Environmental Microbiology

Papers
(The TQCC of Environmental Microbiology is 12. 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 2021-05-01 to 2025-05-01.)
ArticleCitations
115
Microbe–sediment interactions in Great Lakes recreational waters: Implications for human health risk96
Prescribed fire selects for a pyrophilous soil sub‐community in a northern California mixed conifer forest96
PeMetR‐mediated sulfur assimilation is essential for virulence and patulin biosynthesis in Penicillium expansum94
Issue Information93
The carnitine degradation pathway ofAcinetobacter baumanniiand its role in virulence87
Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy77
ArsV and ArsW provide synergistic resistance to the antibiotic methylarsenite76
Prevalence, complete genome, and metabolic potentials of a phylogenetically novel cyanobacterial symbiont in the coral‐killing sponge, Terpios hoshinota70
Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch60
Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies59
The toxicological spectrum of the Bacillus cereus toxin cereulide points towards niche‐specific specialisation59
Microbial community origin and fate through a rural wastewater treatment plant58
When the going gets tough, the tough get going—Novel bacterial AAA+ disaggregases provide extreme heat resistance54
A lipopolysaccharide‐dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance53
An atlas of bacterial secondary metabolite biosynthesis gene clusters53
Assembly and comparative analyses of the Geosiphon pyriformis metagenome52
Enrichment of nosZ‐type denitrifiers by arbuscular mycorrhizal fungi mitigates N2O emissions from soybean stubbles52
Beyond purified dietary fibre supplements: Compositional variation between cell wall fibre from different plants influences human faecal microbiota activity and growth in vitro52
Enhanced ability of freshwater bacteria to secrete extracellular vesicles upon interaction with virus51
Single‐amplified genomes reveal most streamlined free‐living marine bacteria49
Distinctive features of the Gac‐Rsm pathway in plant‐associated Pseudomonas48
Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi48
Validation of key sponge symbiont pathways using genome‐centric metatranscriptomics48
How does metal soil pollution change the plant mycobiome?47
One substrate, many fates: different ways of methanol utilization in the acetogen Acetobacterium woodii47
Genomic differentiation of three pico‐phytoplankton species in the Mediterranean Sea46
Particle‐associated and free‐living bacterial communities in an oligotrophic sea are affected by different environmental factors46
Late Pleistocene‐dated divergence between South Hemisphere populations of the non‐conventional yeast L. cidri46
Specificity and genetic polymorphism in the Vfm quorum sensing system of plant pathogenic bacteria of the genus Dickeya45
Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure44
Life strategies and metabolic interactions of core microbes during thiosulphate‐based denitrification42
The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits42
Intra‐genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing42
The acetoin assimilation pathway of Pseudomonas putida KT2440 is regulated by overlapping global regulatory elements that respond to nutritional cues41
Drivers of fungal diversity and community biogeography differ between green roofs and adjacent ground‐level green space41
A meta‐analysis study of the robustness and universality of gut microbiota–shrimp diseases relationship40
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Physiological stage drives fungal community dynamics and diversity in Leptospermum scoparium (mānuka) flowers39
Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks38
High diversity of pathogenic Escherichia coli clones carrying mcr‐1 among gulls underlines the need for strategies at the environment–livestock–human interface38
Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt38
Low phosphate mitigates cadmium‐induced oxidative stress in Saccharomyces cerevisiae by enhancing endogenous antioxidant defence system38
Issue Information38
Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars37
Oak Wilt Disease May Reduce the Initial Decay Rate of Dead Quercus serrata Stems by Altering Fungal Communities in the Wood37
New Insight Into the Mechanism of Nitrite Enhancement on Heterotrophic Nitrification and Aerobic Denitrification Bacterium in Gene Expression37
How do soil microbes exert impact on soil respiration and its temperature sensitivity?37
Biodegradation of pollutants by exoelectrogenic bacteria is not always performed extracellularly36
At least three families of hyphosphere small secreted cysteine‐rich proteins can optimize surface properties to a moderately hydrophilic state suitable for fungal attachment36
Anaerobic methanotrophy is stimulated by graphene oxide in a brackish urban canal sediment35
Fine‐scale mapping of physicochemical and microbial landscapes of the coral skeleton35
Toward an accurate mechanistic understanding of Wolbachia‐induced cytoplasmic incompatibility35
CARD‐FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes35
Wolbachia in scale insects: a distinct pattern of infection frequencies and potential transfer routes via ant associates35
Coral holobiont research needs spatial analyses at the microbial scale35
Protein acetylation and deacetylation in plant‐pathogen interactions35
Biogeography of culturable marine bacteria from both poles reveals that ‘everything is not everywhere’ at the genomic level34
Bacterial community dynamics on bats and the implications for pathogen resistance34
Volatile Organic Compounds of Diverse Origins and Their Changes Associated With Cultivar Decay in a Fungus‐Farming Termite34
Carbon substrate re‐orders relative growth of a bacterium using Mo‐, V‐, or Fe‐nitrogenase for nitrogen fixation33
Lysobacter enzymogenes antagonizes soilborne bacteria using the type IV secretion system32
Ornithine decarboxylase of the fungal pathogenColletotrichum higginsianumplays an important role in regulating global metabolic pathways and virulence32
Organoarsenical tolerance in Sphingobacterium wenxiniae, a bacterium isolated from activated sludge31
Environmental vibrio phage–bacteria interaction networks reflect the genetic structure of host populations31
Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient31
Discovery of the non‐cosmopolitan lineages in Candidatus Thermoprofundales31
Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA31
Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome31
Symbiotic germination and development of fully mycoheterotrophic plants convergently targeting similar Glomeraceae taxa31
A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota30
Distribution, causal agents, and infection dynamic of emerging ink disease of sweet chestnut in Southern Switzerland30
Diversity and ecology of Radiolaria in modern oceans30
Horizontal gene transfer (HGT) and microbial evolution30
Time after time: detecting annual patterns in stream bacterial biofilm communities30
Molecular mechanisms underlying glyphosate resistance in bacteria30
Optimal Cell Length for Exploration and Exploitation in Chemotactic Planktonic Bacteria29
Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs29
Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics29
Environmental exposure more than plastic composition shapes marine microplastic‐associated bacterial communities inPacificversusCaribbeanfield incubations29
Ferroptosis induced by the biocontrol agent Pythium oligandrum enhances soybean resistance to Phytophthora sojae29
Geography and environmental pressure are predictive of class‐specific radioresistance in black fungi29
Metabolic Segregation and Functional Gene Clusters in Anaerobic Digestion Consortia29
Long‐range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies28
Dissection of FixK2 protein–DNA interaction unveils new insights into Bradyrhizobium diazoefficiens lifestyles control28
Fate of glacier surface snow‐originating bacteria in the glacier‐fed hydrologic continuums28
Evidence for reciprocal evolution of the global repressor Mlc and its cognate phosphotransferase system sugar transporter27
Correction to “Preventing multiresistance: New insights for managing fungal adaptation”27
Issue Information27
A novel soluble di‐iron monooxygenase from the soil bacterium Solimonas soli27
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Synthesis of the unusual lipid bis(monoacylglycero)phosphate in environmental bacteria27
Unexpected role of electron‐transfer hub in direct degradation of pollutants by exoelectrogenic bacteria26
The fitness benefit of pyoverdine cross‐feeding by Pseudomonas protegens Pf‐526
Phytoplankton exudates provide full nutrition to a subset of accompanying heterotrophic bacteria via carbon, nitrogen and phosphorus allocation26
Seasonal shifts in Fe‐acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling26
Comprehensive analysis of the regulatory network of blue‐light‐regulated conidiation and hydrophobin production in Trichoderma guizhouense26
Site‐directed mutagenesis of the succinate dehydrogenase subunits B and D from Corynespora cassiicola reveals different fitness costs and sensitivities to succinate dehydrogenase inhibitors26
Novel oil‐associated bacteria in Arctic seawater exposed to different nutrient biostimulation regimes25
MoOpy2 is essential for fungal development, pathogenicity, and autophagy in Magnaporthe oryzae25
Revealing human impact on natural ecosystems through soil bacterial DNA sampled from an archaeological site25
The filamentous γ‐prefoldin chaperone is not essential for growth and thermal adaptation in Methanocaldococcus jannaschii25
Widespread formation of intracellular calcium carbonates by the bloom‐forming cyanobacterium Microcystis25
AwMelWolbachiavariant inAedes aegyptifrom field‐collectedDrosophila melanogasterwith increased phenotypic stability under heat stress25
Nitrogen fertilization differentially affects the symbiotic capacity of two co‐occurring ectomycorrhizal species25
Highly Dynamic Archaeal and Bacterial Communities From the Surface to the Deep in the Atlantic Ocean25
How good are global DNA‐based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation25
Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov)24
Linear scaling between microbial predator and prey densities in the global ocean24
Core rhizosphere microbiome ofPanax notoginsengand its associations with belowground biomass and saponin contents24
Dynamics of Baltic Sea phages driven by environmental changes24
Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions24
Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria24
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Correction to “Five structural genes required for ceramide synthesis in Caulobacter and for bacterial survival”24
Environmental Microbiology and Environmental Microbiology Reports 2023 and onwards23
The brown root rot fungus Phellinus noxius affects microbial communities in different root‐associated niches of Ficus trees23
Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin23
Issue Information23
Biodegradation in wastewater treatment plants: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology23
Long‐term unsustainable patterns of development rather than recent deforestation caused the emergence of Orthocoronavirinae species23
Genome‐Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts23
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Ecology of Listeria monocytogenes and Listeria species in India: the occurrence, resistance to biocides, genomic landscape and biocontrol23
Phylogenomics, epigenomics, virulome and mobilome of Gram‐negative bacteria co‐resistant to carbapenems and polymyxins: a One Health systematic review and meta‐analyses23
Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts)22
Sarracenia pitcher plant‐associated microbial communities differ primarily by host species across a longitudinal gradient22
Elevated O3 concentrations alter the compartment‐specific microbial communities inhabiting rust‐infected poplars22
Novel virulent and temperate cyanophages predicted to infect Microcoleus associated with anatoxin‐producing benthic mats22
Water Quality and Land Use Shape Bacterial Communities Across 621 Canadian Lakes22
An ArsRC fusion protein enhances arsenate sensing and detoxification22
Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses22
CotG controls spore surface formation in response to the temperature of growth in Bacillus subtilis22
Does diet breadth affect the complexity of the phytophagous insect microbiota? The case study of Chrysomelidae22
Oxic–anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors22
Microbiome Stability Is Linked to Acropora Coral Thermotolerance in Northwestern Philippines21
Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist21
Isolation and evaluation of the biocontrol potential of Talaromyces spp. against rice sheath blight guided by soil microbiome21
Viable but non‐cultivable state: a strategy for Staphylococcus aureus survivable in dual‐species biofilms with Pseudomonas aeruginosa?21
Membrane lipid renovation in Pseudomonas aeruginosa ‐ implications for phage therapy?21
Novel broad‐spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases21
A perspective on insect–microbe holobionts facing thermal fluctuations in a climate‐change context21
The quorum‐sensing systems of Vibrio campbelliiDS40M4 and BB120 are genetically and functionally distinct21
The pH signalling transcription factor PacC modulate growth, development, stress response and pathogenicity of Trichothecium roseum21
Exploring the Exclusive Isolation of Pseudomonas syringae in Peltigera Lichens via Metabolite Analysis and Growth Assays21
Microscale imaging sheds light on species‐specific strategies for photo‐regulation and photo‐acclimation of microphytobenthic diatoms21
Functional characterization of a high‐affinity iron transporter (PiFTR) from the endophytic fungus Piriformospora indica and its role in plant growth and development21
Experimental evidence that lignin‐modifying enzymes are essential for degrading plant cell wall lignin byPleurotus ostreatususingCRISPR/Cas921
Countrywide inter‐epidemic region migration pattern suggests the role of southwestern population in wheat stripe rust epidemics in China21
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Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters20
From ubiquity to specificity: The diverse functions of bacterial thioredoxin systems20
Toward a molecular understanding of fluoride stress in a model Pseudomonas strain20
Stability of a dominant sponge‐symbiont in spite of antibiotic‐induced microbiome disturbance20
Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia20
Golgi‐localized calcium/manganese transporters FgGdt1 and FgPmr1 regulate fungal development and virulence by maintaining Ca2+ and Mn2+ homeostasis in Fu20
Adaptation ofListeria monocytogenesto perturbation ofc‐di‐AMPmetabolism underpins its role in osmoadaptation and identifies a fosfomycin uptake system20
Rehabilitation of the ‘bad guys’ for biocontrol applications19
Microbial biofilms: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology19
Warm temperature inhibits cytoplasmic incompatibility induced by endosymbiotic Rickettsiella in spider hosts19
Microbial metabolism and adaptations in Atribacteria‐dominated methane hydrate sediments19
The two Pseudomonas aeruginosa DksA stringent response proteins are largely interchangeable at the whole transcriptome level and in the control of virulence‐related traits19
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Issue Information19
High salinity gradients and intermediate spatial scales shaped similar biogeographical and co‐occurrence patterns of microeukaryotes in a tropical freshwater‐saltwater ecosystem19
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Differential apicomplexan presence predicts thermal stress mortality in the Mediterranean coral Paramuricea clavata19
Diversification of Bacillus subtilis during experimental evolution on Arabidopsis thaliana and the complementarity in root colonization of evolved subpop19
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Metagenomic evidence of a novel family of anammox bacteria in a subsea environment18
Genetic Analysis of Polyunsaturated Fatty Acids Biosynthesis Pathway Determines Four Distinct Thraustochytrid Types18
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Azole‐resistant Aspergillus fumigatus is highly prevalent in the environment of Vietnam, with marked variability by land use type18
Diverse viruses of marine archaea discovered using metagenomics18
Towards risk assessment for antibiotic resistant pathogens in recycled water: a systematic review and summary of research needs18
Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air18
Production and utilization of pseudocobalamin in marine Synechococcus cultures and communities18
Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field18
The cAMP‐PKA signalling pathway regulates hyphal growth, conidiation, trap morphogenesis, stress tolerance, and autophagy in Arthrobotrys oligospora18
Uniform selective pressures within redox zones drive gradual changes in microbial community composition in hadal sediments18
Airborne and indigenous microbiomes co‐drive the rebound of antibiotic resistome during compost storage18
Interactions between Bdellovibrio and like organisms and bacteria in biofilms: beyond predator–prey dynamics18
Bacterial inoculation ofQuercus pyrenaicatrees alters co‐occurrence patterns but not the composition of the rhizosphere bacteriome in wild conditions18
Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings18
Multi‐omics analysis of antagonistic interactions among free‐living Pseudonocardia from diverse ecosystems18
Denitrification fractionates N and O isotopes of nitrate following a ratio independent of carbon sources in freshwaters18
Water deficit affects inter‐kingdom microbial connections in plant rhizosphere18
Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum17
Microecosystem of yak rumen on the Qinghai‐Tibetan Plateau is stable and is unaffected by soil or grass microbiota17
Employing a triple metabarcoding approach to differentiate active, dormant and dead microeukaryotes in sediments17
Selective Pressure Influences Inter‐Biome Dispersal in the Assembly of Saline Microbial Communities17
Genetic Diversity and Anatoxin Profiles of Freshwater Benthic Cyanobacteria From Nova Scotia (Canada)17
Distinct strategies of the habitat generalists and specialists in sediment of Tibetan lakes17
Experimental evolution of Pseudomonas putida under silver ion versus nanoparticle stress17
The current situation and potential effects of climate change on the microbial load of marine bivalves of the Greek coastlines: an integrative review17
Isolation and characterization of a phage collection against Pseudomonas putida17
The tetrameric assembly of 2‐aminomuconic 6‐semialdehyde dehydrogenase is a functional requirement of cofactor NAD+ binding17
Bacteriophages vehiculate a high amount of antibiotic resistance determinants of bacterial origin in the Orne River ecosystem17
The bianchetto truffle (Tuber borchii) a lead‐resistant ectomycorrhizal fungus increases Quercus cerris phytoremediation potential17
Microbial Community of a Sandy Beach Subterranean Estuary is Spatially Heterogeneous and Impacted by Winter Waves17
Coexistence Theory for Microbial Ecology, and Vice Versa17
Identification of dominant taxa of sooty moulds and their impact on the leaf microbiome16
Marine microbes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology16
Web Alert: Microbes and plastics: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology16
Reaching out in anticipation: bacterial membrane extensions represent a permanent investment in polysaccharide sensing and utilization16
Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra16
Proteomic profiling and glycomic analysis of the yeast cell wall in strains with Aflatoxin B1 elimination ability16
Fluid dynamics and cell‐bound Psl polysaccharide allows microplastic capture, aggregation and subsequent sedimentation by Pseudomonas aeruginosa in water16
Isolation and characterization of a novel methanogen Methanosarcina hadiensis sp. nov. from subsurface Boom Clay pore water16
Following the flow—Microbial ecology in surface‐ and groundwaters in the glacial forefield of a rapidly retreating glacier in Iceland16
Comparative transcriptome analysis reveals different adaptation mechanisms for degradation of very long‐chain and normal long‐chain alkanes in Dietzia sp. DQ12‐45‐1b16
Cold Surface Waters of the Sub‐Antarctic Pacific Ocean Support High Cyanophage Abundances and Infection Levels16
Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples16
Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae16
Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils16
Continuous Rice Cultivation Increases Celery Yield by Enhancing Plant Beneficial Bacteria in Rice‐Celery Rotations16
Biosolids for safe land application: does wastewater treatment plant size matters when considering antibiotics, pollutants, microbiome, mobile genetic elements and associated resistance genes?16
The 2‐methylpropene degradation pathway in Mycobacteriaceae family strains16
Virulence of Vibrio harveyiORM4 towards the European abalone Haliotis tuberculata involves both quorum sensing and a type III secretion system16
Proteomic response of the marine ammonia‐oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity16
New Strains of the Deep Branching Streptophyte Streptofilum: Phylogenetic Position, Cell Biological and Ecophysiological Traits, and Description of Streptofilum arcticumsp. nov16
The Influence of Symbiont Identity on the Proteomic and Metabolomic Responses of the Model Cnidarian Aiptasia to Thermal Stress16
Warming Seawater Temperature and Nutrient Depletion Alters Microbial Community Composition on a Foundational Canopy Kelp Species16
Microplastic ingestion affects hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber16
Long‐term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil16
Short‐term plastisphere colonization dynamics across six plastic types15
Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter15
Physiology and genetics of ethanologenesis in the acetogenic bacterium Acetobacterium woodii15
Proteomic responses of the coccolithophore Emiliania huxleyi to zinc limitation and trace metal substitution15
Issue Information15
Adaptive Responses of Cyanobacteria to Phosphate Limitation: A Focus on Marine Diazotrophs15
Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning15
Gene Expression by a Model Fungus in the Ascomycota Provides Insight Into the Decay of Fungal Necromass15
Evolution under low antibiotic concentrations: a risk for the selection of Pseudomonas aeruginosa multidrug‐resistant mutants in nature15
Antidepressants: A new front in the war against antibiotics resistance15
Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea15
Complex and flexible catabolism in Aromatoleum aromaticumpCyN115
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Diversity of dimethylsulfide‐degrading methanogens and sulfate‐reducing bacteria in anoxic sediments along the Medway Estuary, UK15
Gene expression in the microbial consortia of colonial Microcystis aeruginosa‐a potential buoyant particulate biofilm15
Bacteria associated with wood tissues of Esca‐diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components15
Plant salt tolerance: ACC deaminase‐producing endophytes change plant proteomic profiles15
Regulation of zinc homeostatic genes by environmental pH in the filamentous fungus Aspergillus fumigatus15
The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet15
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Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms15
Microbial community composition controls carbon flux across litter types in early phase of litter decomposition15
Ability of phages to infect Acinetobacter calcoaceticus‐Acinetobacter baumannii complex species through acquisition of different pectate lyase depolymerase domains15
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