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Toward a Census of Bacteria in Soil

https://doi.org/10.1371/journal.pcbi.0020092

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Total bacterial diversity in soil and sediment communities—A review

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Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities

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Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution

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Santa Rosalia revisited: Why are there so many species of bacteria?

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Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation‐independent surveys

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Predicting microbial species richness

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Estimating prokaryotic diversity and its limits

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Prokaryotes: The unseen majority

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Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA

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Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

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Stopping Rules and Estimation for Recapture Debugging with Unequal Failure Rates

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A new DNA sequence assembly program

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rrndb: the Ribosomal RNA Operon Copy Number Database

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The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

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ARB: a software environment for sequence data

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The Soil and the Microbe

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Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology

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Intraspecific Variation in Small-Subunit rRNA Sequences in GenBank: Why Single Sequences May Not Adequately Represent Prokaryotic Taxa

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Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms

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Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes.

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Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases

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Comparative Metagenomics of Microbial Communities

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Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil

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High diversity in DNA of soil bacteria

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Microbial Community Changes in a Perturbed Agricultural Soil Investigated by Molecular and Physiological Approaches

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Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples

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Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning

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Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures

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Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity

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Empirical and Theoretical Bacterial Diversity in Four Arizona Soils

inferredcites →https://doi.org/10.1128/aem.70.4.2429-2436.2004openalex-snapshot

Exploring Nitrilase Sequence Space for Enantioselective Catalysis

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Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor

inferredcites →https://doi.org/10.1128/aem.71.3.1501-1506.2005openalex-snapshot

Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

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Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity

inferredcites →https://doi.org/10.1128/mmbr.68.4.686-691.2004openalex-snapshot

Status of the Microbial Census

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Phylogenetic identification and in situ detection of individual microbial cells without cultivation

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Metagenomics: Genomic Analysis of Microbial Communities

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Robust Estimation of Population Size When Capture Probabilities Vary Among Animals

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Measuring biological diversity

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Biodiversity restated: > 99.9% of global species in Soil Biota

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Comparative Metagenome Analysis Using MEGAN

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GeoChip: A High‐Throughput Metagenomics Technology for Dissecting Microbial Community Functional Structure

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Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters

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To Grow or Not to Grow: Isolation and Cultivation Procedures in the Genomic Age

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Metaproteomics to unravel major microbial players in leaf litter and soil environments: C hallenges and perspectives

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Quantitative stable isotope probing with H 2 18 O to measure taxon‐specific microbial growth

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Protocols for Investigating the Microbiology of Drilling Fluids, Hydraulic Fracturing Fluids, and Formations in Unconventional Natural Gas Reservoirs

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Clone Libraries of Ribosomal RNA Gene Sequences for Characterization of Microbial Communities

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DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy

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Rhizosphere Meta Transcriptomics

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Microbial Communities, Structure, and Function

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Microarray-Based Amplification Product Detection and Identification

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Soil Metagenomics

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Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning

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Molecular Methods to Study Complex Microbial Communities

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inferred← citeshttps://doi.org/10.1007/978-3-030-73507-4_18openalex-snapshot

Global Scenario of Soil Microbiome Research: Current Trends and Future Prospects

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Diversity of Plant-Growth-Promoting Rhizobacteria Associated with Maize (Zea mays L.)

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Developing Disease-Suppressive Soil Through Agronomic Management

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Metagenomic Mining of Enzyme Diversity

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Metagenomic Mining of Enzyme Diversity

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Enhancing Metagenomic Approaches Through Synthetic Biology

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Effects of Spatial Structure and Reduced Growth Rates on Evolution in Bacterial Populations

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Tree Endophytes: Cryptic Drivers of Tropical Forest Diversity

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Clone Libraries of Ribosomal RNA Gene Sequences for Characterization of Bacterial and Fungal Communities

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Functional Marker Gene Assays for Hydrocarbon Degrading Microbial Communities: Aerobic

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Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil

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Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information

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Soil Bacteria and Bacteriophages

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Identification and Analysis of Prophages and Phage Remnants in Soil Bacteria

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Studying the Life Cycle of Aerobic Endospore-forming Bacteria in Soil

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Probiotics for Plants: Importance of Rhizobacteria on Aboveground Fitness in Plants

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Climate Change Influences the Interactive Effects of Simultaneous Impact of Abiotic and Biotic Stresses on Plants

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Bacterial colonies as complex adaptive systems

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Archaea in dry soil environments

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Speciation

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Principles of taxonomy

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Learning what counting tells us

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Classification logic

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Inflection of the root microbiome by plants: Plant growth promotion and disease management

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Applications of Functional Gene Microarrays for Profiling Microbial Communities

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New Developments and Applications of Microarrays for Microbial Community Analysis in Natural and Impacted Ecosystems

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Emerging approaches to manipulate the plant microbiome and implications

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Characterization of bacteria isolated from maize roots: Emphasis on Serratia and infestation with corn rootworms (Chrysomelidae: Diabrotica)

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Humusica 1, article 8: Terrestrial humus systems and forms – Biological activity and soil aggregates, space-time dynamics

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Investigating the effect of biochar and fertilizer on the composition and function of bacteria in red soil

inferred← citeshttps://doi.org/10.1016/j.apsoil.2020.103849openalex-snapshot

Detection of Azospirillum brasilense by qPCR throughout a maize field trial

inferred← citeshttps://doi.org/10.1016/j.biocon.2011.03.001openalex-snapshot

Food for thought: Risks of non-native species transfer to the Antarctic region with fresh produce

inferred← citeshttps://doi.org/10.1016/j.biocontrol.2015.04.019openalex-snapshot

Rhizospheric changes of fungal and bacterial communities in relation to soil health of multi-generation apple orchards

inferred← citeshttps://doi.org/10.1016/j.catena.2026.110293openalex-snapshot

Fire severity alters soil microbial diversity and community stability in a subtropical forest ecosystem

inferred← citeshttps://doi.org/10.1016/j.chemosphere.2013.07.073openalex-snapshot

Diversity of chlorobiphenyl-metabolizing bacteria and their biphenyl dioxygenases in contaminated sediment

inferred← citeshttps://doi.org/10.1016/j.chom.2015.04.009openalex-snapshot

Microbiota and Host Nutrition across Plant and Animal Kingdoms

inferred← citeshttps://doi.org/10.1016/j.coal.2008.05.001openalex-snapshot

Characterization of a methanogenic consortium enriched from a coalbed methane well in the Powder River Basin, U.S.A.

inferred← citeshttps://doi.org/10.1016/j.copbio.2011.12.021openalex-snapshot

Applications of functional gene microarrays for profiling microbial communities

inferred← citeshttps://doi.org/10.1016/j.cub.2022.02.002openalex-snapshot

Microbial communities: The metabolic rate is the trait

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2021.112707openalex-snapshot

Application, release, ecotoxicological assessment of biocide in building materials and its soil microbial response

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2026.120191openalex-snapshot

Heavy metals, gastrointestinal polymer-related materials, and gut microbiome in an Indo-Pacific bottlenose dolphin (Tursiops aduncus) recovered from a fisheries bycatch-related event in the East China Sea

inferred← citeshttps://doi.org/10.1016/j.ecohyd.2023.08.013openalex-snapshot

No trophy for the trophy? - How lake trophy impacts bacterial assemblages of biofilm on microplastic

inferred← citeshttps://doi.org/10.1016/j.ejsobi.2011.11.010openalex-snapshot

Measuring the effects of pesticides on bacterial communities in soil: A critical review

inferred← citeshttps://doi.org/10.1016/j.envsoft.2013.12.001openalex-snapshot

Optimizing biodiversity prediction from abiotic parameters

inferred← citeshttps://doi.org/10.1016/j.foreco.2021.118989openalex-snapshot

The impact of fire on soil-dwelling biota: A review

inferred← citeshttps://doi.org/10.1016/j.gene.2019.02.099openalex-snapshot

Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India

inferred← citeshttps://doi.org/10.1016/j.geoderma.2023.116455openalex-snapshot

The role of inherited characteristics from parent materials in shaping bacterial communities in agricultural soils

inferred← citeshttps://doi.org/10.1016/j.ijantimicag.2013.05.004openalex-snapshot

Alternative natural sources for a new generation of antibacterial agents

inferred← citeshttps://doi.org/10.1016/j.jare.2014.10.005openalex-snapshot

Assessing the global phylum level diversity within the bacterial domain: A review

inferred← citeshttps://doi.org/10.1016/j.jenvman.2023.119885openalex-snapshot

Effect of fire and post-fire management on soil microbial communities in a lower subtropical forest ecosystem after a mountain fire

inferred← citeshttps://doi.org/10.1016/j.jhazmat.2012.05.031openalex-snapshot

Improved detection of microbial risk of releasing genetically modified bacteria in soil by using massive sequencing and antibiotic resistance selection

inferred← citeshttps://doi.org/10.1016/j.jprot.2014.01.007openalex-snapshot

Non-model organisms, a species endangered by proteogenomics

inferred← citeshttps://doi.org/10.1016/j.jprot.2019.103623openalex-snapshot

The total microbiome functions in bacteria and fungi

inferred← citeshttps://doi.org/10.1016/j.mib.2010.08.005openalex-snapshot

Antibiotic resistance in the environment: a link to the clinic?

inferred← citeshttps://doi.org/10.1016/j.mib.2011.04.010openalex-snapshot

Metagenomic exploration of antibiotic resistance in soil

inferred← citeshttps://doi.org/10.1016/j.micres.2015.02.007openalex-snapshot

The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea

inferred← citeshttps://doi.org/10.1016/j.micres.2021.126732openalex-snapshot

Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation

inferred← citeshttps://doi.org/10.1016/j.micres.2021.126943openalex-snapshot

Combined application of H2S and a plant growth promoting strain JIL321 regulates photosynthetic efficacy, soil enzyme activity and growth-promotion in rice under salt stress

inferred← citeshttps://doi.org/10.1016/j.mimet.2008.05.009openalex-snapshot

Species richness in soil bacterial communities: A proposed approach to overcome sample size bias

inferred← citeshttps://doi.org/10.1016/j.mimet.2011.10.007openalex-snapshot

Nonlinear electrophoresis for purification of soil DNA for metagenomics

inferred← citeshttps://doi.org/10.1016/j.pedobi.2016.03.004openalex-snapshot

Soil biota in a megadiverse country: Current knowledge and future research directions in South Africa

inferred← citeshttps://doi.org/10.1016/j.resmic.2014.05.036openalex-snapshot

Seasonal changes in dominant bacterial taxa from acidic peatlands of the Atlantic Rain Forest

inferred← citeshttps://doi.org/10.1016/j.rhisph.2023.100769openalex-snapshot

Plant mediates soil water content effects on soil microbiota independently of its water uptake

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2016.05.185openalex-snapshot

Environmental drivers of soil microbial community structure and function at the Avon River Critical Zone Observatory

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2021.144966openalex-snapshot

Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2021.152515openalex-snapshot

Four-year biochar study: Positive response of acidic soil microenvironment and citrus growth to biochar under potassium deficiency conditions

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2023.164506openalex-snapshot

Diversity of Fungal Microbiome Obtained from Plant Rhizoplanes

inferred← citeshttps://doi.org/10.1016/j.soilbio.2010.04.017openalex-snapshot

Optimizing the indirect extraction of prokaryotic DNA from soils

inferred← citeshttps://doi.org/10.1016/j.soilbio.2012.11.009openalex-snapshot

Soil enzymes in a changing environment: Current knowledge and future directions

inferred← citeshttps://doi.org/10.1016/j.still.2023.105920openalex-snapshot

Comparative analysis of rhizobial and bacterial communities in experimental cotton fields: Impacts of conventional and conservation soil management in the Texas High Plains

inferred← citeshttps://doi.org/10.1016/j.watres.2010.05.039openalex-snapshot

Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids

inferred← citeshttps://doi.org/10.1016/s1002-0160(19)60826-xopenalex-snapshot

A new perspective on functional redundancy and phylogenetic niche conservatism in soil microbial communities

inferred← citeshttps://doi.org/10.1017/cbo9780511777592.002openalex-snapshot

Biodiversity discovery and its importance to conservation

inferred← citeshttps://doi.org/10.1021/acs.est.0c03566openalex-snapshot

Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management

inferred← citeshttps://doi.org/10.1038/455724aopenalex-snapshot

Soil ecology: What lies beneath

inferred← citeshttps://doi.org/10.1038/ismej.2007.53openalex-snapshot

Pyrosequencing enumerates and contrasts soil microbial diversity

inferred← citeshttps://doi.org/10.1038/ismej.2008.106openalex-snapshot

Diversity rankings among bacterial lineages in soil

inferred← citeshttps://doi.org/10.1038/ismej.2008.5openalex-snapshot

Evaluating different approaches that test whether microbial communities have the same structure

inferred← citeshttps://doi.org/10.1038/ismej.2008.69openalex-snapshot

The rational exploration of microbial diversity

inferred← citeshttps://doi.org/10.1038/ismej.2009.136openalex-snapshot

Biogeography of soil archaea and bacteria along a steep precipitation gradient

inferred← citeshttps://doi.org/10.1038/ismej.2009.43openalex-snapshot

Abundance, composition, diversity and novelty of soil Proteobacteria

inferred← citeshttps://doi.org/10.1038/ismej.2009.83openalex-snapshot

Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing

inferred← citeshttps://doi.org/10.1038/ismej.2011.151openalex-snapshot

Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle

inferred← citeshttps://doi.org/10.1038/ismej.2011.170openalex-snapshot

The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

inferred← citeshttps://doi.org/10.1038/ismej.2013.10openalex-snapshot

Robust estimation of microbial diversity in theory and in practice

inferred← citeshttps://doi.org/10.1038/ismej.2013.180openalex-snapshot

Species matter: the role of competition in the assembly of congeneric bacteria

inferred← citeshttps://doi.org/10.1038/ismej.2015.198openalex-snapshot

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

inferred← citeshttps://doi.org/10.1038/ismej.2015.54openalex-snapshot

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils

inferred← citeshttps://doi.org/10.1038/ng.2536openalex-snapshot

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

inferred← citeshttps://doi.org/10.1038/nrmicro1969openalex-snapshot

Wolbachia: master manipulators of invertebrate biology

inferred← citeshttps://doi.org/10.1038/nrmicro2259openalex-snapshot

Bacterial competition: surviving and thriving in the microbial jungle

inferred← citeshttps://doi.org/10.1038/nrmicro3400openalex-snapshot

Ecology and exploration of the rare biosphere

inferred← citeshttps://doi.org/10.1038/nrmicro3468openalex-snapshot

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

inferred← citeshttps://doi.org/10.1038/s41396-018-0162-5openalex-snapshot

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship

inferred← citeshttps://doi.org/10.1038/s41467-019-10542-0openalex-snapshot

Probing the active fraction of soil microbiomes using BONCAT-FACS

inferred← citeshttps://doi.org/10.1038/s41467-024-53989-6openalex-snapshot

Cell shape affects bacterial colony growth under physical confinement

inferred← citeshttps://doi.org/10.1038/s41589-018-0100-xopenalex-snapshot

The evolving interface between synthetic biology and functional metagenomics

inferred← citeshttps://doi.org/10.1038/s41598-019-43031-xopenalex-snapshot

Predicting Growth and Carcass Traits in Swine Using Microbiome Data and Machine Learning Algorithms

inferred← citeshttps://doi.org/10.1038/s41598-020-71102-xopenalex-snapshot

Comparative analysis of racial differences in breast tumor microbiome

inferred← citeshttps://doi.org/10.1038/s42254-025-00849-xopenalex-snapshot

On the growth and form of bacterial colonies

inferred← citeshttps://doi.org/10.1038/s43016-024-01024-8openalex-snapshot

Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management

inferred← citeshttps://doi.org/10.1038/s43017-026-00806-xopenalex-snapshot

Heterotrophic respiration by soil microbes in a changing climate

inferred← citeshttps://doi.org/10.1038/srep01413openalex-snapshot

The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing

inferred← citeshttps://doi.org/10.1038/srep03895openalex-snapshot

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi indicated by metagenomics

inferred← citeshttps://doi.org/10.1038/srep28628openalex-snapshot

Induction of a stable sigma factor SigR by translation-inhibiting antibiotics confers resistance to antibiotics

inferred← citeshttps://doi.org/10.1038/srep33239openalex-snapshot

Soil bacteria as sources of virulence signal providers promoting plant infection by Phytophthora pathogens

inferred← citeshttps://doi.org/10.1039/d1np00044fopenalex-snapshot

Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites

inferred← citeshttps://doi.org/10.1042/etls20160017openalex-snapshot

Novel therapeutics for bacterial infections

inferred← citeshttps://doi.org/10.1071/sr19067openalex-snapshot

Soil biodiversity and biogeochemical function in managed ecosystems

inferred← citeshttps://doi.org/10.1073/pnas.1711842115openalex-snapshot

The biomass distribution on Earth

inferred← citeshttps://doi.org/10.1073/pnas.2208019119openalex-snapshot

Morphological instability and roughening of growing 3D bacterial colonies

inferred← citeshttps://doi.org/10.1080/00103624.2023.2211605openalex-snapshot

Impact of Cover Crops and Nitrogen Management on Soil Bacterial Alpha Diversity

inferred← citeshttps://doi.org/10.1080/00103624.2024.2380492openalex-snapshot

Effect of Different Approaches of Nutrient Application on Soil Quality Index Under Maize-Wheat Cropping System in Mollisol Region of Uttarakhand

inferred← citeshttps://doi.org/10.1080/00207233.2020.1845533openalex-snapshot

Geoecological study of the soil microbial communities of the natural and agricultural ecosystems in the south-eastern Baltic sea region

inferred← citeshttps://doi.org/10.1080/00288233.2018.1428203openalex-snapshot

Managing soil microbiology: realising opportunities for the productive land‐based sectors

inferred← citeshttps://doi.org/10.1080/09593331003789511openalex-snapshot

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota

inferred← citeshttps://doi.org/10.1080/09670874.2016.1211771openalex-snapshot

Occurrence of soil insect pests: insight from classical identification supplemented with DNA barcoding

inferred← citeshttps://doi.org/10.1080/10643389.2011.592735openalex-snapshot

Adaptation of Soil Microorganisms to Trace Element Contamination: A Review of Mechanisms, Methodologies, and Consequences for Risk Assessment and Remediation

inferred← citeshttps://doi.org/10.1080/11263500903374724openalex-snapshot

Bacterial and fungal communities associated with Tuber magnatum ‐productive niches

inferred← citeshttps://doi.org/10.1080/23766808.2021.1920296openalex-snapshot

DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador

inferred← citeshttps://doi.org/10.1086/701597openalex-snapshot

Watershed hydrology and salinity, but not nutrient chemistry, are associated with arid-land stream microbial diversity

inferred← citeshttps://doi.org/10.1089/ast.2009.0443openalex-snapshot

High-Density 16S Microarray and Clone Library–Based Microbial Community Composition of the Phoenix Spacecraft Assembly Clean Room

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