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Title: The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

Abstract

Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses. Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils. In conclusion, this study provides a holistic understanding of microbiome structure within amore » bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [3]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  2. East Carolina Univ., Greenville, NC (United States). Brody School of Medicine, East Carolina Diabetes & Obesity Inst., Dept. of Biochemistry & Molecular Biology
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
Publication Date:
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)
OSTI Identifier:
1423095
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Populus deltoides; Populus trichocarpa × deltoides hybrid; 16S rRNA; ITS2; Fungal pathogen

Citation Formats

Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A., and Schadt, C. W. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. United States: N. p., 2018. Web. doi:10.1186/s40168-018-0413-8.
Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A., & Schadt, C. W. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. United States. doi:10.1186/s40168-018-0413-8.
Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A., and Schadt, C. W. Mon . "The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome". United States. doi:10.1186/s40168-018-0413-8. https://www.osti.gov/servlets/purl/1423095.
@article{osti_1423095,
title = {The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome},
author = {Cregger, M. A. and Veach, A. M. and Yang, Z. K. and Crouch, M. J. and Vilgalys, R. and Tuskan, G. A. and Schadt, C. W.},
abstractNote = {Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses. Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils. In conclusion, this study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.},
doi = {10.1186/s40168-018-0413-8},
journal = {Microbiome},
issn = {2049-2618},
number = 1,
volume = 6,
place = {United States},
year = {2018},
month = {2}
}

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