7. Biodegradation Pathways Flashcards
Mineralization
- Complete breakdown or degradation by a microorgnaism of organic compounds into inorganic compudns
- Products: CO2 + water + energy (ATP) + biomass
Biotransformation
Transformation by a microorganism of an organic or inorganic compound into another organic compound or inorganic compound, respectively
Cometabolism
- The gratuitous (freely given) metabolic transformation of a substance by a microbe growing on another substrate.
- The cometabilized substrate is not incorporated into the microorganism’s biomass and the microorganism does not derive energy from the transformation of the substrate.
- Organism A does cometabolism. It has an enzyme that transforms the pollutant to a product but organism A doesn’t get a benefit from this
- Organism B comes along and uses the product to biodegrade the product into something innocuous and it gives itself energy
What is an example of cometabolism?
Cyclohexane is cometabolized in the presence of propane by M.vaccae, allowing for commensal growth of Pseudomonas on cyclohexane
How might you stimulate the biodegradation of cyclohexane?
You would introduce propane
When biodegraded, cyclohexane becomes cyclohexanol which is a mildly toxic solvent
Cometabolism of cyclohexane detailed
- M. vaccae cells have an enzyme to oxidize propane
- This enzyme also, by chance, oxidizes cyclohexane
- As M. vaccae cells have no use for cyclohexanol, this reaction does not benefit them
- The Pseudomonas species benefits because it can metabolize cyclohexanol, but cannot oxidize cyclohexane
- The M. vaccae cells co-metabolize cyclohexane in the presence of propane
- Note that cyclohexane degradation may not occur in the absence of propane, because expression of the M. vaccae enzyme may require propane for induction, and M. vaccae may require propane for growth
- → To stimulate biodegradation of cyclohexane: add propane (etc)
Biodegradation of hydrocarbons (5)
- Biodegradability of crude oil hydrocarbons, not surprisingly, depends upon molecular complexity
- Very complex compounds (long chain alkanes, complex polyaromatics, highly branched compounds) are recalcitrant
- These compounds are also quite inaccessible to microbes due to their low solubility in /miscibility with water, and the fact that many are solids at the low temperatures of that environment
- These compounds tend to remain at spill sites for many years in the form of insoluble tars, asphalts, and oil mousse, on the surface but even more just under the surface
- The lightest alkanes are toxic to microbes but tend to volatilize quickly
BTEX
Benzene, toluene, ethylbenzene, xylene
PAHs: smaller ones effect on solubility
Smaller ones are more soluble in water
PAHs: size and biodegradation
The bigger they are the harder they are to degrade
4 major steps of mineralization of an alkane via oxidation
- Oxidation of an alkane to a primary alchohol via a monooxygenase or a dioxygenase (requires O2)
- Formation of a fatty acid (requires O2)
- Beta-oxidatin of fatty acids to acetyl-CoA
- Oxidation of acetyl-CoA via the TCA cycle and the glyoxylate shunt
Bioremediation of Aromatics and PAHs (3 steps)
- Typically, aromatic compounds are first oxidized to catechol under aerobic conditions
- The enzymes responsible (monooxygenases, dioxygenases) require molecular oxygen (O2)
- Next step is the cleavage of the catechol phenolic ring structure (aka breaking the ring)
Monooxygenases (3 points)
- One oxygen atom is transferred to the substrate, and the other is reduced, yielding water
- i.e., Methane Monooxygenase (MMO) oxidizes CH4 to CH3OH
- Alkane monooxygenase oxidizes alkanes to alcohols
Dioxygenases (2 points)
- Both oxygen atoms are transferred to the substrate
- i.e., catechol dioxygenases oxidizes catechol (NB two O atoms) to cis, cis-muconic acid (NB four O atoms)
Aromatic hydrocarbon ring cleavage (2 pathways to do this)
- Ortho cleavage: breaking between the OH groups
- Meta cleavage: breaking beside one of the OH groups
