Composition and Diversity of Endophytic Bacterial Community in Seeds of Upland Rice Resources from Different Origin Habitats in Yunnan Province of China

Abstract Upland rice has the characteristics of strong drought tolerance and wide adaptability. Cultivating upland rice with high yield and high quality can solve the contradiction between food shortage, water shortage, and population increase in countries all over the world, and is of great significance to the sustainable development of agriculture. This study aims to reveal the "core microbiota" of the endophytic bacteria in upland rice seeds in the Yunnan Province of China by examining their diversity and community structures. Through the correlation analysis with upland rice habitat environmental factors, the effects of climate and altitude on the structure and diversity of endophytic bacterial community in upland rice seeds were further revealed. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to investigate the structure and diversity of endophytic bacterial communities using 12 upland rice variety seeds from different areas in Yunnan Province of China as materials. Here, 39 endophytic OTUs (0.68%) were found to coexist in all samples. At the phylum level, the first dominant phyla in the 12 seed samples were Proteobacteria (66.92–99.98%). At the genus level, Pantoea (9.75–99.24%), Pseudomonas (0.11–37.24%), Curtobacterium (0.01–19.90%), Microbacterium (0.01–14.95%), Methylobacterium (0.40–5.86%), Agrobacterium (0.01–4.53%), Sphingomonas (0.04–1.56%), Aurantimonas (0.01–1.45%) and Rhodococcus (0.11–1.09%), which represent the core microbiota in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. Environmental factors such as temperature, precipitation and altitude have great influences on the structure of endophytic bacterial community in upland rice seeds. This study is of great significance to explore the relationship between upland rice and its endophytic bacteria and to tap the resources of drought-tolerant bacteria to improve the yield of local upland rice.