Assessment of various methods for extraction of metagenomic DNA from saline habitats of coastal Gujarat (India) to explore molecular diversity

Authors


Satya P. Singh, Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India. E-mail: satyapsingh@yahoo.com, satyapsingh125@gmail.com

Abstract

Aims:  To develop total DNA extraction protocol from saline soil for further metagenomic applications.

Methods and Results:  The protocols combine the application of mechanical (Beads and Sonicator) and Soft Lysis (SDS and enzymes) method for the isolation of total DNA from saline soil of coastal Gujarat followed by its quantification and purity assessment. The quality and purity of metagenomic DNA was quite consistent and reliable, although it contained residual concentartions of humic acid. The extracted DNA was used to successfully amplify 16S rRNA region. The amplicons were suitable for further applications such as diversity-based analysis by denaturing gradient gel electrophoresis (DGGE).

Conclusions:  The methods appear to have wide applicability in investigating molecular diversity and exploring functional genes from the total DNA.

Significance and Impact of the Study:  The protocol is simple, short and facilitates rapid isolation of PCR amplifiable total genomic DNA from saline soil. The method yielded good quality of the DNA suitable for metagenomic studies. The results are also significant as only few extreme environments, particularly saline habitats, are explored for their metagenomic potential.

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