ISME Journal

Papers
(The TQCC of ISME Journal is 24. 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 2020-12-01 to 2024-12-01.)
ArticleCitations
Environmental stress destabilizes microbial networks664
Erosion reduces soil microbial diversity, network complexity and multifunctionality412
Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes277
Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens206
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions198
Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer172
Open challenges for microbial network construction and analysis163
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life157
Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress144
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity142
Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress139
Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species136
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities129
Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi125
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem124
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities123
Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome122
Increasing flavonoid concentrations in root exudates enhance associations between arbuscular mycorrhizal fungi and an invasive plant121
Unraveling negative biotic interactions determining soil microbial community assembly and functioning116
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen112
Prokaryotic taxonomy and nomenclature in the age of big sequence data111
Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems107
Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation102
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms100
Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome100
The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization96
The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?94
Solutions in microbiome engineering: prioritizing barriers to organism establishment93
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health92
Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress89
Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates88
Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype87
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria87
Fecal filtrate transplantation protects against necrotizing enterocolitis87
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation84
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes84
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria83
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika83
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe83
Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization82
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups81
Interspecies bacterial competition regulates community assembly in the C. elegans intestine80
Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes79
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance77
In vitro interaction network of a synthetic gut bacterial community77
Social networks strongly predict the gut microbiota of wild mice77
Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs75
Nitrogen cycling and microbial cooperation in the terrestrial subsurface74
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa73
A genomic view of the microbiome of coral reef demosponges73
Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene72
Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles68
Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations68
Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome68
Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients67
Diversity and distribution of viruses inhabiting the deepest ocean on Earth67
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing65
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling64
Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes63
A mycovirus modulates the endophytic and pathogenic traits of a plant associated fungus62
Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist61
Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt60
Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome59
Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool59
Ecological dynamics of the gut microbiome in response to dietary fiber59
Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium58
Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process58
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient58
Decline in symbiont-dependent host detoxification metabolism contributes to increased insecticide susceptibility of insects under high temperature57
Seasonal niche differentiation among closely related marine bacteria56
Microbial storage and its implications for soil ecology56
Inter-species interactions alter antibiotic efficacy in bacterial communities56
The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide56
Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity54
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides54
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents54
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments54
Life history strategies among soil bacteria—dichotomy for few, continuum for many54
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle53
Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom53
Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments53
Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity52
Light exposure mediates circadian rhythms of rhizosphere microbial communities52
Viral lysis modifies seasonal phytoplankton dynamics and carbon flow in the Southern Ocean50
Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer50
T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer50
Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture50
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips50
The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance49
Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants48
The rates of global bacterial and archaeal dispersal48
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations48
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil46
Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition45
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway45
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean44
Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria43
Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations43
Community context matters for bacteria-phage ecology and evolution42
Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms42
Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments42
Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling42
Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages41
Phages in the infant gut: a framework for virome development during early life41
Highly diverse flavobacterial phages isolated from North Sea spring blooms41
Predicting spatial patterns of soil bacteria under current and future environmental conditions40
Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology40
Locally adapted gut microbiomes mediate host stress tolerance40
Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons40
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets39
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates39
Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential39
Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues39
Microbial keystone taxa drive succession of plant residue chemistry39
Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers38
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae38
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds38
Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions38
The occurrence and ecology of microbial chain elongation of carboxylates in soils38
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones38
Network structure of resource use and niche overlap within the endophytic microbiome38
Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments38
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean37
Unexpected diversity among small-scale sample replicates of defined plant root compartments37
Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants37
Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network37
Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications37
Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments37
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean36
Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium36
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting36
Global and seasonal variation of marine phosphonate metabolism36
Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor35
Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees35
Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions35
Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean35
Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks35
Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community35
Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities35
Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness34
Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms34
Microbially facilitated nitrogen cycling in tropical corals33
Nitrification and beyond: metabolic versatility of ammonia oxidising archaea33
Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene33
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients33
Salt tolerance-based niche differentiation of soil ammonia oxidizers33
Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem33
Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions33
Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut33
Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria33
Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas33
Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages33
Soil minerals affect taxon-specific bacterial growth33
Bacterial controlled mitigation of dysbiosis in a seaweed disease32
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system32
Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning32
Pervasive prophage recombination occurs during evolution of spore-forming Bacilli32
Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef32
Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism32
Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems32
Predator-induced defence in a dinoflagellate generates benefits without direct costs32
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development32
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages31
Evolutionary stasis of a deep subsurface microbial lineage31
Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics31
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome31
In-depth analysis of N2O fluxes in tropical forest soils of the Congo Basin combining isotope and functional gene analysis31
Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis31
Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone31
Experimental identification and in silico prediction of bacterivory in green algae30
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi30
Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland30
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley30
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins30
The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution30
Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties30
Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus29
Fungal phytopathogen modulates plant and insect responses to promote its dissemination29
The effect of Quorum sensing inhibitors on the evolution of CRISPR-based phage immunity in Pseudomonas aeruginosa29
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts29
Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community29
Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing29
Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis29
Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes29
A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen29
Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments28
Methane-dependent selenate reduction by a bacterial consortium28
Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks28
Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits28
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily28
Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes28
Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways28
Microbial drivers of methane emissions from unrestored industrial salt ponds28
Extreme summers impact cropland and grassland soil microbiomes28
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community28
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot27
Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater27
Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)27
Founder cell configuration drives competitive outcome within colony biofilms27
Morphological complexity affects the diversity of marine microbiomes27
Plant-associated fungi support bacterial resilience following water limitation27
Causes and consequences of pattern diversification in a spatially self-organizing microbial community27
Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape27
Biofilm matrix cloaks bacterial quorum sensing chemoattractants from predator detection27
Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria27
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes27
Functional mutants of Azospirillum brasilense elicit beneficial physiological and metabolic responses in Zea mays contributing to increased host iron assimilation27
Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate27
Decreased efficacy of antimicrobial agents in a polymicrobial environment27
Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria27
Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock27
Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms27
Decreased thermal niche breadth as a trade-off of antibiotic resistance26
Ecologically coherent population structure of uncultivated bacterioplankton26
Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress26
Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility26
Microbial N2O consumption in and above marine N2O production hotspots26
Reductive dissolution of pyrite by methanogenic archaea26
Sinking Trichodesmium fixes nitrogen in the dark ocean26
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures26
Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions26
Pantothenate mediates the coordination of whitefly and symbiont fitness26
Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world’s oceans26
Chemolithoautotroph distributions across the subsurface of a convergent margin26
Transitions in symbiosis: evidence for environmental acquisition and social transmission within a clade of heritable symbionts26
Dissimilatory nitrate reduction by a freshwater cable bacterium26
Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments26
Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean26
Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels25
Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling25
Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions25
Bacterial ectosymbionts in cuticular organs chemically protect a beetle during molting stages25
Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability25
Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals25
Metagenome-derived virus-microbe ratios across ecosystems25
Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying25
Pseudomonas aeruginosa polysaccharide Psl supports airway microbial community development25
Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment25
Impact of intraspecific variation in insect microbiomes on host phenotype and evolution25
Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota25
Host genotype and genetic diversity shape the evolution of a novel bacterial infection25
Genomic network analysis of environmental and livestock F-type plasmid populations25
A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen25
Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea24
Specific inactivation of an antifungal bacterial siderophore by a fungal plant pathogen24
Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake24
Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse24
Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants24
Lifestyle of sponge symbiont phages by host prediction and correlative microscopy24
Identification of nosZ-expressing microorganisms consuming trace N2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales24
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