Extraction of the metagenomic DNA and assessment of the bacterial diversity from the petroleum-polluted sites

Abstract

The assessment of the microbial diversity of the entire community of a given habitat requires the extraction of the total environmental DNA. Metagenomic investigations of a petroleum-polluted habitat have its unique challenges. The specific methods were developed for the extraction of high-quality metagenome in good quantity from the petroleum-polluted saline and non-saline sites in Gujarat (India). The soil samples were washed to remove the toxic, hazardous organic pollutants which might interfere with the recovery of the metagenomic DNA. The metagenomic DNA extraction results were encouraging with the mechanical bead beating, soft lysis, and combination of both. The extracted DNA was assessed for its purity and yield followed by its application in the amplification of the 16S rRNA region. The amplicons were used for judging the molecular diversity by the denaturing gradient gel electrophoresis (DGGE). The microbial diversity was also analyzed statistically by calculating various diversity indices and principal component analysis (PCA). The results on the metagenomic diversity of the bacterial population among the three cohorts based on the culture-independent technique exhibited significant difference among the PAH sites and Okha-Madhi and Porbandar Madhavpur habitats.

Avaliação integrada da contaminação por metais potencialmente tóxicos em área de disposição de resíduo de mineração de chumbo - Adrianópolis (PR)

“…A diversidade da comunidade microbiana é um índice sensível da qualidade do solo, que pode variar com a concentração de MPT (BÅÅTH, 1989;OTHMANI et al, 2015). As técnicas moleculares independentes da cultura, como a reação em cadeia da polimerase (RCP ou PCR) e a eletroforese em gel com gradiente desnaturante (EEGD ou DGGE), podem fornecer informações, como riqueza, diversidade (H') e dominância (D), que podem auxiliar na avaliação da contaminação de um sítio (MÜLLER et al, 2001;LI et al, 2006;WANG et al, 2007;DELL'AMICO et al, 2008;MARTÍNEZ-IÑIGO et al, 2009;QU et al, 2011;AKBARI;PANDYA;SINGH, 2014).…”