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Microorganisms in Terrestrial Ecosystems
CHAPTER OVERVIEW
This chapter discusses the different types of microorganisms associated with soils. The interactions of
microorganisms with plants are discussed. The subsurface biosphere is discussed.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:
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describe the various environmental conditions found in soils
discuss the various types of associations between plants and microorganisms
discuss the interactions of microorganisms and plants
discuss organic matter accumulation and decomposition in soils
discuss the subsurface biosphere
CHAPTER OUTLINE
I.
II.

Soil as a Microbial Habitat
A. Soil consists primarily of inorganic geological materials, which are modified by the biotic
community
B. Soil varies in terms of the amount of oxygen available to microorganisms
1. Highly oxygenated areas are found on particle surfaces; microorganisms are often found in
thin films of water on these surfaces
2. Under certain conditions, soil may contain isolated pockets of water, which serve as miniaquatic environments; oxygen concentrations are generally lower in these pockets of water
3. Waterlogged soil is very similar to anaerobic lake sediments
4. Changes in water content, gas fluxes, and the growth of plant roots can affect the concentration
of carbon dioxide and other gases in the soil
C. Soils can be categorized by their gross composition; mineral soil contains less than 20% organic
carbon, while organic soil contains more; most soils are mineral
D. Soil organic matter (SOM)
1. Helps retain nutrients, maintain soil structure, and hold water for plants; plowing, irrigation,
and other soil disturbances can increase microbial degradation of this organic matter, thereby
decreasing soil fertility
2. Nonhumic SOM has not undergone significant degradation; humic SOM (humus) has been
converted into a complex blend of organic materials that are recalcitrant (resist degradation)
3. Breakdown of plant material to SOM occurs in three steps:
a. Soluble carbohydrates and proteins are easily converted to CO2 and biomass
b. Complex carbohydrates (e.g., cellulose) are degraded with extracellular enzymes to
smaller sugars that are readily assimilated
c. Resistant materials (e.g., lignin) degrade slowly and accumulate in soils
E. Nitrogen is an important element in soil ecosystems; carbon to nitrogen ratios affect the activity of
microbial communities; exogenous nitrogen is derived from agricultural fertilizers
F. Phosphorus fertilizers can cause eutrophication of surface waters when excess phosphorus runs off
of soils
Microorganisms in the Soil Environment
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A.
Bacteria in soils are remarkably diverse and numerous with thousands of species in each gram of
soil; the vast majority of rRNA genes are from novel genera that lie within nine phyla; fungal and
archaeal diversity may rival that of bacteria
B. Bacteria are found primarily on the surfaces of soil particles, most frequently on surfaces of pores in
these particles; this probably protects them from predation by protozoa and gives them access to
soluble nutrients
C. Filamentous fungi form bridges between separated particles or aggregates called peds; this exposes
the fungi to high levels of oxygen; filamentous fungi move nutrients and water over great distances
in the soil
D. The microbial loop in soils differs from that of the open ocean; in soils plants (not microbes) are
primary producers; microbes still rapidly turn over organic matter, making the nutrients available to
higher trophic levels (predatory protozoa); degradative enzymes released from animals, plants,
insects, and microbes contribute to soil biochemistry
III. Microorganism Associations with Vascular Plants
A. Many types of plant-microbe interactions exist; commensalism is a relationship wherein one partner
is benefited, while mutualism benefits both partners; epiphytes live on plant surfaces; endophytes
colonize internal tissues; plant exudates support bacterial growth and competing saprotrophic and
pathogenic fungi
B. Phyllosphere microorganisms—a wide variety of microorganisms (Sphingomonas, Pseudomonas,
Erwinia) are found on and in the aerial surfaces of plants (phyllosphere), where they can utilize
organic compounds released by the leaves and stems
C. Rhizosphere and rhizoplane microorganisms
a. The rhizosphere is the volume of soil around plant roots influenced by materials released
by the plants; the rhizoplane is the root surface; both provide unique environments for
microorganisms; microorganisms in the rhizosphere serve as a labile source of nutrients
and play a critical role in organic matter synthesis and degradation
b. Numerous rhizosphere bacteria influence plant growth through the release of auxins,
gibberellins, cytokinins, and other molecules
c. Associative nitrogen fixation—nitrogen fixation carried out by bacteria on the
rhizoplanes and in the rhizosphere
D. Mycorrhizae
1. Mutualistic fungus-root associations in which the fungi are not saprophytic, but use
photosynthetically derived host carbohydrates
2. Six associations have been described; they fall into two broad categories:
a. Ectomycorrhizae
1) Ascomycete or basidiomycete fungi that grow as an external sheath around the root
and may grow between (but not within) cortical root cells, forming the Hartig net
2) Fungal hyphae can aggregate in soils, forming rhizomorphs that bring nutrients to
the plant
b. Endomycorrhizae
1) Fungi that penetrate the outer cortical cells of the plant root
2) Arbuscular mycorrhizae form characteristic structures known as arbuscules within
invaginations in the plasma membrane of cortical root cells; they protect from
disease and drought, and bring nutrients to the plant
3) Orchid endomycorrhizae are saprophytic and bring nutrients to the plant
3. Mycelia extend far into the soil, forming a mycorrhizosphere, and mediate nutrient transfer to
the plant; mycorrhizae increase the competitiveness of the plant and increase water uptake by
the plant in arid environments; they also make it possible to share resources (e.g., carbon,
minerals, and water); mycorrhizal helper bacteria aid in the development of the mycorrhizal
relationships
E. Nitrogen-fixing bacteria
1. Symbiotic nitrogen fixation (conversion of nitrogen gas to ammonia) by bacteria associated
with plants is crucial for global nitrogen cycles and agriculture; often performed by Rhizobium
in root nodules on legumes
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2.
The Rhizobia
a. Rhizobium—a prominent member of the rhizosphere community; it can also establish an
endosymbiotic association with legumes and fix nitrogen for use by the plant
b. The initial reaction of the plant is an oxidative burst; the Rhizobium survives this because
of its antioxidant abilities and it is subsequently stimulated (by plant flavonoid inducer
molecules) to produce Nod factors, which activate the host responses necessary for root
hair infection and nodule development
c. The bacterium induces formation of an infection thread by the plant; the infection thread
grows down into the root hair
d. Rhizobium spreads within the infection thread into the underlying root cells, eventually
giving rise to the nodule
e. Bacteria terminally differentiate into bacteroids that are enclosed by a plant-derived
membrane called the peribacteroid membrane
f.
Further growth and differentiation lead to the formation of nitrogen-fixing forms called
symbiosomes
g. Nitrogen fixation occurs within symbiosomes within the root nodules which are protected
from oxygen by leghemoglobin; the nitrogen is then assimilated into various organic
compounds and distributed throughout the plant
3. Stem-nodulating rhizobia—bacteria that form nodules at the base of adventitious roots
branching out of the stem above the soil surface; observed primarily in tropical legumes; the
nodulation process differs from that of the rhizobia
4. Actinorrhizae—actinomycete-root associations between members of the genus Frankia and
woody plants; Frankia can fix nitrogen and are important in the life of woody, shrublike
plants; the nodules take the form of lateral root clusters
F. Agrobacterium
1. Members of this genus that contain the Ti (tumor-inducing) plasmid cause the formation of
crown galls (tumors) on the plant
2. Gall formation is a complex process that involves transfer of Ti DNA into the plant host and
expression of a set of vir (virulence) genes
3. The Ti plasmid is an important biotechnology tool for transfer of new genetic characteristics
into plants
G. Other plant pathogens—Fungi, protists, and bacteria as plant pathogens—many fungi and bacteria
are plant pathogens, causing rusts, blights, rots, and other plant diseases; many viruses infect plants
and cause disease and economic losses (e.g., tobacco mosaic virus)
IV. The Subsurface Biosphere
A. Studied by examining outcrops, surface excavations, petroleum hydrocarbons, well corings, and
materials from deep mine sites
B. The subsurface biosphere may contain about one-third of the Earth's living biomass
C. Microbial processes take place in different regions
1. Shallow subsurface aquifers where water flowing from the surface moves below the plant root
zone
2. Subsurface regions where organic matter has been transformed by chemical and biological
processes to yield coal, kerogens, and oil and gas; mobile materials move up into more porous
geological structures where microorganisms can be active
3. Deeper biogenic zones where methane is being synthesized using geologic hydrogen as an
energy source
TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1.
An initial response by plants to root nodule-forming
bacteria; it involves the production of a mixture that
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____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
can contain superoxide radicals, hydrogen peroxide,
and N2O
Porous geological structures below the plant root zone,
through which water often flows
The volume of soil around a plant root that is
influenced by materials released from the root
Tumorigenic plasmid carried by Agrobacterium strains
Bacteria and fungi that infect and live within plants
Heterogeneous soil aggregates formed partly by
bacterial and fungal growth in soil
Substances that activate the host symbiotic processes
necessary for infection of root hairs by Rhizobium
Rhizobial cells found in root nodules; when fully
differentiated they are capable of nitrogen fixation
Nutrients available in a soluble form
Organisms found growing on the surface of a plant
Fungi that form symbiotic relationships with plant
roots bringing nutrients to the plant
The above-ground portions of a plant that acts as a
home for a microbial community
Bacteria that form symbiotic relationships with plant
roots, forming nodules, and fixing nitrogen
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
aquifers
bacteroids
dissolved organic matter
endophytes
epiphyte
mycorrhizae
Nod factors
oxidative burst
peds
phyllosphere
rhizobia
rhizosphere
Ti plasmid
FILL IN THE BLANK
1.
2.
3.
4.
5.
Plants can develop relationships with two or three different types of microorganisms. Several examples
are known. One involves a host plant,
, and rhizobia. Another involves a host
plant, endomycorrhizae, and
(association with actinomycetes). A third association
involves a host plant,
, and actinorrhizae.
Certain bacterial genera (e.g., Azotobacter and Azospirillum) carry out nitrogen fixation on the surface of
plant roots (i.e., the
). This type of nitrogen fixation is called ____________ nitrogen
fixation.
Associations between fungi and plant roots are referred to as mycorrhizae: if this association involves the
growth of the fungi as a sheath around the root tip with limited penetration of the hyphae into the cortical
region of the root, it is called
; however, if extensive penetration of the fungal hyphae into
the cortical regions of the plant root occurs, then it is called
. Certain of the latter type of
mycorrhizae have a characteristic structure called the ____________, and fungi with this structure are
called
fungi.
Certain tropical legumes are infected by
, which form nodules at the base of
adventitious roots branching out of the stem just above the soil surface.
Members of the genus Rhizobium infect the root hairs of legumes, stimulating the plant to form an
____________ ____________ down which the bacteria travel. Eventually the bacteria are released into a
host cell and are surrounded by a plant membrane to become
. After further differentiation
they become nitrogen-fixing
and are located in swollen structures called
.
MULTIPLE CHOICE
For each of the questions below select the one best answer.
1.
Which of the following is NOT used by
soil microorganisms to support their
growth?
a.
b.
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
moisture contained in soil pores
dissolved nutrients associated with soil
particles or in pores
c.
2.
3.
4.
organic matter released from the
plant roots
d. All of the above are used to support
growth of soil microorganisms.
Which of the following is NOT a benefit
to the plant involved in a mycorrhizal
association?
a. increased nutrient availability in
moist environments
b. increased water availability in arid
environments
c. increased utilization of
photosynthate
d. All of the above are benefits to the
plant of mycorrhizal associations.
Mycorrhizal helper bacteria (MHBs) help
with which of the following?
a. ectomycorrhizal development
b. endomycorrhizal development
c. Both (a) and (b) are correct.
d. Neither (a) nor (b) is correct.
Which of the following types of
compounds are released by
microorganisms and influence plant
growth?
a. auxins
b. gibberellins
c. cytokinins
d. all of the above
5.
6.
7.
8.
Which term refers to the aerial surfaces of
plants?
a. mycorrhizosphere
b. phyllosphere
c. residuesphere
d. subsurface biosphere
Bacterial symbionts have been identified in the
cytoplasm of arbuscular mycorrhizal fungi.
What is the role of these bacteria thought to be?
a. They act as an energy source for the
fungus.
b. They synthesize amino acids needed by the
plant and fungus.
c. They inhibit the growth of the fungus and
disrupt the mycorrhizae.
d. none of the above
Which microorganisms play a predominant role
in the decomposition of lignin-containing
materials of woody plants?
a. bacteria
b. archaea
c. fungi
d. viruses
In which of the following mycorrhizal
associations does the fungus invade plant cells?
a. orchid endomycorrhizae
b. ericoid endomycorrhizae
c. arbuscular mycorrhizae
d. all of the above
TRUE/FALSE
____ 1.
____ 2.
Soils that are very wet tend to be anaerobic.
Endomycorrhizae are detrimental to desert plants because they limit water uptake by the plant,
which is growing in an already arid environment.
____ 3. Agrobacterium, a tumor-producing bacterium that infects plants, has been of recent interest because
of its possible use as a vector for genetically engineering plants.
____ 4. The vast majority of microorganisms found in soils have been cultivated in the
laboratory.
____ 5. Soil consists of both organic and inorganic materials.
____ 6. Microorganisms inhabit five major subsurface zones.
____ 7. In an ideal soil, microorganisms function in thin water films that have close contact with
air.
____ 8. Most microbes in soil are embedded in the anoxic zones of soil particles.
____ 9. Soil organic matter tends to remain the same regardless of environmental conditions.
____ 10. Decomposition seems to be maximal at a carbon-to-nitrogen ratio of 30.
____ 11. Although the phyllosphere is a stable environment, it is nearly devoid of microbial life.
____ 12. Arbuscular fungi develop within folds in the plasma membrane of host plant cells.
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CRITICAL THINKING
1.
Draw a cross section of a soil aggregate (ped), showing the location of bacteria, fungi, and protozoa, and
showing the relative availability of oxygen throughout the aggregate.
2.
Describe the process of nodulation by rhizobia. What factors are important for host responses? What is
the nature of the symbiosis? How might this relationship have occurred evolutionarily?
ANSWER KEY
Terms and Definitions
1. h, 2. a, 3. l, 4. m, 5. d, 6. i, 7. g, 8. b, 9. i, 10. e, 11. f, 12. j, 13. k
Fill in the Blank
1. endomycorrhizae; actinorrhizae; ectomycorrhizae 2. rhizoplane; associative 3. ectomycorrhizae;
endomycorrhizae; arbuscule; arbuscular mycorrhizal 4. stem-nodulating rhizobia 5. infection thread;
bacteroids; symbiosomes; root nodules
Multiple Choice
1. d, 2. c, 3. a, 4. d, 5. b, 6. b, 7. c, 8. d
True/False
1. T, 2. F, 3. T, 4. F, 5. T, 6. F, 7. T, 8. F, 9. F, 10. T, 11. F, 12. T
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