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Complete genome sequence of Desulfomicrobium baculatum type strain (X)

Alex Copeland et al. Stand Genomic Sci. .

Abstract

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X(T) is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO(2). 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 deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords: Desulfomicrobiaceae; Gram-negative; Sulfate reducer; anaerobe; free-living; freshwater; mesophile; non-pathogenic.

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Figures

Figure 1
Figure 1
Phylogenetic tree of D. baculatum strain XT and all type strains of species within members of the family Desulfomicrobiaceae, inferred from 1,457 aligned characters [4,5] of the 16S rRNA gene sequence under the maximum likelihood criterion [6]. The tree was rooted with all members from the Desulfonatronaceae, another family in the order Desulfovibrionales. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Strains with a genome-sequencing project registered in GOLD [7] are printed in blue; published genomes in bold.
Figure 2
Figure 2
Scanning electron micrograph of D. baculatum XT (Manfred Rohde, Helmholtz Centre for Infection Biology, Braunschweig)
Figure 3
Figure 3
Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.
See this image and copyright information in PMC

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References

    1. Rozanova EP, Nazina TN. A mesophilic, sulfate-reducing, rod-shaped, nonsporeforming bacterium. Mikrobiologiya 1976; 45:825-830 - PubMed
    1. List Editor Validation of the publication of new names and new combinations previously effectively published outside the ISJB. Int J Syst Bacteriol 1984; 34:355-357
    1. Rozanova EP, Nazina TN, Galushko AS. Isolation of a new genus of sulfate-reducing bacteria and description of a new species of this genus, Desulfomicrobium apsheronum gen. nov., sp. nov. Mikrobiologiya 1988; 57:634-641
    1. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464 10.1093/bioinformatics/18.3.452 - DOI - PubMed
    1. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552 - PubMed