The diversity and organ distribution of endophytic bacteria of sweet cherry

Endophytic bacteria are widely distributed in plants and play an important function and potential role in promoting plant growth and acting against stresses. To examine the diversity and distribution of the endophytic bacteria in the sweet cherry of Dalian, China, the community structures in sweet cherry varieties and organs were investigated using Illumina-HiSeq sequencing. A total of 18,797,077 effective tags corresponding to 16S rRNA gene V3-V4 regions were obtained from all the samples. Consequently, 512-1200 operational taxonomic units (OTUs) per sample and 24 prokaryotic phyla in total were revealed. Among these, Proteobacteria was the dominant phylum, followed by Actinobacteria, Firmicutes, and Bacteroidetes. Based on the alpha diversity and beta diversity analyses, a marked difference in endophytic bacterial diversity was evident among different organs; particularly, the diversity was higher in root than in stem or bark. Furthermore, there was significant correlation between the endophytic bacterial community and sweet cherry varieties. Identification of organ-specific OTUs, an indicator of organ-specific endophytic bacteria, and Linear Discriminant Analysis (LEfSe) revealed that there were 46 taxa differentially distributed among the three organs analyzed. In conclusion, by revealing the endophytic bacterial distribution among sweet cherry varieties and organs, our results suggested that organ type, but not genotype, can affect the composition of the endophytic microbiota of the sweet cherry.