Characterization of cucumber rhizosphere bacterial community with high-throughput amplicon sequencing

Cucumber rhizosphere and bulk soils were sampled from a greenhouse, which has been continuously monocropped with cucumber. Bacterial community composition was analyzed by high-throughput sequencing of 16S rRNA genes on an Illumina Miseq platform. A total of 211,027 quality sequences were obtained and were classified into more than 1,800 Operational taxonomic units at the 97% sequence similarity. Cucumber rhizosphere soil sample had lower bacterial alpha diversity than bulk soil sample. Bacterial community composition also differed between the rhizosphere and bulk soils. Rhizosphere soil sample was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria phyla and classes of Gammaproteobacteria, Alphaproteobacteria, Cyanobacteria, Bacilli and Actinobacteria. Compared with the bulk soil, cucumber rhizosphere soil had higher relative abundances of Bacillus, Lysobacter, Streptomyces, Microbacterium and Rhizobium spp. and lower relative abundances of Clostridium sensu stricto 1, Sphingomonas and Microvirga spp. (P < 0.05).