Structural and functional differentiation of the root-associated bacterial microbiomes of perennial ryegrass

The microbiomes inhabiting plant roots and their adjacent soil environment play significant roles in plant growth, health, and ecological services. Recent studies have provided detailed insights into many phytomicrobiomes, but our understanding of the root-associated microbiomes of perennial ryegrass is still very limited. Here we carried out a stratified rhizobox experiment involving a fluvo-aquic soil and red soil under elevated (750 ppm) and ambient (350–400 ppm) CO2, and used deep amplicon sequencing to investigate the ryegrass root-associated bacterial microbiomes across compartments (the bulk soil, 2-mm outer rhizosphere, rhizosphere, rhizoplane, and endosphere). We observed increased relative abundances of Proteobacteria (mainly Rhizobiaceae and Enterobacteriaceae) in the rhizosphere, rhizoplane, and endosphere compared with the bulk soil and outer rhizosphere. The dominant bacterial genera (mainly Methylobacterium, Rhizobium, Pseudomonas, Stenotrophomonas, and Enterobacter) which facilitate plant growth and soil nutrient cycling were enriched in the rhizosphere, rhizoplane, and endosphere compared with outer rhizosphere. PICRUSt predicted moderate functional differentiation of bacterial microbiomes across compartments. The bacterial α-diversity showed a decreased trend along a spatial gradient from the bulk soil to the endosphere. The β-diversity and network analyses indicated significant differences in the root-associated bacterial microbiomes between the fluvo-aquic soil and red soil. In conclusion, our study suggests that the filtration and acquisition of the ryegrass root-associated bacterial microbiomes are largely controlled by indigenous soil microbial communities, rather than the changes in root rhizodeposition caused by elevated CO2.