Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))

Abstract

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.

Keywords: Deltaproteobacteria; Desulfohalobiaceae; GEBA; Gram-negative; Proteobacteria; hydrogen utilization; hypersaline lake; mesophile; moderately halophilic; strictly anaerobic; sulfate-reducer.

Figure 1

Phylogenetic tree highlighting the position of strain HR₁₀₀^T, D. retbaense DSM 5692, relative to the other type strains within the family. The tree was inferred from 1,386 aligned characters [6,7] of the 16S rRNA gene sequence under the maximum likelihood criterion [8] and rooted in accordance with the type strain of 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%. Lineages with type strain genome sequencing projects registered in GOLD [9] are shown in blue, published genomes in bold.

Figure 2

Scanning electron micrograph of cells of D. retbaense strain HR₁₀₀^T

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.

Figure 4

Proposed organization of the electron transfer chain in D. retbaense with H₂ as electron donor and sulfate as electron acceptor. Gene products are designated according to the information given in Supplementary Table 1. Subunits of multiprotein complexes are labeled with capital letters. Abbreviations: APS, adenosine-5'-phosphosulfate; AMP, adenosine monophosphate; MQ, menaquinone; MQH2, dihydromenaquinone.