Comparative Microbiome Analysis of Pesticide-Contaminated and Pristine Agricultural Soils of Hot Arid Rajasthan

Abstract

Comparative microbial community structure analysis of agricultural soil located in hot, western Rajasthan with long term history of chemical pesticides vis-à-vis pristine soil has been attempted using the technique of PCR-RFLP. Pesticide contaminated (24 nos.) and pristine (10 nos.) soil samples were collected from different locations of the vegetable growing agricultural fields. Metagenomic DNA was extracted each from pooled-contaminated and pooled-pristine soils and amplified with universal 16S rRNA gene primers. Amplification products were cloned in to E. coli DH5α cells to obtain 78 and 39 16S rDNA clones from contaminated and pristine soils respectively. The clones were subjected to RFLP analysis using three restriction enzymes (AluI, AvaII and MspI) followed by phylogenetic tree construction. The studies revealed differences in microbial community structures of both types of arid, agricultural soils. We also detected the presence of pesticide-degrading naphthalene dioxygenase gene (nahA) controlling the initial step of the degradation process in contaminated soil.