Nature 428, 37-43 (4 March 2004) | ; Received 24 November 2003; Accepted 19 January 2004; Published online 1 February 2004

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

Gene W. Tyson1, Jarrod Chapman3,4, Philip Hugenholtz1, Eric E. Allen1, Rachna J. Ram1, Paul M. Richardson4, Victor V. Solovyev4, Edward M. Rubin4, Daniel S. Rokhsar3,4 & Jillian F. Banfield1,2

  1. Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
  2. Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
  3. Department of Physics, University of California, Berkeley, California 94720, USA
  4. Joint Genome Institute, Walnut Creek, California 94598, USA

Correspondence to: Jillian F. Banfield1,2 Email:
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession code AADL00000000. The version described in this paper is the first version, AADL01000000.


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.


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