Abstract
The field of microbial genomics has embarked in a new direction, as shown by sequence analysis of a community of microbes from a biofilm growing on the surface of acid mine drainage (AMD) at the Richmond mine at Iron Mountain in California. The underground AMD site has a community with a low diversity of microorganisms (based on 16S rRNA analysis), which is probably not surprising given that the environment consists of a pH of 0.83, a temperature of 42 °C and high concentrations of several heavy metals. Tyson and colleagues [ 1 Tyson, G.W. et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 10.1038/nature02340 (http://www.nature.com). Google Scholar ] have reported the successful application of the whole-genome shotgun strategy, the assembly of nearly complete genomes of two species and also partial recovery of three other species from this environmental sample. Scaffolds generated from the assembly of 103 462 sequence reads, totaling more than 76 million bp of DNA, were initially separated into low (<43.5%) and high (>43.5%) G+C bins. Each bin included scaffolds with ∼10-fold sequence coverage, each associated with a single 16S rRNA gene. These two sets of scaffolds were found to represent the nearly complete genome sequences of a Leptospirillum group II bacterium (estimated genome size of 2.23 Mb) and a Ferroplasma type II archaeon (estimated genome size of 1.9 Mb). In addition, three partial genome sequences from more distantly related species of the Leptospirillum group III, Ferroplasma type I and G-plasma were also obtained.
Published Version
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