Soil Microbiology and Biochemistry
Soil Sci./Bact. 523 Exam II
Due Apr. 23, 2004
Name:______
Part I. Answer all questions. (50 pts).
1. Microbial interactions underlay most or all of the processes important in biogeochemical cycling. Two examples discussed in class were 1) the interactions that occur in interspecies H2 transfer that drive oxidation of organic acids such as acetate in and interspecies H2 transfer and 2) the collective action of the nitrifying bacteria which effects nitrification. Please answer the following regarding these processes. (20 pts).
a.) Define the process of interspecies H2 transfer. This definition should address the two types of organisms involved in the interaction, the physiological activity each organism contributes to the interaction, how the physiological activities of each organism affect the other, and the characteristics of the environment that affect the activity of each organism.
b.) Define the process of nitrification. This definition should address the two types of organisms involved in the interaction, the physiological activity each organism contributes to the interaction, how the physiological activities of each organism affect the other, and the characteristics of the environment that affect the activity of each organism.
c.) Compare and contrast the processes of interspecies H2 transfer and nitrification. How are the two similar? How do they differ?
2. The data in the table below are from a study on the effects of different grass species on nitrogen cycling. Use the data given to fill in the missing values, calculate how much nitrogen is required for microbial growth in each grass system, and estimate the annual net nitrogen mineralization rate for the Grass B system. Assume that roots are the only plant input, that roots are 45% carbon, and all the grass nitrogen is available, that lignin carbon is unavailable, and that 80% of the non-lignin carbon is metabolized in one week (k = 1.6 yr-1). The microbial growth yield is 0.5 and the microbial C/N ratio is 8. State any other assumptions you think are necessary and show your work. (10 pts)
3. Ammonia oxidation is a key step in the N cycle and the ammonia-oxidizing bacteria (AOB) are essentially the only organisms in soil that mediate this transformation. However, the AOB characteristically comprise an almost insignificant fraction of the microbial biomass in soil. Why? Your answer should include both physiological characteristics of AOB and the environment that may be relevant. (10 pts)
4. Biological nitrogen fixation (BNF) is a key process supporting life on earth. Please answer the following regarding this activity. (10 pts)
a) Describe how nitrogenase works. Your answer should include a description of the biochemical requirements of the enzyme including biochemical factors that positively and negatively affect its activity.
b) Explain how the ability of and organism to carry out BNF is affected by growth as a free-living organism and how growth in a symbiotic association may alleviate some of the restrictions on BNF that free-living organisms face.
c) Is it inherently better for organisms to mediate BNF as symbiotic organisms? If so, why do you think it is that all bacteria capable of BNF (or at least many more species of these) do not establish symbiotic associations with plants.
Part II. Answer five of the following six questions. (50 pts).
5. Four symbiotic associations discussed in class were those between rhizobia-legumes cyanobacteria-fungi, mycorrhizal fungi-woody and mycorrhizal fungi and non-woody plants. Compare and contrast each of these with associations with respect to the benefits each partner gains from the interaction, and the structural adaptations that each partner develops in the symbiosis. (10 pts)
6. A tripartite association often forms between legumes, nitrogen-fixing bacteria, and mycorrhizal fungi. Why would a legume especially benefit form colonization by the two microbial symbionts? How might mycorrhizal fungi benefit from the tripartite association? What might the benefits be to the rhizobia? (10 pts)
7. Microbial processes underlying biogeochemical cycling of elements in soil are affected by a variety of factors that act at different levels. As such, “level of control” diagrams like that shown below for denitrification can be used to illustrate these factors, their relative importance, and possible interactions. (10 pts)
a) For the denitirification figure shown below, please explain the relative importance of the proximate physiological factors and how the (distal) soil factors in affecting the physiological (proximal) factors.
b) Explain the relative importance of the proximate physiological factors and how the (distal) soil factors in affecting the physiological factors that you have indicated in your diagram.
c) Comparing the distal and proximal factors, which might you expect to be more variable? Why?
8. Is the growth and activity of organisms in anaerobic environments generally limited by the availability of electron donors or electron acceptors? Explain your answer. (5 pts)
In addition to their role in cycling natural organic matter, Sulfate-reducing bacteria are also known to transform some xenobiotic chlorinated organic compounds in anaerobic environments. Do the occurrence of these transformations make sense considering your answer to the first part of this question. (5 pts)
9. Compare and contrast the following processes with respect to the types of organisms mediating the transformations, what physiological benefit each organism type derives from the activity, and the biological diversity of organisms mediating each process. (10 pts)
Methane consumption vs. methane formation
Nitrogen gas (N2) consumption vs. nitrogen gas (N2) formation
Sulfide consumption vs. sulfide formation
10. Hydrocarbon degradation is an important part of the carbon cycle, and is a process affected by both the nature (structure, chemical composition) of the electron donor (hydrocarbon) and the types of electron acceptors available.
a) Explain how and why these transformations are affected by the nature of the electron donor. As part of your answer, discuss the enzymatic mechanisms that aerobes and anaerobes have evolved to allow metabolism of these compounds. (5 pts)
b) Explain how and why these transformations are affected by the nature of the electron acceptor. As part of your answer, use hydrocarbon-contaminated groundwater as an example and discuss how the presence of the hydrocarbons would affect electron acceptor availability and how availability of differing types of electron acceptors may affect the pattern of hydrocarbon degradation (e.g., the types of hydrocarbons). (5 pts)
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