Decoding Soil Microbiomes: Metagenomic Insights into Pesticide-Contaminated Agro-Ecosystems

Abstract: Soil contamination from excessive pesticide use is a global issue, threatening human health and environmental sustainability. Pesticides disrupt soil microbiomes, leading to a decline in beneficial microorganisms, impaired nutrient cycling, and long-term ecosystem disturbances. Microorganisms play a crucial role in environmental preservation by breaking down xenobiotics, including pesticides. However, the pathways of pesticide degradation by microorganisms are not well understood due to limitations in current culturing techniques. To address this knowledge gap, we utilized 16S rRNA V3-V4 metagenomic sequencing to analyze farming soils in Dehradun with a history of pesticide application. Our results revealed a relative abundance of the phyla Proteobacteria, Acidobacteria, Firmicutes, and Actinobacteria in contaminated zones. Bacillus, Solibacter, and Nitrospira were the most prevalent taxa, indicating nitrogen and carbon fixation and regulation of biogeochemical cycles in extreme environments. Predictive metagenome analysis showed that core-degrading orthologs involved in membrane transport, the TCA cycle, carbohydrate metabolism, and xenobiotic degradation (such as atrazine and chlorocyclohexane degradation) were prevalent in contaminated soils. Our findings highlight the implications of abundant microbes in contaminated soils through comprehensive metagenomic approaches, paving the way for further research on gene expression frequencies and major enzyme assays for pesticide degradation.

Keywords: Metagenomics, Microbial diversity, Pesticide degradation, Taxonomy