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

Marlen C. Rice; Jeanette M. Norton; Frederica Valois; Annette Bollmann; Peter J. Bottomley; Martin G. Klotz; Hendrikus J. Laanbroek; Yuichi Suwa; Lisa Y. Stein; Luis Sayavedra-Soto; Tanja Woyke; Nicole Shapiro; Lynne A. Goodwin; Marcel Huntemann; Alicia Clum; Manoj Pillay; Nikos Kyrpides; Neha Varghese; Natalia Mikhailova; Victor Markowitz; Krishna Palaniappan; Natalia Ivanova; Dimitrios Stamatis; T. B.K. Reddy; Chew Yee Ngan; Chris Daum

doi:10.1186/s40793-016-0168-4

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

Marlen C. Rice, Jeanette M. Norton^*, Frederica Valois, Annette Bollmann, Peter J. Bottomley, Martin G. Klotz, Hendrikus J. Laanbroek, Yuichi Suwa, Lisa Y. Stein, Luis Sayavedra-Soto, Tanja Woyke, Nicole Shapiro, Lynne A. Goodwin, Marcel Huntemann, Alicia Clum, Manoj Pillay, Nikos Kyrpides, Neha Varghese, Natalia Mikhailova, Victor MarkowitzKrishna Palaniappan, Natalia Ivanova, Dimitrios Stamatis, T. B.K. Reddy, Chew Yee Ngan, Chris Daum

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Article number	46
Journal	Standards in Genomic Sciences
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/s40793-016-0168-4
Publication status	Published - 28 Jul 2016

Keywords

Agricultural soil
Ammonia monooxygenase
Ammonia-oxidizing bacteria
Chemolithotroph
Nitrification
Nitrosospira
Nitrous oxide

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Rice, M. C., Norton, J. M., Valois, F., Bollmann, A., Bottomley, P. J., Klotz, M. G., Laanbroek, H. J., Suwa, Y., Stein, L. Y., Sayavedra-Soto, L., Woyke, T., Shapiro, N., Goodwin, L. A., Huntemann, M., Clum, A., Pillay, M., Kyrpides, N., Varghese, N., Mikhailova, N., ... Daum, C. (2016). Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. Standards in Genomic Sciences, 11(1), Article 46. https://doi.org/10.1186/s40793-016-0168-4

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title = "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.",

keywords = "Agricultural soil, Ammonia monooxygenase, Ammonia-oxidizing bacteria, Chemolithotroph, Nitrification, Nitrosospira, Nitrous oxide",

author = "Rice, {Marlen C.} and Norton, {Jeanette M.} and Frederica Valois and Annette Bollmann and Bottomley, {Peter J.} and Klotz, {Martin G.} and Laanbroek, {Hendrikus J.} and Yuichi Suwa and Stein, {Lisa Y.} and Luis Sayavedra-Soto and Tanja Woyke and Nicole Shapiro and Goodwin, {Lynne A.} and Marcel Huntemann and Alicia Clum and Manoj Pillay and Nikos Kyrpides and Neha Varghese and Natalia Mikhailova and Victor Markowitz and Krishna Palaniappan and Natalia Ivanova and Dimitrios Stamatis and Reddy, {T. B.K.} and Ngan, {Chew Yee} and Chris Daum",

year = "2016",

month = jul,

day = "28",

doi = "10.1186/s40793-016-0168-4",

language = "English",

volume = "11",

journal = "Standards in Genomic Sciences",

issn = "1944-3277",

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Rice, MC, Norton, JM, Valois, F, Bollmann, A, Bottomley, PJ, Klotz, MG, Laanbroek, HJ, Suwa, Y, Stein, LY, Sayavedra-Soto, L, Woyke, T, Shapiro, N, Goodwin, LA, Huntemann, M, Clum, A, Pillay, M, Kyrpides, N, Varghese, N, Mikhailova, N, Markowitz, V, Palaniappan, K, Ivanova, N, Stamatis, D, Reddy, TBK, Ngan, CY & Daum, C 2016, 'Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil', Standards in Genomic Sciences, vol. 11, no. 1, 46. https://doi.org/10.1186/s40793-016-0168-4

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T1 - Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil

AU - Rice, Marlen C.

AU - Norton, Jeanette M.

AU - Valois, Frederica

AU - Bollmann, Annette

AU - Bottomley, Peter J.

AU - Klotz, Martin G.

AU - Laanbroek, Hendrikus J.

AU - Suwa, Yuichi

AU - Stein, Lisa Y.

AU - Sayavedra-Soto, Luis

AU - Woyke, Tanja

AU - Shapiro, Nicole

AU - Goodwin, Lynne A.

AU - Huntemann, Marcel

AU - Clum, Alicia

AU - Pillay, Manoj

AU - Kyrpides, Nikos

AU - Varghese, Neha

AU - Mikhailova, Natalia

AU - Markowitz, Victor

AU - Palaniappan, Krishna

AU - Ivanova, Natalia

AU - Stamatis, Dimitrios

AU - Reddy, T. B.K.

AU - Ngan, Chew Yee

AU - Daum, Chris

PY - 2016/7/28

Y1 - 2016/7/28

N2 - 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.

AB - 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.

KW - Agricultural soil

KW - Ammonia monooxygenase

KW - Ammonia-oxidizing bacteria

KW - Chemolithotroph

KW - Nitrification

KW - Nitrosospira

KW - Nitrous oxide

UR - http://www.scopus.com/inward/record.url?scp=84979573577&partnerID=8YFLogxK

U2 - 10.1186/s40793-016-0168-4

DO - 10.1186/s40793-016-0168-4

M3 - Article

AN - SCOPUS:84979573577

SN - 1944-3277

VL - 11

JO - Standards in Genomic Sciences

JF - Standards in Genomic Sciences

IS - 1

M1 - 46

ER -

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

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Keywords

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