Identification of chlorpyrifos-degrading microorganisms in farmland soils via cultivation-independent and -dependent approaches

Abstract

Microorganisms have important roles in the bioremediation of organophosphorus pesticides (OPs) in farmland soils. However, the majority of functional microorganisms (>99%) are yet to be cultivated. In this study, magnetic nanoparticle-mediated isolation (MMI) coupled with high-throughput sequencing was applied to identify the microorganisms responsible for chlorpyrifos (CPF) degradation in farmland soils. Various microorganisms have been identified as CPF degraders via MMI, in which the roles of genera Citrobacter, Exiguobacterium, Azoarcus, Azohydromonas and Massilia have not previously been related to CPF degradation. Two organophosphorus hydrolase genes (ophB and ophC) were involved in CPF metabolism in MMI enrichments, compared to only ophB found in the cultivable CPF degrader Alcaligenes L1. Also, a more thorough degradation of CPF was found in MMI enrichments, where 3,5,6-trichloro-2-pyridinol (TCP), O,O-diethyl thiophosphate (DETP), 2,3,5-trichloro-6-methoxypyridine (TMP) and O,O,S-trimethyl phosphorothioate were identified as the biodegradation products. This work suggests that MMI is a promising technology for separating functional microorganisms from complex microbiota, with deeper insight into their ecological functions, providing fundamental knowledge on soil bioremediation strategies.