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Title: Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria

Abstract

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 association 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 symbioticand 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. Lastly, 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:
 [1];  [2];  [2];  [1];  [1];  [3];  [1]
  1. Joint Genome Institute, Walnut Creek, CA (United States)
  2. Murdock Univ., Murdoch (Australia)
  3. 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 Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
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. doi: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. doi: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 = {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 association 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 symbioticand 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. Lastly, 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 = {2015},
month = {11}
}

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