Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria
Abstract
© 2015, Nature Publishing Group. All rights reserved. Root nodule bacteria (RNB) or "rhizobia" are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic as sociation and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.
- Authors:
-
- Joint Genome Institute, Walnut Creek, CA (United States)
- Murdock Univ., Murdoch (Australia)
- Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1241030
- Alternate Identifier(s):
- OSTI ID: 1378655
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 5; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; applied microbiology; comparative genomics; data mining; symbiosis
Citation Formats
Seshadri, Rekha, Reeve, Wayne G., Ardley, Julie K., Tennessen, Kristin, Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N. Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria. United States: N. p., 2015.
Web. doi:10.1038/srep16825.
Seshadri, Rekha, Reeve, Wayne G., Ardley, Julie K., Tennessen, Kristin, Woyke, Tanja, Kyrpides, Nikos C., & Ivanova, Natalia N. Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria. United States. https://doi.org/10.1038/srep16825
Seshadri, Rekha, Reeve, Wayne G., Ardley, Julie K., Tennessen, Kristin, Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N. Fri .
"Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria". United States. https://doi.org/10.1038/srep16825. https://www.osti.gov/servlets/purl/1241030.
@article{osti_1241030,
title = {Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria},
author = {Seshadri, Rekha and Reeve, Wayne G. and Ardley, Julie K. and Tennessen, Kristin and Woyke, Tanja and Kyrpides, Nikos C. and Ivanova, Natalia N.},
abstractNote = {© 2015, Nature Publishing Group. All rights reserved. Root nodule bacteria (RNB) or "rhizobia" are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic as sociation and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.},
doi = {10.1038/srep16825},
journal = {Scientific Reports},
number = ,
volume = 5,
place = {United States},
year = {Fri Nov 20 00:00:00 EST 2015},
month = {Fri Nov 20 00:00:00 EST 2015}
}
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Legionella
journal, October 2020
- Mondino, Sonia; Schmidt, Silke; Buchrieser, Carmen
- mBio, Vol. 11, Issue 5
High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia
journal, January 2017
- Klonowska, Agnieszka; López-López, Aline; Moulin, Lionel
- Standards in Genomic Sciences, Vol. 12, Issue 1
High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr
journal, March 2017
- Reeve, Wayne; van Berkum, Peter; Ardley, Julie
- Standards in Genomic Sciences, Vol. 12, Issue 1
Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach
journal, April 2016
- Lyngwi, Nathaniel A.; Nongkhlaw, Macmillan; Kalita, Debajit
- PLOS ONE, Vol. 11, Issue 4
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil
posted_content, February 2020
- Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie
- Research Square [preprints]
Taxonomy and systematics of plant probiotic bacteria in the genomic era
journal, January 2017
- Carro, Lorena; Nouioui, Imen
- AIMS Microbiology, Vol. 3, Issue 3