Soil Science/Bacteriology 523
Exam I, Spring 2004
Answer 10 of 11 questions(10 pts ea.)
Due March 4, 2004
Name: _______________________
1. The inorganic and organic materials that constitute soils collectively create a unique habitat
for microorganisms.
a) What are the major minerals types that comprise soil, and what are their affects on soil
properties or microbial nutrition?
b) Define soil texture and explain how this is related to mineralogy.
c) How are soil texture and soil porosity related?
d) What are the major organic components of soil?
e) How does the organic matter content of soil affect the porosity?
f) Explain the concept of “habitable pore space” as it relates to soil bacteria. How is the
amount of habitable pore space in a soil related to its texture?
g) Which of the graphs below do think would you depict the theoretical relationship between the
biomass of bacteria in soil and the habitable pore space? Why? (
A
B
Bacterial Biomass
C
Habitable pore space
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2. Several schemes for classifying Compare and contrast autocthonous/zymogenousoligotroph/copiotroph-r/K strategist as functional categories. Considering the pools of carbon
present in soil, explain why these terms have come to be applied to soil bacteria. Give an
example of organism that may fit into each category and explain your reasons.
3. What characteristics define an organism as being a saprotroph, biotroph or necrotroph? In
your answer give an example of an organism (genus name or physiological type) and explain
why it fits the definition. Can the r/K characterization be applied to each of these groups? For
example, can saprotrophs be considered as being r or K strategists? If so, are they all r, all K
or possibly a mix of both? Apply the same question to the biotrophs and necrotrophs
4. Define the characteristics of an lithoautotroph and chemoorganotroph. Give four examples of
each, specifying whether in the example given the organism is an aerobe, facultative
anaerobe, or ananerobe. Explain how the activity affects the cycling of one or more elements.
5. Soil microbes are typically considered to inhabit an energy-limited environment. Explain why
this is so. Consider in your discussion how this statement may be applied equally to
organisms that grow as organoheterotrophs as well as lithoautotrophs. As part of your answer
regarding lithoautotrophs, list the major types of these organisms that inhabit soil.
6. Cultural and molecular approaches, such as those based on PCR amplification of nucleic
acids, are potentially complementary for use in investigating soil microbial communities. What
are the strengths and weaknesses of PCR? Contrast and compare these with regards to
strengths and weaknesses of culturing approaches. How might these approaches be used
together to gain an understanding of microbial communities that is more comprehensive than
that obtained by either alone. Give an example.
7. What information about a microbe does analysis of the 16S rRNA gene provide? Why is this
useful as a molecular tool for analysis of microbial communities? What are the limitations of this
type of analysis in terms of gaining an understanding of microbial community activities?
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8. Explain the basis for repetitive element PCR (REP-PCR). How does this information differ
form that obtained from analysis of 16S rRNA genes? Explain how REP-PCR was applied to
investigate endemic communities of fluorescent pseudomonads in the study that was discussed
in class.
9. There is great interest in understanding the impacts of plants on soil microbial communities
and identifying the communities of organisms that associate with plants. In class, we discussed
a study focusing on Pseudomonas in rhizospheres. Explain DGGE and how it was used to
investigate this issue.
10 a) Explain how substrate level, substrate degradation rate and substrate are related in first
order degradation.
b) Data given below are for degradation of carbofuran in an aerobic soil. Determine k from
this data. (5 pts).
Time (months)
mg/Kg soil
0 (application)
200
1
120
2
80
3
75
4
40
5
35
c) If the soil were flooded, how might this affect k for the degradation of carbofuran?
d) List four factors that may affect the decomposition rate of carbofuran and explain how these
may effect the process. Are some factors more important than others or are they all equally
important? Explain.
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11. Explain the roles that both biotic and abiotic reactions may have in the formation of soil
organic matter (SOM). Compare and contrast the polyphenol and modified lignin theories for
soil organic matter formation. In both theories lignin has a central role, why? Propose an
experiment in which you could test the extent to which one or both may be operative in humus
formation (10 pts).
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