The last time most people probably thought about metabolism was to comment that theirs is different than it used to be! For environmental engineers, however, the metabolic processes of in situ microorganisms can shape daily on-site activities and workflows.
Bioremediation – the utilization of microorganisms to degrade contaminants at impacted sites – is a staple strategy in the environmental sector. Because biodegradation is so complex, it is easy for decision-makers to simplify the myriad metabolic pathways undertaken at a single site to the statement, “The microbes degrade the contaminant.” While this is true, diving in a bit deeper to understand how that biodegradation takes place empowers site managers to both conceptualize the effects of site conditions and treatments on the degradation pathway and choose the appropriate analytical tools to guide their decisions.
Below, we discuss 2 primary mechanisms of contaminant biodegradation: the compound as a carbon source and the compound as an electron acceptor. The specifics of a metabolic pathway vary by contaminant and often by microorganism, but the intent of the below descriptions and diagrams is to offer a conceptual framework for the application of Stable Isotope Probing analysis. As such, the diagrams and statements below are very simplified and are not demonstrative of specific metabolic pathways.
An Introduction to SIP
Stable Isotope Probing (SIP) is an innovative method that combines MI’s proprietary Bio-Trap® technology with specially synthesized carbon-13 (13C) compounds to prove the occurrence of contaminant biodegradation at sites undergoing remediation. Because 13C is uncommon in nature, contaminants made with 13C provide “tracers” that can be followed to the end products of microbial metabolism to prove that biodegradation of the contaminant of concern is occurring at the site.
For more information on SIP analysis, see:
The Contaminant as a Carbon Source
Just like us humans, when microbes “eat” a compound, they can use that “food” for energy or growth. Microbes transform “food” into energy via cellular respiration. Briefly, a cell takes in a compound such as a carbohydrate or protein and transforms that into pyruvate and later acetyl~S-coenzyme A (or a similar molecule). Acetyl~coA then enters the Kreb’s Cycle, a series of reactions that generates some energy and decarboxylates Acetyl~coA to carbon dioxide (CO2). Finally, some bacteria proceed to oxidative phosphorylation, a series of oxidation-reduction reactions that drive ATP production and require a terminal electron acceptor.
For many petroleum hydrocarbon contaminants, the biodegradation pathway begins with the microbe taking in a contaminant molecule and transforming it into one of the intermediaries required for the Kreb’s Cycle (2). This is the crux of why SIP can be used for these compounds. Because the reactions of the Kreb’s Cycle transform the contaminant into various products and release CO2, the 13C from the compound supplied for SIP analysis can be identified in that CO2.
Similarly, the same intermediary compounds used in the Kreb’s Cycle also play a major role in fatty acid synthesis (1). Fatty acids can then be incorporated into phospholipid fatty acids (PLFAs), which are a major component in bacterial cell membranes (1). Through this pathway, contaminants are transformed and eventually incorporated into microbial membranes and thus bacterial biomass, allowing the 13C introduced via SIP analysis to be detected through PLFA testing.
The diagram below summarizes these processes, and the locales of 13C detection in SIP analysis are denoted in red.

Contaminant as an Electron Acceptor
Reduction-oxidation (redox) reactions are fundamental to the natural world and, in the simplest terms, involve the transfer of electrons from one atom or molecule to another. When these reactions are mediated by bacteria, the electrons from the electron donor molecule are moved through the microbe’s electron transport chain as part of cellular respiration’s final stage to generate energy (ATP).
Because these biodegradation pathways do not involve the direct metabolism of the contaminant and because the carbon atoms in the contaminant molecule are not “touched” in any way, SIP analysis cannot be used to prove biodegradation occurred for those contaminants.
As an example, the diagram below shows the reductive dechlorination pathway for chlorinated ethenes. These reactions are believed to take place on the cell membrane (3, 4), so it is useful to oversimplify and think of these reactions as “external” to the bacteria cell. When we think of these reactions as external as opposed to the “internal” reactions associated with direct metabolism pathways as described above, it is easier to understand how SIP cannot be used for certain contaminants that are not “brought in” to the cell. Similarly, because these reactions for chlorinated ethenes do not involve the carbon in the molecules, the 13C supplied through SIP analysis cannot be tracked to the end products of microbial metabolism.

If you would like to know if SIP analysis is applicable to the contaminants at your site, reach out to our Project Success team here:

Written by: Hannah Ward, Project Manager