Abstract
Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB) capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 3.8-Mb genome sequence to provide further insight into microbial mercury methylation.
Methylmercury (MeHg) is primarily produced by sulfate-reducing bacteria (SRB), for example, species of the genus Desulfovibrio, as well as Fe(III)-reducing bacteria (IRB), such as Geobacter spp. (2, 4, 6, 10). MeHg bioaccumulates in aquatic and terrestrial food webs, with neurotoxicological effects on humans and damage to ecosystems (12, 14). Given the ability of D. desulfuricans ND132 to methylate mercury while several other Desulfovibrio species are unable to do so, a genome sequence was determined and is summarized here. ND132 was isolated from mesohaline Chesapeake Bay sediments (7), which are moderately Hg contaminated and support de novo MeHg production (8).
The genome size is ∼3.8 Mb, which is based upon averages of ∼40× and ∼122× genome coverage for 454 and Illumina data, respectively (11). The genome is defined as “noncontiguous finished,” which indicates a high-quality assembly with automated and manual improvements (3), and the production methods used have been described previously (5). Only six gaps (<100 bp) that are recalcitrant to resolution remain. A 20-bp high-GC-content repeat pattern (GCCTCCGGCGGCCGGGGGAA) occurs 60 times in the genome at 100% identity, and other copies exist with a 1-bp mismatch. This repeat sequence is within 20 bp of two gaps and within 250 bp of three more gaps and occurs within 400 bp of a 17-bp version of the repeat. In all six cases, the gap is 3′ of a repeat.
The 16S rRNA gene sequence of D. desulfuricans ND132 indicates that its phylogenetic placement should be reconsidered. The genome contains two separate and identical rRNA operons, each containing 16S, 23S, and 5S rRNA genes. The 16S rRNA gene is 98 to 99% similar to those of Desulfovibrio dechloracetivorans strains SF3 (AF230530), Mic42c03 (AB546253), Mic1c02 (AB546252), and Mic13c06 (AB546251). D. dechloracetivorans SF3 is able to couple the oxidation of acetate to the reductive dechlorination of ortho-chlorophenol and phenol production (15). D. desulfuricans ND132 is unable to grow by sulfate respiration with acetate, but its ability to couple acetate oxidation to reductive dechlorination has not been tested (C. Gilmour, unpublished). The 16S rRNA genes of D. desulfuricans ND132 are only 88 to 90% similar to those of Desulfovibrio desulfuricans subsp. desulfuricans strain Essex (AF192153), Desulfovibrio desulfuricans subsp. desulfuricans ATCC 27774 (CP001358), and Desulfovibrio G20 (CP000112).
A total of 3,455 candidate protein-encoding-gene models were predicted and curated by the Prodigal and GenePRIMP algorithms (9, 13). As expected, the D. desulfuricans ND132 genome carries genes typical for SRB, such as DND132_2809-10 (dissimilatory sulfite reductase genes dsrAB), DND132_3240-41 (Ni-Fe hydrogenase subunits), and DND132_0486-7 (Fe-hydrogenase subunits). Mercury resistance and organomercury lyase genes of the mer operon are relatively well characterized (1) and were not detected in the ND132 genome. The ND132 genome sequence will allow comprehensive comparisons with other SRB and IRB for further investigations into the mechanisms of mercury methylation.
Nucleotide sequence accession number.
The sequence determined in this whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under accession no. AEUJ00000000. The version described in this paper is the first version (accession no. AEUJ01000000).
ACKNOWLEDGMENTS
We thank Tamar Barkay for confirming the absence of known mer genes in the ND132 genome.
This research was supported by the Office of Biological and Environmental 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 and grant DE-FG02-073464396 (J.D.W.). Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
Footnotes
Published ahead of print on 25 February 2011.
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