Community structure and metabolism through reconstruction of microbial genomes from the environment

Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, Paul M. Richardson, Victor V. Solovyev, Edward M. Rubin, Daniel S. Rokhsar and Jillian F. Banfield ()
Additional contact information
Gene W. Tyson: University of California
Jarrod Chapman: University of California
Philip Hugenholtz: University of California
Eric E. Allen: University of California
Rachna J. Ram: University of California
Paul M. Richardson: Joint Genome Institute
Victor V. Solovyev: Joint Genome Institute
Edward M. Rubin: Joint Genome Institute
Daniel S. Rokhsar: University of California
Jillian F. Banfield: University of California

Nature, 2004, vol. 428, issue 6978, 37-43

Abstract: Abstract Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.

Date: 2004
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DOI: 10.1038/nature02340

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