Further description:-  Microbiology 

Glossary Entry
inform about Microorganism and their effects on contaminant degradation in soil and groundwater 




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.



Redox equivalents

Carbon source


(energy generation by light)


(oxidation of organic compounds)


(carbon from organic compounds)


(energy generation by chemical oxidation)


(oxidation of inorganic compounds)


(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: I. John Wiley & Sons. New York, Chichester, Weinheim, Brisbane, Singapore, Toronto.


The University of Minnesota Biocatalysis/Biodegradation Database: biodegradation pathways for most environmental relevant pollutants





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