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The metagenomics of soil

Key Points

  • Soil is probably the most complex and heterogeneous microbial habitat on earth. The diversity of soil microbial communities exceeds that of other environments.

  • Soil metagenomics is a cultivation-independent molecular approach to explore and exploit the enormous diversity of soil microbial communities. This technology comprises isolation of soil DNA and production and screening of clone libraries.

  • The protocols for isolation of high-quality DNA from soil samples are based either on the recovery of cells and subsequent lysis, or on the direct lysis of cells in the sample followed by DNA purification.

  • Purified soil DNA is used to construct small-insert libraries in plasmid vectors or large-insert libraries in cosmid, fosmid or BAC (bacterial artificial chromosome) vectors. Small-insert libraries are useful to identify single genes or small operons that encode new metabolic functions, and large-insert libraries to recover complex pathways encoded by gene clusters and to characterize genomic fragments of uncultured soil microorganisms.

  • The screening strategies for metagenomic soil libraries are based either on activities of the library clones or on sequence similarities with known genes.

  • Screening of metagenomic soil libraries, especially by activity-based approaches, has led to the identification of various novel biomolecules, including enzymes and antibiotics of industrial importance. To increase gene detection frequencies, enrichment steps for soil microorganisms harbouring the desired traits can be used prior to library construction.

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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Figure 1: Essential steps to explore and exploit the genomic diversity of soil microbial communities by metagenomics.
Figure 2: Examples of activity-based screens.

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Acknowledgements

R.D. is supported by funds of the Competence Network Göttingen 'Genome Research on Bacteria', financed by the German Federal Ministry of Education and Research and by a European Commission grant.

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∫–LIBSHUFF

Glossary

BIOTA

The organisms that occupy an ecosystem.

HUMUS

A complex of heteropolymeric substances, including humic acids, humin and fulvic acids.

ABIOTIC

Non-living objects, substances or processes.

SUBSURFACE

The geological zone below the surface of the Earth. It is not exposed to the Earth's surface.

CONSORTIUM

Physical association between cells of two or more types of microorganisms. Such an association might be advantageous to at least one of the microorganisms.

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Daniel, R. The metagenomics of soil. Nat Rev Microbiol 3, 470–478 (2005). https://doi.org/10.1038/nrmicro1160

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