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

Journal Article · Thu Jan 01 04:00:00 EST 2004 · Nature

DOI:https://doi.org/10.1038/nature02340· OSTI ID:834233

Tyson, Gene W ^[1]; Chapman, Jarrod; Hugenholtz, Phillip; Allen, Eric E; Rachna, Ram J; Richardson, Paul M; Solovyev, Victor V; Rubin, Edward M; Rokhsar, Daniel S; Banfield, Jillian F

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1. LBNL Library

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.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director. Office of Science. Office of Biological and Environmental Research. Microbial Genomics Program; National Science Foundation. Biocomplexity Program (US)
• DOE Contract Number: AC03-76SF00098
• OSTI ID: 834233
• Report Number(s): LBNL--55327
• Journal Information: Nature, Journal Name: Nature Vol. 428
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
CARBON
COMMUNITIES
DNA
ECOSYSTEMS
GENES
METABOLISM
MICROORGANISMS
NITROGEN FIXATION
NUCLEOTIDES
RECOMBINATION
STRAINS