biodegradation and detoxification
DESCRIPTION
Biodegradation and Detoxification. June 3, 2014 Joonhong Park. Definitions. Terms. Disappearances of a polluting chemical Abiotic transformation of a chemical Biotic transformation of a chemical (Biodegradation) Detoxification Activation Cometabolic vs. Metabolic Biodegradation. - PowerPoint PPT PresentationTRANSCRIPT
Biodegradation and Detoxification
June 3, 2014
Joonhong Park
Definitions
Terms
a. Disappearances of a polluting chemical
b. Abiotic transformation of a chemical
c. Biotic transformation of a chemical (Biodegradation)
d. Detoxification
e. Activation
f. Cometabolic vs. Metabolic Biodegradation
Detoxification
Detoxification
The most important role of microorganisms in the transformation of pollutants
Detoxification refers to the change in a molecule that renders it less harmful to one ore more susceptible species (human, animals, plants and microorganisms)
Toxin
ToxinInactiveProduct
Metab.Seq. A
Metab.Seq. B
AtypicalProduct
CO2
TypicalProduct
DetoxificationReaction
Mineralization
Transformation processes resulting in detoxification
a. Hydrolysis: addition of water
b. Hydroxylation: addition of OH
c. Dehalogenation: removal of Cl or halogens; (i) reductive dehalogenation, (ii) hydrolytic dehalogenation, and (iii) dehydrodehalogenation
d. Demethylation or other dealkylation
e. Methylation: R-OH => R-O-CH3
f. Nitro reduction: R-NO3 => R-NH2
g. Deamination: metamitron, Figure 4.5
h. Ether cleavage: 2,4-D, Figure 4.5
i. Conversion of nitrile to amide: R-C≡N => R-C(=O)-NH2
j. Conjugation: A product of a toxicant combined with a natural metabolite
Activation
Activation
One of the more surprising, and possibly the most undesirable, aspects of microbial transformations in nature is the formation of toxicants.
Often, by-products of biodegradation are more toxic than their parental compounds
Important to know about the pathway of biodegradation including activation and its degradation products (intermediates)
Mechanisms of Activation (I)
a. Dehalogenation:PCE => TCE => DCE => VC => ethaneb. Halogenation: fungi, algae and bacteria add chloride or
bromine to organic compoundsc. Nitrosamine formation
R R NH + NO2
- = N-N=O + OH- R’ R’ (nitrosamine)
d. Epoxidation O -HC=CH- => -HC-CH- (ex. Aldrin to Dieldrin)
e. Conversion of phosphorothinate to phosphateRO S RO ORO -P-OX => RO - P – OX (cf. phosphorodithoates)
Mechanisms of Activation (II)
f. Metabolism of Phenoxyalkanoic Acids: beta-oxidation (2,4-D, Figure 5.5; 4-nonlyphenol Figure 5.6)
g. Oxidation of Thioethers O O -C-S-C- => -C-S-C => -C-S-C- Oh. Hydrolysis of Esters O O RCOR’ + H2O => RCOH + HOR’
i. Other Activations - Production of TCDD by peroxidases - Methylation (organics, mercury, arsenic, tin etc.) - Demethylation - Anaerobic degradation of RDX into 1,1-and1,2-dimethylhydrazine
Discussion: Risks of Biodegradation
The products of microbial biodegradation of a pollutant may or may not be more toxic to human, animals, plants or other ecosystems.
Is biodegradation always good?
What should be the ultimate goal of bioremediation?
What measurements are required for answering the above questions?
Effect of Chemical Structure on Biodegradation
Chemical Factors Affecting Biodegradation
Many possible chemical reactions are foreign to microorganisms (xenobiotics)
Biodegradation rates vs. Xenobiotic metabolism(growth-linked metabolism vs. cometabolism)
Chemical Factors Affecting Biodegradation
Xenophores (substituents): Table 11.2 in B&B- Cl, Br, NO2, SO3H, CN or CF3 (strong xenophores)- CH3, NH2, OH and OCH3 (often acting as xenophores)- OH, COOH, amide, anhydride etc. (stimulaitng
biodegradation)
The addition of xenophore: Table 11.2 in B&B- The more addition, the less biodegradable.
The position of xenophore: Table 11.3 in B&B
Chemical Factors Affecting Biodegradation
Methylbranching vs. beta-oxidation-Linear ABS vs. ABS with a quaternary C
Molecules containing an aromatic and alky/aliphatic acid moiety
PAH biodegradability (Figure 11.5 in B&B): 3 rings (biodegradable) vs. 4 and more rings (little biodegradable)
Chlorinated Hydrocarbon Biodegradability
Degree of Halogenation vs. Biodegradation
C C
Cl
Cl
Cl
Cl
C C
Cl
Cl
H
Cl C C
H
Cl
Cl
H
C C
Cl
Cl
H
H
C C
H
H
Cl
H
C C
H
H
H
H
Tetrachloroethene(Perchloroethene, PCE)
Trichloroethene(TCE, Cs = 1,100 mg/L)
cis-Dichloroethene(cDCE)
trans-Dichloroethene(tDCE)
monochloroethene(vinyl chloride, 발암물질 )
ethene
가장 산화됨
가장 환원됨
Monochlorinated Polychlorinated0.25 4
Degree of Chlorination
So
rpti
on
on
to S
ub
surf
ace
Mat
eria
l
Deg
rad
atio
n R
ateSorption
Reductive dechlorination
Aerobic degradation
BiodegradabilityThe apliphatic and aromatic hydrocarons are readily biodegradable by a
range of aerobic bacteria and fungi. The key is that molecular O2 is needed to activate the molecules via initial oxygenation reactions.
Evidence of anaerobic biodegradation of aromatic hydrocarbons is growing. Anaerobic biodegradation rates are slower than aerobic rates, but they can be important when fast kinetics are not essential.
Most halogenated aliphatics can be reductively dehalogenated, although the rate appears to slow as the halogen substituens are removed.
Highly chlorinate aromatics, including PCBs, can be reductively dehalogenated to less halogenated species.
Lightly halogenated aromatics can be aerobically biodegraded via initial oxygenation reactions.
Many of the common organic contaminants show inhibitory effects on microorganism growth and metabolism. Due to their strongly hydrophobic nature, many of the inhibitory responses are caused by intereactions with the cell membrane. In some cases, intermediate products of metabolism can be more toxic than the original contaminant.
Predicting Biodegrability?Structure-Activity Relationship (SAR) or
Structure-Biodegradation Relationship (SBR)
Biodegradation rate of a compound = f(waster solubility, melting/boiling points, molecular weight, molecular volume, molar refractivity, density, logKow, van der Waals radius, van der Waals volume, Hammett’s sigma, pKa, dipole moment, etc.)
Microbial Physiology
Microbial Ecology
Environmental Abiotic Factors
Acclimation
Factors Affecting Acclimation
Environmental Factors (temperature, pH and aeration)
The concentration of N, P or both (nutrients) (cf. the degradation of P- and N-containing organic
compounds is inhibited in the presence of nutrients)
The concentration of the compound that is being metabolized- Threshold- Detection limit
Site specific microbial communities- Biodegradation population- Interaction with other population members
Explanations for the Acclimation Phase
(a) Proliferation of small populations (Figure 3.3 in B&B)
(b) Presence of toxins (Figure 3.4 in B&B)
(c) Predation by protozoa (Figures 3.5 and 3.6 in B&B)
(d) Appearance of new genotypes (mutation or gene transfer)
(e) Enzyme Induction and Lag Phase (the regulations of gene expression and enzyme induction, diauxie, catabolic repression, etc.)
Predicting Biodegradation Intermediates (Pathways)
Biodegradation Pathway Databases
Biocatalysis/Biodegradation Database (Univ. of Minnesota)
http://umbbd.ethz.ch/index.html
List of 219 pathways, 1503 reactions, 1396 compounds993 enzymes, 543 microorganism entries, 249 biotransformation rules
KEGG Pathway Database – GenomeNet
http://www.genome.jp/kegg/pathway.html
Mono-cyclic Aromatics (BTEX): Upstream
Johnson, Park, Kukor and Abriola, 2006, Biodegradation
Hydroxylation via mono- and di-oxygenases
Ketone formation
Ring cleavage
Mono-cyclic Aromatics (BTEX): Upstream
Carboxylation (anaerobic conditions)
Mono-cyclic Aromatics (BTEX): Downstream
Mono-cyclic Aromatics (BTEX):
Reduction of Double Bonds
Benzene Cyclohexene
COOH COOH COOH
Benzoic acid 1-cyclohexenecarboxylic acid
cyclohexanecarboxylic acid
CH3
Toluene 4-methycyclohexanol
CH3HO
Cycloalkanes:
oxidation
-CH2-CH2- -CH-CH2-
OH
-C-CH2-
O
-HC=CH-
Hydroxylation
Ketone formation
Dehydrogenation
Methyl Groups (RCH3):
(terminal) oxidation
R-CH3 R-CH2
OH
R-CH
O
Alcohol
Aldehyde
Carboxylic acid R-C-OH
O
R could be alkanes and aromatics in oil products, surfactants etc.
Alkanes (CH3(CH2)nCH3):
Dehydrogenation
R-CH2-CH2-R’ R-CH=CH-R’
Ex. The conversion of eicosane (C20H42) to eicos-9-ene in soil The formation of 1-dodecene from tetradecane by anaerobes
Alkyl Groups (R(CH2)nCH3):
Sub-terminal Oxidation (hydroxylation or keto formation)
Ar-CH2-CH3
Ar-CH2-Ar
Ar-CH-CH3
O
Ar-CH-Ar
ethylbenzene
O
Alkenes and Others with Double Bonds:
Reduction, Oxidation, Hydration and Epoxide Formation
R-CH2-CH2-R’ R-CH=CH-R’
R-COH-CH2-OH R-CH=CH2
R’ R’
R-CHCH2-OH R-CH=CH2
R’ R’
R-CH-CH-R’ R-CH=CH-R’
O
Alkynes and Others with Triple Bonds:
Reduction
R-CH=CH2R-C≡CH
HC≡CH H2C=CH2
acetylene ethene (ethylene)
The acetylene reduction is done by bacterial nitrogen fixation
Carboxylic Acids (R-COOH):
Decarboxylation and Reduction
ArCOOH
CH3 Decarboxylation
ArH
R-CH-COOH R-CH2CH3
R-COOH R-CHO R-CH2OH
Reduction
Carboxylic Acids and Alcohols:
Ester Formation
R’-COOHR-CH2OH +
Ester
R-CH2OCR’
O
Esters: Hydrolysis
R’-COOHR-CH2OH +R-CH2OCR’
O
Microbial hydrolysis of malathion, bromoxynil, etc.
Alkanoic Acids [R(CH2)nCOOH], Alkanes [H(CH2)nCH3], and Alkyl Groups [R(CH2)nCH3]:
Beta-oxidation
CH3-COOH
R-(CH2)nCH2CH2COOH R-(CH2)nCH=CHCOOH
R-(CH2)nCHCH2COOH
OH
R-(CH2)nCCH2COOH
O
β-position
R-(CH2)nCOOH
+
Hydroxyl Groups (ROH):
Methylation and Ether (ROR’) Formation
R-OH R-OCH3
ArOCH2COOH
Ar ArOH ArOCH3 PAH
ArOH ArOCH3Phenoxyherbicides
ArOH ArOCH2CH3 O-ethylation
CH3
Ar
Ar
CH-O-CH
Ar
Ar
Ar
Ar
diphenylmetahne to1,1,1’1’-tetraphenyl-dimethyl ether
Ether (ROR):Cleavage
Table 12.9
Halogenated Aromatics:
Reductive Dehalogenation
Cl Cl
Cl
Cl
Cl
Cl
Cl Cl
Cl
Cl
Cl
H
+ [2H]
+ H+ + Cl-
Cl Cl
Cl
Cl
H
H
Cl Cl
H
Cl
H
Cl
Cl H
Cl
Cl
H
Cl
isomers
ArCl6 => HArCl5 => H2ArCl4 => H3ArCl3 => H4ArCl2 => H5ArCl
Halogenated Alkanes and Alkenes:
Reductive Dehalogenation
CCl4 => HCCl3 => H2CCl2
CCl4 + [2H] HCCl3 + H+ + Cl-
Cl2CHCHCl2 => Cl2CHCH2Cl => ClCH2CH2Cl => ClCH2CH3
C C
Cl
Cl
Cl
Cl
C C
Cl
Cl
H
ClC C
H
Cl
Cl
H
C C
Cl
Cl
H
HC C
H
H
Cl
H
C C
H
H
H
H
PCE
TCE
cDCE
tDCE
MCE (VC)
ethene
Halogenated Compounds:Hydrolytic Dehalogenation, Dehydrodehlogenation, Halogen Migration
R2CHCCl3 R2C=CCl2
RCl + H2O ROH + H+ + Cl- Hydrolytic Dehalogenation
Ex. Trans-1,3-dichloropropen into trans-3-chloroallyl alcohol
+ H+ + Cl-
R2CHCHCl2 R2C=CHCl
R2CHCH2Cl R2C=CH2
+ H+ + Cl-
+ H+ + Cl-
Dehydro-Dehalogenation
Ex. DDT metabolism (DDT=>DDE=>DDMU)
C C
Cl
Cl
H
ClTCE
C
Cl
Cl
H
Cl 1,1,1-trichloro-ethanol
C OH
H
HalogenMigration
Other Halogenated Compounds
ArCl ArSCH3
From THM (trihalomethyl)-containing compounds
RCCl3 RCOOH
To methylthio derivatives
Amines
Reductive deamination
RCH2CHCOOH RCH2CH2COOH
NH2
RCH2CHCOOH
OHHydrolyticdeamination
RCH=CHCOOH
Dehydro-deamination
N-methylation
N-acylation
ArNH2 ArNHCCH3
O
N-oxidation
RNH2 RNHOH RNO RNO2
N heterocycle
Aniline
2-methylquinoline
Amines
R-NH + NO2- R-N-NO + OH-
Dimerization
ArNH2 ArN=NAr
S-addition
RN-Alk2 RNH2
R’ R’
N-nitrosation
ArNH2 ArNHSCH3
O
Dealkylation
RN-Alk
ArN=NAr’ ArNH2 + Ar’NH2
Reduction
Carbamates and Amides: Cleavage
Carbamate Cleavage
RCNHR’ RCOOH + H2NR’
O
Amide Cleavage
RCNH2 RCOOH + H3N
O
Nitriles (RC≡N)
RC≡N
Dihalogenated benzonitriles used as pesticides
RCNH2
O
RCOH
O
Azobenzenes: Reduction to Amines
ArN=NAr’ ArNH2 + H2NAr’
N-Nitroso Compounds (Nitrosamines):
R-N-NO R-N-H
R’ R’Denitrosation
Nitro Compounds (RNO2)
ArNO2
Reduction
Hydrolytic Denitration
ArNO ArNHOH ArNH2(nitroso-) (hydroxylamino-) (amino-)
RNO2 + H2O ROH + NO2- + H+
ArNO2
Reductive Denitration
ArH
Nitrate Esters (RONO2)Cleavage RONO2 ROH
R(ONO2)3 HOR(ONO2)2 (HO)2RONO2 (OH)3R
C-S Bond: Cleavage
Thiols (RSH):
ArSH ArSCH3 RSH RSSR
Sulfate Esters (ROSO3H):Cleavage
ROSO3H ROH
Thioethers (RSR’): Oxidation
RSR’ RSR’ RSR’ O O
O
= ==
Disulfides(RSSR): Cleavage
RSSR RSH
RSR’ RSH (+ HR’) RSR’ ROH
Methylation Dimerization
CHSR’’ C=O RSO3H ROHR
R’
R
R’
Phosphate Esters
PhoshorothioatesCleavage
P-ORAlkO O
AlkO
=
P-ORAlkO
HO
=O
HOP-OR
HO O=
POHAlkO O
AlkO=
P-ORAlkO S
AlkO
= P-OHAlkO S
HO
=
P-OHAlkO S
AlkO
=
P-OHAlkO O
HO=
P-OHAlkO O
AlkO
=
PSRAlkO O
AlkO
=
Degradation
PSHAlkO O
AlkO
=
P-OHAlkO O
AlkO
=
Phoshoro-Di-thioatesCleavage
P-SRAlkO S
AlkO
=
PSRAlkO S
HO
= P-SHAlkO S
AlkO
=
P-OHAlkO O
AlkO
=
PhoshonatesCleavage
RP-OH + H2O RH + HOP-OHS
OH
=
OH
= O
Triarly PhoshonatesCleavage
ArOP-OAr ArOPOAr + ArOHO
OAr
=
OH
= O
P=SConversion to P=O
PSRAlkO S
AlkO=
PSRAlkO O
HO
=
Addition Reactions
ArH ArCH3
ArH ArNO2
CHCCl3
ROH + H2SO4 ROSO3H + H2O
Ar
ArCHC≡N
Ar
Ar
ArNO2
ArSCH3
Methyl-
Nitro-
Nitrile
Sulfonate
Methylthio-