MICROM 518 - ESC 518

MENU Course Description and Prerequisites Stuart Strand 518/542 Home Page Syllabus (15 January 2003) download pdf Representative Answers to Previous Exam - 1 Five questions and satisfactory answers to three questions from a previous exam are presented here. Download pdf. Representative Answers for Exam 1, Winter 2003 Better answers from different students and a good references cited list As signed Reading Student Oral Presentations Student Presentation Groups, Topics, and Suggested Reading Student Presentation Tips and Evaluation Forms Student PowerPoint Presentation Files Group 1 Group 2 Group 3 Group 4 Links to Bioremediation Web Sites Herwig Home Page Email Dr. Herwig
	MICROM 518 ESC 518 CEE 542 Bioremediation Science (formerly known as Microbial Degradation of Toxic Contaminants) Winter Quarter 2003 Russell P. Herwig University of Washington

		Lectures Notes (revision date) Environmental Contaminants & Working with Microorganisms (01/08/03) Genera/Species and 16S rRNA (01/08/03) Basics of Metabolism (01/08/03) Petroleum Hydrocarbons - I (01/12/03) Petroleum Hydrocarbons - II (01/12/03) Aerobic Toluene Biodegradation and Biodegradation Plasmids - (01/20/03) Chlorinated Solvents, Reductive Dechlorination, Cometabolism - (01/30/03) Dechlorinating Bacteria - DCB-1 Consortium (02/03/03) Polychlorinated Biphenyls (PCBs) (02/03/03)


	Course Description Bioremediation Science is a University of Washington course that is jointly listed as MICROM 518, ESC 518, and CEE 542. It is a 3-credit interdisciplinary graduate class offered during Winter Quarter 2002. The class consists of two 1.5 hour lecture periods each week on Tuesday and Thursday morning. This course is co-taught with Dr. Stuart Strand, a Research Professor in the College of Forest Resources. Besides hearing lectures from Dr. Herwig and Dr. Strand, students prepare an oral PowerPoint presentation, and hear lectures from guest speakers from academia, agencies, and local firms involved with bioremediation. This course was formerly known as Microbial Degradation of Toxic Contaminants.
	Course Prerequisites and Suggested Background Prerequisites: A course in biological sciences or biological aspects of environmental engineering. Recommended courses or their equivalents: organic chemistry, BIOL 201, 202, 303; CHEM 231, 235, 236. Suggested: MICROM 410, 411, 412; BIOCHEM 440, 441. Qualified undergraduate students and nonmatriculated students may take the course with permission of the instructor.

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Assigned Reading

Working with Microorganisms

1. Madsen, E.L. 1997. Methods for determining biodegradability, p. 709-720. In C. J. Hurst (ed.), Manual of environmental microbiology. ASM Press, Washington, D.C. Download pdf

16S rRNA and Phylogenetics

2. Woese, C. 2000. Interpreting the universal phylogenetic tree. PNAS 97:8392-8396. Download pdf

3. Dojka, M.A., P. Hugenholtz, S.K. Haack, and N.R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent contaminated aquifer undergoing intrinsic bioremediation. Appl. Eniviron. Microbiol. 64:3869-3877. Download pdf

Basics of Metabolism

No required reading. Please review Chapter 4 in Brock Biology of Microorganisms for clarifications and additional information about microbial metabolism.

Microbial Degradation of Petroleum Hydrocarbons

4. Leahy, J.G., and R.R. Colwell. 1990. Microbial degradation of hydrocarbons in the environment. Microbiol. Rev. 54:305-315. Download pdf

5. Mearns, A.J. 1997. Cleaning oiled shores: putting bioremediation to the test. Spill Science Technol. Bull. 4:209-217. Download pdf

6. Swannell, R.P.J., K. Lee, and M. McDonagh. 1996. Field evaluations of marine oil spill bioremediation. Microbiol. Rev. 60:342-365. Download pdf

7. Venosa, A.D., M.T. Suidan, B.A. Wrenn, K.L. Strohmeier, J.R. Haines, B.L. Eberhart, D. King, and E. Holder. 1996. Bioremediation of an experimental oil spill on the shoreline of Delaware Bay. Environ. Sci. Technol. 30:1764-1775. Download pdf

8. Widdel, F., and R. Rabus. 2001. Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr. Opin. Biotechnol. 12: 259-275. Download pdf

Biodegradative Plasmids and Aerobic Toluene Degradation

9. Top, E.M., D. Springael, and N. Boon. 2002. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol. Ecol. 42: 199-208. Download pdf

10. Whyte L.G., L. Bourbonniere, and C.W. Greer. 1997. Biodegradation of petroleum hydrocarbons by psychrotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways. Appl. Environ. Microbiol. 63:3719-3723. Download pdf

Aerobic PAH Degradation

11. Dyksterhouse, S.E., J.P. Gray, R.P. Herwig, J.C. Lara, and J.T. Staley. 1995. Cycloclasticus pugetii , gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int. J. System. Bacteriol. 45: 116-123. Download pdf

12. Geiselbrecht, A.D., R.P. Herwig, J.W. Deming, and J.T. Staley. 1998. Enumeration and phylogenetic analysis of polycyclic aromatic hydrocarbon-degrading marine bacteria from Puget Sound sediments. Appl. Environ. Microbiol. 62: 3344-3349. Download pdf

13. Samanta, S.K., O.V. Singh, and R.K. Jain. 2002. Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation. Trends Biotechnol. 20: 243-248. Download pdf

Reductive Dechlorination

14. Fetzner, S. 1998. Bacterial dehalogenation. Appl. Microbiol. Biotechnol. 6:633-657. Download pdf

15. Holliger, C., G. Wohfarth, and G. Diekert. 1999. Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22:383-398. Download pdf

16. Smidt, J., A.D.L. Akkermans, J. van der Oost, W. M de Vos. 2000. Halorespiring bacteria--molecular characterization and detection. Enzyme Microb. Technol. 27:812-820. Download pdf

Microbial Transformation of Polychlorinated Biphenyls

17. Abraham, W.-R., B. Nogales, P.N. Golyshin, D.H. Pieper, K.N. Timmis. 2002. Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr. Opin. Microbiol. 5: 246-253. Download pdf

18. Brown, J.F., Jr., D.L. Bedard, M.J. Brennan, J.C. Carnahan, H. Feng, and R.E. Wagner. 1987. Polychlorinated biphenyl dechlorination in aquatic sediments. Science (Wash.) 236:709-712. Download pdf

19. Quensen, J.F., III, J.M. Tiedje, and S.A. Boyd. 1988. Reductive dechlorination of polychlorinated biphenyls by anaerobic microorganisms from sediments. Science (Wash.) 242:752-754. Download pdf

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Oral Presentations and Readings
Presentation Groups
Group	Members	Presentation Date	Detailed Outline Due PowerPoint Presentation Draft Due	Topic (Assigned Readings)
1	Alli, Rebecca Hodges, John Fraser, Whitney Bost, Heather	February 18	February 4 February 11	Degradation of pollutants by white rot and other ligninolytic fungi



2	Walker, Chris Miller, Jonathon Harris, Audrey Johnson, Lara	February 20	February 6 February 13	Use of genetically engineered microbial strains for bioremediation and monitoring

3	Lu, Junhe Satterberg, Jessi Banes, Robin Perrins, Jake	March 4	February 18 February 25	Transformation and degradation of pollutants by rhizosphere microorganisms

4	Nicoll, Greg Bui, Todd Mantel, Veronica Lu, Sharon	March 6	February 20 February 27	TBA