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Detection of Microbial Indicators and Human Microbial Pathogens in Artificial Recharge Studies

By Dale W. Griffin, Ph.D., MSPH
U.S.Geological Survey Center for Coastal Studies, St. Petersburg, Florida 33701

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One of the needs in studying artificial recharge is determining microbial water quality within the recharge zone. Indicator organisms such as the fecal coliforms and alternate indicators such as enterococci, Clostridium perfringens and bacteriophage can be used to determine if a recharge zone is being impacted by viable microorganisms of fecal origin via the recharge water source or surrounding contaminated ground waters. Using emerging technologies, some indicator organisms such as Escherichia coli (a fecal coliform), enterococci and certain types of bacteriophage (viruses whose hosts are bacteria) can be used to determine the source of the pollution when questions arise concerning human versus animal inputs. Examples of emerging technologies that have allowed this type of resolution include ribotyping (DNA fingerprinting of bacteria isolates) and genetic probe assays (group typing of F+ specific RNA coliphage). The alternate to determining source via these types of assays are to screen water samples for host specific pathogens (human or animal). One group of host specific pathogens are the human enteroviruses (a group which includes polioviruses, echoviruses and Coxsackie viruses) and Hepatitis A viruses. These viruses have successfully been utilized by a number of researchers to determine if human waste was impacting a given body of water. Assays that are utilized to determine the presence of these pathogens include cell culture and many variants of the polymerase chain reaction (PCR).

Another useful tool in determining the susceptibility of a recharge zone to contamination or in determining the potential impact of recharge water on surrounding ground waters is tracer studies. Tracer studies can be carried out with gases, dyes and/or microorganisms. A number of tracer studies, which utilized bacteriophage to determine wastewater/groundwater movement, have been successfully carried out in the State of Florida. A common trend that was noted in these studies was that the phage tracers typically moved faster than dye tracers that were or had been utilized in the same regions for similar purposes. One of the conclusions from these studies was that phage tracers better reflect actual microbial groundwater movement.

This presentation will cover the microorganisms of interest and the methodology used to determine microbe presence and viability in groundwater studies. Issues such as source tracking, selection of the appropriate organism or suite of organisms and the pros and cons of various methodologies will be addressed. Below are several papers where many of these issues are addressed.


Griffin, D., C.J. Gibson III, E.K. Lipp, K. Riley, J.H. Paul, and J.B. Rose (1999). Detection of Viral Pathogens by Reverse Transcriptase PCR and of Microbial Indicators by Standard Methods in the Canals of the Florida Keys. Applied and Environmental Microbiology 65(9): 4118-4125.

Griffin, D.W., E.K. Lipp, M. McLaughlin and J.B. Rose (2001). Marine Recreation and Public Health Microbiology: Quest for the Ideal Indicator. BioScience 51(10): 817-825

Harvey, R.W. (1997). Microorganisms as tracers in groundwater injection and recovery experiments: A review. FEMS Microbiology Reviews 20(3-4): 461-472

Paul, J.H., J.B. Rose, S.C. Jiang, X. Zhou, P. Cochran, C. Kellogg, J.B. Kang, D. Griffin, S. Farrah and J. Lukasik. (1997). Evidence for Groundwater and Surface Marine Water Contamination by Waste Disposal Wells in the Florida Keys. Water Research 31(6) :1448-1454

Yates, M.V. and Yates S.R. (1988). Modeling Microbial Fate in the Subsurface Environment. CRC Critical Reviews in Environmental Control. 17(4): 307-344

In George R. Aiken and Eve L. Kuniansky, editors, 2002, U.S. Geological Survey Artificial Recharge Workshop Proceedings, Sacramento, California, April 2-4, 2002: USGS Open-File Report 02-89

The use of firm, trade, and brand names in this report is for identification purposes only and does not consitute endorsement by the U.S. Government.

For additonal information write to:

Regional Hydrologist
Southeast Regional Office
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Suite 160
Norcross, GA 30092

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Denver, CO 80225-0286

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