Geoscience Reference
In-Depth Information
New approaches to next-generation DNA-sequencing technologies offer
the promise of characterizing healthy water by ensuring the absence of harmful
biotic organisms, even rare ones (see Appendix C for background information
on genomics tools and technologies). Just as the human microbiome studies are
examining the diversity and ecology of microorganisms in the intestinal tract,
DNA-sequencing methods are being used to explore the water microbiome in
polluted, pristine, and unique environments, although finding rare microbial
populations that will exhibit genetic characteristics with the potential for harm to
humans is difficult. Metagenomics of the wastewater system, and in particular
the viral genome, provide insight into the complex world of water microbiotas,
but is only being used for exploration. Current efforts are being spent in devel-
oping methods and generating large amounts of data (Table 3-2); the methods
are able to identify which microorganisms (including potentially pathogenic
organisms) are present, but their viability and functional activity are often not
known. Finally, genomic data have not been used much to inform microbial risk
assessment. In the next decade, environmental microbiome studies and data will
need to move toward sophisticated data interpretation and modeling, and sub-
stantial investment in bioinformatics will be necessary. With the growing under-
standing of the ecosystem microbiome and its interaction with human health and
the environment, it is becoming evident that the microbiome plays an important
role in modulating health risks posed by broader environmental exposures. Un-
derstanding such interactions will have important implications for understanding
individual and population susceptibility and the observed variability in risks
posed by environmental exposures.
Other recent advances that are facilitating the use of molecular tools in-
clude new techniques for increasing sample concentration—such as ultrafiltra-
tion, continuous filtration, and new types of filters—for improved recovery and
automated extraction of nucleic acids with less contamination, less inhibition,
and more rapid throughput (Hill et al. 2005; Srinivasan et al. 2011). New quanti-
tative PCR approaches for monitoring the viability of pathogens of concern are
of particular interest, and several approaches show some promise. Such dyes as
ethidium monoazide and propidium monoazide have been used to distinguish
between live cells and heat-killed cells, but the dyes are not able to penetrate
apparently killed cells when applied to disinfected treated sewage samples, so
the signals that are produced through quantitative PCR methods are comparable
with counts made before and after disinfection with or without use of the dyes
(Varma et al. 2009; Srinivasan et al. 2011). More work is needed to address the
possible presence of viable but nonculturable cells in disinfected effluents. An
approach to examining viability associated with bacteria is to use quantitative
PCR methods to target the precursors of ribosomal RNA (rRNA). That was done
to quantify viable cells of
Aeromonas
and mycobacteria in water (Cangelosi et
al. 2010) and showed promise for both saltwater and freshwater and for post-
chlorination monitoring. Those types of methods will require verification in the
monitoring of disinfected drinking water and wastewater. There may be a need
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