Illumina high-throughput sequencing and comparative analysis of bacterial communities in cherry orchard soil

Microbial diversity in the rhizosphere is affected by soil physical and chemical properties, which may be determined by plant species and growth stage. Exploring the bacterial communities in cherry rhizospheres may help in monitoring and conservation of soil quality. The aim of this study was to characterize the bacterial community structure between bulk soil and rhizosphere, using Illumina pyrosequencing of bacterial 16S rRNA genes, to determine the effect of soil types and seasons on bacterial diversity in cherry orchard. Sequences of 199,615 (30,162–35,399/sample) genes were obtained. Rhizosphere communities shared features with the surrounding bulk soil, such as predominance of Proteobacteria, Acidobacteria, and Actinobacteria. The relative abundance of certain bacterial lineages differed: Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were more abundant in the rhizosphere than in bulk soil. At the genus level, Burkholderia, Rhodococcus, Streptomyces, and Varivorax were more abundant in the rhizosphere, compared with the bulk. Specifically, Burkholderia and Rhodanobacter were abundant in the rhizosphere and bulk soil, respectively, and changed greatly with different growth stages. These results indicated that season variations and soil types affected the bacterial community composition in cherry orchard soil, which may have implications for understanding the status of cherry orchard nutrients in North China.