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Prescott’s Microbiology, 9th Edition
31
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.
LEARNING OUTCOMES
After reading this chapter you should be able to:
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differentiate between a mineral and an organic soil, and describe the role of microbes in generating soil
organic matter
explain why lignin degradation is confined to only a few types of microbes
predict how a specific carbon to nitrogen ratio will influence the microbial community within a given soil
estimate the relative microbial populations in several soil types
list the microbial genera that are easily cultured from soil
describe the different ecological niches occupied by microbes in soil and how microbes have evolved to
take advantage of the niches
compare the soil microbial loop with an aquatic microbial loop
describe mechanisms by which plants and microbes communicate
differentiate between the phyllosphere, rhizophere, and rhizoplane environments and the microbes that
dwell there
explain the importance of mycorrhizae to the growth of vascular plants
contrast and compare the ectomycorrhizal life cycle and that of the arbuscular fungi
diagram the steps that result in the formation of rhizobium nodules on a leguminous plants
compare the process of stem nodulation with root nodulation
discuss other microbes, in addition to the rhizobia, that fix nitrogen
explain how Agrobacterium tumefaciens cause tumors in plants
list at least five plant pathogens other than Agrobacterium tumefaciens and the diseases they cause
identify a plant disease that is likely to be found near your home or school
relate the metabolic processes that occur in the subsurface biosphere to the free energy released during
the use of each successive compound as a terminal electron acceptor
describe the distribution of subsurface methane production
explain at least one new discovery that has come from exploring the “deep hot biosphere”
CHAPTER OUTLINE
I.
Soils 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
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
Prescott’s Microbiology, 9th Edition
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 CO 2 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
II. Microorganisms in the Soil Environment
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. Microbe-Plant Interactions
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
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
Prescott’s Microbiology, 9th Edition
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
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
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution
in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.

Prescott’s Microbiology, 9th Edition
1.
2.
3.
Shallow subsurface aquifers where water flowing from the surface moves below the plant root
zone
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
Deeper biogenic zones where methane is being synthesized using geologic hydrogen as an
energy source
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?
3.
Tropical soils throughout the world are under intense pressure to be developed into agricultural land.
What microbial approaches may be employed to develop and maintain soils for this purpose?
4.
Considering the oxygen concentration gradient along nutrient and waste product gradients, is there a
typical soil microenvironment? Explain.
CONCEPT MAPPING CHALLENGE
Construct a concept map using the words below; provide your own linking terms.
Symbionts Mycorhizzae Root nodule Rhizobia Phosphate N 2fixation Rhizomorphs
Mutualism Actinorhizae Ectomychorrhizae Endomychorrizal Tripartite association
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution
in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
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