Lecture 5: biodegradation

Sweet spot for bioremediation

overlab between matrix, contaminant, and organism

C + G rich microbes

arthrobacter, rhodococcus

Petroleum biodegrading psychrophiles

Rhodococcus

biotransformation

microbe transforms organic/inorganic compound into different compound

cometabolism

gratuitous metabolic transformation of substance by microbe growing on another substrate, does not use the substrate for energy or biomass

M vaccae

metabolises propane and accidentally cyclohexane (toxic) into cyclohexanol (less toxic)

pseudomonas

Consumes cometabolized cyclohexanol and makes energy

cyclohexane

nonpolar solvent in chemical industry, produces adipic acid and caprolactam both used for nylon production, is toxic

recalcitrant hydrocarbons

very complex, long Chan alkanes, complex polyaromatics, highly branched compounds, inaccessible to microbes and low solubility

tars, asphalts, oil mousse

recalcitrant hydrocarbons

subterminal alkane biodegradation

cleaves subterminal carbon in compound as first mineralization step

terminal alkane biodegradation

cleaves terminal carbon in compound as first mineralization step

Alkane mineralization step 1

oxidation of alkane to primary alcohol by mono or di oxygenase

alkane mineralization step 2

formation of fatty acid (requires o2)

alkane mineralization step 3

ß-oxidation of fatty acids to acetyl-CoA

alkane mineralization step 4

oxidation of acetyl-CoA in TCA cycle and glyoxylate shunt

complex aromatic compound biodegradation

oxidezed to catechol in aerobic conditions by mono or dioxygenases then the ring is cleaved

Catechol ortho cleavage

cleaved between the two OH groups, leads to more direct pathway for use in TCA Cycle and cell

Catechol meta cleavage

cleaved beside OH group, leads to more complex degradation needed, not direct pathway to TCA cycle

Monooxygenase

one oxygen atom transferred to substrate and other reduced to water

dioxygenase

both oxygen atoms transferred to substrate

PAHs degradation by fungi

cytochrome p450/methane oxygenase make Arlene oxide then phenol and trans dihydrodiol

PAHs degradation by bacteria

dioxygenase and dehydrogenase make catechol then perform meta or ortho cleavage, making cis muronic acid or hydroxymuconic semialdehyde

PAH degradation by white rot fungi

make PAH quinone then cleave ring

fates of contaminants

water, groundwater, soil and sediment, air

bioaccumulation

increase in concentration of compound within an organism compared to environment

biomagnification

increase in tissue of an organism of a pollutant up trophic levels

xenobiotic

compounds alien to existing life, often toxic, carcinogenic, and recalcitrant

recalcitrance

compounds attacked poorly or not at all by microbial enzymes because of molecular complexity

oligomerization examples

cellulose, polystyrene, plastics

halogen substitution

H replaced by chlorine, fluorine, bromine

other substitution

H replaced by nitro-sulfa groups

branched molecules

alkylated molecules

large molecules

to large to fit into enzyme pockets and are less soluble in water and less bio available

aeration of soil

stimulates denitrification of soil because O2 terminal electron receptor, often rate limiting compound for petroleum degradation

aeration strategies

tilling, adding bulking agent, venting aquifers

Anaerobic conditions for bioremediation

BTEX, PAH, halogenated organic compounds, allows reductive de chlorination

reductive dechlorination

substitution of Cl with H in anaerobic environment, because the halogenated hydrocarbon is serving as terminal electron acceptor

pH bioremediation strategies

add lime to acidic soil to raise pH

psychrophiles

0-20 optimum is under 20

psychrotroph

0-35 optimum is greater than 20

mesophiles

10-50, 40 degree optimum

thermophiles

50-110 optimum is less than 65

Q10 value

temperature coefficient, a 10 degree change can increase or decrease enzyme activity two fold

soil moisture content

% water, amount of water in the soil is dry weight/wet weight

water activity (Aw)

Water available for biological use

water holding capacity

amount of water soil can hold before saturation

soil moisture bioremediation strategies

Optimal aerobic is 60-80%, for hydrocarbon degradation 30-90%

anoxic soil

waterlogged, can decrease with gypsum or bulking agents like alfalfa

non contaminated environment limiting nutrient

carbon

contaminated environment limiting nutrient

N and P

20:1

carbon to nitrogen ratio for bacteria

50:1

carbon to phosphorus ration for bacteria

nutrient supply bioremediation strategies

add NO3 or NH4

oleophilic fertilizers

used in aqueous systems, hydrophobic with N and P and remain associate with oil contaminant