Bacterial community structure in the Cerasus sachalinensis Kom. rhizosphere based on the polymerase chain reaction - denaturing gradient gel electrophoresis (PCR-DGGE) method

Abstract

The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial community diversity in the cultivated C. sachalinensis rhizosphere was always higher than the wild, while the evenness and dominance indices followed a different pattern as compared to band richness in the wild and cultivated conditions. The plant growth stages also had an influence on the bacterial community structures. The richness and diversity of the bacteria both corresponded to: budbreaking phase > growing phase > defoliation phase. Cluster analysis based on DGGE banding patterns showed that the bacterial community structures were affected by growth conditions and agricultural management practices. Accordingly, the dendrogram was divided into Clusters I and II, which respectively contained the cultivated and wild soil samples. Additionally, specific bacterial species were found in the wild and cultivated C. sachalinensis rhizosphere. 13 dominant DGGE bands were excised, sequenced, and divided into eight groups, in which 3 bands were identified as Actinobacteria, 2 as Sphingobacteria, 2 as α-Proteobacteria, 2 as Firmicutes, and the remaining 4 as γ-Proteobacteria, Acidobacteria, Gemmatimonadetes and unclassified bacteria, respectively. Uncultivable bacteria were predominant in the total bacterial groups.

Key words: Cerasus sachalinensis Kom., bacteria, community structure, denaturing gradient gel electrophoresis (DGGE), diversity.