Environmental distribution of prokaryotic taxa

BackgroundThe increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa.ResultsWe used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB.ConclusionsThis is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.

• Publication year

  2010

• Venue

  BMC Microbiology

• Publication date

  2010-03-22

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/1471-2180-10-85PMID 20307274PMCID 2850351
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Encyclopedia of Inland Waters

  2009cited by this paper
• EnvDB, a database for describing the environmental distribution of prokaryotic taxa.

  2009cited by this paper
• The minimum information about a genome sequence (MIGS) specification

  2008cited by this paper
• A Molecular Study of Microbe Transfer between Distant Environments

  2008cited by this paper
• Worlds within worlds: evolution of the vertebrate gut microbiota

  2008cited by this paper
• Confusing Kinships

  2008cited by this paper
• The minimum information about a genome sequence (MIGS) specification

  2008cited by this paper
• Short pyrosequencing reads suffice for accurate microbial community analysis

  2007cited by this paper
• Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

  2007cited by this paper
• Accuracy and quality of massively parallel DNA pyrosequencing

  2007cited by this paper
• Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

  2007cited by this paper
• Trait Evolution, Community Assembly, and the Phylogenetic Structure of Ecological Communities

  2007cited by this paper
• Global patterns in bacterial diversity

  2007influential reference
• Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

  2007cited by this paper
• Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

  2007cited by this paper
• Microbial diversity in the deep sea and the underexplored “rare biosphere”

  2006cited by this paper
• Microbial biogeography: putting microorganisms on the map

  2006cited by this paper
• An Introduction to the Family Flavobacteriaceae

  2006cited by this paper
• Spatial scaling of microbial biodiversity.

  2006cited by this paper
• The Family Succinivibrionaceae

  2006cited by this paper
• Global patterns of diversity and community structure in marine bacterioplankton

  2006cited by this paper
• Phylogenetic clustering and overdispersion in bacterial communities.

  2006cited by this paper
• Toward a Census of Bacteria in Soil

  2006cited by this paper
• Opinion: Re-evaluating prokaryotic species.

  2005cited by this paper
• Re-evaluating prokaryotic species

  2005cited by this paper
• Comparative genomics of gene-family size in closely related bacteria

  2004cited by this paper
• An ecological perspective on bacterial biodiversity

  2004cited by this paper
• Environmental Genome Shotgun Sequencing of the Sargasso Sea

  2004cited by this paper
• Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins.

  2004cited by this paper
• Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

  2003cited by this paper
• Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts

  2003cited by this paper
• Soil Type Is the Primary Determinant of the Composition of the Total and Active Bacterial Communities in Arable Soils

  2003cited by this paper
• Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea

  2003cited by this paper
• Global Dispersal of Free-Living Microbial Eukaryote Species

  2002cited by this paper
• What are bacterial species?

  2002cited by this paper
• The structure of microbial communities in soil and the lasting impact of cultivation

  2001cited by this paper
• Clustering of highly homologous sequences to reduce the size of large protein databases

  2001cited by this paper
• Biogeography and Degree of Endemicity of Fluorescent Pseudomonas Strains in Soil

  2000cited by this paper
• Prokaryotes: the unseen majority.

  1998cited by this paper
• Polyphasic Taxonomy , a Consensus Approach to Bacterial Systematics

  1996cited by this paper
• Polyphasic taxonomy, a consensus approach to bacterial systematics

  1996cited by this paper
• Microbial ecology on land and sea

  1994cited by this paper
• Diversity and Evenness: A Unifying Notation and Its Consequences

  1973cited by this paper

• Analysis of Multitrophic Biodiversity Patterns in the Irtysh River Basin Based on eDNA Metabarcoding

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• Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities

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• Salinity Is a Key Factor Shaping Bacteriobenthos in Floodplain Lakes of a Neotropical Coastal Wetland

  2025cites this paper
• Determination of Antibiotic Resistance Genes in the Interior Bay of Puno-Peru, Lake Titicaca

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• Assessment of Aquatic Ecosystem Health in the Irtysh River Basin Using eDNA Metabarcoding

  2025cites this paper
• Detection of Antibiotic-Resistance Genes in Drinking Water: A Study at a University in the Peruvian Amazon

  2025cites this paper
• Shifts in organic matter character and microbial assemblages from glacial headwaters to downstream reaches in the Canadian Rocky Mountains

  2025cites this paper
• Diversity of Culturable Bacteria in Gut of White Grub Maladera Insanabilis (Brenske)

  2024cites this paper
• Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic

  2024cites this paper
• Diversity and biogeography of bacterial community in the Ili River network varies locally and regionally.

  2024cites this paper
• A matter of salt: global assessment of the effect of salt ionic composition as a driver of aquatic bacterial diversity

  2024cites this paper
• Quantifying microbial guilds

  2024cites this paper
• Shifts in organic matter character and microbial community structure from glacial headwaters to downstream reaches in Canadian Rocky Mountain rivers

  2023cites this paper
• Comparing diversity patterns and processes of microbial community assembly in water column and sediment in Lake Wuchang, China

  2023cites this paper
• From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian

  2023cites this paper
• 16S-based metagenomics analysis of microbial communities associated with toxic and non-toxic dinoflagellate cultures

  2023cites this paper
• Differences of Nitrogen Transformation Pathways and Their Functional Microorganisms in Water and Sediment of a Seasonally Frozen Lake, China

  2023cites this paper
• Microbiological Status, Physico-chemistry and Plant Performance in Spent Lubricating Oil (SLO) Polluted Soils Amended with Spiked Organic Fertilizer

  2023cites this paper
• Anion-type modulates the effect of salt stress on saline lake bacteria

  2022cites this paper
• Linkages between bacterial community and extracellular enzyme activities crossing a coastal front

  2022cites this paper
• Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity

  2022cites this paper
• Host–Pathogen Interactions of Marine Gram-Positive Bacteria

  2022cites this paper
• The Role of Thermokarst Lake Expansion in Altering the Microbial Community and Methane Cycling in Beiluhe Basin on Tibetan Plateau

  2022cites this paper
• Characterization of the bacterioplankton community and the influencing factors in the upper reaches of the Han River basin

  2021cites this paper
• Co-existing water and sediment bacteria are driven by contrasting environmental factors across glacier-fed aquatic systems.

  2021cites this paper
• The Origin of Niches and Species in the Bacterial World

  2021cites this paper
• Seasonal Dynamics in the Number and Composition of Coliform Bacteria in Drinking Water Reservoirs

  2021cites this paper
• Response of bacterial and fungal communities to high petroleum pollution in different soils

  2021cites this paper
• Metagenomic Analysis of The Effects of Salinity On Microbial Diversity and Functional Gene Diversity in Kongsfjorden Estuary

  2021influential citation
• ReviewUnderestimated cyanobacterial diversity: trends and perspectives of research in tropical environments

  2021cites this paper
• Recent technological advancements in studying biodegradation of polycyclic aromatic hydrocarbons through theoretical approaches

  2021cites this paper
• Protistan and fungal diversity in soils and freshwater lakes are substantially different

  2020cites this paper
• Many roads to bacterial generalism.

  2020cites this paper
• Unravelling the composition of tap and mineral water microbiota: Divergences between next-generation sequencing techniques and culture-based methods.

  2020cites this paper
• Bacterial Communities in Stream Biofilms in a Degrading Grassland Watershed on the Qinghai–Tibet Plateau

  2020cites this paper
• Isolation and Characterization of Carbonoclastic Bacteria Diversity in Oil-contaminated Soil in Cape Coast Metropolis, Ghana

  2020cites this paper
• Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria

  2020cites this paper
• Hydrological variations shape diversity and functional responses of streambed microbes.

  2020cites this paper
• The bacterial communities of surface soils from desert sites in the eastern Utah (USA) portion of the Colorado Plateau.

  2020cites this paper
• Bacterial Diversity in a Dynamic and Extreme Sub-Arctic Watercourse (Pasvik River, Norwegian Arctic)

  2020cites this paper
• Temporal and spatial changes in bacterial diversity in mixed use watersheds of the Great Lakes region

  2019cites this paper
• Assessment of the Microbial Biomass Carbon (MB-C), Nitrogen (MB-N) and Phosphorus (MB-P) in Soil Spiked with Pesticides (Carbofuran and Paraquat)

  2019cites this paper
• Spatial ecology of soil nematodes: Perspectives from global to micro scales

  2019cites this paper
• Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions

  2019cites this paper
• Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate

  2019cites this paper
• Bacterioplankton Community Composition Along Environmental Gradients in Lakes From Byers Peninsula (Maritime Antarctica) as Determined by Next-Generation Sequencing

  2019cites this paper
• Meta-16S rRNA Gene Phylogenetic Reconstruction Reveals the Astonishing Diversity of Cosmopolitan Myxobacteria

  2019cites this paper
• Microbial diversity and distribution differ between water column and biofilm assemblages in arid-land waterbodies

  2019cites this paper
• Selection-based model of prokaryote pangenomes

  2019cites this paper
• Meta-16S rRNA gene phylogenetic reconstruction reveals astonishing diversity of the cosmopolitan myxobacteria

  2019cites this paper
• Metagenomic Achievements in Microbial Diversity Determination in Croplands

  2019cites this paper
• Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment

  2019cites this paper
• Statistical determination of crucial taxa indicative of pollution gradients in sediments of Lake Taihu, China.

  2019cites this paper
• Soil available phosphorus content drives the spatial distribution of archaeal communities along elevation in acidic terrace paddy soils.

  2019cites this paper
• Coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community in a coastal watershed of Southeast China.

  2019cites this paper
• Intra-species diversity ensures the maintenance of functional microbial communities under changing environmental conditions

  2019cites this paper
• Prokaryotic footprints in urban water ecosystems: A case study of urban landscape ponds in a coastal city, China.

  2018cites this paper
• Cultivable anaerobic and aerobic bacterial communities in the fermentation chambers of Holotrichia parallela (coleoptera: scarabaeidae) larvae

  2018cites this paper
• Experimental insights into the importance of ecologically dissimilar bacteria to community assembly along a salinity gradient

  2018cites this paper
• Infection dynamics of insecticide-degrading symbionts from soil to insects in response to insecticide spraying

  2018cites this paper
• Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons

  2018cites this paper
• Ugly ducklings—the dark side of plastic materials in contact with potable water

  2018cites this paper
• Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay

  2018cites this paper
• Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China

  2018cites this paper
• Latent environment allocation of microbial community data

  2018cites this paper
• Dynamics of the bacterial community in a channel catfish nursery pond with a cage-pond integration system.

  2018cites this paper
• Microbial Diversity: The Gap between the Estimated and the Known

  2018cites this paper
• Exploring biogeographic patterns of bacterioplankton communities across global estuaries

  2018cites this paper
• Indicators of arable soils fatigue – Bacterial families and genera: A metagenomic approach

  2018cites this paper
• Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs

  2018cites this paper
• Endemicity and climatic niche differentiation in three marine ciliated protists

  2018cites this paper
• Storm Events Restructured Bacterial Community and Their Biogeochemical Potentials

  2018cites this paper
• Applications of Metagenomics in Microbial Bioremediation of Pollutants

  2018cites this paper
• Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens.

  2017cites this paper
• Microbial community structure of an oil polluted site in Effurun , Nigeria

  2017cites this paper
• Strong impact of anthropogenic contamination on the co‐occurrence patterns of a riverine microbial community

  2017cites this paper
• Therapeutic Opportunities in the Vaginal Microbiome

  2017cites this paper
• Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica.

  2017cites this paper
• Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands)

  2017cites this paper
• Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa

  2017cites this paper
• Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change

  2017cites this paper
• Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

  2017cites this paper
• Interplay between stochastic and deterministic processes in the maintenance of alternative community states in Verrucomicrobia-dominated shallow lakes.

  2017cites this paper
• Longitudinal variation of microbial communities in benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams

  2017cites this paper
• ISOLATE AND IDENTIFICATION OF PSEUDOMONAS AERUGINOSA FROM CONTAMINATED SOIL WITH HYDROCARBONS DISCHARGED FROM GAS FILLING REFINERIES

  2017cites this paper
• Long-term chronological shifts in bacterial communities and hydrolytic extracellular enzyme activities in the forty years following a land-use change from upland fields to paddy fields

  2016cites this paper
• Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes

  2016cites this paper
• Water mass dynamics shape Ross Sea protist communities in mesopelagic and bathypelagic layers

  2016cites this paper
• Identification of growing bacteria during litter decomposition in freshwater through H218O quantitative stable isotope probing.

  2016cites this paper
• Stream Biofilm Responses to Flow Intermittency: From Cells to Ecosystems

  2016cites this paper
• Characteristics of aquatic bacterial community and the influencing factors in an urban river.

  2016cites this paper
• Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

  2016cites this paper
• Duration-Related Variations in Archaeal Communities after a Change from Upland Fields to Paddy Fields.

  2016cites this paper
• Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios.

  2016cites this paper
• Proteobacteria become predominant during regrowth after water disinfection.

  2016cites this paper
• Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water.

  2016cites this paper
• Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms

  2016influential citation
• The use of high throughput DNA sequence analysis to assess the endophytic microbiome of date palm roots grown under different levels of salt stress.

  2016cites this paper
• Xenobiotic Metabolism and Gut Microbiomes

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• Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

  2016cites this paper