“Innovative Methods to Quantify Microorganisms Associated with the Biodegradation of the Chlorinated Solvents and 1,4-Dioxane” by Dr. Alison Cupples
Reductive dechlorination by Dehalococcoides mccartyi plays a vital role in the bioremediation of chlorinated solvent sites. The presence of D. mccartyi is commonly monitored using quantitative PCR (qPCR) targeting genes which encode for distinct reductive dehalogenases. In this research, we evaluated two alternative quantification methods to qPCR. The first method, loop mediated isothermal amplification (LAMP), involves a one-step amplification reaction that occurs at a single temperature. As LAMP does not require a real time thermal cycler, the method is less expensive and potentially field deployable. In this research, an approach was developed requiring only basic, low-cost laboratory equipment, which requires less time and resources compared to qPCR. The method includes concentrating biomass from groundwater and LAMP amplification of the cell templates without a DNA extraction step. The amplified DNA are detected by a simple visual color change (orange/green). A second method uses shotgun sequencing with both taxonomic and functional analyses to examine chlorinated solvent and 1,4-dioxane degrading microorganisms in contaminated groundwater. The second approach is advantageous over current methods because an unlimited number of functional genes could potentially be quantified.
Several organism- and process-specific genes are biomarkers which can be used to monitor reductive dechlorination. Whereas the presence of reductive dehalogenase genes provides a measure of potential reductive dechlorination, the presence of reductive dehalogenase proteins can provide information about actual reductive dechlorination activity. The objectives of this project are to demonstrate that (1) quantitative proteomics measures reductive dehalogenase proteins over a wide range of Dehalococcoides (Dhc) cell densities and (2) reductive dehalogenase protein abundances correlate with in situ reductive dechlorination rates. This webinar will describe how reductive dehalogenase biomarker abundances and reductive dechlorination rates were quantified and correlated in a series of laboratory microcosms established with aquifer material from a chlorinated solvent-contaminated aquifer. Further, the potential utility of this reductive dechlorination rate estimation approach for application at sites undergoing monitored natural attenuation and active bioremediation will be discussed.
is an associate professor in the Department of Civil and Environmental Engineering at Michigan State University in East Lansing, Michigan. Alison’s current area of research focuses on the use of molecular methods to quantify microorganisms involved in contaminant biodegradation. Alison has served as the Principal Investigator on several grants to examine microbial communities associated with the biodegradation of 1,4-dioxane, RDX, chlorinated solvents and pharmaceuticals methods using methods such as quantitative PCR, stable isotope probing and high throughput sequencing. She has authored more than 50 peer-reviewed research papers and conference proceedings, including several on the chlorinated solvents. Alison earned a bachelor’s degree in environmental sciences from the University of East Anglia in England (1997), a master’s degree (1999) in natural resources and environmental sciences from the University of Illinois and a doctoral degree (2003) in environmental engineering and Science from Stanford University.
Dr. Mandy Michalsen is a research engineer with the U.S. Army Engineer Research Development Center (ERDC) in Seattle, Washington. Mandy’s current research areas focus on novel applications of groundwater remediation technologies to accelerate cleanup of explosives- and chlorinated solvent-contaminated aquifers, and polymeric samplers for measuring freely-dissolved contaminants in sediment porewater. Since joining U.S. Army Corps of Enginners (USACE) in 2008, Mandy has served as Principal Investigator and lead engineer on field-scale technology demonstrations and full-scale groundwater remedy optimization projects, resulting in multiple peer-reviewed research papers. She received her bachelor’s degree in civil engineering from University of Iowa, and both her master’s and doctoral degrees in civil engineering from Oregon State University. Prior to joining ERDC in November 2014, Mandy was chief of soils at the USACE Seattle District.
Dr. Kate Kucharzyk is a principal research scientist with Battelle Memorial Institute in Columbus, Ohio. Since joining Battelle in 2014, Kate has served as a Principal Investigator on projects focusing on applying and monitoring bioremediation processes in contaminated sites. With detailed knowledge of molecular biological tools and experience in assessment of remediation technologies, Kate is currently a Principal Investigator at Battelle’s Chemical, Biological, Radiological, Nuclear, and Explosives (CBRNE) Advanced Omics BU aiding in study design, assay selection, and result interpretation. Her project experience and fields of expertise include soil, groundwater and sediment remediation, biochemical basis of bioremediation of munition constituents and omic technologies in performance monitoring. She has reviewed and interpreted data for optimization of remedial technologies and geochemical and biological characterization of contaminated sites. She received her master’s degree in biochemistry from Maria Curie University in Poland and a doctoral degree in environmental microbiology from the University of Idaho.