Phil Dennis (ON) will present “Combining Molecular Tools and Compound-Specific Isotope Analysis for Natural Attenuation Assessment” at the Clemson Hydrogeology Symposium (Virtually) at Clemson University in Anderson, SC on October 21, 2021.

Phil’s co-presenters are Silvia Mancini, PhD, Julie Konzuk, Ph.D. & Carol Cheyne (Geosyntec Consultants) and Anko Fischer, Ph.D. & Kevin Kuntze (Isodetect).

Phil is a Principal Molecular Biologist with more than 20 years of experience focused environmental microbiology, molecular genetic testing, enhanced bioremediation and technology commercialization. He currently directs the molecular testing services, next generation sequencing and is the innovation lead for SiREM’s research and development program. He has also played a leading role in developing relationships with many universities and serves on the Board for University of Waterloo Center for Microbial Research.

The Clemson Hydrogeology Symposium is an ongoing effort to engage and educate the hydrogeological community at large whether from industry or academia. Their primary focus is on geologic and hydrologic issues in the southeast US but it is not restricted to any geographic extent. The long-term goal has been to offer an opportunity for industry related projects to intermingle with academic research and bridge the gap that has traditionally separated these two endeavors.

The Department of Environmental Engineering and Earth Sciences (EEES) at Clemson University has a synergistic blend of environmental engineering, biosystems engineering, environmental science, geology and earth sciences, and nuclear environmental engineering and science. The offer several academic options to our students.

At the undergraduate level, they are committed to providing the next generation of environmental engineers and earth scientists a comprehensive understanding and skill set to tackle complex environmental issues and challenges. Their  environmental engineering curriculum is versatile, allowing students to pursue a core curriculum that emphasizes areas that are traditionally associated with environmental engineering (e.g., water and wastewater treatment, solid and hazardous waste management, air pollution control, pollution prevention, natural systems, and risk assessment). Biosystems engineering combines the application of engineering science and design with biological and agricultural sciences.

Environmental quality and natural resources are important aspects of the discipline. They emphasize two areas of biosystems engineering – bioprocessing and ecological engineering. For the geology degree, they provide specialization in traditional geology, environmental science, and hydrogeology. Unique to Clemson, all of their undergraduate geology students participate in research with a faculty member from their sophomore through senior year.

At the graduate level, they offer five degrees and their programs are nationally recognized for their quality. The environmental engineering and science graduate program has been consistently ranked in the top 25 by U.S. News and World Report. Their graduates find employment across the United States. Today, more than 1000 people have earned graduate degrees from EEES. Overall, their diverse, dynamic, and talented faculty and comprehensive curriculum provide a rich, scholarly, and challenging educational experience to their students.


Assessing natural attenuation potential, progress and degradation rates is critical for decision making regarding the feasibility of monitored natural attenuation (MNA) remedies for sites with chlorinated solvents, petroleum hydrocarbons, 1,4-dioxane, and other contaminants. While numerous tests are employed in evaluating natural attenuation, the combination of compound-specific stable isotope analysis (CSIA) and molecular tools can be particularly useful. CSIA indicates the extent of degradation and quantifies bond breaking processes over non-degradative losses such as sorption. CSIA also has the potential for estimating long-term degradation rates. Molecular tools, including quantitative polymerase chain reaction (qPCR) tests and next generation sequencing (NGS) that quantify key biodegradative microorganisms, functional genes and whole microbial communities, provide insight into whether observed degradation can be explained by biotic processes. CSIA and molecular tools are tertiary lines of evidence in MNA protocols, and provide compelling data to answer the questions (1) Has degradation occurred and to what extent? and (2) Which microbes are responsible for any observed biodegradation?

CSIA and molecular genetic data were collected from several sites undergoing MNA assessments. The CSIA data (mainly for carbon: 13C/12C as δ13C, but also in combination with chlorine: 37Cl/35Cl as δ37Cl and/or hydrogen: 2H/1H as δ2H) was used to determine if contaminant degradation processes were evident, or absent, based on enrichment of the heavy isotope (13C, 37Cl, 2H) in the remaining undegraded contaminant fraction. Corresponding molecular genetic data, including qPCR was used to determine if biodegradative microbes were present, and at quantities able to meaningfully impact contaminant degradation. NGS microbial community profiles were also compared to geochemical data to determine if microbial community composition was consistent with CSIA results and geochemistry.

In several cases, the combination of CSIA and molecular genetic testing data indicated natural attenuation processes were occurring or ruled them out. At a site in Alaska, trichloroethene to cis-1,2-dichloroethene (cDCE) degradation was conclusively as confirmed by CSIA but further cDCE degradation by reductive or oxidative processes was inconclusive. By correlating the extent of 13C-enrichment in cDCE with the proportion of dechlorinators as determined by molecular tools the case for natural attenuation of cDCE was more compelling. At another site, inconclusive evidence for degradation of cDCE in both the CSIA and the microbial data, suggested that natural attenuation of cDCE had not occurred and enhanced bioremediation was likely necessary. At a third site, isotopic evidence suggested that abiotic degradation pathways may be important for natural attenuation while anaerobic pathways dominated in source areas where an active remedy is in place.

Overall, the combination of CSIA and molecular tools allows conclusions to be drawn on natural attenuation processes that are not easily arrived at by using other analytical methods.

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