Application of T-RFLP analysis to the study of bacterial community structure in the rhizosphere

Abstract

To analyze the structure of the bacterial communities in the spinach rhizosphere, we used a terminal-restriction fragment length polymorphism (TRFLP) analysis. The T-RFLP electropherograms revealed several large peaks and smaller peaks, which were ascribed to various bacterial species composing each of the bacterial communities. It is considered that T-RFLP analysis is a convenient method for assessing the microbial diversity or community structure in the rhizosphere. Bacterial DNA from colonies on d~lution plates and directly extracted bacterial DNA of rhizosphere samples were analyzed by TRFLP in order to determine whether agar-grown colonies are representative of the dominant bacterial groups in the rhizosphere. The T-RFLP patterns obtained by using bacterial colonies from dilution plates as the source of target DNA were different from those found with the direct DNA extracts. The results indicated that many bacterial groups grown on agar media selective for the rhizosphere are not likely to be dominant in the rhizosphere.