ISME Journal

Article	Citations
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	257
Aminolipids in bacterial membranes and the natural environment	182
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	138
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	133
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	129
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	126
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	123
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides	116
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	109
Inositol phosphates as an overlooked phosphorous source in marine ecosystems	107
Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress	106
Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans	106
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	97
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	90
Understanding prokaryotic adaptation through advanced DNA methylation detection techniques	89
Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux	86
Co-cultivation rescues suicidal Paenibacillus amylolyticus swarms	85
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	85
Endosymbionts modulate virus effects on aphid-plant interactions	85
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes	84
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	81
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	81
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	79
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system	78
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	78

Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms	75
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	74
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	73
Colonization history of snow algae on Hawai‘i island	72
Genetic and species rearrangements in microbial consortia impact biodegradation potential	68
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	65
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	64
Transportome remodeling of a symbiotic microalga inside a planktonic host	64
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	63
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	63
Drug delivery dynamics dictate evolution of bacterial antibiotic responses	63
Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	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
Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean	59
Catabolic protein degradation in marine sediments confined to distinct archaea	59
Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistillata	57
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	57
Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability	57
Metabolic potential of Nitrososphaera-associated clades	56
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	55
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	55
Phyllosphere symbiont promotes plant growth through ACC deaminase production	54
Hot moment of N2O emissions in seasonally frozen peatlands	54
Gut microbiota contribute to variations in honey bee foraging intensity	54
Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater	54
Microbial cross-feeding stabilized by segregation of a dependent mutant from its independent ancestor	53
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	53
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	53
Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems	52
Celebrating 15 years of The ISME Journal	51
Dietary protein source alters gut microbiota composition and function	50
Mixed heavy metal stress induces global iron starvation response	50
MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi	50
Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science	50
Chlorine redox chemistry is widespread in microbiology	49
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	49
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	49
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	49
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	49
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	49
Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods	48
Correction to: Ice nucleation in a Gram-positive bacterium isolated from precipitation depends on a polyketide synthase and non-ribosomal peptide synthetase	48
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	48
Metabolic labour division trade-offs in denitrifying microbiomes	48
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	47
Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction	47
Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism	47
Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri	47
Microbial solutions must be deployed against climate catastrophe	46

Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	46
Microbial community composition predicts bacterial production across ocean ecosystems	46
Diversity and Evolution of Prokaryotic Viral Lytic Proteins	46
Endofungal bacteria as hidden facilitators of biotic interactions	45
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	45
Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems	45
Unexplored diversity and ecological functions of transposable phages	45
Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria	45
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	45
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	45
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	44
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity	44
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	44
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	44
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	43
α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats	43
Tailless and filamentous prophages are predominant in marine Vibrio	43
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	43
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants	42
Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism	42
Extreme summers impact cropland and grassland soil microbiomes	42
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	41
Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide	41
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	40
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	40
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	40
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	40
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	40
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	40
Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks	40
Specialized digestive mechanism for an insect-bacterium gut symbiosis	39
Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont	38
Thermal stress triggers productive viral infection of a key coral reef symbiont	38
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	37
Transglobal spread of an ecologically relevant sea urchin parasite	37
Bridging ecological assembly process and community stability upon bacterial invasions	37
The atmosphere: a transport medium or an active microbial ecosystem?	37
Metabolic interactions underlying phyllosphere microbiota assembly	37
Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site	37
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	37
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	37
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	37
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	36
Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome	36
Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales	36
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	36
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	36
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria	36
Engineering plant holobionts for climate-resilient agriculture	36
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	36
Sulfide stress tolerance as a controller of methane production in temperate wetlands	35
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	35
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly	35
Biofilm lifestyle across different lineages of ammonia-oxidizing archaea	35
Mechanisms underlying interactions between two abundant oral commensal bacteria	35
Pathogen-pathogen interactions during co-infections	35
Altered rhizosphere microbiome composition associated with B-subgenome cultivars of diploid and triploid banana plants	35
Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms	35
High niche specificity and host genetic diversity of groundwater viruses	35
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily	34
Dysbiotic gut fungi exacerbate Klebsiella pneumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation	34
Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics	34
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus–bacterial coexistence	34
Spatio-temporal pattern formation of living organisms at the edge of chaos	34
Polyphenol rewiring of the microbiome reduces methane emissions	34
Microbial dispersal into surface soil is limited on a meter scale	34
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	34
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	33
Cooperative Microbial Metabolism Enhances Tryptophan-Mediated Insecticide Detoxification in the Fall Armyworm	33
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	33
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	32
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	32
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	32
Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils	31
Trophic modulation of endophytes by rhizosphere protists	31
Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	31
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	31
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	31
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	31
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes	31

Correction to 29 articles due to inaccurate manuscript submission dates	30
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	30
Decreased efficacy of antimicrobial agents in a polymicrobial environment	30
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	30
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits	30
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	30
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	30
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	30
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	29
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	29
Siderophores and competition for iron govern myxobacterial predation dynamics	29
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	29
Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis	29
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	29
Host-specific viral predation network on coral reefs	28
Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host	28
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	28
Taeniasis impacts human gut microbiome composition and function	27
Seed-mediated vertical transmission of Pantoea core endophytes	27
Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former	27
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	27
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response	27
Function-based selection of synthetic communities enables mechanistic microbiome studies	27
Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments	27
Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia	27
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments	26
Correction: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria	26
Structured interactions explain the absence of keystone species in synthetic microcosms	26
Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning	26
Two-step localization driven by peptidoglycan hydrolase in interbacterial predation	26
Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice	26
Spatial sensing as a strategy for public goods regulation by gut microbes	25
Collective protection against the type VI secretion system in bacteria	25
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	25
Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group	25
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	25
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids	25
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	25
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	25
Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean	25
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	25
Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus	25
Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool	25
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle	24
Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail	24
High resolution functional analysis and community structure of photogranules	24
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes	24
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	24
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	24
Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins	24
Correction to: Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil	24
Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria	23
Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas diversity	23
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts	23
Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion	23
Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation	23
Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert	23
Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria	23
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean	23
Nitrogen availability shapes evolution of phage resistance in cyanobacteria	23
Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi	22
Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti	22
Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions	22
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide	22
Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae	22
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression	22
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome	22
Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean	22
Ecological and evolutionary responses of earthworm holobionts to environmental changes	22
Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens	22
Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis	22
Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies	22
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations	22
Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders	22
Polyhydroxybutyrate production by freshwater SAR11 (LD12)	22
Net rate of lateral gene transfer in marine prokaryoplankton	21
Leveraging genome-scale metabolic models to understand aerobic methanotrophs	21
Competition for iron shapes metabolic antagonism betweenBacillus subtilisandPseudomonas marginalis	21
Correction: Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia	21
Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer	21
Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming	21
Gut microbiota facilitate adaptation of invasive moths to new host plants	21
Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms	21
Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation	20
SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen	20
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population	20
Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining–impacted habitats	20
Genome reduction occurred in early Prochlorococcus with an unusually low effective population size	20
SeqCode in the golden age of prokaryotic systematics	20
Identification and cultivation of anaerobic bacterial scavengers of dead cells	20
Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene	20
Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae	20
Correction to: Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus?	20
Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage	20
Predatory protists impact plant performance by promoting plant growth-promoting rhizobacterial consortia	20