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

Publication ,  Journal Article
Cregger, MA; Veach, AM; Yang, ZK; Crouch, MJ; Vilgalys, R; Tuskan, GA; Schadt, CW
Published in: Microbiome
February 2018

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.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.

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Published In

Microbiome

DOI

EISSN

2049-2618

ISSN

2049-2618

Publication Date

February 2018

Volume

6

Issue

1

Start / End Page

31

Related Subject Headings

  • Soil Microbiology
  • Sequence Analysis, DNA
  • Rhizosphere
  • Populus
  • Plant Stems
  • Plant Roots
  • Plant Leaves
  • Organ Specificity
  • Microbiota
  • High-Throughput Nucleotide Sequencing
 

Citation

APA
Chicago
ICMJE
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Cregger, M. A., Veach, A. M., Yang, Z. K., Crouch, M. J., Vilgalys, R., Tuskan, G. A., & Schadt, C. W. (2018). The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome, 6(1), 31. https://doi.org/10.1186/s40168-018-0413-8
Cregger, M. A., A. M. Veach, Z. K. Yang, M. J. Crouch, R. Vilgalys, G. A. Tuskan, and C. W. Schadt. “The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.Microbiome 6, no. 1 (February 2018): 31. https://doi.org/10.1186/s40168-018-0413-8.
Cregger MA, Veach AM, Yang ZK, Crouch MJ, Vilgalys R, Tuskan GA, et al. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome. 2018 Feb;6(1):31.
Cregger, M. A., et al. “The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.Microbiome, vol. 6, no. 1, Feb. 2018, p. 31. Epmc, doi:10.1186/s40168-018-0413-8.
Cregger MA, Veach AM, Yang ZK, Crouch MJ, Vilgalys R, Tuskan GA, Schadt CW. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome. 2018 Feb;6(1):31.
Journal cover image

Published In

Microbiome

DOI

EISSN

2049-2618

ISSN

2049-2618

Publication Date

February 2018

Volume

6

Issue

1

Start / End Page

31

Related Subject Headings

  • Soil Microbiology
  • Sequence Analysis, DNA
  • Rhizosphere
  • Populus
  • Plant Stems
  • Plant Roots
  • Plant Leaves
  • Organ Specificity
  • Microbiota
  • High-Throughput Nucleotide Sequencing