Complete genome sequence of Desulfomicrobium baculatum type strain (X T)

Alex Copeland, Stefan Spring, Markus Göker, Susanne Schneider, Alla Lapidus, Tijana Glavina del Rio, Hope Tice, Jan Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna PalaniappanMiriam Land, Loren Hauser, Yun Juan Chang, Cynthia C. Jeffries, Linda Meincke, David Sims, Thomas Brettin, John C. Detter, Cliff Han, Patrick Chain, Jim Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans Peter Klenk, Susan Lucas

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X T is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO 2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Original languageEnglish (US)
Pages (from-to)29-37
Number of pages9
JournalStandards in Genomic Sciences
Volume1
Issue number1
DOIs
StatePublished - 2009
Externally publishedYes

Fingerprint

Genome
Sulfates
Encyclopedias
Bacteria
Replicon
Archaea
Carbon Monoxide
Pyruvic Acid
Lactic Acid
Acetates
RNA
Water
Growth
Genes
Proteins
manganese carbonate

Keywords

  • Anaerobe
  • Desulfomicrobiaceae
  • Free-living
  • Freshwater
  • Gram-negative
  • Mesophile
  • Non-pathogenic
  • Sulfate reducer

ASJC Scopus subject areas

  • Genetics

Cite this

Copeland, A., Spring, S., Göker, M., Schneider, S., Lapidus, A., del Rio, T. G., ... Lucas, S. (2009). Complete genome sequence of Desulfomicrobium baculatum type strain (X T). Standards in Genomic Sciences, 1(1), 29-37. https://doi.org/10.4056/sigs.13134

Complete genome sequence of Desulfomicrobium baculatum type strain (X T). / Copeland, Alex; Spring, Stefan; Göker, Markus; Schneider, Susanne; Lapidus, Alla; del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia C.; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter; Lucas, Susan.

In: Standards in Genomic Sciences, Vol. 1, No. 1, 2009, p. 29-37.

Research output: Contribution to journalArticle

Copeland, A, Spring, S, Göker, M, Schneider, S, Lapidus, A, del Rio, TG, Tice, H, Cheng, JF, Lucas, S, Chen, F, Nolan, M, Bruce, D, Goodwin, L, Pitluck, S, Ivanova, N, Mavromatis, K, Ovchinnikova, G, Pati, A, Chen, A, Palaniappan, K, Land, M, Hauser, L, Chang, YJ, Jeffries, CC, Meincke, L, Sims, D, Brettin, T, Detter, JC, Han, C, Chain, P, Bristow, J, Eisen, JA, Markowitz, V, Hugenholtz, P, Kyrpides, NC, Klenk, HP & Lucas, S 2009, 'Complete genome sequence of Desulfomicrobium baculatum type strain (X T)', Standards in Genomic Sciences, vol. 1, no. 1, pp. 29-37. https://doi.org/10.4056/sigs.13134
Copeland A, Spring S, Göker M, Schneider S, Lapidus A, del Rio TG et al. Complete genome sequence of Desulfomicrobium baculatum type strain (X T). Standards in Genomic Sciences. 2009;1(1):29-37. https://doi.org/10.4056/sigs.13134
Copeland, Alex ; Spring, Stefan ; Göker, Markus ; Schneider, Susanne ; Lapidus, Alla ; del Rio, Tijana Glavina ; Tice, Hope ; Cheng, Jan Fang ; Lucas, Susan ; Chen, Feng ; Nolan, Matt ; Bruce, David ; Goodwin, Lynne ; Pitluck, Sam ; Ivanova, Natalia ; Mavromatis, Konstantinos ; Ovchinnikova, Galina ; Pati, Amrita ; Chen, Amy ; Palaniappan, Krishna ; Land, Miriam ; Hauser, Loren ; Chang, Yun Juan ; Jeffries, Cynthia C. ; Meincke, Linda ; Sims, David ; Brettin, Thomas ; Detter, John C. ; Han, Cliff ; Chain, Patrick ; Bristow, Jim ; Eisen, Jonathan A ; Markowitz, Victor ; Hugenholtz, Philip ; Kyrpides, Nikos C. ; Klenk, Hans Peter ; Lucas, Susan. / Complete genome sequence of Desulfomicrobium baculatum type strain (X T). In: Standards in Genomic Sciences. 2009 ; Vol. 1, No. 1. pp. 29-37.
@article{42789c464343498bba1c9e20b3942f3c,
title = "Complete genome sequence of Desulfomicrobium baculatum type strain (X T)",
abstract = "Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X T is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6{\%} (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO 2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.",
keywords = "Anaerobe, Desulfomicrobiaceae, Free-living, Freshwater, Gram-negative, Mesophile, Non-pathogenic, Sulfate reducer",
author = "Alex Copeland and Stefan Spring and Markus G{\"o}ker and Susanne Schneider and Alla Lapidus and {del Rio}, {Tijana Glavina} and Hope Tice and Cheng, {Jan Fang} and Susan Lucas and Feng Chen and Matt Nolan and David Bruce and Lynne Goodwin and Sam Pitluck and Natalia Ivanova and Konstantinos Mavromatis and Galina Ovchinnikova and Amrita Pati and Amy Chen and Krishna Palaniappan and Miriam Land and Loren Hauser and Chang, {Yun Juan} and Jeffries, {Cynthia C.} and Linda Meincke and David Sims and Thomas Brettin and Detter, {John C.} and Cliff Han and Patrick Chain and Jim Bristow and Eisen, {Jonathan A} and Victor Markowitz and Philip Hugenholtz and Kyrpides, {Nikos C.} and Klenk, {Hans Peter} and Susan Lucas",
year = "2009",
doi = "10.4056/sigs.13134",
language = "English (US)",
volume = "1",
pages = "29--37",
journal = "Environmental Microbiomes",
issn = "1944-3277",
publisher = "BioMed Central Ltd.",
number = "1",

}

TY - JOUR

T1 - Complete genome sequence of Desulfomicrobium baculatum type strain (X T)

AU - Copeland, Alex

AU - Spring, Stefan

AU - Göker, Markus

AU - Schneider, Susanne

AU - Lapidus, Alla

AU - del Rio, Tijana Glavina

AU - Tice, Hope

AU - Cheng, Jan Fang

AU - Lucas, Susan

AU - Chen, Feng

AU - Nolan, Matt

AU - Bruce, David

AU - Goodwin, Lynne

AU - Pitluck, Sam

AU - Ivanova, Natalia

AU - Mavromatis, Konstantinos

AU - Ovchinnikova, Galina

AU - Pati, Amrita

AU - Chen, Amy

AU - Palaniappan, Krishna

AU - Land, Miriam

AU - Hauser, Loren

AU - Chang, Yun Juan

AU - Jeffries, Cynthia C.

AU - Meincke, Linda

AU - Sims, David

AU - Brettin, Thomas

AU - Detter, John C.

AU - Han, Cliff

AU - Chain, Patrick

AU - Bristow, Jim

AU - Eisen, Jonathan A

AU - Markowitz, Victor

AU - Hugenholtz, Philip

AU - Kyrpides, Nikos C.

AU - Klenk, Hans Peter

AU - Lucas, Susan

PY - 2009

Y1 - 2009

N2 - Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X T is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO 2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

AB - Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X T is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO 2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

KW - Anaerobe

KW - Desulfomicrobiaceae

KW - Free-living

KW - Freshwater

KW - Gram-negative

KW - Mesophile

KW - Non-pathogenic

KW - Sulfate reducer

UR - http://www.scopus.com/inward/record.url?scp=79960730905&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79960730905&partnerID=8YFLogxK

U2 - 10.4056/sigs.13134

DO - 10.4056/sigs.13134

M3 - Article

C2 - 21304634

AN - SCOPUS:79960730905

VL - 1

SP - 29

EP - 37

JO - Environmental Microbiomes

JF - Environmental Microbiomes

SN - 1944-3277

IS - 1

ER -