Plant Phylogeny Affects the Structure and Function of the Rhizosphere Microbiome

The plant rhizosphere microbiome is essential for plant health and growth. One of the key roles the rhizosphere microbiome plays in plant health is nitrogen cycling. Indeed, while plants are unable to obtain nitrogen from the environment in its most common form (i.e., N2), a reduced group of microbes can cycle nitrogen through its various forms and provide usable forms to plants. Previous research has established that multiple factors influence the composition of the rhizosphere microbiome including plant species, soil properties, plant root exudates, and season. However, little research has been done to discriminate these factors in examining their effect on the microbiome. Here, I took advantage of an ongoing common garden experiment to further investigate how plant phylogeny impacts the rhizosphere microbiome. The phylogeny of 27 grasses with different geographic origins was established by chloroplast DNA sequencing whereas the structure and function of their rhizosphere microbiomes was established using whole (meta)genome sequencing. Based on annotated reads, the most abundant taxa, with a conserved set of functions, formed a core microbiome across plants. Beside these taxa, some less abundant and more specialized lineages drove dissimilarity in the structure and functional potential of the microbiomes. Variation in grass phylogeny was compared in the microbiomes and the relatedness among plants correlated with fluctuation of the rhizosphere microbiome structure and functional potential based on annotated sequences. Overall, these results suggest that (i) traits for nitrogen cycling are not randomly distributed in microbiomes and (ii) plants actively control the structure and/or functional potential of their rhizosphere microbiomes. Finally, these results provide a framework for future studies to discover the mechanisms that plants use to regulate their rhizosphere microbiomes