A Synergistic Consortium Involved in rac -Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis

Abstract

Rac-dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in Rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in Rac-dichlorprop degradation remain largely unknown. In this study, DNA-stable isotope probing and metagenomics analysis were integrated to reveal the key microbial consortium responsible for Rac-dichlorprop degradation in a Rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the ¹³C-Rac-dichlorprop-labeled heavy DNA fractions. A Rac-dichlorprop degrader, Sphingobium sp. L3, was isolated from the enrichment by traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomics analysis of the associations between Rac-dichlorprop-degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of Rac-dichlorprop. Importance Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide of Rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of microbial consortium and the interactions between community members during the biodegradation of Rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomics analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of Rac-dichlorprop. Our study provides new insights into the synergistic degradation of Rac-dichlorprop at the community level and implies the existence of novel degrading genes for Rac-dichlorprop in nature.