The Plant-Microbe Interfaces Scientific Focus Area (SFA) is one of several SFAs for National Laboratory research funded by the Office of Biological and Environmental Research (BER) within the U.S. Department of Energy’s (DOE’s) Office of Science. The SFA is created in 2008 to take advantage of the multidisciplinary, team-oriented research that is a strength of a national laboratory such as ORNL.
PMI Sampling Trip
Location: Oct 2015
PMI Blount County Louisville TN Sampling Trip
While there have been numerous studies of the microbial associations of individual plant environments (e.g. the rhizosphere, phylosphere or endosphere) very few have simultaneously examined variation across habitats of the plant as a whole. Simultaneous examination should allow us to better understand microbial niche specialization and niche overlap of symbiotic partners across the overall tree environment. This will allow us to build an “atlas” of microbial interactors of Populus trees and better links to their potential functions across Populus. We conducted sampling the week of August 11th that will enable us comprehensively survey rRNA based microbial diversity across approximately 30 different tissue level habitats in Populus. These are replicated within individual trees, between five replicate clonal trees, and across two contrasting genotypes (P. deltoides and P. deltoides X trichocarpa). Selected plant habitats are also to be examined using metagenome DNA sequencing to include soils, rhizospheres, root endospheres, heartwood, and leaves, replicated from samples pooled across the individual tree habitats. Samples are also being used for culture isolation and single cell genomics of targeted species (ectomycorrhizae, Atractiella, Acenitobacter, etc.)
PMI Oregon Sample Trip
Populus trichocarpa root collection in Clatskanie and Corvallis, OR common gardens occurred in May 2012. 32 genotypes from 1100 P. trichocarpa genotypes were selected based on their phenotypic diversity and their genomic regions. Fine roots, soils sample, and fungal sporocarps were collected from (and around) each tree.
Common Garden Root Sample Processing
Roots collected from the various genotypes of P. trichocarpa in the North West common gardens being washed and cut for distribution among the various researchers for their respective studies.
Live cell imaging of a plant-microbe interaction
A Pantoea strain isolated from the poplar rhizosphere was engineered by post-doc Amber Bible to produce GFP when a gene encoding a diguanylate cyclase is activated. The plant-associated bacteria fluoresces green against a background of red autofluoresence from a wheat plant. Images were collected from live plant-microbe co-cultures using confocal microscopy by Jenny Morrell-Falvey. Although this Pantoea strain is often found associated with the plant surface, this movie shows the bacteria living inside a plant cell.