7. Biodegradation Pathways

Question 1

Mineralization

Answer 1

• Complete breakdown or degradation by a microorgnaism of organic compounds into inorganic compudns
• Products: CO2 + water + energy (ATP) + biomass

Question 2

Biotransformation

Answer 2

Transformation by a microorganism of an organic or inorganic compound into another organic compound or inorganic compound, respectively

Question 3

Cometabolism

Answer 3

• 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

Question 4

What is an example of cometabolism?

Answer 4

Cyclohexane is cometabolized in the presence of propane by M.vaccae, allowing for commensal growth of Pseudomonas on cyclohexane

Question 5

How might you stimulate the biodegradation of cyclohexane?

Answer 5

You would introduce propane

When biodegraded, cyclohexane becomes cyclohexanol which is a mildly toxic solvent

Question 6

Cometabolism of cyclohexane detailed

Answer 6

• 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)

Question 7

Biodegradation of hydrocarbons (5)

Answer 7

• 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

Question 8

BTEX

Answer 8

Benzene, toluene, ethylbenzene, xylene

Question 9

PAHs: smaller ones effect on solubility

Answer 9

Smaller ones are more soluble in water

Question 10

PAHs: size and biodegradation

Answer 10

The bigger they are the harder they are to degrade

Question 11

4 major steps of mineralization of an alkane via oxidation

Answer 11

1. Oxidation of an alkane to a primary alchohol via a monooxygenase or a dioxygenase (requires O2)
2. Formation of a fatty acid (requires O2)
3. Beta-oxidatin of fatty acids to acetyl-CoA
4. Oxidation of acetyl-CoA via the TCA cycle and the glyoxylate shunt

Question 12

Bioremediation of Aromatics and PAHs (3 steps)

Answer 12

1. Typically, aromatic compounds are first oxidized to catechol under aerobic conditions
2. The enzymes responsible (monooxygenases, dioxygenases) require molecular oxygen (O2)
3. Next step is the cleavage of the catechol phenolic ring structure (aka breaking the ring)

Question 13

Monooxygenases (3 points)

Answer 13

• 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

Question 14

Dioxygenases (2 points)

Answer 14

• 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)

Question 15

Aromatic hydrocarbon ring cleavage (2 pathways to do this)

Answer 15

• Ortho cleavage: breaking between the OH groups
• Meta cleavage: breaking beside one of the OH groups

Question 16

Which ring cleavage pathway is favored?

Answer 16

Ortho (between the OH groups)

Question 17

Diffrence between fungi (and other eukaryotic cells) and bacteria in the way they oxidize aromatic compounds

Answer 17

• Fungi and other eukaryotic cells form trans-diols
• Bacteria form cis-diols