Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment

Gilmour, Cynthia C.; Soren, Ally Bullock; Gionfriddo, Caitlin M.; Podar, Mircea; Wall, Judy D.; Brown, Steven D.; Michener, Joshua K.; Urriza, Maria Goñi; Elias, Dwayne A.

doi:10.1099/ijsem.0.004697

Title: Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment

Journal Article · Thu Feb 11 00:00:00 EST 2021 · International Journal of Systematic and Evolutionary Microbiology

DOI:https://doi.org/10.1099/ijsem.0.004697· OSTI ID:1767872

^[1];

^[2];

^[3];

^[4];

^[5];

^[3];

^[6];

^[3]

Smithsonian Environmental Research Center, Edgewater, MD (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Smithsonian Environmental Research Center, Edgewater, MD (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of Missouri, Columbia, MO (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); LanzaTech, Skokie, IL (United States)
Université de Pau et des Pays de l’Adour (UPPA), Pau (France). Inst. of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM)

The sulfate-reducing, mercury-methylating strain ND132^T was isolated from the brackish anaerobic bottom sediments of Chesapeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132^T has been widely used as a model strain to study the process and to determine the genetic basis of Hg methylation. Originally called Desulfovibrio desulfuricans ND132^T on the basis of an early partial 16S rRNA sequence, the strain has never been formally described. Phylogenetic and physiological traits place this strain within the genus Pseudodesulfovibrio, in the recently reclassified phylum Desulfobacterota (formerly Deltaproteobacteria ). ND132^T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1^T and Pseudodesulfovibrio indicus J2T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88 % ANI between P. hydrargyri BerOc1T and ND132T, and 84 % similarity between ND132T and P. indicus J2^T. These cut-off scores <95 %, along with a multi-gene phylogenetic analysis of members of the family Desulfovibrionacea, and differences in physiology indicate that all three strains represent separate species. The Gram-stain-negative cells are vibrio-shaped, motile and not sporulated. ND132^T is a salt-tolerant mesophile with optimal growth in the laboratory at 32 °C, 2 % salinity, and pH 7.8. The DNA G+C content of the genomic DNA is 65.2 %. It is an incomplete oxidizer of short chain fatty acids, using lactate, pyruvate and fumarate with sulfate or sulfite as the terminal electron acceptors. ND132^T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C_{15 :0}, anteiso-C_{15 : 0}, iso-C_{17 : 0}, iso-C_{17 : 1}ω9c and anteiso-C_{17 : 0}. We propose the classification of strain ND132^T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); University of Maryland; Harvard School of Public Health

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1767872

Journal Information:: International Journal of Systematic and Evolutionary Microbiology, Vol. 71, Issue 3; ISSN 1466-5026

Publisher:: International Union of Microbiological SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

References (59)

Desulfovibrio profundus sp. nov., a Novel Barophilic Sulfate-Reducing Bacterium from Deep Sediment Layers in the Japan Sea Bale, S. J.; Goodman, K.; Rochelle, P. A. International Journal of Systematic Bacteriology, Vol. 47, Issue 2 https://doi.org/10.1099/00207713-47-2-515	journal	April 1997
Desulfovibrio tunisiensis sp. nov., a novel weakly halotolerant, sulfate-reducing bacterium isolated from exhaust water of a Tunisian oil refinery Ben Ali Gam, Z.; Oueslati, R.; Abdelkafi, S. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 5 https://doi.org/10.1099/ijs.0.000943-0	journal	April 2009
Intracellular Hg(0) Oxidation in Desulfovibrio desulfuricans ND132 Wang, Yuwei; Schaefer, Jeffra K.; Mishra, Bhoopesh Environmental Science & Technology, Vol. 50, Issue 20 https://doi.org/10.1021/acs.est.6b03299	journal	October 2016
Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations Christensen, Geoff A.; Gionfriddo, Caitlin M.; King, Andrew J. Environmental Science & Technology, Vol. 53, Issue 15 https://doi.org/10.1021/acs.est.8b06389	journal	July 2019
Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation Warthmann, Rolf; Vasconcelos, Crisogono; Sass, Henrik Extremophiles, Vol. 9, Issue 3 https://doi.org/10.1007/s00792-005-0441-8	journal	April 2005
The Influence of Sulfide on Solid-Phase Mercury Bioavailability for Methylation by Pure Cultures of Desulfobulbus propionicus (1pr3) Benoit, J. M.; Gilmour, C. C.; Mason, R. P. Environmental Science & Technology, Vol. 35, Issue 1 https://doi.org/10.1021/es001415n	journal	January 2001
Overview of Mercury Methylation Capacities among Anaerobic Bacteria Including Representatives of the Sulphate-Reducers: Implications for Environmental Studies Ranchou-Peyruse, M.; Monperrus, M.; Bridou, R. Geomicrobiology Journal, Vol. 26, Issue 1, p. 1-8 https://doi.org/10.1080/01490450802599227	journal	January 2009
Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea Khelaifia, Saber; Fardeau, Marie-Laure; Pradel, Nathalie International Journal of Systematic and Evolutionary Microbiology, Vol. 61, Issue 11 https://doi.org/10.1099/ijs.0.028670-0	journal	November 2011
Cobalamin-mediated mercury methylation by Desulfovibrio desulfuricans LS. Choi, S. C.; Bartha, R. Applied and Environmental Microbiology, Vol. 59, Issue 1 https://doi.org/10.1128/AEM.59.1.290-295.1993	journal	January 1993
Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation Cooper, Connor J.; Zheng, Kaiyuan; Rush, Katherine W. Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-1047-5	journal	June 2020
Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment Ranchou-Peyruse, Magali; Goñi-Urriza, Marisol; Guignard, Marion International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 5 https://doi.org/10.1099/ijsem.0.002173	journal	May 2018
Sequencing Intractable DNA to Close Microbial Genomes Hurt, Richard A.; Brown, Steven D.; Podar, Mircea PLoS ONE, Vol. 7, Issue 7, Article No. e41295 https://doi.org/10.1371/journal.pone.0041295	journal	July 2012
Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio Cao, Junwei; Gayet, Nicolas; Zeng, Xiang International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 10 https://doi.org/10.1099/ijsem.0.001286	journal	October 2016
Mercury Methylation by Novel Microorganisms from New Environments Gilmour, Cynthia C.; Podar, Mircea; Bullock, Allyson L. Environmental Science & Technology, Vol. 47, Issue 20 https://doi.org/10.1021/es403075t	journal	September 2013
Diversity and origin of Desulfovibrio species: phylogenetic definition of a family. Devereux, R.; He, S. H.; Doyle, C. L. Journal of Bacteriology, Vol. 172, Issue 7 https://doi.org/10.1128/JB.172.7.3609-3619.1990	journal	January 1990
Isolation and Characterization of Desulfovibrio dechloracetivorans sp. nov., a Marine Dechlorinating Bacterium Growing by Coupling the Oxidation of Acetate to the Reductive Dechlorination of 2-Chlorophenol Sun, B.; Cole, J. R.; Sanford, R. A. Applied and Environmental Microbiology, Vol. 66, Issue 6 https://doi.org/10.1128/AEM.66.6.2408-2413.2000	journal	June 2000
Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria Hu, Haiyan; Lin, Hui; Zheng, Wang Nature Geoscience, Vol. 6, Issue 9 https://doi.org/10.1038/ngeo1894	journal	August 2013
Aspects of Bioavailability of Mercury for Methylation in Pure Cultures of Desulfobulbus propionicus (1pr3) Benoit, J. M.; Gilmour, C. C.; Mason, R. P. Applied and Environmental Microbiology, Vol. 67, Issue 1 https://doi.org/10.1128/AEM.67.1.51-58.2001	journal	January 2001
Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury Methylation Gilmour, Cynthia C.; Elias, Dwayne A.; Kucken, Amy M. Applied and Environmental Microbiology, Vol. 77, Issue 12, p. 3938-3951 https://doi.org/10.1128/AEM.02993-10	journal	April 2011
Robust Mercury Methylation across Diverse Methanogenic Archaea Gilmour, Cynthia C.; Bullock, Allyson L.; McBurney, Alyssa mBio, Vol. 9, Issue 2 https://doi.org/10.1128/mBio.02403-17	journal	April 2018
Note: Desulfovibrio aespoeensis sp. nov., a mesophilic sulfate-reducing bacterium from deep groundwater at aspo hard rock laboratory, Sweden Motamedi, M.; Pedersen, K. International Journal of Systematic Bacteriology, Vol. 48, Issue 1 https://doi.org/10.1099/00207713-48-1-311	journal	January 1998
Relative Reactivity and Bioavailability of Mercury Sorbed to or Coprecipitated with Aged Iron Sulfides Rivera, Nelson A.; Bippus, Paige M.; Hsu-Kim, Heileen Environmental Science & Technology, Vol. 53, Issue 13 https://doi.org/10.1021/acs.est.9b00768	journal	June 2019
Mercury Methylation by Desulfovibrio desulfuricans ND132 in the Presence of Polysulfides Jay, J. A.; Murray, K. J.; Gilmour, C. C. Applied and Environmental Microbiology, Vol. 68, Issue 11 https://doi.org/10.1128/AEM.68.11.5741-5745.2002	journal	November 2002
Enzymatic catalysis of mercury methylation by Desulfovibrio desulfuricans LS. Choi, S. C.; Chase, T.; Bartha, R. Applied and Environmental Microbiology, Vol. 60, Issue 4 https://doi.org/10.1128/AEM.60.4.1342-1346.1994	journal	January 1994
Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation Smith, Steven D.; Bridou, Romain; Johs, Alexander Applied and Environmental Microbiology, Vol. 81, Issue 9 https://doi.org/10.1128/AEM.00217-15	journal	February 2015
Mercury Uptake by Desulfovibrio desulfuricans ND132: Passive or Active? An, Jing; Zhang, Lijie; Lu, Xia Environmental Science & Technology, Vol. 53, Issue 11 https://doi.org/10.1021/acs.est.9b00047	journal	May 2019
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments Criscuolo, Alexis; Gribaldo, Simonetta BMC Evolutionary Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2148-10-210	journal	January 2010
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Desulfovibrio portus sp. nov., a novel sulfate-reducing bacterium in the class Deltaproteobacteria isolated from an estuarine sediment Suzuki, Daisuke; Ueki, Atsuko; Amaishi, Aya The Journal of General and Applied Microbiology, Vol. 55, Issue 2 https://doi.org/10.2323/jgam.55.125	journal	January 2009
Anaerobic microbial methylation of inorganic tin in estuarine sediment slurries Gilmour, Cynthia C.; Tuttle, Jon H.; Means, Jay C. Microbial Ecology, Vol. 14, Issue 3 https://doi.org/10.1007/BF02012943	journal	November 1987
The Genetic Basis for Bacterial Mercury Methylation Parks, J. M.; Johs, A.; Podar, M. Science, Vol. 339, Issue 6125, p. 1332-1335 https://doi.org/10.1126/science.1230667	journal	February 2013
Global prevalence and distribution of genes and microorganisms involved in mercury methylation Podar, Mircea; Gilmour, Cynthia C.; Brandt, Craig C. Science Advances, Vol. 1, Issue 9 https://doi.org/10.1126/sciadv.1500675	journal	October 2015
Nanomolar Copper Enhances Mercury Methylation by Desulfovibrio desulfuricans ND132 Lu, Xia; Johs, Alexander; Zhao, Linduo Environmental Science & Technology Letters, Vol. 5, Issue 6 https://doi.org/10.1021/acs.estlett.8b00232	journal	May 2018
Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov. Kim, Yun Jae; Yang, Jhung-Ahn; Lim, Jae Kyu Journal of Microbiology, Vol. 58, Issue 4 https://doi.org/10.1007/s12275-020-9376-0	journal	February 2020
Effects of Cellular Sorption on Mercury Bioavailability and Methylmercury Production by Desulfovibrio desulfuricans ND132 Liu, Yu-Rong; Lu, Xia; Zhao, Linduo Environmental Science & Technology, Vol. 50, Issue 24 https://doi.org/10.1021/acs.est.6b04041	journal	November 2016
Genome Sequence of the Mercury-Methylating Strain Desulfovibrio desulfuricans ND132 Brown, S. D.; Gilmour, C. C.; Kucken, A. M. Journal of Bacteriology, Vol. 193, Issue 8, p. 2078-2079 https://doi.org/10.1128/JB.00170-11	journal	February 2011
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB Date, Swapneeta S.; Parks, Jerry M.; Rush, Katherine W. Applied and Environmental Microbiology, Vol. 85, Issue 13 https://doi.org/10.1128/AEM.00438-19	journal	April 2019
Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. Miller, L. T. Journal of Clinical Microbiology, Vol. 16, Issue 3 https://doi.org/10.1128/JCM.16.3.584-586.1982	journal	January 1982
Isolation and Characterization of Desulfovibrio halophilus sp. nov., a Halophilic Sulfate-reducing Bacterium Isolated from Solar Lake (Sinai) Caumette, Pierre; Cohen, Yehuda; Matheron, Robert Systematic and Applied Microbiology, Vol. 14, Issue 1 https://doi.org/10.1016/S0723-2020(11)80358-9	journal	January 1991
Distinct Microbial Behavior of Re Compared to Tc: Evidence Against Microbial Re Fixation in Aquatic Sediments Dolor, Marvourneen K.; Gilmour, Cynthia C.; Helz, George R. Geomicrobiology Journal, Vol. 26, Issue 7 https://doi.org/10.1080/01490450903060822	journal	September 2009
A sulfate-reducing bacterium from the oxic layer of a microbial mat from Solar Lake (Sinai), Desulfovibrio oxyclinae sp. nov. Krekeler, Daniel; Sigalevich, Pavel; Teske, A. Archives of Microbiology, Vol. 167, Issue 6 https://doi.org/10.1007/s002030050457	journal	May 1997
Contrasting Effects of Dissolved Organic Matter on Mercury Methylation by Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132 Zhao, Linduo; Chen, Hongmei; Lu, Xia Environmental Science & Technology, Vol. 51, Issue 18 https://doi.org/10.1021/acs.est.7b02518	journal	August 2017
Dissolved Organic Matter Enhances Microbial Mercury Methylation Under Sulfidic Conditions Graham, Andrew M.; Aiken, George R.; Gilmour, Cynthia C. Environmental Science & Technology, Vol. 46, Issue 5 https://doi.org/10.1021/es203658f	journal	February 2012
Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities Waite, David W.; Chuvochina, Maria; Pelikan, Claus International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 11 https://doi.org/10.1099/ijsem.0.004213	journal	November 2020
Anaerobic oxidation of Hg(0) and methylmercury formation by Desulfovibrio desulfuricans ND132 Colombo, Matthew J.; Ha, Juyoung; Reinfelder, John R. Geochimica et Cosmochimica Acta, Vol. 112 https://doi.org/10.1016/j.gca.2013.03.001	journal	July 2013
Microbial mercury methylation in Antarctic sea ice Gionfriddo, Caitlin M.; Tate, Michael T.; Wick, Ryan R. Nature Microbiology, Vol. 1, Issue 10 https://doi.org/10.1038/nmicrobiol.2016.127	journal	August 2016
Sulfurization of Dissolved Organic Matter Increases Hg–Sulfide–Dissolved Organic Matter Bioavailability to a Hg-Methylating Bacterium Graham, Andrew M.; Cameron-Burr, Keaton T.; Hajic, Hayley A. Environmental Science & Technology, Vol. 51, Issue 16 https://doi.org/10.1021/acs.est.7b02781	journal	July 2017
The Cellular Fatty Acids of the Sulphate-reducing Bacteria, Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio desulfuricans Taylor, J.; Parkes, R. J. Microbiology, Vol. 129, Issue 11 https://doi.org/10.1099/00221287-129-11-3303	journal	November 1983
Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains Goñi-Urriza, Marisol; Klopp, Christophe; Ranchou-Peyruse, Magali Research in Microbiology, Vol. 171, Issue 1 https://doi.org/10.1016/j.resmic.2019.10.003	journal	January 2020
Detailed Assessment of the Kinetics of Hg-Cell Association, Hg Methylation, and Methylmercury Degradation in Several Desulfovibrio Species Graham, Andrew M.; Bullock, Allyson L.; Maizel, Andrew C. Applied and Environmental Microbiology, Vol. 78, Issue 20, p. 7337-7346 https://doi.org/10.1128/AEM.01792-12	journal	August 2012
GenBank Sayers, Eric W.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky989	journal	October 2018
Active transport, substrate specificity, and methylation of Hg(II) in anaerobic bacteria Schaefer, J. K.; Rocks, S. S.; Zheng, W. Proceedings of the National Academy of Sciences, Vol. 108, Issue 21 https://doi.org/10.1073/pnas.1105781108	journal	May 2011
Fractionation of Mercury Stable Isotopes during Microbial Methylmercury Production by Iron- and Sulfate-Reducing Bacteria Janssen, Sarah E.; Schaefer, Jeffra K.; Barkay, Tamar Environmental Science & Technology, Vol. 50, Issue 15 https://doi.org/10.1021/acs.est.6b00854	journal	July 2016
Desulfovibrio africanus sp. n., a New Dissimilatory Sulfate-reducing Bacterium Campbell, L. Leon; Kasprzycki, Mary A.; Postgate, John R. Journal of Bacteriology, Vol. 92, Issue 4 https://doi.org/10.1128/JB.92.4.1122-1127.1966	journal	January 1966
Extractable and lipopolysaccharide fatty acid and hydroxy acid profiles from Desulfovibrio species. Edlund, A.; Nichols, P. D.; Roffey, R. Journal of Lipid Research, Vol. 26, Issue 8 https://doi.org/10.1016/S0022-2275(20)34302-9	journal	August 1985
Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes Jones, Daniel S.; Walker, Gabriel M.; Johnson, Nathan W. The ISME Journal, Vol. 13, Issue 7 https://doi.org/10.1038/s41396-019-0376-1	journal	February 2019
Desulfovibrio senegalensis sp. nov., a mesophilic sulfate reducer isolated from marine sediment Thioye, Abdoulaye; Gam, Zouhaier Ben Ali; Mbengue, Malick International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 9 https://doi.org/10.1099/ijsem.0.001997	journal	September 2017
Evidence against incorporation of exogenous thymidine by sulfate-reducing bacteria Gilmour, C. C.; Leavitt, M. E.; Shiaris, M. P. Limnology and Oceanography, Vol. 35, Issue 6 https://doi.org/10.4319/lo.1990.35.6.1401	journal	September 1990

Similar Records

Transcriptional Control of hgcAB by an ArsR-Like Regulator in Pseudodesulfovibrio mercurii ND132

Journal Article · Thu Mar 23 00:00:00 EDT 2023 · Applied and Environmental Microbiology · OSTI ID:1767872

Gionfriddo, Caitlin M.; Soren, Ally Bullock; Wymore, Ann M.; +5 more

Adsorption and intracellular uptake of mercuric mercury and methylmercury by methanotrophs and methylating bacteria

Journal Article · Sat May 13 00:00:00 EDT 2023 · Environmental Pollution · OSTI ID:1767872

Zhang, Lijie; Kang-Yun, Christina S.; Lu, Xia; +5 more

Contrary effects of phytoplankton Chlorella vulgaris and its exudates on mercury methylation by iron- and sulfate-reducing bacteria

Journal Article · Fri Apr 01 00:00:00 EDT 2022 · Journal of Hazardous Materials · OSTI ID:1767872

Yin, Xixiang; Wang, Lihong; Liang, Xujun; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
incomplete oxidizer
methylmercury
sulfate-reducer

Title: Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment

Citation Formats

References (59)

Similar Records

Related Subjects