CSS360 Exam 1 Review Questions and Study Guide I. Questions Based on Lecture Materials: A. Soil Properties: 1. What contributions to overall soil health do soil aggregates provide? For example, what soil properties are influenced by the presence of aggregates? 2. What differentiates the O, A, and E horizons in a soil profile? 3. In a highly reduced soil (e.g. a waterlogged or saturated soil), what is the source of the small, red “dots” (as in slide 17 of lecture 1)? 4. Given the soil textural triangle below, indicate what soil texture is composed of 60% silt and 20% sand. 5.
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A sample of soil reveals that 3 cm3 of soil has a mass of 6.30 g. What is the bulk density of the soil? What will happen to the bulk density and particle density of a mineral soil when organic matter is incorporated? Why is this the case? Differentiate between micropores and macropores. What roles do they play in water holding capacity and water movement? What is the matric potential of a soil? What happens to the matric potential as soils begin to dry out? What is the difference between gravitational water and field capacity? B. Soil Carbon 1. Why is soil organic carbon important to overall soil health? 2. Why does tilling reduce soil organic carbon over time? 3. How does the active carbon pool differ from the slow and passive carbon pools? What type of matter constitutes each pool? 4. Which carbon pool responds the fastest to changes in soil management? 5. What are some methods that can be used to build soil carbon? 6. How does the C:N ratio of a substrate (e.g. manure, compost, plant litter) that is incorporated into a soil influence N availability to plants and the build-­‐up of soil organic matter? 7. An N poor amendment is added to a soil with a C:N ratio of 36:1. What happens to the nitrogen in the amendment and how does this affect the microbial community? 8. What is lignin? How does the lignin:N ratio affect the speed of decomposition? Why? 9. What are some controls over soil aggregate formation and stability? C. Soil Bacterial Genetics and Gene Exchange 1. What is the difference between prokaryotes and eukaryotes? What are the 3 domains of life? How do archaea differ from bacteria? 2. Name three different types of bacterial shapes 3. Why is endospore formation important in soils? 4. What is the difference between a Gram + and Gram – bacteria? 5. Bacteria A has a Ks of 40 mmol while bacteria B has a Ks of 110 mmol while growing on glucose. Based on this information, which bacteria would you expect to have a competitive advantage at a substrate concentration of 30? 6. What is the difference between a copiotroph and an oligotroph? Assuming that both can grow on the same substrate, which would “win” when the limiting substrate is at a high concentration? 7. What is the central dogma of molecular biology? 8. What is the structural difference between RNA and DNA? 9. What is the ribosome and why is it important in cell function? 10. What is the difference between transcription and translation? 11. Why is the 16S rRNA gene the current basis for bacterial taxonomy? 12. Name one problem encountered by using 16S rRNA gene for bacterial taxonomy. 13. What is the role of the plasmid in bacteria? 14. Name three methods by which genetic material is exchanged among soil bacteria. 15. Why is conjugation the most important pathway of genetic exchange among bacteria? 1.
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D. Bacterial Diversity, Viruses, and Metabolism What soil properties have been proposed to control bacterial diversity? What are the properties of viruses? How do they differ from bacteria? What are the two life cycles of bacteriophages? How can bacteriophages increase bacterial genetic diversity? Why are bacteriophages not as important in soil as they are in the aquatic environment? 6. A bacteria obtains its carbon from CO2 and its energy from photosynthesis. What is the class of this bacteria? 7. Differentiate between a chemoheterotroph and a chemoautotroph. 8. What is being reduced (accepting electrons) and what is being oxidized (donating electrons) in the following reaction: C6H12O6 (aq) + 6 O2 (g) → 6 CO2 (g) + 6 H2O (l) 9. Name four electron acceptors in bacterial metabolism and place them in order of the highest energy yielding to the lowest energy yielding. 10. Where would you expect to find aerobic respiration occurring in a flooded soil? 11. Where would you expect to find anaerobic respiration occurring in a well aerated soil? 12. What are siderophores? 13. How does sulfate reduction and CO2 reduction (methanogenesis) differ from the other methods of metabolism in regard to their C source? 14. What is the advantage of using enzymes in a chemical reaction? 15. What is the role of cofactors in enzymes? 16. How are enzyme kinetics (Vmax and Km in the graphs) related to bacterial growth kinetics? 17. Name two environmental factors that control enzyme activities. 18. What is the difference between an ectoenzyme and an exoenzyme? E. Nitrogen Cycling 1.What is meant by “redox power” in terms of electron flow from a donor to an acceptor? 2. Name three input sources of nitrogen to soil 3. What regulates N fixation? 4. What is a heterocyst? Who uses them? 5. Name the three types of N fixation discussed in lecture. 6. Discuss the general steps of Rhizobia infection of legume root hairs 7. What is the advantage to the plant and to the bacteria in symbiotic N fixation? 8. Discuss the difference between N mineralization and N immobilization. 9. What are the possible fates of NH4+ released from N mineralization in soil? 10. In what conditions would N loss from ammonia volatilization be most pronounced? 11. What are some possible fates of nitrate produced from nitrification? 12. Where in the soil, under what conditions would you expect denitrification to occur? 13. What is anammox? How does anammox differ from denitrification? 14. Why was the anammox process overlooked for so long? II. Questions Based on Reading Assignments: Condron et al., pp. 87-­94 1. Condron et al. discussed the effects plant communities have on the microbial community and how plant productivity is affected or affects the microbial community. Briefly discuss this. 2. What is the relationship between soil organic matter and microbial biomass? 3. What are the general differences between soils that are dominated by fungi and those dominated by bacteria? 4. What is meant by “functional redundancy” in the microbial community? Condron et al., pp. 98-­108 1. According to this manuscript, what is the consequence of nitrogen addition on the microbial community composition and abundance? 2. Compare the stoichiometric decomposition theory with the nitrogen mining hypothesis. 3. What is the affect of nitrogen fertilization on lignin degradation? 4. Give some examples of why the microbial biomass carbon is an important carbon source in soil. Smith et al., Eutrophication 1. Give some examples of how human activities have drastically impacted the global nitrogen cycle. 2. What are 3 fates of N added to soil as fertilizer? 3. What is eutrophication? 4. What are some ways that eutrophication affects lakes? 5. How does eutrophication affect coastal marine systems? 6. How does eutrophication (or overall N addition) affect terrestrial systems? 7. What relationship did the authors show between the anthropogenic addition of N to the ecosystem and atmospheric CO2? (e.g. what affect may increased N additions have on CO2 uptake and storage by soil? The two nitrogen readings are supplementary to the lecture. Use them to clear up any questions you may have. The exam will only cover what is covered in the N lecture, not the two reading assignments. III. Synthesis Questions: (Variations on these types of questions should be expected on the exam. Typically I will give you a choice of a few questions—these are “essay” questions, there will likely be two or more of these on the exam. Answers should be in complete sentences with all the support for your answer you can muster.) 1. Discuss the decay continuum of plant material as it falls to the soil surface. Include how substrate quality affects litter decay and how soil moisture may affect the cycling of nutrients. 2. Mineralization of NH4+ to NO-­‐ is a reaction in the overall process of organic matter breakdown. Describe this N mineralization in relation to : a) the microorganisms involved, b) the affect of anaerobic conditions, c) the effect of soil pH and d) the effect of adding straw with a C:N ratio of 80:1. 3. Describe the process of how N2 gas is fixed and incorporated into the soil-­‐plant system. 4. A flooded, stable, saturated soil forms an oxygen diffusion gradient at the soil surface. All electron acceptors are found in this soil. A.) Discuss how the microbial communities would be organized with depth according to electron acceptor. B.) How can two or more electron acceptors be used at the same time by different microbial populations in the same general depth (think soil structure). 5. Describe how sulfate reducers and methanogens are dependent on fermentating bacteria. 6. Draw a graph showing growth curves comparing an oligotroph and copiotroph who both use the same substrate for growth. What is a possible outcome if they use different substrates for growth? 7. Pick one “strange bacteria” that was discussed in class and describe their morphology, unique properties, etc. that relate to that bacteria. 8. What may be the advantage of incorporating cover crops with different C:N ratios in terms of nutrient availability for a crop? Why is this the case? 9. Why may it be difficult to both restore soil organic matter with the addition of litter, manure, compost, etc. AND supply crops with the nutrients contained within the SOM or associated with it? 10. Discuss how plant roots in saturated soils may influence the nitrogen cycle of a soil. 11. Why would microbial RNA rather than DNA be targeted for analysis in a soil? Give an example of a question that this would address. 12. Your goal is to eliminate nitrogen losses from a field. Would you target nitrification or denitrification and why?