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Announcement
19 January 2017

Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain

ABSTRACT

Desulfovibrio BerOc1 is a sulfate-reducing bacterium isolated from the Berre lagoon (French Mediterranean coast). BerOc1 is able to methylate and demethylate mercury. The genome size is 4,081,579 bp assembled into five contigs. We identified the hgcA and hgcB genes involved in mercury methylation, but not those responsible for mercury demethylation.

GENOME ANNOUNCEMENT

Desulfovibrio BerOc1 is a vibrio-shaped motile sulfate-reducing bacterium isolated from the highly oil-contaminated sediments of the Berre lagoon. It has been isolated from an anaerobic enrichment with octadecane as the sole carbon source (1). BerOc1 grows under sulfate reduction, fumarate respiration, and pyruvate fermentation. Lactate, pyruvate, and ethanol are used as carbon sources, but not acetate. BerOc1 is able to methylate and demethylate mercury (2). The strain BerOc1 has already been used as a model organism to better understand the mercury species distribution (3), their isotopic fractionation (4), and the physiology of the methylation (5). The potential of mercury methylation of BerOc1 varied depending on growing conditions (5), with a maximum potential occurring under fumarate respiration, probably because the absence of sulfide allows the inorganic mercury to be more available (6).
The total DNA of BerOc1 was extracted using an UltraClean microbial DNA isolation kit (Mo Bio). The genome was sequenced with 454 Roche Technology, using 454 GS FLEX Titanium version. Sequences were assembled using Newbler 2.6 (454 Life Sciences). We obtained 36 contigs, with a mean depth of coverage of 45×. Contigs were reordered using Promer (7) and the Desulfovibrio desulfuricans ND132 genome (RefSeq GenBank accession no. NC_016803) as the template. They were further extended by PCR. The draft genome includes five contigs, with the longest and shortest sequences being 2,803,249 and 2,705 bp, respectively. The total size of the genome is 4,081,579 bp, with a G+C content of 63.79%. The final assembly was annotated using Prokka version 1.10 (8) and identified 3,686 coding regions, three rRNAs, 59 tRNAs, and one transfer-messenger RNA (tmRNA). While no plasmid amplicon was detected, five putative genomic islands (29,653 bp, 27,947 bp, 11,484 bp, 19,691 bp, and 7,691 bp) were predicted using IslandViewer (9). There were three transposases annotated and four integrases; the presence of a bacteriophage is suspected by the presence of prophage-derived endonuclease YokF precursor and some proteins involved in tail constitution. No clustered regularly interspaced short palindromic repeat (CRISPR) could be detected using the CRISPR Recognition Tool (CRT) version 1.0 software (10).
The products of the hgcA and hgcB genes have been described to be involved in mercury methylation (11). The HgcA protein, belonging to Pterin-binding superfamily, shared 69% identity with HgcA of D. desulfuricans ND132 and Desulfovibrio aespoeensis (GenBank accession no. NC_014844). Notably, the motif NVWCAAGKG, known to be necessary for mercury methylation, was identical (12). HgcB shared 77% and 63% identity with HgcB of D. desulfuricans ND132 and Desulfovibrio aespoeensis, respectively. The operon mer, involved in methylmercury demethylation, could not be detected in the BerOc1 genome, suggesting that this process is performed through another unknown metabolic pathway.
Mostly all of the Desulfovibrio strains tested are able to demethylate mercury, but few strains are able to methylate it (13). The comparison of the genomes of Desulfovibrio strains sharing the capacity to produce this highly toxic mercury species with those unable to drive this process will give new tracks in the understanding of methylmercury production by bacteria.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LKAQ00000000 . The version described in this paper is version LKAQ01000000.

ACKNOWLEDGMENTS

This work has been funded by the CNRS EC2CO Microbien funding agency, project BIOMER (AO2012- 792147). The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.

REFERENCES

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Goñi-Urriza M, Corsellis Y, Lanceleur L, Tessier E, Gury J, Monperrus M, and Guyoneaud R. 2015. Relationships between bacterial energetic metabolism, mercury methylation potential, and hgcA/hgcB gene expression in Desulfovibrio dechloroacetivorans BerOc1. Environ Sci Pollut Res Int22:13764–13771.
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Hsu-Kim H, Kucharzyk KH, Zhang T, and Deshusses MA. 2013. Mechanisms regulating mercury bioavailability for methylating microorganisms in the aquatic environment: a critical review. Environ Sci Technol47:2441–2456.
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Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, and Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol5:R12.
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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, and Liang L. 2013. The genetic basis for bacterial mercury methylation. Science339:1332–1335.
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Smith SD, Bridou R, Johs A, Parks JM, Elias DA, Hurt RA, Brown SD, Podar M, and Wall JD. 2015. Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation. Appl Environ Microbiol81:3205–3217.
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Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 5Number 319 January 2017
eLocator: 10.1128/genomea.01483-16

History

Received: 4 November 2016
Accepted: 14 November 2016
Published online: 19 January 2017

Contributors

Authors

Marisol Goñi Urriza
Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l’Adour, IBEAS, Pau, France
Claire Gassie
Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l’Adour, IBEAS, Pau, France
Oliver Bouchez
GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
Christophe Klopp
Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
Rémy Guyoneaud
Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l’Adour, IBEAS, Pau, France

Notes

Address correspondence to Marisol Goñi Urriza, [email protected].

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