Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Rice and the aquatic macrophyte duckweed are two monocotyledonous plants that coexist in paddy fields naturally. While presence of duckweed in paddy fields has been shown to significantly improve rice productivity, the interplay between microbes and the two plant hosts in this agroecosystem remains unexplored. Here, we compared the bacterial microbiome structure between duckweed and rice, and between rice roots and aerial tissues from multiple rice paddy fields in Guizhou, China. Our results indicate that host-specific and tissue-dependent factors can reproducibly sculpt the bacterial community structure in the plant hosts. This conclusion is corroborated by results from culture-dependent approaches in which Pantoea spp. isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of their low representation in the duckweed microbiome. Characterizing auxin-producing bacteria isolates from both plants identified potential plant growth-promoting bacteria that may help improve growth for both duckweed and rice in paddy fields. Results from this work should help pave the way for deployment of synthetic communities of plant associated microbes from paddy fields for more sustainable rice production