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 bugsThree big categories- no one told bugs

• 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 less the more substituents it has and less water soluble- the slower it degradeswater soluble- the slower it degrades

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- need Large molecules cannot enter cells- need

extracellular enzymesextracellular enzymes Surfaces often not wetable so water and Surfaces often not wetable so water and

enzyme does not see moleculeenzyme 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 less Slower than aerobic processes- 19X less energyenergy

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 – not Use a variety of electron acceptors – not

OO22 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 one What may be too high or too low in one

environment may be degraded in 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 effectbiologically available to have a toxic effect

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 most supplies of inorganic nutrients in most environmentsenvironments

Where there are large amounts of Where there are large amounts of organic materials need to add N and Porganic materials need to add N and P

Most often seen in oil spills where lots Most often seen in oil spills where lots of carbon has been addedof 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