Abstract
Sulfolane is an industrial solvent and emerging organic contaminant affecting groundwater around the world, but little is known about microbes capable of biodegrading sulfolane or the pathways involved. We combined DNA-based stable isotope probing (SIP) with genome-resolved metagenomics to identify microorganisms associated with sulfolane biodegradation in a contaminated subarctic aquifer. In addition to 16S rRNA gene amplicon sequencing, we performed shotgun metagenomics on the 13C-labeled DNA to obtain functional and taxonomic information about the active sulfolane-degrading community. We identified the primary sulfolane degrader, comprising ~85% of the labeled community in the amplicon sequencing dataset, as closely related to Rhodoferax ferrireducens strain T118. We obtained a 99.8%-complete metagenome-assembled genome for this strain, allowing us to identify putative pathways of sulfolane biodegradation. Although the 4S dibenzothiophene desulfurization pathway has been proposed as an analog for sulfolane biodegradation, we found only a subset of the required genes, suggesting a novel pathway specific to sulfolane. DszA, the enzyme likely responsible for opening the sulfolane ring structure, was encoded on both the chromosome and a plasmid. This study demonstrates the power of integrating DNA-SIP with metagenomics to characterize emerging organic contaminant degraders without culture bias and expands the known taxonomic distribution of sulfolane biodegradation.
Highlights
Molecular techniques like stable isotope probing (SIP) are powerful tools for examining the active members from environmental microbial communities involved in the biodegradation of emerging organic contaminants such as sulfolane. 13C-based SIP is the process of exposing a microbial community to a chemical compound highly enriched in 13C, which otherwise accounts for roughly 1% of all carbon
Using DNA-SIP combined with metagenomics, we have identified a single operational taxonomic units (OTUs) as the primary sulfolane-degrading organism in subarctic aquifer substrate and provided DNA evidence that strongly suggests it is a member of the Rhodoferax genus (Fig. 3)
Of the 178 OTUs detected in the 13C-labled SIP fractions, OTU1 was identified as the dominant microorganism incorporating carbon from sulfolane in this subarctic aquifer substrate
Summary
Molecular techniques like stable isotope probing (SIP) are powerful tools for examining the active members from environmental microbial communities involved in the biodegradation of emerging organic contaminants such as sulfolane. 13C-based SIP is the process of exposing a microbial community to a chemical compound highly enriched in 13C, which otherwise accounts for roughly 1% of all carbon. Molecular techniques like stable isotope probing (SIP) are powerful tools for examining the active members from environmental microbial communities involved in the biodegradation of emerging organic contaminants such as sulfolane. The environmental microorganisms known to be capable of degrading sulfolane to date have all been isolated from temperate regions. We performed DNA-SIP with 13C-labeled sulfolane in contaminated North Pole, Alaska, aquifer substrate to elucidate the identity of subarctic sulfolane degraders while circumventing culture bias. We combined DNA-SIP with shotgun metagenomics to taxonomically identify microbes involved in sulfolane degradation as well as to gain insights into their genetic potential and possible degradation pathways that may be used to process sulfolane. This study demonstrates that, by combining these techniques, it is possible to identify and obtain high-quality draft genomes of unknown emerging contaminant degraders from environmental samples
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