Studying the Plant-Microbe Interface of Populus Using Constructed Microbial Communities

The association of plant and microbes at the root-soil interface exemplifies a complex, multi-organism system that is shaped by the participating organisms and environmental forces. The plant microbe interface is a dynamic boundary across which a plant detects, interacts with, and may alter its associated biotic environment in order to maintain or improve its performance. Poor understanding of the mechanics of the plant-microbe interface represents a critical knowledge gap. Our goal was to investigate key areas of this gap: (a) microbial community assembly dynamics on Populus host root systems, (b) potential host specificity of two Populus species, and (c) the effect of environmental factors in structuring the root microbiome of Populus. This study used constructed communities in which specific microbes are combined with an axenic host in a controlled fashion. The process used two communities of 10 bacterial strains isolated from two poplar species; the 10 bacterial strains represented abundant members both functionally and phylogenetically from Populus natural microbiomes. The two communities were inoculated onto two Populus host species, and microbial community structure and abundance was assayed by qPCR and/or 16S rRNA amplicon sequencing. A time course study revealed that Pantoea dominates the community at all sampled time points and Paraburkholderia emerges as a dominant member as time progresses. In addition, species of Populus were dominated by Paraburkholderia and Pantoea or Rahnella strains regardless of original host species isolated from. Community members colonized in similar abundances compared to colonization by individual members of the communities. The shade treatment had no effect on the structure of the bacterial community, although stem length and root area of the plant increased significantly with the 10-member community. This study demonstrates the feasibility and analysis of model communities to study microbiome function in plant systems.