Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

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

doi:10.1186/s40793-015-0080-3

Title: Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1^T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

Abstract

Â© 2015 Berben et al. Thioalkalivibrio thiocyanodenitrificans strain ARhD 1 T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 proteincoding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1 T was sequenced as part of the DOE Joint Genome Institute Community Science Program.

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, 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:: 1323224

Alternate Identifier(s):: OSTI ID: 1378606

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; soda lakes; sp-nov; tool

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 Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification.  United States: N. p., 2015. 
Web.  doi:10.1186/s40793-015-0080-3.

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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 Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification.  United States.  https://doi.org/10.1186/s40793-015-0080-3

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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 Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification".  United States.  https://doi.org/10.1186/s40793-015-0080-3.  https://www.osti.gov/servlets/purl/1323224.

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@article{osti_1323224,

  title        = {Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification},

  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 thiocyanodenitrificans strain ARhD 1 T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 proteincoding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1 T was sequenced as part of the DOE Joint Genome Institute Community Science Program.},

  doi          = {10.1186/s40793-015-0080-3},

  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/s40793-015-0080-3

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Works referencing / citing this record:

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

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 Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

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

A critical review on destruction of thiocyanate in mining effluents journal, July 2012

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

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

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

Anaerobic growth of the haloalkaliphilic denitrifying sulfur-oxidizing bacterium Thialkalivibrio thiocyanodenitrificans sp. nov. with thiocyanate journal, July 2004

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

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment journal, March 1998

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities journal, March 1998

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

Consed: A Graphical Tool for Sequence Finishing journal, March 1998

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

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176 journal, October 2015

Solexa Ltd journal, June 2004

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

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

A critical review on destruction of thiocyanate in mining effluents journal, July 2012

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

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

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

Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing journal, July 2020

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

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

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

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

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities journal, March 1998

Consed: A Graphical Tool for Sequence Finishing journal, March 1998

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

Solexa Ltd journal, June 2004

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

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

Title: Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1^T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

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

A critical review on destruction of thiocyanate in mining effluents
journal, July 2012

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

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

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

Anaerobic growth of the haloalkaliphilic denitrifying sulfur-oxidizing bacterium Thialkalivibrio thiocyanodenitrificans sp. nov. with thiocyanate
journal, July 2004

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

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
journal, March 1998

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998

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

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

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

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176
journal, October 2015

Solexa Ltd
journal, June 2004

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

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

A critical review on destruction of thiocyanate in mining effluents
journal, July 2012

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

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

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

Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing
journal, July 2020

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

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

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

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

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

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

Solexa Ltd
journal, June 2004

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

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