Pesticides, their ecological impacts, and omics-based approaches for elucidating degradation pathways: a systematic review

Pesticides are extensively used in modern agriculture but pose significant hazards to soil, water, air, and overall ecosystem health. This systematic review synthesizes findings from studies published between 2000 and 2025 to evaluate pesticide-induced ecological risks and the potential of omics-driven microbial degradation strategies for their mitigation. The analysis identifies major pesticide classes, including organophosphates, organochlorines, and herbicides, as key contributors to environmental persistence, toxicity, and disruption of microbial and trophic dynamics. Evidence from genomics, transcriptomics, proteomics, and metabolomics studies highlights the role of specific functional genes and metabolic pathways in facilitating pesticide degradation and detoxification. Importantly, integration of multi-omics approaches provides a comprehensive understanding of microbial responses and enhances the prediction of degradation efficiency, thereby supporting targeted and effective bioremediation strategies. These processes contribute directly to hazard mitigation by reducing pesticide persistence, toxicity, and environmental exposure. However, challenges such as limited field-scale validation, variability in omics methodologies, and data integration constraints remain. Overall, this review emphasizes the importance of integrating omics-based approaches with risk-oriented frameworks to develop sustainable and scalable solutions for pesticide management.