Single Strand Conformational Polymorphism as a Molecular Marker for Detection of Variation between the Small Length ss DNA of Azospirillum, Phosphobacteria and Pseudomonas from the inoculated Bhendi field (COBH 1)

Abstract

Single strand conformational polymorphism is used to identify specific microorganism from the microbial ecosystem at field level. Here the double strand DNA of each organism is converted to single strand and allowed to run in polyacrylamide gel. SSCP can differentiate small variation within same length DNA of different organism due to the difference in retention time, temperature, ionic strength and electrophorotic mobility of ss DNA. This concept is used in this experiment to identify the inoculated microbial consortium from the field by comparison with microbial consortium and pure culture. Azospirillum (Azospirillum brasilense sp 7) and phosphobacteria (Bacillus megaterium var. phosphaticum) and Pseudomonas fluorescens (Pf 1) cultures were used for development of liquid microbial consortium for precision farming system. Inoculated microbes from the field were identified through SSCP –PCR analysis. Appearance of unique domain of V₁ to V₉ region of 16srRNA is universal for all bacteria and archae microbial community. Universal primers were used to amplify the V₁ to V₂ region of 16srRNA gene of pure culture, microbial consortium and soil sample from inoculated field for SSCP gel electrophoresis. This study revealed that similar banding pattern was observed between soil sample from inoculated field, microbial consortiums and pure cultures. This experiment proved that SSCP gel electrophoresis is a powerful technique to find specific microorganism in the field in comparison with its pure culture strains without characterization of microorganism.