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Soil Microbes: Metagenomic Approaches

Source:  Janet Jansson

Soil contains 109-1010 microbial cells per gram, and these cells conduct life-sustaining functions for our planet.

From a microbiological perspective, soil is largely unexplored, even though we know it has a rich diversity of microbial life—it contains billions to trillions of microbial cells per gram, including tens of thousands of different bacterial, archaeal, and fungal species, plus viruses and protists.

Soil microbes carry out life-sustaining functions for our planet, including cycling of nutrients and promoting plant growth. Respiring soil microorganisms, producing metabolic byproducts such as carbon dioxide and methane, cycle enormous volumes of carbon-containing gases from the terrestrial ecosystem into the atmosphere. Perturbing this ecosystem—for example, when global warming raises temperatures—potentially alters the flux of these gases. Despite the immensity of the carbon reservoir in soil (approximately 2,300 gigatons), how this reservoir affects climate change is not known.

The high diversity of soil microbial communities makes them difficult to study. Exacerbating this difficulty, few soil microorganisms are amenable to isolation and cultivation, steps that in conventional terms are crucial for elucidating microbial physiology and biochemistry. Although most isolated soil bacteria, such as pseudomonads and actinobacteria, are opportunistic and capable of growth on laboratory media, 16S rRNA gene surveys reveal that few species from the great bulk of soil bacteria have cultured representatives. For example, members of the Acidobacteria phylum are widespread in soil but are notoriously difficult to cultivate.

To address these issues, a team of ESD microbial ecologists led by Janet Jansson—including Regina Lamendella (E.O. Lawrence Fellow), Jenni Hultman, Neslihan Tas, and Maude David —are using a metagenomics approach, sequencing DNA from a wide variety of soil samples and from different climates, regions, and conditions—to develop a better grasp of microbial identities and their potential functions in soils. (Note that the ESD team works in collaboration with Joint Genome Institute colleagues Eddy Rubin, Susannah Tringe, Rachel Mackelprang, Nikos Kyrpides, and others—as well as cooperating with scientists throughout the world pursuing similar investigations.)


Suggested Reading:

  • Fierer, N., and R. B. Jackson (2006), The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626-631. Gilbert, J. A., and C. L. Dupont (2011), Microbial metagenomics: beyond the genome. Annu. Rev. Mar. Sci. 3:357-371.
  • Tringe, S. G., C. von Mering, A. Kobayashi, A. A. Salamov, K. Chen, H. W. Chang, M. Podar, J. M. Short, E. J. Mathur, J. C. Detter, P. Bork, P. Hugenholtz, and E. M. Rubin (2005), Comparative metagenomics of microbial communities. Science 308:554-557
  • Vogel, T. M., P. Simonet, J. K. Jansson, P. R. Hirsch, J. M. Tiedje, J. D. Van Elsas, M. J. Bailey, R. Nalin, and L. Philippot (2009), TerraGenome: a consortium for the sequencing of a soil metagenome. Nature Rev. Microbiol. 7:1.
  • Yergeau, E., H. Hogues, L. G. Whyte, and C. W. Greer (2010), The functional potential of high arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J. 4:1206-1214.
  • Yilmaz, P., R. Kottmann, d. Field, R. Knight, J.R. Cole, et al. (2011), Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotech. 29, 415–419.


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