Dynamic changes in microbial communities during the bioremediation of herbicide (chlorimuron-ethyl and atrazine) contaminated soils by combined degrading bacteria

A Novel Pathway of Chlorimuron-Ethyl Biodegradation by Chenggangzhangella methanolivorans Strain CHL1 and Its Molecular Mechanisms

Chlorimuron-ethyl is a widely used herbicide in agriculture. However, uncontrolled chlorimuron-ethyl application causes serious environmental problems. Chlorimuron-ethyl can be effectively degraded by microbes, but the underlying molecular mechanisms are not fully understood. In this study, we identified the possible pathways and key genes involved in chlorimuron-ethyl degradation by the Chenggangzhangella methanolivorans strain CHL1, a Methylocystaceae strain with the ability to degrade sulfonylurea herbicides. Using a metabolomics method, eight intermediate degradation products were identified, and three pathways, including a novel pyrimidine-ring-opening pathway, were found to be involved in chlorimuron-ethyl degradation by strain CHL1. Transcriptome sequencing indicated that three genes (atzF, atzD, and cysJ) are involved in chlorimuron-ethyl degradation by strain CHL1. The gene knock-out and complementation techniques allowed for the functions of the three genes to be identified, and the enzymes involved in the different steps of chlorimuron-ethyl degradation pathways were preliminary predicted. The results reveal a previously unreported pathway and the key genes of chlorimuron-ethyl degradation by strain CHL1, which have implications for attempts to enrich the biodegradation mechanism of sulfonylurea herbicides and to construct engineered bacteria in order to remove sulfonylurea herbicide residues from environmental media.

Impact of Paenarthrobacter ureafaciens ZF1 on the soil enzyme activity and microbial community during the bioremediation of atrazine-contaminated soils

Bioremediation of atrazine-contaminated soil is considered a safe and effective approach in removing contaminates from the soil. However, the effects of adding foreign organisms to assist bioremediation on soil environmental quality and ecosystem are unclear. Here, the ecological remediation potential of strain Paenarthrobacter ureafaciens ZF1 on atrazine-contaminated soil was investigated through miniature experiments using variations in soil enzymes and bacterial communities as indicators. The results showed that strain ZF1 accelerated atrazine degradation, which could completely degrade atrazine at concentrations of 100 mg·L^− 1 atrazine within 2 h in liquid medium and could remove up to 99.3% of atrazine (100 mg·kg^− 1 in soil) within 6 days. During soil bioremediation, atrazine promoted the activities of urease and cellulase, and inhibited the activities of sucrase and catalase, while the strain ZF1 significantly promoted the activities of these four enzymes. High-throughput sequencing of 16S rRNA genes showed that ZF1 affected the relative abundance and bacterial community structure, and promoted bacterial diversity and evenness. Furthermore, redundancy analysis revealed a certain correlation among the strain ZF1, atrazine residue, soil enzyme activity, and soil bacterial community. The strain ZF1 in this work demonstrated remarkable potential for ecological restoration, and can be an effective and environmentally friendly alternative in remediating atrazine-contaminated soil.