The metagenomics of soil
Abstract
Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil microbial communities. This approach has already led to the identification of novel biomolecules. However, owing to the complexity and heterogeneity of the biotic and abiotic components of soil ecosystems, the construction and screening of soil-based libraries is difficult and challenging. This review describes how to construct complex libraries from soil samples, and how to use these libraries to unravel functions of soil microbial communities.
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Soil, roots, and the phyllosphere harbour complex microbiomes of thousands of bacterial and fungal species that may suppress diseases, act as pathogens, or affect plant health and growth.
“Soil, roots, and the phyllosphere harbour complex microbiomes consisting of thousands of bacterial and fungal species that may suppress diseases, act as pathogens, or affect plant health and growth by various other mechanisms [5–8].”
From Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi (2017) · cites this paper as [8]
Cites
Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · cited 1× · see citing works
“Soil is an important reservoir for organic carbon, and prokaryotes are an essential component of the soil decomposition syste”
BackgroundZengler, K., Toledo, G., Rappé, M., Elkins, J., Mathur, E. J., Short, J. M., & Keller, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252630999 · Cited by 796 · see citing works
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Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776 · see citing works
The ecology and biogeochemistry of stream biofilms
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Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
Morgan, J. L., Darling, A. E., & Eisen, J. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010209 · Cited by 248 · see citing works
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- Authors
- Daniel, R.
- Affiliations
- University of Göttingen (DE)
- Corresponding author
- Daniel, Rolf
- ORCID
- Daniel, Rolf
- Venue
- Nature Reviews Microbiology
- Published
- 2005-06
- Volume
- 3
- Issue
- 6
- Pages
- 470-478
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- OpenAlex
- W2167046694
- Cited by
- 862
- References
- 2
- Citations by year
- 2026: 16 · 2025: 41 · 2024: 51 · 2023: 41 · 2022: 41 · 2021: 55 · 2020: 49 · 2019: 53 · 2018: 37 · 2017: 54 · 2016: 42 · 2015: 60 · 2014: 38 · 2013: 36 · 2012: 43
- FWCI
- 2.41
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- GRO (submittedVersion)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- soil metagenomics, soil microbial communities, prokaryotic diversity, microbial community function
- MeSH terms
- DNA, Soil Microbiology, Gene Library, Genomics
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