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

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

doi:10.1186/s40793-015-0078-x

Cited by 4 publications

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References 17 publications

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“…Sequencing and annotation procedures were described in detail elsewhere ( Berben et al, 2015a , b , c ). Basic genome properties are summarized in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

et al. 2017

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Thiocyanate is a C1 compound containing carbon, nitrogen, and sulfur. It is a (by)product in a number of natural and industrial processes. Because thiocyanate is toxic to many organisms, including humans, its removal from industrial waste streams is an important problem. Although a number of bacteria can use thiocyanate as a nitrogen source, only a few can use it as an electron donor. There are two distinct pathways to use thiocyanate: (i) the “carbonyl sulfide pathway,” which has been extensively studied, and (ii) the “cyanate pathway,” whose key enzyme, thiocyanate dehydrogenase, was recently purified and studied. Three species of Thioalkalivibrio, a group of haloalkaliphilic sulfur-oxidizing bacteria isolated from soda lakes, have been described as thiocyanate oxidizers: (i) Thioalkalivibrio paradoxus (“cyanate pathway”), (ii) Thioalkalivibrio thiocyanoxidans (“cyanate pathway”) and (iii) Thioalkalivibrio thiocyanodenitrificans (“carbonyl sulfide pathway”). In this study we provide a comparative genome analysis of these described thiocyanate oxidizers, with genomes ranging in size from 2.5 to 3.8 million base pairs. While focusing on thiocyanate degradation, we also analyzed the differences in sulfur, carbon, and nitrogen metabolism. We found that the thiocyanate dehydrogenase gene is present in 10 different Thioalkalivibrio strains, in two distinct genomic contexts/genotypes. The first genotype is defined by having genes for flavocytochrome c sulfide dehydrogenase upstream from the thiocyanate dehydrogenase operon (present in two strains including the type strain of Tv. paradoxus), whereas in the second genotype these genes are located downstream, together with two additional genes of unknown function (present in eight strains, including the type strains of Tv. thiocyanoxidans). Additionally, we found differences in the presence/absence of genes for various sulfur oxidation pathways, such as sulfide:quinone oxidoreductase, dissimilatory sulfite reductase, and sulfite dehydrogenase. One strain (Tv. thiocyanodenitrificans) lacks genes encoding a carbon concentrating mechanism and none of the investigated genomes were shown to contain known bicarbonate transporters. This study gives insight into the genomic variation of thiocyanate oxidizing bacteria and may lead to improvements in the application of these organisms in the bioremediation of industrial waste streams.

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“…Sequencing and annotation procedures were described in detail elsewhere ( Berben et al, 2015a , b , c ). Basic genome properties are summarized in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

et al. 2017

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“…The genome of T. thiocyanoxidans ARh 2 T (GenBank accession no. NZ_ARQK00000000.1) was previously sequenced and annotated ( 40 ). The FASTA file containing the genome sequences (in a total of 61 contigs) and the GFF file containing all of the sequence annotations were downloaded from the NCBI RefSeq FTP server.…”

Section: Methodsmentioning

confidence: 99%

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2^TUsing Transcriptomics

et al. 2017

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Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.

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“…Ten out of 85 strains of Thioalkalivibrio isolated from soda lakes can grow with thiocyanate (SCN À ) as a the sole energy source (Sorokin et al, 2013). The genome of one of these strains, T. paradoxus ARh 1 (Berben et al, 2015), contains five copies of gene clusters that encode proteins homologous to FCC. The amino-acid sequence identity between the flavin-binding subunits encoded by the different copies of the FCC gene is up to 73%.…”

Section: Introductionmentioning

confidence: 99%

Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1

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et al. 2018

Acta Cryst Sect D Struct Biol

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

Cited by 4 publications

References 17 publications

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2^TUsing Transcriptomics

Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1

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

Cited by 4 publications

References 17 publications

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2TUsing Transcriptomics

Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1

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Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2^TUsing Transcriptomics