Microbial engineering for pesticide degradation: current insights and future directions for sustainable agriculture

Abstract

Pesticides are synthetic agrochemicals widely used to protect crops from pests and diseases; however, their limited biodegradability and indiscriminate application pose serious risks to non-target organisms, soil fertility, human health, and overall environmental sustainability. Conventional physical and chemical remediation strategies often fall short in restoring contaminated ecosystems, highlighting the urgent need for effective and sustainable pesticide mitigation approaches. In recent years, in situ bioremediation has emerged as a promising, eco-friendly, and cost-effective strategy for pesticide degradation in agricultural soils. Under favourable conditions, microorganisms utilise pesticides as sources of carbon, sulphur, and electrons, facilitating their breakdown through diverse metabolic pathways, with enzymatic degradation playing a central role in chemical transformation. Microbial consortia exhibit enhanced degradation efficiency by leveraging functional diversity and synergistic interactions among their microbial members. For instance, a consortium comprising Azospirillum , Cloacibacterium , and Ochrobacterium achieved 100% degradation of 50 mg L −1 glyphosate within 36 h. Advances in microbiome engineering have further expanded the scope of bioremediation by enabling the targeted manipulation of microbial communities to improve degradation specificity and performance. Notably, the recombined genomes of Psathyrella candolleana and Pseudomonas putida , generated through protoplast fusion, degraded 78.98% of pentachlorophenol in contaminated water. Additionally, engineering the rhizosphere with plant growth–promoting microorganisms, combined with microbial genetic modification, has demonstrated significant potential in enhancing pesticide degradation while simultaneously improving crop growth and productivity. Such integrative approaches represent a sustainable pathway towards resilient agroecosystems. This review synthesises current knowledge on the impacts of pesticides on crop physiology and metabolism, explores conventional and advanced microbe-mediated degradation strategies, and highlights the role of microbial engineering and consortia-based systems. Furthermore, it discusses emerging technologies, environmental and economic benefits, and recent patentable innovations, underscoring their relevance for sustainable agriculture and ecological restoration.

Key findings

• ▸Pesticides pose significant risks to soil fertility, non-target organisms, and human health due to their limited biodegradability.
• ▸In situ bioremediation is identified as an eco-friendly and cost-effective strategy for mitigating pesticide contamination in agricultural soils.
• ▸Microbial consortia demonstrate superior degradation efficiency by utilizing diverse metabolic pathways and synergistic interactions among members.
• ▸Specific bacteria like Azospirillum are utilized within these consortia to facilitate the breakdown of pesticides as carbon and energy sources.

Keywords

Identifiers

DOI

10.3389/fmicb.2026.1751932

Journal

Frontiers in Microbiology

Year

2026