Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors
Abstract
Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecologicalmore »
- Authors:
-
[1];
[1];
[1];
[2];
[3];
[3]
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1807272
- Alternate Identifier(s):
- OSTI ID: 1821201
- Report Number(s):
- PNNL-SA-158824
Journal ID: ISSN 2379-5042
- Grant/Contract Number:
- AC05-00OR22725; AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mSphere
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 3; Journal ID: ISSN 2379-5042
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 16S rRNA; ITS; microbial ecology; microbial community assembly; microbial source tracking; null modeling; plant endosphere; plant-microbe interactions; phyllosphere; rhizosphere
Citation Formats
Dove, Nicholas C., Veach, Allison M., Muchero, Wellington, Wahl, Toni, Stegen, James C., Schadt, Christopher W., and Cregger, Melissa A. Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors. United States: N. p., 2021.
Web. doi:10.1128/msphere.01316-20.
Dove, Nicholas C., Veach, Allison M., Muchero, Wellington, Wahl, Toni, Stegen, James C., Schadt, Christopher W., & Cregger, Melissa A. Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors. United States. https://doi.org/10.1128/msphere.01316-20
Dove, Nicholas C., Veach, Allison M., Muchero, Wellington, Wahl, Toni, Stegen, James C., Schadt, Christopher W., and Cregger, Melissa A. Wed .
"Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors". United States. https://doi.org/10.1128/msphere.01316-20. https://www.osti.gov/servlets/purl/1807272.
@article{osti_1807272,
title = {Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors},
author = {Dove, Nicholas C. and Veach, Allison M. and Muchero, Wellington and Wahl, Toni and Stegen, James C. and Schadt, Christopher W. and Cregger, Melissa A.},
abstractNote = {Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.},
doi = {10.1128/msphere.01316-20},
journal = {mSphere},
number = 3,
volume = 6,
place = {United States},
year = {Wed Jun 09 00:00:00 EDT 2021},
month = {Wed Jun 09 00:00:00 EDT 2021}
}
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