Biodegradation of atrazine and nicosulfuron by Streptomyces nigra LM01: Performance, degradative pathway, and possible genes involved

Microbial herbicide degradation is an efficient bioremediation method. In this study, a strain of Streptomyces nigra, LM01, which efficiently degrades atrazine and nicosulfuron, was isolated from a corn field using a direct isolation method. The degradation effects of the identified strain on two herbicides were investigated and optimized using an artificial neural network. The maximum degradation rates of S. nigra LM01 were 58.09% and 42.97% for atrazine and nicosulfuron, respectively. The degradation rate of atrazine in the soil reached 67.94% when the concentration was 108 CFU/g after 5 d and was less effective than that of nicosulfuron. Whole genome sequencing of strain LM01 helped elucidate the possible degradation pathways of atrazine and nicosulfuron. The protein sequences of strain LM01 were aligned with the sequences of the degraded proteins of the two herbicides by using the National Center for Biotechnology Information platform. The sequence (GE005358, GE001556, GE004212, GE005218, GE004846, GE002487) with the highest query cover was retained and docked with the small-molecule ligands of the herbicides. The results revealed a binding energy of −6.23 kcal/mol between GE005358 and the atrazine ligand and −6.66 kcal/mol between GE002487 and the nicosulfuron ligand. Atrazine and nicosulfuron are commonly used herbicides that remain in the environment for several hundred days. They are often used in combination in corn fields and can cause severe damage to non-corn crops, including soybeans and wheat. This phenomenon often interferes with crop rotation and is not conducive to sustainable agriculture. In this study, a strain of Streptomyces nigra LM01 was isolated from soil, and it was effective in degrading atrazine and nicosulfuron. This study elucidated the degradation mechanism of strain LM01 in detail, providing a reference for understanding the degradation of atrazine and nicosulfuron in the environment.