The characterization of bacterial community structure in the rhizosphere of watermelon ( Citrullus vulgaris SCHARD.) using culture-based approaches and terminal fragment length polymorphism (T-RFLP)

Abstract

To test the hypothesis that the culturable portion of soil bacterial community occupies the majority of bacterial biomass, we selected bacteria from the rhizosphere of watermelon ( Citrullus vulgaris SCHARD.) grown on an experimental farm in Miryang, South Korea, to identify the phenotypes and genotypes of soil bacteria. After the phenotype identification of the bacteria was completed with Gram tests and API tests, the bacterial strains were isolated and the 16S rRNA gene regions of each bacteria colony were sequenced. Total soil DNA was extracted from the rhizosphere of watermelon from the same experimental farm for terminal restriction fragment length polymorphism (T-RFLP) analysis. The API tests identified several strains of Pseudomonas and Bacillus, while six genera were identified through DNA sequence comparison. In contrast, T-RFLP resulted in 51–66 restriction fragment peaks. Comparison between the expected restriction fragment lengths from the sequence data of cultures and restriction fragment profiles from the total soil DNA showed that only 4.0–4.2% of total restriction peak areas were areas of matched peaks with the expected restriction fragments. These results show that bacterial community analysis through medium culture appears to represent only a minor portion, in terms of the numbers and the biomass, of the bacterial community in the rhizosphere of watermelon.