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Soil genomics

Nature Reviews Microbiology volume 7, page 756 (2009)Cite this article

The recent editorial on the TerraGenome consortium by Vogel et al. (TerraGenome: a consortium for the sequencing of a whole-soil metagenome. Nature Rev. Microbiol. 7, 252 (2009))1 elegantly highlighted the needs, requirements and challenges for sequencing the genomes of soil microorganisms in line with human genome and marine metagenomic projects. Microorganisms are the most diverse and abundant group of organisms and constitute 60% of the Earth's biomass. A current global estimate suggests that soil contains 4–5 × 1030 microbial cells (excluding viruses), 10 times more than the seas. In addition to reservoirs of industrial products worth UK£100s of billions, microorganisms play vital parts in biogeochemical cycling and sustainability2. Therefore, understanding microbial community structure, diversity, functions and stability is essential to our understanding of evolution, community formation and sustainability of life on the Earth. However, obtaining this information has been difficult, owing to our inability to grow microorganisms in laboratory conditions. It is estimated that >99% of microorganisms are currently unculturable under laboratory conditions3. Recent developments in technologies such as metagenomics offer a real opportunity for discoveries in the fundamental science of evolution and community formation.

Although large-scale genome sequencing has become cheaper, metagenomics is still an expensive and time-consuming approach. Based on current estimates of the diversity of soil microbial communities, it is estimated that at least 2 million metagenomic clones will need to be sequenced before we can consider statistically that all of the initial genomes have been included in the metagenomic library4. A large and interdisciplinary consortium is therefore needed to accomplish such an objective, and TerraGenome provides an important start for such an initiative if it is able to secure funding. However, for all practical purposes, this is just a first step forward, and many more concerted approaches will be needed in the future before we can even start to understand soil microbial diversity and community structure. The site (Park Grass) will provide a well-studied and highly relevant reference site. However, there is huge variability in the soil microbial community owing to space, time and management, and therefore many more soils need to undergo metagenomic analysis. Soils in different locations are vastly different in their properties at the landscape scale, but heterogeneity in habitat also occurs at the micro-scale. This creates habitats within habitats at a range of scales from microenvironment (rhizospheres) through aggregates, soil profiles, profile sequences and management units (fields) to landscapes. However, because of cost and logistical reasons, metagenomics for many types of soils is not possible yet.

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References

  1. Vogel, T. M. et al. TerraGenome: a consortium for the sequencing of a soil metagenome. Nature Rev. Microbiol. 7, 252 (2009).

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  2. Curtis, T. P. & Sloan, W. T. Exploring microbial diversity — a vast below. Science 309, 1331–1333 (2006).

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  4. Ginolhac, A. et al. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl. Environ. Microbiol. 70, 5522–5527 (2004).

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  5. He, Z. L. et al. Geochip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 1, 67–77 (2007).

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Authors and Affiliations

  1. Brajesh K. Singh and Colin D. Campbell are at the Macaulay Land Use Research Institute, Aberdeen, AB15 8QH, UK.,

    Brajesh K. Singh & Colin D. Campbell

  2. Soren J. Sorenson is at the Institute of Biology, University of Copenhagen, DK-1307 Copenhagen, Denmark.,

    Soren J. Sorenson

  3. Jizhong Zhou is at the Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma 73072, USA.,

    Jizhong Zhou

Authors
  1. Brajesh K. Singh
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  2. Colin D. Campbell
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  3. Soren J. Sorenson
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  4. Jizhong Zhou
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Correspondence to Brajesh K. Singh.

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Singh, B., Campbell, C., Sorenson, S. et al. Soil genomics. Nat Rev Microbiol 7, 756 (2009). https://doi.org/10.1038/nrmicro2119-c1

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