Cultivated rice rhizomicrobiome is more sensitive to environmental shifts than that of wild rice in natural environments

Asian cultivated rice (Oryza sativa L.) domesticated from common wild rice (Oryza rufipogon Griff.) is one of the most consumed staple foods in the world. The rhizomicrobiome plays a vital role in the growth and production of rice. However, the responses of rhizomicrobial community structures to rice cultivation (including agricultural management and rice breeding) and natural environmental shifts are largely unknown. In this study, the rhizomicrobiomes of cultivated rice grown in paddy fields and wild rice grown in natural ecosystems were compared on a regional scale using high-throughput sequencing. For the same location, the cultivated rice showed less selective pressure on the rhizomicrobiome than wild rice. Specifically, compared to the rhizomicrobiome of wild rice, that of cultivated rice had 1) more complicated networks with stronger connections among different groups and 2) higher diversity, as evidenced by the Shannon, Simpson, ACE and Chao1 indices. For different locations, the rhizomicrobiome of cultivated rice was more sensitive to environmental shifts than that of wild rice. Compared to natural ecosystems, in paddy fields, 1) the rhizomicrobial diversity changed more drastically; 2) the number of rhizomicrobial groups cooccurring in different regions was lower at almost all taxonomic levels; and 3) the differences among samples examined by ANOSIM and PERMANOVA tests were more significant. In addition, we observed that the effects of rice cultivation on the rhizomicrobiome were more significant than those of natural environmental shifts on a large scale. Taken together, our results indicate that rice cultivation has profound effects on the rice rhizomicrobiome and that the rhizomicrobiome of cultivated rice in agricultural ecosystems is more sensitive to environmental shifts than that of wild rice in natural ecosystems.