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Integrated Analysis of Bacteroidales and Mitochondrial DNA for Fecal Source Tracking in Environmental Waters

Kapoor, Vikram
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1406821605

Abstract Details

2014, PhD, University of Cincinnati, Engineering and Applied Science: Environmental Engineering.
Identifying the source of surface water fecal contamination is paramount to mitigating pollution and risk to human health. Fecal bacteria such as E. coli have been staple indicator organisms for over a century; however there remains uncertainty with E. coli-based metrics since these bacteria are abundant in the environment. In this study we have shown that human-specific Bacteroidales correlates much more closely to a direct indicator of human waste in the form of human mitochondrial DNA (R =0.62), relative to E. coli (R =0.33), for an urban creek system afflicted by combined sewer overflows. The Duck Creek watershed, which includes Duck Creek, Deerfield Creek and the Little Miami River, was used for sampling due to continued fecal contributions to the Little Miami River recreational waterway. We identified and quantified potential sources of fecal pollution from combined sewer overflows (CSO), and watershed runoff by employing molecular tools for an integrated analysis of Bacteroidales and mitochondrial DNA (mtDNA). The correlation between the presence of human mtDNA, human-specific Bacteroidales and E. coli at sampling sites was studied to design an integrated and reliable fecal source tracking strategy for environmental waters. By comparing a direct indicator (human mtDNA) with bacterial markers, we were able to overcome the limitations of traditional methods which yield false positives from bacteria already living in the stream. Furthermore, we investigated the biodiversity of Bacteroidales 16S rRNA gene sequences derived from some of the water samples to substantiate the evidence of human wastes in the watershed, and to examine their relative abundance among sampling sites. Unlike previous microbial-based correlative investigations, we demonstrate that Bacteroidales closely follow the dynamics of human mitochondrial DNA concentration changes, indicating that these obligate anaerobes are more accurate than E. coli, lending further support to risk overestimation using coliforms. Ion Torrent was used to sequence human mitochondrial hypervariable region II (HVRII) from water samples obtained from CSO sites at different time points accounting for spatial-temporal resolution of human contamination in the watershed. We investigated the occurrence of HVRII allelic frequencies of human mtDNA and used these SNPs to form site-specific genetic barcodes (HVR fingerprint) for evaluating anthropogenic watershed inputs. Altogether, several molecular tools were applied, namely PCR, multiplex PCR, qPCR, and sequencing for elucidating fecal contaminant input and relative contributions. The rigorous sampling procedure followed takes into account wet and dry weather variation, storm event input and diurnal variation. Specifically, the information from this study will not only assist MSDGC with pollution source location and best management practices for mitigating Duck Creek bacterial contributions to the Little Miami River, but will also serve as an invaluable tool for future waste source tracking efforts in general by providing improved methodology.
David Wendell, Ph.D. (Committee Chair)
Ting Lu, Ph.D. (Committee Member)
Ronald Debry, Ph.D. (Committee Member)
Margaret Kupferle, Ph.D. P.E. (Committee Member)
George Sorial, Ph.D. (Committee Member)
149 p.
Environmental Science
Fecal source tracking; Bacteroidales; Mitochondrial DNA; Microbial source tracking; Fecal indicators; Human mitochondrial hypervariable region

Recommended Citations

Citations

  • Kapoor, V. (2014). Integrated Analysis of Bacteroidales and Mitochondrial DNA for Fecal Source Tracking in Environmental Waters [Doctoral dissertation, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1406821605

    APA Style (7th edition)

  • Kapoor, Vikram. Integrated Analysis of Bacteroidales and Mitochondrial DNA for Fecal Source Tracking in Environmental Waters. 2014. University of Cincinnati, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1406821605.

    MLA Style (8th edition)

  • Kapoor, Vikram. "Integrated Analysis of Bacteroidales and Mitochondrial DNA for Fecal Source Tracking in Environmental Waters." Doctoral dissertation, University of Cincinnati, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1406821605

    Chicago Manual of Style (17th edition)

ucin1406821605
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© 2014, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.