ISME Journal

Article	Citations
Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function	261
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment	244
Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities	191
Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism	182
SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway	162
Spatial separation of ribosomes and DNA in Asgard archaeal cells	154
In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection	148
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin	137
Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2	136
Aminolipids in bacterial membranes and the natural environment	135
Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil	126
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants	124
Endosymbionts modulate virus effects on aphid-plant interactions	113
Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms	111
Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves	109
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides	107
Population differentiation of Rhodobacteraceae along with coral compartments	104
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments	102
Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments	101
Community context matters for bacteria-phage ecology and evolution	101
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil	101
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system	96
Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes	94
Gut microbiota contribute to variations in honey bee foraging intensity	92
Bacterial type VI secretion system helps prevent cheating in microbial communities	91

Cryptochrome PtCPF1 regulates high temperature acclimation of marine diatoms through coordination of iron and phosphorus uptake	89
Transportome remodeling of a symbiotic microalga inside a planktonic host	86
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana	85
Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources	84
Metabolic potential of Nitrososphaera-associated clades	84
Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability	80
Correction: Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation	79
Hot moment of N2O emissions in seasonally frozen peatlands	78
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities	77
Fireworms are a reservoir and potential vector for coral-infecting apicomplexans	76
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont	75
Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth	75
Genetic and species rearrangements in microbial consortia impact biodegradation potential	75
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay	75
Asgard ESCRT-III and VPS4 reveal conserved chromatin binding properties of the ESCRT machinery	75
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation	74
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment	71
Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean	68
Catabolic protein degradation in marine sediments confined to distinct archaea	67
Phyllosphere symbiont promotes plant growth through ACC deaminase production	66
Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities	64
Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system	64
Unraveling negative biotic interactions determining soil microbial community assembly and functioning	63
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota	61
Dietary protein source alters gut microbiota composition and function	61
Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater	61
Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods	59
Chlorine redox chemistry is widespread in microbiology	59
Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass	58
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis	56
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley	56
Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia	56
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles	56
Metabolic labour division trade-offs in denitrifying microbiomes	55
Celebrating 15 years of The ISME Journal	55
Mechanisms driving genome reduction of a novel Roseobacter lineage	54
Correction: Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum	54
MicroRNA-mediated regulation of lipid metabolism in virus-infected Emiliania huxleyi	52
Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor	51
Mixed heavy metal stress induces global iron starvation response	51
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot	51
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs	51
Tailless and filamentous prophages are predominant in marine Vibrio	50
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean	49
Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects	49
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity	49
Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis	49
Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum	49
Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere	49
Microbial solutions must be deployed against climate catastrophe	48

Correction to: Ice nucleation in a Gram-positive bacterium isolated from precipitation depends on a polyketide synthase and non-ribosomal peptide synthetase	48
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions	48
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series	48
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean	47
Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria	46
Microbial community composition predicts bacterial production across ocean ecosystems	46
Network structure of resource use and niche overlap within the endophytic microbiome	46
Unexplored diversity and ecological functions of transposable phages	46
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders	45
Long-term maintenance of a heterologous symbiont association in Acropora palmata on natural reefs	44
Functional convergence in slow-growing microbial communities arises from thermodynamic constraints	44
Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments	44
α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats	43
Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments	43
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia	42
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
Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks	41
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing	41
Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes	41
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms	41
Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism	41
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria	41
Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems	41
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction	41
Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site	40
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice	40
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle	40
The atmosphere: a transport medium or an active microbial ecosystem?	40
Reductive dissolution of pyrite by methanogenic archaea	40
Extreme summers impact cropland and grassland soil microbiomes	40
Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria	40
Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms	40
Specialized digestive mechanism for an insect-bacterium gut symbiosis	39
Transglobal spread of an ecologically relevant sea urchin parasite	39
Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy	39
Bridging ecological assembly process and community stability upon bacterial invasions	39
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera	39
Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction	39
Rethinking CSR theory to incorporate microbial metabolic diversity and foraging traits	39
Thermal stress triggers productive viral infection of a key coral reef symbiont	38
Mechanisms underlying interactions between two abundant oral commensal bacteria	38
The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss	38
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups	38
The rates of global bacterial and archaeal dispersal	38
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes	38
Microbial drivers of methane emissions from unrestored industrial salt ponds	37
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains	37
High niche specificity and host genetic diversity of groundwater viruses	37
Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales	37
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate	37
Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues	37
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron	36
Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness	36
Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12	36
Episomal virus maintenance enables bacterial population recovery from infection and promotes virus-bacterial coexistence	36
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity	36
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria	35
Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments	35
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily	35
High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean	35
Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution	35
Copper stress shapes the dynamic behavior of amoebae and their associated bacteria	35
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes	35
Spatio-temporal pattern formation of living organisms at the edge of chaos	35
Correction to 29 articles due to inaccurate manuscript submission dates	34
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses	34
Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses	34
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits	34
Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing	34
Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders	34
Correction to: Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption	34
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health	34
Siderophores and competition for iron govern myxobacterial predation dynamics	34
First come, first served: superinfection exclusion in Deformed wing virus is dependent upon sequence identity and not the order of virus acquisition	34
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions	34
Host-specific viral predation network on coral reefs	33
Decreased efficacy of antimicrobial agents in a polymicrobial environment	33
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action	33
Cell surface carbohydrates of symbiotic dinoflagellates and their role in the establishment of cnidarian–dinoflagellate symbiosis	33

Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates	33
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis	33
Taeniasis impacts human gut microbiome composition and function	33
Trophic modulation of endophytes by rhizosphere protists	32
Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape	32
Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus	32
Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests	32
Correction: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria	32
Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity	32
Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients	32
Spatial sensing as a strategy for public goods regulation by gut microbes	32
Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice	31
Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments	31
Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages	31
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes	31
Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef	31
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis	31
Collective protection against the type VI secretion system in bacteria	31
Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks	31
Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins	31
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean	31
High resolution functional analysis and community structure of photogranules	30
Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals	30
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis	30
Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean	30
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids	30
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance	30
Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group	30
Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus	30
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean	30
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response	30
Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool	30
Correction: Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia	29
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle	29
Ecological and evolutionary responses of earthworm holobionts to environmental changes	29
Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas diversity	29
Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone	29
Drosophila attack inhibits hyphal regeneration and defense mechanisms activation for the fungus Trichoderma atroviride	29
Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies	29
Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria	29
Identification and cultivation of anaerobic bacterial scavengers of dead cells	29
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil	29
Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene	29
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean	29
Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways	28
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population	28
Correction to: Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil	28
Ongoing diversification of the global fish pathogenPiscirickettsia salmonisthrough genetic isolation and transposition bursts	28
Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae	28
Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens	28
Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean	28
Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis	28
Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming	28
Competition for iron shapes metabolic antagonism betweenBacillus subtilisandPseudomonas marginalis	27
Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation	27
Gut microbiota facilitate adaptation of invasive moths to new host plants	27
Response to substrate limitation by a marine sulfate-reducing bacterium	27
Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions	27
Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria	27
Leveraging genome-scale metabolic models to understand aerobic methanotrophs	27
Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion	27
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations	26
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression	26
Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert	26
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide	26
Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti	26
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem	26
Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage	26
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome	26
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean	26
Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining–impacted habitats	26
Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders	25
Ecologically coherent population structure of uncultivated bacterioplankton	25
Holobiont perspectives on tripartite interactions among microbiota, mosquitoes, and pathogens	25
Polyhydroxybutyrate production by freshwater SAR11 (LD12)	25
Correction to: Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation	25
Phycosphere pH of unicellular nano- and micro- phytoplankton cells and consequences for iron speciation	25
Predatory protists impact plant performance by promoting plant growth-promoting rhizobacterial consortia	25
Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation	25
Modeling host-associating microbes under selection	25
Correction to: Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus?	24
A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen	24
Abundant and active community members respond to diel cycles in hot spring phototrophic mats	24
SeqCode in the golden age of prokaryotic systematics	24
Global and seasonal variation of marine phosphonate metabolism	24
Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae	24
Diel investments in metabolite production and consumption in a model microbial system	24
Genome reduction occurred in early Prochlorococcus with an unusually low effective population size	24