Whole genome sequence and 16S rRNA gene amplicon metagenomics of enhanced in-situ reductive dechlorination at a tetrachloroethene-contaminated superfund site

Abstract

The application of environmental DNA analysis techniques to guide the bioremediation strategy for tetrachloroethene-contaminated groundwater is exemplified by the North Railroad Avenue Plume (NRAP) Superfund site located in New Mexico, USA. Enhanced reductive dechlorination (ERD) was selected as the remedy due to the presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera Dehalococcoides and Dehalobacter, and associated reductive dehalogenase genes detected prior to remediation. DNA extracted from groundwater samples collected prior to remedy application and after four, 23 and 39 months was subjected to 16SrRNA gene amplicon and whole genome sequencing (WGS). The goals were to compare the potential of these methods as tools for environmental engineers and to highlight how advancements in DNA techniques can be used to understand ERD. The response of the indigenous NRAP microbiome to the injection and recirculation of electron donors and hydrogen sources is consistent with results obtained from microcosms, dechlorinating consortia, and other contaminated sites. WGS detects three times as many phyla and six times as many genera as 16S rRNA gene amplicons. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. No methane was detected before remediation, its appearance after biostimulation corresponds to the increase in methanogenic Archaea. Assembly of WGS reads produced scaffolds containing reductive dehalogenase genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance at NRAP include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing at the aquifer-soil interface or by microbes that have the potential to produce O2 via chlorite dismutation. Results from next-generation sequencing-based methods are consistent with current hypotheses regarding syntrophy in environmental microbiomes and reveals novel taxa and genes that may contribute to ERD.