Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium

Jan Kuever, Michael Visser, Claudia Loeffler, Matthias Boll, Petra Worm, Diana Z. Sousa, Caroline M. Plugge, Peter J. Schaap, Gerard Muyzer, Ines A C Pereira, Sofiya N. Parshina, Lynne A. Goodwin, Nikos C. Kyrpides, Janine Detter, Tanja Woyke, Patrick Chain, Karen W. Davenport, Manfred Rohde, Stefan Spring, Hans Peter Klenk & 1 others Alfons J M Stams

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA path-way, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.

Original languageEnglish
Pages (from-to)821-839
Number of pages19
JournalStandards in genomic sciences
Volume9
Issue number3
DOIs
Publication statusPublished - 30 Oct 2014

Fingerprint

Desulfotomaculum
Sulfates
Genome
Bacteria
formic acid
Peptococcaceae
Autotrophic Processes
Heterotrophic Processes
Genes
Chromosomes, Human, Pair 4
Acetyl Coenzyme A
Spores
Fresh Water
Carbon Dioxide
Vitamins
Fatty Acids
RNA
Growth
Proteins

Keywords

  • Anaerobic degradation of aromatic compounds
  • Autotrophic
  • Clostridiales
  • Complete oxidizer
  • Peptococcaceae
  • Spore-forming anaerobes
  • Sulfate reduction

Cite this

Kuever, Jan ; Visser, Michael ; Loeffler, Claudia ; Boll, Matthias ; Worm, Petra ; Sousa, Diana Z. ; Plugge, Caroline M. ; Schaap, Peter J. ; Muyzer, Gerard ; Pereira, Ines A C ; Parshina, Sofiya N. ; Goodwin, Lynne A. ; Kyrpides, Nikos C. ; Detter, Janine ; Woyke, Tanja ; Chain, Patrick ; Davenport, Karen W. ; Rohde, Manfred ; Spring, Stefan ; Klenk, Hans Peter ; Stams, Alfons J M. / Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium. In: Standards in genomic sciences. 2014 ; Vol. 9, No. 3. pp. 821-839.
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abstract = "Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA path-way, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.",
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Kuever, J, Visser, M, Loeffler, C, Boll, M, Worm, P, Sousa, DZ, Plugge, CM, Schaap, PJ, Muyzer, G, Pereira, IAC, Parshina, SN, Goodwin, LA, Kyrpides, NC, Detter, J, Woyke, T, Chain, P, Davenport, KW, Rohde, M, Spring, S, Klenk, HP & Stams, AJM 2014, 'Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium', Standards in genomic sciences, vol. 9, no. 3, pp. 821-839. https://doi.org/10.4056/sigs.5209235

Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium. / Kuever, Jan; Visser, Michael; Loeffler, Claudia; Boll, Matthias; Worm, Petra; Sousa, Diana Z.; Plugge, Caroline M.; Schaap, Peter J.; Muyzer, Gerard; Pereira, Ines A C; Parshina, Sofiya N.; Goodwin, Lynne A.; Kyrpides, Nikos C.; Detter, Janine; Woyke, Tanja; Chain, Patrick; Davenport, Karen W.; Rohde, Manfred; Spring, Stefan; Klenk, Hans Peter; Stams, Alfons J M.

In: Standards in genomic sciences, Vol. 9, No. 3, 30.10.2014, p. 821-839.

Research output: Contribution to journalArticle

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T1 - Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium

AU - Kuever, Jan

AU - Visser, Michael

AU - Loeffler, Claudia

AU - Boll, Matthias

AU - Worm, Petra

AU - Sousa, Diana Z.

AU - Plugge, Caroline M.

AU - Schaap, Peter J.

AU - Muyzer, Gerard

AU - Pereira, Ines A C

AU - Parshina, Sofiya N.

AU - Goodwin, Lynne A.

AU - Kyrpides, Nikos C.

AU - Detter, Janine

AU - Woyke, Tanja

AU - Chain, Patrick

AU - Davenport, Karen W.

AU - Rohde, Manfred

AU - Spring, Stefan

AU - Klenk, Hans Peter

AU - Stams, Alfons J M

PY - 2014/10/30

Y1 - 2014/10/30

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KW - Clostridiales

KW - Complete oxidizer

KW - Peptococcaceae

KW - Spore-forming anaerobes

KW - Sulfate reduction

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