Rice endophytic communities are strongly dependent on microbial communities specific to each soil

This study aims to investigate the effects of soil as a microbial source on the assemblage of the endophytic bacterial communities in rice roots. Rice seedlings were grown hydroponically with the addition of a permeable bag filled with one of five soil types collected from different geographical locations in Japan. After 3 and 6 weeks, the endophytic bacterial communities in rice roots were analyzed using the Illumina Miseq-based 16SrRNA gene amplicon sequencing method. The results showed that the bacterial community in the soils added as a microbial source differed among the soil types, which affected the bacterial community in the hydroponic solution and consequently reflected in the endophytic bacterial community assemblage. Bacterial diversity and richness differed significantly with respect to the microbial sources. As a result, a conserved group of 16 endophytic bacterial taxa at the genus level, dominated by Burkholderia-Caballeronia-Paraburkholderia , and independent of the soil type were shared across all microbial sources, thereby underlining the ability of rice plants to selectively recruit their endophytic inhabitants. Altogether, this study demonstrates the importance of the microbial source as a crucial driving force for the formation of the endophytic bacterial communities in rice roots.