ISME Journal

Article	Citations
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	567
Distinct transcriptomic strategies underlie differential heat tolerance in Symbiodiniaceae symbionts	201
Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialog and adaptive strategies with the fungus	185
Aminolipids in bacterial membranes and the natural environment	177
Inositol phosphates as an overlooked phosphorous source in marine ecosystems	156
Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits	153
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	140
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	132
Understanding prokaryotic adaptation through advanced DNA methylation detection techniques	130
Rapid adaptive evolution of oxylipin-based chemical defense against algicidal bacteria in a bloom-forming diatom	123
Co-cultivation rescues suicidal Paenibacillus amylolyticus swarms	120
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	114
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	108
Land use drives drug resistance in an airborne human fungal pathogen	107
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	99
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	98
Endosymbionts modulate virus effects on aphid-plant interactions	94
Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux	93
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	91
Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces	90
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	89
Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome	86
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	86
Standardized and batch effect–independent technologies enable global collaboration in microbiome research	83
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	83

Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	82
Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance	80
Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans	80
Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress	80
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	79
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	77
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	76
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	76
Drug delivery dynamics dictate evolution of bacterial antibiotic responses	73
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	73
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	73
Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	72
Rapid resistance evolution against phage cocktails	71
Bacterial type VI secretion system helps prevent cheating in microbial communities	71
Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts	67
Symbiont diversity within Loripes orbiculatus and the case for multiple hosts	66
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	66
Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistillata	66
Transportome remodeling of a symbiotic microalga inside a planktonic host	65
Hot moment of N2O emissions in seasonally frozen peatlands	65
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	65
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	64
Colonization history of snow algae on Hawai‘i island	64
Upregulated jasmonate signaling shifts Arabidopsis microbiota interactions and stress adaptations through a positive feedback loop	64
Metabolic potential of Nitrososphaera-associated clades	64
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	63
Phyllosphere symbiont promotes plant growth through ACC deaminase production	62
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	61
Genetic and species rearrangements in microbial consortia impact biodegradation potential	61
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	58
Celebrating 15 years of The ISME Journal	57
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	57
Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems	57
Gut microbiota contribute to variations in honey bee foraging intensity	57
MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi	56
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	55
Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis	55
Chlorine redox chemistry is widespread in microbiology	54
Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales	53
Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific	53
Dietary protein source alters gut microbiota composition and function	52
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	52
Growth promotion of milk-associated Candida zeylanoides by a cyclic lipopeptide produced by Pseudomonas	52
Microbial cross-feeding stabilized by segregation of a dependent mutant from its independent ancestor	51
Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin	51
Mixed heavy metal stress induces global iron starvation response	50
Metabolic labour division trade-offs in denitrifying microbiomes	50
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	49
Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science	49
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	49

Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature	49
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	48
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	48
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	48
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	47
Microbial solutions must be deployed against climate catastrophe	47
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	46
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	46
Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods	46
Impact of diazotrophs on marine food webs and the biological carbon pump: progress and remaining challenges	46
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	45
Tailless and filamentous prophages are predominant in marine Vibrio	44
Latitudinal diversity in circadian and light-sensing genes in an ecologically vital group of marine picoeukaryote algae	44
Microbiome-mediated polyphosphate accumulation enhances the resilience of sponge holobionts to future climate scenarios	44
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	44
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	44
Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide	44
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	43
Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri	43
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	43
Diversity and evolution of prokaryotic viral lytic proteins	43
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	43
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants	43
Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont	43
Endofungal bacteria as hidden facilitators of biotic interactions	43
α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats	42
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	41
Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction	41
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	41
Unexplored diversity and ecological functions of transposable phages	41
Extreme summers impact cropland and grassland soil microbiomes	40
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	40
Microbial community composition predicts bacterial production across ocean ecosystems	40
Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept	39
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	39
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	39
Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	38
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	38
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	38
Specialized digestive mechanism for an insect-bacterium gut symbiosis	38
Bridging ecological assembly process and community stability upon bacterial invasions	37
Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges	37
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria	37
Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance	36
Intra-colony light gradients drive variation in coral symbiont morphology and carbon storage	36
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	36
Metabolic interactions underlying phyllosphere microbiota assembly	36
Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont	36
Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean	36
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	36
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	36
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	36
Transglobal spread of an ecologically relevant sea urchin parasite	36
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	36
The atmosphere: a transport medium or an active microbial ecosystem?	35
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	35
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	35
Altered rhizosphere microbiome composition associated with B-subgenome cultivars of diploid and triploid banana plants	35
Spatio-temporal pattern formation of living organisms at the edge of chaos	34
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	34
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly	34
Kinetic plasticity of nitrite-oxidizing bacteria containing cytoplasmic nitrite oxidoreductase	34
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	34
DNA virus–host patterns in lake and marine environments over the last glacial cycle	34
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	34
Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms	34
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus–bacterial coexistence	34
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	34
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	34
Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases	34
Biofilm lifestyle across different lineages of ammonia-oxidizing archaea	33
Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics	33
Bioplastic biodegradability shapes microbial communities in a coastal brackish environment	33
Temperature alters interactions and keystone taxa in the marine microbiome	33
Oxylipin-mediated metabolic signatures of symbiosis homeostasis and thermal stress in a model sea anemone	32
Sulfide stress tolerance as a controller of methane production in temperate wetlands	32
Polyphenol rewiring of the microbiome reduces methane emissions	32
Early transcription factor activation distinguishes symbiotic from non-symbiotic bacteria during microbiome processing in a sponge	32
Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer	32
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	31

Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	31
Pathogen-pathogen interactions during co-infections	31
Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems	31
Cooperative microbial metabolism enhances tryptophan-mediated insecticide detoxification in the fall armyworm	31
Microbial dispersal into surface soil is limited on a meter scale	31
High niche specificity and host genetic diversity of groundwater viruses	31
Dysbiotic gut fungi exacerbate Klebsiella pneumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation	31
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	31
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	31
Global terrestrial distribution of N2O-reducing Acidobacteriota members	31
Engineering plant holobionts for climate-resilient agriculture	30
Endozoicomonas acroporae enhances coral thermal resilience through host–microbe coordination	30
Acidifying bacteria inhibit pathogenic bacteria more strongly with increasing glucose	30
Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome	30
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	30
Taeniasis impacts human gut microbiome composition and function	29
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	29
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes	29
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	29
Correction to 29 articles due to inaccurate manuscript submission dates	29
Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	28
Trophic modulation of endophytes by rhizosphere protists	28
Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis	28
Correction to: Horizontal transmission of heat-evolved microalgal symbionts in adult corals	28
Hydrological regime of a continental river system predicts bacterial macroecological patterns	28
Predator–prey dynamics of Vibrio cholerae on chitin suggest an alternative mode of biofilm formation in marine snow conditions	28
Host-specific viral predation network on coral reefs	28
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	28
Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments	27
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	27
Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host	27
Carbon metabolic versatility underpins Bathyarchaeia ecological significance across the global deep subsurface	27
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	27
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	27
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	27
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	27
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	27
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	27
Siderophores and competition for iron govern myxobacterial predation dynamics	27
Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils	27
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	27
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	26
Spatial sensing as a strategy for public goods regulation by gut microbes	26
Two-step localization driven by peptidoglycan hydrolase in interbacterial predation	26
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response	26
Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice	26
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	26
Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia	26
Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils	26
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	26
High resolution functional analysis and community structure of photogranules	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	25
Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments	25
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids	25
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	25
Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning	25
Seed-mediated vertical transmission of Pantoea core endophytes	25
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes	25
Collective protection against the type VI secretion system in bacteria	25
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	25
Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus	25
Advancing microbial ecology, microbiomes, and One Health in Africa: from regional initiatives to pan-African flagship programs	25
Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group	25
Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR–NF-κB axis	24
Structured interactions explain the absence of keystone species in synthetic microcosms	24
Correction: Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia	24
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	24
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	24
Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former	24
Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors	24
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments	24
Function-based selection of synthetic communities enables mechanistic microbiome studies	24
Milk IgA promotes symbionts and limits pathobionts in the early life gut	24
Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene	23
Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas	23
Gut microbiota facilitate adaptation of invasive moths to new host plants	23
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population	23
Polyhydroxybutyrate production by freshwater SAR11 (LD12)	23
Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer	23
Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert	23
Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti	23
Ecological and evolutionary responses of earthworm holobionts to environmental changes	23
Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies	23
Nitrogen availability shapes evolution of phage resistance in cyanobacteria	23
Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae	23
Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens	23
Net rate of lateral gene transfer in marine prokaryoplankton	23
Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions	23
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression	23
Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia	22
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts	22
AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential	22
Identification and cultivation of anaerobic bacterial scavengers of dead cells	22
Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean	22