Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

Matthew Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo

Deposition and secretion from roots influences the composition of the microbial communities surrounding them in the rhizosphere, and microbial activities influence the growth and health of the plant. Different host plant genotypes result in differences in those microbial communities. Crop genomes may have a narrow genetic base because of bottlenecks that occurred when domesticated crops were derived from small populations within the progenitor species. Desirable traits influencing root-associated microbial communities might therefore have been lost in the transition from wild species to modern cultivars. To investigate the diversity of bacterial communities associated with wild and cultivated rice, we surveyed a series of plant species and cultivars spanning the Oryza genus, growing them in the same nutrient-poor soil and assessing the bacterial composition of their rhizospheres and the surrounding soil using 16S rDNA sequencing. Root-associated bacterial communities showed small but significant differences dependent on the plant genotype. We found that differences between bacteria associated with differing plant genotypes were only weakly correlated with the phylogenetic distance between the Oryza wild species and cultivars. In ordination plots, domesticated and wild samples could be separated on the basis of their associated bacterial communities. Taxa of the Anaerolineae were overrepresented in wild samples compared to domesticated ones. Certain methanotrophs were overrepresented in the earliest diverged part of the Oryza genus. Bacterial populations associated with the rhizosphere of wild rice species displayed differences with those associated with cultivars, suggesting that root traits selected in domestication could have significant influence on the rhizosphere microbiota composition. Variation within the genus seems to influence the representation of methanotrophs. This suggests that greenhouse emissions from paddy fields could be altered by manipulating plant genotypes through the introgression of wild rice genetic material.