High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of Ginkgo biloba

BACKGROUND: The narrow region of soil, in contact with and directly influenced by plant roots, is called the rhizosphere. Microbes living in the rhizosphere are considered to be important factors for the normal growth and development of plants. In this research, the structural and functional diversities of microbiota between the Ginkgo biloba root rhizosphere and the corresponding bulk soil were investigated. METHODS: Three independent replicate sites were selected, and triplicate soil samples were collected from the rhizosphere and the bulk soil at each sampling site. The communities of bacteria and fungi were investigated using high-throughput sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) of the rRNA gene, respectively. RESULTS: A number of bacterial genera showed significantly different abundance in the rhizosphere compared to the bulk soil, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira. Functional enrichment analysis of bacterial microbiota revealed consistently increased abundance of ATP-binding cassette (ABC) transporters and decreased abundance of two-component systems in the rhizosphere community, compared to the bulk soil community. In contrast, the situation was more complex and inconsistent for fungi, indicating the independency of the rhizosphere fungal community on the local microenvironment.