Abstract
Desulfovibrio alaskensis G20 (formerly Desulfovibrio desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7-Mb genome sequence to provide insights into its physiology.
GENOME ANNOUNCEMENT
Desulfovibrio desulfuricans G100A is a deltaproteobacterium that was isolated from a producing oil well in Ventura County, California (8). Strain G20 is a spontaneously nalidixic acid-resistant derivative of G100A that is also lacking the endogenous cryptic 2.3-kb plasmid, pBG1 (6).
Strictly anaerobic sulfate-reducing bacteria (SRB) of the Desulfovibrio genus have provided a rich experimental system for understanding energy conversion because of their ability to respire sulfate, ferment organic acids, and live in syntrophic associations. Hydrogen metabolism appears to be fundamental for these growth modes. In 1981, Odom and Peck (4) proposed the hydrogen-cycling model as an explanation for the hydrogen transients seen during growth on organic acids with sulfate. This model requires both cytoplasmic and periplasmic hydrogenases. As the second SRB to have a complete genome sequence available, G20 revealed the lack of conservation of annotated cytoplasmic hydrogenases necessary for this cycle. Therefore, either “hydrogen cycling” does not make an essential contribution to the SRB energy budget or different members of the genus have derived different solutions to the electron flow to sulfate. Importantly, these electron pathways are critical to understanding ferrous metal corrosion (5) and the capacity for reduction of toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms (3).
It was observed that the 16S rRNA gene sequence of D. desulfuricans G20 was >97% identical to those of Desulfovibrio alaskensis. DNA-DNA hybridization results (performed by Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH) between the G20 strain, D. alaskensis (ID 04-514), and the D. desulfuricans subsp. desulfuricans type strain DSM 642T showed that G20 and D. alaskensis were 84.3% similar. With a 70% threshold value for definition of bacterial species (7), these strains are related at the species level. Neither belongs to the D. desulfuricans species. We propose reclassification of D. desulfuricans G20 as Desulfovibrio alaskensis G20.
The original genome annotation was performed as described in reference 1. To update the gene predictions, the gene-calling algorithm Prodigal (2) was used, and the two sets of gene calls were compared. All original genes not predicted by Prodigal were eliminated unless there were shotgun proteomic or gene expression array data to support their inclusion (A. Arkin, personal communication). All other differences were resolved manually. The updated annotation is available at http://genome.ornl.gov/microbial/ddes.
The D. alaskensis G20 genome is 57.8% GC and contains 3.7 Mbps, 66 tRNA genes, and 4 rRNA cistrons. The original annotation predicted 3,775 protein coding genes and 9 pseudogenes, whereas the updated annotation predicts 3,258 protein coding genes and 25 pseudogenes. The updated annotation confirmed 2,834 genes, lengthened 74, shortened 280, added 54, deleted 554 genes, changed 19 to pseudogenes, changed 2 pseudogenes to real genes, added 4 new pseudogenes, deleted 5 pseudogenes, and modified 14 other genes. Approximately 25% of the original protein coding genes were changed in some way.
Nucleotide sequence accession number.
This genome has been deposited at DDBJ/EMBL/GenBank under the accession number CP000112. The version described in this paper is the second version.
Acknowledgments
This research was supported by the Office of Biological and Environmental Research (OBER), Office of Science, U.S. Department of Energy (DOE), in part through ENIGMA—Ecosystems and Networks Integrated with Genes and Molecular Assemblies under contract no. DE-AC02-05CH11231 (M.N.P., S.D.B., J.D.W., and K.L.K.), by Genomics Program: GTL BioHydrogen Production and BioEthanol contract DE-FG02-083464691 (J.D.W., K.L.K., and S.D.B.), and by the DOE Office of Basic Energy Sciences, contract DE-FG02-87ER13713 (J.D.W. and B.J.R.-G.). Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the DOE under contract DE-AC05-00OR22725. The work conducted by the DOE Joint Genome Institute is supported by the Office of Science under contract no. DE-AC02-05CH11231. A portion of the research was performed by EMSL, a national scientific user facility sponsored by the DOE OBER and located at the Pacific Northwest National Laboratory.
Footnotes
Published ahead of print on 17 June 2011.
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