Metagenomic characterization of a novel enrichment culture responsible for dehalogenation of 1,2,3-trichloropropane to allyl chloride

Abstract

Degradation of 1,2,3-trichloropropane (TCP) to allyl chloride (AC) by Dehalogenimonas (Dhg), the only reported TCP anaerobic reductive dechlorinating microorganism so far, has been demonstrated to be effective for in-situ bioremediation (ISB) of groundwater. This process is found viable when augmented with the fermentable organic substrate, yet its environmental implication is not yet clear and limited due to the complex environmental conditions and indigenous microbial communities. In this study, using yeast extract as biostimulant, an enrichment culture capable of dechlorinating TCP derived from groundwater well sludge at a chlorinated aliphatic hydrocarbon (CAH)-contaminated site was incubated. Geochemical methods, 16 S rRNA gene and shotgun metagenomic sequencing were used to systematically monitor the TCP biodegradation kinetics and unravel the functional microbial communities that play pivotal roles in this process. The decrease of TCP, along with the increase of AC (the product of TCP degradation) and δ13C-TCP values indicated active biodegradation of TCP. The 16S rRNA phylogenetic tree showed the absence of Dhg, suggesting a putative novel culture for dechlorinating TCP. Several potential anaerobic reductive functional genes and dominant microorganisms were identified and mutualistic interactions were found. Hydrogenase (H2ase) genes, responsible for producing the hydrogen, were harbored by Desulfovibrio. Cobalamin synthase (CobS) genes, responsible for synthesizing the cobalamin, an important co-factor for dehalogenation, were harbored by Desulfovibrio, Gracilibacter, Thermococcus. By obtaining the electron donor (hydrogen) and essential cofactors (cobalamin), the reductive dehalogenase (Rdh) gene were harbored by Parabacteroides, Caldisalinibacter, and Desulfovibrio. Based on these findings, Desulfovibrio was deduced to be the most promising genus for TCP degradation. The identified microbial community could collaboratively play critical roles in TCP degradation, and therefore, a new method is expected to be developed.