Determinants of extent and rate of contaminant biodegradation

1. Determinants of extent and rate of contaminant biodegradation • Genetic potential of microbes to mutate key genes in such a way that gene product • transport protein can take up the contaminant from the environment • enzyme can catalyze step in contaminant degradation • This requires period of time for such adaptation to occur (weeks, months, years, decades, centuries?)

2. Determinants of extent and rate of contaminant biodegradation • Bioavailability • First step in biodegradation process is the uptake of the contaminant compound by the cell in order for intracellular enzymes to access the contaminant • If contaminant is not water-soluble, it is difficult for cell to access and take up contaminant. Low-density, non-aqueous phase liquid (hydrocarbon, benzene H2O Dense, non-aqueous phase liquid (TCE, PCBs)

3. Determinants of extent and rate of contaminant biodegradation • Bioavailability • Production of surfactants • attachment to liquid-liquid interface Low-density, non-aqueous phase liquid (hydrocarbon, benzene Flow H2O Dense, non-aqueous phase liquid (TCE, PCBs)

4. Determinants of extent and rate of contaminant biodegradation • Bioavailability • Production of surfactants • attachment to liquid-liquid interface • make cell surface more hydrophobic Low-density, non-aqueous phase liquid (hydrocarbon, benzene H2O Dense, non-aqueous phase liquid (TCE, PCBs)

5. Particle Contaminant Determinants of extent and rate of contaminant biodegradation • Bioavailability • Sorption of contaminant to soil particles • Diffusion of contaminant into soil matrix Bacterial cell Soil particles

6. Determinants of extent and rate of contaminant biodegradation • Bioavailability • Sorption of contaminant to soil particles • Diffusion of contaminant into soil matrix Contaminant no longer available to microbes contaminant Soil particles

7. Determinants of extent and rate of contaminant biodegradation • Contaminant structure • Steric effects active site for enzyme blocked

8. Determinants of extent and rate of contaminant biodegradation • Contaminant structure • Electronic effects • as electronegativity of substituents increased, biodegradation rates decreased

9. Electonic Effects

10. Determinants of extent and rate of contaminant biodegradation • Environmental factors • organic matter (source of carbon and energy) • subsurface, unsaturated zones have low organic matter concentrations • oxygen availability • nutrient (N,S, P) availability • temperature • pH • Eh • salinity • water activity

11. Most important factors controlling contaminant biodegradation

12. Economics of in-situ vs. ex-situ remediation of contaminated soils • Cost of treating contaminated soil in place $80-$100 per ton • Cost of excavating and trucking contaminated soil off for incineration is $400 per ton. • Over 90% of the chemical substances classified as hazardous today can be biodegraded.

13. Above ground bioreactors • Bioreactors have been developed to achieve better control over the environmental conditions. • Controlling factors such as temperature, pH, oxygen concentrations, nutrient input help accelerate biodegradation process. • When you carry out bioremediation in the natural environment, changes in temperature can really affect rates of bioremediation.

14. Bioreactors • Wastewater Treatment • ToileTronic-peat moss in a chamber under the toilet holds 2x its weight in water. A mechanical rotator mixes the human waste in with the peat moss and introduces lots of oxygen. • A typical family of 4 produces a shoebox-size product over a 1-month period that is harmless and can be sprinkled in the yard as fertilizer.

16. Volatile organic compounds (VOC) • These are major contributors to air pollution • Paint industry • Pharmaceutical industry • bakeries • printers • dry cleaners • auto body shops

17. These industries are being asked to filter out the VOC before release into the atmosphere. • A bioreactor technology was developed in Europe: • directs the fumes through troughs filled with peat moss, wood waste or compost loaded with bacteria, which are aerated. • As the vapors travel along the trough, the pollutants become a wet film covering the filter particles. • Once trapped in that form, they are easily attacked by the bacteria on the particles and converted to carbon dioxide and water.

18. Using microbes to minimize release of contaminants into the environment • Microbes can make some compounds more "user-friendly" • dibenzothiothene (DBT) is an aromatic compound associated with coal that adheres tenaciously to hydrocarbon molecules. It is converted to sulfur dioxide when ignited. • The Institute of Gas Technology has just patented a strain of bacteria that degrades DBT without attacking the hydrocarbon molecule.

19. Using microbes to minimize release of contaminants into the environment • Microbes and plants can be genetically engineered to do jobs that, until now, only toxic chemicals have done. • pesticides that are biological products (BT toxin) • Microbes can help attack stubborn metals and radioactive wastes. • produce enzymes that convert uranium from a form that is soluble in water to one that is insoluble in water.

20. Hard to degrade contaminants • Chlorinated hydrocarbons • solvents • lubricants • plasticizers • insulators • herbicides and pesticides.

21. Degradation of chlorinated hydrocarbons • Degradation of organic toxins requires the participation of entire biochemical pathways involving many enzymes coded for by many genes. • Some of the genes exist on the chromosome while other genes reside on plasmids.

22. Catechol is a common intermediate for metabolizing many aromatic compounds and utilizes enzymes encoded by the catA, catB, catC, and catD genes

23. p ORF1pheBpheA ORF2 Promoter forms 2 complexes with catR in absence of inducer and 1 complex with catR in presence of inducer catC catB p catR plasmid activation CatR chromosome phenol, cis, cis-muconate are inducers

27. Phenol-degrading dmp operon is regulated by DmpR, a NtrC-like positive regulator.

29. The chlorocatechol degradative pathway is used to degrade these chlorinated compounds. • Similar to catechols, chlorocatechols are common intermediates of the degradation of chloroaromatics such as chlorobenzenes and chlorophenoxyacetates. • Chlorocatechol-degrading genes that have been isolated from bacteria: • clc for chlorocatechol • tcb for trichlorobenzene • tfd for 2,4-dichlorophenoxyacetate

30. The layout of the genes involved in chlorocatechol-degradation on the plasmid is similar to the layout of the catechol-degrading genes on the chromosome

31. The clcABD operon is positively regulated by the clcR gene product, just as the catBC operon is controlled by the catR gene product. • The clcA, tcbC and tfdC genes, all of which encode a similar chlorocatechol dioxygenase activity, have high nucleotide sequence identity. • The clcB, tcbD and tfdD genes, all of which encode a similar chloromuconate cyclosomerase activity, have high nucleotide sequence identity.

32. Each of these chlorocatechol-degrading genes closely resembles the corresponding catechol-degrading cat genes, implying they evolved from common ancestral genes. • CatR and ClcR cross-bind each other’s target promoter regions, indicating that the regulatory regions have considerable homology. • CatR can regulate the clcABD operon but ClcR cannot regulate the catBC operon.

33. Summary • Many factors control biodegradability of a contaminant in the environment • Before attempting to employ bioremediation technology, one needs to conduct a thorough characterization of the environment where the contaminant exists, including the microbiology, geochemistry, mineralogy, geophysics, and hydrology of the system