifunctionality under increasing grazing stress - Shaoyu Li; Bin Zhang; Yanan Li; Tianqi Zhao; Jiahua Zheng; Jirong Qiao; Feng Zhang; Guodong Han; Ton Bisseling; Mengli Zhao (Applied Soil Ecology, 2025)

Long-term effects of nitrogen fertilization and Bradyrhizobium inoculation on diazotrophic community structure and diversity in soybean cultivation - Wanling Wei; Mingchao Ma; Xin Jiang; Fenliang Fan; Fangang Meng; Fengming Cao; Huijun Chen; Dawei Guan; Li Li; Jun Li (Applied Soil Ecology, 2025)

Field inoculation with a local arbuscular mycorrhizal (AM) fungal consortium promotes sunflower agronomic traits without changing the composition of AM fungi coexisting inside the crop roots - Myriam Arcidiacono; Laura Ercoli; Gaia Piazza; Elisa Pellegrino (Applied Soil Ecology, 2025)

Potential protocol for earthworm monitoring under adverse soil conditions or in small plots - P. Euteneuer; K.R. Butt (Applied Soil Ecology, 2025)

Co-inoculation with rhizobacterial community and an ectomycorrhizal fungus promotes poplar ectomycorrhization - Haiyun Zi; Yun Wang; Yangwenke Liao; Shuikuan Bei; Jinchi Zhang; Xiaogang Li (Applied Soil Ecology, 2025)

Impact of plant diversity in potato-ley strip-cropping systems on soil microbial communities - L.G.A. Riggi; T. Ranheim Sveen; C. Castaño; P. Onorati; D.F. van Apeldoorn; M. Berri; L. Mommer; K.E. Clemmensen; M. Bahram (Applied Soil Ecology, 2025)

The responses of oribatid mites to grazer exclusion in a boreal forest over different time scales - Maria Väisänen; Inkeri Markkula (Applied Soil Ecology, 2025)

Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies - Soumyadev Sarkar; Anna Kazarina; Paige M. Hansen; Kaitlyn Ward; Christopher Hargreaves; Nicholas Reese; Qinghong Ran; Willow Kessler; Ligia F.T. de Souza; Terry D. Loecke; Marcos V.M. Sarto; Charles W. Rice; et al. (Applied Soil Ecology, 2025)

Soil and vegetation drivers of microbial attributes in a microhabitat mosaic at different successional stages after restoration of inland sand dunes - Kaja Skubała; Karolina Chowaniec; Małgorzata Stanek; Janusz Błaszkowski; Maciej Móll; Szymon Zubek (Applied Soil Ecology, 2025)

Soil pore structure may affect microbial communities involved in carbon cycling during thaw slumps development - Yunduo Zhao; Xia Hu (Applied Soil Ecology, 2025)

Seed inoculation of Hartmannibacter diazotrophicus does not alter the rhizosphere bacterial microbiome of wheat and barley in a three-year field trial - Santiago Quiroga; Stefan Ratering; David Rosado-Porto; Azin Rekowski; Franz Schulz; Christian Zörb; Sylvia Schnell (Applied Soil Ecology, 2025)

The community diversity and metabolic function of symbiont bacteria associated with soil amoebae (dictyostelids) in free-living habitats - Zhaojuan Zhang; Yingkun Yang; Yujing Du; Yue Zou; Steven L. Stephenson; Yu Li; Pu Liu (Applied Soil Ecology, 2025)

Redundancy of microbial P mobilization in beech forest soils with contrasting P stock: A microbial dilution experiment - Yijie Shi; Sasya Samhita; Sebastian Loeppmann; Iris Zimmermann; Michaela A. Dippold; Sandra Spielvogel (Applied Soil Ecology, 2025)

Inoculation of cadmium-tolerant bacteria mitigates the impact of cadmium pollution on soil bacterial community assembly processes - Shangqi Xu; Meng Na; Xiaoyang Xu; Jihai Zhou (Applied Soil Ecology, 2025)

Rice rhizosphere and microplastic synergistically reshaping antibiotic resistome in soil - Xiangmiao Su; Xinjian Huang; Yanyu Bao (Applied Soil Ecology, 2025)

Chronosequence changes in soil microbes under Populus simonii × P. nigra stands: Implications for soil health restoration in Mollisols - Jia Yang; Qinghua Liu; Keyi Liu; Shunzhong Wang; Huiyan Gu (Applied Soil Ecology, 2025)

Effect of Eisenia foetida on enzyme activity and microbial community in phytoremediation of petroleum-contaminated soil using three plant species - Xiang Li; Junhua Hou; Jinjin Yang; Genwang Chang; Genmao Zhong; Junjie Wang; Tong Li; Shaokang Li (Applied Soil Ecology, 2025)

Assaying the microbial features in rhizosphere of Panax quinquefolium L. under plant-derived smoke water based on metagenomic sequencing - Wanying Duan; Xiaoli Chen; Rui Li; Zhifang Ran; Lei Fang; Lanping Guo; Jie Zhou (Applied Soil Ecology, 2025)

Barriers and prospects for soil biodiversity research in the Balkans - M. Topole; J. Marinko; V. Podpečan; P. Mylona; M. Debeljak (Applied Soil Ecology, 2025)

Higher endogenous labile organic carbon decreases the temperature sensitivity of soil organic matter decomposition in two subtropical forests - Di Ma; Yu Sun; Min Liu; Huajun Fang; Xingliang Xu (Applied Soil Ecology, 2025)

Large-scale organic farming enhances soil properties and earthworm communities in relation to conventional farming in the Pampas region of Argentina - M.P. Rodríguez; A. Domínguez; J.C. Bedano (Applied Soil Ecology, 2025)

Lithological impact on topsoil organic carbon storage of karst forest soils shaped by aggregate pool complexity and their molecular composition - Qingmei Lin; Shuotong Chen; Xiao Feng; Thammavongsa Sounilan; Kun Cheng; Xuhui Zhang; Rongjun Bian; Xiaoyu Liu; Yan Wang; Marios Drosos; Jufeng Zheng; Lianqing Li; et al. (Applied Soil Ecology, 2025)

Bacillus thuringiensis (Bt) rice straw mulching and earthworms mediated changes in soil N2O and CO2 emissions driven by N-cycling and C-utilizing microbial communities - Fuyuan Duan; Huiru Zhan; Shiqiang Ge; Zixuan Wang; Yangbeijia Liu; Zhenggao Xiao; Fengxiao Tan; Jianwu Wang; Yinghua Shu (Applied Soil Ecology, 2025)

Impacts of continuous potato cropping on soil microbial assembly processes and spread of potato common scab - Lichun Wang; Song Liu; Guokui Tian; Yang Pan; Haiyan Wang; Guangwei Qiu; Fengyun Li; Ze Pang; Kaixin Ding; Jinpeng Zhang; Hong Xue; Xinyuan Li; et al. (Applied Soil Ecology, 2025)

Deciphering the mechanisms through which arbuscular mycorrhizal symbiosis reduces nitrogen losses in agroecosystems - Sulaimon Basiru; Khadija Ait Si Mhand; Mohamed Hijri (Applied Soil Ecology, 2025)

Converting paddy to upland alters soil neutral sugars by influencing microbial community and life history strategy - Liuming Yang; Quancheng Wang; Xia Yun; Yuexin Fan; Weiqi Wang (Applied Soil Ecology, 2025)

Forest gaps reduce soil organic carbon stability by decreasing fungal necromass carbon and mineral-associated organic carbon in a calcareous forest - Wenjing Chen; Kelu Chen; Fuzhong Wu (Applied Soil Ecology, 2025)

Effects of agricultural plastic films on crop growth and soil health in tobacco fields: A comparative study - Hao Xia; Jia Shen; Muhammad Riaz; Fafen Ran; Tingming Cheng; Xueying Wang; Qing Dong; Chaolong Zu; Bo Liu; Saba Babar; Chaoqiang Jiang (Applied Soil Ecology, 2025)

Identifying bacterial fixation pathway of mediating soil carbon stock changes along tropical forest restoration - Mingliu Wang; Shaojun Wang; Mei Lu; Minkun Chen; Zhe Zhang; Hong Wang (Applied Soil Ecology, 2025)

Long-term biochar-based fertilizer substitution promotes carbon, nitrogen, and phosphorus acquisition enzymes in dryland soils by affecting soil properties and regulating bacterial community - Jun Wang; Lijuan Sun; Yafei Sun; Shiyan Yang; Qin Qin; Yong Xue (Applied Soil Ecology, 2025)

Warming-induced response of microbial diversity and functions regulated microbial necromass and soil multifunctionality - Zhuonan Hou; Wenzu Liu; Shaoqi Xu; Su Chang; Xinjun Zhang; Ruihong Wang; Daqing Luo; Baorong Wang; Shaoshan An; Yuhui Qiao; Zhangliu Du; Yuquan Wei (Applied Soil Ecology, 2025)

Microbial recruitment and microbial ecological roles in soil nutrient cycling of Populus cathayana males and females - Junhua Wang; Liangliang Chen; Liyun Ye; Yingtao Sun; Miao Liu (Applied Soil Ecology, 2025)

A density-based method to objectively quantify earthworm activity - Péter Garamszegi; Tullia Calogiuri; Mathilde Hagens; Alix Vidal; Jan Willem Van Groenigen (Applied Soil Ecology, 2025)

Inoculation of plant growth-promoting rhizobacteria and rhizobia changes the protist community of alfalfa rhizosphere soil under saline-alkali environment - Yang Sun; Lu Tang; Ying Cui; Dihe Yang; Hong Gao; Jiaxin Chen; Ziying Zheng; Changhong Guo (Applied Soil Ecology, 2025)

Editorial Board (Advances in Water Resources, 2025)

On the permeability-surface area-porosity relationship for dissolving porous media - Kai Li; Ran Hu; Ya-Nan Zhang; Zhibing Yang; Yi-Feng Chen (Advances in Water Resources, 2025)

Three-dimensional saturated-unsaturated flow to a well in an alluvial fan wedge-shaped aquifer - Mohammad M. Sedghi; Hongbin Zhan (Advances in Water Resources, 2025)

A well-balanced conservative high-order alternative finite difference WENO (A-WENO) method for the shallow water equations - Ziyao Xu; Chi-Wang Shu (Advances in Water Resources, 2025)

A hybrid CNN-transformer surrogate model for the multi-objective robust optimization of geological carbon sequestration - Zhao Feng; Bicheng Yan; Xianda Shen; Fengshou Zhang; Zeeshan Tariq; Weiquan Ouyang; Zhilei Han (Advances in Water Resources, 2025)

Incorporating geological structure into sensitivity analysis of subsurface contaminant transport - Lisa Bigler; Tara LaForce; Laura Swiler (Advances in Water Resources, 2025)

A training trajectory random walk model for upscaling colloid transport under favorable and unfavorable conditions - Bashar M. Al-Zghoul; William P. Johnson; Diogo Bolster (Advances in Water Resources, 2025)

Global sensitivity analysis of mass transfer and reaction dynamics for electrokinetic transport in porous media - R. Sprocati; A. Guadagnini; L. Ceresa; A. Gallo; M. Rolle (Advances in Water Resources, 2025)

On the modeling of the foam dynamics in heterogeneous porous media - Jhuan B. Cedro; Filipe F. de Paula; Grigori Chapiro (Advances in Water Resources, 2025)

Stochastic model for subsurface water flow in Swiss catchments - M.C. Bovier; S. Fedotov; S. Ferraris; A. Gentile; B. Toaldo (Advances in Water Resources, 2025)

Investigating solute transport and reaction using a mechanistically coupled geochemical and geophysical modeling approach - Flore Rembert; Nicole M. Fernandez; Linda Luquot; Roger Guérin; Damien Jougnot (Advances in Water Resources, 2025)

Reactive transport modeling to reveal the impacts of beach morphodynamics, storm floods and seasonal groundwater recharge on the biogeochemistry of sandy subterranean estuaries - Stephan L. Seibert; Gudrun Massmann; Rena Meyer; Vincent E.A. Post; Janek Greskowiak (Advances in Water Resources, 2025)

Reactive precipitation during overlaying CO2 dissolution into brine: The role of porous structure - Shuai Zheng; Ke Xu; Dongxiao Zhang (Advances in Water Resources, 2025)

Conversion between suspended sediment concentration and turbidity of summer surface water in Zhejiang offshore area - Jinduo Li; Jihai Lai; Yue Duan; Yejuan Jiang (Discover Oceans, 2025)

Underexplored rare bacterial biosphere associated with corals of the northeastern Tropical Eastern Pacific - Joicye Hernández-Zulueta; Rubén Araya; Ofelia Vargas-Ponce; Alma Paola Rodríguez-Troncoso; Alex Echeverria-Vega; Andrés López-Pérez; Eduardo Ríos-Jara; Fabián A. Rodríguez-Zaragoza (Discover Oceans, 2025)

Adverse effects of dichlofluanid on neotropical marine organisms - Ana Carolina Feitosa Cruz; Renan Canute Kamikawachi; Guacira de Figueiredo Eufrasio Pauly; Bruno Galvão Campos; Ítalo Braga Castro; Denis Moledo de Souza Abessa (Discover Oceans, 2025)

Microplastics contamination in seaweed: impacts on human health and mitigation approaches - Md. Simul Bhuyan; Venkatramanan Senapathi; Sivakumar Karthikeyan; Mrityunjoy Kunda; Md. Tarikul Islam; Stanley Iheanacho; Amita Kumari Choudhury (Discover Oceans, 2025)

Lifetime assessment for container ship by multimodal Gaidai risk evaluation method - Oleg Gaidai; Alia Ashraf; Yu Cao; Yan Zhu; Jinlu Sheng; Zirui Liu (Discover Oceans, 2025)

Editorial Board (Applied Soil Ecology, 2025)

Influence of land-use type on earthworm diversity and distribution in Yunnan: Insights from soil properties - Chang-E Liu; Qing-Rui Luo; Yan-Lan Xiao; Hong-Yang Li; Hong-Juan Dong; Chang-Qun Duan (Applied Soil Ecology, 2025)

Breeding-induced changes in the rhizosphere microbial communities in Lima bean (Phaseolus lunatus) - Karla Annielle da Silva Bernardo Brito; Sandra Mara Barbosa Rocha; Ângela Celis de Almeida Lopes; Verônica Brito Silva; Regina Lucia Ferreira Gomes; Carlos Humberto Aires Matos Filho; Arthur Prudêncio de Araujo Pereira; Vania Maria Maciel Melo; Erika Valente de Medeiros; Lucas William Mendes; Ana Roberta Lima de Miranda; Ademir Sérgio Ferreira Araujo (Applied Soil Ecology, 2025)

Plant richness reshuffles the soil microbiome in permafrost ecosystems - Zhong-Miao Liu; Gui-Feng Gao; Nai-Li Zhang; Hai-Yan Chu; Xiang-Yun Zhu (Applied Soil Ecology, 2025)

Bacillus velezensis SS-20 as a potential and efficient multifunctional agent in biocontrol, saline-alkaline tolerance, and plant-growth promotion - Zhaoliang Chen; Haiyun Zhang; Weiguang Lv; Siyi Zhang; Linna Du; Shuangxi Li; Hanlin Zhang; Xianqing Zheng; Juanqin Zhang; Tinglin Zhang; Naling Bai (Applied Soil Ecology, 2025)

Natural succession and artificial management have different effects on soil microbial ecological patterns in wetland resulting from land-use change - Yijing Wang; Guodong Zheng; Changchao Li; Yongkang Zhao; Junyu Dong; Zhiliang Wang; Guohong Lu; Zongcheng Chen; Zhoubin Dong; Kang Liu; Huaizhi Bo; Jian Liu (Applied Soil Ecology, 2025)

Phenolic acids alleviated consecutive replant problems in lily by regulating its allelopathy on rhizosphere microorganism under chemical fertiliser reduction with microbial agents in conjunction with organic fertiliser application - Jia Han; Yuanpeng Li; Hui Li; Hongyu Yang; Shilei Luo; Huali Man; Guiying Shi (Applied Soil Ecology, 2025)

Plant litter crust enhances nitrogen accumulation by regulating microbial diversity and urease activity in semi-arid sandy soils - Zhen Cheng; Wei Liu; Zhigang Li; María José Carpio; Juan Carlos García-Gil; Zhanjun Wang; Gao-Lin Wu (Applied Soil Ecology, 2025)

Snow and nitrogen manipulation do not alter the dominant role of fungi in the N2O production of biocrusts in a temperate desert - Yongxing Lu; Benfeng Yin; Yonggang Li; Yongxin Zang; Xiaobing Zhou; Yuanming Zhang (Applied Soil Ecology, 2025)

Land-use change from native forest to avocado orchards: Effects on soil nutrient transformation and microbial communities - Brenda Baca-Patiño; Antonio González-Rodríguez; Felipe García-Oliva; Ariana García; Ingrid Lara-De La Cruz; Roberto Garibay-Orijel; Amisha Poret-Peterson; Yurixhi Maldonado-López; Pablo Cuevas-Reyes; Alberto Gómez-Tagle; Yunuen Tapia-Torres (Applied Soil Ecology, 2025)

Simple rain-shelter cultivation controls soilborne root-rot disease and improves the quality of Panax notoginseng - Mengxin Shi; Haoji Wang; Huilin Guan; Fugang Wei; Shaozhou Yang; Ping Xiang; Huimei Pu; Ying Liu; Wumei Xu (Applied Soil Ecology, 2025)

Resilience of Collembola communities to extreme drought is moderated by land use at a regional scale - Sophie Joimel; Jonathan Bonfanti; Julie Bahri; Pierre Ganault; Alain Rakoto; Paul-Olivier Redon; Jérôme Cortet (Applied Soil Ecology, 2025)

Tree mycorrhizal associations strongly mediate soil microbial β-diversity along an elevational gradient in a warm-temperate forest - Xinyue Wang; Yaru Wang; Yu Wang; Jieyan Yang; Hongyi He; Yuchen Ren; Chenlin Wang; Haibo Li; Xiongzhi Zhang; Huifang Zhang; Jingjing Wang; Xiuqing Yang; et al. (Applied Soil Ecology, 2025)

Changes in soil microbial community and carbon use efficiency in freeze-thaw period restored after growth season under warming and straw return - Minghui Liu; Zhiming Zhang; Peng He; Yifei Zhang; Lu-Jun Li (Applied Soil Ecology, 2025)

Nitrogen deposition changes the root nutrient uptake strategies by affecting microbial diversity of the rhizosphere - Gaoqiang Zhu; Guoyong Yan; Guancheng Liu; Yajuan Xing; Qinggui Wang (Applied Soil Ecology, 2025)

Effects of irrigation-mediated continuously moist and dry-rewetting pattern on soil physicochemical properties, structure and bacterial community - Fuhui Yang; Pute Wu; Lin Zhang; Yuqing Hang; Yiqian Wei (Applied Soil Ecology, 2025)

Impact of soil inoculation on crop residue breakdown and carbon and nitrogen cycling in organically and conventionally managed agricultural soils - Sophie Q. van Rijssel; Eva Kuipers; Kyle Mason-Jones; Guusje J. Koorneef; Wim H. van der Putten; G.F. (Ciska) Veen (Applied Soil Ecology, 2025)

Bacterial community structure drives soil multifunctionality along a precipitation gradient in the Inner Mongolian shrublands - Bo Liu; Xu Li; Wenxu Cao; Qinghe Li (Applied Soil Ecology, 2025)

Accumulation of metals and metalloids in soil cover, road dust, and their PM10 fraction in Ulan-Ude: Spatial variation and source apportionment - Sycheva Daria; Kosheleva Natalia (Applied Soil Ecology, 2025)

Distance-dependent, species-specific effects of legumes on nitrogen utilization by companion non-legumes in the Gurbantunggut desert, Northern China - Yuxin Xiao; Xinyu Zhang; Boyi Song; Nargiza Galip; Weiwei Zhuang (Applied Soil Ecology, 2025)

Impact of bacterial inoculations on Pisum sativum L. biometric parameters and associated bacterial and AM fungal communities under semi-arid field conditions in Tunisia - Houda Ilahi; Alice Calvo; Sana Dhane; Mustapha Missbah El Idrissi; Lahcen Ouahmane; Mohamed Najib Alfeddy; Thomas Reitz; Fabiano Sillo; Raffaella Balestrini; Bacem Mnasri (Applied Soil Ecology, 2025)

High-rate nitrogen loading accelerates organic phosphorus loss through enzymatic and non-enzymatic processes in a semi-arid grassland - Nan Jiang; Qi Wang; Dongqi Jiang; Chenran Wu; Jiahui Pu; Wenjing Huang; Zimeng Yao; Zhenhua Chen; Yulan Zhang; Lijun Chen (Applied Soil Ecology, 2025)

Addition of bacterial-feeding nematodes contributes to soil phosphorus availability by affecting the mineralization of moderately labile organic phosphorus - Jigao Wang; Kai Wei; Jialiang Tang; Chaoyan Yuan; Yanling Wang; Xiaoming Sun; Bo Zhu (Applied Soil Ecology, 2025)

Increased diversification of crop rotation systems induces plant-beneficial rhizobiomes to facilitate crop performance - Shunran Hu; Qi Shao; Yongliang Chen; Jan Kammenga; Stefan Geisen (Applied Soil Ecology, 2025)

Bacterial communities and tetracycline resistance genes in the soil-rice continuum upon tetracycline exposure - Qing Li; Bin Zhang; Yang Zhang; Jian Hu; Qigen Dai (Applied Soil Ecology, 2025)

Editorial Board (Advances in Water Resources, 2025)

Corrigendum to “Investigating Steady Unconfined Groundwater Flow using Physics Informed Neural Networks” [Advances in Water Resources Volume 177 (2023), 104445] - Mohammad Afzal Shadab; Dingcheng Luo; Eric Hiatt; Yiran Shen; Marc Andre Hesse (Advances in Water Resources, 2025)

A computationally efficient hybrid neural network architecture for porous media: Integrating convolutional and graph neural networks for improved property predictions - Qingqi Zhao; Xiaoxue Han; Ruichang Guo; Cheng Chen (Advances in Water Resources, 2025)

Pore-scale modeling of biofilm formation and biofilm-induced anomalous transport features in heterogenous porous media - Xueying Li; Xiaofan Yang (Advances in Water Resources, 2025)

Fully coupled morphological modelling under the combined action of waves and currents - Wei Li; Yiming Zhang; Peng Hu (Advances in Water Resources, 2025)

Study on the effects of non-uniformity of microbial growth on permeability changes in porous media - Gengyang Zang; Lijian Huang; Shilin Wang; Taijia Lu; Yanfeng Gong; Liping Chen (Advances in Water Resources, 2025)

Acropora coral pore morphology and its internal hydrodynamics - Yanmei Tian; Rongrong Tian; Xiangbo Gao; Liang Lei; S.A. Galindo-Torres; Ling Li (Advances in Water Resources, 2025)

Water vapor condensation in porous media: Effects of fracture, porosity, and flow rate revealed by rapid 4D neutron imaging - Arash Nemati; Bratislav Lukić; Alessandro Tengattini; Matthieu Briffaut; Philippe Séchet (Advances in Water Resources, 2025)

Experimental validation of an image-based dynamic pore-network model for spontaneous imbibition in sandstones - Xin Wang; Chaozhong Qin; Bo Guo; Sorin Pop; Jian Tian (Advances in Water Resources, 2025)

Modeling parametric uncertainty in PDEs models via Physics-Informed Neural Networks - Milad Panahi; Giovanni Michele Porta; Monica Riva; Alberto Guadagnini (Advances in Water Resources, 2025)

On transient qanat discharge in an unconfined aquifer underlain by a fractured aquifer - Mohammad M. Sedghi; Hongbin Zhan (Advances in Water Resources, 2025)

Visualization experiment for characterizing the influence of an open fracture on CO2 behavior in fractured porous media - Seung-Wook Ha; Ji-Young Baek; In-Woo Park; Kang-Kun Lee (Advances in Water Resources, 2025)

An extension of the box method discrete fracture model (Box-DFM) to include low-permeable barriers with minimal additional degrees of freedom - Ziyao Xu; Dennis Gläser (Advances in Water Resources, 2025)

In search of non-stationary dependence between estuarine river discharge and storm surge based on large-scale climate teleconnections - Georgios Boumis; Hamed R. Moftakhari; Danhyang Lee; Hamid Moradkhani (Advances in Water Resources, 2025)

A novel geometry-informed drag term formulation for pseudo-3D Stokes simulations with varying apertures - David Krach; Felix Weinhardt; Mingfeng Wang; Martin Schneider; Holger Class; Holger Steeb (Advances in Water Resources, 2025)

Phase diagram of invasion patterns in «capillary number, wetting angle, disorder» coordinates: A lattice Boltzmann study - T.R. Zakirov; A.S. Khayuzkin; A.N. Kolchugin; I.V. Malevin (Advances in Water Resources, 2025)

Numerical investigation of multiphase flow through self-affine rough fractures - Prakash Purswani; Javier E. Santos; Jeffrey D. Hyman; Eric J. Guiltinan (Advances in Water Resources, 2025)

A Modeling framework for flocculated cohesive sediment transport in the current bottom boundary layer - Jorge A. Penaloza-Giraldo; Liangyi Yue; Tian-Jian Hsu; Bernhard Vowinckel; Andrew Manning; Eckart Meiburgc (Advances in Water Resources, 2025)

Relating flow resistance to equivalent roughness - Octavia Crompton; Gabriel Katul; Sally E. Thompson (Advances in Water Resources, 2025)

On the flow behaviour of unconfined dual porosity aquifers with sloping base - Konstantinos N. Moutsopoulos; John N.E. Papaspyros; Antonis D. Koussis; Frederick Delay; Marwan Fahs (Advances in Water Resources, 2025)

Implications of Microalgal–Bacterial Interactions in Modern Aquaculture Practices: A Review of the Current Knowledge - Sardar Ali; Waqas Waqas; Md. Akibul Hasan Bakky; Sahib Zada; Uddin Md Saif; Md Tawheed Hasan; Muhammad Shafiq; Tariq Dildar; Wang Hui (Reviews in Aquaculture, 2025)
Microalgae play a crucial role in aquaculture due to their nutritional value and antimicrobial properties, yet harvesting them can be energy intensive. To address this, microalgal–bacterial interactions have emerged as a sustainable approach, enhancing growth rates and wastewater treatment efficiency but also significantly improve nutrient cycling, particularly through the removal of ammonia and phosphorus. These interactions range from mutualism to antagonism, influencing nutrient exchange and ecological niche formation. Despite their potential, the integration of bacterial–microalgal consortia remains limited in aquaculture. This review aims to expand understanding of these interactions, their benefits, and their role in optimizing aquaculture systems. Various aspects of microalgae–bacterial interactions, including mutualistic and commensal relationships, antibiotics production by algae, and the algicidal role of bacteria, are discussed. Factors influencing these interactions, such as nutrient availability, the physical environment, chemical signaling, and microbial community composition, are also explored. The potential effects of microalgae–bacterial interactions on aquaculture, including enhanced revenue, efficiency, and ecological sustainability, are highlighted. Further research is needed to identify bacterial groups' influence on microalgal output and their potential for enhancing productivity in commercial aquaculture systems. Understanding and leveraging these microbial interactions could significantly improve aquaculture practices.

Shrimp Intestinal Microbiota Homeostasis: Dynamic Interplay Between the Microbiota and Host Immunity - Kai‐Min Zhou; Ping‐Ping Liu; Jia‐Yun Yao; Gerardo R. Vasta; Jin‐Xing Wang; Xian‐Wei Wang (Reviews in Aquaculture, 2025)
The shrimp intestine harbors a microbiota that has pivotal roles for host's physiology. Imbalance of shrimp intestinal microbiota has been shown closely related to the occurrence of diseases. The morphological and biological features of the shrimp intestine are considered suboptimal for stable microbial colonization, making the intestinal microbiota composition highly susceptible to the impact of environmental changes or stressors, and particularly unstable. Therefore, the relative unsteadiness of the microbiota composition represents a continuous threat to host survival. Shrimp intestinal microbiota homeostasis is achieved through a dynamic interplay between the microbiota and the host's innate immunity. The shrimp intestine possesses effective innate immune mechanisms that can suppress the uncontrolled proliferation of microbiota components, and simultaneously protect the microbiota from elimination. The mechanism(s) by which the microbial components and the intestinal innate immunity interact with each other to achieve homeostasis represents an interesting interplay between host and microbiota. This review summarizes the current knowledge about intestinal microbiota colonization in shrimp, as well as the intricate mechanisms employed by the intestinal immune system to regulate this microbiota. Moreover, the potential intervention strategies to promote and protect shrimp intestinal homeostasis by modulating the microbiota are also discussed. Thus, this review seeks to comprehensively analyze the current information and contribute to a deeper understanding of the complex interplay between the shrimp intestinal microbiota and innate immunity in maintaining shrimp intestinal homeostasis and overall health. This enhanced understanding may potentially open new avenues for aquaculture management and disease mitigation strategies, ultimately benefiting the shrimp farming industry.

Twenty Years of Commercial Farming of Kappaphycus alvarezii in India: A Look Back at Learnings and the Way Forward - Vaibhav A. Mantri (Reviews in Aquaculture, 2025)
Kappaphycus alvarezii continues to be driving force in marine agronomy. Along with Euchema spp. it contributes to 11.6 million tonnes feedstock globally. Among 30 countries where it was introduced, only, Tanzania and India could reach commercial‐scale farming. In India the feedstock production reached 8088 t (dry) worth ~USD 2,390,184 (between 2005 and 2020). The commercial farming has provided diversification of livelihood to the fishermen involved in un‐organized sector of natural seaweed gathering. At the cusp of its strategic expansion this review based on 20 years of research and developmental efforts provided a broad‐brushstroke picture of information on: (i) new innovations; novel, high‐value products; (ii) use as a biological source of commercially relevant genes to combat abiotic stress tolerance in crops; (iii) evolution in farming techniques and models; (iv) conscious efforts in skill‐set development; (v) policy guidelines to support industry; (vi) environmental concerns, disease outbreak, and biosecurity framework; (vii) sustainable seed‐supply management; (viii) cost–benefit analysis through perspective of profitability assessment parameters; and (ix) role of private sector in taking this initiative ahead. K. alvarezii farming in India seems to be successful example of achieving “triple bottom line” objectives of balanced economic, social and environmental out‐come as proposed by United Nations Department of Economic and Social Affairs (UNDESA) and World Bank (WB).

A Comprehensive Review of Diatom‐Bacterial Interactions Inferred From Bibliometric Analysis - Caiqin Hu; Zhen Shi; Tiehuan Hu; Yuan Gao; Qianfu Liu; Chao Wang (Reviews in Aquaculture, 2025)
Diatoms and bacteria have coexisted and coevolved for more than 200 million years, and their interactions have driven the processes of underlying major biogeochemical cycles. These complex and heterogeneous interactions span the range from synergistic to competitive and antagonistic, and they are regulated by diverse metabolites and biochemical mediators. Despite the significance of diatom–bacterial interactions in shaping aquatic food webs, driving nutrient cycles, and controlling algal blooms, the field currently lacks a comprehensive review of the current literature, research contents, and future research trends and perspectives. This review presents a comprehensive analysis of diatom–bacterial interactions by summarizing the information from current publications, including temporal trends, the most productive authors, journals, and countries, and illustrating current research contents, including regions, methods, foci, the interaction mechanisms and the environmental regulation. In addition, we discuss future research trends and perspectives. Our results indicate that most of the current research has been conducted in the ocean, using the methods of co‐culture experiments or field investigation combined with high‐throughput sequencing. The current research foci include the mechanisms of multiple cell‐to‐cell synergistic, competitive, antagonistic interactions, and multiple interactions regulated by biochemical molecules, and potential biotechnological applications. Furthermore, the future trends in this research field concern the underlying mechanisms of variation in diatom–bacterial interactions influenced by environmental changes and the possible applications. This review provides a comprehensive perspective on diatom‐bacterial relationships as well as a guide to future research.

Ecological Restoration of Inland Aquaculture in Land‐Locked Europe: The Role of Semi‐Intensive Fishponds and Multitrophic Technologies in Transforming Food Systems - Koushik Roy; Marc C. J. Verdegem; Jan Mraz (Reviews in Aquaculture, 2025)
Pond aquaculture and water protection in Europe suffer from conflicts, whereas multitrophic freshwater aquaculture technologies face hardships with over‐regulations in Europe. As such, inland freshwater aquaculture in land‐locked Europe has not given its contribution or echoed its importance in regional food system dialogues. The emphasis on marine cages and RAS‐based aquaculture is enormous. Almost if they are the only viable way to carry the future European aquaculture forward. In this scoping review, we have hypothesized that semi‐intensive fishponds and freshwater multitrophic aquaculture could be an overlooked component in the European food system. The analysis we present reviewed: (1) current positioning of inland freshwater aquaculture in European food system; (2) European fishponds' current positioning within food system and inland freshwater aquaculture; (3) way forward for semi‐intensive European fishponds through ecological pond nutrition research; (4) ecological technologies for realizing ‘net zero’ aquatic foods in land‐locked Europe; (5) risks and potential for making the transition. We conclude ample circular technologies and nature‐based solutions in pond and multitrophic freshwater aquaculture in land‐locked Europe. They have the potential to transform food systems locally with low‐impact aquatic food. European inland freshwater aquaculture may be a sleeping giant among EU's planetary healthy diet ambitions. As an example, 0.25 million hectares available Central Eastern European fishponds have the potential to ecologically substitute 1 billion marine fish oil capsules (EPA + DHA in 1 kt marine fish oil) and 11.9 kt of casein (leucine from 0.45 billion litres milk) equivalents, fulfilling singlehandedly annual leucine or EPA + DHA requirements of 1.2–3 million adults.

The Importance of Addressing Evolutionary Mismatches in the Production Management of Aquaculture Species - Thomas S. Mock; Davis S. Francis; Antoine M. Dujon (Reviews in Aquaculture, 2025)
To achieve production goals, aquaculture often modifies the environments of farmed species, creating conditions that differ significantly from their natural habitats. These alterations can result in evolutionary mismatches, where traits that evolved to optimise survival and reproduction in the wild become maladaptive in farming settings. This can lead to a conflict between traits desired for farming and those favoured by natural selection. In this opinion piece, we examine cases where such evolutionary mismatches arise, their impact on production, and strategies to mitigate these effects. We provide examples of species and farming practices that have been optimised through selective breeding and evolutionary studies and highlight practical solutions that can be applied to the many aquaculture species for which farming practices remain suboptimal. Additionally, we suggest directions for future research to deepen our understanding of evolutionary mismatches in aquaculture.

Cell Death in Crustacean Immune Defense - Zeyan Chen; Muhammad Tayyab; Defu Yao; Jude Juventus Aweya; Zhihong Zheng; Xianliang Zhao; Zhongyang Lin; Yueling Zhang (Reviews in Aquaculture, 2025)
Cell death mechanisms in crustaceans are a complex interplay of processes essential for maintaining cellular homeostasis and immune defense. Modes of cell death like apoptosis, necroptosis, and necrosis are well‐documented in crustaceans, serving crucial roles in removing damaged or infected cells. Unlike in other organisms, crustaceans likely lack pyroptosis, a type of programmed cell death associated with innate immunity and inflammation, because they do not possess the gasdermin genes essential for this process. Recently, NETosis and ferroptosis have emerged as significant mechanisms in pathogen defense. NETosis, involving the release of DNA fibers and antimicrobial proteins, helps trap and neutralize pathogens, while ferroptosis, an iron‐dependent form of cell death, contributes to lipid peroxidation and immune responses. Cuproptosis, although not yet studied in the context of crustacean immunity, shows potential crosstalk with ferroptosis, particularly in the regulation of metal ion homeostasis, oxidative stress, and cellular metabolism. Understanding these mechanisms offers promising applications in aquaculture, such as developing targeted immune modulators and enhancing disease resistance in economically important crustacean species.

Recent Research Advances on the Hippo‐Yki Pathway of Crustaceans: Current Knowledge and Potential Applications in Crustacean Aquaculture - Linwei Yang; Yushi Gan; Hengwei Deng; Jianguo He; Xiaopeng Xu (Reviews in Aquaculture, 2025)
The Hippo‐YAP/Yki pathway is critical for the regulation of physiological responses in various biological processes from invertebrates to mammals. Crustaceans, in particular shrimp and crabs, are important food sources worldwide. In response to the needs of crustacean aquaculture and disease control, the regulatory mechanisms of crustacean life activities, especially immunity, have been increasingly emphasized. Emerging clues suggest that Hippo‐Yki pathway is important for immunity and regeneration in crustaceans. In this review, the structure, activation pattern, response mechanism to pathogen invasion, and crosstalk with other signaling cascades of the Hippo‐Yki pathway in aquaculture crustaceans are summarized and its similarities and differences with those in mammals and Drosophila are investigated. Based on this, the roles of the Hippo‐Yki pathway in crustacean immune response and limb regeneration are further discussed, and the application potential of strategies pharmacologically or biologically targeting this pathway for crustacean disease control and breeding is theoretically explored.

Environmental and Biological Factors of Relevance to Shellfish Production in Northern Ireland: Insights From 20 Years of Regional Monitoring Data - Diana Senovilla‐Herrero; Yuwei Chen; Chaoran Liu; Subbulakshmi Suresh; Heather Moore; April McKinney; Sarah Helyar; Lenka Mbadugha; Katrina Campbell (Reviews in Aquaculture, 2025)
A historical analysis was conducted to evaluate monitoring data in the coastal and estuarine waters of Northern Ireland over the 20‐year period between 2001 and 2022 to identify current and emerging concerns and gaps in analysis relative to the sustainability of the aquaculture industry. The effects of biological factors such as the presence of harmful algal bloom phytoplankton and marine biotoxins, and environmental factors such as chemical contamination and the water quality on shellfish production were analysed. The influence of key meteorological factors, such as sea temperature, rainfall and sunshine hours, on the levels of environmental factors was also examined. The evaluation included a socio–economic perspective, exploring the impact of the shellfish industry on the Northern Irish economy and the surrounding communities. The article examined the challenges faced by shellfish producers in terms of regulatory compliance and market access, and provides suggestions for comprehensive environmental monitoring strategies, in particular improved sampling plans to be employed to address these challenges. Overall, the compilation analysis discovered that while the shellfish industry in Northern Ireland faces a number of challenges, it remains a valuable source of local employment and income, and has the potential for growth in the coming years. The findings presented will be of interest to researchers and policymakers in the aquaculture industry, and presents a valuable historical contribution on the evaluation of chemical and microbiological contaminants affecting shellfish production that may be useful for other production areas.

Fish Genomics and Its Application in Disease‐Resistance Breeding - Yu Huang; Zeyu Li; Mengcheng Li; Xinhui Zhang; Qiong Shi; Zhen Xu (Reviews in Aquaculture, 2025)
Global aquaculture production has been rising for several decades, with up to 76% of the total production from fish. However, the problem of fish diseases is becoming more and more prominent in today's context of pursuing sustainable aquaculture. Since the first fish genome assembly reported in 2002, genomic approaches have been successfully implemented in fish breeding to enhance disease resistance and reduce economic losses caused by diverse fish diseases. Here, we present a review of the current progress in fish genomics and its application in disease‐resistance breeding. First, assembly data for all publicly available fish genomes were curated and statistical analysis of these data were performed. Subsequently, genomics‐assisted breeding approaches (including quantitative trait loci mapping, genome‐wide association study, marker‐assisted selection, genomic selection, gene transfer, and genome editing) that have been applied in practical disease–resistance breeding programs are outlined. In addition, candidate genetic markers that could possibly be utilized in breeding were summarized. Finally, remaining challenges and further directions were discussed. In summary, this review provides insight into fish genomics and genomics‐assisted breeding of disease‐resistant fish varieties.

Lipid Droplets in Aquatic Animals: Diversity, Biogenesis, and Functional Implications - Si Zhu; Zhimeng Lv; Qinghui Ai; Chenghua Li (Reviews in Aquaculture, 2025)
Amid the aquaculture boom, chemical contaminants, diseases, and improper nutrition persist as threats to the sustainability of aquaculture. The accumulation of lipid droplets in different tissues has emerged as a hallmark in aquatic animals exposed to these stressors. While abundant knowledge is available on lipid droplets in mammals, relatively little is known in aquatic animals. Recently, interest in lipid droplets has grown in parallel with the recognition that they are actively engaged in the regulation of stress responses, metabolic modulation, infections, and immune response in different aquatic animals. This review first outlines the diversity of lipid droplets protein in various aquatic animals and discusses the function of lipid droplets in maintaining cellular homeostasis by contacting other organelles. Subsequently, the mechanisms of lipid droplet biogenesis in response to various chemical contaminants are summarized. Additionally, we describe the complex roles of lipid droplets in the host‐pathogen dynamic and the link between excessive lipid droplets accumulation and unwanted metabolic diseases in several aquatic animals. Finally, the potential application of lipid droplets in aquaculture is presented. A better understanding of the dynamics and functions of lipid droplets will facilitate the development of lipid droplets‐based therapeutic strategies, thereby improving the sustainability of aquaculture.

Macrophytes Used as Multifaceted Benefits Including Feeding, Bioremediation, and Symbiosis in Freshwater Aquaculture—A Review - Rathidra Nath Mandal; Pujadebi Bera (Reviews in Aquaculture, 2025)
The utility of macrophytes in freshwater aquaculture is diverse. We review the benefits of macrophytes in aquaculture into broadly three useful perspectives: (i) Feeding, (ii) Bioremediation, and (iii) Symbiosis. Macrophytes are used as direct food by herbivores for their potential nutrient values with a maximal protein content of 35% (D/W basis) and as ingredients for fish feed preparation with optimal 50% protein inclusion to reduce feed cost in commercial aquaculture. Macrophytes are used for wastewater treatments to eliminate contaminants, including As, Cu, Cd, Cr, Hg, and Pb, to 99.9%, and to reduce BOD (Biological Oxygen Demand) to improve water quality. Intake of remedied wastewater into aquaculture enhances water productivity through phytoplankton growth. An estimate is that 1.0 L of remedied wastewater, particularly sewage effluent adds an average of 0.05 g N & P and 0.99‐L freshwater into aquaculture to yield an average of 0.309 g fish. Macrophytes are integrated with fish in commercial aqua‐farming. Plants and fish are farmed together in aquaponics. They are used as substrates for some commercial fish species to lay eggs in farming. They are raised with ornamental fish for benefits in aquariums. Nevertheless, extensive studies are required to harness more benefits from macrophytes.

CRISPR /Cas Technology in Disease Prevention and Control of Aquatic Animals - Nan Lin; Jiexin Zhang; Yilei Wang; Ziping Zhang (Reviews in Aquaculture, 2025)
The CRISPR/Cas genome editing technology, with its advantages of simplicity, high efficiency, and cost‐effectiveness, has become a key tool for dissecting gene function, knocking out harmful/undesirable genes, and repairing defective genes. It has also shown great potential in the genome editing of aquatic animals such as tilapia, carp, salmon, and sea urchins. Disease prevention and control are core areas of aquatic animal research and the aquaculture industry. Novel technologies based on CRISPR/Cas, such as rapid diagnostic kits for aquatic diseases and species‐specific drugs against parasites, have been developed in the disease diagnosis, treatment, and prevention of aquatic animals. Based on our work in these fields, this review summarizes the relevant new technologies and latest progress, aiming to provide readers with a quick and comprehensive understanding of the application status and future trends of CRISPR/Cas technology in the prevention and control of aquatic diseases and to provide a reference for related fields.

The Transformative Role of Prebiotics, Probiotics, and Microbiomes in Biofloc Systems for Sustainable Aquaculture: A Comprehensive Review - Ramasamy Ramasubburayan; Santhiyagu Prakash; Grasian Immanuel; Davoodbasha Mubarakali; Govindasamy Rajakumar; Durairaj Thirumurugan; Arunachalam Palavesam (Reviews in Aquaculture, 2025)
Global demand for animal protein has increased dramatically due to the exponential development of the human population, which in turn led to intensification of aquaculture. However, the aforementioned fact impose stress on cultivable organisms, resulting in susceptibility to infectious diseases. Alternatively, this situation warranted the search for an environmentally friendly approach to replace the application of various chemical, physical, and biological processes that fail to cope with the required standards. In this context, biofloc technology (BFT) has emerged as a viable technique for aquaculture management with a sustainable and environmentally benign approach that has proven to have no adverse effects. BFT provides a conducive environment for cultivable aquatic species and system sustainability. Also, by maintaining the C:N ratio, the microbiome of BFT offers an appropriate carbon source and recycles waste. As well, the addition of probiotics and prebiotics (polysaccharides) in BFT certainly improves the host's antioxidant status, innate immunity, and disease resistance. Numerous studies on the use of BFT for various aquatic farmed species have been carried out recently, and it has evolved as a promising technique for the growth of sustainable aquaculture. BFT uses less water, increases productivity, provides biosecurity, and improves the health status of numerous aquaculture species. This review aims to compile and validate the scientific data about the benefits of biofloc in ensuring the health, biosecurity, and sustainability of aquaculture in light of the transformative role of probiotics, prebiotics, and microbiomes.

Toward Understanding Mechanistic Regulation of Body Size and Growth Control in Bivalve Mollusks - Ahmed Mokrani; Jian‐an Li; Qi Li; Shikai Liu (Reviews in Aquaculture, 2025)
Bivalves possess a pair of valves connected to a stretchable ligament that facilitates the opening and closing of the shell. The growth bioprocess commences when the supplemental materials secreted from the edge are added to the early‐constructed shell. Here, we endeavor to provide a glimpse into physiological responses, mechanistic control, and omics applications toward understanding this complex trait. In the first section, we review studies that have been performed to investigate the effects of food availability, temperature, salinity, contaminants, and climate change in natural ecosystems and under experimental conditions. These conditions affect some internal promotors and alter the concentration of particular neuropeptides and neurotransmitters that induce neuroendocrinal signals crucial for regulating this peculiar process. Besides, we provide a predicted concept for organs' size control and maintaining body size homeostasis via intertwining networks, including the Hippo pathway. On the other hand, we discuss the findings of studies employing genomics, transcriptomics, proteomics, and metabolomics approaches to uncover the mechanistic modulation of growth‐related traits in different bivalve species. We recommend further research to decipher organ size control and its intricate relationship with the entire body homeostasis. Future genetic dissection studies are also recommended to identify new key genes with a major effect that profoundly influences this trait, facilitating their potential editing to develop new strains with enhanced growth rates.

Recent Advances and Applications of Passive Acoustic Monitoring in Assessing Shrimp Feeding Behaviour Under Laboratory and Farm Conditions - Silvio Peixoto; Roberta Soares (Reviews in Aquaculture, 2025)
The use of passive acoustic monitoring (PAM) has recently been integrated with other noninvasive ethological methodologies to enhance the understanding of shrimp feeding behaviour, as their mandibles emit click sounds during food intake. This review aims to compile recent advances and various applications of PAM in assessing shrimp feeding behaviour under controlled laboratory and farm conditions. It includes a description of key concepts, terms and general methodologies in the field of bioacoustics to facilitate understanding of acoustic characterisation, specific methodologies and the main uses of PAM in shrimp research. Among the primary contributions of PAM in laboratory studies are acoustic characterisation of clicks and mandibular structures associated with their emission for different species; variations in acoustic click parameters related to animal size, feed texture and pellet size; and effects on feeding behaviour caused by shrimp size, stocking density and specific characteristics of artificial diets (texture, formulations, additives and pellet sizes). Finally, future perspectives and recommendations for laboratory studies using PAM are provided. The review highlights the contribution of PAM, which, allied with other ethological methodologies, emerges as a novel tool for researching shrimp behaviour and optimising feed management in aquaculture.

Potential Functions of the Gut Microbiome and Modulation Strategies for Improving Aquatic Animal Growth - Zhimin Zhang; Qiushi Yang; Haokun Liu; Junyan Jin; Yunxia Yang; Xiaoming Zhu; Dong Han; Zhigang Zhou; Shouqi Xie (Reviews in Aquaculture, 2025)
The increase in the body weight of animals, a pivotal indicator closely tied to production, is important to the aquaculture industry. Despite remarkable variability in gut microbiomes, which are intricately associated with their hosts and affect overall performance, fitness, and physiological outcomes, across individuals and species, the development and practical application of gut microbiota modulation in aquaculture remain underdeveloped. In this review, we systematically examine the advancements with a focus on the gut microbiomes of aquatic animals with different growth rates by literature search, summarizing the existing knowledge regarding the diversity, composition, and significance of the microbiome in individual growth. The comparative analysis reveals substantial alterations in the gut microbiome that correspond to changes in the growth rate of aquatic animals, with a species bias toward more carnivorous fish, and shrimps and sea cucumbers in nonfish species. The present review also discusses comparative gut microbiome research in aquaculture as an emerging field with great potential for advancing our understanding of animal growth, screening candidate probiotics, and facilitating microbiome modulation strategies. Besides, the present gaps in the knowledge of the gut microbiome associated with the growth and production of farmed animals have been highlighted. We propose potential directions to address emerging challenges and opportunities in this field, such as priority effects on gut microbiome establishment, especially in the early stage, and screening of host‐derived probiotics across various aquatic animals. Finally, we provide a conceptual framework for enhancing animal farming practices in aquaculture through intensified gut microbiome research.

The Molecular Mechanism of Embryonic Development in Decapod Crustaceans - Ardavan Farhadi; Qun Zhao; Karsoon Tan (Reviews in Aquaculture, 2025)
In recent decades, the decapod aquaculture industry has grown significantly in many parts of the world. Despite this progress, production levels still fall short of market demands, indicating a need for further efforts to increase the production. Investigations into the molecular mechanisms underlying embryonic development in decapods provide valuable insights into the complex embryonic development processes of this economically and ecologically important animal group. In this review, we explore the molecular mechanisms underlying decapod embryonic development, focusing on key genes, signaling pathways, and microRNAs (miRNAs) involved in the embryogenesis. Numerous genes have been identified that regulate various aspects of embryogenesis including egg activation, maternal‐to‐zygotic transition (MZT), mesoderm development, segmentation, nervous system development, sex determination, germline development, and exoskeleton formation. We also discuss the pivotal role of signaling pathways such as Hedgehog, Wnt, Notch, MAPK, TGF‐β, Jak‐STAT, VEGF, and Ecdysteroid in the regulation of embryogenesis. Additionally, this review identifies current research gaps in decapod embryogenesis and proposes directions for future investigation. This review is anticipated to be especially beneficial for researchers delving into the molecular mechanisms driving embryonic development in decapods.

Mitigating the role of aquaculture in crustacean invasions - Eléna Manfrini; Franck Courchamp; Boris Leroy (Reviews in Aquaculture, 2025)

Copper Homeostasis and Its Impact on Innate Immunity in Crustaceans - Hejia Chen; Xi Huang; Muhammad Tayyab; Mingming Zhao; Defu Yao; Zhihong Zheng; Xianliang Zhao; Yongzhen Zhao; Xiuli Chen; Bobo Zhang; Qiongqiong Yang; Yueling Zhang; et al. (Reviews in Aquaculture, 2025)
Copper, an essential micronutrient in crustaceans, plays vital roles in enzymatic processes, oxygen transport, pigmentation, and structural protein synthesis, including collagen and elastin. Recent research has elucidated its pivotal role in innate immunity of crustaceans, enhancing the immune response by promoting phagocytic activity, antimicrobial peptide production, and modulation of immune gene expression. Copper ions exhibit antimicrobial effects by disrupting cell membranes and inhibiting microbial proliferation. Furthermore, copper governs antioxidant defense mechanisms, protecting crustaceans against oxidative stress and infection. However, excessive copper can lead to toxicity, highlighting the need for strict maintenance of copper homeostasis. This review explores the complex processes of copper homeostasis in crustaceans, detailing transport mechanisms, storage proteins, and detoxification pathways. It emphasizes copper's critical physiological and immunological functions, contributing to a comprehensive understanding of its multifaceted roles in crustaceans and laying groundwork for further exploration of copper homeostasis as a strategy for boosting crustacean immunity. Aquaculture practices significantly influence copper levels in crustaceans. Effective copper management, including monitoring techniques, water treatment strategies, and regulatory frameworks, is crucial for both crustacean welfare and environmental sustainability.

Erythropoiesis in Teleost Fishes: The Fantastic Biological Process - Aihua Zhong; Xiaojun Yan (Reviews in Aquaculture, 2025)
Global fish production exceeds 170 million tons in 2023, and provides a high‐quality protein source for humans. However, various factors may contribute to hypoxic stress and anemia, which contribute to yield loss in fish production. Elevated red blood cell counts or activation of erythropoiesis are well‐known responses to anemia and hypoxia stress in fish. Erythropoiesis is the process of formation of new erythrocytes, from hemopoietic stem cells, through the differentiation of erythroblasts, to the maturation of red blood cells. This step‐wise process is governed by complex transcriptional, post‐translational, and epigenetic programs in response to extracellular signals. This review summarizes developing knowledge regarding erythropoiesis in teleosts, including the wave and site of erythropoiesis, specification of the erythroid lineage, and molecular regulation mechanisms. A summary of research gaps is presented, to be addressed by future research on teleosts. Understanding erythropoiesis facilitates improved fish husbandry and selective breeding of hypoxia‐tolerance fish, to ultimately contribute to increased production.

The Immune Priming in Aquaculture Invertebrates: Inspiration From Cellular Perspective and Future Investigation - Weilin Wang; Lingling Wang; Linsheng Song (Reviews in Aquaculture, 2025)
Aquatic invertebrates account for more than 33.4% of global aquaculture production and are important aquaculture animals worldwide. Although the frequent outbreaks of diseases and the lack of disease prevention strategies have greatly hindered further development of the invertebrate aquaculture industry. Immune priming is a phenomenon that invertebrates mount a faster and stronger secondary response than that of the primary response when encountered with a given microbe. It has been demonstrated to be present in a wide range of aquaculture species and would provide a fresh idea for disease prevention. As the main executors of immune defense in invertebrates, the circulating hemocytes are short‐lived, and the solution for the paradox of keeping a long‐lasting immune protection might lie in the formation of long‐lived memory cells in immune priming. As a reference for the access of memory cell formation processes in aquaculture invertebrates, the cellular kinetics including expansion, contraction, and memory formation of lymphocytes in the adaptive immunity of vertebrates are discussed. Then the features of hemocytes in aquaculture invertebrates, and their kinetic changes of cell number and immune capacity during immune priming are summarized for the knowledge of a stronger secondary immune response. The regulatory roles of epigenetic modification and metabolic reprogramming in immune priming and their possible functions in memory cell formation and identification are proposed to be preferentially investigated for further clarifying the mechanism of immune priming, which might provide a novel entrance for understanding the mechanisms of immune priming and developing disease prevention strategy in aquaculture invertebrates.

The Effect of Probiotics and Prebiotics on Feed Intake in Cultured Fish - Inês Guerreiro; Aires Oliva‐Teles; Paula Enes (Reviews in Aquaculture, 2025)
With aquaculture intensification, improving feed intake in order to increase fish growth as well as to reduce production costs and environmental impacts assume a high importance. In this sense, probiotics and prebiotics' capacity to positively modulate animals' appetite is of high interest and has been the focus of several studies in mammals, while in fish these studies are scarce, and available information is dispersed. Probiotics and prebiotics' role in appetite regulation mechanisms can be mediated by short‐chain fatty acids produced by gut microbiota, or by several other microbial‐derived metabolites, proteins, and lipopolysaccharides. The possible way these molecules may affect fish appetite is the focus of this review, which also highlights novel research directions for better elucidation of the impact of probiotics and prebiotics in the regulation of fish appetite, contributing to the definition of better feeding strategies, that optimize feed utilization efficiency and fish growth, leading to a more sustainable aquaculture production.

Advancing Aquaculture Sustainability: A Comprehensive Review of Biofloc Technology Trends, Innovative Research Approaches, and Future Prospects - Gang Liu; Marc Verdegem; Zhangying Ye; Jian Zhao; Jinxing Xiao; Xingguo Liu; Qinlang Liang; Kun Xiang; Songming Zhu (Reviews in Aquaculture, 2025)
Biofloc technology (BFT), initially adapted for shrimp farming in the 1970s, represents a sophisticated ecosystem of microorganisms designed to enhance aquaculture productivity and sustainability. Despite its established history, research into BFT is surprisingly still at an early stage globally. This review conducted a bibliometric analysis of 612 articles from major aquaculture journals spanning 2008–2023 to systematically explore the development, trends, and focal points of BFT research. The analysis revealed that the bulk of significant contributions originates from Brazil and China, and highlighting areas of interest can be categorized into four hotspots, such as (1) efficient nitrogen transformation, (2) biofloc microbiology, (3) biofloc's immunostimulant properties, and (4) the evaluation of research methodologies. At the end, the microecology concept was introduced, and the cross‐discipline methods were promoted in the aquaculture field. Notably, much of the BFT research is still at an exploratory phase, with numerous functional bacteria unidentified and optimization strategies for BFT underdeveloped. These gaps present opportunities for enhancing aquaculture through improvements in wastewater management, product quality, safety, and yield. Furthermore, the review notes a growing trend in applying microbiome research and microecological analysis in aquaculture, with high‐throughput sequencing data increasingly used to understand microbial interactions and nitrogen transformation within bioflocs. This direction promises to unlock further insights into the complex microbial ecosystems of bioflocs and their applications in sustainable aquaculture.

Exposed Aquaculture Operations: Strategies for Safety and Fish Welfare - Hans Vanhauwaert Bjelland; Ole Folkedal; Heidi Moe Føre; Esten Ingar Grøtli; Ingunn Marie Holmen; Eivind Lona; Hans Tobias Slette; Kristine Vedal Størkersen; Trine Thorvaldsen (Reviews in Aquaculture, 2025)
The expansion of aquaculture production into more exposed harsh and remote ocean environments presents both new opportunities and challenges. To manage the complexities of exposed operations, research into fish welfare, personnel safety, and facilitating technology is thus of key importance. This paper reviews recent research advances in the areas of safety, fish welfare, and technology, while the focus is on the Norwegian salmon farming industry, the results could benefit exposed fish farming internationally. Regarding fish welfare, the study summarizes the current knowledge status of salmon coping abilities and welfare indicators in strong currents and waves. On the safety front, there has been significant progress in operational safety management, accident analysis, and emergency preparedness, all of which are crucial for human personnel in these demanding settings. Human safety and fish welfare also rely on structures and equipment, and recent research results include advances in environmental load analysis, vessel design, simulations of fish farms. Notably, the development of contact‐free, autonomous lifting operations, and hole detection methods represents a significant leap in maintaining aquaculture infrastructure. This multidisciplinary study underscores the need for integrated research approaches to address exposed aquaculture, emphasizing that while recent innovations have enhanced safety and robustness, ongoing research and new strategies are critical for safety and fish welfare in exposed aquaculture operations.

Influence of Dietary Fatty Acids on Fish Sperm Tolerance to Cryopreservation - Elías Figueroa Villalobos; Wellison Amorim Pereira; Maritza Pérez‐Atehortúa; Leydy Sandoval‐Vargas; J. Romero; Ricardo P. S. Oliveira; Iván Valdebenito; Alejandro Villasante (Reviews in Aquaculture, 2025)
To meet growing fish demand, aquaculture must develop sustainable, cost‐effective, and high‐performance fish feed formulations for industry advancement. Plant‐based lipids are a viable alternative to forage fish ingredients in finfish diets. However, most plant‐derived lipids lack long‐chain polyunsaturated fatty acids (LC‐PUFA) like EPA and DHA, which are nutritionally essential for fish. This review summarizes recent findings on the nutritional aspects of fish brood stock and sperm quality, emphasizing the effects of fatty acids on reproductive outcomes. Studies indicate that substituting fish oil with plant oils alters the fatty acid profiles in fish tissues and gametes, potentially compromising sperm quality, cryopreservation success, and progeny viability. Sperm membrane lipids, including EPA, DHA, and ARA, are vital for motility and fertilization rates post‐thaw. Additionally, cryopreservation has been linked to molecular and epigenetic alterations in sperm, which may negatively affect offspring quality. The role of mRNA and noncoding RNA in regulating sperm function and embryonic development is well known, and thus any damage to these molecules as a consequence of cryopreservation might induce long‐term effects on offspring. Proteomic analyses reveal that cryopreservation can lead to significant protein loss in sperm, diminishing their functional and fertilization capabilities. Optimizing cryoprotectant protocols and freezing techniques is crucial to reduce damage, while dietary fatty acids play a key role in preserving sperm quality during cryopreservation stress. Further research with omic technologies is crucial to fully understand sperm tolerance to cryopreservation, which will improve reproductive outcomes and enhance sustainability and quality in aquaculture.

Optimising Outbreak Investigation, Surveillance and Discovery of Pathogens in Aquaculture Using Unbiased Metatranscriptomics - Vincenzo A. Costa; Richard J. Whittington; Charles Caraguel; Joy A. Becker; Kerrie E. Wiley; Christine Huynh; Jeremy Carson; Francisca Samsing (Reviews in Aquaculture, 2025)
Emerging infectious diseases are a major threat to global aquaculture production and are projected to increase in frequency due to anthropogenic stressors and climate change. Our ability to screen the global aquatic ‘infectome’ is dramatically improving through unbiased metatranscriptomic (i.e., total RNA) sequencing. Despite recent advances in molecular diagnostics and next‐generation sequencing, outbreak investigation in aquaculture often encounters limitations due to the targeted nature of conventional techniques, which may only capture a small portion of the diverse array of disease‐causing agents present in nature, sometimes requiring years to resolve. Here, we propose that unbiased metatranscriptomic sequencing serves as a cost‐effective and powerful technique for characterising pathogens during disease outbreaks and in surveillance programmes. In doing so, we offer a diagnostic framework to mitigate infectious disease threats to global aquaculture. We emphasise the importance of combining rapid metatranscriptomics with traditional techniques for a holistic examination of the causes of unknown aetiologies in aquatic animals, and how it can be used to examine host responses in parallel with pathogen discovery. We suggest that the integration of metatranscriptomics into aquaculture will require upskilling, proficiency testing, user‐friendly bioinformatic tools and open data sharing. Furthermore, it is essential to establish a reporting framework—with analytical guidelines—that ensures the protection of animal industries while safeguarding trade interests.

Epigenetic Resources: Gaps in Aquatic Animal Germplasm Research - Fangcheng Li; Junfang Zhang; Xiangbing Cheng; Xinyao Cui; Jiamin Sun; Qigen Liu (Reviews in Aquaculture, 2025)
Aquatic animal germplasm research plays a vital role in biodiversity conservation and sustainable aquaculture. The traditional view is that diversity of germplasm resources is commonly attributed to genetic variation. However, recent studies in transgenerational epigenetics have shown that epigenetic information can also be passed down to offspring, which is consistent with the definition of germplasm. Therefore, it is necessary to define epigenetic information, such as DNA methylation, histone modifications, and ncRNAs, which can be passed down through generations, as epigenetic resources and incorporate them into the concept of germplasm. Germplasm resources should include not only genetic resources but also epigenetic resources. Epigenetic variation can arise from genetic, environmental, or stochastic factors. Genetic and epigenetic variation co‐determine phenotypic traits. It has been demonstrated that epigenetic information can be inherited across generations in aquatic animals. DNA methylation, histone modification, and ncRNAs are involved in addressing environmental challenges, maintaining genetic diversity, improving breeding strategies, combating inbreeding decline, and age determination. Therefore, future research on epigenetic resources is important for germplasm conservation, development, and utilization. This review proposes a new theoretical framework to elucidate the place of epigenetic resources in germplasm research and collects articles from the past 8 years that explore the inheritance of epigenetic information in aquatic animals. Integrating epigenetic research into germplasm studies enhances our understanding of population dynamics, adaptation, and evolutionary processes, thereby informing conservation strategies and enhancing aquaculture practices. By considering both genetic and epigenetic resources, we can address the challenges facing germplasm diversity and sustainable aquaculture more comprehensively.

Cracking the myth: Bivalve farming is not a CO 2 sink - Fabrice Pernet; Sam Dupont; Jean‐Pierre Gattuso; Marc Metian; Frédéric Gazeau (Reviews in Aquaculture, 2025)
Bivalve farming was usually considered as a CO 2 source through respiration and calcification, but recent studies suggest its potential as a CO 2 sink, prompting exploration of its inclusion in carbon markets. Here we reviewed the scientific basis behind this idea and found that it is not supported by observational and experimental studies. This idea indeed arises from carbon budget models that are based on theoretical misconceptions regarding seawater carbonate chemistry. The main misunderstanding consists of assuming that the carbon trapped in the shell originates from atmospheric CO 2 when it mostly comes from (bi)carbonate ions. While these ions originate from atmospheric CO 2 through the erosion of minerals over geological time scales, their incorporation into shells does not prompt short‐term CO 2 compensation. The opposite occurs—calcification releases CO 2 in seawater and limits or even prevents the uptake of atmospheric CO 2 . Some authors suggest that considering the bivalve farm ecosystem could change the perspective on the source/sink issue but there is no evidence for that now. Most ecosystem‐based carbon budget models rely on several unverified assumptions and estimates. Although challenging, field measurements must be conducted for monitoring, reporting, and verifying atmospheric CO 2 uptake before qualifying for carbon credits. To achieve scientific consensus, we need reinforcing measurement‐based studies of CO 2 fluxes in shellfish ecosystems, integrating carbon balance models with observational and experimental science, and fostering interdisciplinary collaboration. Although bivalve farming provides numerous environmental benefits and is vital for sustainable aquaculture, there is currently no evidence that it contributes to CO 2 capture.

Assessing Changes in China's Pond Water Quality From 1989 to 2020: Implications for Green Development in Aquaculture - Yuanshuai Duan; Lu Liu; Rong Tang; Shouqi Xie; Mingmei Yang; Zhimin Zhang; Dapeng Li (Reviews in Aquaculture, 2025)
Since 1989, China has become the world's largest aquaculture producer through pond culture, significantly contributing to global food security but potentially posing environmental threats. However, little is known about the changes in the pond water quality at broad spatial and temporal scales, thus creating challenges in the sustainability of pond aquaculture. Herein, we explore changes in water quality in China's aquaculture ponds from 1989 to 2020 and assess the waterbody's health status to optimize sustainable management strategies. This study highlights pond water quality changes closely associated with China's aquaculture practices, development, and related policies. Seasonal and regional farming variations significantly impact water quality, with peak aquaculture seasons and Central China and North China associated with the lowest water quality scores. Pond water quality initially declined with the rise of intensive aquaculture but improved after 2012 with the adoption of ecological engineering measures, eco‐farming practices, and policies supporting green development. Under a scenario combining these efforts, the water quality score in 2035 is projected to increase by 57% of the 2020 level. These findings reveal that national ecological initiatives and advancements in green aquaculture techniques and public policies can significantly enhance the water quality of China's aquaculture ponds, offering valuable insights into environmental governance in global agriculture.

Issue Information (Reviews in Aquaculture, 2025)

Emerging Contaminants Related to Brazilian Aquaculture - Juliana Barros da Mota; Thiago de Alencar Neves; Daniel Pereira da Costa; Maria Clara Vieira Martins Starling; Camila Costa de Amorim; Kleber Campos Miranda‐Filho (Reviews in Aquaculture, 2025)
Research efforts around the world have focused on identifying the occurrence of emerging contaminants in aquaculture areas. In the Brazilian context, studies have aimed to identify emerging contaminants in water used for this activity. This systematic review covered studies published without a specific time frame with the following criteria: research conducted in aquaculture areas or with species and cultured water in Brazil and analysis of emerging contaminants. Out of the 42 studies identified, 132 emerging contaminants were observed. The Southeast and South regions accounted for most of these studies, with limited research conducted in the North and Northeast regions. Tilapia was the most studied species, followed by mollusks. In toxicity tests, animals showed several effects, such as decreased oxygen consumption and swimming patterns, histopathological changes, inhibition of sperm production, cardiac edema, spinal deformity, and antimicrobial resistance. In conclusion, advancements in research on emerging contaminants in Brazilian aquaculture are needed as the number of existing studies is lower compared to global numbers. Few studies have focused on analyzing cultivation sites to identify the contaminants present and their sources. Also noteworthy is the scarcity of work in the Northern region of Brazil and on native species. Characterizing these environments in terms of the types of contaminants and main sources of contamination is essential to finding ways to mitigate ecological and human health risks, as well as developing specific legislation for these contaminants because they are currently not part of routine monitoring programs and are therefore not regulated, especially in aquaculture environments.

Assessing the Feasibility of Sustainable Aquaculture for Common Snook Centropomus undecimalis - María de Jesús Contreras‐García; Wilfrido M. Contreras‐Sánchez; Manuel Mendoza‐Carranza (Reviews in Aquaculture, 2025)
Common Snook ( Centropomus undecimalis ) is widely distributed across the tropical Atlantic Coasts and has a significant economic impact. This review aims to assess the knowledge status of common snook, contributing significantly to the development of sustainable aquacultural practices. The review was conducted using Web of Science and Google Scholar to identify scientific articles analysing the biology and ecology, the status of snook fisheries and developments in aquaculture production. Researchers in the USA, Mexico and Brazil have conducted 37.95%, 25.52% and 26.21% of published research, respectively, focusing mainly on reproduction in natural environments, status of fisheries and aquaculture production. From an environmental perspective, it is essential to understand the factors impacting C . undecimalis populations. Climate change effects and human alterations to river courses pose significant threats. In addition to fishing regulations, there is a promising potential for further fisheries research and to deepen the understanding of the life cycle to support the implementation of sound aquacultural practices to replenish exploited stocks and to develop commercial aquaculture. Currently, C . undecimalis populations in Mexico and the United States are overexploited, focusing on México, which now has a management plan. Advances in controlled reproduction and larval development have been made. However, many challenges remain unclear, such as larval conditions that continue to represent a bottleneck to block continuous and large‐scale aquaculture production, larval nutrition, disease management and culture systems. However, aquaculture holds the potential to enhance the sustainability of this species by reducing fishing pressure and aiding population recovery.

Water Quality Impact on Fish Behavior: A Review From an Aquaculture Perspective - Kaisheng Zhang; Zhangying Ye; Ming Qi; Wenlong Cai; João L. Saraiva; Yanci Wen; Gang Liu; Ze Zhu; Songming Zhu; Jian Zhao (Reviews in Aquaculture, 2025)
Changes in water quality significantly shape fish behavior, a crucial index reflecting the growth and welfare status of fish. Given the centrality of this relationship to aquaculture practices, a comprehensive understanding of how water quality dynamics influence fish behavior is imperative. While there have been some summaries of the effects of water quality parameters on fish physiology and growth, few reviews on their effects on fish behavior have been reported yet. This article reviews several water quality parameters which are of great concern in aquaculture from multiple facets of actual production, including physical parameters (water temperature and turbidity), chemical parameters (dissolved oxygen, salinity, pH, and inorganic nitrogen), and chemical pollutants (microplastics and crude oil), which have gained increasing attention from the researchers and aquaculture practitioners over the past decades. Variations in these water quality parameters can exert profound effects on fish physiology, metabolism, internal tissues and organs, and sensory perception, which influences fish behaviors such as swimming, schooling, feeding, predation, anti‐predation, aggression, courtship, as well as adaptive and stress‐related behaviors such as exploration, avoidance response, and anxiety‐like behavior. By synthesizing the behavioral changes caused by specific water quality parameters, this review aims to provide strong support for further water quality‐related research, thereby fostering environments conducive to both fish welfare and aquaculture productivity.

Current disease treatments for the ornamental pet fish trade and their associated problems - E. Larcombe; M. E. Alexander; D. Snellgrove; F. L. Henriquez; K. A. Sloman (Reviews in Aquaculture, 2025)
The trade in live ornamental fishes to be held as companion animals or displayed in public aquaria has an estimated global annual value of US$15–20 billion. Supply chains for ornamental pet fishes often involve many more parties than for fish farmed as food fishes, and at each stage, fishes are exposed to stressors including handling, confinement, crowding, mechanical disturbance, and poor water quality. If chronic, these stressors can compromise their immune system, making fishes more susceptible to pathogens. Mortality and morbidity from infectious disease can result in considerable welfare impacts and massive economic losses for the industry, and the range of infective agents seen in ornamental species is well documented. However, treating these diseases is not straightforward with practices varying greatly across the trade and with several approaches having unintended consequences, such as the emergence of resistant strains of pathogens. While disease treatments for a handful of fish species (e.g., koi, goldfish) have received focused research attention, for the home aquarium owner, there is an increasing reliance on products based on natural compounds which have received far less scientific attention. This review aims to highlight the gaps in our knowledge surrounding the range of disease treatments used across the ornamental pet fish trade, with a particular focus on freshwater tropical species destined for home aquaria. Consideration is given to the potential problems arising from these treatments, including microbial resistance and effects of treatments themselves on fish health and welfare.

Which Novel Ingredient Should be Considered the “Holy Grail” for Sustainable Production of Finfish Aquafeeds? - Nikolas Panteli; Katerina Kousoulaki; Efthimia Antonopoulou; Chris G. Carter; Ioannis Nengas; Morgane Henry; Ioannis T. Karapanagiotidis; Elena Mente (Reviews in Aquaculture, 2025)
The immense production of fishmeal and fish oil is dramatically intensifying the severe state of pelagic fisheries overexploitation. The latter in conjunction with the increasing demand for low‐cost protein‐rich food supply prompt aquaculture to employ new practice. Several novel dietary ingredients are currently under evaluation for potential incorporation in aquafeeds in an effort to shift the aquaculture sector toward a more sustainable and economic production. The present review aims to summarize the existing findings regarding the effects of studied alternatives to fishmeal and fish oil on the most valuable and commercially produced marine ( Sparus aurata and Dicentrarchus labrax ) and freshwater ( Salmo salar and Oncorhynchus mykiss ) finfish species in European aquaculture. Alternative protein sources, including macroalage (marine plants), krill (marine fishery), insects (terrestrial), terrestrial animal by‐products (processed/rendered), and single cell ingredient (biotechnology), are discussed for their efficiency in promoting the growth and the welfare of both fry and adult cultured finfish species. Applicability of these ingredients is reviewed in terms of nutrient composition, dietary inclusion level, performance output, digestibility, and health benefits. In addition, a meta‐analysis was conducted based on data from peer‐reviewed scientific publications in order to assess whether novel ingredients meet the dietary protein (amino acid) and lipid requirements of finfishes. Aquafeed reformulation strategies should ensure the recommended daily nutritional requirements and additionally indicate the meta‐analysis alternatives, such as microalgae, which are deficient in essential amino acids. The sustainable expansion of aquaculture is on the horizon, but which novel ingredients may be regarded as the key drivers to its establishment?

Salmon lice biology, environmental factors, and smolt behaviour with implications for the Norwegian salmon farming management system: A critical review - Solveig van Nes; Albert Kjartan Dagbjartarson Imsland; Simon R. M. Jones (Reviews in Aquaculture, 2025)
In 2017, a new regulatory management system, the traffic light system (TLS), was implemented to estimate the effects of salmon lice from Norwegian salmon aquaculture on marine survival of wild Atlantic salmon and forms the basis of aquaculture capacity regulation. The TLS relies on observational data and a set of models to estimate the risk for negative impact on wild salmon populations. This review of the literature that forms the basis for the TLS as well as other relevant studies is presented in the context of the currently practiced TLS and suggestions are made for immediate and long‐term improvements. The main findings of this review are that: (1) assumed timing and duration of smolt migration contribute to unreliable observational and modelled data and overestimates of infection pressure; (2) production of lice larvae from farmed salmon is overestimated; (3) TLS model systems rely on or are calibrated by the same potentially flawed data; (4) lice‐associated mortality in wild salmon smolts may be overestimated; and (5) lice infection levels on farms are not associated with measurable effects on wild salmon. Recommendations to improve the accuracy and reliability of the TLS, and hence its environmental efficiency include the more complete use of available biological and physical environmental variables, adjusting the time period that observational data are registered and modelled data are integrated, adjusting the interpretation of data including recognition of uncertainty in model outcomes, and use of more realistic assumptions concerning lice‐induced mortality thresholds.

Genome Manipulation Advances in Selected Aquaculture Organisms - Jinhai Wang; Yu Cheng; Baofeng Su; Rex A. Dunham (Reviews in Aquaculture, 2025)
With the rising global demand for seafood and the challenges posed by overfishing and climate change, the aquaculture sector has become increasingly important in providing high‐quality protein for human consumption. Although traditional selection breeding programs have made great strides in genetic improvement of aquaculture species over the past decades, faster and more precise breeding tools, such as genome manipulation, are needed for performance enhancement of aquaculture stock. This review presents a comprehensive overview of the current status of three major genome manipulation tools, including RNA interference (RNAi), gene transfer, and genome editing in aquaculture species, and discusses the advances made, challenges faced, and potential future directions of this fast‐developing field. Taking catfish as an example, this paper reviews the specific applications of these techniques to improve traits such as growth, disease resistance, reproduction, and nutritional profiles in various commercially important fishes and crustaceans, highlighting successful applications and ongoing research efforts. We also propose CRISPR/Cas9‐mediated multiplex genome editing for the knockout or replacement of multiple genes in parallel to improve multiple traits in fish. Collectively, this review provides insights into the evolving landscape of genome manipulation in aquaculture and sheds light on its implications for sustainable practices and responsible innovation.

Assessing the Sustainability and Food Security Implications of Introduced Pangasianodon hypophthalmus (Sauvage, 1878) and Clarias gariepinus (Burchell, 1822) Into Indian Aquaculture: A OneHealth Perspective - Atul K. Singh (Reviews in Aquaculture, 2025)
The introduced striped catfish ( Pangasianodon hypophthalmus , Sauvage, 1878) and North African catfish ( Clarias gariepinus , Burchell, 1822) are popular choices in Indian aquaculture due to their high productivity and ease of management. Among all introduced non‐native fish species, catfish production is particularly notable, with P. hypophthalmus contributing 1.6 million metric tons (mmt) and C. gariepinus reaching 0.4 mmt. This paper examines the ecological, biodiversity, environmental, and disease concerns associated with the intensive aquaculture of the non‐native catfish species, using a OneHealth approach to assess sustainability. Generated information on biological plasticity, resource competition, genetic interactions, invasion risks, biodiversity impacts, food safety, and disease risks in extensive aquaculture of non‐native catfish are presented. A risk assessment (RA) was performed using an Excel–based developed module having 28 attributes and rated on a scale of 1 to 5. The results indicated significant risks, particularly for C. gariepinus , which had a risk score of 116 out of total 140 response points obtained from 65 farmers, manifesting 82.85% risk. In comparison, P. hypophthalmus had a response score of 85, displaying 60.71% risk. The findings suggest that C. gariepinus poses a higher ecological risk than P. hypophthalmus , primarily due to poorly controlled aquaculture practices, inadequate biosecurity, and insufficient regulatory measures. To tackle these issues, it is recommended that stringent policy with clear regulatory framework on the OneHealth approach will ascertain safe interconnectedness of aquaculture, environment, fish, and human health while improving the biosafety of non‐native catfish aquaculture practices safeguarding human health, fish populations, and overall ecosystem health.

Beyond the Win–Win Discourse: Designing Seaweed Farming for Long‐Term Success - Tomas Chaigneau; Giulia Nicolini; Katharine Orchel; Carly Daniels; Ian Ashton (Reviews in Aquaculture, 2025)
Communication about seaweed aquaculture has so far been dominated by its many socio‐economic and ecological advantages. A key risk of this ‘hype’ is the potential loss of support from communities affected by seaweed cultivation if reality fails to live up to expectations. This could have justice and equity implications for impacted communities, and undermine potential benefits for those communities, as well as affecting the long‐term success of emerging industries. This paper highlights experiences from other marine sectors in which a similar emphasis on benefits has drowned out discussion of potential costs, often leading to initial success but long‐term failure. We highlight the importance of clearly communicating possible negative impacts, and meaningfully engaging stakeholders to shape marine interventions. Finally, we recommend further research into the social dimensions of seaweed farming in geographies where this practice is nascent, and increased attention to the potential trade‐offs of scaling up seaweed cultivation.

Managing the Dissolved Oxygen Balance of Open Atlantic Salmon Sea Cages: A Narrative Review - Evelina Veronica Christina Berntsson; Tor Kristian Stevik; Asbjørn Bergheim; David Persson; Marit Stormoen; Kristian Hovde Liland (Reviews in Aquaculture, 2025)
As Atlantic salmon depend on dissolved oxygen (DO) to survive and grow, managing DO is essential for welfare and growth. However, the dynamics of DO in the open sea cages are complex, caused by a range of factors that interact and create compounding effects. To understand DO dynamics, two pillars of knowledge are essential: the supply of DO to the cages and the consumption of DO in the cages. The components of these two pillars vary greatly across both time and space, with factors including ambient sea temperature and current, density stratification, fish size, health and metabolism, biomass density and distribution, topography, production routines and farm configuration. In the production environment, these factors often interact, making related analyses on effects, causality and effective management highly challenging. Exacerbating matters, existing knowledge is fragmented across multiple disciplines, making it challenging for end‐users to access. Using sensors is often necessary to understand and manage the complexity of DO, and the interest to implement digital technologies to aquaculture operations and utilize big data analyses is growing, but to succeed in the application, an in‐depth understanding of the relevant dynamics is necessary. Consequently, this review is produced to compile existing knowledge on the many factors that influence the consumption or supply of DO in the sea cages, and their relationship to each other. In this narrative review, we explore the known interactions and compounding effects between these factors, and synthesize it in a causal diagram for holistic analyses of the DO balance.

Impacts of Global Warming on Quality of Male Fishes: Evidence From A Meta‐Analysis of Temperature Effects on Sperm Motility Kinematics - Yu Cheng; Jinhai Wang; Sayyed Mohammad Hadi Alavi; Songpei Zhang; Zuzana Linhartová; Deepali Rahi Roy; Nururshopa Eskander Shazada; Borys Dzyuba; Otomar Linhart (Reviews in Aquaculture, 2025)
Studies have demonstrated adverse effects of global warming on aquatic ecosystems. However, the effects of increased water temperature (IWT) on fish reproduction are still doubtful in species spawning at low or high temperatures. In this meta‐analysis, we elucidated the effects of global warming on spermatozoa functions, key determinants of male fertility. We recruited 245 data records from 20 studies spanning 20 cold‐ and warm‐water fishes to identify the effects of IWT on sperm quality. Data were re‐processed and re‐analyzed to determine the overall effects of IWT on sperm kinetics such as percentage of motile spermatozoa (MOT), duration of spermatozoa motility (DSM), curvilinear velocity (VCL), straight line velocity (VSL), average path velocity (VAP), as well as on enzymatic activities for energy supply (EAES) and antioxidant enzyme activity (ANEA). The standardized mean difference was calculated for each study, with positive values indicating higher performance under IWT. Results showed that (a) the overall effect size for MOT was larger negative in cold‐water fishes (−1.22) than in warm‐water fishes (−0.95). (b) Each 1°C increase in the activation medium reduced MOT by 1.30% (cold‐water fishes) and 3.47% (warm‐water fishes). (c) IWT negatively affected DSM, decreasing it by 10 s (cold‐water species) and 5.64 s (warm‐water species) per degree of IWT. (d) Spermatozoa velocity (VCL and VSL) increased by IWT in warm‐water species. (e) In cold‐water species, IWT‐induced detrimental effects on EAES were associated with adverse impacts on sperm motility kinetics. In conclusion, IWT negatively affects sperm motility kinetics, suggesting an impact of global warming on fish reproduction.

The Research Advances in Distant Hybridization and Gynogenesis in Fish - Qizhi Liu; Shi Wang; Chenchen Tang; Min Tao; Chun Zhang; Yi Zhou; Qinbo Qin; Kaikun Luo; Chang Wu; Fangzhou Hu; Yude Wang; Qingfeng Liu; et al. (Reviews in Aquaculture, 2025)
Distant hybridization and gynogenesis are two prevalent breeding techniques for fishes. Drawing from the research achievements of our team and the existing literature, we summarize the reproductive traits and genetic features of fishes derived from distant hybridizations and gynogenesis, and we deduce the fundamental mechanisms of these two methods and compare them, discerning their common and different characteristics. Both distant hybridization and gynogenesis techniques can alter genotypes and phenotypes, thus establishing them as significant breeding methods. Additionally, the genetic principles and the basic biological characteristics of distant hybridization and gynogenesis in fish have been inferred. We propose the concepts of macro‐hybrid and micro‐hybrid based on extensive experimental findings from fish distant hybridizations and gynogenesis. The term “macro‐hybrid” refers to offspring from distant hybridization that possess two distinct subgenomes, each inherited from one of the two parental species, such as allodiploid and allotetraploid lineages. The concept of “micro‐hybrid” refers to offspring, including autodiploid and autotetraploid lineages, as well as those resulting from artificial gynogenesis, whose genome almost originates solely from the maternal parent but in which certain DNA fragments derived from the paternal parent insert. Distant hybridization and gynogenesis are vital techniques in fish genetics, breeding, and evolution. We highlight the prospective paths for research and application of distant hybridization and gynogenesis in fishes.

Current Advances in the Black Tiger Shrimp Penaeus monodon Culture: A Review - Khor Waiho; Yang Ling; Mhd Ikhwanuddin; Alexander Chong Shu‐Chien; Nor Afiqah‐Aleng; Youji Wang; Menghong Hu; Honjung Liew; Nor Azman Kasan; Jia Hui Peh; Hanafiah Fazhan (Reviews in Aquaculture, 2025)
The increasing high‐end market demand for the black tiger shrimp Penaeus monodon has brought tremendous industry opportunities. Although the industry has tried its best to increase production, according to the report data from the Food and Agriculture Organization (FAO), annual global production has shown no significant upward trend over the past decade. Besides that, newly implemented policies such as seafood safety and food security negatively impacted the industry and reduced production. However, P. monodon cultivation is still promising due to its larger body size and higher market acceptance as a premium product. Over the years, numerous studies have been conducted to increase the production of P. monodon by optimizing its culture conditions, implementing new culture system, increasing disease resistance to disease such as WSSV, AHPND, WFD, implementation of pre‐ and probiotics in feed, and selective breeding programs to increase genetic diversity and population of P. monodon broodstock. This review provides an overview of the current advances in P. monodon broodstock cultivation, thereby providing an essential baseline for P. monodon aquaculture. Areas needing urgent research focus are also highlighted. Future research should take great strides and take into account the impact of future climate change scenario during P. monodon culture and optimization, and increase biosecurity measures to prevent its introduction as an alien species in wild settings.

Salmon Aquaculture in Chile: Production Growth and Socioeconomic Impacts - Adams Ceballos‐Concha; Frank Asche; Roberto Cárdenas‐Retamal (Reviews in Aquaculture, 2025)
Global aquaculture production has been rapidly increasing in recent decades. Associated with this growth, there has been a discussion with respect to the industry's socioeconomic impact. In particular, the industry's ability to make a positive difference in the communities where it is conducted is often questioned. This is a difficult topic to address due to limited data availability. However, it is a critical question concerning the aquaculture industry's long‐term viability. Some recent studies have addressed specific indicators such as poverty reduction in a given country. However, no studies review the impact of an aquaculture industry on a broad set of indicators over time. In this paper, we review the impact of the Chilean salmon industry on three broad socioeconomic indicators: employment, salary level and migration; as well as several narrower indicators. While data beyond production initially are scarce and mostly found in the gray literature, the information they provide connects well with newer data sets as they become available. Not unexpectedly, employment in the Chilean aquaculture industry increases with production. The industry pays relatively well, and it has a societal impact as opportunities created by the industry first reverse outward migration and then lead to inward migration. This is also associated with reduced poverty, a more even income distribution, a higher female labor participation ratio, and higher education levels. While the overall socioeconomic impacts of the industry are positive, they are also disrupted by severe environmental crises and show that the socioeconomic benefits are conditioned on environmental sustainability.

Shrimp Processing Waste in Aquaculture Feed: Nutritional Value, Applications, Challenges, and Prospects - Kylian Manon Eggink; Renata Gonçalves; Peter Vilhelm Skov (Reviews in Aquaculture, 2025)
The global shrimp processing industry generates substantial amounts of solid waste (head, abdominal exoskeleton, and tail), with a considerable part currently being disposed of in landfills. It holds significant potential as an alternative ingredient in aquaculture feed due to its relatively high crude protein content, balanced amino acid profile, and presence of bioactive compounds. However, one of the main challenges with shrimp processing waste is its rapid spoilage. Consequently, shrimp solid processing waste must undergo further refinement to produce shrimp‐derived products suitable as aquaculture feed ingredients, such as meal, hydrolysate, or silage. This literature review describes the nutritional value, applications, challenges, and prospects of these shrimp‐derived products in aquaculture feed. Among the investigated shrimp‐derived products, shrimp hydrolysate has the highest nutritional value considering the high crude protein content, balanced amino acid profile, low chitin content, and low ash content. However, producing shrimp hydrolysate requires extensive processing, which can be costly, limiting its applications to high‐value aquaculture species. On the other hand, shrimp meal and shrimp silage, which require less energy‐intensive processing, may be more suitable for lower‐value aquaculture species that naturally consume feeds high in ash and chitin. The prospects for using shrimp‐derived products in aquafeed are promising, with advances in processing technologies showing potential to reduce costs, improve nutritional value, and enhance product quality and safety. Ultimately, shrimp‐derived products could replace current aquafeed ingredients while simultaneously utilizing current shrimp solid waste streams, provided that quality and safety measures are carefully considered.

Biosafety in Norwegian Aquaculture—Risks and Measures in RAS Facilities and Well‐Boats - Hans Tobias Slette; Cecilie Salomonsen; Kristine Størkersen; Guro Møen Tveit; Andreas Misund; Eivind Lona (Reviews in Aquaculture, 2025)
Biosafety is a central concern in Norwegian salmon farming, as diseases and parasites are common. Continued production depends on preventing and controlling diseases and parasites. A critical part of the farmed salmon's life is during smolt production and the following well‐boat transport out to sea. Biosafety here is thus essential, and there is a need for an overview of risk factors and measures. Biosafety is related to the technical solutions' design, construction, cleaning, and maintenance, that can be studied through field work, interviews, and document analysis. This paper presents results from a study identifying risk factors related to technical solutions in smolt production (with RAS—recirculating aquaculture systems) and well‐boats, and potential measures to reduce risk. Risk factors for RAS facilities are divided into four main groups: Introduction of pathogens to the facility, spread of pathogens inside the facility, growth of pathogens inside the facility, and additional risks. Risk factors for well‐boats are divided into three main groups: Introduction of pathogens through intake water, spread of pathogens between fish groups, and spread of pathogens from well‐boat to the environment. Measures are proposed to mitigate the identified risk factors. The lists are not exhaustive, and risk magnitude is not quantified, so effect of measures is not calculated. Still, the measures' potential for risk reduction and implementation (cost/benefit) are discussed, suggesting measures vital for biosafety in RAS facilities and well‐boats.

Cover Image - Diana Senovilla‐Herrero; Yuwei Chen; Chaoran Liu; Subbulakshmi Suresh; Heather Moore; April McKinney; Matt Service; Sarah Helyar; Lenka Mbadugha; Katrina Campbell (Reviews in Aquaculture, 2025)
The cover image is based on the article Environmental and Biological Factors of Relevance to Shellfish Production in Northern Ireland: Insights From 20 Years of Regional Monitoring Data by Katrina Campbell et al., https://doi.org/10.1111/raq.12998 . image

Antibiotic Resistance in Vibrio parahaemolyticus : Mechanisms, Dissemination, and Global Public Health Challenges—A Comprehensive Review - Yingpeng Li; Gongshi Lin; Theerakamol Pengsakul; Qingpi Yan; Lixing Huang (Reviews in Aquaculture, 2025)
Vibrio parahaemolyticus , a ubiquitous pathogen in marine and estuarine environments, is a foodborne microorganism whose infections have become a global public health challenge. In recent years, the overuse and misuse of antibiotics have led to the emergence of increasing numbers of antibiotic‐resistant strains of V. parahaemolyticus worldwide. These strains harbor resistance genes that mediate various resistance mechanisms, presenting a significant challenge to antibiotic therapy. Furthermore, horizontal gene transfer (HGT) of resistance genes and the accelerating impacts of global climate change have facilitated the formation and spread of resistance, contributing to the proliferation of resistant strains and exacerbating the public health threat. This review aims to provide a comprehensive overview of the resistance genes and mechanisms in V. parahaemolyticus , the effects of climate change on its resistance, and strategies to curb the transmission of resistant strains. Additionally, we conducted a statistical analysis of resistance data from 6727 V. parahaemolyticus isolates obtained from 27 countries across Asia, Africa, the Americas, and Europe, through the literature review, to better understand the distribution and trends of resistance in this pathogen. We hope that this study will serve as an important reference for controlling the spread of antibiotic resistance in V. parahaemolyticus and addressing this critical public health issue.

A Review on the Role of 2–8 Carbon Chain Carboxylates in Enhancing Aquaculture Performance - Moussa Gouife; Lefei Jiao; Fei Kong; Tinghong Ming; Pascal Saikaly; Jorge Galindo‐Villegas; Jiajie Xu (Reviews in Aquaculture, 2025)
Aquaculture is a key sector for global food security, but its sustainability and productivity remain constantly questioned. Using 2–8 carbon chain carboxylates (2–8 CCs) has proven to be a promising and beneficial strategy for various fields, including aquaculture. Within the 2–8 CCs, short‐chain fatty acids (SCFAs) have received significantly more attention from researchers than the relatively less‐explored medium‐chain fatty acids (MCFAs). Applying these compounds in aquaculture has improved growth performance, feed efficiency, immune responses, intestinal health, antioxidant capacity, and water quality, thus promoting aquaculture organisms' productivity and sustainability. Furthermore, 2–8 CCs offer significant environmental benefits by reducing the reliance on antibiotics and promoting a healthier gut microbiota, thereby mitigating some ecological impacts of aquaculture. They also contribute to improved waste management practices and developing a more circular economy within aquaculture systems. This review comprehensively examines the current understanding of 2–8 CCs' effects in aquaculture, discussing their roles, environmental impacts, benefits, challenges, and future research directions. The findings underscore the potential of 2–8 CCs to significantly enhance the sustainability and productivity of aquaculture systems, offering a hopeful outlook for the future of the field.

Fish Sludge as Feed in Circular Bioproduction: Overview of Biological and Chemical Hazards in Fish Sludge and Their Potential Fate via Ingestion by Invertebrates - Kristin S. Pettersen; Veronika Sele; Pedro Araujo; Ikram Belghit; Sylvie L. Benestad; Aksel Bernhoft; Andy M. Booth; Gunnar S. Eriksen; Julia Farkas; Aleksander H. Handå; Bjørn Henrik Hansen; Kari O. Helgesen; et al. (Reviews in Aquaculture, 2025)
Aquaculture farming discharges large volumes of fish sludge, consisting of particulate organic matter from feed spill and feces. Fish sludge from land‐based salmonid aquaculture systems can potentially be used to feed low‐trophic species such as marine polychaetes and insects. Further use of these invertebrates as feed may provide a more sustainable feed chain. However, food security must not compromise feed or food safety. The use of fish sludge as feed is currently not permitted in the European Union (EU). A regulatory assessment that considers the integration of fish sludge in the circular bioeconomy requires knowledge of the potential chemical and biological risks involved. This review has compiled data from existing literature on the occurrence of chemical and biological hazards, as well as the physical properties of fish sludge. The potential risks along this feed chain, from fish sludge to novel feed ingredient production, are discussed in light of the EU regulatory framework. Within the available, but scarce, literature on biological hazards in fish sludge, there is no clear evidence that fish sludge is unsafe for use as a feed material for invertebrates if treatment criteria established in the EU regulations are followed. Scarcity implies a level of uncertainty, but not necessary of risk. For the chemical hazards, some elements are of concern and may exceed regulatory limits, and there are limited data on the occurrence of organic pollutants. This review highlights considerable knowledge gaps concerning the use of fish sludge in a circular feed and food system.

The Roles of Chemical Cues in the Life Cycle of Bivalves: Spawning, Settlement, and Metamorphosis - Ana Rato; Sandra Joaquim; Domitília Matias; Peter C. Hubbard (Reviews in Aquaculture, 2025)
Spawning, settlement, and metamorphosis represent the most challenging events for hatchery bivalve production. To enhance bivalve aquaculture, hatcheries have relied on a range of chemical compounds to induce these biological processes. Yet, despite the apparent importance of chemical cues, there is little knowledge on chemosensory systems and the role of chemical communication in bivalves. This review aims to compile the existing knowledge of the chemicals used in hatcheries to induce spawning and to improve settlement and metamorphosis in some economically important bivalves. A lack of recent studies regarding this topic has resulted in stagnation in the development of new approaches and products for use in aquaculture. This review explores the natural chemical cues and how they act in the natural environment, and the efforts made by hatcheries, through the use of synthetic inducers, to optimize bivalve production and overcome the challenges associated with spawning, settlement, and metamorphosis. Furthermore, it discusses the current knowledge on the chemical nature of spawning‐inducing pheromones. The synthesis of synthetic pheromones for spawning, settlement, and metamorphosis induction may improve bivalve aquaculture and efficiency. Nevertheless, more research is needed to fully understand the chemical communication and chemosensory systems of bivalves.

Fish Tracking, Counting, and Behaviour Analysis in Digital Aquaculture: A Comprehensive Survey - Meng Cui; Xubo Liu; Haohe Liu; Jinzheng Zhao; Daoliang Li; Wenwu Wang (Reviews in Aquaculture, 2025)
Digital aquaculture leverages advanced technologies and data‐driven methods, providing substantial benefits over traditional aquaculture practices. This article presents a comprehensive review of three interconnected digital aquaculture tasks, namely, fish tracking, counting, and behaviour analysis, using a novel and unified approach. Unlike previous reviews which focused on single modalities or individual tasks, we analyse vision‐based (i.e., image‐ and video‐based), acoustic‐based, and biosensor‐based methods across all three tasks. We examine their advantages, limitations, and applications, highlighting recent advancements and identifying critical cross‐cutting research gaps. The review also includes emerging ideas such as applying multitask learning and large language models to address various aspects of fish monitoring, an approach not previously explored in aquaculture literature. We identify the major obstacles hindering research progress in this field, including the scarcity of comprehensive fish datasets and the lack of unified evaluation standards. To overcome the current limitations, we explore the potential of using emerging technologies such as multimodal data fusion and deep learning to improve the accuracy, robustness, and efficiency of integrated fish monitoring systems. In addition, we provide a summary of existing datasets available for fish tracking, counting, and behaviour analysis. This holistic perspective offers a roadmap for future research, emphasizing the need for comprehensive datasets and evaluation standards to facilitate meaningful comparisons between technologies and to promote their practical implementations in real‐world settings.

Rab Proteins as Potential Therapeutic Targets Applied to Crustacean Aquaculture: Rab7 Case Analysis - Carlos Fajardo; Marcos De Donato; Patai Charoonnart; Vanvimon Saksmerprome; Harry O. Jackson; Juan Miguel Mancera; Benjamin Costas (Reviews in Aquaculture, 2025)
Rab proteins constitute an important subfamily of molecular effectors whose function is related to the modulation of several important cellular and metabolic processes, including controlling intracellular endocytic vesicle trafficking, phagosome formation, endosome maturation, and innate immunity. In crustaceans, the study and characterization of these proteins have garnered great interest, mainly due to their pivotal role in the innate immune response mechanisms against infections. Among the Rab family, the Rab7 stands out as a prominent example of the potential of these proteins as therapeutic targets for the development of genetic therapies to control viral pathogens in crustacean aquaculture. In this review, a compendium of the information currently available in relation to Rab proteins in crustaceans is made, taking the Rab7 protein as a model, emphasizing not only its general aspects of functioning at the molecular level, but also describing in‐depth both mechanisms of action and potential interactions, as well as its implications in relation to the immune system, particularly in shrimp.

Seasonality and diversity variations of planktonic tintinnids (Ciliophora) in the tropical Cochin estuary, southwest coast of India - Twinkle Sathish; Aishwarya Purushothaman; Renju Mohan; K. H. Afnitha; Lathika Cicily Thomas; K. B. Padmakumar (Discover Oceans, 2024)

Correction: First record of two species of brachyuran crab (Crustacea: Decapoda) Austruca albimana (Kossmann, 1877) and Tirmilyra concinnus (Ghani and Tirmizi, 1995) from India - Deep D. Dudiya; Pranav J. Pandya; Mansi S. Goswami; Reza Naderloo (Discover Oceans, 2024)

Making the case for gender-inclusive fisheries governance, policies and climate adaptation - Ayodele Oloko; Louise Teh; Philippe Le Billon; William Cheung; Sarah Harper; Ussif Rashid Sumaila (Discover Oceans, 2024)

Editorial Board (Applied Soil Ecology, 2024)

Arbuscular mycorrhizal fungi regulation of soil carbon fractions in coal mining restoration: Dominance of glomalin-related soil proteins revealed by stable carbon isotopes (δ13C) - Mingchao Li; Yinli Bi; Kejing Yin; Xinpeng Du; Lexuan Tian (Applied Soil Ecology, 2024)

Effects of biochar on plant and microbial communities in landfill soil - Jiaxin Liao; Guangcun Hao; Haowen Guo; Hongqi CHEN (Applied Soil Ecology, 2024)

Litter quality regulates cover crop litter decay alongside altered microbial facets - Guilong Li; Ke Leng; Wenjing Qin; Xiaofen Chen; Yongxin Lin; Ming Liu; Meng Wu; Jianbo Fan; Xiaoyue Wang; Yuji Jiang; Jia Liu (Applied Soil Ecology, 2024)

Sustainable strategies for enhancing soil carbon sequestration and their beneficial impacts on soil fertility: A comprehensive review - Mathiyazhagan Narayanan; Christo Ananth; M. Ayyandurai; Arivalagan Pugazhendhi; Mohammed Ali Alshehri; Ying Ma (Applied Soil Ecology, 2024)

Niche differentiation shapes the community assembly of fungi associated with evergreen trees in the Horqin desert - Xuan Liu; Pei-shan Zhao; Guang-lei Gao; Yue Ren; Guo-dong Ding; Ying Zhang (Applied Soil Ecology, 2024)

Microbial mechanisms underlying active organic carbon pool increases via rhizodeposition by Moso bamboo under in situ crown 13CO2 enrichment - Man Shi; Hang Chen; Junbo Zhang; Zhenxiong Chen; Zhikang Wang; Tingting Cao; Quan Li; Xinzhang Song (Applied Soil Ecology, 2024)

Organic materials return suppressed soil N2O emissions by changing the composition instead of abundance of denitrifying microbial community - Lin Chen; Qing Liu; Hailun Du; Jixiao Cui; Yuanquan Chen (Applied Soil Ecology, 2024)

Nitrifying and denitrifying microbes exhibit distinct community structure and activity responses to different crop rotation systems in subtropical paddy soils - Huifang Xu; Ke Li; Rong Sheng; Hongling Qin; Yi Liu; Anlei Chen; Haijun Hou; Baoli Zhu; Wenxue Wei; Wenzhao Zhang (Applied Soil Ecology, 2024)

Impacts of long-term organic fertilization on metabolomic and metagenomic characteristics of soils in a greenhouse vegetable production system - Yun-Cheng Hsieh; Chun-Han Su; Tzung-Han Lee; Lean-Teik Ng (Applied Soil Ecology, 2024)