Does Populus deltoides select for a unique microbiome?

Background/Question/Methods

Populushas become of great interest to bioenergy researchers for the production of cellulose-derived biofuels. The genetically diverse and clonal nature of Populus allows it to grow within a wide range of temperate habitat types. The ease that Populus clones can be propagated, tractable genome and fast growth rates have made it a leading candidate for bioenergy and fibre production and a model system for forest genetics. Our goal is to understand the microbiome associated with Populus, the host genotypic and environmental characteristics that effect the composition of the microbiome, and the role of the microbiome in plant health and productivity. The aim of the current study is to further parse the degree to which plant species vs other local environmental factors influences microbiome assembly in the habitats in which they co-occur

Native P. deltoides samples were collected within the lower Caney Fork River basin in Tennessee. At each site P. deltoidesthree adjacent heterospecific tree species were sampled. Replicate samples of bulk soil and root samples for rhizosphere, and endophytes were collected from each tree. High throughput sequencing data was generated for both bacterial and fungal communities via 454 pyro-sequencing. Denoising and quality filtering was performed via Ampliconnoise and ChimeraSlayer respectively. Taxonomic assignment, OTU picking, and all other downstream analyses were performed using QIIME.

Results/Conclusions

A total of 64 bacterial communities (399,674 reads) and 39 fungal communities (120,461 reads) remained after quality filtering and removal of singeltons. Initial phylogenetic and OTU-based analyses show minimal community differences between P. deltoides and adjacent heterospecifics for both bacterial and fungal communities. However, some specific differences in endophytic communities between species as apparent.  For example P. deltoides have a significantly higher proportion of Pseudomonas(Bonferroni p-val < 0.001) compared to heterospecific endophytic communities. Bulk soil and rhizosphere samples contained higher relative abundances of Acidobacteria and Proteobacteria, while endophyte communities contained higher relative abundances of Actinobacteria.  Although analysis of fungal community data is ongoing, we have observed increased representation of fungi from the Chytridiomycota and Mortierellomycotina (Bonferroni p-val < 0.001) in soil and rhizosphere communities compared to endophytic communities.

 With the exception of increased relative abundance of Pseudomonas within the root system, P. deltoides does not appear to affect the overall composition of fungal and bacterial communities differently than adjacent heterospecific trees. These results suggest that local soil properties and processes may predominately affect microbial community assembly.