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Chapter 9 : Microbial Source Tracking

Authors: Valerie J. Harwood1, Ryu Hodon2, Jorge Santo Domingo3
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Affiliations: 1: Department of Integrative Biology, University of South Florida, Tampa, FL 33620; 2: ORD/NRMRL/WSWRD/MCCB U.S. Environmental Protection Agency, Cincinnati, OH 45268; 3: ORD/NRMRL/WSWRD/MCCB U.S. Environmental Protection Agency, Cincinnati, OH 45268
Content Type: Monograph
Publication Year: 2011

Category: Applied and Industrial Microbiology; Environmental Microbiology

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Abstract:

This chapter uses the term microbial source tracking (MST) to collectively refer to a number of methods developed to specifically determine the sources of fecal contamination and/or fecal indicator bacteria in water, because the chapter focuses on the use of microbial-based assays, rather than analyzing for chemical compounds such as coprostanol or host animal genes (i.e., mitochondrial genes). The chapter outlines the scientific questions and regulatory needs that have led to the burgeoning growth of this area of environmental microbiology. A section discusses some of the new tools and approaches that can be used to examine environmental samples and how they can be used in tracking sources of fecal pollution. Nucleic acid microarrays can be used to screen for the presence of DNA or RNA (i.e., expression arrays) obtained from pure cultures or from complex microbial communities. The power of multilocus sequence typing (MLST) in combination with metagenomic sequencing data was illustrated in recent application in which the presence of -like bacteria was confirmed by comparing typing data with metagenomic sequences from the Sargasso Sea. A promising technology in source tracking and in microbial ecology in general, is called hierarchical oligonucleotide primer extension. This fingerprint technique uses combinations of hierarchical primers to target different bacteria within a phylogenetic group.

Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
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Microbial Source Tracking
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Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
/content/10.1128/9781555816865.ch09.ch09fig01
FIGURE 1
Some factors that influence the composition of the microbiota of the gastrointestinal tract of host species. Some of these factors are constrained by the host anatomical and physiological conditions and the diet and dietary supplements such as antibiotics, whereas others involve interactions between the different members of the resident microbiota and the host.
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10.1128/9781555816865/f0190-01.gif
Image of FIGURE 1
FIGURE 1

Some factors that influence the composition of the microbiota of the gastrointestinal tract of host species. Some of these factors are constrained by the host anatomical and physiological conditions and the diet and dietary supplements such as antibiotics, whereas others involve interactions between the different members of the resident microbiota and the host.

Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
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/content/10.1128/9781555816865.ch09.ch09fig02
FIGURE 2
Examples of the fecal sources contributing to the pollution of environmental waters. The sources can range from anthropogenic impacts such as sewage and septic systems to agricultural waste and wild animals. In some cases, multiple sources can impact a given water body, increasing complexity of MST efforts.
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10.1128/9781555816865/f0192-01.gif
Image of FIGURE 2
FIGURE 2

Examples of the fecal sources contributing to the pollution of environmental waters. The sources can range from anthropogenic impacts such as sewage and septic systems to agricultural waste and wild animals. In some cases, multiple sources can impact a given water body, increasing complexity of MST efforts.

Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
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/content/10.1128/9781555816865.ch09.ch09fig03
FIGURE 3
Source tracking methods can be divided into two general groups: library-dependent methods and library-independent methods. Molecular techniques are used in both general methods and, in some of the library-independent methods, the first step involves a culture/enrichment step.
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10.1128/9781555816865/f0196-01.gif
Image of FIGURE 3
FIGURE 3

Source tracking methods can be divided into two general groups: library-dependent methods and library-independent methods. Molecular techniques are used in both general methods and, in some of the library-independent methods, the first step involves a culture/enrichment step.

Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
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FIGURE 4
MST method development from source material to target identification using emerging technologies, followed by assay development/validation, and eventually field application.
10.1128/9781555816865/f0203-01_thmb.gif
10.1128/9781555816865/f0203-01.gif
Image of FIGURE 4
FIGURE 4

MST method development from source material to target identification using emerging technologies, followed by assay development/validation, and eventually field application.

Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
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Tables

Microbial Source Tracking
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Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9
/content/10.1128/9781555816865.ch09.ch09tab01
TABLE 1
Examples of fecal pathogens and their fecal sources
Generic image for table
TABLE 1

Examples of fecal pathogens and their fecal sources

Citation: Harwood V, Hodon R, Santo Domingo J. 2011. Microbial Source Tracking, p 189-216. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch9

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