Data from: Whole-genome duplication and host genotype affect rhizosphere microbial communities

The composition of microbial communities found in association with plants
is influenced by host phenotype and genotype. Yet, the ways in which
specific genetic architectures of host plants shape microbiomes is
unknown. Genome duplication events are common in the evolutionary history
of plants, influence many important plant traits, and, thus, they may
affect associated microbial communities. Using experimentally induced
whole genome duplication (WGD), we tested the effect of WGD on rhizosphere
bacterial communities in Arabidopsis thaliana. We performed 16S rRNA
amplicon sequencing to characterize differences between microbiomes
associated with specific host genetic backgrounds (Columbia vs. Landsberg)
and ploidy levels (diploid vs. tetraploid). We modeled relative abundances
of bacterial taxa using the Dirichlet and multinomial distributions via a
hierarchical Bayesian approach. We found that host genetic background and
ploidy level affected rhizosphere community composition. We then tested to
what extent microbiomes derived from a specific genetic background or
ploidy level affected plant performance by inoculating sterile seedlings
with microbial communities harvested from a prior generation. We found a
negative effect of the tetraploid Columbia microbiome on growth of all
four plant genetic backgrounds. These findings suggest an interplay
between host genetic architecture and bacterial community assembly with
potential ramifications for host fitness. Moreover, we uncovered an
intriguing role of ploidy-level for shaping plant microbiomes. Given the
prevalence of ploidy-level variation in both wild and managed plant
populations, the effects on microbiomes of this aspect of host genetic
architecture could be a widespread driver of differences in plant
microbiomes.