Proposed Syllabus for Environmental Microbiology - EEES 5510
Lecturer: Daryl F. Dwyer
Office: BO 3096H
Office Hours: T, Th 11:00 am until 12:00 noon
Text: Environmental Microbiology. R. M. Maier, C. P. Gerba, and I. L. Pepper. Academic Press Inc. ISBN 0124975704
Grading: Exams (3 x 100 Points) 300 Points
Problem Sets (4 x 50 Points) 200 Points
Total 500 Points
Problem sets will be handed out on a Monday and will be due the following Monday in class. Late problem sets will not be accepted, as the answers will be discussed in class on the day that they are due.
Each exam will only cover the material preceding it. The final exam will not be comprehensive. Students will be responsible for lecture material as well as reading assignments. If you miss an exam without a valid excuse, you will receive an incomplete until the exam is taken. Copying problem sets and cheating on exams will result in a letter grade of F. Letter grades for the course will be awarded on a percentage basis: A > 93%, A- = 90-92%, B+ = 87-89%, B = 83-86%, B- = 80-82%, C+ = 76-79%, C = 72-75%, C- = 68-71%, D = 60-67%, F < 60%. The percentages may change, but only to the advantage of the students.
Graduate students will be required to review a scientific paper that relates to one of the course topics. The review will consist of a paper that is at a maximum of five pages (typed) in length and an oral presentation of the review (15 minutes in length). The goal is to have each student relate to the class an application of microbiology in solving an environmental problem. The format for the paper and presentation will be discussed in class.
Week 1 1, 2, 3 Microbes in the Environment and Measurement of
Bacterial Growth
Week 2 4, 6 Terrestrial and Aquatic Environments
Week 3 7 Microbial Transport
Week 4 8, 9 Collection and Processing of Environmental Samples
Week 6 10, 11 Cultural and Physiological Methods of Identification
Week 7 12, 13 Immunological and Nucleic Acid-Based Methods of
Identification
Week 8-10 14, 15 Biogeochemical Cycling and Energy Flow in the Microbial
World
Week 11-12 16, 17 Pollution with Organic Compounds and Metals
Week 13 19-20 Pathogens and Indicator Microorganisms
Week 14 21-22 Treatment of Domestic Wastes and Drinking Water
Week 15 24 Risk Assessment
Environmental Microbiology Name: ___________________________
Exam #1
February 23, 2003
True or False (10 Points)
___ 1. Virus particles consist primarily of an inner nucleic acid genome and an outer protein capsid.
___ 2. Virus particles require a host cell in which to replicate, as they cannot metabolize on their own.
___ 3. Prokaryotic cells contain mitochondria that are used in cell respiration.
___ 4. Both prokaryotic and eukaryotic cells contain proteins in the cytoplasmic membrane that aid in transport of molecules through the membrane.
___ 5. The basic chemical formula for photosynthesis is:
2 H2O + CO2 ΰ CH2O + O2 + H2O
___ 6. Endogenous metabolism is responsible for the growth of cells during the stationary phase of the microbial growth cycle.
___ 7. A photolithotroph uses H2O as its electron donor, CO2 as its carbon source and sunlight as the energy source for photosynthesis.
___ 8. Blue-green bacteria, now commonly known as cyanobacteria, primarily carry out symbiotic nitrogen fixation.
___ 9. Starch is present in both leaves and muscle tissue as a polymer of glucose and is used for the purpose of energy storage.
___ 10. The vegetative structure of protozoa is referred to as a thallus.
Short Problems
1. A bacterial culture is using glucose as its substrate with aerobic conditions. Provide (a) a balanced equation for the metabolism of glucose, (b) the amount of cell mass that can be derived from 1 g glucose (mw = 180 g/mol), and the mass of CO2 that is produced. How many moles of O2 (32 g/mol) will be needed for the culture to metabolize 1 g of glucose? (10 Points)
2. Provide a diagram of the sulfur cycle. Number and name all the different components. For each component give a short explanation of what is occurring (10 Points)
3. Draw a generalized eukaryotic cell and provide 5 organelles within your drawing. Label each organelle (1 through 5) and underneath your drawing make a list in which you name the appropriately numbered organelles and describe each ones function. (5 Points)
4. Use a diagram to provide an explanation of how photosynthesis works, both as an energy yielding and an anabolic process. (10 Points)
5. Explain how one can obtain the basic growth parameters for a bacterium that is growing in chemostat culture. There are three basic growth parameters to be determined. Do not forget to explain why the system must be at steady state. (10 Points)
6. Provide a diagram(s) and explain how the electron transport system sets up a proton motive force; describe what the proton motive force is and how it functions during cellular metabolism (10 Points)
7. Using the flowing data, calculate values for umax and Ks. For this purpose, create a Line-Weaver Burke (reciprocal) plot. What is the generation time for the bacterium during exponential growth? What is the specific growth rate for a substrate concentration of 3 mg/L? (10 Points)
u [S]
0.25 h-1 5 mg/L
0.62 10
0.90 15
0.98 20
1.0 25
8. Balance the following reactions and determine the energy yield associated with 500 micromoles of substrate being oxidized. (15 Points)
a.
CH3CH2OH + O2
b.
CH3COOH + H2SO4
c.
H2S + Fe3+
9. Describe in some
detail the process of biological nitrogen fixation, both for symbiotic
associations and for free-living organisms.
Do not forget to discuss how the organisms deal with the process being
anaerobic in nature. (10 Points)
As part of the required work, each graduate student is required to review a scientific paper that relates to one of the subjects in class. At first, I considered assigning the paper, but then thought it might be better to have each of you look through some journals and select one on your own. This is a good way to see what kind of papers are out there these days. So check the list below and see the topic that I would like each of you to cover:
Barnswell Biodegradation using electron-acceptor(s) other than O2, and that makes use of electro-potentials
Kassem Fermentation in which products and pathways are described
Mileyeva-Biebesheimer Anaerobic metabolism involving hydrogenase activity
Saunders Metabolism measured either by respirometry or dark-light bottles for photosynthesis
Sharma Use of kinetics to describe either in situ competition (preferred choice) or rates of biodegradation as a predictive tool
Wilt Measurement of limiting factors in microbial growth
Now select a paper that was published in 2002-3. You need to prepare a five- page summary of the paper (typed, double-spaced). On Wednesday, April 7, 2004, I would like to hear the title of the paper that you have selected, and at that time we will go over what should be in your summation. Note: its a good idea to have more than one paper title for selection, because we might like some but not all of the ones you have chosen. I will have a handout for you on Critical Thinking to help in preparing your summation; many of you have already seen this. Please note you will be required to do a presentation of your summary in the last week of classes (15 minute duration).
As for the journals, I would consider looking in: Applied and Environmental Microbiology, Microbial Ecology, Canadian Journal of Microbiology, Environmental Science and Technology, Environmental Monitoring and Assessment, Biogeochemistry, and there are many more .
Problem Set Due dates will be announced in class. This will be ongoing, so please check for updates.
Date: April 12, 2004
Chapter 11 Questions 1, 2, 3, 5
Chapter 13 Questions 1, 2, 3, 6, 8
Chapter 14 Questions 3, 5
Chapter 16 Questions 1, 2, 3, 4, 5, 7
Chapter 21 Questions 2, 12