ISME Journal

Article	Citations
Environmental stress destabilizes microbial networks	664
Erosion reduces soil microbial diversity, network complexity and multifunctionality	412
Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes	277
Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens	206
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions	198
Ecology and evolution of antimicrobial resistance in bacterial communities	182
Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer	172
Open challenges for microbial network construction and analysis	163
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life	157
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere	146
Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress	144
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification	143
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity	142
Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress	139
Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species	136
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities	129
Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi	125
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem	124
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities	123
Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome	122
Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant	121
Unraveling negative biotic interactions determining soil microbial community assembly and functioning	116
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen	112
Engineering rhizobacteria for sustainable agriculture	112
Prokaryotic taxonomy and nomenclature in the age of big sequence data	111

“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems	107
Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation	106
Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation	102
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms	100
Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome	100
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters	97
The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization	96
The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?	94
Solutions in microbiome engineering: prioritizing barriers to organism establishment	93
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health	92
Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress	89
Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates	88
Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype	87
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria	87
Fecal filtrate transplantation protects against necrotizing enterocolitis	87
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation	84
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes	84
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria	83
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika	83
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe	83
Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization	82
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups	81
Interspecies bacterial competition regulates community assembly in the C. elegans intestine	80
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis	79
Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes	79
In vitro interaction network of a synthetic gut bacterial community	77
Social networks strongly predict the gut microbiota of wild mice	77
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	77
Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs	75
Nitrogen cycling and microbial cooperation in the terrestrial subsurface	74
A genomic view of the microbiome of coral reef demosponges	73
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions	73
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa	73
Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene	72
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo	72
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations	68
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome	68
Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles	68
Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients	67
Diversity and distribution of viruses inhabiting the deepest ocean on Earth	67
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing	65
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling	64
Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes	63
A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus	62
Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist	61
Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt	60
Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome	59
Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool	59
Ecological dynamics of the gut microbiome in response to dietary fiber	59
Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium	58

Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process	58
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient	58
Decline in symbiont-dependent host detoxification metabolism contributes to increased insecticide susceptibility of insects under high temperature	57
Seasonal niche differentiation among closely related marine bacteria	56
Microbial storage and its implications for soil ecology	56
Inter-species interactions alter antibiotic efficacy in bacterial communities	56
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide	56
Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity	54
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides	54
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents	54
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments	54
Life history strategies among soil bacteria—dichotomy for few, continuum for many	54
Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments	53
Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom	53
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle	53
Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity	52
Light exposure mediates circadian rhythms of rhizosphere microbial communities	52
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips	50
Viral lysis modifies seasonal phytoplankton dynamics and carbon flow in the Southern Ocean	50
Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture	50
T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer	50
Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer	50
The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance	49
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations	48
Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants	48
The rates of global bacterial and archaeal dispersal	48
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment	48
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil	46
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway	45
Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition	45
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean	44
Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations	43
Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria	43
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning	43
Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments	42
Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms	42
Community context matters for bacteria-phage ecology and evolution	42
Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling	42
Highly diverse flavobacterial phages isolated from North Sea spring blooms	41
Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages	41
Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment	41
Phages in the infant gut: a framework for virome development during early life	41
Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology	40
Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation	40
Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons	40
Locally adapted gut microbiomes mediate host stress tolerance	40
Predicting spatial patterns of soil bacteria under current and future environmental conditions	40
Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential	39
Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues	39
Microbial keystone taxa drive succession of plant residue chemistry	39
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets	39
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	39
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae	38
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds	38
Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions	38
Network structure of resource use and niche overlap within the endophytic microbiome	38
Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments	38
Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers	38
The occurrence and ecology of microbial chain elongation of carboxylates in soils	38
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones	38
Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments	37
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean	37
Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications	37
Unexpected diversity among small-scale sample replicates of defined plant root compartments	37
Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants	37
Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network	37
Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance	37
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean	36
Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium	36
Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function	36
Global and seasonal variation of marine phosphonate metabolism	36
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting	36
Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean	35
Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees	35
Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions	35
Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community	35
Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks	35
Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor	35
Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities	35
Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness	34

Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms	34
Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge)	33
Salt tolerance-based niche differentiation of soil ammonia oxidizers	33
Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas	33
Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages	33
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients	33
Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria	33
Nitrification and beyond: metabolic versatility of ammonia oxidising archaea	33
Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene	33
Soil minerals affect taxon-specific bacterial growth	33
Microbially facilitated nitrogen cycling in tropical corals	33
Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem	33
Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions	33
Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut	33
Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems	32
Predator-induced defence in a dinoflagellate generates benefits without direct costs	32
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development	32
Bacterial controlled mitigation of dysbiosis in a seaweed disease	32
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system	32
Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning	32
Pervasive prophage recombination occurs during evolution of spore-forming Bacilli	32
Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef	32
Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism	32
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages	31
Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis	31
Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone	31
In-depth analysis of N2O fluxes in tropical forest soils of the Congo Basin combining isotope and functional gene analysis	31
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome	31
Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics	31
Evolutionary stasis of a deep subsurface microbial lineage	31
The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution	30
Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties	30
Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures	30
Experimental identification and in silico prediction of bacterivory in green algae	30
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi	30
Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland	30
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley	30
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins	30
Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus	29
Fungal phytopathogen modulates plant and insect responses to promote its dissemination	29
The effect of Quorum sensing inhibitors on the evolution of CRISPR-based phage immunity in Pseudomonas aeruginosa	29
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts	29
Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community	29
Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing	29
Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis	29
Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes	29
A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen	29
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits	28
Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments	28
Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes	28
Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways	28
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily	28
Extreme summers impact cropland and grassland soil microbiomes	28
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community	28
Microbial drivers of methane emissions from unrestored industrial salt ponds	28
Methane-dependent selenate reduction by a bacterial consortium	28
Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks	28
Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)	27
Founder cell configuration drives competitive outcome within colony biofilms	27
Morphological complexity affects the diversity of marine microbiomes	27
Plant-associated fungi support bacterial resilience following water limitation	27
Causes and consequences of pattern diversification in a spatially self-organizing microbial community	27
Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate	27
Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria	27
Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria	27
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	27
Functional mutants of Azospirillum brasilense elicit beneficial physiological and metabolic responses in Zea mays contributing to increased host iron assimilation	27
Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape	27
Decreased efficacy of antimicrobial agents in a polymicrobial environment	27
Biofilm matrix cloaks bacterial quorum sensing chemoattractants from predator detection	27
Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock	27
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes	27
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	27
Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater	27
Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility	26
Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions	26
Reductive dissolution of pyrite by methanogenic archaea	26
Ecologically coherent population structure of uncultivated bacterioplankton	26
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures	26
Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments	26
Pantothenate mediates the coordination of whitefly and symbiont fitness	26
Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world’s oceans	26
Chemolithoautotroph distributions across the subsurface of a convergent margin	26
Sinking Trichodesmium fixes nitrogen in the dark ocean	26
Dissimilatory nitrate reduction by a freshwater cable bacterium	26
Microbial N2O consumption in and above marine N2O production hotspots	26
Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean	26
Decreased thermal niche breadth as a trade-off of antibiotic resistance	26
Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress	26
Transitions in symbiosis: evidence for environmental acquisition and social transmission within a clade of heritable symbionts	26
Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals	25
Metagenome-derived virus-microbe ratios across ecosystems	25
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	25
Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels	25
Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling	25