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Title: Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)

Abstract

Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na(+) ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [3] more »;  [3];  [4];  [4];  [5];  [6];  [7];  [5];  [5];  [5];  [1];  [8];  [9];  [10];  [5];  [1] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. Jomo Kenyatta Univ. of Agriculture and Technology (Kenya)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States);Jomo Kenyatta Univ. of Agriculture and Technology (Kenya)
  9. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  10. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
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); German Research Foundation (DFG)
OSTI Identifier:
1630578
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-2
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; strictly aerobic; motile by gliding; Gram-negative; flexirubin-synthesizing; mesophilic; chemoorganotrophic Cryomorphaceae; GEBA

Citation Formats

Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J., Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T). United States: N. p., 2011. Web. doi:10.4056/sigs.2124912.
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Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J., Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, & Kyrpides, Nikos C. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T). United States. https://doi.org/10.4056/sigs.2124912
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Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J., Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C. Sat . "Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)". United States. https://doi.org/10.4056/sigs.2124912. https://www.osti.gov/servlets/purl/1630578.
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@article{osti_1630578,
title = {Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)},
author = {Woyke, Tanja and Chertkov, Olga and Lapidus, Alla and Nolan, Matt and Lucas, Susan and Del Rio, Tijana Glavina and Tice, Hope and Cheng, Jan-Fang and Tapia, Roxanne and Han, Cliff and Goodwin, Lynne and Pitluck, Sam and Liolios, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Huntemann, Marcel and Mavromatis, Konstantinos and Mikhailova, Natalia and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Brambilla, Evelyne-Marie and Rohde, Manfred and Mwirichia, Romano and Sikorski, Johannes and Tindall, Brian J. and Göker, Markus and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Klenk, Hans-Peter and Kyrpides, Nikos C.},
abstractNote = {Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na(+) ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.2124912},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 5,
place = {United States},
year = {Sat Oct 15 00:00:00 EDT 2011},
month = {Sat Oct 15 00:00:00 EDT 2011}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.4056/sigs.2124912
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Cited by: 21 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of F. taffensis relative to the type strains of the other species within the family Cryomorphaceae. The tree was inferred from 1,429 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion. Rooting was done initially using the midpointmore » method and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 300 ML bootstrap replicates (left) and from 1,000 maximum parsimony bootstrap replicates (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD are labeled with one asterisk, those also listed as 'Complete and Published' (as well as the target genome) with two asterisks.« less
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    Distribution and microbial community structure analysis of a single-stage partial nitritation/anammox granular sludge bioreactor operating at low temperature
    journal, February 2016

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    • Applied and Environmental Microbiology, Vol. 80, Issue 8
    • DOI: 10.1128/aem.04105-13
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