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

Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 6978: 37-43. doi:10.1038/nature02340


Author Tyson, Gene W.
Chapman, Jarrod
Hugenholtz, Philip
Allen, Eric E.
Ram, Rachna J.
Richardson, Paul M.
Solovyev, Victor V.
Rubin, Edward M.
Rokhsar, Daniel S.
Banfield, Jillian F.
Title Community structure and metabolism through reconstruction of microbial genomes from the environment
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
1476-4687
Publication date 2004-03-04
Year available 2004
Sub-type Article (original research)
DOI 10.1038/nature02340
Open Access Status
Volume 428
Issue 6978
Start page 37
End page 43
Total pages 7
Place of publication London
Publisher Nature Publishing Group
Language eng
Subject 03 Chemical Sciences
0304 Medicinal and Biomolecular Chemistry
0305 Organic Chemistry
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.
Keyword Microbes
Structure
Metabolism
Microbial
Genomes
Environment
Acidophilic biofilm
Leptospirillum
Ferroplasma
Q-Index Code C1
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Wed, 23 Dec 2009, 21:48:34 EST by Macushla Boyle on behalf of Faculty of Science