Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil
Abstract
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:
- more »
- 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:
- 1618958
- Alternate Identifier(s):
- OSTI ID: 1379530
- Grant/Contract Number:
- CSP 2010 project 1012224; AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; nitrosospira; ammonia-oxidizing bacteria; nitrification; agricultural soil; ammonia monooxygenase; nitrous oxide; chemolithotroph
Citation Formats
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 Kingdom: N. p., 2016.
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 Kingdom. https://doi.org/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. Thu .
"Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil". United Kingdom. https://doi.org/10.1186/s40793-016-0168-4.
@article{osti_1618958,
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 Kingdom},
year = {Thu Jul 28 00:00:00 EDT 2016},
month = {Thu Jul 28 00:00:00 EDT 2016}
}
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