Alison M. Cupples, Ph.D.

Professor, Civil and Environmental Engineering
Environmental Microbiology

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Peer Reviewed Journal Articles (Web of Science H-Index: 22)
    1. Vera, Andrea, Paes Wilson, Fernanda and A. M. Cupples. In press. Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated Naval Sites. Applied Microbiology and Biotechnology. 
    2. A.M. Cupples and Thelusmond, J.R. In press. Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms. Journal of Microbiological Methods.
    3. 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.
    4. 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. 
    5. 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): 43094327.
    6. Ramalingam, V. and A. M Cupples.2020. Anaerobic 1,4-dioxane biodegradation and microbial community analysis in microcosms inoculated with soils or sediments and different electron acceptors. Applied Microbiology and Biotechnology. 104 (9):4155-4170.
    7. Ramalingam, V. and A. M Cupples.2020. Enrichment of novel Actinomycetales and detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula. Applied Microbiology and Biotechnology. 104 (5):2255-2269. doi: 10.1007/s00253-020-10376-7.
    8. Fang, Y. 1, G. Vanzin 1, A. M. Cupples, Timothy J. Strathmann. 2020. Influence of terminal electron-accepting conditions on the soil microbial community and degradation of organic contaminants of emerging concern. Science of the Total Environment.706:135327 doi:10.1016/j.scitotenv.2019.135327.
    9. Collier, J. M.,B. Chai, J. R. Cole, M. M. Michalsen and A. M. Cupples. 2019. High throughput quantification of the functional genes associated with RDX biodegradation using the SmartChip real-time PCR system. Applied Microbiology and Biotechnology. 103 (17): 7161-7175.
    10. Thelusmond, J.R., Strathmann, T. J. and A. M. Cupples. 2019. Carbamazepine, triclocarban and triclosan biodegradation and the phylotypes and functional genes associated with xenobiotic degradation in four agricultural soils. Science of the Total Environment. 657: 1138-1149.
    11. Dang, H., Kanitkar, Y. H., Stedtfeld, R. D., Hatzinger, P. B., Hashsham, S. A. and A. M. Cupples. 2018. Abundance of chlorinated solvent and 1,4-dioxane degrading microorganisms  at five chlorinated solvent contaminated sites determined via shotgun sequencing. Environmental Science and Technology. 52 (23): 13914–13924.
    12. Xikun, L., Y. Wu, F. Paes, K. Yu, C. Lintner, A. M. Cupples and T. Mattes. 2018. Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride. FEMS Microbiology Ecology. 94: 1-14.
    13. Thelusmond, J. R., Kawka, E., Strathmann, T. J. and A. M. Cupples. 2018. Diclofenac, carbamazepine and triclocarban biodegradation in agricultural soils and the microorganisms and metabolic pathways affected. Science of the Total Environment. 640-641: 1393-1410.
    14. Kanitkar, Y. H.Stedtfeld, R. D., Hatzinger. P. B., Hashsham, S. A. and A. M. Cupples. 2017. Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples. Journal of Microbiological Methods.143:44-49.
    15. Kanitkar, Y. H., Stedtfeld, R. D., Hatzinger. P. B., Hashsham, S. A. and A. M. Cupples. 2017. Development and application of a rapid, user-friendly and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater. Applied Microbiology and Biotechnology.101: 4827–4835.
    16. Ahmad. F., R. D. Stedtfeld, H. Waseem, M. R. Williams, A.M. Cupples, J. M. Tiedje and S. A. Hashsham. 2017. Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in < 25 min. Journal of Microbiological Methods. 132: 27-33.
    17. Stedtfeld, R. D., T. M. Stedtfeld, F. Samhan, Y. H. Kanitkar, P. B. Hatzinger, A. M. Cupples, and S. A. Hashsham. 2016. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater. Journal of Microbiological Methods. 131: 61-67.
    18. Thelusmond, J.R., Strathmann, T. J. and A. M. Cupples. 2016. The identification of carbamazepine biodegrading phylotypes and phylotypes sensitive to carbamazepine exposure in two soil microbial communities. Science of the Total Environment. 571: 1241-1252.
    19. Paes Wilson F., X. Liu, T. E. Mattes, and A. M. Cupples. 2016. Nocardioides, Sediminibacterium, Aquabacterium, Variovorax and Pseudomonas linked to carbon uptake during aerobic vinyl chloride biodegradation. Environmental Science and Pollution Research. 23: 19062-19070.
    20. Cupples, A. M. 2016. A review: contaminant degrading microorganisms identified using stable isotope probing. Chemical Engineering and Technology. 39: 1593-1603.
    21. Paes Wilson, F. and A. M. Cupples. 2016. Microbial community characterization and functional gene quantification in RDX degrading microcosms derived from sediment and groundwater at two Naval sites. Applied Microbiology and Biotechnology, 100: 7297-7309.
    22. Kanitkar, Y. H.,  Stedtfeld, R. D., Steffan, R. J., Hashsham, S. A. and A. M. Cupples. 2016. Development of loop mediated isothermal amplification (LAMP) for rapid detection and quantification of Dehalococcoides spp. biomarker genes in commercial reductive dechlorinating cultures KB-1 and SDC-9. Applied and Environmental Microbiology.82:1799-1806.
    23. Seyrig, G., Stedtfeld, R. D., Tourlousse, D. M., Farhan, A., Towery, K., Cupples, A. M, Tiedje, J. M. and S. A. Hashsham. 2015. Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. Journal of Microbiological Methods. 119: 223-227.
    24. Paes, F., Liu, X., Mattes, T. E. and A. M. Cupples. 2015. Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing. Applied Microbiology and Biotechnology. 99: 7735-7743.
    25. Jayamani, I. and A. M Cupples. 2015. Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site. Environmental Science and Pollution Research. 22: 10340-10350.
    26. Jayamani, I. and A. M. Cupples. 2015. A comparative study of microbial communities in four soil slurries capable of RDX degradation using Illumina sequencing. Biodegradation. 26: 247-257.
    27. Jayamani, I. and A. M. Cupples. 2015. Stable isotope probing and high throughput sequencing implicates Xanthomonadaceae and Rhodocyclaceae in ethylbenzene degradation. Environmental Engineering Science. 32:240-249.
    28. Ding, L. and A. M. Cupples. 2015. The effect of the potential fuel additive isobutanol on benzene, toluene, ethylbenzene, p-xylene degradation in aerobic soil microcosms. Environmental Technology, 36: 237-244.
    29. Song, Y., Xiao, L., Jayamani, I., He, Z. and A.M. Cupples. 2015. A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing. Journal of Microbiological Methods, 108:4-11.
    30. Stedtfeld, R., Stedtfeld, T., Kronlein, M., Seyrig, G., Steffan, R., Cupples, A.M. and S. A. Hashsham. 2014. DNA extraction-free quantification of Dehalococcoides spp. in groundwater using a hand-held device. Environmental Science and Technology, 36:237-244.
    31. Sun, W., Sun, X. and A. M. Cupples. 2014. Presence, diversity and enumeration of functional genes (bssA and bamA) relating to toluene degradation across a range of redox conditions and inoculum sources. Biodegradation, 25:109-203.
    32. Sun, W., Sun, X. and A. M. Cupples. 2014. Identification of Desulfosporosinus as toluene-assimilating microorganisms from a methanogenic consortium. International Biodeterioration and Biodegradation, 88: 13-19.
    33. A. M. Cupples. 2013. RDX degrading microbial communities and the prediction of microorganisms responsible for RDX bioremediation. International Biodeterioration and Biodegradation, 85: 260-270.
    34. Jayamani, I., Manzella, M. P. and Cupples, A. M. 2013. RDX degradation potential in soils previously unexposed to RDX and the identification of RDX degrading species in one agricultural soil using stable isotope probing. Water, Air and Soil Pollution, 224:1745
    35. Jayamani, I. and A. M. Cupples. 2013. Effect of isobutanol on toluene biodegradation in nitrate amended, sulfate amended & methanogenic enrichment microcosms. Biodegradation, 24: 657-663.
    36. Sun, W., X. Sun and A.M. Cupples. 2012. Anaerobic MTBE degrading microorganisms identified in wastewater treatment plant samples using stable isotope probing. Applied and Environmental Microbiology, 78: 2973-2980.
    37. Sun, W. and A. M. Cupples. 2012. Diversity of five anaerobic toluene degrading microbial communities investigated using stable isotope probing (SIP). Applied and Environmental Microbiology, 78: 972-980.
    38. Cha, J. and A. M. Cupples. 2012. Determination of triclocarban and triclosan in biosolid and soil samples by application of pressurized liquid extraction and liquid chromatography with tandem mass spectrometry. Geosystem Engineering, 15:280-291.
    39. Cupples, A. M. 2011. The use of nucleic acid based stable isotope probing to identify the microorganisms responsible for anaerobic benzene and toluene biodegradation. Journal of Microbiological Methods, 85, 83-91.
    40. Xie, S., W. Sun, C. Luo and A. M. Cupples. 2011. Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation, 22, 71-81.
    41. Cha, J. and A. M. Cupples. 2010. Triclocarban and triclosan biodegradation at field concentrations and the resulting leaching potentials in three agricultural soils. Chemosphere, 81, 494-499.
    42. Xie, S., W. Sun, C. Luo and A. M. Cupples. 2010. Stable isotope probing identifies novel m-xylene degraders in soil microcosms from contaminated and uncontaminated sites. Water, Air and Soil Pollution, 212, 113-122.
    43. Sun, W., S. Xie, C. Luo and A. M. Cupples. 2010. Direct link between toluene degradation in contaminated-site microcosms and a Polaromonas strain. Applied and Environmental Microbiology, 76: 956-959.
    44. Luo, C., S. Xie, W. Sun, X. Li and A. M. Cupples. 2009. Identification of a novel toluene-degrading bacterium from the candidate phylum TM7 as determined by DNA-stable isotope probing. Applied and Environmental Microbiology, 75: 4644-4647.
    45. Cha, J. and A. M. Cupples. 2009. Detection of the antimicrobials triclocarban and triclosan in agricultural soils following land application of municipal biosolids. Water Research, 43: 2522-2530.
    46. Cupples, A. M. 2008. Real-time PCR quantification of Dehalococcoides populations: methods and applications. Journal of Microbiological Methods, 72: 1-11.
    47. Cupples, A. M., E. A. Shaffer, J. C. Chee-Sanford, and G. K. Sims. 2007. DNA buoyant density shifts during 15N DNA stable isotope probing. Microbiological Research, 162: 328-334.
    48. Cupples, A. M. and G. K. Sims. 2007. Identification of in situ 2,4-dichlorophenoxyacetic acid-degrading soil microorganisms using DNA-stable isotope probing. Soil Biology and Biochemistry, 39: 232-238.
    49. Cupples, A. M., R. A. Sanford, and G. K. Sims. 2005. Dehalogenation of the herbicides bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) and ioxynil (3,5-diiodino-4-hydroxybenzonitrile) by Desulfitobacterium chlororespirans . Applied and Environmental Microbiology. 71: 3741-3746.
    50. Cupples, A. M., A. M. Spormann and P. L. McCarty. 2004. Comparative evaluation of chloroethene dechlorination to ethene by Dehalococcoides -like microorganisms. Environmental Science and Technology, 38: 4768-4774.
    51. Cupples, A. M., A. M. Spormann and P. L. McCarty. 2004. Vinyl chloride and cis-dichloroethene dechlorination kinetics and microorganism growth under substrate limiting conditions. Environmental Science and Technology, 38: 1102-1107.
    52. Cupples, A. M., A. M. Spormann, and P. L. McCarty. 2003. Growth of a Dehalococcoides -like microorganism on vinyl chloride and cis-dichloroethene as electron acceptors as determined by competitive PCR. Applied and Environmental Microbiology. 69: 953-959.
    53. Cupples, A. M., G. K. Sims, R. P. Hultgen and S. E. Hart. 2000. Effect of soil conditions of the degradation of chloransulam-methyl. Journal of Environmental Quality 29: 786- 794.
    54. Sims, G. K. and A. M. Cupples. 1999. Factors controlling degradation of pesticides in soil. Pesticide Science 55: 598-601.
    55. David, M. B., A. M. Cupples, G. B. Lawrence, G. Shi, K. Vogt and P. M. Wargo. 1998. Effect of chronic nitrogen additions on soil nitrogen fractions in Red Spruce stands. Water, Air and Soil Pollution 105: 183-192.

     

    Conference Proceedings, Book Chapters and Reports

    1. Cupples, A.M. 2020. Examining the effectiveness of short, voluntary on-line tutorials in a large undergraduate class. Conference Proceedings, American Society of Engineering Education (ASEE), June 22-26th, 2020. Virtual Conference.
    2. Cupples, A.M. 2019. The development of anaerobic bioremediation approaches for chlorinated solvent and dioxane co-contaminated sites (SERDP Final Report)
    3. Dang, H., Kanitkar, Y. H., Stedtfeld, R. D., Hatzinger, P. B., Hashsham, S. A. and A. M. Cupples. 2019. Abundance of chlorinated solvent and 1,4-dioxane degrading microorganisms at five chlorinated solvent contaminated sites determined via shotgun sequencing. The Fifth International Symposium on Bioremediation and Sustainable Environmental Technologies, April, 15-18, 2019, in Baltimore, Maryland Best Student Paper Award (Conference Proceeding).
    4. Ramalingam, V. and A. M. Cupples. 2019. 1,4-Dioxane biodegradation potential in aerobic and anaerobic microcosms inoculated with agricultural soil and contaminated sediments. The Fifth International Symposium on Bioremediation and Sustainable Environmental Technologies, April, 15-18, 2019, in Baltimore, Maryland (Conference Proceeding).
    5. Cupples, A.M, S. A. Hashsham, R. Stedtfeld & P. B. Hatzinger. Development of LAMP to detect Dehalococcoides and Dehalobacter spp. genes without DNA extraction (SERDP Final Report, 2018)
    6. Ramalingam, V. and A. M. Cupples. 2018. The development of microcosms to achieve anaerobic and aerobic 1,4-dioxane biodegradation. The Eleventh International Conference on Remediation of Chlorinated and Recalcitrant Compounds, April 8-12, 2018, Palm Springs, California (Conference Proceeding).
    7. Collier, J. M., B. Chai, J. R. Cole and A. M. Cupples. 2018. High throughput quantification of the functional genes associated with RDX degradation using the WaferGen SmartChip Platform. The Eleventh International Conference on Remediation of Chlorinated and Recalcitrant Compounds, April 8-12, 2018, Palm Springs, California (Conference Proceeding).
    8. Dang, H., Y. H. Kanitkar, R. D. Stedtfeld, S. A. Hashsham, P. B. Hatzinger and A. M. Cupples. 2018. Microbial community characterization at five chlorinated solvent sites following bioaugmentation with Dehalococcoides enriched culture, SDC-9. The Eleventh International Conference on Remediation of Chlorinated and Recalcitrant Compounds, April 8-12, 2018, Palm Springs, California (Conference Proceeding).
    9. Strathmann, T. Y. and Cupples, A. M. Biological and biologically mediated abiotic transformation of contaminants of emerging concern in anaerobic soils (USDA Final Report, Sept 2017).
    10. Cupples, A. M. 2016. Collaborative research: stable isotope-based differentiation of vinyl chloride assimilators from cometabolizers in contaminated groundwater. (NSF Final Report, Aug 2016).
    11. Cupples, A. M. 2016. Development of biomarkers for assessing in situ RDX biodegradation potential. Project Number: ER 1606 (SERDP Final Report).
    12. Liu X., Yu K., Paes F., Linter C.K., Cupples A.M and Mattes T.E. 2016. Microbial adaptation to vinyl chloride in groundwater microcosms as revealed by metagenomics and other molecular tools. Proceedings of the Tenth International Conference on Remediation of Chlorinated and Recalcitrant Compounds. Best Student Paper Award for X. Liu (Conference Proceeding).
    13. Paes, F., Liu, X., Mattes, T. and A. M. Cupples. 2015.Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing. The Third International Symposium on Bioremediation and Sustainable Environmental Technologies, May 18–21, 2015, in Miami, Florida. Best Student Paper Award (conference proceeding).
    14. Cupples, A. M., W. Sun, and S. Masten. 2013. The use of active learning to address ABET course learning objectives in a large undergraduate environmental engineering class (ASEE Conference Paper).
    15. Cupples, A. M. 2013. Stable isotope probing to assess bioremediation of LUST contaminants: addressing existing MTBE/BTEX and probable future ethanol/BTEX contamination (NSF, Final Report).
    16. Cupples, A. M., W. Sun, and S. Masten. 2012. The use of active learning to address ABET course learning objectives in a large undergraduate environmental engineering class (Lilly Program Report).
    17. Cupples, A. M. and I. Jayamani. Final Report SERDP. 2010. Development of biomarkers for assessing in situ RDX biodegradation potential. Project Number: ER 1606 (SEED project, SERDP Final Report).
    18. Cupples, A. M., J. B. Rose, and I. Xagoraraki. 2010. New molecular methods for detection of water-borne pathogens, Environmental Microbiology, Wiley Publications (Book Chapter).