Biology 11 - Lecture 20: Bioremediation
Important Tables and Figures: Fig 16.57, 16.61, 16.62b, Table 16.6
I. Environmental pollutants: Pesticides, effluents,
		spills, fertilizers.... EPA priority list .
	Ideal pesticide: Persists, functions, biodegrades.
    	Stabilize by chlorination - 24D, PCB, DDT
II. Fate of pollutants: 
 A. Degradation - Naturals will degrade under right conditions -
	accumulate under adverse conditions.
	What about unnatural compounds? Xenobiotics (Fig 16.61)
	Photo and Biodegradation (Bio is faster)
	Biodegradation  -------------------------- Recalcitrant 
	 (CO2, NH3, P)		(same or modified)
	Mineralization vs modification.
	Billions of years of evol -> enz pool ->
		rapid evol -> common pathways
	Most synthetics - similar enough to naturals, so degraded.
B. Recalcitrant - No enzyme, Not induced, 
	No permease, Insoluble
	Cl or N on ring is electron withdrawing -> ring stabilization -> 
		recalicitrant (TNT, DDT, DNP)
C. Biomagnification - Ex. DDT fat soluble -> 
		magnified in food chain -> 
	5 ppm in US humans when used
III. Biodegradation
A. General Concepts
	1.  Organisms - Pseudomonas (metabolic diversity), 
		White Rot Fungus
		 Toluene, TNT, and lignin degradation pathways
	2. Pathways 
		Hydroxylation - dioxygenase (O2) - common
		Ortho (intradiol) or meta (extradiol) -> TCA
		Pathway - Remove side chain, remove side groups, 
			hydroxylate, open ring (Fig 16.62b)
	3. Role of plasmids - Broad host range, self transmissible
		TOL plasmid - toluene, xylene
		Two operons (upper and lower) - Tol -> benzoate -> Kreb Cycle
		Regulation by xylR and S - Transcriptional activators.
		Broad substrate specificity of upper enzymes.
	4. Genetic engineering
	a. Molecular breeding - 2,4,5-T 
		Force genes into one organism
		Ananda Chakrabarty - oil degradation 1974 -> 
			1980 Supreme Court patent OK.
		Also with chlorophenols and chlorobenzoate
	b. Clone and change substrate specificity
B. Major bioremediation strategies - 
	Using microbes to clean up environment
	1. Slow degradation: Endogenous organisms, 
		but conditions poor.
		 - low  nutrients, low temp, low DO, low organics, 
			low surface area (tar balls)
	2. Alter environment - temp, pH, water, O2, nutrients
	a. O2 - Drainage, soil tilling, bioreactor, pump H2O2 
		(degrades to O2)- Used in xylene spills.
		Anaerobic digestion - rice fields
	b. Nutrient addition - Oleophilic nitrogen - 
		places it at oil/water interface.
		(Commercial - Elf Aquitaine Corp, Product = Inipol EAP22
		Urea nitrogen, lauryl phosphate and oleic acid - 
			Used at Prince William Sound)
	c. Landfarming - Dilute oil sludge into soil 
		(approx 5 % in upper 20 cm)
		pH 7 with limestone; N and P fertilizer added; 
		Used in US
		Before starting: characterize site for level of
		 contaminant and subsurface plume
	3. Seeding - Current market for inoculum - $10 million.
		Petroleum, formaldehyde adapted inoculum sold.
		Most Pseudomonas, Phanerochaete - 
			lignin, DDT, plastics.
	4. Addition of enzymes - to pesticide containers
C. Application - 60 % of bioremediation practiced is petroleum - 
	Some examples:
	1. Dehalogenation - 
		PCP - Koppers in Oroville
		TCE - by methane monooxygenase - 
			broad substrate specificity
			ie Use Methanotrophs (aerobes)
		DDT - Degraded by consortium
			Completely by Phanerochaete
		PCB - Coolant/insulator in transformers, inks, paint,
			 flame retardant, plasticizer
			1 ppm in random sample of US humans.
			Biphenyl and some PCB degraded.
			1978 banned (still inold transformers, etc.)
			Complete degradation by White rot fungus, 
				 Alcaligenes, anaerobes.
			Degradation products (dioxin) - 
				highly toxic and carcinogen.
	2. Plastics - 50 million tons in US/yr
		90 % = polystyrene, polyvinyl chloride, 
			polyethylene - not biodegraded.
		Plasticizers (make pliable) are degraded.
		Facilitate biodegradation by pyrolysis -> 
			<500 MW -> Biodegradable.
		Alternative: Biopolymers produced by 
			Alcaligenes, Bacillus, Pseudomonas (cost 7x more)
	3. Petroleum hydrocarbons - 
		Enter environment by natural seepage
		Crude is mixture of many compounds
		Difficult to physically clean up: 
			Detergents are cosmetic only
			Some are carcinogenic, damage bird and marine life
		Recalcitrant: long chain and branched
	a. First - mono and dioxygenases -> alcohol -> FA -> 
		B-oxidation -> Acetyl CoA
		Aerobic - Use endogenous since mixed 
			components in crude
			Dispersal helps - lots of O2
	b. Benzene --->  Dihydroxybenzene
	4. Pesticides - 1000s registered in US
		Silent Spring (1962) Rachel Carson - alert to danger of DDT
		Most biodegrade in one growing season - 2,4-D