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Title: Plant compartment and genetic variation drive microbiome composition in switchgrass roots

Abstract

Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.

Authors:
ORCiD logo [1];  [2];  [3];  [1];  [2]
  1. Department of Energy Joint Genome Institute Walnut Creek CA USA
  2. Department of Integrative Biology, University of Texas Austin Austin TX USA
  3. School of Integrative Plant Science, Cornell University Ithaca NY USA
Publication Date:
Research Org.:
Univ. of Texas, Austin, TX (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division
OSTI Identifier:
1501730
Alternate Identifier(s):
OSTI ID: 1511072; OSTI ID: 1591807; OSTI ID: 1594754
Grant/Contract Number:  
SC0014156; AC02‐05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Environmental Microbiology Reports
Additional Journal Information:
Journal Name: Environmental Microbiology Reports Journal Volume: 11 Journal Issue: 2; Journal ID: ISSN 1758-2229
Publisher:
Wiley-Blackwell
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Singer, Esther, Bonnette, Jason, Kenaley, Shawn C., Woyke, Tanja, and Juenger, Thomas E. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. United States: N. p., 2019. Web. doi:10.1111/1758-2229.12727.
Singer, Esther, Bonnette, Jason, Kenaley, Shawn C., Woyke, Tanja, & Juenger, Thomas E. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. United States. doi:10.1111/1758-2229.12727.
Singer, Esther, Bonnette, Jason, Kenaley, Shawn C., Woyke, Tanja, and Juenger, Thomas E. Thu . "Plant compartment and genetic variation drive microbiome composition in switchgrass roots". United States. doi:10.1111/1758-2229.12727.
@article{osti_1501730,
title = {Plant compartment and genetic variation drive microbiome composition in switchgrass roots},
author = {Singer, Esther and Bonnette, Jason and Kenaley, Shawn C. and Woyke, Tanja and Juenger, Thomas E.},
abstractNote = {Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.},
doi = {10.1111/1758-2229.12727},
journal = {Environmental Microbiology Reports},
issn = {1758-2229},
number = 2,
volume = 11,
place = {United States},
year = {2019},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1111/1758-2229.12727

Citation Metrics:
Cited by: 3 works
Citation information provided by
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