Biomedical Engineering Reference
In-Depth Information
12.3.3 The Much-Maligned Microcosm and the Need
for Activity-Based Tests
A microcosm is a small, representative system serving as an analogy to a larger system in
constitution, configuration or development. The word is derived originally from Greek,
meaning “little world” ( micros kosmos ).
Microcosms are frequently used to represent or mimic the subsurface environment and the
interplay of physical, chemical and microbial activity within. Their design ranges from very
simple batch microcosms, consisting of subsurface material and groundwater in a sealed bottle,
to more complex flowing columns and increasingly larger tank systems (Da Silva et al., 2006 ;
Reeves et al., 1999 ). Microcosms can be designed to mimic as closely as possible the in situ
environmental conditions or can be used to explore the effects of defined perturbations, such as
the addition of specific nutrients, donors or acceptors, or the modification of parameters such
as pH, redox or temperature.
The conditions imposed on the microcosm will define the niche and therefore which
microbes grow, and careful planning of the imposed enrichment conditions is critical. Micro-
cosm studies have been the source of practically all contaminant-degrading enrichment cultures
and isolates. From the perspective of subsurface remediation, microcosms prepared with
material from long time, historically-impacted environments have been the most successful.
In such environments, the native microbes have been chronically exposed to the contaminants,
and have had a much longer time to adapt to prevailing contaminants. Microcosms and the
subsequent enrichment cultures derived from them continue to be a wonderful resource for
discovering novel microbial activities.
The microcosm study, particularly the relatively rapid and easily parallelizable batch
microcosm study, has long been a powerful diagnostic and decision tool in bioremediation.
But recently, with the advent of molecular biological tools (MBTs) (MBTs - DNA based
detection) to detect biomarkers correlated with activity, the use of the microcosm has been
sidelined. The attraction to MBTs is clear. The analyses are easily done on extracted ground-
water, as with other chemical analyses, and turnaround times can be less than a few weeks.
Costs are comparable to chemical analyses too.
However, MBTs are only as good as what you know, as they target only known organisms
and genes. Moreover, DNA-based assays, which are by far the most common owing to their
ease, do not provide quantitative data on rates. RNA-based methods are problematic as well, as
it is difficult to correlate transcript levels with expression and rate. Comparatively, activity-
based assays, such as the microcosm, or derivatives thereof, provide valuable kinetic informa-
tion without the need for any a priori knowledge of the system.
The lack of a requirement for such a priori information is one of several advantages
microcosm studies have over the newer MBT techniques. Specifically, microcosms provide
valuable information for determining:
Which contaminants at a site can be degraded at all
The products of degradation
Relative rates - or rates normalized to some total biomass estimation
Matrix effects of the subsurface on degradation
Cocontaminant effects
If bioaugmentation is needed
If inhibitors are present
Which electron donors, nutrients, and electron acceptors are most effective
What conditions can be changed to enhance activity (e.g., pH, temperature, and redox).
Search WWH ::




Custom Search