Microbiology
1. Summary
Microbiology is the study of microorganisms,
comprising prokaryotes (eubacteria,
archaea)
and eukaryotes (fungi, algae, protists). Microorganisms are ubiquitous and degrade numerous
pollutants, thus responsible for the most important Natural Attenuation (NA)
and Enhanced Natural Attenuation (ENA) process. The use of different electron
acceptors during pollutant degradation in contaminated lands lead to the
development of different redox zones, underlining the
importance of anaerobic microbial processes for NA or ENA.
2. Microorganisms
Microorganisms are an
heterogeneous group of organisms normally detectable for the human eye only by
means of magnifying instruments (microscops). Phylogenetically, prokaryotes, being the oldest known form
of life and comprising the domains eubacteria and archaea, are separated from eukaryotes, including fungi,
algae and protists. Microorganisms
can be found almost everywhere in the earth’s atmosphere, hydrosphere and
lithosphere. They are the driving forces in the global cycling of biologically
essential elements, e.g. carbon, nitrogen and sulfur.
3. Microorganisms
in contaminated lands
From an anthropogenic view, the most important function of microorganisms in contaminated lands is to degrade pollutants,
which is in general the basis for Natural Attenuation (NA) and Enhanced Natural
Attenuation (ENA) remediation technologies. Almost every natural occurring
organic compound can be degraded by microorganisms.
Even xenobiotic organic substances are degradable,
sometimes after a certain length of time, due to co-metabolic (see below)
reactions or rearrangements in the genome of microorganisms,
leading to the evolution of new degradation pathways.
3.1 Metabolic types of microorganisms in contaminated lands
Pollutants in contaminated lands can be degraded by numerous metabolic
pathways of microorganisms. The following overview describes
some terms often used in the context of biodegradation.
·
Mineralisation vs. transformation or co-metabolism
Mineralisation means the complete oxidation of organic
compounds to inorganic end products (e.g. carbon dioxide, ammonia); toxic
organic compounds are, therefore, always detoxified by this process. Mineralisation is usually linked to microbial growth, since
microorganisms gain the maximal energy of a substrate
by complete oxidation. In contrast, transformation or co-metabolism
(a somewhat not precisely defined term) both mean an incomplete degradation of
compounds, leading to the (sometimes transient) accumulation of intermediates.
These intermediates can be more toxic ore less toxic than the original
substances. Transformation and co-metabolism are based on incomplete or partly
inhibited microbial degradation pathways and must not be linked to microbial
growth.
·
Aerobic vs anaerobic degradation
Microorganisms are called aerobic when
using oxygen as terminal electron acceptor (TEA). Since oxygen is the
thermodynamically most favourable TEA, aerobic microorganisms
usually grow fast and reach high growth yields. Besides oxygen, microorganisms can use a lot of alternative terminal
electron acceptors, e. g. nitrate, sulfate, carbon
dioxide, ferric iron; these organisms are called in general anaerobes.
Anaerobes are almost exclusively prokaryotes. Figure 1 illustrates some electron
accepting processes relevant in contaminated lands and the respective energy
released during electron transfer.
Figure
1: Redox potential of different terminal electron
accepting reactions (after Wiedemeier et al., 1999)
Complicating, it is possible that the same microorganism
can use, dependent from the environmental conditions, more than a single
electron acceptor; if one of these electron acceptors is oxygen, these
organisms are called facultative aerobes or facultative anaerobes (indeed,
both terms mean the same). Many microorganisms are
true anaerobes, thus not able to use oxygen as terminal electron acceptor,
often even killed by the presence of low amounts of oxygen.
Additionally,
oxygen is often required already in the degradation pathways of the pollutants,
since these are usually activated by microbial enzymes called mono- or dioxygenases which introduce oxygen into the molecules.
That is the reason why the anaerobic degradation pathway for a distinct
compound is always completely different from the respective aerobic degradation
pathway - under anoxic conditions, activation
reactions with oxygen are simply not possible.
·
Types of metabolism
Although the metabolic types of microorganisms
are highly divers, the fundamental principles can be illustrated in a simple
scheme (which is in fact guilty for all forms of life on earth), which might be
helpful to learn by heart (Table 1). In the left column, reactions for gaining
energy are listed, in the middle column those for gaining redox
equivalents, in the right column those for gaining carbon. A human being lives
therefore chemo-organo-heterotrophically, as also
most pollutant degrading microorganisms in
contaminated lands. Microorganisms can carry out
every possible combination illustrated in Table 1.
|
Energy |
Redox equivalents |
Carbon source |
Photo-(energy generation by light) |
Organo-(oxidation of organic compounds) |
Heterotroph(carbon from organic compounds) |
Chemo-(energy generation by chemical oxidation) |
Litho-(oxidation of inorganic compounds) |
Autotroph(carbon from carbon dioxide) |
Table
1: Fundamental metabolic principles of microorgansims
3.2 Redox zones
In plumes, after a certain time different redox
zones develop, due to the use and consumption of different electron
acceptors by microorganisms. Until some years ago, it
was believed that the electron acceptors used follow a succession strongly
determined by thermodynamic rules: first consumption of all available oxygen,
next consumption of all available nitrate, followed by consumption of the next
available, most energy releasing electron acceptor (see Figure 1). Such a
succession would end in a plume, in which the centre is dominated by carbon
dioxide reduction (methanogenesis). Sulfate reduction zones and iron reduction zones would
develop in between the centre and the fringes of the plume, whereas aerobic and
nitrate reducing processes would exist only in small zones at the fringes. The
outline of such an assumption is that the developing redox
zones would be all more or less clearly separated by each other. Today, there
are indications that different electron acceptors like ferric iron and sulfate could be indeed reduced simultaneously in
proximity, leading to redox zones not as clear
separable as believed before. Without doubt, however, play aerobic processes in
older plumes only at the plume fringes a role, thus underlining the general
importance of anaerobic degradation processes for NA and ENA.
3.3 Nutrients
Microorganisms need nutrients for growth.
Macro-nutrients are those which are needed in relatively high concentrations;
the most important are nitrogen (in form of nitrate, ammonia or dinitrogen), sulfur (in form of sulfate) and phosphorous (in form of phosphate).
Micro-nutrients are as well essential, but needed only in trace amounts, e.g.
magnesium, potassium, cobalt. Normally, in contaminated lands, nutrients should
be available in excess. However, if an aquifer or soil is contaminated with
pollutants in high concentrations, a shortage of one ore more nutrients could
come true during pollutant degradation, leading to reduced or collapsing
degradation reactions.
4. Literature and links
Madigan, M. T., Martinko J. M., Parker, J.
(2003): Brock - Biology of microorganisms, 10th ed.,
Prentice Hall Inc., ISBN 0-13-085264-3.
Wiedemeier, T. H., Rifai, H.
S., Newell, C. J., Wilson, J. T. (1999): Natural attenuation of fuels and
chlorinated solvents in the subsurface. In:
The
http://umbbd.ahc.umn.edu/
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