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Title: Exploration of the Biosynthetic Potential of the Populus Microbiome

Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NPmore » diversity trends seen in the metagenomic samples. In our paper, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome.« less
Authors:
ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [1] ;  [1] ; ORCiD logo [1] ; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 3; Journal Issue: 5; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (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; biosynthetic gene clusters; natural product biosynthesis; plant-microbe interactions; quorum sensing; rhizosphere-inhabiting microbes; siderophores
OSTI Identifier:
1479788

Blair, Patricia M., Land, Miriam L., Piatek, Marek J., Jacobson, Daniel A., Lu, Tse-Yuan S., Doktycz, Mitchel John, and Pelletier, Dale A.. Exploration of the Biosynthetic Potential of the Populus Microbiome. United States: N. p., Web. doi:10.1128/mSystems.00045-18.
Blair, Patricia M., Land, Miriam L., Piatek, Marek J., Jacobson, Daniel A., Lu, Tse-Yuan S., Doktycz, Mitchel John, & Pelletier, Dale A.. Exploration of the Biosynthetic Potential of the Populus Microbiome. United States. doi:10.1128/mSystems.00045-18.
Blair, Patricia M., Land, Miriam L., Piatek, Marek J., Jacobson, Daniel A., Lu, Tse-Yuan S., Doktycz, Mitchel John, and Pelletier, Dale A.. 2018. "Exploration of the Biosynthetic Potential of the Populus Microbiome". United States. doi:10.1128/mSystems.00045-18.
@article{osti_1479788,
title = {Exploration of the Biosynthetic Potential of the Populus Microbiome},
author = {Blair, Patricia M. and Land, Miriam L. and Piatek, Marek J. and Jacobson, Daniel A. and Lu, Tse-Yuan S. and Doktycz, Mitchel John and Pelletier, Dale A.},
abstractNote = {Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NP diversity trends seen in the metagenomic samples. In our paper, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome.},
doi = {10.1128/mSystems.00045-18},
journal = {mSystems},
number = 5,
volume = 3,
place = {United States},
year = {2018},
month = {10}
}

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