COS 119-3 - Dissecting the microbiome of Populus tree species from the soil to the canopy using amplicon sequencing and shotgun metagenomic analyses

Wednesday, August 9, 2017: 2:10 PM
D139, Oregon Convention Center
Melissa A. Cregger1, Allison M. Veach1, Miranda Crouch1, Ian Hodges1, Zamin Yang1, Debbie Weighill1, Piet Jones1, Carissa Bleker1, Armin Geiger1, Mircea Podar1, Rytas Vilgalys2, Timothy Rials3, Susannah G. Tringe4, Dale A. Pelletier1, Daniel Jacobson1 and Christopher W. Schadt1, (1)Oak Ridge National Laboratory, (2)Department of Biology, Duke University, Durham, NC, (3)University of Tennessee Institute of Agriculture, Knoxville, TN, (4)DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA

The microbiome associated with plants serve important functions in promoting plant growth and survival. However since most studies have only addressed microbiome composition of one plant tissue type at a time, our current understanding of the variation in microbiome composition across the myriad of habitats represented by a tree from the soil to the canopy, is not adequate. Using Populus trees as a model ecosystem coupled with next generation amplicon sequencing, this study characterized the microbiome – specifically the archaea, bacteria, and fungi - across 30 different potential niches of five replicate Populus deltoides and five hybrid Populus trichocarpa X deltoides (TxD)clones grown in adjacent sections of a three year old experimental plantation in Tennessee.


The microbiome varied across plant niches from the leaves to the soil with diversity varying across habitats and specifically, greater fungal diversity in P. deltoides habitats. The oldest woody stem tissues were also distinguishable from 1st and 2nd year tissues, and enriched in Firmicutes consistent with potentially anaerobic environments. Within the leaf, stem, root, and soil habitats, bacterial and fungal community structure in P. deltoides samples could be differentiated from TxD hybrid samples. Leaf niches of the TxD hybrid had high abundances of the fungal pathogens Septoria musciva and Marssonina brunnea relative to P. deltoides leaf samples and suggest the differential abundance of these pathogens may be driving changes in the overall microbiome structure. Comparative metagenomic analyses and amplicon-based datasets were completed for root endophyte, rhizosphere and soil samples, show a high degree of congruence and confirm our methods reduced host DNA contamination to < 2%. Metagenome functional gene profiles based on ordination and network analyses of PFAM enrichment patterns, show distinct clustering based on habitat type (endosphere, rhizosphere, and soil) and host genotype (P. deltoides vs. TxD hybrids). Results from this and future work should enhance our community and functional understanding of plant microbiomes in this important model species.