Natural microbial communities generally have complex compositions and unclear metabolic interactions, posing constraints on their applications. Clarifying these intricate interactions within microbial communities is challenging for traditional experiment‐based methods. Here, we developed a simulation‐based approach to design synthetic communities (SynComs) by simplifying complex microbial communities through metabolic modellin...

Radiation resistance in bacteria is a critical trait with implications for biotechnology, medicine and environmental science. Deinococcus species possess unique genomic features that enable their extraordinary survival in extreme environments. However, the diversity of radiation resistance mechanisms across bacteria remains poorly explored. Here, we analysed the genomic diversity and functional gene repertoire of Deinococcus a...

Viruses play essential roles in shaping the structure and function of microbial communities, including those inhabiting extreme environments. The Qaidam Basin is a unique Mars‐analog desert characterised by hyperaridity, oligotrophy and high soil salinity. We hypothesise that viruses contribute to microbial adaptability and biogeochemical cycling through virus‐host interactions in desert ecosystems. Here, we investigated viral...

Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai‐Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon ind...

Thaumarchaeota are predominant in oligotrophic habitats such as deserts and arid soils, but their adaptations to these arid conditions are not well understood. In this study, we assembled 23 Thaumarchaeota genomes from arid and semi‐arid soils collected from the Inner Mongolia Steppe and the Qinghai‐Tibet Plateau. Using a comparative genomics approach, integrated with 614 Thaumarchaeota genomes from public databases, we identi...

Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil–plant continuums. However, the drivers of community structure, assembly mechanisms, co‐occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associate...

Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi‐functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal‐dynamics of antibiotic res...

The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co‐occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east‐central China. At higher pH sites, the taxonomic co‐occurrence network of...

Saline springs within the Illinois Basin result from the discharge of deep‐seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communiti...

Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae . In this study, we reveal that the global regulatory protein RsmA3 from the RetS‐Gac/Rsm signalling pathway modulates RpoS in the early‐log growth phase in the P . syringae wild‐type strain MB03, thereby regulating oxidative tolerance to H 2 O 2 and ultimately affecting pathogenicity to the host plant. Following increased H 2...

Understanding countrywide pathogen population structure and inter‐epidemic region spread is crucial for deciphering crop potential losses. Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease that affects worldwide wheat production, widespread in China, representing largest epidemic region globally. This study aimed to understand the population structure and migration route of P . striiformi...

Summary The mechanisms underlying microbial community dynamics and co‐occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co‐occurrence patterns in bacterial and fungal communities across a well‐established chronosequence of post‐mining lands spanning 54 years of recovery. Bacterial community structures...

Summary Filamentous prophages in Pseudomonas aeruginosa PAO1 are converted to superinfective phage virions during biofilm development. Superinfection exclusion is necessary for the development of resistance against superinfective phage virions in host cells. However, the molecular mechanisms underlying the exclusion of superinfective Pf phages are unknown. In this study, we found that filamentous prophage‐encoded structural pr...

Summary Common in fungal extracellular membrane (CFEM) domain is unique in fungal proteins and some of which contribute to iron acquisition in yeast. However, their roles in iron acquisition remain largely unknown in filamentous fungi. In this study, 12 CFEM‐containing proteins were bioinformatically identified in the filamentous entomopathogenic fungus Beauveria bassiana , and the roles of 11 genes were genetically characteri...

Summary The development and pathogenicity of the fungus Magnaporthe oryzae , the causal agent of destructive rice blast disease, require it to perceive external environmental signals. Opy2, an overproduction‐induced pheromone‐resistant protein 2, is a crucial protein for sensing external signals in Saccharomyces cerevisiae . However, the biological functions of the homologue of Opy2 in M. oryzae are unclear. In this study, we...

Summary Magnaporthe oryzae is an important plant pathogen that causes rice blast. Hse1 and Vps27 are components of ESCRT‐0 involved in the multivesicular body (MVB) sorting pathway and biogenesis. To date, the biological functions of ESCRT‐0 in M. oryzae have not been determined. In this study, we identified and characterized Hse1 and Vps27 in M. oryzae . Disruption of MoHse1 and MoVps27 caused pleiotropic defects in growth, c...

Summary Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate‐ or metal‐reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcos...

Summary Coronavirus disease 2019 (COVID‐19) pandemic has caused high number of infections and deaths of healthcare workers globally. Distribution and possible transmission route of SARS‐CoV‐2 in hospital environment should be clarified. We herein collected 431 environmental (391 surface and 40 air) samples in the intensive care unit (ICU) and general wards (GWs) of three hospitals in Wuhan, China from February 21 to March 4, 2...

Summary Termites are pivotal ecosystem engineers in tropical and subtropical habitats, where they construct massive nests (‘mounds’) that substantially modify soil properties and promote nutrient cycling. Yet, little is known about the roles of termite nesting activity in regulating the spread of antimicrobial resistance (AMR), one of the major Global Health challenges. Here, we conducted a large‐scale (> 1500 km) investigatio...

Summary Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large‐scale investigation of Eucalyptus phyllospheric micro...

Summary The clinical and environmental infections caused by AmpC β‐lactamases have been increasingly reported recently. In this study, we characterize the novel chromosome‐encoded AmpC β‐lactamase SFDC‐1 identified in Serratia fonticola strain R28, which was isolated from a rabbit raised on a farm in southern China. SFDC‐1 shared the highest amino acid identity of 79.6% with the functionally characterized AmpC β‐lactamase gene...

Summary Interspecific interaction happens frequently among bacterial species and can promote the colonization of polymicrobial community in various environments. However, it is not clear whether the intervention of antibiotics, which is a common therapeutic method for infectious disease, will influence the interacting dynamics of different pathogenic bacteria. By using the frequently co‐isolated bacteria Pseudomonas aeruginosa...

Summary Fungi can parasitize microalgae, exerting profound impacts on both the aquatic ecosystems and microalgal mass cultures. In this study, the unicellular green alga Haematococcus pluvialis and the blastocladialean fungus Paraphysoderma sedebokerense were used as a model system to address the mechanisms underlying the fungal parasitism on the algal host. High‐throughput metabolic assay indicated that P . sedebokerense can...

Summary FtsZ is a tubulin‐like GTPase that polymerizes to initiate the process of cell division in bacteria. Heterocysts are terminally differentiated cells of filamentous cyanobacteria that have lost the capacity for cell division and in which the ftsZ gene is downregulated. However, mechanisms of FtsZ regulation during heterocyst differentiation have been scarcely investigated. The patD gene is NtcA dependent and involved in...

Summary Termites are ubiquitous insects in tropical and subtropical habitats, and some of them construct massive nests (‘mounds’), which substantially promote substrate heterogeneity by altering soil properties. Yet, the role of termite nesting process in regulating the distribution and diversity of soil microbial communities remains poorly understood, which introduces uncertainty in predictions of ecosystem functions of termi...