1. IntroductionThe use of integrate

1. Introduction
The use of integrated river basin management planning is
necessary to mitigate the impacts of climate change and to
protect water resources. In Europe, this is being implemented
through the ‘Programs of Measures’ as outlined in
Article 11 of Directive 2000/60/EC, the Water Framework
Directive. Climate change will undoubtedly influence water
quality in rivers, lakes and marine waters used for drinking
water abstraction, recreational activities, shellfish harvesting
and assimilation of point and diffuse fluxes of human
and livestock effluents. Thus, the risk profile and treatment
interventions necessary for sewage and potable waters
must be changed. The fourth assessment report of the
Intergovernmental Panel on Climate Change (IPCC) noted
that higher temperatures, changes in precipitation regimes
and more frequent weather-related disasters are primary
changes that represent risks for agriculture, food, and
particularly water supplies. Moreover, increasing urban
expansion and associated intensification of farm production
are increasing microbial loads, which are then discharged
into receiving waters worldwide. Achieving legal water
quality criteria will, therefore, require intelligent and integrated
application of sustainable treatment and urban
drainage technologies (SUDs), upgrade of wastewater
treatment plants (WWTP), enhanced storm water retention
facilities, and application of agricultural best management
practices (BMPs) designed to reduce diffuse pollution from
livestock farming.
There is increasing concern regarding the levels of fecal
pollution in surface waters due to point-source discharges
from community sewage treatment plants and livestock
concentrations derived from slaughterhouse discharges
(Collins et al., 2005; Jamieson et al., 2004). Also, non-point
diffuse microbial pollution may originate from direct fecal
voiding by grazing livestock, manure spreading or urban surface
water runoff, which can derive from roof and road
surfaces contaminated with avian, domestic and wild animal
feces and also from cross-connections to urban sewerage
system, all of which can exhibit high microbial loads (Llopart-
Mascaro´ et al., 2010; Brownell et al., 2007; Bercu et al., 2011).
The identification of fecal contamination sources in water
using specific markers is a key step for good management and
remediation protocols.
Microbial Source Tracking (MST) encompasses a group of
methodologies that aim to identify and, in some cases,
quantify the dominant sources of fecal contamination in the
environment, particularly in water resources (Field et al.,
2004; Fong and Lipp, 2005). MST plays a very important
role in informing remediation strategies directed against
specific pollutant sources. Molecular markers used for MST
are target sequences in host-associated microorganisms or
sequences derived directly from the host. These can come
from prokaryotes, eukaryotes and viruses. Widely-used
human and animal-associated markers have been identified
in the order Bacteroidales (Bernhard and Field, 2000a, b)
and other bacteria. Polymerase chain reaction (PCR) assays
have been developed and validated for markers of fecal
contamination from humans and a diversity of animals
(reviewed in Roslev and Bukh, 2011). Although these molecular
markers represent interesting methods for MST,
they do have significant limitations. For example, (i) there is
a lack of absolute host specificity among human- and
animal-associated microbial markers; (ii) there is a lack of
temporal stability of some host-associated microbial
markers in different host groups and (iii) non-fecal sources
of markers potentially exist (Roslev and Bukh, 2011;
Stapleton et al., 2009). The use of highly host specific,
ubiquitous and stable MST markers that produce persistent
excretions in their human or animal hosts could overcome
these limitations.
In recent years, many studies have examined human
adenovirus (HAdV) and JC polyomavirus (JCPyV) as human
fecal indicators, as they are persistently excreted by infected
humans both with and without clinical symptoms in the feces