OOIR: Observatory of International Research

Papers

(The median citation count of FEMS Microbiology Ecology is 9. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-11-01 to 2023-11-01.)

Article	Citations
Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism	176
Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils	111
Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists	58
Antibiotic-induced gut metabolome and microbiome alterations increase the susceptibility to Candida albicans colonization in the gastrointestinal tract	51
Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in a mountain ecosystem	51
Salinity reduces bacterial diversity, but increases network complexity in Tibetan Plateau lakes	51
Soil characteristics and land-use drive bacterial community assembly patterns	46
Microbial abundance, composition, and function in nectar are shaped by flower visitor identity	39
Different community assembly mechanisms underlie similar biogeography of bacteria and microeukaryotes in Tibetan lakes	35
Four decades of soil water stress history together with host genotype constrain the response of the wheat microbiome to soil moisture	35
Temporal dynamics of bacterial communities during seed development and maturation	34
Root microbiomes as indicators of seagrass health	32
Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil and phyllosphere	32
Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay	29
Supplemental selenium source on gut health: insights on fecal microbiome and fermentation products of growing puppies	28
Microbial indicators are better predictors of wheat yield and quality than N fertilization	28
Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers	28
Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network	28
Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in cattle rumen	28
Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA	28
Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling	27
Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost	25
Water management and phenology influence the root-associated rice field microbiota	25
The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity?	25
Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir	25

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem	24
Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil	24
The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community	24
Seasonal variation of epiphytic bacteria in the phyllosphere of Gingko biloba, Pinus bungeana and Sabina chinensis	24
Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life	23
Effects of simulated drought on biological soil quality, microbial diversity and yields under long-term conventional and organic agriculture	22
Editorial: The Environmental Dimension of Antibiotic Resistance	22
Functional convergence in the decomposition of fungal necromass in soil and wood	21
Temporal changes in water temperature and salinity drive the formation of a reversible plastic-specific microbial community	21
Methanogenic response to long-term permafrost thaw is determined by paleoenvironment	21
Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica	20
Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics	20
Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis	20
Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warm	20
Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology	20
Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome	20
Diversity and genetic lineages of environmental staphylococci: a surface water overview	20
Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest	19
The marine intertidal zone shapes oyster and clam digestive bacterial microbiota	19
Vegetation type determines spore deposition within a forest–agricultural mosaic landscape	19
Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA	19
Distribution of phenotypic and genotypic antimicrobial resistance and virulence genes in Vibrio parahaemolyticus isolated from cultivated oysters and estuarine water	19
The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica	19
Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats	18
Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria	18
No evidence for phylosymbiosis in western chipmunk species	18
Diversity of cyanobacteria at the Alaska North Slope with description of two new genera: Gibliniella and Shackletoniella	18
Response of a methane-driven interaction network to stressor intensification	18
MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data	18
Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design	17
Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment	17
Redox stratification within cryoconite granules influences the nitrogen cycle on glaciers	17
Body site-specific microbiota reflect sex and age-class among wild spotted hyenas	17
Diversity of methicillin-resistant staphylococci among wild Lepus granatensis: first detection of mecA-MRSA in hares	17
Weekly variations of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in shallow waters of the central Red Sea	17
Bacterial community dynamics across developmental stages of fungal fruiting bodies	17
Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome	17
Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity	17
Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load	17
Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish	16
Novel rhizobia exhibit superior nodulation and biological nitrogen fixation even under high nitrate concentrations	16
Local factors drive bacterial and microeukaryotic community composition in lake surface sediment collected across an altitudinal gradient	16
The proficiency of the original host species determines community-level plasmid dynamics	16
Mucoidy, a general mechanism for maintaining lytic phage in populations of bacteria	15
Tannin supplementation modulates the composition and function of ruminal microbiome in lambs infected with gastrointestinal nematodes	15
Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake	14
Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities	14
Larval density affects phenotype and surrounding bacterial community without altering gut microbiota in Drosophila melanogaster	14
16S rRNA gene-based primer pair showed high specificity and quantification accuracy in detecting freshwater Brocadiales anammox bacteria	14
Biopolymers modulate microbial communities in municipal organic waste digestion	14

Minerals play key roles in driving prokaryotic and fungal communities in the surface sediments of the Qinghai-Tibetan lakes	14
Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water	14
Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India	14
Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota ofMus musculusare modulated byTrichuris murisinfection	14
Illuminating the dynamic rare biosphere of the Greenland Ice Sheet's Dark Zone	13
Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling	13
Surface ammonium loading rate shifts ammonia-oxidizing communities in surface water-fed rapid sand filters	13
Structure and distribution of nitrite-dependent anaerobic methane oxidation bacteria vary with water tables in Zoige peatlands	13
AHL-priming for enhanced resistance as a tool in sustainable agriculture	13
Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest	13
Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics	13
Environmental control of Vibrio spp. abundance and community structure in tropical waters	12
Metal-induced bacterial interactions promote diversity in river-sediment microbiomes	12
Diversity of carotenogenic microalgae in the White Sea polar region	12
Relative contributions of egg-associated and substrate-associated microorganisms to black soldier fly larval performance and microbiota	12
The roles of environmental variation and spatial distance in explaining diversity and biogeography of soil denitrifying communities in remote Tibetan wetlands	12
Plant-associated fungal biofilms—knowns and unknowns	12
The driving factors of nematode gut microbiota under long-term fertilization	12
Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants	12
Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam	12
Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities and prokaryotic community profiles in Argentinean semi-arid soils	12
Protecting the outside: biological tools to manipulate the skin microbiota	12
PbS biomineralization using cysteine: Bacillus cereus and the sulfur rush	12
Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America	12
Intestinal Enterococcus abundance correlates inversely with excessive weight gain and increased plasma leptin in breastfed infants	12
Bacteria but not fungi respond to soil acidification rapidly and consistently in both a spruce and beech forest	12
Warming and disturbance alter soil microbiome diversity and function in a northern forest ecotone	12
Stochastic processes dominate marine free-living Vibrio community assembly in a subtropical gulf	12
Macroecological diversification and convergence in a clade of keystone symbionts	12
Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum	12
Microhabitats are associated with diversity–productivity relationships in freshwater bacterial communities	12
A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization	12
Biochar as electron donor for reduction of N2O by Paracoccus denitrificans	11
Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium	11
Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes	11
Safeguarding the fragile rice–wheat ecosystem of the Indo-Gangetic Plains through bio-priming and bioaugmentation interventions	11
Insights into the structure and role of seed-borne bacteriome during maize germination	11
Cell Architecture of the Giant Sulfur Bacterium Achromatium oxaliferum: Extra-cytoplasmic Localization of Calcium Carbonate Bodies	11
miCROPe 2019 – emerging research priorities towards microbe-assisted crop production	11
Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils	11
Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics	11
Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop	11
Columbia spotted frogs (Rana luteiventris) have characteristic skin microbiota that may be shaped by cutaneous skin peptides and the environment	10
Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin	10
Heterogeneity–disease relationship in the human microbiome-associated diseases	10
Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability	10
Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand	10
Restoring degraded microbiome function with self-assembled communities	10
Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain)	10
Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals	10
Mitochondrial sequences of Rhipicephalus and Coxiella endosymbiont reveal evidence of lineages co-cladogenesis	9
Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change	9
The association between initial adhesion and cyanobacterial biofilm development	9
Characterizing the culturable surface microbiomes of diverse marine animals	9
Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas	9
Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection	9
A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer	9
Long-lasting effects of antibiotics on bacterial communities of adult flies	9
Arbuscular mycorrhiza has little influence on N2O potential emissions compared to plant diversity in experimental plant communities	9
Soil fungal community composition and functional similarity shift across distinct climatic conditions	9
Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem	9
Role of amoebae for survival and recovery of ‘non-culturable’ Helicobacter pylori cells in aquatic environments	9
Shifts in short-chain fatty acid profile, Fe(III) reduction and bacterial community with biochar amendment in rice paddy soil	9
Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system	9
Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition	9
Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere	9
A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination	9