Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

doi:10.1186/s40793-017-0303-x

Title: Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565 ^T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

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Abstract

A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82 ^T (DSM 21565 ^T = KCTC 5659 ^T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82 ^T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operonmore »« less

Authors:

Díaz-Cárdenas, Carolina ^[1]; López, Gina ^[1]; Alzate-Ocampo, José David ^[2]; González, Laura N. ^[2]; Shapiro, Nicole ^[3]; Woyke, Tanja ^[3]; Kyrpides, Nikos C. ^[3]; Restrepo, Silvia ^[2];

^[1]

Pontificia Univ. Javeriana, Bogotá (Colombia)
Univ. de los Andes, Bogotá (Colombia)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: 2017-12-20

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1544025

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Standards in Genomic Sciences

Additional Journal Information:: Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Microbiology; Dethiosulfovibrio salsuginis; Synergistetes; Halophilic; Anaerobe; Fermentation of amino acids; Saline spring

Citation Formats


                    Díaz-Cárdenas, Carolina, López, Gina, Alzate-Ocampo, José David, González, Laura N., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Restrepo, Silvia, and Baena, Sandra. Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring.  United States: N. p., 2017. 
        Web.  doi:10.1186/s40793-017-0303-x.

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                    Díaz-Cárdenas, Carolina, López, Gina, Alzate-Ocampo, José David, González, Laura N., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Restrepo, Silvia, & Baena, Sandra. Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring.  United States.  doi:10.1186/s40793-017-0303-x.

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                    Díaz-Cárdenas, Carolina, López, Gina, Alzate-Ocampo, José David, González, Laura N., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Restrepo, Silvia, and Baena, Sandra. Wed .  
        "Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring".  United States.  doi:10.1186/s40793-017-0303-x.  https://www.osti.gov/servlets/purl/1544025.

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@article{osti_1544025,

  title        = {Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring},

  author       = {Díaz-Cárdenas, Carolina and López, Gina and Alzate-Ocampo, José David and González, Laura N. and Shapiro, Nicole and Woyke, Tanja and Kyrpides, Nikos C. and Restrepo, Silvia and Baena, Sandra},

  abstractNote = {A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565 T = KCTC 5659 T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.},

  doi          = {10.1186/s40793-017-0303-x},

  journal      = {Standards in Genomic Sciences},

  number       = 1,

  volume       = 12,

  place        = {United States},

  year         = {2017},

  month        = {12}

}

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Title: Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565 T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

Abstract

Citation Formats

Title: Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565 ^T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring