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Unveiling the novel biodegradation mechanisms of acephate by Pandoraea pnomenusa: Catalytic pathway, functional enzyme, and environmental bioremediation.

Ziqiu Lin,Mingqiu Liu,Shimei Pang,Wenjuan Chen,Sandhya Mishra,M. A. Ghorab,Shao-Fang Chen

Published 2025 in Bioresource Technology

ABSTRACT

Acephate, a commonly used organophosphorus pesticide, poses significant risks to ecosystems and human health. However, the currently available acephate-degrading microbes are not optimal. In addition, the molecular mechanism underlying the microbial degradation of acephate is still unknown. Here, Pandoraea pnomenusa ZQ05, a highly efficient acephate degrader isolated from the previous acephate-degrading microbial consortium ZQ01, was identified and characterized. ZQ05 achieved the fastest degradation of acephate by a pure culture reported so far, with 96.8 % degradation in water within 18 h and complete degradation in soil within 15 h. ZQ05 effectively degraded acephate across concentrations of 25 to 800 mg·L-1, with a half-life ranging from 5.6 to 9.0 h. It utilizes a novel metabolic pathway that initially breaks the amide bond, followed by phosphate bond degradation and further metabolism, achieving complete degradation of acephate. Furthermore, a key amidase involved in acephate biodegradation, designated Aca, was the first time to be identified for acepahte degradation using whole-genome sequencing and proteomics. Purified Aca effectively degraded acephate across temperatures between 15℃ and 65℃ and pH levels between 4.0 and 10.0, with optimal performance at pH 7.0 and 35℃. Multi-omics analysis and molecular docking studies further revealed that Aca possesses the conserved amidase catalytic triad Ser183-Ser163-Lys84, which constitutes the catalytic center responsible for hydrolyzing acephate. These findings shed a new light into the microbial catabolism of acephate, providing a theoretical basis for utilizing microbes and enzymes in acephate contamination remediation.

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