Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing

Vinyl chloride (VC), a known human carcinogen, is a common and persistent groundwater pollutant at many chlorinated solvent contaminated sites. The remediation of such sites is challenging because of the lack of knowledge on the microorganisms responsible for in situ VC degradation. To address this, the microorganisms involved in carbon assimilation from VC were investigated in a culture enriched from contaminated site groundwater using stable isotope probing (SIP) and high-throughput sequencing. The mixed culture was added to aerobic media, and these were amended with labeled ((13)C-VC) or unlabeled VC ((12)C-VC). The cultures were sacrificed on days 15, 32, and 45 for DNA extraction. DNA extracts and SIP ultracentrifugation fractions were subject to sequencing as well as quantitative PCR (qPCR) for a functional gene linked to VC-assimilation (etnE). The gene etnE encodes for epoxyalkane coenzyme M transferase, a critical enzyme in the pathway for VC degradation. The relative abundance of phylotypes was compared across ultracentrifugation fractions obtained from the (13)C-VC- and (12)C-VC-amended cultures. Four phylotypes were more abundant in the heavy fractions (those of greater buoyant density) from the (13)C-VC-amended cultures compared to those from the (12)C-VC-amended cultures, including Nocardioides, Brevundimonas, Tissierella, and Rhodoferax. Therefore, both a previously identified VC-assimilating genus (Nocardioides) and novel microorganisms were responsible for carbon uptake. Enrichment of etnE with time was observed in the heavy fractions, and etnE sequences illustrated that VC-assimilators harbor similar Nocardioides-like etnE. This research provides novel data on the microorganisms able to assimilate carbon from VC.