ISME Journal

Article	Citations
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	489
Understanding prokaryotic adaptation through advanced DNA methylation detection techniques	179
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	174
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	163
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	136
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	130
Endosymbionts modulate virus effects on aphid-plant interactions	130
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	128
Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance	123
Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits	119
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	115
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	114
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	113
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	106
Land use drives drug resistance in an airborne human fungal pathogen	103
Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux	101
Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces	94
Inositol phosphates as an overlooked phosphorous source in marine ecosystems	88
Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress	88
Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides	86
Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialog and adaptive strategies with the fungus	86
Distinct transcriptomic strategies underlie differential heat tolerance in Symbiodiniaceae symbionts	83
Co-cultivation rescues suicidal Paenibacillus amylolyticus swarms	82
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes	82
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	82

Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	80
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	80
Aminolipids in bacterial membranes and the natural environment	79
Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans	76
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	76
Colonization history of snow algae on Hawai‘i island	74
Drug delivery dynamics dictate evolution of bacterial antibiotic responses	73
Genetic and species rearrangements in microbial consortia impact biodegradation potential	73
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	72
Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	72
Rapid resistance evolution against phage cocktails	71
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	70
Transportome remodeling of a symbiotic microalga inside a planktonic host	70
Metabolic potential of Nitrososphaera-associated clades	67
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	66
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	66
Symbiont diversity within Loripes orbiculatus and the case for multiple hosts	66
Hot moment of N2O emissions in seasonally frozen peatlands	66
Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts	65
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	65
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	64
Gut microbiota contribute to variations in honey bee foraging intensity	63
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	63
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	63
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	62
Bacterial type VI secretion system helps prevent cheating in microbial communities	61
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	61
Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistillata	60
Phyllosphere symbiont promotes plant growth through ACC deaminase production	60
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	60
Mixed heavy metal stress induces global iron starvation response	59
MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi	59
Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature	57
Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales	56
Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems	56
Celebrating 15 years of The ISME Journal	56
Microbial cross-feeding stabilized by segregation of a dependent mutant from its independent ancestor	55
Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science	55
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	54
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	53
Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis	53
Metabolic labour division trade-offs in denitrifying microbiomes	52
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	52
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	51
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	50
Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific	50
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	49
Growth promotion of milk-associated Candida zeylanoides by a cyclic lipopeptide produced by Pseudomonas	49
Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin	49
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	48

Chlorine redox chemistry is widespread in microbiology	48
Dietary protein source alters gut microbiota composition and function	47
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	47
Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods	47
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	47
Microbial solutions must be deployed against climate catastrophe	47
Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri	46
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	46
Tailless and filamentous prophages are predominant in marine Vibrio	46
Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont	46
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	45
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	45
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	45
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	44
Unexplored diversity and ecological functions of transposable phages	44
Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide	44
Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems	44
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	44
α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats	43
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	42
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	42
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	42
Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction	41
Microbial community composition predicts bacterial production across ocean ecosystems	41
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	41
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	41
Latitudinal diversity in circadian and light-sensing genes in an ecologically vital group of marine picoeukaryote algae	41
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	41
Extreme summers impact cropland and grassland soil microbiomes	41
Endofungal bacteria as hidden facilitators of biotic interactions	40
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants	40
Impact of diazotrophs on marine food webs and the biological carbon pump: progress and remaining challenges	40
Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean	39
Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	39
Specialized digestive mechanism for an insect-bacterium gut symbiosis	39
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	39
The atmosphere: a transport medium or an active microbial ecosystem?	39
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	39
Diversity and evolution of prokaryotic viral lytic proteins	39
Intra-colony light gradients drive variation in coral symbiont morphology and carbon storage	38
Bridging ecological assembly process and community stability upon bacterial invasions	38
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	38
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	37
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	37
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	37
Metabolic interactions underlying phyllosphere microbiota assembly	37
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	37
Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont	37
Transglobal spread of an ecologically relevant sea urchin parasite	37
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria	36
Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges	36
Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance	36
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	35
Spatio-temporal pattern formation of living organisms at the edge of chaos	35
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	35
Altered rhizosphere microbiome composition associated with B-subgenome cultivars of diploid and triploid banana plants	35
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	35
Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms	35
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly	35
High niche specificity and host genetic diversity of groundwater viruses	34
Polyphenol rewiring of the microbiome reduces methane emissions	33
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	33
Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer	33
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	33
Bioplastic biodegradability shapes microbial communities in a coastal brackish environment	33
Cooperative microbial metabolism enhances tryptophan-mediated insecticide detoxification in the fall armyworm	33
Biofilm lifestyle across different lineages of ammonia-oxidizing archaea	32
Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics	32
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	32
Microbial dispersal into surface soil is limited on a meter scale	32
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	31
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	31
DNA virus–host patterns in lake and marine environments over the last glacial cycle	31
Sulfide stress tolerance as a controller of methane production in temperate wetlands	31
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	31
Dysbiotic gut fungi exacerbate Klebsiella pneumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation	31
Global terrestrial distribution of N2O-reducing Acidobacteriota members	31
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	31
Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome	31
Pathogen-pathogen interactions during co-infections	31

Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases	31
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus–bacterial coexistence	30
Carbon metabolic versatility underpins Bathyarchaeia ecological significance across the global deep subsurface	30
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	30
Temperature alters interactions and keystone taxa in the marine microbiome	30
Taeniasis impacts human gut microbiome composition and function	30
Kinetic plasticity of nitrite-oxidizing bacteria containing cytoplasmic nitrite oxidoreductase	30
Engineering plant holobionts for climate-resilient agriculture	30
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	30
Hydrological regime of a continental river system predicts bacterial macroecological patterns	29
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	29
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	29
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	29
Correction to: Horizontal transmission of heat-evolved microalgal symbionts in adult corals	29
Predator-prey dynamics of Vibrio cholerae on chitin suggest an alternative mode of biofilm formation in marine snow conditions	29
Host-specific viral predation network on coral reefs	29
Correction to 29 articles due to inaccurate manuscript submission dates	28
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	28
Trophic modulation of endophytes by rhizosphere protists	28
Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis	28
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes	28
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	28
Siderophores and competition for iron govern myxobacterial predation dynamics	28
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	28
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	28
Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	28
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	28
Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host	27
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	27
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	27
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	27
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits	27
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	27
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	26
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	26
Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR–NF-κB axis	26
Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils	26
Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils	26
Seed-mediated vertical transmission of Pantoea core endophytes	26
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes	26
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	26
Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection	26
Structured interactions explain the absence of keystone species in synthetic microcosms	26
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	25
Spatial sensing as a strategy for public goods regulation by gut microbes	25
Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former	25
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids	25
Function-based selection of synthetic communities enables mechanistic microbiome studies	25
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	25
Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus	25
High resolution functional analysis and community structure of photogranules	25
Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia	25
Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning	25
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response	25
Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice	24
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments	24
Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments	24
Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming	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
Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis	24
Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors	24
Collective protection against the type VI secretion system in bacteria	24
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	24
Correction: Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia	24
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	24
Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion	23
Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail	23
Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene	23
Identification and cultivation of anaerobic bacterial scavengers of dead cells	23
Leveraging genome-scale metabolic models to understand aerobic methanotrophs	23
Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions	23
Nitrogen availability shapes evolution of phage resistance in cyanobacteria	23
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression	23
Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean	23
Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies	23
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population	23
Milk IgA promotes symbionts and limits pathobionts in the early life gut	23
Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage	23
Polyhydroxybutyrate production by freshwater SAR11 (LD12)	23
Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert	23
Net rate of lateral gene transfer in marine prokaryoplankton	23
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts	23
Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria	22
Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae	22
Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens	22
Sensitivity of microbial spatial self-organization to surface friction depends on metabolic interactions	22
Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas	22
Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi	22
Predatory protists impact plant performance by promoting plant growth-promoting rhizobacterial consortia	22
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms	22
Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti	22
Ecological and evolutionary responses of earthworm holobionts to environmental changes	22
Gut microbiota facilitate adaptation of invasive moths to new host plants	22
Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer	21