ISME Journal

Article	Citations
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	283
Spatial separation of ribosomes and DNA in Asgard archaeal cells	276
Endosymbionts modulate virus effects on aphid-plant interactions	159
Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms	158
Understanding Prokaryotic Adaptation through Advanced DNA Methylation Detection Techniques	139
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	126
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	125
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides	121
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system	118
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes	117
Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans	116
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	114
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	110
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	102
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	101
Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux	99
Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress	94
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	90
Aminolipids in bacterial membranes and the natural environment	87
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	86
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	83
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	82
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	79
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	79
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	78

Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	78
Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system	77
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	77
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	76
Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater	76
Catabolic protein degradation in marine sediments confined to distinct archaea	76
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	75
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	73
Hot moment of N2O emissions in seasonally frozen peatlands	73
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	68
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	67
Drug delivery dynamics dictate evolution of bacterial antibiotic responses	66
Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistilatta	64
Metabolic potential of Nitrososphaera-associated clades	63
Phyllosphere symbiont promotes plant growth through ACC deaminase production	62
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	62
Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability	61
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	60
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	59
Correction: Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation	58
Genetic and species rearrangements in microbial consortia impact biodegradation potential	56
Gut microbiota contribute to variations in honey bee foraging intensity	55
Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean	55
Transportome remodeling of a symbiotic microalga inside a planktonic host	55
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	55
Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	55
Chlorine redox chemistry is widespread in microbiology	54
Bacterial type VI secretion system helps prevent cheating in microbial communities	54
Celebrating 15 years of The ISME Journal	53
Correction: Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum	53
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	51
Mixed heavy metal stress induces global iron starvation response	50
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	50
Microbial cross-feeding stabilized by segregation of a dependent mutant from its independent ancestor	50
Metabolic labour division trade-offs in denitrifying microbiomes	50
MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi	49
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	49
Dietary protein source alters gut microbiota composition and function	49
Correction to: Ice nucleation in a Gram-positive bacterium isolated from precipitation depends on a polyketide synthase and non-ribosomal peptide synthetase	48
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley	48
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	48
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	48
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	48
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	48
α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats	46
Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	46
Unexplored diversity and ecological functions of transposable phages	46
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	46
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants	46
Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria	45

Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks	45
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	45
Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems	45
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	45
Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism	45
Network structure of resource use and niche overlap within the endophytic microbiome	45
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	44
Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism	44
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	44
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	44
Microbial solutions must be deployed against climate catastrophe	44
Endofungal bacteria as hidden facilitators of biotic interactions	43
Tailless and filamentous prophages are predominant in marine Vibrio	43
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	43
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	43
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	43
Microbial community composition predicts bacterial production across ocean ecosystems	43
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	42
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	42
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	42
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	42
Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction	42
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	42
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity	41
Extreme summers impact cropland and grassland soil microbiomes	41
The atmosphere: a transport medium or an active microbial ecosystem?	40
Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms	40
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	40
Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site	40
Thermal stress triggers productive viral infection of a key coral reef symbiont	40
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	40
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	39
Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy	39
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	39
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	39
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	38
Specialized digestive mechanism for an insect-bacterium gut symbiosis	38
Bridging ecological assembly process and community stability upon bacterial invasions	38
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	38
Transglobal spread of an ecologically relevant sea urchin parasite	38
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria	37
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	37
Mechanisms underlying interactions between two abundant oral commensal bacteria	37
Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales	36
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	36
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	35
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	35
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	35
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	35
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	35
Pathogen-pathogen interactions during co-infections	35
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily	35
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly	35
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	35
Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome	35
High niche specificity and host genetic diversity of groundwater viruses	34
Spatio-temporal pattern formation of living organisms at the edge of chaos	34
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	34
Polyphenol rewiring of the microbiome reduces methane emissions	34
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	34
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus–bacterial coexistence	34
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	33
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits	33
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	33
Decreased efficacy of antimicrobial agents in a polymicrobial environment	33
Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis	33
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	33
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	33
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	33
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	33
Engineering Plant Holobionts for Climate-Resilient Agriculture	33
Host-specific viral predation network on coral reefs	32
Taeniasis impacts human gut microbiome composition and function	32
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	32
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	32
Correction to 29 articles due to inaccurate manuscript submission dates	32
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	32
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	32
Siderophores and competition for iron govern myxobacterial predation dynamics	31
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes	31

Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	31
Trophic modulation of endophytes by rhizosphere protists	31
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	30
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	30
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	30
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	30
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	30
Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice	30
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	30
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	30
Correction: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria	30
Collective protection against the type VI secretion system in bacteria	30
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	29
Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins	29
Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean	29
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle	29
Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia	28
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	28
Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus	28
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response	28
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments	28
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes	28
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	28
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids	28
Spatial sensing as a strategy for public goods regulation by gut microbes	28
Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool	28
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome	27
Presence of a biofilm beneficiary alters the evolutionary trajectory of a biofilm former	27
Correction to: Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil	27
Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways	27
Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis	27
Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas diversity	27
High resolution functional analysis and community structure of photogranules	27
Identification and cultivation of anaerobic bacterial scavengers of dead cells	27
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide	27
Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group	27
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	27
Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion	27
Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene	26
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts	26
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean	26
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean	26
Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation	25
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population	25
Ecological and evolutionary responses of earthworm holobionts to environmental changes	25
Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens	25
Legume-specific recruitment of rhizobia by hyphae of arbuscular mycorrhizal fungi	25
Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage	25
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression	25
Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert	25
Predatory protists impact plant performance by promoting plant growth-promoting rhizobacterial consortia	25
Gut microbiota facilitate adaptation of invasive moths to new host plants	25
Competition for iron shapes metabolic antagonism betweenBacillus subtilisandPseudomonas marginalis	24
Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria	24
Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae	24
Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions	24
Correction: Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia	24
Antibiotic-altered gut microbiota explain host memory plasticity and disrupt pace-of-life covariation for an aquatic snail	24
Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining–impacted habitats	24
Polyhydroxybutyrate production by freshwater SAR11 (LD12)	24
Leveraging genome-scale metabolic models to understand aerobic methanotrophs	24
Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer	24
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
Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti	23
Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming	23
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations	23
Correction to: Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation	23
Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders	23
Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria	23
Plant-associated fungi support bacterial resilience following water limitation	23
Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network	22
Potential effects of gut microbiota on host cancers: focus on immunity, DNA damage, cellular pathways, and anticancer therapy	22
Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis	22
Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes	22
Diel investments in metabolite production and consumption in a model microbial system	22
Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability	22
Holobiont perspectives on tripartite interactions among microbiota, mosquitoes, and pathogens	22
Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation	22
Global and seasonal variation of marine phosphonate metabolism	22
Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus	22