Alison Cupples

Alison Cupples

Alison Cupples



Research Interests

The application of microbiology to understand and treat soil and water contamination

  • The identification of the microorganisms and functional genes involved in biodegradation of traditional, problematic contaminants (chlorinated solvents, BTEX, MTBE, RDX, 1,4-dioxane) and emerging contaminants (antimicrobials, pharmaceuticals and personal care products)
  • The application of molecular methods to environmental microbiology including quantitative PCR, TRFLP, stable isotope probing, LAMP, high throughout sequencing
  • The occurrence and fate of emerging contaminants in engineered and natural systems

Current Projects

  • The fate and biodegradation of contaminants of emerging concern in agricultural soils
  • The application of high throughput sequencing and PICRUSt to identify microbial communities capable of rapid contaminant biodegradation
  • The development of LAMP assays to detect functional genes associated with the reductive dechlorination of the chlorinated solvents
  • The development of microbial cultures capable to 1,4-dioxane biodegradation
  • The application of stable isotope probing to identify microorganisms involved in the degradation of agricultural chemicals


2015-2016, Withrow Teaching Excellence Award
2011-2012, Lilly Teaching Fellow, MSU
2011, Excellence in Review Award, Environmental Science & Technology
2009, SETAC North American Endowment Environmental Engineering Travel Award
2005, Superior Research in Environmental Microbiology, USDA-ARS
2004, Superior Research Accomplishments in Microbiology, USDA-ARS
Ph.D., Environmental Engineering and Science, Stanford University 2003
M.S., Natural Resources and Environmental Sciences, University of Illinois 1999
B.S., Environmental Sciences, University of East Anglia (England) 1997
Vera, Andrea, Paes Wilson, Fernanda and A. M. Cupples. 2022. Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated Naval Sites. Applied Microbiology and Biotechnology, 106 (2), 835-853.
A.M. Cupples and Thelusmond, J.R. 2022. Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms. Journal of Microbiological Methods, 193, 106401.
Dang, Hongyu and A. M. Cupples. 2021. Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms. Science of the Total Environment. Volume 794, 10 November 2021, 148690.
Dang, Hongyu and A. M. Cupples. 2021. Diversity and abundance of the functional genes and bacteria associated with RDX degradation at a contaminated site pre- and post- biostimulation. Applied Microbiology and Biotechnology, 105, 6463-6475.
Li, Zheng and A. M. Cupples. 2021. Diversity of nitrogen cycling genes at a Midwest Long Term Ecological Research Site with different management practices. Applied Microbiology and Biotechnology. 105 (10): 4309–4327.