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Reassessment of PCR primers targeting 16S rRNA genes of the organohalide-respiring genus Dehalogenimonas

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Abstract

Representatives from the genus Dehalogenimonas have the metabolic capacity to anaerobically transform a variety of environmentally important polychlorinated aliphatic compounds. In light of the recent isolation of additional strains, description of a new species, and an expanded number of uncultured DNA sequences, PCR primers and protocols intended to uniquely target members of this organohalide-respiring genus were reevaluated. Nine of fourteen primer combinations reported previously as genus-specific failed to amplify 16S rRNA genes of recently isolated Dehalogenimonas strains. Use of alternative combinations or modified genus-specific primers, however, allowed detection of all presently known Dehalogenimonas strains. Use of a modified primer set in qPCR revealed an approximately two-order of magnitude increase in concentration of Dehalogenimonas 16S rRNA gene copies following subsurface injection of electron donors at a Louisiana Superfund site, demonstrating the utility of the newly developed protocol and suggesting that the genus Dehalogenimonas can respond to biostimulation remediation strategies in a manner similar to that previously reported for other dechlorinating genera such as Dehalococcoides.

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Acknowledgments

This research was funded by the Governor’s Biotechnology Initiative of the Louisiana Board of Regents grant BOR#015 and a consortium of petrochemical companies. The authors gratefully acknowledge Jyoti Rao and Rachel Stebbing for assistance with groundwater community DNA extractions.

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Authors and Affiliations

  1. Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA

    Jie Chen, Kimberly S. Bowman & William M. Moe

  2. Department of Biological Sciences, University of Alaska at Anchorage, Anchorage, AK, 99508, USA

    Fred A. Rainey

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  1. Jie Chen
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  2. Kimberly S. Bowman
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  3. Fred A. Rainey
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  4. William M. Moe
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Correspondence to William M. Moe.

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Chen, J., Bowman, K.S., Rainey, F.A. et al. Reassessment of PCR primers targeting 16S rRNA genes of the organohalide-respiring genus Dehalogenimonas . Biodegradation 25, 747–756 (2014). https://doi.org/10.1007/s10532-014-9696-z

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  • DOI: https://doi.org/10.1007/s10532-014-9696-z

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