Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A.; Woyke, Tanja; Muyzer, Gerard

doi:10.1186/s40793-015-0078-x

Title: Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2^T

Abstract

Â© 2015 Berben et al. Thioalkalivibrio thiocyanoxidans strain ARh 2 T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na + . This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. This organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

Authors:

Berben, Tom ^[1]; Sorokin, Dimitry Y. ^[2]; Ivanova, Natalia ^[3]; Pati, Amrita ^[3]; Kyrpides, Nikos ^[3]; Goodwin, Lynne A. ^[3]; Woyke, Tanja ^[3];

^[1]

Univ. of Amsterdam, Amsterdam (The Netherlands)
Winogradsky Institute of Microbiology, RAS, Moscow (Russia); Delft Univ. of Technology, Delft (The Netherlands)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: Mon Oct 26 00:00:00 EDT 2015

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1323183

Alternate Identifier(s):: OSTI ID: 1378605

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Standards in Genomic Sciences

Additional Journal Information:: Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; haloalkaliphilic; Soda lakes; sulfur-oxidizing bacteria; Thiocyanate; sp-nov

Citation Formats


                    Berben, Tom, Sorokin, Dimitry Y., Ivanova, Natalia, Pati, Amrita, Kyrpides, Nikos, Goodwin, Lynne A., Woyke, Tanja, and Muyzer, Gerard. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T.  United States: N. p., 2015. 
Web.  doi:10.1186/s40793-015-0078-x.

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                    Berben, Tom, Sorokin, Dimitry Y., Ivanova, Natalia, Pati, Amrita, Kyrpides, Nikos, Goodwin, Lynne A., Woyke, Tanja, & Muyzer, Gerard. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T.  United States.  https://doi.org/10.1186/s40793-015-0078-x

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                    Berben, Tom, Sorokin, Dimitry Y., Ivanova, Natalia, Pati, Amrita, Kyrpides, Nikos, Goodwin, Lynne A., Woyke, Tanja, and Muyzer, Gerard. Mon .  
"Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T".  United States.  https://doi.org/10.1186/s40793-015-0078-x.  https://www.osti.gov/servlets/purl/1323183.

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@article{osti_1323183,

  title        = {Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T},

  author       = {Berben, Tom and Sorokin, Dimitry Y. and Ivanova, Natalia and Pati, Amrita and Kyrpides, Nikos and Goodwin, Lynne A. and Woyke, Tanja and Muyzer, Gerard},

  abstractNote = {Â© 2015 Berben et al. Thioalkalivibrio thiocyanoxidans strain ARh 2 T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na + . This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. This organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.},

  doi          = {10.1186/s40793-015-0078-x},

  journal      = {Standards in Genomic Sciences},

  number       = 1,

  volume       = 10,

  place        = {United States},

  year         = {Mon Oct 26 00:00:00 EDT 2015},

  month        = {Mon Oct 26 00:00:00 EDT 2015}

}

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https://doi.org/10.1186/s40793-015-0078-x

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Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors
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Sorokin, D. Y.; van den Bosch, P. L. F.; Abbas, B.
Applied Microbiology and Biotechnology, Vol. 80, Issue 6
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Microbial diversity and biogeochemical cycling in soda lakes
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Sorokin, Dimitry Y.; Berben, Tom; Melton, Emily Denise
Extremophiles, Vol. 18, Issue 5
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The minimum information about a genome sequence (MIGS) specification
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Field, Dawn; Garrity, George; Gray, Tanya
Nature Biotechnology, Vol. 26, Issue 5
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Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
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Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

Tamura, Koichiro; Stecher, Glen; Peterson, Daniel
Molecular Biology and Evolution, Vol. 30, Issue 12
DOI: 10.1093/molbev/mst197

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

Lowe, Todd M.; Eddy, Sean R.
Nucleic Acids Research, Vol. 25, Issue 5
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Ludwig, W.
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Works referencing / citing this record:

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics
journal, December 2017

Berben, Tom; Balkema, Cherel; Sorokin, Dimitry Y.
mSystems, Vol. 2, Issue 6
DOI: 10.1128/msystems.00102-17

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes
journal, February 2017

Berben, Tom; Overmars, Lex; Sorokin, Dimitry Y.
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.00254

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway
journal, July 2019

Ahn, Anne-Catherine; Cavalca, Lucia; Colombo, Milena
Frontiers in Microbiology, Vol. 10
DOI: 10.3389/fmicb.2019.01514

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes
journal, February 2017

Berben, Tom; Overmars, Lex; Sorokin, Dimitry Y.
Frontiers in Microbiology, Vol. 8
DOI: 10.3389/fmicb.2017.00254

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Title: Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

Abstract

Citation Formats

The minimum information about a genome sequence (MIGS) specification journal, May 2008

Class I. Alphaproteobacteria class. nov. book, January 2005

Haloalkaliphilic Sulfur-Oxidizing Bacteria book, January 2006

Gene Ontology: tool for the unification of biology journal, May 2000

ARB: a software environment for sequence data journal, February 2004

Microbial diversity and biogeochemical cycling in soda lakes journal, August 2014

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal, June 1990

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence journal, March 1997

Prodigal: prokaryotic gene recognition and translation initiation site identification journal, March 2010

Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors journal, August 2008

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 journal, October 2013

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal, February 2008

High-quality draft assemblies of mammalian genomes from massively parallel sequence data journal, December 2010

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes journal, May 2010

Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes. journal, March 2002

Validation of publication of new names and new combinations previously effectively published outside the IJSEM journal, November 2005

Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors journal, August 2008

Microbial diversity and biogeochemical cycling in soda lakes journal, August 2014

The minimum information about a genome sequence (MIGS) specification journal, May 2008

Dietary palmitic acid promotes a prometastatic memory via Schwann cells journal, November 2021

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. journal, June 1990

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 journal, October 2013

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence journal, March 1997

ARB: a software environment for sequence data journal, February 2004

Reassignment of the Genus Ectothiorhodospira Pelsh 1936 to a New Family, Ectothiorhodospiraceae fam. nov., and Emended Description of the Chromatiaceae Bavendamm 1924 journal, July 1984

Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes. journal, March 2002

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal, February 2008

Prodigal: prokaryotic gene recognition and translation initiation site identification journal, March 2010

The Microbial Sulfur Cycle at Extremely Haloalkaline Conditions of Soda Lakes journal, January 2011

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics journal, December 2017

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes journal, February 2017

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway journal, July 2019

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes journal, February 2017

Title: Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2^T

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

Class I. Alphaproteobacteria class. nov.
book, January 2005

Haloalkaliphilic Sulfur-Oxidizing Bacteria
book, January 2006

Gene Ontology: tool for the unification of biology
journal, May 2000

ARB: a software environment for sequence data
journal, February 2004

Microbial diversity and biogeochemical cycling in soda lakes
journal, August 2014

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors
journal, August 2008

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes.
journal, March 2002

Validation of publication of new names and new combinations previously effectively published outside the IJSEM
journal, November 2005

Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors
journal, August 2008

Microbial diversity and biogeochemical cycling in soda lakes
journal, August 2014

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

ARB: a software environment for sequence data
journal, February 2004

Reassignment of the Genus Ectothiorhodospira Pelsh 1936 to a New Family, Ectothiorhodospiraceae fam. nov., and Emended Description of the Chromatiaceae Bavendamm 1924
journal, July 1984

Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes.
journal, March 2002

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

The Microbial Sulfur Cycle at Extremely Haloalkaline Conditions of Soda Lakes
journal, January 2011

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics
journal, December 2017

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes
journal, February 2017

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway
journal, July 2019

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes
journal, February 2017