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

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

doi:10.1099/ijsem.0.004697

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

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

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

Abstract

The sulfate-reducing, mercury-methylating strain ND132^T was isolated from the brackish anaerobic bottom sediments of Ches-apeake 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 J2^T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88% ANI between P. hydrargyri BerOc1^T and ND132^T, and 84% similarity between ND132^T 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.

Original language	English
Article number	004697
Journal	International Journal of Systematic and Evolutionary Microbiology
Volume	71
Issue number	3
DOIs	https://doi.org/10.1099/ijsem.0.004697
State	Published - 2021

Funding

Author affiliations: 1Smithsonian Environmental Research Center, Edgewater, Maryland, USA; 2Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; 3Department of Biochemistry, University of Missouri, Columbia, Missouri, USA; 4Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM UMR 5254, Pau, France. *Correspondence: Cynthia C. Gilmour, [email protected] Keywords: incomplete oxidizer; methylmercury; sulfate-reducer. Abbreviations: ANI, average nucleotide identity; DSRB, dissimilatory sulfate-reducing bacterium; MAG, metagenome-assembled genome. †Present address: LanzaTech, Skokie, Illinois, USA. The GenBank accession number for the complete genome of Pseudodesulfovibrio mercurii ND132T is GCA_000189295.2 This manuscript has been authored in part by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). One supplementary figure and one supplementary table are available with the online version of this article.

Keywords

Incomplete oxidizer
Methylmercury
Sulfate-reducer

Access to Document

10.1099/ijsem.0.004697

Cite this

@article{3145cca2c87346b8ad4c2aec24499e9e,

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

abstract = "The sulfate-reducing, mercury-methylating strain ND132T was isolated from the brackish anaerobic bottom sediments of Ches-apeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132T 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 ND132T 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). ND132T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1T 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 J2T. 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. ND132T 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. ND132T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, iso-C17:1 ω9c and anteiso-C17:0 . We propose the classification of strain ND132T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.",

keywords = "Incomplete oxidizer, Methylmercury, Sulfate-reducer",

author = "Gilmour, {Cynthia C.} and Soren, {Ally Bullock} and Gionfriddo, {Caitlin M.} and Mircea Podar and Wall, {Judy D.} and Brown, {Steven D.} and Michener, {Joshua K.} and Urriza, {Maria Soledad Go{\~n}i} and Elias, {Dwayne A.}",

year = "2021",

doi = "10.1099/ijsem.0.004697",

language = "English",

volume = "71",

journal = "International Journal of Systematic and Evolutionary Microbiology",

issn = "1466-5026",

publisher = "Microbiology Society",

number = "3",

}

TY - JOUR

T1 - Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment

AU - Gilmour, Cynthia C.

AU - Soren, Ally Bullock

AU - Gionfriddo, Caitlin M.

AU - Podar, Mircea

AU - Wall, Judy D.

AU - Brown, Steven D.

AU - Michener, Joshua K.

AU - Urriza, Maria Soledad Goñi

AU - Elias, Dwayne A.

PY - 2021

Y1 - 2021

N2 - The sulfate-reducing, mercury-methylating strain ND132T was isolated from the brackish anaerobic bottom sediments of Ches-apeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132T 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 ND132T 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). ND132T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1T 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 J2T. 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. ND132T 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. ND132T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, iso-C17:1 ω9c and anteiso-C17:0 . We propose the classification of strain ND132T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.

AB - The sulfate-reducing, mercury-methylating strain ND132T was isolated from the brackish anaerobic bottom sediments of Ches-apeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132T 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 ND132T 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). ND132T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1T 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 J2T. 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. ND132T 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. ND132T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, iso-C17:1 ω9c and anteiso-C17:0 . We propose the classification of strain ND132T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.

KW - Incomplete oxidizer

KW - Methylmercury

KW - Sulfate-reducer

UR - http://www.scopus.com/inward/record.url?scp=85103283600&partnerID=8YFLogxK

U2 - 10.1099/ijsem.0.004697

DO - 10.1099/ijsem.0.004697

M3 - Article

C2 - 33570484

AN - SCOPUS:85103283600

SN - 1466-5026

VL - 71

JO - International Journal of Systematic and Evolutionary Microbiology

JF - International Journal of Systematic and Evolutionary Microbiology

IS - 3

M1 - 004697

ER -

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

Abstract

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this