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Title: Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil

Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [4] ;  [9] ;  [9] ;  [10] ;  [9] ;  [9] ;  [9] ;  [9] ;  [9] ;  [9] ;  [9] more »;  [9] ;  [9] ;  [9] ;  [9] ;  [9] ;  [9] « less
  1. Utah State Univ., Logan, UT (United States)
  2. Woods Hole Research Center, Falmouth, MA (United States)
  3. Miami Univ., Oxford, OH (United States)
  4. Oregon State Univ., Corvallis, OR (United States)
  5. City Univ. (CUNY), Flushing, NY (United States). Queens College; Xiamen Univ. (China). Inst. of Marine Microbes and Ecospheres
  6. Netherlands Inst. of Ecology, Wageningen (Netherlands); Utrecht Univ. (Netherlands)
  7. Chuo Univ., Tokyo (Japan)
  8. Univ. of Alberta, Edmonton, AB (Canada)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  10. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Biosciences Division
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; nitrosospira; ammonia-oxidizing bacteria; nitrification; agricultural soil; ammonia monooxygenase; nitrous oxide; chemolithotroph
OSTI Identifier:
1379530

Rice, Marlen C., Norton, Jeanette M., Valois, Frederica, Bollmann, Annette, Bottomley, Peter J., Klotz, Martin G., Laanbroek, Hendrikus J., Suwa, Yuichi, Stein, Lisa Y., Sayavedra-Soto, Luis, Woyke, Tanja, Shapiro, Nicole, Goodwin, Lynne A., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Kyrpides, Nikos, Varghese, Neha, Mikhailova, Natalia, Markowitz, Victor, Palaniappan, Krishna, Ivanova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, and Daum, Chris. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. United States: N. p., Web. doi:10.1186/s40793-016-0168-4.
Rice, Marlen C., Norton, Jeanette M., Valois, Frederica, Bollmann, Annette, Bottomley, Peter J., Klotz, Martin G., Laanbroek, Hendrikus J., Suwa, Yuichi, Stein, Lisa Y., Sayavedra-Soto, Luis, Woyke, Tanja, Shapiro, Nicole, Goodwin, Lynne A., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Kyrpides, Nikos, Varghese, Neha, Mikhailova, Natalia, Markowitz, Victor, Palaniappan, Krishna, Ivanova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, & Daum, Chris. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. United States. doi:10.1186/s40793-016-0168-4.
Rice, Marlen C., Norton, Jeanette M., Valois, Frederica, Bollmann, Annette, Bottomley, Peter J., Klotz, Martin G., Laanbroek, Hendrikus J., Suwa, Yuichi, Stein, Lisa Y., Sayavedra-Soto, Luis, Woyke, Tanja, Shapiro, Nicole, Goodwin, Lynne A., Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Kyrpides, Nikos, Varghese, Neha, Mikhailova, Natalia, Markowitz, Victor, Palaniappan, Krishna, Ivanova, Natalia, Stamatis, Dimitrios, Reddy, T. B. K., Ngan, Chew Yee, and Daum, Chris. 2016. "Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil". United States. doi:10.1186/s40793-016-0168-4. https://www.osti.gov/servlets/purl/1379530.
@article{osti_1379530,
title = {Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil},
author = {Rice, Marlen C. and Norton, Jeanette M. and Valois, Frederica and Bollmann, Annette and Bottomley, Peter J. and Klotz, Martin G. and Laanbroek, Hendrikus J. and Suwa, Yuichi and Stein, Lisa Y. and Sayavedra-Soto, Luis and Woyke, Tanja and Shapiro, Nicole and Goodwin, Lynne A. and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Kyrpides, Nikos and Varghese, Neha and Mikhailova, Natalia and Markowitz, Victor and Palaniappan, Krishna and Ivanova, Natalia and Stamatis, Dimitrios and Reddy, T. B. K. and Ngan, Chew Yee and Daum, Chris},
abstractNote = {Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.},
doi = {10.1186/s40793-016-0168-4},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 11,
place = {United States},
year = {2016},
month = {7}
}

Works referenced in this record:

Evolution and classification of the CRISPR–Cas systems
journal, May 2011
  • Makarova, Kira S.; Haft, Daniel H.; Barrangou, Rodolphe
  • Nature Reviews Microbiology, Vol. 9, Issue 6, p. 467-477
  • DOI: 10.1038/nrmicro2577

Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009