Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T))

Abstract

Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

Keywords: CSP 2009; Clostridiales; Peptococcaceae; anaerobic; hydrogen sulfide; incomplete oxidizer; mesophilic; mixotrophic; motile; sporulating; sulfate-reducer.

Figure 1

Neighbor-joining tree based on 16S rRNA sequences showing the phylogenetic affiliation of Desulfotomaculum and related species. D. ruminis is printed in bold type. The sequences of different Thermotogales were used as outgroup, but were pruned from the tree. Closed circles represent bootstrap values between 75 and 100%. The scale bar represents 2% sequences difference.

Figure 2

Scanning electron micrograph of D. ruminis DL^T.

Figure 3

Graphical map of the chromosome. From outside to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content (black), GC skew (purple/olive).

Figure 4

Venn diagram showing a comparison of three different Desulfotomaculum genomes, D. ruminis DSM 2154^T, D. acetoxidans DSM 771^T and D. nigrificans DSM 564^T. The number of overlapping protein genes is given inside the areas of the circles and the total number of derived protein sequences used for each strain is shown in parentheses. The figure was created using the program Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center [51].

Figure 5A

Organization of dsrAB and neighboring genes for three Desulfotomaculum species. Other genes are indicated by their locus tags.

Figure 5B

Organization of qmoBA, aprAB and hdrBC and neighboring genes for three Desulfotomaculum species. Other genes are indicated by their locus tags.

Figure 6A

Phylogenetic tree of the dsrAB protein sequences. The trees (6A and 6B) were inferred from proteins sequences using RAxML (maximum-likelihood) in the software program ARB. The sequences of Archaeoglobus fulgidus, A. profundus, and A. veneficus were used as outgroup, but were pruned from the tree. The sequence of D. ruminis is written in bold. The black circles are bootstrap values between 100-75%, the white circles are values between 75-50%. The scale bar corresponds to 10% estimated sequence divergence.

Figure 6B

Phylogenetic tree of the aprBA protein sequence.