ISME Journal

Article	Citations
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	596
Aminolipids in bacterial membranes and the natural environment	209
Inositol phosphates as an overlooked phosphorous source in marine ecosystems	189
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	183
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	171
Land use drives drug resistance in an airborne human fungal pathogen	166
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	134
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	126
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	123
Rapid adaptive evolution of oxylipin-based chemical defense against algicidal bacteria in a bloom-forming diatom	120
Co-cultivation rescues suicidal Paenibacillus amylolyticus swarms	111
Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome	111
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	106
Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces	100
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	96
Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance	94
Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux	93
Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits	93
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	92
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	88
Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress	88
Standardized and batch effect–independent technologies enable global collaboration in microbiome research	87
Architectural Intelligence: Toward a Spatial Framework for Interpreting Microbiome-Associated Human Disease.	86
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	85
Distinct transcriptomic strategies underlie differential heat tolerance in Symbiodiniaceae symbionts	84

Deterministic Recruitment Limitation during Soybean Pod Development Shapes Seed-Transmitted Microbiota Assembly	83
Photosynthesis-driven interactions in the phycosphere enhance bacterial extracellular superoxide production	82
Endosymbionts modulate virus effects on aphid-plant interactions	82
Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialog and adaptive strategies with the fungus	81
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	80
Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans	80
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	78
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	77
Understanding prokaryotic adaptation through advanced DNA methylation detection techniques	76
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	76
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	75
Drug delivery dynamics dictate evolution of bacterial antibiotic responses	72
Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistillata	68
Symbiont diversity within Loripes orbiculatus and the case for multiple hosts	68
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	67
Rapid resistance evolution against phage cocktails	67
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	67
Colonization history of snow algae on Hawai‘i island	66
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	66
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	65
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	64
Genetic and species rearrangements in microbial consortia impact biodegradation potential	64
Transportome remodeling of a symbiotic microalga inside a planktonic host	64
Upregulated jasmonate signaling shifts Arabidopsis microbiota interactions and stress adaptations through a positive feedback loop	63
Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts	62
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	61
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	61
Hot moment of N2O emissions in seasonally frozen peatlands	60
Metabolic potential of Nitrososphaera-associated clades	60
Phyllosphere symbiont promotes plant growth through ACC deaminase production	59
Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	58
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	57
Bacterial extracellular vesicles exhibit distinct functional potential across biogeographic provinces of the South Pacific Ocean	56
Gut microbiota contribute to variations in honey bee foraging intensity	55
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	55
Bacterial type VI secretion system helps prevent cheating in microbial communities	55
Celebrating 15 years of The ISME Journal	54
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	54
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	53
Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales	53
Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems	53
Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific	53
Microbial cross-feeding stabilized by segregation of a dependent mutant from its independent ancestor	52
Growth promotion of milk-associated Candida zeylanoides by a cyclic lipopeptide produced by Pseudomonas	52
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	51
Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science	51
Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis	51
Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin	51
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	50
Mixed heavy metal stress induces global iron starvation response	49

Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature	49
Field strains of the unicellular alga Chlamydomonas reinhardtii exhibit multicellular characteristics that shape their interactions	48
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	48
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	47
Dietary protein source alters gut microbiota composition and function	46
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	46
Chlorine redox chemistry is widespread in microbiology	46
Metabolic labour division trade-offs in denitrifying microbiomes	45
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	45
Influence of cell-cell distance on the ecology and evolution of microbial communities	45
Microbial solutions must be deployed against climate catastrophe	45
Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods	44
Tailless and filamentous prophages are predominant in marine Vibrio	44
Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont	44
Microbiome-mediated polyphosphate accumulation enhances the resilience of sponge holobionts to future climate scenarios	44
Impact of diazotrophs on marine food webs and the biological carbon pump: progress and remaining challenges	44
Diversity and evolution of prokaryotic viral lytic proteins	44
Latitudinal diversity in circadian and light-sensing genes in an ecologically vital group of marine picoeukaryote algae	44
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	43
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	43
Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri	43
Unexplored diversity and ecological functions of transposable phages	42
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	41
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	41
Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction	41
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	40
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	40
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants	40
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	40
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	40
Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept	40
Endofungal bacteria as hidden facilitators of biotic interactions	39
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	39
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	39
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	39
Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	39
Extreme summers impact cropland and grassland soil microbiomes	39
Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide	39
Microbial community composition predicts bacterial production across ocean ecosystems	38
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	38
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	38
Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges	37
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	37
Specialized digestive mechanism for an insect-bacterium gut symbiosis	37
Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance	37
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	37
Intra-colony light gradients drive variation in coral symbiont morphology and carbon storage	36
Metabolic interactions underlying phyllosphere microbiota assembly	36
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	36
Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont	36
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria	36
Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean	36
Bridging ecological assembly process and community stability upon bacterial invasions	36
Transglobal spread of an ecologically relevant sea urchin parasite	35
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	35
The atmosphere: a transport medium or an active microbial ecosystem?	35
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	35
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus–bacterial coexistence	35
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	35
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	35
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	35
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	34
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	34
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	34
Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases	34
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	34
Pathogen-pathogen interactions during co-infections	33
DNA virus–host patterns in lake and marine environments over the last glacial cycle	33
Bioplastic biodegradability shapes microbial communities in a coastal brackish environment	33
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	33
Biofilm lifestyle across different lineages of ammonia-oxidizing archaea	33
Acidifying bacteria inhibit pathogenic bacteria more strongly with increasing glucose	32
Oxylipin-mediated metabolic signatures of symbiosis homeostasis and thermal stress in a model sea anemone	32
Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome	32
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	32
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	32
Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics	32
Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer	31
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	31
Cooperative microbial metabolism enhances tryptophan-mediated insecticide detoxification in the fall armyworm	31

Spatio-temporal pattern formation of living organisms at the edge of chaos	31
Endozoicomonas acroporae enhances coral thermal resilience through host–microbe coordination	31
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly	31
Early transcription factor activation distinguishes symbiotic from non-symbiotic bacteria during microbiome processing in a sponge	31
Dysbiotic gut fungi exacerbate Klebsiella pneumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation	31
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	31
Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems	31
Microbial dispersal into surface soil is limited on a meter scale	31
Host community activity, but not always composition, explains viral biogeography in bulk and rhizosphere soils over a tomato growing season	30
Global terrestrial distribution of N2O-reducing Acidobacteriota members	30
Temperature alters interactions and keystone taxa in the marine microbiome	30
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	30
Altered rhizosphere microbiome composition associated with B-subgenome cultivars of diploid and triploid banana plants	30
Engineering plant holobionts for climate-resilient agriculture	30
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	29
Polyphenol rewiring of the microbiome reduces methane emissions	29
Correction to 29 articles due to inaccurate manuscript submission dates	29
Kinetic plasticity of nitrite-oxidizing bacteria containing cytoplasmic nitrite oxidoreductase	29
Sulfide stress tolerance as a controller of methane production in temperate wetlands	29
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes	29
High niche specificity and host genetic diversity of groundwater viruses	29
Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms	29
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	28
Correction to: Horizontal transmission of heat-evolved microalgal symbionts in adult corals	28
Predator–prey dynamics of Vibrio cholerae on chitin suggest an alternative mode of biofilm formation in marine snow conditions	28
Trophic modulation of endophytes by rhizosphere protists	28
Taeniasis impacts human gut microbiome composition and function	28
Hydrological regime of a continental river system predicts bacterial macroecological patterns	28
Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis	28
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	27
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	27
Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils	27
Siderophores and competition for iron govern myxobacterial predation dynamics	27
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	27
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	27
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	27
Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	27
Host-specific viral predation network on coral reefs	27
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	27
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	27
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	27
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	26
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	26
Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host	26
Carbon metabolic versatility underpins Bathyarchaeia ecological significance across the global deep subsurface	26
Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments	26
Accumulation of antimicrobial resistance genes in wild chimpanzees	26
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	25
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments	25
Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice	25
Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus	25
Structured interactions explain the absence of keystone species in synthetic microcosms	25
Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection	25
Advancing microbial ecology, microbiomes, and One Health in Africa: from regional initiatives to pan-African flagship programs	25
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	25
Spatial sensing as a strategy for public goods regulation by gut microbes	25
Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments	25
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	25
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	25
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	25
Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia	25
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes	25
Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils	24
Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former	24
High resolution functional analysis and community structure of photogranules	24
Collective protection against the type VI secretion system in bacteria	24
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response	24
Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR–NF-κB axis	24
Two-step localization driven by peptidoglycan hydrolase in interbacterial predation	24
Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group	24
Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning	24
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	24
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	23
Function-based selection of synthetic communities enables mechanistic microbiome studies	23
Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail	23
Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage	23
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids	23
Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions	23
Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer	23
Correction: Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia	23
Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean	23
Seed-mediated vertical transmission of Pantoea core endophytes	23
Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene	23
Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi	23
Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors	23
Milk IgA promotes symbionts and limits pathobionts in the early life gut	22
Identification and cultivation of anaerobic bacterial scavengers of dead cells	22
AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential	22
Net rate of lateral gene transfer in marine prokaryoplankton	22
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts	22
Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia	22
Polyhydroxybutyrate production by freshwater SAR11 (LD12)	22
Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming	22
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms	22
Sensitivity of microbial spatial self-organization to surface friction depends on metabolic interactions	22