Examples of Previous Final Examinations
Biology 447 Final Exam - Example #1
Answer 4 (four) questions (Originally this Final Exam had 9 questions - the ones removed were on topics no longer covered.)
1. The Niagara River is depositing many toxic chemicals into Lake Ontario from leaking landfill sites along the American side of the river. How would you design a sampling scheme and methodology to assess the effects of these toxic chemicals on the natural levels of activity of the phytoplankton in the affected waters?
2. It has been suggested that it would be possible to improve the water quality (reducing algal biomass, reducing organic contents, lowering phosphorus and nitrate levels, etc.) of Toronto Harbour by "ecosystem control" measures such as installing underwater constructions to stimulate growth of communities. How would this work?
3. You have been given a new organic chemical to test for its environmental effects. It is a complex, four ring aromatic compound, heavily substituted with bromine atoms. It has some long aliphatic branched side chains each with a total length of 23 carbon atoms, but each branch is more than 6 and less than 10 carbon atoms in length. What procedures would you use to assess the effects of this compound on microbial activities in soil?
4. Explain in detail how you would experimentally distinguish between metabolism and cometabolism in the case of a compound present in a water system at levels of a few mg per litre?
5. What are the main problems associated with the operation of landfill sites? How are these problems affected by the presence of bacteria in the landfill site and the groundwater below and near the landfill site?
6. a). How can bacteria be used to extract minerals from sulfide-containing ores? b). How can microorganisms be used to produce cheaper fuels?
7. Explain the following observations as completely as you can: a). Gasoline components are found in groundwater in different concentrations to those in the spilled gasoline. b). Most hydrocarbons are degraded more slowly in anaerobic than in aerobic environments. c). Bioaccumulation of organic molecules can be assessed by their octanol/water partition coefficients. d). Some attempts to reduce eutrophication in lakes have involved deliberate mixing of the layers of the lake. The results have varied - sometimes an improvement is noted, sometimes not.
Biology 447 Final Exam - Example #2
Answer 5 (five) questions (This exam originally had 10 questions)
1. Surface freshwater systems are often subject to man-made pollution. Describe the main types of pollution and show how they affect the cycling of nutrients in freshwater lakes such as the Great Lakes.
2. The "safety" of water supplies or water used for recreational purposes is usually monitored by testing for the presence of coliform bacteria. What us the rationale for these tests and what do the results mean in assessing water quality? (60%) How could you improve this testing procedure?(40%)
3. Why do the biodegradation rates of naturally occurring polymers such as proteins, cellulose and lignins vary so widely? (70%) What effect do environmental conditions have on these biodegradation rates? (30%)
4. a). Aliphatic hydrocarbons occurring in crude oil samples degrade at different rates if spilled into water or into soil. Describe what variations you would expect to see between the degradation of different types of aliphatic hydrocarbon molecules. (70%) b). Aliphatic hydrocarbon biodegradation only occurs in the water phase, not in the hydrocarbon phase itself - why? (30%)
5. The chemical formula of an aromatic hydrocarbon, especially the type and extent of halogen substitution, has a marked effect on its biodegradability. Show examples of this and explain the observations as far as possible.
6. There are a series of microbial activities occurring along the flow direction of groundwater initially containing some organic materials. Describe the reactions and explain why they occur in the observed sequence.
7. Different aromatic contaminants move at different rates through the groundwater matrix and at different rates in comparison to the actual rate of groundwater flow. Why? (60%) What are the biological methods available to remove such contaminants and "clean up" contaminated groundwater? (25%) What other types of methods are available? (15%)
8. What is meant by the following terms;
i) Shikimic acid pathway ii) Stable toxic intermediate iii) Hydroperoxidation iv) Epoxidation v) Subterminal oxidation vi) Ecosystem control to treat eutrophication of fresh water
9. Explain the difference between the following:
i) Biotransformation and biodegradation ii) Co-metabolism versus secondary substrate utilization iii) "Headquarters" and "range" for human indigenous microorganisms iv) Zero and first order reaction types.
Biology 447 Final Exam - Example #3
Answer 4 (four) questions (This exam originally had 9 questions)
1. How would you assess both the degree of success and the contribution of microorganisms to an in-situ bioremediation using addition of "native bacteria" (isolated from the site and grown in quantity before re-introduction) and nutrients to a site where polyaromatic hydrocarbons (PAHs) had been spilled on the ground? Give the main criteria for success and contribution and explain briefly how you would determine these experimentally.
2. A reservoir has been found to be contaminated with Escherichia coli bacteria at very high levels (more than 2500 per 100 mL). What are the likely sources for this kind of contamination? The reservoir is used for "body contact recreation" such as swimming, and as a source of water for a water purification plant piping water after treatment into the water system of a nearby city. What problems would there be for these uses because of the contamination? How would you attempt to assess the cause and seriousness of the situation and how would you attempt to correct it?
3. Hamilton Harbour is heavily contaminated with heavy metals, organic carbon from sewage plants and other nutrients. A proposal to clean up the harbour sediment involves aeration of the water and physically disturbing and suspending the sediment in the water column to promote precipitation and metabolism of the various contaminants. How would you monitor these processes to make sure that satisfactory results are being obtained? What measurements would you make? What would be the potential disadvantages of such an approach?
4. In general terms, if the chemical structure and water solubility of an organic chemical is known, the biodegradation pathways and breakdown kinetics can be predicted with a fair degree of accuracy. Do you agree with this statement? Give examples to justify your answer.
5. Thermodynamics can predict whether a compound or material is potentially biodegradable under given environmental conditions. Show why this is true (details are not required). The speed of breakdown is not generally predicted by thermodynamic considerations - why not?
6. What is meant by the following terms:
b) Secondary substrate metabolism
c) First order kinetics (of breakdown)
d) Ecosystem control of aquatic systems
e) Integrated pest management procedures
f) Stable toxic intermediate
g) epoxidation reactions
h) octanol/water partition coefficients
7. Why does ground water move? Show how the input of organic materials into ground water from any source leads to the development of distinct zones of microbial activity. Explain the presence and relative location of these zones.
Biology 447 Final Exam - Example #4
Biology 447 - Environmental Microbiology 2001
Answer 4 (four) questions only
Time allowed - 3 hours
All parts of multi-part questions have equal marks
1. Groundwater conditions change along the flow path in a predictable manner when organic, biodegradable materials enter the aquifer. This leads to a changing environment for microbial growth and activity. Describe these changes (use diagrams to make your answer clear) and explain why different bacteria are found in different regions of the groundwater along the flow path from where the organic material enters the system.
2. A new pesticide chemical has been developed with the following properties. It is an aromatic structure with 2 aromatic rings having one side group on one ring with 15 carbon atoms in the side group - the side group is linear and not branched. The other aromatic ring has a chlorine atom attached to the meta position. What could you predict about: a). The biodegradation of this compund (*given the limited amount of information at your disposal. - What features of the molecule would you need to know to perform a better prediction? b). its biodegradation in the field - How would you test that biodegradability in the laboratory and in the field?
3. Groundwater entering a local water-works system through a drilled well has been contaminated with very high levels of Escherichia coli from a local farming operation. What does this mean in terms of potential or actual safety concerns? What precautions would you take to ensure a safe drinking water supply? How would you check the groundwater supply and the drinking water to ensure that it is safe to drink? Would you advise the residents to drink the water in Walkerton after it has been declared safe?
4. Some bacteria are able to grow in extreme conditions. Explain how bacteria are able to grow:
i). At extreme depths in the oceans
ii). At very low temperatures in the oceans
iii). Under high salinity conditions in groundwater and the oceans
iv). At depths in the ground where very small amounts of nutrients are available
v). Under extremely anaerobic conditions with very high sulphate levels in the bottom of polluted lakes
vi). With carbon dioxide as their sole carbon source in anaerobic environments in lakes
5. The thermodynamic laws only predict whether a reaction is possible (i.e. will generate sufficient energy for growth of microorganisms). Explain why this is so and also explain why the kinetic models for growth rates are required to more fully understand the growth of microorganisms in any environment.
6. Explain the following observations as completely as you can:
a) Placing old car tires in a shallow area of the sea or in a lake increases biodiversity
b) Polyaromatic hydrocarbons (PAHs) are degraded biologically very slowly if at all when they have more than 4 aromatic rings in their molecular structure
c) The cyclodiene pesticides often produce so-called "stable toxic intermediates" upon degradation
d) 2,4-dichlorophenoxyacetic acid is more biodegradable than 2,4,5-trichlorophenoxyacetic acid
e) Some wells drilled into groundwater aquifers have water flow without requiring any pumping.
f) Some compounds are biodegraded even though there are no organisms present that can gain energy from their metabolism
g) A very high octanol/water partition coefficient predicts many other properties of an organic molecule
7. Why do the biodegradation rates of naturally occurring polymers such as proteins, cellulose and lignins vary so widely? What effect do environmental conditions in soils and groundwater have on these biodegradation rates? What effect would particle size of the mineral materials in soils and groundwater aquifers have on this decomposition?
Biology 447 Final Exam - Example #5
Final Examination - Biology 447 - Environmental Microbiology
Time allowed 3 hours - No aids permitted
Answer 4 questions only
1. A new pesticide chemical has been developed and it has the following properties. It is an aromatic organic molecule with 2 aromatic rings each having side chains with 22 carbon atoms, At the end of one of these side chains is a methoxy group (OCH3) and the other has a carboxylic acid group (COOH). Each aromatic group has 1 chlorine atom substituted at the meta position on the ring
Using this information, answer the following questions:
a). What could you predict about the biodegradation of this compound given the limited information at your disposal?
b). What other features of the chemical would you have to know to better predict its biodegradability?
c). Given that is to be used on field crops such as corn and wheat to control weeds, how would you test the biodegradability in the laboratory and in the field?
2. Discuss the use of Escherichia coli and total coliform counts as indicators of pollution of water by pathogenic organisms. Provide evidence for both the advantages and disadvantages involved in using these organisms as indicators.
3. Why do plumes of groundwater that have become contaminated with high levels of organic carbon and other nutrients from a leaking landfill site exhibit a very consistent progressive change in the types of microorganisms present, their activities, and the products formed in the plume? What factors control these processes?
compounds move in a complex manner in groundwater. What factors control this
movement? Answer this question using named examples if you can.
5. What is meant by the following:
· First order kinetics
· Second order kinetics
· Zero order kinetics
· Ecosystem control measures in a river drainage basin (watershed)
· Octanol-water partition coefficient
· Subterminal oxidation of aliphatic hydrocarbons
· Stable toxic intermediate (in pesticides)
· Autotrophic microorganisms
· Photoautotrophic microorganisms
· Heterotrophic microorganisms
6. A major gasoline spill (over 25,000 gallons) has occurred in a service station. There is a proposal to treat it by pumping the bulk of the liquid gasoline from the surface of the groundwater and then allowing "intrinsic remediation" or "natural attenuation" to take care of the remainder of the gasoline components in the soil and in the groundwater. You have been asked to comment on this proposed treatment. What factors would you recommend be examined before treatment occurs, during treatment and after treatment? What data would convince you that the proposal would work satisfactorily?
7. Explain the following observations:
· Escherichia coli can, under certain conditions, cause severe disease symptoms and death
· DDT is biodegraded slowly, if at all, and the products may be more toxic than DDT
· Estuaries are extremely productive ecosystems and lead to highly productive off-shore marine environments
· There are very few cities in coastal regions or very close to sea that carry out sewage treatment to any extent.
· Artesian wells can be found miles from surrounding hills or mountains
· Cryptosporidium contamination can be found in water chlorinated to kill bacteria
· Contamination by Cryptosporidium species is difficult to detect in treated water supplies
· Chlorinated hydrocarbons tend to be degraded under anaerobic soil or groundwater conditions
· Lignin, although a naturally occurring plant product, degrades slowly in soils.
· Bioremediation of complex mixtures of compounds is usually difficult and often unsuccessful.
Biology 447 Exam - Example 6
Biology 447 Environmental Microbiology – Final Examination December 2004
3 hours – no aids permitted Answer 4 (four) questions only
Q1: You have been asked to design a sampling and assay scheme for
that will be used to measure the activities of aquatic bacteria in the lake. How would you go about designing such a scheme? What factors would control where samples were taken? How could you measure the general “activity” of aquatic bacteria? Lake Ontario
Q2: Explain the following observations that have been made in lakes and oceans:
a). Only around the periphery of a lake are photosynthetic bacteria found at the surface of the sediment layer
b). When bottles of lake water were incubated at the surface of the lake, black glass bottles (no light penetration, therefore no photosynthetic activity) still showed uptake of C14-labelled CO2 into the biomass of organisms in the lake water sample – but at a much lower level than that in clear glass bottles
c). Radio-labelled P32 added as inorganic phosphate to lake water disappeared from the water within a few minutes
d). There is a “balance” between photosynthesis and respiration in oceans in terms of the cycling of the main nutrients (C, H, O, N, and P) that does not occur in many freshwater lakes
Q3: List the main differences between the conditions in freshwater lakes and oceans. Give one example for each of how these differences affect microbial growth and activities in the two ecosystems. The estuarine ecosystem (where rivers meet the sea) are a combination of marine and freshwater systems – explain why they are such productive environments.
Q4: Why are biofilms important to microbial growth and activities in aquatic systems and in water treatment and distribution systems? Explain these effects.
Q5: Coliform bacteria and/or Escherichia coli are often used as indicators of pollution of water by faecal materials. What are the advantages and disadvantages of using these organisms as indicators? What are the alternatives?
Q6: In biodegradation studies what is meant by:
a). Sorption b). Cometabolism c). Recalcitrance d). Toxicity e). Hydroxylation f). Dehydrogenation g). Ortho cleavage of aromatic ring structures h). Polyaromatic hydrocarbons (PAHs) g). Stable toxic intermediate h) Zero order kinetics i) First order kinetics j) Redox reactions
Q7: The biodegradation of pesticides is determined to a large degree by their chemical structures. Give three examples where this is the case from each of the insecticide and herbicide groups of pesticides (detailed biochemistry of biodegradation is NOT required) and explain how these differences in persistence (biodegradability) are related to the chemical structures.
Q8: Explain as completely as you can the observation that there are “zones” with different redox potentials produced along the flow path after high levels or organic materials (such as those from leaking landfill sites) enter a groundwater system. Describe the factors controlling the development of those zones and indicate the role of bacteria in the development of the zones.
Q9: You have been asked to determine whether the hydrocarbon contamination in the sediment in a small lake can be reduced to below legal standards or eliminated completely using bioremediation options (either in-situ or ex-situ). How would you go about answering this question? Details of hydrocarbon biodegradation are NOT required to answer this question. This question is concerned with site characterization and preliminary testing protocols; not producing a detailed plan of bioremediation.
Biology 447 Exam - Example 7
Biology 447 – Environmental Microbiology – December 2004 - Version 1
3 hours – No aids permitted
Answer 4 questions only
Each part of multi-part questions has equal value
1. It has been suggested that it would be possible to improve the water quality (reducing algal biomass, reducing organic contents, lowering phosphorus and nitrate levels, etc.) of
by "ecosystem control" measures such as installing underwater constructions to stimulate growth of communities, harvesting biomass from the harbour, etc. Describe these ecosystems control measures and explain the theoretical basis for these approaches Hamilton Harbour
2. The chemical formula of an aromatic hydrocarbon, including the type, position and extent of halogen substitution, has a marked effect on its biodegradability. Show examples of the effects of chemical formulae of aromatic compounds on biodegradation and explain the observations as far as possible.
3. What is meant by the following terms:
b) Secondary substrate metabolism
c) First order kinetics (of breakdown)
d) Integrated pest management procedures
e) Stable toxic intermediate
f ) epoxidation reactions
4. Discuss the use of Escherichia coli and total coliform counts as indicators of pollution of water by pathogenic organisms. Provide evidence for both the advantages and disadvantages involved in using these organisms as indicators.
5. What are the important differences between the freshwater and marine environments that determine microbial growth and activity?
6. Explain the following observations as completely as you can:
a). Soluble gasoline components such as benzene, toluene, xylenes and ethylbenzene are found in groundwater in different proportions to those in the spilled gasoline.
b). Most hydrocarbons are degraded more slowly in anaerobic than in aerobic environments.
c). Bioaccumulation of organic molecules can be assessed by their octanol/water partition coefficients.
7. What are the main problems involved in carrying out a successful bioremediation of contaminated sediment in a freshwater environment? Discuss these problems while outlining the steps involved in designing such a bioremediation process.
8. Explain the significance and roles of biofilms in aquatic environments.
9. What are the main impacts of
a). manure production and disposal from large-scale farming
b). sewage sludge disposal on farm lands