Journal article
Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing
Applied microbiology and biotechnology, Vol.99(18), pp.7735-7743
09/2015
DOI: 10.1007/s00253-015-6606-1
PMID: 25981993
Abstract
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 (13C-VC) or unlabeled VC (12C-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 13C-VC- and 12C-VC-amended cultures. Four phylotypes were more abundant in the heavy fractions (those of greater buoyant density) from the 13C-VC-amended cultures compared to those from the 12C-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.
Details
- Title: Subtitle
- Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing
- Creators
- Fernanda Paes - Department of Civil and Environmental Engineering Michigan State University East Lansing MI 48824 USAXikun Liu - Department of Civil and Environmental Engineering University of Iowa Iowa City IA 52242 USATimothy Mattes - Department of Civil and Environmental Engineering University of Iowa Iowa City IA 52242 USAAlison Cupples - Department of Civil and Environmental Engineering Michigan State University East Lansing MI 48824 USA
- Resource Type
- Journal article
- Publication Details
- Applied microbiology and biotechnology, Vol.99(18), pp.7735-7743
- Publisher
- Springer Berlin Heidelberg; Berlin/Heidelberg
- DOI
- 10.1007/s00253-015-6606-1
- PMID
- 25981993
- ISSN
- 0175-7598
- eISSN
- 1432-0614
- Language
- English
- Date published
- 09/2015
- Academic Unit
- Civil and Environmental Engineering
- Record Identifier
- 9984001094502771
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