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Title: Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)

Abstract

'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [2];  [3];  [3];  [3];  [3];  [3];  [1];  [4];  [3];  [3];  [3];  [3];  [3];  [3];  [5];  [5];  [6];  [6];  [6] more »;  [6];  [3];  [3];  [1];  [7];  [7];  [2];  [8];  [3];  [3];  [9];  [5];  [3];  [3];  [10];  [3] « less
+ Show Author Affiliations
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. American Type Culture Collection (ATCC), Manassas, VA (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  7. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  8. Montana State Univ., Bozeman, MN (United States)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
  10. German Collection of Microorganism and Cell Cultures, Braunschweig (Germany)
Publication Date:
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:
1630546
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 3; Journal Issue: 2; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; extreme thermal soil; thermoacidophile; Gram-positive; nonmotile; non-spore-forming; obligate aerobe; Incertae sedis; Chloroflexi; GEBA

Citation Formats

Kiss, Hajnalka, Cleland, David, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Lu, Megan, Brettin, Thomas, Detter, John C., Göker, Markus, Tindall, Brian J., Beck, Brian, McDermott, Timothy R., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Cheng, Jan-Fang. Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T). United States: N. p., 2010. Web. doi:10.4056/sigs.1153107.
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Kiss, Hajnalka, Cleland, David, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Lu, Megan, Brettin, Thomas, Detter, John C., Göker, Markus, Tindall, Brian J., Beck, Brian, McDermott, Timothy R., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, & Cheng, Jan-Fang. Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T). United States. https://doi.org/10.4056/sigs.1153107
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Kiss, Hajnalka, Cleland, David, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Lu, Megan, Brettin, Thomas, Detter, John C., Göker, Markus, Tindall, Brian J., Beck, Brian, McDermott, Timothy R., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Cheng, Jan-Fang. Sun . "Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)". United States. https://doi.org/10.4056/sigs.1153107. https://www.osti.gov/servlets/purl/1630546.
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@article{osti_1630546,
title = {Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)},
author = {Kiss, Hajnalka and Cleland, David and Lapidus, Alla and Lucas, Susan and Del Rio, Tijana Glavina and Nolan, Matt and Tice, Hope and Han, Cliff and Goodwin, Lynne and Pitluck, Sam and Liolios, Konstantinos and Ivanova, Natalia and Mavromatis, Konstantinos and Ovchinnikova, Galina and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Chang, Yun-Juan and Jeffries, Cynthia D. and Lu, Megan and Brettin, Thomas and Detter, John C. and Göker, Markus and Tindall, Brian J. and Beck, Brian and McDermott, Timothy R. and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter and Cheng, Jan-Fang},
abstractNote = {'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.1153107},
journal = {Standards in Genomic Sciences},
number = 2,
volume = 3,
place = {United States},
year = {Sun Oct 31 00:00:00 EDT 2010},
month = {Sun Oct 31 00:00:00 EDT 2010}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.4056/sigs.1153107
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Cited by: 9 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of ‘T. terrenum’ strain YNPT relative to the type strains of the other species within the phylum Chloroflexi . The trees were inferred from 1,316 aligned characters of the 16S rRNA gene sequence under the maximum likelihood criterion and rooted in accordance withmore » the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD are shown in blue, published genomes and GenBank records [CP000804,CP000875,CP000909,CP001337] in bold, e.g. the GEBA genome S. thermophilus.« less
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    Works referencing / citing this record:

    Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring
    journal, March 2018

    • Lee, Li Sin; Goh, Kian Mau; Chan, Chia Sing
    • MicrobiologyOpen, Vol. 7, Issue 6
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    Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)
    journal, October 2011

    • Chang, Yun-juan; Land, Miriam; Hauser, Loren
    • Standards in Genomic Sciences, Vol. 5, Issue 1
    • DOI: 10.4056/sigs.2114901
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