Biodegradation
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Transcript of Biodegradation
BiodegradationBiodegradation
Why study?Why study?• One of few fate processes where One of few fate processes where
material is gone from the environmentmaterial is gone from the environment• Change concentrations that are present Change concentrations that are present
to have effectto have effect• We can play with microbial communities We can play with microbial communities
to get them to do some things we wantto get them to do some things we want
BiodegradationBiodegradation
Three big categories- no one told Three big categories- no one told bugsbugs• Rapid breakdown- days to weeksRapid breakdown- days to weeks• Slow breakdown- months to yearsSlow breakdown- months to years• Almost no breakdown- many yearsAlmost no breakdown- many years
Chemical structure importantChemical structure important Biodegradation requires the presence Biodegradation requires the presence
of the appropriate organism, the of the appropriate organism, the chemical in an available form, and the chemical in an available form, and the right environmental conditions for right environmental conditions for organisms to functionorganisms to function
Molecular Recalcitrance and Molecular Recalcitrance and Microbial FallibilityMicrobial Fallibility
100 yrs of everything breaking down-100 yrs of everything breaking down- In 50’s and 60’s synthetic organics In 50’s and 60’s synthetic organics
appear that do not break downappear that do not break down No prior exposure of microbes to No prior exposure of microbes to
chemicalschemicals Could not find bugs to grow on themCould not find bugs to grow on them Therefore, there are recalcitrant Therefore, there are recalcitrant
compoundscompounds Began a variety of studies on breakdown Began a variety of studies on breakdown
in the environmentin the environment Can find degraders for many of these Can find degraders for many of these
compounds now- evolution?compounds now- evolution?
Chemical StructureChemical Structure
Structure has to relate to Structure has to relate to degradability since it dictates what degradability since it dictates what kind of enzyme is neededkind of enzyme is needed
There have been few systematic There have been few systematic studiesstudies
Most with TOC in screening testsMost with TOC in screening tests Many of the chemicals you need are Many of the chemicals you need are
not available.not available. Generally the larger the molecule, Generally the larger the molecule,
the more substituents it has and the more substituents it has and less water soluble- the slower it less water soluble- the slower it degradesdegrades
First substituent on ring
For others number, type and position all have large influence
Kinetics = How fast does it goKinetics = How fast does it go
If something degrades the next If something degrades the next question is how fastquestion is how fast
To predict how long it will persist To predict how long it will persist need some idea of kineticsneed some idea of kinetics
In most environments first order In most environments first order works for most chemicalsworks for most chemicals
More later on concentration More later on concentration effectseffects
First Order V= K[S]
Second Order V= K[B][S]
Rapid BiodegradationRapid Biodegradation
Compounds that are identical or Compounds that are identical or very similar to naturally very similar to naturally occurring materialsoccurring materials
Use same or similar metabolic Use same or similar metabolic pathways as natural materialspathways as natural materials
Usually support growth of some Usually support growth of some group of organismsgroup of organisms
Many examples- petroleum, Many examples- petroleum, pesticides, industrial chemicalspesticides, industrial chemicals
R-CH2-CH3
R-CH2-CH2OH
R-CH2-CHO
Only in microbes
Very common
Ortho dihydroxy intermediates
Oxygenase enzymes all over the place
Most Common herbicide
Persists 2 mo
Isolate bact that grow on it
Pathway well understoood
Slowly DegradedSlowly Degraded
Tends to be compounds with more Tends to be compounds with more than one substituent, or halogensthan one substituent, or halogens
Usually not present in high Usually not present in high concentrationsconcentrations
Generally do not support growth of Generally do not support growth of degradersdegraders
Partial degradation products commonPartial degradation products common COMETABOLISMCOMETABOLISM
CometabolismCometabolism
They are small changes- one or two steps- then stops
Why partial metabolism?Why partial metabolism? Very common way for xenobiotic to Very common way for xenobiotic to
degradedegrade Either from unusual structure or very low Either from unusual structure or very low
concentrationconcentration The enzymes early in a pathway are not The enzymes early in a pathway are not
very specific- so attack more than one very specific- so attack more than one thingthing
As pathways proceed the enzymes As pathways proceed the enzymes become more specific- so it stops at some become more specific- so it stops at some pointpoint
Function of non-specific enzymesFunction of non-specific enzymes
MMO
AMOPMO
Almost Non-DegradableAlmost Non-Degradable
Mostly polymers – monomers often Mostly polymers – monomers often degradabledegradable
Even natural polymers slowly Even natural polymers slowly degradabledegradable
Large molecules cannot enter cells- Large molecules cannot enter cells- need extracellular enzymesneed extracellular enzymes
Surfaces often not wetable so water Surfaces often not wetable so water and enzyme does not see moleculeand enzyme does not see molecule
Many examplesMany examples
Simple Molecules linked Simple Molecules linked
COOH
COOH
Terphthalic acid
CO-O-CH2-CH2-O-CO- CO-O-CH2-CH2-O-CO-
DACRON
Environmental FactorsEnvironmental Factors
Presence of electron acceptorsPresence of electron acceptors Concentration of the chemicalConcentration of the chemical Availability of nutrientsAvailability of nutrients Bioavailability of the chemical to Bioavailability of the chemical to
the organismsthe organisms Almost anything else you can Almost anything else you can
think of can sometimes have an think of can sometimes have an effect effect
Characteristic of Anaerobic Characteristic of Anaerobic ProcessesProcesses
Slower than aerobic processes- 19X Slower than aerobic processes- 19X less energyless energy
Less oxidized processesLess oxidized processes Methane a common mineralization Methane a common mineralization
productproduct Consortia of organisms almost always Consortia of organisms almost always
involvedinvolved Use a variety of electron acceptors – Use a variety of electron acceptors –
not Onot O22
Do many reactions not possible by Do many reactions not possible by aerobesaerobes
Anaerobic Consortia
Polysaccharides
Aromatics
Pollutants
Acetate, H2, CO2
Lactate, Propionate, Butyrate
Fermenters
Acetogens
CH4, CO2
MethanogensEnergy yielding
Energy requiring
For at least some microbes the halogenated are electron acceptors
Anaerobically the more halogenated the better the e- acceptor
ConcentrationConcentration
Microbes have sophisticated ways to Microbes have sophisticated ways to control enzyme productioncontrol enzyme production
Thresholds do occur- some Thresholds do occur- some concentrations are too low to turn on concentrations are too low to turn on enzyme synthesisenzyme synthesis
Most Cpds do not have thresholdsMost Cpds do not have thresholds Toxicity often seen at high Toxicity often seen at high
concentrationsconcentrations What may be too high or too low in What may be too high or too low in
one environment may be degraded in one environment may be degraded in anotheranother
Bioavailability of chemicalsBioavailability of chemicals Early observation that high organic Early observation that high organic
contaminated sediments did not show contaminated sediments did not show toxicity to aquatic critterstoxicity to aquatic critters
Toxicity related to pore water Toxicity related to pore water concentrationconcentration
Material sorbed to sediment was not Material sorbed to sediment was not biologically available to have a toxic biologically available to have a toxic effecteffect
At same time saw that microbes did not At same time saw that microbes did not degrade material sorbed to soil or degrade material sorbed to soil or sedimentsediment
Effect of nutrient availabilityEffect of nutrient availability
Most of the time there are adequate Most of the time there are adequate supplies of inorganic nutrients in supplies of inorganic nutrients in most environmentsmost environments
Where there are large amounts of Where there are large amounts of organic materials need to add N and organic materials need to add N and PP
Most often seen in oil spills where Most often seen in oil spills where lots of carbon has been addedlots of carbon has been added
Important consideration in Important consideration in remediation effortsremediation efforts
Even though the compounds are degradable they do not unless N and P are added
What can we use this for?What can we use this for? Bioremediation= lets use Bioremediation= lets use
microbes to clean up our messmicrobes to clean up our mess In US right nowIn US right now
• 100,000 petroleum leaks100,000 petroleum leaks• 15,000 VOC spills15,000 VOC spills• 8,000 wood treating sites8,000 wood treating sites• Many othersMany others
Most can be bio-cleaned Most can be bio-cleaned cheaper than other methodscheaper than other methods
Bedtime ReadingBedtime Reading BooksBooks
• Microbial Transformations and Degradation of Toxic Microbial Transformations and Degradation of Toxic Organic Chemicals- Young and Cerniglia- WileyOrganic Chemicals- Young and Cerniglia- Wiley
• Biology of Anaerobic Microorgansism- Zehnder- WileyBiology of Anaerobic Microorgansism- Zehnder- Wiley• Biodegradation and Bioremediation- Alexander- Biodegradation and Bioremediation- Alexander-
WileyWiley JournalsJournals
• Applied and Environmental MicrobiologyApplied and Environmental Microbiology• Environmental Science and TechnologyEnvironmental Science and Technology• BiodegradationBiodegradation• Environmental Toxicology and ChemistryEnvironmental Toxicology and Chemistry
WebsitesWebsites• ASMUSA.org- lots of good stuffASMUSA.org- lots of good stuff• EPA.gov- search under biodegradationEPA.gov- search under biodegradation