Soil Microbiology Final Exam Study Questions – Linda
3,8,13,18,23,28,33,38,43,48,58
3. Draw a table showing the main characteristics of VAM, ectomycorrhizae, ericoid, arbutoid
and orchid mychorrhiza.
From handout discussed in lecture 10/23-10/25
Ecto
AM
Ericoid
Arbutoid
Orchid
Fungi
X
X
X
X
Septate
Hyphae
Penetrate
X
X
X
X
Cell Wall
Mantle –
Fungal
X
X
Sheath
(Sock)
Hartig Net
X
X
Hyphal
Coils in
X
X
X
X
Cell
Vesicles in
Cells or
X/Tissues
External
?only short roots
Not very far
?connected to
Hyphae
Extensive
Extensive
are extensively
(mats)
another tree?
???????
infected?
Type of
Basidiomycete Zygomycete Ascomycete Basidiomycete
Basidiomycete
Fungus
Ascomycete
Zygomycete
Range
Boreal
Tropical
8. Explain how Doug-fir needles and Red Alder leaves differ in their decomposition.
Short-term decomposition (less than 2 years)
Red Alder>Doug-Fir>Western Hemlock>Pacific Silver Fir
Long-term decomposition
Doug-Fir>Western Hemlock>Red Alder>Pacific Silver Fir
Too high an amount of nitrogen can actually slow down decomposition after 2 years because it
complexes locking up carbon and nitrogen making them less bioavailable. Complexes refers to
being tied up in a lignin molecule. Lignin is an amorphous molecule that is constantly changing.
We don’t know exactly what it is except that it’s a mass of stuff that’s been recombined. This is
what happens with Red Alder, this phenomenon can also occur in other high nitrogen situations
such as biosolids applications. If there is less nitrogen then carbon will remain more bioavailable
(ie proper C:N ratio for uptake) as is the case with Doug-Fir needles. So initially Red Alder
leaves decompose much faster but then slows way down. Doug-Fir needles decompose slowly,
but at a more constant rate, so after two years the rate is faster than Red Alder leaves.
13. Give an example of microbial transformation of P, S, Fe, Hg, or Cd.
P mineralization: Organic P is released as phosphate by Sclerotium, Fusarium, Aspergillus, and
others. Aerobic.
P immobilization: Microbial uptake of P by Bacteria or Fungi. Aerobic.
S mineralization: Organic s is released by many genera of bacteria in anaerobic environments
(this is the smelly thing)
Fe ferrous oxidation: FeS2 FeSO4 + H2SO4 by Thiobacillus ferroxidans in aerobic
conditions. The acid generated corrodes Fe pipes.
Hg methylation: Hg2+  CH3Hg+  CH3HgCH3 Can happen in aerobic or anaerobic
conditions by Bacillus, Clostridium, Pseudomonas,…. Methylated mercury is the toxic form.
Cd methylation: Cd2+  CH3Cd+ by Pseudomonas in aerobic conditions.
18. Describe the process of microbial succession on decomposing conifer needles.
Microbial Ecology handout from lecture 10/16-10/21 and lab report.
Succession is when one species seems to be clearing the way for the next. First the molecules
with relatively simple bonds are broken down, sugars, starches and simple proteins. The fungi
responsible for this have relatively short life spans and are prolific spore producers. Next
cellulose is decomposed. Cellulose is more complex than sugars and so more difficult to break
down. Finally, the complex molecule lignin is left and is broken down last. Peroxidase enzyme
is the enzyme typically associated with lignin decomposition. Because lignin decomposition is
slow these fungi have a longer life span. They tend to be basidiomycetes (have to produce
mushrooms). Bob also discussed initial floristics vs relay floristics, initial is when all the species
are present at the beginning some are long-lived and some are short-lived. Relay floristics is
succession, later species are not present initially.
If you want more detail on species composition here is an excerpt from our lab report…….
Our results provide strong evidence of a fungal succession based on the changing nature of the available substrates.
On the green needle that was still on the tree we observed colonies of Zygomycetes and Deuteromycetes. The
Zygomycota are typically found on more readily decomposed materials such as dung or other soil organic matter.
The Deuteromycetes are the asexual molds. The substrates that they are commonly found on are simple substrates
similar to the Zygomycota, and also less readily decomposed substrates such as leaves (Trudell). Up to 10% of plant
dry weight can be made up of the simple molecules such as sugars that are readily broken down. These soluble
molecules are readily leached from plants and quickly utilized by microorganisms (Paul and Clark). This
information suggests that the fungal colonies present on the green needles are utilizing the plants glucose molecules
as their substrate. On the needle that had recently fallen off the tree and was on the top of the litter layer we
observed Deuteromycetes and Basidiomycetes. This shows a shift in the colonies, we no longer saw Zygomycetes
and saw a new type of fungi, the Basidiomycetes. The Basidiomycetes are mostly found on large woody debris,
twigs, cones and leaves (Trudell). This suggests that the simple molecules that were supporting the fungal growth on
the green needle have been used up and the Deuteromycetes and Basidiomycetes are using a more complex
molecule such as cellulose as their substrate. On the needle that was further down in the humus portion of the litter
layer we only observed one type of Basidiomycete. This suggests that the only substrate left at this stage of
decomposition is the more complex lignin molecules. Other types of fungal colonies are no longer observed
because the substrates that support them have been used up. The green needle and the recently fallen needle had
more types of fungal colonies present on them. There are more types of organisms that have the enzymes to
breakdown these simple molecules, but far less that have enzymes that can degrade lignin.
23. Describe the three basic ways that N fixation rates are determined.
Acetylene reduction activity (ARA): The enzyme nitrogenase is responsible for dinitrogen
fixation. It is a 3-step process, at each step a bond is broken and 2Hs are added. It was
discovered that nitrogenase will also reduce acetylene to ethylene (HCCH  H2CCH2), this fact
is used in a common (and relatively cheap and easy) method to determine relative rates of Nfixation. You add 10% acetylene by volume to a gas-tight system with your N-fixer in there, let
the reaction run a period of time, remove a gas sample and analyze on the GC for the amount
ethylene produced. This will be proportionate to the rate of N-fixation.
15
N-isotope dilution – Add ‘labelled’ nitrogen to a system and see where it ends up.
Accretion with time – (Primary succession) This method looks at nitrogen in a system that was
known to not have any nitrogen in the system at a previous time in history providing you with a
rate of N fixation. An example of this would be looking at soil nitrogen in an area that was
exposed due to glacial retreat at a known time.
28. Define: hyphae, conidia, rhizomorph, flagella
Hyphae: “Typically fungi form slender filaments or hyphae, either branched or unbranched,
septate or nonseptate, and commonly multinucleate”(Paul and Clark p92). “A filament that
collectively makes up the body of a fungus” (Campbell, Reese and Mitchell). “Their body plan
is filamentous (hyphal), made up of numerous microscopic thread-like hyphae that collectively
are called a mycelium” (Trudell).
Conidia: “A naked, asexual spore produced at the ends of hyphae in ascomycetes” (Campbell,
Reese and Mitchell).
Rhizomorph:????????
Flagella: “A long cellular appendage specialized for locomotion, formed from a core of nine
outer doublet microtubules and two inner single microtubules, ensheathed in an extension of
plasma membrane” (Campbell, Reese and Mitchell).
33. What is the rhizosphere and why is it so important in soil microbiology.
The rhizosphere is the 1-2mm area surrounding roots. The chemistry of the rhizosphere is much
different than in the surrounding soil as a result of root exudates such as CO2, organic acids
(acetate), enzymes, protons, and bicarbonate. These exudates are food stuff for bacteria, this
area supports many more bacteria than surrounding soil. The pH of the rhizosphere can be up to
two pH units more acidic because plants use H+ pumps to move ions across cell walls.. This
change in chemistry can help attract nutrients that are in the form of cations (NH4+) that are
adsorbed to negatively charged clay particles in the vicinity, and solubulize phosphate for uptake
by the plant.
38. Describe the process of log decomposition. Why is N immobilized in logs for so long?
The decomposition of logs is a slow process because of the biochemical makeup of trees. The
stages of decomposition are leaching, weathering and biological action (most important aspect
except fire). Sugars are decomposed rapidly, waxes and amino acids are decomposed more
slowly but still relatively rapidly. Extractives (phenolic compounds that give wood its color)
give wood decay resistance but are still more easily decayed than cellulose and lignin. Cellulose
and lignin are the most difficult molecules to decompose and so control the rate of
decomposition. Cellulose is composed of ‘tons and tons’ of glucose molecules and forms the
vertical structure of wood. Cellulase is the complex of enzymes responsible for breakdown of
cellulose molecules. This energy source is relatively available to fungi (but not bacteria). They
‘chew’ cellulose at the O molecule breaking it up into the constituent glucose molecules. Lignin
is the ‘glue’ holding cellulose together. It is a complex arrangement of phenolic rings and 3 C
straight chain linkages and is much more difficult than cellulose to degrade. Peroxidase is the
enzyme frequently associated with lignin decomposition.
In addition to these biochemical factors the ratio and concentration of chemical factors also plays
a role. The ideal C:N ratio for microbial uptake is between 20 and 30, logs have C:N ratio of 45
(Doug-fir) to 100 (Pacific Silver Fir). Also playing a role are the lignin concentration and
Lignin:N ratio. Nitrogen is immobilized in logs for so long because all these factors contribute
to slow decomposition rates. Microbes liberate N from the logs in a proportionate C:N ratio,
fungi need about 10 carbon molecules for every nitrogen molecule.
The rate of decomposition will also be affected by physical factors such as temperature,
moisture, size, location (buried, clear cut, …)
43. Describe the roles of Azotobacter, Rhizobium, Glomus, Boletus, Frankia, Nitrobacter,
Desulfvibrio, Thiobacillus.
Azotobacter: Free-living nitrogen fixer
Rhizobium: Symbiotic nitrogen fixer, lives in association with legumes
Glomus: Most common AM
Boletus: EM fungi (can tell a Boletus because it has pores not gills)
Frankia: Symbiotic nitrogen fixer, lives in association with woody perennials such as Ceanothus
and Alnus rubra.
Nitrobacter: Key bacteria in nitrification. Oxidizes nitrite to nitrate.
Desulfovibrio: Reduces inorganic sulfur in anaerobic conditions. SO4-  H2S.
Thiobacillus: Oxidizes inorganic sulfur in aerobic and anaerobic conditions. Also involved in
Fe oxidation. SO42- that is generated is corrosive to Fe pipes.
48. How do anaerobic environments influence soil organisms?
Bacteria are the only soil organisms that can live in anaerobic conditions (no fungi or protozoa
Archae are anaerobic). Anaerobic bacteria can be obligate anaerobes or facultative. Microbially
mediated redox reactions that occur as a soil changes from an aerobic to anaerobic state will shift
from most oxidized (aerobic) to most reduced (anaerobic). An example of an aerobic redox
reaction is O2  H2O. Examples of anaerobic redox reactions are CO2  CH4 and SO42- 
S2-. Anaerobic metabolisms are not as efficient as aerobic metabolisms and result in incomplete
decomposition of organic matter with gas production (methane, hydrogen sulfide,
denitrification).
58. What are nonmycorrhizal, facultatively mycorrhizal and obligate mycorrhizal plants. Where
are you likely to find nonmycorrhizal plants?
Mycorrhiza describes a fungus/root association.
Nonmycorrhizal plant: does not form a fungus/root association.
Faculatively mycorrhizal plants: can form a fungus/root association but does not have to for its
survival
Obligate mycorrhizal plants: has to form a fungus/root association for its survival.
Nonmycorrhizal plants tend to be ‘weedy’ species or more recently evolved plant species. An
example is the mustard family. You would tend to find these plants growing in soil where there
are a sufficient amount of available nutrients because they do not have the assistance of the fungi
in nutrient uptake.