Identification and Characterization of a Dominant Sulfolane-Degrading Rhodoferax sp. via Stable Isotope Probing Combined with Metagenomics

Scientific Reports
Christopher P KasankeMary Beth Leigh

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 chromoso...Continue Reading

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Datasets Mentioned

BETA
K00299
AB051429.1
SRP136637
QEII00000000

Methods Mentioned

BETA
PCR
amplicon sequencing

Software Mentioned

VizBin
MiSeq SOP
Seaview
UCHIME
R
CheckM
MUSCLE
RAST
vegan
PhyML

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