Joanne Chee-Sanford

Phone: (217) 265-0959

USDA / Agricultural Research Service



About Us


Research Projects

Research Team





-B.S., Univ. of Washington, Microbiology, 1984

-Ph.D, Michigan State Univ., Microbiology and Environmental Toxicology, 1996



Our research is examining available weed management strategies for key weed species in vegetable and row crops in the midwest area. The goal is to develop fundamental knowledge of weed biology/microbiology, and develop ecology to enhance environmentally safe weed control. Additionally, new directions for biologically based management of these weed species will be proposed, in close collaboration with key customers and stakeholders, universities and extension laboratories. A regional approach to solving these problems collaboratively will be developed.

The approach of this research unit is to study critical physiological/biochemical, environmental, and ecological phenomena of economically important weeds in vegetable and row crop systems. These include factors important to weeds, weed seeds, microbial communities and function, and their relationship to the environment. With this knowledge, improved weed management systems can be developed that integrate and utilize biological control weed sensors, reduced herbicide inputs, reduced tillage, crop rotations, and enhancement/reduction of factors affecting microbial-mediated weed seed bank depletion or other non-chemical management strategies.




Shaffer, E., Sims, G.K., Cupples, A.M., Smyth, C., Chee Sanford, J.C. 2010. Atrazine Biodegradation in a Cisne Soil Exposed to a Major Spill. International Journal of Soil, Sediment, and Water. 3(2):1-26.


Koike, S., Aminov, R.I., Yannarell, A.C., Gans, H.D., Krapac, I.G., Chee Sanford, J.C., Mackie, R.I. 2010. Molecular Ecology of Macrolide-Lincosamide-Streptogramin B Methylases in Waste Lagoons and Subsurface Waters Associated with Swine Production. Microbial Ecology. 59(3):487-498.


Chee Sanford, J.C., Mackie, R.I., Koike, S., Krapac, I., Maxwell, S., Lin, Y., Aminov, R.I. 2009. Fate and Transport of Antibiotic Residues and Antibiotic Resistance Genetic Determinants During Manure Storage, Treatment, and Land Application. Journal of Environmental Quality. 38(3):1086-1108.


Chee-Sanford, J.C. 2008.  Weed seeds as nutritional resources for soil Ascomycota and characterization of specific associations between plant and fungal species.  Biol Fertil Soils 44:763–771. 

Koike, S., Krapac, I.G., Oliver, H.D., Yannarell, A.C., Chee-Sanford, J.C., Aminov, R.I. and Mackie, R.I.  2007.  Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a three-year period.  Appl. Environ. Microbiol. 73:4813-4823. 

Lundgren, J.G., Lehman, R.M. and Chee-Sanford, J.  2007.  Bacterial communities within digestive tracts of ground beetles (Cleoptera: Carabidae).  Annals of the Entomological Society of America 100:275-282. 

Mackie, R.I., Koike, S., Krapac, I., Chee-Sanford, J., Maxwell, S. and Aminov, R.I. 2006. Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilities. Anim. Biotech. 17: 157-176.


Cupples, A.M., Shaffer, E.A., Chee-Sanford, J.C. and Sims, G.K.  2006.  DNA buoyant density shifts during 15N-DNA stable isotope probing.  Microbiol. Research.162:328-334. 

Chee-Sanford, J.C., Williams II, M.M., Davis, A.S. and Sims, G.K. 2006.  Do microbes influence seed bank dynamics? Weed Sci.  54:575-587.

Krapac, I.G., Koike, S., Meyer, M.T., Snow, D.D., Chou, S.–F.J., Mackie, R.I., Roy, W.R. and Chee-Sanford, J.C. 2004. Long-term monitoring of the occurrence of antibiotic residues and antibiotic resistance genes in groundwater near swine confinement facilities. 4th Int. Conference on Pharmaceuticals and Endocrine Disrupting Chemicals in Water, National Ground Water Association, Westerville, Ohio, p. 158-172.


R. I. Aminov, Chee-Sanford, J. C. , Garrigues, N., Teferedegne, B., Krapac, I.J., White, B.A. and Mackie, R.I.  2002.  Development, validation, and application of PCR primers for detection of tetracycline efflux genes of gram-negative bacteria.  Appl. Environ. Microbiol. 68: 1786-1793. 

Kirisits, M.J., Snoeyink, V.L., Chee-Sanford, J.C., Daugherty, B.J., Brown, J.C. and Raskin, L.M.  2002.  Effect of column design and operating conditions on bromate removal efficiency in BAC filters.  J. Amer. Waterworks Assoc. 94:182-193. 


Chee-Sanford, J. C., Aminov, R.I., Krapac, I.J., Garrigues-Jeanjean, N. and Mackie, R.I. 2001. Occurrence and diversity of tetracycline-resistance genes in lagoons and groundwater underlying two swine production facilities. Appl. Environ. Microbiol. 67:1494-1502.

 Kirisits, M.J., Snoeyink, V.L., Inan, H., Chee-Sanford, J.C., Raskin, L.M. and Brown, J.C. 2001.  Water quality factors affecting bromate reduction in biologically active carbon filters.  Water Research, 35:891-900.


 Rockne, K.J., Chee-Sanford, J.C. (corresponding author), Sanford, R.A., Hedlund, B., Staley, J.T. and Strand, S.E. 2000. Anaerobic naphthalene degradation by microbial pure cultures under nitrate-reducing conditions.  Appl. Environ. Microbiol. 66:1595-1601.


 Chee-Sanford, J.C., Frost, J.W., Fries, M.R., Zhou, J.-Z. and Tiedje, J.M. 1996. Evidence for acetyl-CoA and cinnamoyl-CoA in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus strain Tol-4.  Appl. Environ. Microbiol. 62:964-973.

 Migaud, M.E, Chee-Sanford, J.C. , Tiedje, J.M. and Frost, J.W. 1996.  Benzylfumaric, benzylmaleic, Z- and E-phenylitaconic acids: synthesis, characterization and correlation with a metabolite generated by Azoarcus tolulyticus strain Tol-4 during anaerobic toluene degradation.  Appl. Environ. Microbiol. 62:974-978.

 Zhou, J.-Z, Fries, M.R., Chee-Sanford, J.C. and Tiedje, J.M. 1995.  Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene: description of Azoarcus tolulyticus sp. nov. Int. J. Sys. Bacteriol. 45:500-506.


Fries, M.R., Zhou, J.-Z. , Chee-Sanford, J.C and Tiedje, J.M. 1994.  Isolation, characterization and distribution of denitrifying toluene degraders from a variety of habitats. Appl. Environ. Microbiol. 60:2802-2810. 

Kirisits,M.J., Snoeyink, V.L., Inan, H., Chee-Sanford, J.C., Raskin, L. and Brown, J.C. 2000. Effect of water quality on bromate reduction in BAC filters. In: Proceedings of the American Water Works Association Annual Conference, Denver, CO.


Brown, J.C., Snoeyink, V.L., Liang, S., Raskin, L., Chee-Sanford, J.C., Coates, J.D., Kirisits, M.J. and Lin, R. 2000. The effect of nitrate on the biological reduction of prechlorate in an activated carbon filter. In: Proceedings of the American Water Works Association Annual Conference, Denver, CO.


Tiedje, J.M., Fries, M., Chee-Sanford, J.C. and Cole, J.. 1994. Anaerobic degradation of aromatic chlorinated and gasoline compounds in soils and aquifers, pp. 364-374, In Proc. 15th Int'l Congress of Soil Science, Acapulco, Mexico, vol. 4A.


Tiedje, J.M., Quensen III, J.F., Chee-Sanford, J.C.,  Schimel, J.P. and Boyd, S.A. 1993. Microbial reductive dechlorination of PCBs. Biodegradation. 4:231-240.


Tiedje, J.M., Fries, M. and Chee-Sanford, J.C. 1993. Is bioremediation of BTEX contaminated soils and aquifers possible under anaerobic conditions. Sec II, In Pacific Basin Conference on Hazardous Wastes, 1993 Proceedings, East-West Center, Honolulu, Hawaii.

Tiedje, J.M., Cole, J.R., 
Chee-Sanford, J.C., Foxworthy, A., and Fathepure, B.Z. 1992. Anaerobic metabolism of chlorobenzoates, phenols, biphenyls, and PCE by novel anaerobes. Microbial Degradation of Environmental Pollutants: Potentials and limitations for practical use. WE—Heraeus Seminars, Physikzentrum Bad Honnef, Germany.

Tiedje, J.M., Quensen, J.F., Chee-Sanford, J.C., Schimel, J.P., and Boyd, S.A. 1992. Microbial reductive dechlorination of PCBs. In Pacific Basin Conference on Hazardous Wastes, 1992 Proceedings, Bangkok, Thailand.

Invited reviews:

Mackie, RI., Koike, S., Krapac, I., Chee-Sanford, J.C., Maxwell, S., Lin, Y.-F. and Aminov, RI. 2006. Fate and transport of antibiotic residues and antibiotic resistance genetic determinants during manure storage, treatment, and land application with emphasis on the environmental persistence and transferability of these determinants. Review of the Critical Literature, National Pork Board.

Peer-Reviewed Publications In Review:

Chee-Sanford, J. C., Mackie, R I., Koike, S., Krapac, I. G., Lin, Y.- F., Yannarell, A C., Maxwell, S., and Aminov, RI. 2008. Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. J. Env. Qual. (Revised manuscript in review).

Chee-Sanford, J.C. 2008. Soil bacterial populations associated with decayed seeds of velvetleaf (Abutilon theophrasti) under conditions of carbon nutrient limitation. Soil BioI. Biochem.

Koike, S., Aminov, RI., Yannarell, AC., Gans, HD., Krapac, I.G., Chee-Sanford, J.C., and Mackie, RI. 2008. A gene ecology of macrolide-Iincosamide­streptogramin B methylases in waste lagoons and subsurface waters associated with swine production. Environ. Microbiol.

Books and Book Chapters:

Kirisits, M.J., Brown, J.C., Snoeyink, V.L., Raskin, L.M., Chee-Sanford, J.C., Liang, S. and Min, J. 2001. Removal of bromate and perchlorate in conventional ozone/GAC systems. Amer. Water Works Assoc. 138 pages.

Aminov, RI., Chee-Sanford, J.C., Garrigues, N., Mehboob, A and Mackie, RI. 2004. Detection of tetracycline resistance genes by PCR. In J.F.T. Spencer and A.L. Ragout de Spencer (eds), Methods in Molecular Biology, Public Health Microbiology, Methods and Protocols, pp. 3-14, Humana Press, Inc., New Jersey.

Chee-Sanford, J.C., Fu, X., Connor, L.M. and Holman, T.J. (Invited, in preparation). Experimental approaches for the study of microorganisms in seed bank processes. In F. Columbus (ed.) Corn Crops: Growth, Fertilization, and Yield (anticipated title), Nova Science Publishers, Inc., Hauppauge, NY.

Environmental Microbiologist, USDA-ARS
Adjunct Professor, Department of Natural Resources and Environmental Sciences, University of Illinois

Joanne Chee-Sanford