ISME Journal

Article	Citations
Environmental stress destabilizes microbial networks	475
Erosion reduces soil microbial diversity, network complexity and multifunctionality	296
Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment	218
Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease	208
Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes	204
Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt	163
Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens	154
Ecology and evolution of antimicrobial resistance in bacterial communities	143
Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation	142
Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer	135
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life	135
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions	131
Open challenges for microbial network construction and analysis	122
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification	121
Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species	117
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere	115
Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation	114
Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress	110
Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation	109
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities	109
Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system	108
Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress	106
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity	101
Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers	98
Air pollution could drive global dissemination of antibiotic resistance genes	98

A network approach to elucidate and prioritize microbial dark matter in microbial communities	97
Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant	96
Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome	94
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities	94
Prokaryotic taxonomy and nomenclature in the age of big sequence data	92
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem	92
Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi	91
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen	90
Engineering rhizobacteria for sustainable agriculture	90
Life-history strategies of soil microbial communities in an arid ecosystem	86
Achieving similar root microbiota composition in neighbouring plants through airborne signalling	85
Unraveling negative biotic interactions determining soil microbial community assembly and functioning	85
Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress	83
Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea	82
Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation	80
“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems	80
Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype	77
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters	77
Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy	77
A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea	77
The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?	76
Drought and plant litter chemistry alter microbial gene expression and metabolite production	76
Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation	75
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria	74
Interspecies bacterial competition regulates community assembly in the C. elegans intestine	74
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups	72
Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping	72
Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses	71
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika	70
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis	69
A genomic view of the microbiome of coral reef demosponges	68
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms	67
Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline	67
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo	66
The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization	66
Solutions in microbiome engineering: prioritizing barriers to organism establishment	66
Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes	65
In vitro interaction network of a synthetic gut bacterial community	65
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions	65
Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization	65
Social networks strongly predict the gut microbiota of wild mice	65
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe	65
Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes	65
Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal	64
Fecal filtrate transplantation protects against necrotizing enterocolitis	64
Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates	63
Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs	63
Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea	62
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation	62
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria	62

CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa	61
Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes	61
A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases	60
Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene	60
Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids	60
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health	60
Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome	60
Selective carbon sources influence the end products of microbial nitrate respiration	60
Diversity and distribution of viruses inhabiting the deepest ocean on Earth	59
Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles	59
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations	59
Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments	58
Intra-colony channels in E. coli function as a nutrient uptake system	56
Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves	55
Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira	55
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient	53
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes	53
Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients	53
Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt	53
Fungal communities decline with urbanization—more in air than in soil	53
Microbial carrying capacity and carbon biomass of plastic marine debris	52
Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations	52
Intracellular symbionts drive sex ratio in the whitefly by facilitating fertilization and provisioning of B vitamins	52
Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi	52
Benchmarking microbial growth rate predictions from metagenomes	51
Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome	51
A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities	51
Host specificity of microbiome assembly and its fitness effects in phytoplankton	50
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling	50
Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogen Erwinia amylovora	50
Microbial storage and its implications for soil ecology	50
Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process	50
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	50
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber	49
A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus	49
Bayesian modeling reveals host genetics associated with rumen microbiota jointly influence methane emission in dairy cows	48
Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist	48
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome	48
Decline in symbiont-dependent host detoxification metabolism contributes to increased insecticide susceptibility of insects under high temperature	47
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents	47
Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog	47
Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool	47
Nitrogen cycling and microbial cooperation in the terrestrial subsurface	46
The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity	46
The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities	46
Inter-species interactions alter antibiotic efficacy in bacterial communities	46
T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer	46
A phylogenetically novel cyanobacterium most closely related to Gloeobacter	46
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing	45
Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection	45
Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity	45
Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments	45
A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus	45
Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival	44
Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage	44
Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium	44
Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation	44
Ecological succession in the vaginal microbiota during pregnancy and birth	44
Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom	43
Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought	43
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips	43
Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria	42
Ecological dynamics of the gut microbiome in response to dietary fiber	42
Light exposure mediates circadian rhythms of rhizosphere microbial communities	42
Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease	42
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide	42
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments	41
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat	41
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway	41
Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture	41
Global distribution of a chlorophyll f cyanobacterial marker	41
Seasonal niche differentiation among closely related marine bacteria	41
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment	41
Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa	41
The rates of global bacterial and archaeal dispersal	41
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil	41
Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity	40
Direct quantification of ecological drift at the population level in synthetic bacterial communities	40
Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment	40
A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances	40

Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer	40
Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits	40
New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods	39
Quorum sensing controls persistence, resuscitation, and virulence of Legionella subpopulations in biofilms	39
A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth	39
Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes	39
Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens	39
Diverse coral reef invertebrates exhibit patterns of phylosymbiosis	39
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean	38
Viral lysis modifies seasonal phytoplankton dynamics and carbon flow in the Southern Ocean	38
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning	38
The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance	38
Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity	37
Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations	37
Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire	37
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle	37
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations	37
Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation	36
Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition	36
Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides	36
Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology	36
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity	36
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline	36
Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments	35
Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria	35
Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes	35
Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment	35
Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential	34
Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies	34
The occurrence and ecology of microbial chain elongation of carboxylates in soils	34
Community context matters for bacteria-phage ecology and evolution	34
Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues	34
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds	34
The saccharibacterium TM7x elicits differential responses across its host range	33
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	33
Anthropogenic dissolved organic carbon and marine microbiomes	33
Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance	33
Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness	33
Division of functional roles for termite gut protists revealed by single-cell transcriptomes	33
Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers	32
Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy	32
Anaerobic metabolism of Foraminifera thriving below the seafloor	32
Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms	32
Life history strategies among soil bacteria—dichotomy for few, continuum for many	32
Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions	32
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean	32
Highly diverse flavobacterial phages isolated from North Sea spring blooms	31
Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants	31
Locally adapted gut microbiomes mediate host stress tolerance	31
Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling	31
Network structure of resource use and niche overlap within the endophytic microbiome	31
Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function	31
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients	31
Unexpected diversity among small-scale sample replicates of defined plant root compartments	31
Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities	31
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones	31
Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium	31
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean	30
Phages in the infant gut: a framework for virome development during early life	30
Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria	30
Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut	30
Lichen-like association of Chlamydomonas reinhardtii and Aspergillus nidulans protects algal cells from bacteria	30
Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions	30
Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments	29
Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees	29
Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages	29
Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms	29
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets	29
Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation	29
Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments	29
Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning	29
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae	29
Biofilm matrix disrupts nematode motility and predatory behavior	29
Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef	29
Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas	28
Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages	28
Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge)	28
Predicting spatial patterns of soil bacteria under current and future environmental conditions	28
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome	28
Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean	28
The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate	28
Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus	28
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system	28
Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene	27
Soil minerals affect taxon-specific bacterial growth	27
Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem	27
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development	27
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community	27
Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone	27
Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures	27
Wildland fire as an atmospheric source of viable microbial aerosols and biological ice nucleating particles	27
Pervasive prophage recombination occurs during evolution of spore-forming Bacilli	27
Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape	27
Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics	27
A spore quality–quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis	27