ISME Journal

Article	Citations
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	343
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	197
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	151
Inositol phosphates as an overlooked phosphorous source in marine ecosystems	147
Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress	139
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	137
Understanding prokaryotic adaptation through advanced DNA methylation detection techniques	128
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	125
Aminolipids in bacterial membranes and the natural environment	122
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	114
Co-cultivation rescues suicidal Paenibacillus amylolyticus swarms	111
Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux	105
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	99
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	99
Endosymbionts modulate virus effects on aphid-plant interactions	97
Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialogue and adaptive strategies with the fungus <	96
Land use drives drug resistance in an airborne human fungal pathogen	92
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	90
Distinct transcriptomic strategies underlie differential heat tolerance in Symbiodiniaceae symbionts	89
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes	87
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	87
Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans	86
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	85
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	84
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	82

Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits	78
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	75
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	74
Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides	74
Colonization history of snow algae on Hawai‘i island	73
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	71
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	70
Transportome remodeling of a symbiotic microalga inside a planktonic host	68
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	68
Drug delivery dynamics dictate evolution of bacterial antibiotic responses	67
Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean	66
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	66
Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistillata	65
Metabolic potential of Nitrososphaera-associated clades	65
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	65
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	64
Gut microbiota contribute to variations in honey bee foraging intensity	64
Bacterial type VI secretion system helps prevent cheating in microbial communities	64
Catabolic protein degradation in marine sediments confined to distinct archaea	62
Phyllosphere symbiont promotes plant growth through ACC deaminase production	61
Genetic and species rearrangements in microbial consortia impact biodegradation potential	60
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	59
Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	58
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	57
Microbial cross-feeding stabilized by segregation of a dependent mutant from its independent ancestor	56
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	56
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	56
MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi	56
Hot moment of N2O emissions in seasonally frozen peatlands	56
Celebrating 15 years of The ISME Journal	55
Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science	54
Chlorine redox chemistry is widespread in microbiology	54
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	53
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	53
Metabolic labour division trade-offs in denitrifying microbiomes	52
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	51
Mixed heavy metal stress induces global iron starvation response	51
Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems	51
Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature	51
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	51
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	51
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	51
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	51
Dietary protein source alters gut microbiota composition and function	50
Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales	50
Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis	50
Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction	49
Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods	49
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	49
Microbial solutions must be deployed against climate catastrophe	48

Microbial community composition predicts bacterial production across ocean ecosystems	48
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity	47
Extreme summers impact cropland and grassland soil microbiomes	47
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	47
Unexplored diversity and ecological functions of transposable phages	47
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	47
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	46
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	46
Diversity and evolution of prokaryotic viral lytic proteins	46
Endofungal bacteria as hidden facilitators of biotic interactions	46
Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide	45
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	45
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	43
Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks	42
Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems	42
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	42
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	42
Latitudinal diversity in circadian and light-sensing genes in an ecologically vital group of marine picoeukaryote algae	41
α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats	41
Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri	41
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	41
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	40
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	40
Specialized digestive mechanism for an insect-bacterium gut symbiosis	39
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	39
Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	39
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	39
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	39
Tailless and filamentous prophages are predominant in marine Vibrio	39
Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont	39
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	39
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants	39
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	38
Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance	38
Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site	38
Metabolic interactions underlying phyllosphere microbiota assembly	38
Thermal stress triggers productive viral infection of a key coral reef symbiont	38
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	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
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	37
Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean	37
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	36
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	36
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	36
Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales	36
The atmosphere: a transport medium or an active microbial ecosystem?	36
Sulfide stress tolerance as a controller of methane production in temperate wetlands	36
Bridging ecological assembly process and community stability upon bacterial invasions	36
Spatio-temporal pattern formation of living organisms at the edge of chaos	35
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	35
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	35
Enrichment of horizontally transferred gene clusters in bacterial extracellular vesicles via non lytic mechanisms	35
Altered rhizosphere microbiome composition associated with B-subgenome cultivars of diploid and triploid banana plants	35
Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome	35
Microbial dispersal into surface soil is limited on a meter scale	34
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus–bacterial coexistence	34
Dysbiotic gut fungi exacerbate Klebsiella pneumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation	34
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	34
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	33
Biofilm lifestyle across different lineages of ammonia-oxidizing archaea	33
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	33
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	33
Pathogen-pathogen interactions during co-infections	33
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	33
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	33
High niche specificity and host genetic diversity of groundwater viruses	32
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	32
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily	32
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly	32
Polyphenol rewiring of the microbiome reduces methane emissions	32
Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics	32
Cooperative microbial metabolism enhances tryptophan-mediated insecticide detoxification in the fall armyworm	31
Engineering plant holobionts for climate-resilient agriculture	31
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	31
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	30
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes	30
Correction to 29 articles due to inaccurate manuscript submission dates	30
Temperature alters interactions and keystone taxa in the marine microbiome	30
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	29

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