ISME Journal

Papers
(The TQCC of ISME Journal is 27. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-06-01 to 2024-06-01.)
ArticleCitations
Environmental stress destabilizes microbial networks506
Erosion reduces soil microbial diversity, network complexity and multifunctionality315
Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment232
Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes214
Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease212
Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt165
Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens164
Ecology and evolution of antimicrobial resistance in bacterial communities149
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions144
Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer142
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life137
Open challenges for microbial network construction and analysis129
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification124
Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species123
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere118
Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation113
Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system113
Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress112
Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress111
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities111
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity106
Air pollution could drive global dissemination of antibiotic resistance genes102
Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers101
Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant101
Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome99
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities98
A network approach to elucidate and prioritize microbial dark matter in microbial communities97
Prokaryotic taxonomy and nomenclature in the age of big sequence data96
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem95
Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi95
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen93
Engineering rhizobacteria for sustainable agriculture93
Life-history strategies of soil microbial communities in an arid ecosystem92
Unraveling negative biotic interactions determining soil microbial community assembly and functioning91
Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation87
Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems86
Achieving similar root microbiota composition in neighbouring plants through airborne signalling86
Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress85
The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?81
Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy80
Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation80
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters79
Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype78
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria77
Interspecies bacterial competition regulates community assembly in the C. elegans intestine75
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups73
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis72
Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping72
Social networks strongly predict the gut microbiota of wild mice72
Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses71
Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline71
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms70
Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome70
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika70
The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization69
Solutions in microbiome engineering: prioritizing barriers to organism establishment69
Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization68
A genomic view of the microbiome of coral reef demosponges68
In vitro interaction network of a synthetic gut bacterial community68
Fecal filtrate transplantation protects against necrotizing enterocolitis68
Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes67
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation67
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe67
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo67
Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal66
Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes66
Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates66
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria66
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions66
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health65
Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea65
Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs64
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa63
A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases63
Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes63
Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene61
Diversity and distribution of viruses inhabiting the deepest ocean on Earth61
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations61
Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids61
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes61
Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles60
Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments58
Intra-colony channels in E. coli function as a nutrient uptake system58
Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira56
Fungal communities decline with urbanization—more in air than in soil55
Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog54
Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt54
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling54
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient54
Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogen Erwinia amylovora54
Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients54
Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations54
Microbial carrying capacity and carbon biomass of plastic marine debris54
Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome53
Benchmarking microbial growth rate predictions from metagenomes53
A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus53
A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities53
Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist52
Intracellular symbionts drive sex ratio in the whitefly by facilitating fertilization and provisioning of B vitamins52
Microbial storage and its implications for soil ecology52
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome52
Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool51
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber51
Host specificity of microbiome assembly and its fitness effects in phytoplankton51
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance51
Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process50
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing50
Decline in symbiont-dependent host detoxification metabolism contributes to increased insecticide susceptibility of insects under high temperature49
Nitrogen cycling and microbial cooperation in the terrestrial subsurface48
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents48
Inter-species interactions alter antibiotic efficacy in bacterial communities48
Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium48
The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity48
T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer47
Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom47
Seasonal niche differentiation among closely related marine bacteria47
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips46
A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus46
Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments46
Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation45
Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity45
Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought45
Ecological dynamics of the gut microbiome in response to dietary fiber45
Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection45
Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival45
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide44
Ecological succession in the vaginal microbiota during pregnancy and birth44
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment44
Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease44
The rates of global bacterial and archaeal dispersal43
Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria43
A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances43
Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity43
Light exposure mediates circadian rhythms of rhizosphere microbial communities43
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat42
Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes42
New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods42
Direct quantification of ecological drift at the population level in synthetic bacterial communities42
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil42
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments42
Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity42
Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture42
Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa41
Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits41
A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth41
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway41
Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer41
Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment41
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean40
Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens40
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle40
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning40
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations39
Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides39
Life history strategies among soil bacteria—dichotomy for few, continuum for many39
Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition39
Quorum sensing controls persistence, resuscitation, and virulence of Legionella subpopulations in biofilms39
Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations38
Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology38
The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance38
Viral lysis modifies seasonal phytoplankton dynamics and carbon flow in the Southern Ocean38
Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire37
Community context matters for bacteria-phage ecology and evolution37
Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies37
Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes37
Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation37
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity36
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline36
Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues36
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds35
Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment35
Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments35
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates35
Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria35
The occurrence and ecology of microbial chain elongation of carboxylates in soils35
Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers35
Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential34
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean34
Highly diverse flavobacterial phages isolated from North Sea spring blooms34
Division of functional roles for termite gut protists revealed by single-cell transcriptomes34
Anthropogenic dissolved organic carbon and marine microbiomes33
Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling33
Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness33
Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy33
The saccharibacterium TM7x elicits differential responses across its host range33
Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance33
Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions32
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients32
Phages in the infant gut: a framework for virome development during early life32
Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria32
Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms32
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones32
Anaerobic metabolism of Foraminifera thriving below the seafloor32
Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants32
Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms32
Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees31
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean31
Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut31
Locally adapted gut microbiomes mediate host stress tolerance31
Unexpected diversity among small-scale sample replicates of defined plant root compartments31
Network structure of resource use and niche overlap within the endophytic microbiome31
Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities31
Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function31
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development31
Predicting spatial patterns of soil bacteria under current and future environmental conditions31
Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments31
Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions31
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae30
Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages30
Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning30
Biofilm matrix disrupts nematode motility and predatory behavior30
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets30
Lichen-like association of Chlamydomonas reinhardtii and Aspergillus nidulans protects algal cells from bacteria30
Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments30
Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas29
Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages29
Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge)29
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages29
Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons29
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome29
Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone29
Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem29
Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation29
Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef29
Wildland fire as an atmospheric source of viable microbial aerosols and biological ice nucleating particles28
Experimental identification and in silico prediction of bacterivory in green algae28
Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean28
Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean28
Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus28
Pervasive prophage recombination occurs during evolution of spore-forming Bacilli28
Microbially facilitated nitrogen cycling in tropical corals28
Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems28
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system28
A spore quality–quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis27
Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism27
A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen27
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins27
Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor27
Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures27
The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution27
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community27
Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene27
Microbial competition reduces metabolic interaction distances to the low µm-range27
Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics27
Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis27
Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape27
Soil minerals affect taxon-specific bacterial growth27
Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts27
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