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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Article
Lawrence Berkeley National Laboratory (2010)

Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column undesirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this marine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome sequence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

    Cover page: Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)
    • Article
    LBL Publications (2008)
    Determining the genetic makeup of predominant microbial taxa with specific metabolic capabilities remains one the major challenges in microbial ecology and bioprospecting, due to the limitations of current cell culturing and metagenomic methods. The complexity of microbial communities and intraspecies variations hinders the assembly of individual genomes from metagenomic shotgun libraries. Here we report the use of single cell genomics to access the genome of a proteorhodopsin-encoding flavobacteria from Gulf of Maine bacterioplankton. We use high throughput fluorescence-activated sorting of single cells, whole genome amplification via multiple displacement amplification, PCR-screening and subsequent shotgun sequencing of this single amplified genome (SAG), allowing the genomic analysis of its novel photometabolic system and the sequence comparison to environmental marine sequence data.
      Cover page: Single Cell Genome Reconstruction of Two Uncultured, Proteorhodopsin-containing Flavobacteria
      • Article
      LBL Publications (2008)
        Cover page: Single Cell Genome Reconstruction of an Uncultured, Proteorhodopsin-Containing Flavobacterium
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2010)
        Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
          Cover page: Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2010)
          'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
            Cover page: Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)
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