Biomedical Engineering Reference
In-Depth Information
To date, few MBTs can address these confounding factors directly. In fact, a combination
of MBTs and microcosms is the most powerful diagnostic choice, and is an ongoing area of
research to further validate cheaper molecular (i.e., MBT) analyses. A related research need
and a worthwhile goal is to develop a mechanism to carry out a rapid activity-based assay for a
given process, e.g., dechlorination of vinyl chloride (VC). A simple system, where one could
take a groundwater sample, add a reagent and measure color formation with time, or a
similarly straightforward assay, would allow determination of VC dechlorination rate normal-
ized to a total biomass or protein measurement.
An assay connecting dechlorination rates directly to biomass would be a powerful tool.
Such measurements are difficult given the typically low biomass concentrations in ground-
water, but should be possible with sensitive detection chemistry. Such assays are similar to
common measurement techniques used in marine and freshwater sediment ecosystems, where
assays to measure methane production rates, sulfate-reduction rates and CO
2
fixation rates are
commonplace. Such rates also would be highly useful input for groundwater and transport
models, increasing the informative nature of this hypothetical assay.
Microcosms and the Need for Activity-Based Tests
Microcosm studies and other direct measurements of microbial activity are the best and most
definitive way to understand complex processes at a given site.
More time-consuming but more informative than simple measurements of chemical
biological markers.
Activity-driven assays do not rely on pre-existing knowledge of microbial identity.
Microcosms are essential to enriching novel microbes.
Microcosms can more readily detect combined abiotic and biotic processes, cometabolism, presence
of inhibitors, and substrate interactions and interferences.
12.3.4 The Enrichment Paradox
When setting up microcosms and subsequent enrichment cultures to explore the biodegra-
dation of a certain contaminant of interest, a researcher is guided by the reductionist principle,
to simplify the system to its essential components. Multiple transfers of enrichment culture into
defined medium are designed to weed out non-essential organisms while maintaining targeted
activity, often while striving for an “isolate” of the organism of interest. However, such
selection techniques, while leading to decreased culture complexity, often also lead to
decreased degradative capacity and decreased culture robustness. The latter are critical com-
ponents of effective bioaugmentation cultures, and thus bioaugmentation and basic research
needs (i.e., enrichment) can be at odds in this regard.
As an example, the dechlorination of 1,1,2-trichloroethane (TCA) requires at minimum two
distinct dechlorinating organisms, a
Dehalobacter
that dihaloeliminates 1,1,2-TCA to VC, and a
Dehalococcoides
that dechlorinates VC to ethene. Depending on the enrichment conditions,
one or the other, or both of these organisms can be maintained in an enrichment culture
(Grostern and Edwards,
2006
) (see Table
12.1
). Enrichment on 1,1,2-TCA supported both
organisms. Enrichment cultures fed both 1,1,2-TCA and 1,2-dichloroethane (1,2-DCA) selected
for
Dehalobacter
at the expense of
Dehalococcoides
. Enrichment on 1,2-DCA and a complex
donor interestingly also supported both
Dehalococcoides
and
Dehalobacter
, as each of these
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