A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees

Journal Article · Tue Jan 01 04:00:00 EST 2013 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0076382· OSTI ID:1097482

Shakya, Migun ^[1]; Gottel, Neil R ^[1]; Castro Gonzalez, Hector F ^[1]; Yang, Zamin ^[1]; Gunter, Lee E ^[1]; Labbe, Jessy L ^[1]; Muchero, Wellington ^[1]; Bonito, Gregory ^[2]; Vilgalys, Rytas ^[2]; Tuskan, Gerald A ^[1]; Podar, Mircea ^[1]; Schadt, Christopher Warren ^[1]

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1. ORNL
2. Duke University

Bacterial and fungal communities associated with plant roots are central to the host- health, survival and growth. However, a robust understanding of root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to it s associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 1097482
• Journal Information: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 10 Vol. 8; ISSN 1932-6203
• Country of Publication: United States
• Language: English

Related Subjects

Bacteria
Endosphere
Fungi
Microbiome
Populus
Rhizosphere