Draft Genome Sequences for Three Mercury-Methylating,
Sulfate-Reducing Bacteria
Steven D. Brown,a Richard A. Hurt, Jr.,a Cynthia C. Gilmour,b Dwayne A. Eliasa
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAa; Smithsonian Environmental Research Center, Edgewater, Maryland, USAb
The genetic basis for bacterial mercury methylation has been described recently. For insights into the physiology of mercury-
methylating bacteria, we present genome sequences for Desulfococcus multivorans strain DSM 2059, Desulfovibrio alkalitolerans
strain DSM 16529, andDesulfovibrio species strain X2.
Received 12 July 2013 Accepted 22 July 2013 Published 15 August 2013
Citation Brown SD, Hurt RA, Jr, Gilmour CC, Elias DA. 2013. Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria. Genome Announc. 1(4):e00618-
13. doi:10.1128/genomeA.00618-13.
Copyright ? 2013 Brown et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Dwayne A. Elias, eliasda@ornl.gov.
Select members of the sulfate-reducing bacteria (SRB) andFe(III)-reducing bacteria (IRB) can methylate inorganic mer-
cury [Hg(II)] to methylmercury (MeHg), a more toxic form that
bioaccumulates (1). For the first time, recent genetic studies have
linked a specific gene cluster (hgcAB) to mercury methylation in
the model SRB Desulfovibrio desulfuricans strain ND132 and IRB
Geobacter sulfureducens strain PCA (2). The hgcAB gene cluster
encodes a putative corrinoid-containing CO dehydrogenase/
acetyl-coenzyme A (CoA) synthase, HgcA, and a 2[4Fe-4S] ferre-
doxin, HgcB, and these are predicted to have roles as a methyl
carrier and an electron donor, respectively.
The potential involvement of the acetyl-CoA pathway in bac-
terial Hg methylation was recognized more than 20 years ago (3),
although the physiology and MeHg formation in incomplete-
oxidizing SRB (conversion of carbon substrates to acetate) and
complete-oxidizing SRB (conversion of carbon to CO2) remain to
be fully elucidated (4, 5). The majority of known Hg-methylating
Deltaproteobacteria are incomplete oxidizers (6). This means that
when they reduce sulfate, these organisms incompletely oxidize
short-chain fatty acids to acetate and do not utilize C-1 substrates,
and thus they do not use the acetyl-CoA pathway as part of their
primary substrate utilization machinery during heterotrophic
growth (7). Detailed assessments and comparisons of mercury
methylation rates for several Desulfovibrio species that are incom-
plete oxidizers, including those investigated in this study, have
been reported (6, 8). Genome sequences for several SRBs known
or predicted to be mercury methylators have been reported (2,
9?12).
Desulfovibrio multivorans is an example of a complete oxidizer
with an acetyl-CoA pathway, and mercury methylation rates have
been reported for several strains (4, 5). D. alkalitolerans strain
DSM16529 is an example of a complete oxidizer that can generate
MeHg (8). Desulfovibrio species strain X2 was isolated from soft
black mid-Chesapeake Bay bottom sediments sampled in May
1985 (13), and it methylates both Sn(IV) (14) and Hg(II) (6), but
its detailed physiology has not been fully assessed.
In this study, we generated draft genomes for D. multivorans
DSM2059,D. alkalitoleransDSM16529, andDesulfovibrio species
strain X2. Sequence data for each genomewere generated using an
Illumina MiSeq instrument (15) and a paired-end approach with
an approximate insert library size of 500 bp and read lengths of
250 bp, according to the manufacturer?s instructions. The CLC
Genomics Workbench (version 6.0.2) was used to trim and filter
reads for quality sequence data and subsequent assemblies. The
resulting assemblies generated 149, 32, and 66 DNA contigs that
represented the draft genome sequences for strains DSM 2059,
DSM 16529, and X2, respectively. The estimated genome sizes
were ~4.4, 3.2, and 3.9 Mb and G
C DNA contents were 56.8%,
64.4%, and 67.9%, and there were 3,838, 2,924, and 3,445 putative
coding sequences (CDS) for DSM 2059, DSM 16529, and X2, re-
spectively. Sequence depth coverage across the genomes was ~205
to 309 times the genome sizes. Draft genome sequences were an-
notated as previously described (16).
The draft genome sequences presented here will facilitate com-
parative studies and assist with investigations into HgcAB native
functions, related pathways, and assessments of MeHg potential
in different ecological niches.
Nucleotide sequence accession numbers. This whole-
genome shotgun project has been deposited at DDBJ/EMBL/
GenBank under the accession numbers ATHJ00000000,
ATHI00000000, and ATHV00000000 for D. multivorans DSM
2059, D. alkalitolerans DSM 16529, and Desulfovibrio species
strain X2, respectively. The versions described in this paper are the
first versions.
ACKNOWLEDGMENTS
WeacknowledgeMiriamLand (ORNL) and SagarUtturkar (University of
Tennessee) for assistance with annotation and deposition of data into the
NCBI GenBank and Sequence Read Archive databases.
This research was supported by the Office of Biological and Environ-
mental Research (OBER), Office of Science, U.S. Department of Energy
(DOE), as part of the Mercury Science Focus Area Program at Oak Ridge
National Laboratory. Oak Ridge National Laboratory is managed by UT-
Battelle, LLC, for the U.S. Department of Energy under contract DE-
AC05-00OR22725.
Genome AnnouncementsJuly/August 2013 Volume 1 Issue 4 e00618-13 genomea.asm.org 1
REFERENCES
1. Hsu-Kim H, Kucharzyk KH, Zhang T, Deshusses MA. 2013. Mechanisms
regulating mercury bioavailability for methylating microorganisms in the
aquatic environment: a critical review. Environ. Sci. Technol. 47:
2441?2456.
2. Parks JM, Johs A, Podar M, Bridou R, Hurt RA, Smith SD, Tomanicek
SJ, Qian Y, Brown SD, Brandt CC, Palumbo AV, Smith JC, Wall JD,
Elias DA, Liang L. 2013. The genetic basis for bacterial mercury methyl-
ation. Science 339:1332?1335.
3. Choi SC, Bartha R. 1993. Cobalamin-mediated mercury methylation by
Desulfovibrio desulfuricans LS. Appl. Environ. Microbiol. 59:290?295.
4. Ekstrom EB, Morel M, FM, Benoit JM. 2003. Mercury methylation inde-
pendent of the acetyl-coenzyme a pathway in sulfate-reducing bacteria.
Appl. Environ. Microbiol. 69:5414?5422.
5. King JK, Kostka JE, Frischer ME, Saunders FM. 2000. Sulfate-reducing
bacteria methylate mercury at variable rates in pure culture and in marine
sediments. Appl. Environ. Microbiol. 66:2430?2437.
6. Gilmour CC, Elias DA, Kucken AM, Brown SD, Palumbo AV, Schadt
CW,Wall JD. 2011. Sulfate-reducing bacteriumDesulfovibrio desulfuricans
ND132 as a model for understanding bacterial mercury methylation. Appl.
Environ. Microbiol. 77:3938?3951.
7. Keller KL, Wall JD. 2011. Genetics and molecular biology of the electron
flow for sulfate respiration in Desulfovibrio. Front. Microbiol. 2:135.
8. Graham AM, Bullock AL, Maizel AC, Elias DA, Gilmour CC. 2012.
Detailed assessment of the kinetics ofHg-Cell Association,Hgmethylation,
andmethylmercury degradation in several Desulfovibrio species. Appl. En-
viron. Microbiol. 78:7337?7346.
9. Brown SD, Gilmour CC, Kucken AM, Wall JD, Elias DA, Brandt CC,
Podar M, Chertkov O, Held B, Bruce DC, Detter JC, Tapia R, Han CS,
Goodwin LA, Cheng JF, Pitluck S, Woyke T, Mikhailova N, Ivanova NN,
Han J, Lucas S, Lapidus AL, Land ML, Hauser LJ, Palumbo AV. 2011.
Genome sequence of themercury-methylating strainDesulfovibrio desulfu-
ricans ND132. J. Bacteriol. 193:2078?2079.
10. Brown SD, Wall JD, Kucken AM, Gilmour CC, Podar M, Brandt CC,
Teshima H, Detter JC, Han CS, Land ML, Lucas S, Han J, Pennacchio
L, Nolan M, Pitluck S, Woyke T, Goodwin L, Palumbo AV, Elias DA.
2011. Genome sequence of the mercury-methylating and pleomorphic
Desulfovibrio africanus strain Walvis Bay. J. Bacteriol. 193:4037?4038.
11. Pagani I, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S,
Cheng JF, Chertkov O, Davenport K, Tapia R, Han C, Goodwin L,
Pitluck S, Liolios K, Mavromatis K, Ivanova N, Mikhailova N, Pati A,
Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD,
Detter JC, Brambilla E, Kannan KP, Djao ODN, Rohde M, Pukall R,
Spring S, Goker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz
V, Hugenholtz P, Kyrpides NC, Klenk HP. 2011. Complete genome
sequence of Desulfobulbus propionicus type strain (1pr3). Stand. Genomic
Sci. 4:100?110.
12. Brown SD, Utturkar SM, Arkin AP, Deutschbauer AM, Elias DA,
Hazen TC, Chakraborty R. 2013. Draft genome sequence for Desulfovib-
rio africanus strain PCS. Genome Announc. 1(2):e00144-13. doi:10.1128
/genomeA.00144-13.
13. Gilmour CC, Tuttle JH, Means JC. 1987. Anaerobic microbial methyl-
ation of inorganic tin in estuarine sediment slurries. Microb. Ecol. 14:
233?242.
14. Gilmour CC, Tuttle JH, Means JC. 1985. Tin methylation in sulfide
bearing sediments, p 239?258. In Sigleo AC, Hattori A (ed), Marine and
estuarine geochemistry. Lewis Publishers, Ann Arbor, MI.
15. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR,
Bertoni A, Swerdlow HP, Gu Y. 2012. A tale of three next generation
sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and
Illumina MiSeq sequencers. BMC Genomics 13:341. doi:10.1186/1471-2
164-13-341.
16. Brown SD, Klingeman DM, Lu TY, Johnson CM, Utturkar SM, Land
ML, Schadt CW, Doktycz MJ, Pelletier DA. 2012. Draft genome se-
quence of Rhizobium sp. strain PDO1-076, a bacterium isolated from
Populus deltoides. J. Bacteriol. 194:2383?2384.
Brown et al.
Genome Announcements2 genomea.asm.org July/August 2013 Volume 1 Issue 4 e00618-13