Diversity Analysis of Endophytic Bacterial Community in Two Citrus Cultivars With Different Resistance to Citrus Canker

The selective infection of Xanthomonas citri pv. citri to citrus cultivars is universally known, but it is not clarified whether there is a relationship between endophytic bacteria and the resistance of host variety to canker disease. In order to explore the relationship, Satsuma mandarin and Newhall navel orange were collected respectively as samples of resistant or susceptible cultivars to citrus canker disease, and endophytic bacterial community of two citrus cultivars were analyzed by using a next-generation, Illumina-based sequencing approach. Simultaneously, the seasonal dynamics of endophytic bacterial community and dominant genera were analyzed. The results showed that there were four dominant groups including Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes in all samples at phylum level. Endophytic bacteria were the most abundant in spring samples, then in summer and autumn samples. There were some differences between endophytic bacterial community of resistant citrus and that of susceptible citrus to canker disease, and the endophytic bacteria of Satsuma mandarin are more abundant than that of Newhall navel orange. According to the analysis of dominant bacteria in two citrus cultivars, it was found that some endophytic bacteria with antagonistic characteristics existed universally in all samples, although the dominant bacteria in different seasonal sample were different. However, in Newhall navel orange of susceptible citrus to canker disease, there were not only some bacteria against Xanthomonas citri pv. citri, but also some cooperative bacteria of canker occurrence like Stenotrophomonas.