Thousands of microbial taxa in the soil form symbioses with host plants and are sufficiently important to plant function that they are often referred to as a “second genome.” Many of these microbes inhabit the zone of soil in close proximity to roots—the rhizosphere—and can promote plant growth, improve nutrient accessibility, suppress diseases, and moderate other host functions. The developmental stage of a host plant could affect rhizosphere microbial assemblage, potentially through an effect of root exudation. Alternatively, this composition could change simply as a consequence of time and opportunity for microbial succession. Previous studies indicate that microbial assemblages in the rhizosphere shift across plant developmental stages, but in these instances, time since germination is entangled with developmental stage. Disentangling these factors is key to understanding the extent to which phenological events of host plants, like flowering or producing fruits, alter their rhizosphere microbiomes relative to how those microbes change over time, independent of phenological status.
We asked how succession and developmental status differentially affect microbial assemblage in the rhizosphere; we focused on flowering as a distinct developmental stage at which to identify the composition of rhizosphere microbiomes. We extricated time since planting from developmental status by using multiple flowering-time mutants of Arabidopsis thaliana within the same genetic background, comparing the wild type against mutants that produced flowers earlier and later. To identify the effects of succession and flowering status on rhizosphere microbes, we first sampled shortly after germination when all genotypes were vegetative, again when early mutants flowered, next when wild type individuals flowered, and finally when late mutants flowered; thus, we could compare microbial communities that had similar time for succession but hosts at different developmental stages. We used 16S rRNA sequencing to characterize rhizosphere microbial composition.
Results/Conclusions
Microbial assemblages were indistinguishable (p > 0.3) among flowering and non-flowering plants within time points. In contrast, the four sampling events were strong predictors of differences in rhizosphere microbe composition regardless of whether or not plants were flowering (p < 0.001). In this case, flowering status did not change the rhizosphere microbiome, and time since planting explained the differences we observed among samples. Our results support the idea that succession accounts for differences in microbial assemblage over time, regardless of host phenological status.