University of Wisconsin–Madison


Professor Katherine Mcmahon (Microbiology 425, Environmental microbiology)

The questions below are all fair game for the final exam. I will select roughly half of the content for the actual exam. The actual exam will also include 5-8 multiple choice questions (not listed here).

For guidance on how much detail to provide in your answer, I am listing the approximate number of lines I would expect you to use on the actual exam, to answer the question. The last page of this document has line numbers to use for calibration purposes.

1. Imagine that after graduation you secure a job at an environmental remediation firm as the resident (micro)biologist, mainly because you took Microbiology 425 and have expertise in environmental microbiology. They hire you to advise a team of ecologists, engineers, and chemists on a range of pollution cleanup and mitigation projects. The first big project you are assigned to is an oil spill that just occurred because an oil tanker sank in Puget Sound, Washington.

a. The engineers propose spraying a chemical dispersant called Corexit on the oil slick because they read about its use for the Deep Water Horizon spill cleanup. The ecologists disagree because they think it is too toxic to wildlife.

i. Explain to both the engineer and the ecologist the purpose of the dispersant (6 lines).

ii. The team wants your advice on whether the dispersant will actually work and to provide evidence from past studies about its effect on microbial processes. Outline the technical report you would provide to them. (20 lines)

iii. Specifically, the team wants to know whether the oil and dispersant degradation rates will be comparable to those reported for the Deep Water Horizon spill. Compare and contrast the conditions at the location of the current spill vs the DWH, in order to answer their question. Focus on conditions that are relevant to the microbes. (15 lines)

b. You are given a large research budget to study the effects of the oil spill on the microbial communities in Puget Sound. Outline THREE datasets that you would collect and briefly describe how you would collect them. (30 lines)

c. Describe the results you would expect to obtain from your studies. Specifically, which organisms do you expect to be enriched in water affected by the spill? (10 lines)

d. Identify at least three genes or pathways you would expect to find enriched in Puget Sound after the spill. (6 lines)

e. One of the ecologists asks whether the team should expect to find a lot of Methylomonas in the water, since he read that this genus was enriched after the DWH spill. Answer her question and explain your answer. (10 lines)

f. One of the engineers asks why oil spills cause dissolved oxygen depletion. She learned about biological oxygen demand in her class on wastewater treatment but doesn’t understand why oil would have the same effect as sewage. Explain the mechanism of hydrocarbon-mediated DO depletion to her. (15 lines)

2. Imagine that you just joined the laboratory of a famous oceanographer who up until recently has not employed many of the more modern molecular techniques to the study of marine microbes. Thus, she is unfamiliar with the strengths and limitations of various molecular methods. She is funding you as a PhD student to study the role of polyamines in the ocean because a recent analysis of metagenomic data showed that genes encoding polyamine transporters were abundant in many marine samples. While doing some background reading, you learn that polyamines are found in marine phytoplankton.

a. The PI asks you to analyze some unassembled metagenomes and tell her which of the major heterotrophic marine bacteria have polyamine transporters in their genomes. You know this is not possible to do without gathering additional data. Explain why this is the case. (8 lines)

b. Propose a workflow that could be used to generate the information your PI is seeking, assuming no budgetary constraints. (15 lines)

c. Now that you know which marine bacteria carry polyamine transporter genes, your PI wants to know which of these bacteria are actively using polyamines, in water off the coast of Georgia. Propose a workflow that could be used to generate the information your PI is seeking. (15 lines)

d. Now imagine that a new undergraduate researcher joins the lab. He has never taken a course in environmental microbiology or marine microbiology. The PI asks you to explain the concept of the Microbial Loop to this new lab member. Outline how you would do this, using the polyamines as an illustrative example. Feel free to draw a diagram if you think it would help. (12 lines)

3. The nitrogen cycle in freshwater lakes is complex. In temperate eutrophic lakes such as Lake Mendota, which thermally stratify during the summer, ammonium accumulates to high concentrations in the hypolimnion. When the lake turns over and mixes in the fall, the ammonium is distributed throughout the water column and persists at concentrations ~ 1 mg-N/L until ice forms. During the winter under the ice, much of the ammonium is gradually converted to nitrate.

a. Identify the individual steps in the conversion of ammonium to nitrate. Write the balanced reactions. (6 lines)

b. Nitrite concentrations under the ice rarely rise above 20 uM. Predict which groups of nitrite oxidizing bacteria would be found under the ice in the winter: Nitrospira or Nitrobacter. Justify your answer. (8 lines)

c. The dissolved oxygen concentrations under the ice tend to be high when the ice forms, but they become depleted during winter leading up to the spring thaw (but not to the point of “hypoxia”). Outline the processes that are leading to this oxygen consumption in the context of the carbon cycle under the ice. Compare and contrast this with what is happening in such lakes during the summer. (15 lines)