waters that do not meet designated use criteria as determined by high densities of
fecal indicator bacteria (FIB). The main area of research activity in MST focuses on
the identification of source-specific genetic markers that can be used to detect
contributions from different hosts such as humans, livestock, and wildlife. However, a variety of other accessible approaches can also be used including detailed
investigations of the watershed and infrastructure, chemical tracers and leak tests,
and increased FIB sampling. This chapter can serve as a guide for decision-making
on where, when, and how to deploy MST. Included are discussions of the main
drivers of MST and how these have shaped the development of past and present
methodological approaches, plus current research initiatives such as community
analysis that could usher in yet another new and improved methodological basis for
the entire field of MST. Finally, a tiered system is presented as a recommended
means to navigate the multiple options for MST analyses that will assist the reader
in how best to use MST within the context of more traditional approaches.
Keywords DNA-based source markers • Fecal indicator bacteria • Fecal pollution •
Microbial community analysis • Microbial source tracking • Recreational water
quality
1 Introduction
The new and expanding field of microbial source tracking (MST) typically involves
sensitive and specific DNA‐based methods that use either presence–absence polymerase chain reaction (PCR) or quantitative PCR (qPCR) to detect and quantify
particular gene fragments that have been found to be relatively source specific (e.g.,
humans, cattle, birds, dogs). These gene fragments are often referred to in the MST
literature as source-specific “markers” [1–3] and frequently exist in the bacterial
genus Bacteroides. Two recent endeavors by the MST community are available that
cover the entire field in detail. The first was a comprehensive book on MST that
included 26 chapters written by 74 authors and coauthors representing 17 countries
and demonstrated the development and application of MST at the international
level [4]. The second was the Source Identification Protocol Project (SIPP), undertaken to identify the best DNA-based methods from 41 that have been developed
within approximately the past decade. This large undertaking involved 27 labs and
resulted in a series of 12 articles published in a special edition of Water Research
[5]. In addition, the SIPP study generated a fecal source identification guidance
manual that framed MST within the context of more conventional and less expensive methodologies and presented a tiered approach for using different methods in a
step-wise and cost-effective manner [6]. This chapter will summarize the lessons
learned within these three key documents, supplemented by recent publications, to
provide practitioners and water quality managers with advice on when, where, and
how to best use MST.
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B. Badgley and C. Hagedorn
fecal indicator bacteria (FIB). The main area of research activity in MST focuses on
the identification of source-specific genetic markers that can be used to detect
contributions from different hosts such as humans, livestock, and wildlife. However, a variety of other accessible approaches can also be used including detailed
investigations of the watershed and infrastructure, chemical tracers and leak tests,
and increased FIB sampling. This chapter can serve as a guide for decision-making
on where, when, and how to deploy MST. Included are discussions of the main
drivers of MST and how these have shaped the development of past and present
methodological approaches, plus current research initiatives such as community
analysis that could usher in yet another new and improved methodological basis for
the entire field of MST. Finally, a tiered system is presented as a recommended
means to navigate the multiple options for MST analyses that will assist the reader
in how best to use MST within the context of more traditional approaches.
Keywords DNA-based source markers • Fecal indicator bacteria • Fecal pollution •
Microbial community analysis • Microbial source tracking • Recreational water
quality
1 Introduction
The new and expanding field of microbial source tracking (MST) typically involves
sensitive and specific DNA‐based methods that use either presence–absence polymerase chain reaction (PCR) or quantitative PCR (qPCR) to detect and quantify
particular gene fragments that have been found to be relatively source specific (e.g.,
humans, cattle, birds, dogs). These gene fragments are often referred to in the MST
literature as source-specific “markers” [1–3] and frequently exist in the bacterial
genus Bacteroides. Two recent endeavors by the MST community are available that
cover the entire field in detail. The first was a comprehensive book on MST that
included 26 chapters written by 74 authors and coauthors representing 17 countries
and demonstrated the development and application of MST at the international
level [4]. The second was the Source Identification Protocol Project (SIPP), undertaken to identify the best DNA-based methods from 41 that have been developed
within approximately the past decade. This large undertaking involved 27 labs and
resulted in a series of 12 articles published in a special edition of Water Research
[5]. In addition, the SIPP study generated a fecal source identification guidance
manual that framed MST within the context of more conventional and less expensive methodologies and presented a tiered approach for using different methods in a
step-wise and cost-effective manner [6]. This chapter will summarize the lessons
learned within these three key documents, supplemented by recent publications, to
provide practitioners and water quality managers with advice on when, where, and
how to best use MST.
268
B. Badgley and C. Hagedorn