Microbial diversity of various agricultural soil sites using denaturing gradient gel electrophoresis (DGGE) community profiling

A.K.R. Emmyrafedziawati, M. Krsek and E.M.H. Wellington

Abstract

PCR-DGGE was applied in this project to compare the diversity of the bacterial populations in two different plots, Tuscany and Basilicata. Tuscany consists of forest and agricultural site while Basilicata consists of biological agricultural and conventional agricultural site. The soil sample from each plot was extracted for the DNA using the combination protocols of conventional method. The DNA was then amplified for the target 16S rRNA genes using the universal primer of P1 (forward) and P2 (reverse) for 35 cycles using the hot start technique. The PCR product was then run on 10% (w/v) of polyacrylamide gel on the denaturing gradient gel electrophoresis (DGGE) to observe the diversity profile with the gradient ranging from 40% to 75%. From the dendogram image, the PCR-DGGE bands in Tuscany showed that there were different soil microbial communities dominant for each site although there was no major difference in banding pattern between the biological agricultural and conventional plots or disturbed and undisturbed forest. In Basilicata, the soil from this site can be categorized as a heterogeneous soil. The correlation analysis indicated that when the aridity index increased and water content decreased, the bacterial number increased although no impact on microbial diversity was observed.

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