Implications of invasive microbes on native microbiome diversity and growth of perennial biofeedstock plants

Jessica A. M. Moore and Joshua K Michener, Bioscience Division, Oak Ridge National Lab, Oak Ridge, TN, Nicholas C. Dove, Biosciences, Oak Ridge National Laboratory, Wellington Muchero, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, Paul E. Abraham, Oak Ridge National Lab, Oak Ridge, TN, Melissa Cregger, Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN

Background/Question/Methods
Bacillus species are ubiquitous bacteria in soils, sometimes forming beneficial mutualisms that promote plant growth. Increasing the diversity and abundance of these organisms in soils may improve plant productivity in managed ecosystems, but novel Bacillus species introduced to an ecosystem may have varying establishment success depending on host genetic factors, environmental conditions, or belowground biotic interactions. After introduction to an ecosystem, Bacillus can spread systemically through the host plant. Due to gene-gene interactions between bacteria and plant hosts, the rate and success of systemic spread can vary among plant hosts. Bacillus associates with Populus trees, an important biofeedstock crop. We have assessed richness and diversity of native Bacillus in a field site in Knoxville, TN. Our study objectives were to characterize (1) the richness and (2) diversity of native Bacillus species. We sequenced amplicons of the 16S rRNA gene region in four different plant-based habitats (rhizosphere, root endosphere, leaf endosphere, and leaf surface) in two host species (Populus trichocarpa and Populus deltoides) and delineated 16S reads into amplicon sequence variants (ASVs). This longitudinal study will inform manipulative experiments where we will examine the efficacy of introducing novel Bacillus species to new environments.
Results/Conclusions
We confirmed presence of the genus Bacillus in the native Populus microbiomes in our study region. We found that ASV richness within the Bacillus genus varied significantly among host tree species (P < 0.001) and among habitats within trees (P = 0.01). Averaged across habitats within the tree system, P. deltoides had 612 Bacillus ASVs while P. trichocarpa had 801. In both host tree species, Bacillus ASV richness was highest in the rhizosphere where c. 1649 ASVs were found. Other habitats contained less half the number of ASVs as the rhizosphere. The root endosphere contained 465, the leaf surface contained 617, and the leaf endosphere contained 269 ASVs. Diversity (inverse Simpson’s index) was similar between the two plant host species (P = 0.23) but varied among the habitats (P < 0.01). Diversity of Bacillus was more than twice as high in the rhizosphere than other habitat zones. While all habitats in the plant system contained Bacillus ASVs, we found their ASV richness and diversity was highest in the rhizosphere of two Populus host species. Our findings suggest that invading Bacillus species may be least successful establishing in the rhizosphere because of high native Bacillus richness and diversity.