Environmental Microbiology Reports

Article	Citations
Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature	113
Deciphering bacterial mechanisms of root colonization	73
Temperature impacts community structure and function of phototrophic Chloroflexi and Cyanobacteria in two alkaline hot springs in Yellowstone National Park	51
Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation	32
ANME‐1 archaea may drive methane accumulation and removal in estuarine sediments	31
Non‐denitrifier nitrous oxide reductases dominate marine biomes	26
Metagenome assembled‐genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils	26
The highly crystalline PET found in plastic water bottles does not support the growth of the PETase‐producing bacterium Ideonella sakaiensis	23
Above‐ground parts of white grapevine Vitis vinifera cv. Furmint share core members of the fungal microbiome	22
Induction of Escherichia coli O157:H7 into a viable but non‐culturable state by high temperature and its resuscitation	22
Autotrophic carbon fixation pathways along the redox gradient in oxygen‐depleted oceanic waters	21
Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process	20
Are we really studying persister cells?	20
Microbiomes in agroecosystem: Diversity, function and assembly mechanisms	20
Soil pH and moisture govern the assembly processes of abundant and rare bacterial communities in a dryland montane forest	20
Development of an electroactive aerobic biocathode for microbial fuel cell applications	20
Cadmium sulfide nanoparticle biomineralization and biofilm formation mediate cadmium resistance of the deep‐sea bacterium Pseudoalteromonas sp. MT33b	19
Anaerobic oxidation of methane mediated by microbial extracellular respiration	19
Global warming impact on the expansion of fundamental niche of Cryptococcus gattii VGI in Europe	18
Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5‐enolpyruvylshikimate‐3‐phosphate synthase	18
Isolation and characterization of potentially pathogenic Vibrio species in a temperate, higher latitude hotspot	18
Tools to map target genes of bacterial two‐component system response regulators	18
Quantitative acetylome analysis reveals involvement of glucosyltransferase acetylation in Streptococcus mutans biofilm formation	18
Bacterial rather than fungal diversity and community assembly drive soil multifunctionality in a subtropical forest ecosystem	18
Hydrostatic pressure is the universal key driver of microbial evolution in the deep ocean and beyond	17

Transmission of the sponge microbiome: moving towards a unified model	16
Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae)	16
Herbivory shapes the rhizosphere bacterial microbiota in potato plants	15
Viruses of freshwater bloom‐forming cyanobacteria: genomic features, infection strategies and coexistence with the host	14
Disentangling soil microbiome functions by perturbation	14
Oxygen metabolism shapes microbial settlement on photosynthetic kelp blades compared to artificial kelp substrates	14
Facility‐specific ‘house’ microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking	14
Global diversity and distribution of mushroom‐inhabiting bacteria	13
Clostridium difficile in soil conditioners, mulches and garden mixes with evidence of a clonal relationship with historical food and clinical isolates	13
Climate change and the aquatic continuum: A cyanobacterial comeback story	13
Towards culturing the microbe of your choice	13
Time as a microbial resource	13
How dead is dead? Viable but non‐culturable versus persister cells	12
An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles	12
Characterization of glyphosate‐resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution	11
Extracellular DNA builds and interacts with vibrio polysaccharide in the biofilm matrix formed by Vibrio cholerae	11
Bacillus thuringiensis RZ2MS9, a tropical plant growth‐promoting rhizobacterium, colonizes maize endophytically and alters the plant's production of volatile organic compounds during	11
Metagenomic and metatranscriptomic analysis reveals enrichment for xenobiotic‐degrading bacterial specialists and xenobiotic‐degrading genes in a Canadian Prairie two‐cell	11
Microbial rhodopsins are increasingly favoured over chlorophyll in High Nutrient Low Chlorophyll waters	11
The ubiquitous soil verrucomicrobial clade ‘Candidatus Udaeobacter’ shows preferences for acidic pH	11
Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?	11
Novel Chlamydiae and Amoebophilus endosymbionts are prevalent in wild isolates of the model social amoeba Dictyostelium discoideum	10
Synergistic role of abiotic factors driving viable but non‐culturable Vibrio cholerae	10
Bacteriophage therapeutics to confront multidrug‐resistant Acinetobacter baumannii ‐ a global health menace	10
Presence of biogenic magnetite in ferromanganese nodules	10
Microbial diversity and adaptive strategies in the Mars‐like Qaidam Basin, North Tibetan Plateau, China	10
Genotypes and phenotypes of methicillin‐resistant staphylococci isolated from shrimp aquaculture farms	10
The physiology and metabolic properties of a novel, low‐abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role	10
Post‐transcriptional deregulation of the tisB/istR‐1 toxin–antitoxin system promotes SOS‐independent persister formation in Escherichia coli	10
Heterogeneity of the white truffle Tuber magnatum in a limited geographic area of Central‐Southern Italy	9
Quantitative proteomics provides an insight into germination‐related proteins in the obligate biotrophic plant pathogen Spongospora subterranea	9
Phthalate hydrolase: distribution, diversity and molecular evolution	9
A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation	9
Subtle bacterioplankton community responses to elevated CO2 and warming in the oligotrophic South Pacific gyre	9
Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds	9
Short‐term microbialite resurgence as indicator of ecological resilience against crises (Catamarca, Argentine Puna)	8
Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose	8
‘Candidatus Gromoviella agglomerans’, a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction	8
Bradyrhizobium sp. strain ORS278 promotes rice growth and its quorum sensing system is required for optimal root colonization	8
Variation of bacterial communities along the vertical gradient in Lake Issyk Kul, Kyrgyzstan	8
Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri	8
What do we mean by viability in terms of ‘viable but non‐culturable’ cells?	8
18S rRNA gene amplicon sequencing combined with culture‐based surveys of maize rhizosphere protists reveal dominant, plant‐enriched and culturable community members	8
Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter	8
Different patterns of belowground fungal diversity along altitudinal gradients with respect to microhabitat and guild types	8
Cyanobacterial community composition and their functional shifts associated with biocrust succession in the Gurbantunggut Desert	8
Theß‐ketoadipate pathway ofAcinetobacter baumanniiis involved in complement resistance and affects resistance against aromatic antibiotics	8
Effects of different short‐term tillage managements on rhizosphere soil autotrophic CO2‐fixing bacteria in a double‐cropping rice paddy field	8
Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum	7
A first response to osmostress inAcinetobacter baumannii: transient accumulation of K+and its replacement by compatible solutes	7

Current perspectives on the occurrence of Q fever: highlighting the need for systematic surveillance for a neglected zoonotic disease in Indian subcontinent	7
Spatiotemporal dynamics of marine microbial communities following a Phaeocystis bloom: biogeography and co‐occurrence patterns	7
Contrasting influences on bacterial symbiont specificity by co‐occurring deep‐sea mussels and tubeworms	7
In it together: Candida–bacterial oral biofilms and therapeutic strategies	7
Physical connections: prokaryotes parasitizing their kin	7
Multiple plant hormone catabolism activities: an adaptation to a plant‐associated lifestyle by Achromobacter spp.	7
Pressure effects on sulfur‐oxidizing activity of Thiobacillus thioparus	7
Pan‐genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11	7
Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation	7
Comparative microbial antibiotic resistome between urban and deep forest environments	7
Unique bacterial communities and potential function along the vertical gradient in the deepest marine blue hole	7
Global 16S rRNA diversity of provannid snail endosymbionts from Indo‐Pacific deep‐sea hydrothermal vents	7
Complete genome assembly of the levan‐positive strain PVFi1 of Pseudomonas savastanoi pv. savastanoi isolated from olive knots in Central Italy	7
Darwinian individuality of extrachromosomal genetic elements calls for population genetics tinkering	6
Soil exposure accelerates recovery of the gut microbiota in antibiotic‐treated mice	6
The potential of Pseudomonas for bioremediation of oxyanions	6
Biodegradation of textile waste by marine bacterial communities enhanced by light	6
Unique phage–bacterium interplay in sponge holobionts from the southern Okinawa Trough hydrothermal vent	6
Sources of protein diet differentially stimulate the gut and water microbiota under freshwater crayfish, marron (Cherax cainii, Austin 2002) culture	6
The growth‐survival trade‐off is hard‐wired in the Lactococcus lactis gene regulation network	6
Light‐dependent niche differentiation in two mixotrophic bacterivores	6
Functional genome mining and taxono‐genomics reveal eco‐physiological traits and species distinctiveness of aromatic‐degrading Pseudomonas bharatica sp. nov.	6
Genome analysis of Streptomyces sp. UH6 revealed the presence of potential chitinolytic machinery crucial for chitosan production	6
Occurrence and phylogenetic analysis of Pseudanabaena sp. producing 2‐methylisoborneol in drinking water source of South Korea	6
Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake	6
Molecular diversity of Extended‐spectrum β‐lactamase‐producing Escherichia coli from vultures in Canary Islands	6
Melanin protects Cryptococcus neoformans from spaceflight effects	6
Two co‐dominant nitrogen‐fixing cyanobacteria demonstrate distinct acclimation and adaptation responses to cope with ocean warming	6
Interruption of Aspergillus niger spore germination by the bacterially produced secondary metabolite collimomycin	6
Plant‐associatedmicrobiota as a source of antagonistic bacteria against the phytopathogenErwinia amylovora	6
Sulfur assimilation in corals with aposymbiotic and symbiotic zooxanthellae	6
Exploration on the Cr(VI) resistance mechanism of a novel thermophilic Cr(VI)‐reducing bacteria Anoxybacillus flavithermusABF1 isolated from Tengchong geotherma	6
The contribution of microbiology toward attainment of sustainable development goals: the need to conserve soil health while maximizing its productivity	6
Antibiotic resistance in mucosal bacteria from high Arctic migratory salmonids	5
O‐acetylesterase activity of Bifidobacterium bifidum sialidase facilities the liberation of sialic acid and encourages the proliferation of sialic acid scavenging Bifidobacterium brev	5
Novel virocell metabolic potential revealed in agricultural soils by virus‐enriched soil metagenome analysis	5
Sessile bacterium unlocks ability of surface motility through mutualistic interspecies interaction	5
A Bacillus subtilis ΔpdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation	5
Molecular and metabolic characteristics of wastewater associated Escherichia coli strains	5
Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms	5
Simulated future conditions of ocean warming and acidification disrupt the microbiome of the calcifying foraminifera Marginopora vertebralis across life stages	5
Rumen protozoa: from background actors to featured role in microbiome research	5
Trophic interrelationships of bacteria are important for shaping soil protist communities	5
Saltmarsh rhizosphere fungal communities vary by sediment type and dominant plant species cover in Nova Scotia, Canada	5
Does sociality drive diversity and composition of airway microbiota in cetaceans?	5
High‐throughput sequencing reveals soil bacterial community structure and their interactions with environmental factors of the grassland fairy ring	5
Mutualistic relationship between Nitrospira and concomitant heterotrophs	5
Microbial diversity and associated metabolic potential in the supraglacial habitat of a fast‐retreating glacier: a case study of Patsio glacier, North‐western Himalaya	5
Picocyanobacterial cells in near‐surface air above terrestrial and freshwater substrates in Greenland and Antarctica	5
Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development	5
ppGpp mediates the growth phase‐dependent regulation of agn43, a phase variable gene, by stimulating its promoter activity	5
The use of different 16S rRNA gene variable regions in biogeographical studies	5
Genomic diversities of ctxB, tcpA and rstR alleles of Vibrio cholerae O139 strains isolated from Odisha, India	4
Metatranscriptomic outlook on green and brown food webs in acid mine drainage	4
Two‐component system in Rahnella aquatilis is impacted by the hyphosphere of the arbuscular mycorrhizal fungus Rhizophagus irregularis	4
Microbial community succession in steam‐sterilized greenhouses infected with Fusarium oxysporum	4
A novel host of MCR‐5 belonging to Enterobacter spp. isolated from hospital sewage water	4
Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria	4
Biogeographic structure of fungal communities in seagrass Halophilia ovalis across the Malay Peninsula	4
Comparative transcriptomic analyses of Chromera and Symbiodiniaceae	4
An uncharacterized clade in the DMSO reductase family of molybdenum oxidoreductases is a new type of chlorate reductase	4
Growth of Stenotrophomonas maltophilia and expression of Sme efflux pumps encoding genes in the presence of supernatants from amoebal and bacterial co‐cultures: towards the role of amoebal seco	4
Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge	4
Drops join to make a stream: high‐throughput nanoscale cultivation to grasp the lettuce root microbiome	4
Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications	4
Nectar compounds impact bacterial and fungal growth and shift community dynamics in a nectar analog	4
Micro‐synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway	4
Chances and limitations when uncovering essential and non‐essential genes of Bacillus subtilis phages with CRISPR‐Cas9	4
Scaling down the microbial loop: data‐driven modelling of growth interactions in a diatom–bacterium co‐culture	4
Salmonella Newport outbreak in Brazilian parrots: confiscated birds from the illegal pet trade as possible zoonotic sources	4
The root‐associated arbuscular mycorrhizal fungal assemblages of exotic alien plants are simplified in invaded distribution ranges, but dominant species are retained: A trans‐continental perspective	4
Metatranscriptomic identification of polyamine‐transforming bacterioplankton in the Gulf of Mexico	4
Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola	4
Death in a sphere: Chromobacterium violaceum secretes outer membrane vesicles filled with antibiotics	4
Who is in the driver's seat? Parvimonas micra: An understudied pathobiont at the crossroads of dysbiotic disease and cancer	4
The bacterial signature offers vision into the machinery of coral fitness across high‐latitude coral reef in the South China Sea	4
Alveolates (dinoflagellates, ciliates and apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves	4
Mostly dead and all dead: response to ‘what do we mean by viability in terms of “viable but non‐culturable cells”’	4
In silico analysis of diversity, specificity and molecular evolution of Stenotrophomonas phages	3
Providing octane degradation capability to Pseudomonas putidaKT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element	3

Disentangling microstructure and environmental conditions in high‐altitude Andean microbialite systems (Catamarca, Argentine Puna)	3
Thermodynamics shapes the biogeography of propionate‐oxidizing syntrophs in paddy field soils	3
A hydrogen‐oxidizing bacterium enriched from the open ocean resembling a symbiont	3
Epigenetic insight into regulatory role of chromatin covalent modifications in lifecycle and virulence of Phytophthora	3
Genome sequencing provides new insights on the distribution of Erwinia amylovora lineages in northern Italy	3
Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction	3
Plant species‐dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves	3
The worm affair: fidelity and environmental adaptation in symbiont species that co‐occur in vestimentiferan tubeworms	3
Global expansion of Vibrio spp. in hot water	3
Linking lifestyle and foraging strategies of marine bacteria: selfish behaviour of particle‐attached bacteria in the northern Adriatic Sea	3
Gliding motility of a uranium‐tolerant Bacteroidetes bacterium Chryseobacterium sp. strain PMSZPI: insights into the architecture of spreading colonies	3
Performance of the melting seawater‐ice elution method on the metabarcoding characterization of benthic protist communities	3
The plant host environment influences competitive interactions between bacterial pathogens	3
Niche differentiation of atmospheric methane‐oxidizing bacteria and their community assembly in subsurface karst caves	3
Growth rate‐dependent synthesis of halomethanes in marine heterotrophic bacteria and its implications for the ozone layer recovery	3
Environmental reservoirs of Vibrio cholerae serogroups in the flowing freshwater environs from the tribal areas of Odisha, Eastern India	3
Temperature enhances the functional diversity of dissolved organic matter utilization by coastal marine bacteria	3
Prevalence, diversity and genetic structure of Escherichia coli isolates from septic tanks	3
Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation	3
Francisella novicida can utilize Paramecium bursaria as its potential host	3
Elucidating the interaction of carbon, nitrogen, and temperature on the biosynthesis of Aureobasidium pullulans antifungal volatiles	3
Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph	3
Coupling methanogenesis with iron reduction by acetotrophic Methanosarcina mazei zm‐15	3
Waiting for Godot: response to ‘How dead is dead? Viable but non‐culturable versus persister cells’	2
AcrAB, the major RND‐type efflux pump of Photorhabdus laumondii, confers intrinsic multidrug‐resistance and contributes to virulence in insects	2
Site‐directed mutagenesis of Bradyrhizobium diazoefficiens USDA 110 aroA improves bacterial growth and competitiveness for soybean nodulation in the presence of gly	2
Dissemination of Vibrio cholerae O1 isolated from Odisha, India	2
Genomic attributes differ between Vibrio parahaemolyticus environmental and clinical isolates including pathotypes	2
The ‘microbiome counterattack’: Insights on the soil and root‐associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event	2
Whole‐genome sequence analysis of Staphylococcus aureus from retail fish acknowledged the incidence of highly virulent ST672‐MRSA‐IVa/t1309, an emerging Indian clone, in Assam, India	2
Comparative genomics reveals the emergence of copper resistance in a non‐pigmented Xanthomonas pathogen of grapevine	2
Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments	2
A potential third‐order role of the host endoplasmic reticulum as a contact site in interkingdom microbial endosymbiosis and viral infection	2
Extracellular sulfite is protective against reactive oxygen species and antibiotic stress in Shewanella oneidensis MR‐1	2
Alarming level of single or multidrug resistance in poultry environments‐associated extraintestinal pathogenic Escherichia coli pathotypes with potential to affect the One Health	2
Wildlife omnivores and herbivores as a significant vehicle of multidrug‐resistant and pathogenic Escherichia coli strains in environment	2
Rapid detection of temperate bacteriophage using a simple motility assay	2
Sinorhizobium meliloti ohrR genes affect symbiotic performance with alfalfa (Medicago sativa)	2
Type‐specific quantification of particulate methane monooxygenase gene of methane‐oxidizing bacteria at the oxic–anoxic interface of a surface paddy soil by digitalPCR	2
SAR11 clade microdiversity and activity during the early spring blooms off Kerguelen Island, Southern Ocean	2
High calcium and strontium uptake by the green microalgaTetraselmis chuiis related to micropearl formation and cell growth	2
Bacterial epiphyte and endophyte communities of seagrass Thalassia hemprichii: the impact of feed extract solution	2
Manipulating indole symbiont signalling	2
Lifestyle of bacteria in deep sea	2
First report on the occurrence of Vibrio cholerae nonO1/nonO139 in natural and artificial lakes and ponds in Serbia: Evidence for a long‐distance transfer of strains and t	2
The potential of bacterial microcompartment architectures for phytonanotechnology	2
Non‐ribosomal peptide biosynthetic potential of the nematode symbiont Photorhabdus	2
Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing	2
Methodological ‘lenses’ influence the characterization of phytoplankton dynamics in a coastal upwelling ecosystem	2
Diversity and putative interactions of parasitic alveolates belonging to Syndiniales at a coastal Pacific site	2
Penicillin‐resistant, ampicillin‐susceptible Enterococcus faecalis isolates are uncommon in non‐clinical sources	2
Rapid formation of mature microbialites in Lake Alchichica, Mexico	2
Exposure to endocrine disruptors promotes biofilm formation and contributes to increased virulence of Pseudomonas aeruginosa	2
Small RNAs in the Antarctic bacterium Pseudomonas extremaustralis responsive to oxygen availability and oxidative stress	2
Lack of kinship with anaerobes is a kind of short‐sightedness of agricultural and environmental microbiologists	2
N‐damo, an opportunity to reduce methane emissions?	2
Dsk2 involves in conidiation, multi‐stress tolerance and thermal adaptation in Beauveria bassiana	2
Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils	2
A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone	2
Metagenomics indicate that public health risk may be higher from flooding following dry versus rainy periods	2
Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta‐analysis involving infants living in sub‐urban areas of Côte d'Ivoire	2
Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines	2
Involvement of membrane vesicles in long‐chain‐AHL delivery in Paracoccus species	2
Latitude and chlorophyll a density drive the distribution of carbohydrate‐active enzymes in the planktonic microbial fraction of the epipelagic zone	2