Impact of a pesticide treatment on bacterial soil community ribosomal DNA fingerprinting

Tan, Lay Har (2007) Impact of a pesticide treatment on bacterial soil community ribosomal DNA fingerprinting. Universiti Malaysia Sabah. (Unpublished)


Download (2MB) | Preview


This research was to investigate a molecular approach to analyzing the changes in genetic diversity of soil bacterial community in pesticide treated and non-pesticide treated agricultural soil by using ribosomal DNA fingerprinting. A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) strategy and conventional cloning method were applied to target small-subunit (SSU) rDNA for profiling microbial community structure. Soil sample with pesticide treatment was collected in an agricultural farm at Kundasang and DNA was extracted by direct lysis hot detergent proteinase K method. The DNA extracted was contaminated by humic acid protein. Impurity samples DNAs were subsequently undergone hydroxyapatite spin-column purification method. After purification, almost all DNA could be used for PCR amplification by 27F-1 492R and GC-968F-140IR primers. Diluted DNA with 500-fold and 1,000- fold dilution had been tested for PCR amplification for both primer set and found out that only the partial 16S rDNA sequence amplification using GC-clamp 968F- 1401R primer was successfully amplified. Thus, the PCR products on gel were cut and purified for subsequent DGGE separation. In this project although some samples could use to amplify the 1,500 bp 16S rDNA sequence, the results were not consistent which might due to the impurity of the samples even though DNA templates after purified with HTP were used. Moreover, the DGGE separation was unfortunately not good enough to be used for fingerprinting analysis because no even one single band was visualized on the gel. In conclusion, the changes of bacterial community in pesticide treated agricultural soil in Kundasang could not be demonstrated.

Item Type: Academic Exercise
Uncontrolled Keywords: DNA fingerprint, diversity, soil bacterial, PCR, DGGE separation, agricultural
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: SCHOOL > School of Science and Technology
Date Deposited: 14 Feb 2014 04:18
Last Modified: 12 Oct 2017 00:01

Actions (login required)

View Item View Item