Marine and Freshwater Fecal Indicators and Source Identification

  • Sandra L. McLellanEmail author
  • Alexandria B. Boehm
  • Orin C. Shanks


Fecal indicators are organisms or chemical constituents found in fecal material or wastewater from humans and other animals can contaminant surface waters and pose a serious threat to the environment and human health. Fecal pollution serves as a vehicle for disease transmission including pathogenic bacteria, viruses, or protozoa. Fecal waste also carries with it harmless commensal organisms that live in the gastrointestinal (GI) tract and are often used as fecal indicators since they are present in high numbers. The type and amount of pathogens found in fecal pollution is dependent on the host source (human, agricultural animal, wildlife) and the prevalence of illness in the host population. Therefore, employing fecal indicators that provide information about human and other animal contributions is critical for estimating the likelihood that pathogens are present and for directing remediation efforts.


Fecal Coliform United States Environmental Protection Agency Much Probable Number Water Quality Criterion Fecal Indicator Bacterium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Alternative fecal indicators

Fecal indicators that have not been fully validated for standard water quality methods, but show potential for increased sensitivity or specificity over current indicators.


The general meaning of this word is sharing of food and originates from the Latin word cum mensa, meaning “sharing a table.” In the context of bacteria and host interactions, the bacteria benefit from the host without causing harm.


The term “enterococci” is a general reference to members of the genus Enterococcus: however, in the context of water quality standards, enterococci often refers to E. faecalis and E. faecium, which can be enumerated using selective and differential media.

Escherichia coli (E. coli)

Gram-negative bacteria found in the gastrointestinal tract of almost all warm-blooded animals. These bacteria are easily cultured and can be enumerated using selective and differential media.

Fecal indicator

A chemical or biological constituent that is found in fecal matter that can be used to demonstrate the presence of contamination.


A microbe or microorganism such as a bacteria, virus, fungi, prion, or protozoan that causes disease in its animal or plant host.

Polymerase chain reaction (PCR)

A scientific technique in molecular biology to amplify a single or few gene copies of a nucleic acid fragment across several orders of magnitude. Amplification results in the generation of thousands to millions of copies of a particular nucleic acid sequence.

Quantitative PCR

A technique based on PCR which simultaneously amplifies and quantifies a targeted nucleic acid molecule.



We would like to thank Dr. Alford Dufour for insightful discussion and for providing historical information on the use of traditional indicators and evolution of water quality criteria. The US Environmental Protection Agency, through its Office of Research and Development, funded and managed, or partially funded and collaborated in, the research described herein. It has been subjected to the Agency’s peer and administrative review and has been approved for external publication. Any opinions expressed in this entry are those of the author(s) and do not necessarily reflect the views of the Agency; therefore, no official endorsement should be inferred. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use.


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Sandra L. McLellan
    • 1
    Email author
  • Alexandria B. Boehm
    • 2
  • Orin C. Shanks
    • 3
  1. 1.School of Freshwater SciencesUniversity of Wisconsin-MilwaukeeMilwaukeeUSA
  2. 2.Environmental and Water Studies, Department of Civil and Environmental EngineeringStanford UniversityStanfordUSA
  3. 3.National Risk Management Research LaboratoryUnited States Environmental Protection AgencyCincinnatiUSA

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