ABSTRACT

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

GENOME ANNOUNCEMENT

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B was isolated from groundwater of well FW-101 at The Field Research Center (FRC) at Oak Ridge National Lab (ORNL). The FRC is part of the Y-12 security complex, located in the Bear Creek drainage. ICP-MS analysis of FW-101 groundwater in late 2001 estimated uranium concentrations between 20 and 250 ppm, and chromium concentrations between 35 and 85 ppm. Previous studies have demonstrated reduction of nitrate and uranium levels in the subsurface upon bio-stimulation with ethanol at the FRC (13). During bio-stimulation, an increase was observed in DNA sequences corresponding to sulfate-reducing bacteria. Groundwater from well FW-101 at the FRC site was collected during the uranium-reduction phase of a previously described biostimulation experiment (3) and used as inoculum for an enrichment culture for sulfate-reducing bacteria. The enrichment was grown at room temperature anaerobically in ES4D medium (pH 6.7). The ES4D medium has the same ingredients as a previously described medium, LS4D, except ethanol replaced the lactate (4).
The genome was sequenced by 454 GS FLX Titanium and paired-end Illumina GAii (2 × 35 bp). The pyrosequencing and Illumina reads were assembled using the Newbler (Roche) and Velvet (5), respectively. Phred/Phrap/Consed (http://www.phrap.com) was used for genome finishing. Genes were identified using Prodigal (6) and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional annotation was performed within the (IMG-ER) platform (7).
Sequence determination revealed a 4.1-Mb genome with 66.5% G+C content, which is comparable to D. carbinoliphilus (63% G+C) and Desulfovibrio vulgaris (63.3% G+C). The COG predictions categorize 581 of the 3,737 protein-encoding genes as pertaining to information storage and processing, 1,183 as cellular processes, 1,576 as metabolism genes, and 596 as poorly characterized functions. Sequencing detected 2 plasmids of different sizes and G+C content, pFW10101 (97,864 bp, 67% G+C) and pFW10102 (21,111 bp, 57.5% G+C).
FW-101-2B was most closely related to D. carbinoliphilus D41T. The ANIb values calculated by JSpecies (8) showed that FW-101-2B was more similar to D. vulgaris Miyazaki (69.11%), D. vulgaris Hildenborough (67.45%), and D. vulgaris DP4 (67.41%) than Syntrophobacter fumaroxidans (64.68) and Desulfovibrio desulfuricans ATCC 27774 (60.93%). The small-subunit (SSU) rRNA gene and sulfite reductase gene (dsrAB) of FW-101-2B was most similar to D. carbinoliphilus D41T at 99% and 92% similarity, respectively.
Although FW-101-2B is phylogenetically very similar to D. carbinoliphilus D41T, physiological evidence would support classification of a new strain. Thus, we propose the classification as D. carbinoliphilus subsp. oakridgensis. This is the first genome sequence of a D. carbinoliphilus strain.

Nucleotide sequence accession numbers.

The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ADFE00000000. The version described in this paper is the version ADFE00000000.2.

ACKNOWLEDGMENTS

Work conducted by ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) is supported by the Office of Science, Office of Biological and Environmental Research, U.S. Department of Energy contract DE-AC02-05CH11231. The work at Lawrence Livermore National Laboratory was supported under contract DE-AC52-07NA27344, and work at Los Alamos National Laboratory was supported under contract DE-AC02-06NA25396.

REFERENCES

1.
Wu W-M, Carley J, Luo J, Ginder-Vogel MA, Cardenas E, Leigh MB, Hwang C, Kelly SD, Ruan C, Wu L, Van Nostrand J, Gentry T, Lowe K, Mehlhorn T, Carroll S, Luo W, Fields MW, Gu B, Watson D, Kemner KM, Marsh T, Tiedje J, Zhou J, Fendorf S, Kitanidis PK, Jardine PM, Criddle CS. 2007. In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environ Sci Technol 41:5716–5723.
2.
Wu W, Carley J, Watson D, Gu B, Brooks S, Kelly SD, Kemner K, van Nostrand JD, Wu L, Xu M, Zhou J, Luo J, Cardenas E, Hwang C, Fields MW, Marsh TL, Tiedje JM, Green SJ, Kostka JE, Kitanidis PK, Jardine PM, Criddle CS. 2011. Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Huanjing Kexue Xuebao 31:449–459.
3.
Hwang C, Wu W, Gentry TJ, Carley J, Corbin GA, Carroll SL, Watson DB, Jardine PM, Zhou J, Criddle CS, Fields MW. 2009. Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J 3:47–64.
4.
Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan X-F, Hazen TC, Arkin AP, Wall JD, Zhou J-Z, Fields MW. 2006. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Appl Environ Microbiol 72:5578–5588.
5.
Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829.
6.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
7.
Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271–2278.
8.
Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 230 April 2015
eLocator: 10.1128/genomea.00092-15

History

Received: 23 January 2015
Accepted: 2 February 2015
Published online: 12 March 2015

Contributors

Authors

Bradley D. Ramsay
Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
Chiachi Hwang
Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
Sue L. Carroll
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Susan Lucas
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
James Han
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Alla L. Lapidus
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Jan-Fang Cheng
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Lynne A. Goodwin
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Samuel Pitluck
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Lin Peters
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Olga Chertkov
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Brittany Held
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
John C. Detter
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Cliff S. Han
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Roxanne Tapia
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Miriam L. Land
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Loren J. Hauser
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Nikos C. Kyrpides
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Natalia N. Ivanova
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Natalia Mikhailova
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Ioanna Pagani
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Tanja Woyke
Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Adam P. Arkin
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
ENIGMA, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Paramvir Dehal
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
ENIGMA, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Dylan Chivian
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
ENIGMA, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Craig S. Criddle
Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
Weimin Wu
Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
Romy Chakraborty
ENIGMA, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Terry C. Hazen
Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
ENIGMA, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, USA
Department of Earth & Planetary Sciences, The University of Tennessee, Knoxville, Tennessee, USA
Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
ENIGMA, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA

Notes

Address correspondence to Terry C. Hazen, [email protected], or Matthew W. Fields, [email protected].

Metrics & Citations

Metrics

Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy