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U.S. Geological Survey - Great Lakes Science Center

Microbial Ecology

Great Lakes beaches are a focal point for public interactions with the lakes and are highly visible and popular recreational areas. In recent years, beaches have been increasingly impacted by periodic closures due to water quality concerns and the effects of microbial contamination. Fecal indicator bacteria (FIB; E. coli, enterococci) have traditionally been used to indicate human- or animal- derived contamination in a nearshore environment. However, there is growing evidence that FIB are being found in nonenteric habitats (e.g., soil, vegetation). Therefore, the USGS-GLSC is working to understand FIB ecology (i.e., survival, persistence, and ambient growth) in nonenteric habitats, as well as population structure and genetic characteristics. This will allow researchers to correctly identify contaminant sources, improve predictive modeling, and identify and quantify risk, as well as protect the public from potential exposure to harmful pathogens in environmental waters.


Problem Statement
Escherichia coli (E. coli) and enterococci occurrence in nonenteric habitats (e.g., soil, vegetation) has been documented since the early 1960s. While the original source of these bacteria remains speculative, recent studies show that populations of E. coli and enterococci are genetically different from those that are commonly found in the gastrointestinal tract of humans. The ability of these bacteria to survive and grow under ambient conditions, as shown in numerous studies, has led many to believe that some human bacterial pathogens with comparable physiology and genetics (of E. coli) (e.g., Salmonella, pathogenic E. coli strains) can similarly survive and may even grow in nonenteric habitats. Thus, a clear understanding of the population structure, genetic relatedness and potential sources of E. coli and other enteric bacteria is especially critical to correctly identify contaminant sources, to determine if there were any ecological roles (e.g., organic matter decomposition, plant protection from pathogens) for these enteric bacteria in soil or other habitats, and importantly to protect the public from exposure to harmful pathogens in contaminated waters.


  1. Examine the population structure and genetic characteristics of FIB (E. coli, enterococci) and enteric bacterial pathogens found in water and beachshed ecosystems using cutting edge technology in traditional microbiology and molecular biology.
    • Determine whether the environmental FIB populations comprise unique genotypes or a range of genotypes capable of colonizing, persisting, and growing under environmental conditions.
  2. To identify sources of microbial contamination in impacted water bodies using microbial source tracking (MST) techniques (chemical, traditional microbiology, and molecular techniques).
    • Determine the relationships between FIB densities and the relative occurrence of MST markers in variously impacted beaches.

Background & Justification
The extraintestinal occurrence of fecal indicator bacteria (FIB), including E. coli and enterococci, has been widely accepted by the scientific community and public health officials [(13)]. Much of the early research in this area was conducted in tropical locations, such as Hawaii, Guam, and Puerto Rico [(1, 7-10)]. Subsequent studies on the continental United States and elsewhere have confirmed the common occurrence of FIB in environments, ranging from subtropical (south Florida) to temperate (Great Lakes, Ireland) biomes [(3-4, 11, 14)]. Significantly, the widespread occurrence of FIB in the environment has been postulated as an adaptive process, leading to the formation of naturalized/adapted populations. However, the mechanism by which this process occurs has not been well understood.

In a series of studies by USGS scientists and their collaborators in the Great Lakes basin, it was found that E. coli population structure in riparian soils comprised both unique genotypes or strains (E. coli was genetically-distinct from E. coli commonly found in humans and wildlife (deer, geese, seagulls, and terns). Similarly, genotypically diverse strains of E. coli presumably adapted to the soil environments has independently been confirmed in studies in Puerto Rico and Ireland [(2, 12)].

Other recent studies have also shown that populations of FIB (E. coli, enterococci), presumably adapted to the environment, are common in other substrates in a range of aquatic and terrestrial habitats: algae/beach wrack, submerged vegetation, and agricultural crops and forage grasses [(5)]. Collectively, these data support the hypothesis that naturalized E. coli populations occur in disparate and geographically-distinct environments. However, the original source(s) of these bacteria and the mechanisms by these bacteria are able to colonize, survive, and grow in nonenteric habitats are not well understood.

Principal Investigator: Murulee Byappanahalli

Problem Statement
There is growing evidence that fecal indicator bacteria (FIB; E. coli, enterococci) that are routinely used as pathogen indicators in environmental waters are also found in nonenteric habitats. Therefore, understanding their ecology (i.e., survival, persistence, and ambient growth) in nonenteric habitats is critical for correctly identifying contaminant sources, improving predictive modeling, developing new or improved criteria, and identifying and quantifying risk, as well as protecting the public from potential exposure to harmful pathogens in environmental waters.


  1. Investigate the nonenteric (nonpoint) sources of FIB in a variety of natural habitats, including beach sand, coastal streams and sediments, riparian soils, and aquatic and terrestrial vegetation.
    • Determine the extent of occurrence and distribution of FIB in a range of environmental substrates (e.g., soil and sediments, beach sand, aquatic vegetation).
    • Determine whether FIB may grow in the environment under specific seasonal and nutrient conditions.
    • Develop more accurate analytical methods for enumerating FIB in environmental substrates using traditional microbiology and molecular methods.
  2. Examine new approaches to source identification at beaches using traditional microbiology and molecular techniques. Candidate organisms may include Bacteroides (human and bovine-specific markers), Catellicoccus sp. (gull-specific), FRNA coliphages, and selected human pathogens (e.g., Salmonella, enteric viruses).

Background & Justification
Fecal indicator bacteria (FIB), such as E. coli and enterococci, have been widely accepted as indicators of fecal (sewage) contamination for recreational waters worldwide [(7)]. Since FIB are found both in humans and warm-blooded animals, identifying their sources (e.g., human vs. nonhuman) remains a challenging task. Traditional culturing methods have limited applications in source identification, and thus, research efforts have been directed toward developing alternate approaches, popularly referred to as microbial source tracking (MST), that incorporate molecular and biochemical techniques for identifying, classifying, and partitioning contaminant sources in recreational waters. Several MST markers have shown promise in this regard: some specific examples include coliphage assays, human- and ruminant-specific Bacteroides markers, virulent genes for pathogens, and fluorescent whitening agents, FWA [(5, 8)]. While many of these markers have been tested across water types, generalizations are difficult because the nature, degree, and extent of contaminant sources seem to vary among beaches. For instance, watershed studies along southern Lake Michigan have shown that beaches are impacted by indicator bacteria from one or more contaminant sources: e.g., mostly non-point sources, such as riparian soils, stream water and sediments, and wildlife; both point- and nonpoint sources; and a mixture of endogenous sources derived at the beach itself (e.g., sand, shore birds, gulls) [(2, 9)]. Thus, beach managers need to understand all of the potential sources of contamination to their beaches so that remediation efforts are better coordinated and management strategies effectively implemented.

It is significant to note that in many instances, FIB vis-à-vis sources/substrates are not entirely independent of each other since interactions are common and dynamic [(2, 9-10)]. Some examples of such interactions include upland soil with stream bed; stream bed with surface water; streams/creeks with receiving beach water [(1)]. Because of the complexity in interactions between the various components, as in the case of watersheds that typically encompass soil, sediments, and stream water that directly influence the downstream beaches (sand, sediments, water, and associated vegetation), Whitman et al recommend that when examining the FIB source, flux, and context, the entire watershed and beach system be referred to as “beachshed,” a dynamic interacting system [(9)].

Growth of indicator bacteria in natural environments has been initially explored in research around the Great Lakes [(3-4, 6, 11)], but the conditions necessary to support growth have yet to be delineated. Fecal indicator bacteria require an abundant nutrient source and likely warm ambient temperatures. Eutrophic conditions in the Great Lakes are greatly limited spatially and temporally, but it has been postulated that fecal indicator bacteria may grow during bloom conditions, such as massive Cladophora growth. Determining the growth potential for indicator bacteria is thus necessary for understanding the nearshore dynamics and coastal processes contributing to net bacteria concentration [(9-10)].

Principal Investigator: Murulee Byappanahalli

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