Analysis of the Bacterial Communities in Paddy Soils in Fujian Province Using 16S rDNA -PCR- DGGE

Abstract:

16S rDNA-PCR-DGGE, a cultivation-independent approach, was used to analyze the bacterial communities in paddy soils in Fujian Province. The bulk soils and rhizosphric soils were sampled from six different ecological soil regions. Total DNA was directly extracted and amplified with the F341GC and R534 primers targeting the 16S rDNA V3. The amplified fragments were analyzed by perpendicular DGGE. Cluster analysis revealed that there was a high diversity of bacterial community compositions among different soil samples tested. Basically they could be grouped to Mindong (East), Minnan (South), Minbei (North) and Minxi (West) ecological regions. 16S rDNA-PCR-DGGE profiles from bulk and rhizospheric soil in the same region showed less bacterial diversity but more similarity. The bacterial community from bulk soil and rhizospheric soil in Longyan shared the most similar DGGE banding patterns, and the banding patterns in Yongtai exhibited the highest diversity. Eleven DGGE bands recovered were re-amplified, sequenced and aligned with Blast. The results indicated that ten of the fragments belong to uncultivated bacteria implying DGGE technique having priority in analyzing uncultivated bacteria in the paddy soils.