Burton’s Microbiology

for the Health Sciences

Section V. Environmental and

Applied Microbiology

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 Burton’s Microbiology
for the Health Sciences

Chapter 10. Microbial Ecology

and Microbial Biotechnology

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Chapter 10 Outline

 Introduction
 Symbiotic Relationships Involving Microorganisms
 Indigenous Microbiota of Humans (Microbiome)
 Beneficial and Harmful Roles of Indigenous Microbiota
 Microbial Communities (Biofilms)
 Agricultural Microbiology
 Microbial Biotechnology

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Introduction

 Ecology is the systematic study of the interrelationships

that exist between organisms and their environment.
 Microbial ecology is the study of the numerous
interrelationships between microbes and the world
around them.
 Most relationships between humans and microbes are
beneficial, rather than harmful.
 Microorganisms are present both on and in our bodies;
collectively, they are referred to as our indigenous
microbiota (older term = normal flora).

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Symbiotic Relationships Involving
Microorganisms #1

 Symbiosis
o Defined as two dissimilar organisms living together in
a close association.
o The organisms in the relationship are referred to as
symbionts.
o Many microorganisms participate in symbiotic
relationships.
 Neutralism
o Refers to a symbiotic relationship in which neither
symbiont is affected by the relationship.

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Symbiotic Relationships Involving
Microorganisms #2
 Commensalism
o A symbiotic relationship that is beneficial to one
symbiont and of no consequence to the other.
o Many organisms in the indigenous microbiota of
humans are considered to be commensals.
 Mutualism
o A symbiotic relationship that is beneficial to both
symbionts; examples include lichens (composed of
an alga, a filamentous fungus and sometimes a
yeast) and the relationship humans have with the
intestinal bacterium Escherichia coli).

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Symbiotic Relationships Involving
Microorganisms #3

 Parasitism
o A symbiotic relationship that is beneficial to one
symbiont (the parasite) and detrimental to the other
symbiont (the host).
 A host is a living organism that harbors another
living organism.
 The parasite may or may not cause disease in the
host.
 A change in conditions can cause one type of symbiotic
relationship to shift to another type.

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Various Symbiotic Relationships

Lichen (a mutualistic Demodex mites in Cause of African

relationship) human hair follicles sleeping sickness (a
(a commensalistic parasitic relationship)
relationship)

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Lichens on a Rock

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Indigenous Microbiota of Humans #1
 Includes all the microbes (bacteria, fungi, protozoa, and
viruses) that reside on and within a person; sometimes
referred to as the human microbiome.
 Our indigenous microbiota is composed of as many as
10,000 different species!
 It is estimated that bacterial protein genes are 360 times
more abundant than human genes.
 Blood, lymph, spinal fluid, and most internal tissues and
organs are normally free of microbes (i.e., they are
sterile).
 Transient microbiota take up temporary residence on
and within humans.
 Destruction of the resident microbiota disturbs the
delicate balance between host and microorganisms. This
is referred to as dysbiosis.
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Areas of the Body Where Most of the
Indigenous Microbiota Reside

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Indigenous Microbiota of Humans #2

 Microbiota of the skin

o Primarily bacteria and fungi—about 30 different
types; most common = Staphylococcus spp.
o Number and variety of microorganisms depend on
 Amount of moisture present
 pH
 Temperature
 Salinity
 Presence of chemical wastes and other microbes

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Indigenous Microbiota of Humans #3

 Microbiota of the ears and eyes

o Middle ear and inner ear are usually sterile; outer ear
and auditory canal contain the same microbes as on
the skin.
o Eye is lubricated and cleansed by tears, mucus, and
sebum—few microbes present.
 Microbiota of the respiratory tract
o Respiratory tract is divided into upper respiratory
tract (nasal passages and throat) and lower
respiratory tract (larynx, trachea, bronchi, and
lungs).

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Indigenous Microbiota of Humans #4

 Microbiota of the respiratory tract—(cont.)

o Upper respiratory tract (nasal passages and throat)
has an abundance of microbes; many are harmless,
some are opportunistic pathogens.
o Carriers harbor virulent pathogens in their nasal
passages or throats, but do not have the diseases
usually caused by these pathogens.
 Example: people harboring the bacteria that
cause diphtheria, pneumonia, meningitis, and
pertussis (whooping cough).
o Lower respiratory tract is usually free of microbes.

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 Indigenous Microbiota of Humans #5

 Microbiota of the oral cavity (mouth)

o Oral cavity affords a shelter for numerous anaerobic and
aerobic bacteria; remaining food particles provide a rich
nutrient medium for bacteria.
o Careless dental hygiene may cause
 Dental caries (tooth decay)
 Gingivitis (gum disease)
 Periodontitis
o The most common organisms within the indigenous
microbiota of the mouth are various species of -
hemolytic streptococci and different anaerobes.

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Indigenous Microbiota of Humans #6

 Microbiota of the gastrointestinal (GI) tract

o The GI tract is designed for digestion of food,
absorption of nutrients, and elimination of
undigested materials.
o The colon (large intestine) contains the largest
number and variety of microbes of any colonized
area of the body: an estimated 500 to 600 different
species—primarily bacteria.
o Colon is anaerobic; bacteria in colon are mostly
obligate, aerotolerant, and facultative anaerobes.
o Many members of the colon microbiota are
opportunists.
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Indigenous Microbiota of Humans #7

 Microbiota of the genitourinary (GU) tract

o The GU tract consists of the kidneys, ureters, urinary
bladder, urethra, and parts of the female/male
reproductive systems.
o Kidney, ureters, and urinary bladder are usually
sterile; the distal urethra and its external opening
harbor many microbes, including bacteria, yeasts,
and viruses.
o Most frequent causes of urethral infections include
Chlamydia trachomatis, Neisseria gonorrhoeae, and
mycoplasmas.
o The male and female reproductive systems are
usually sterile, with the exception of the vagina.
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Beneficial and Harmful Roles of the
Indigenous Microbiota #1

 Humans derive many benefits from their indigenous

microbiota (e.g., vitamins K and B12).
 Microbial antagonism
o This means “microbes versus microbes”
o Many members of our indigenous microbiota are
beneficial, in that they prevent other microbes from
becoming established.
o Other examples of microbial antagonism involve the
production of antibiotics and bacteriocins
(antibacterial proteins); an example is colicin,
produced by E. coli.

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Beneficial and Harmful Roles of the
Indigenous Microbiota #2
 Opportunistic pathogens and biotherapeutic agents
o Opportunistic pathogens are those microbes that
“hang around,” waiting for the opportunity to cause
infection.
 Examples: E. coli, other members of the family
Enterobacteriaceae, S. aureus, and Enterococcus
spp.
o The delicate balance of the indigenous microbiota
can be disturbed by antibiotics, other types of
chemotherapy, and changes in pH.
o Bacteria and yeasts used to stabilize the microbial
balance are called biotherapeutic agents or
probiotics.
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Microbial Communities #1

 It is rare to find an ecologic niche in which only one type

of microbe is causing a particular effect.
 Microbes are often organized into biofilms—complex
communities of assorted organisms. Biofilms are
everywhere (e.g., dental plaque).
 Biofilms consist of a variety of different species of
bacteria plus a gooey polysaccharide that the bacteria
secrete; the bacteria grow in tiny clusters called
microcolonies, separated by water channels.
 Biofilms have medical significance; they form on urinary
catheters, prosthetic joints, venous and arterial
catheters, and medical equipment and can cause
diseases like endocarditis and prosthetic joint infections.
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Microbial Communities #2

 Microbes commonly associated with biofilms on medical

devices include the yeast, Candida albicans, and bacteria
such as Staphylococcus aureus, Enterococcus spp.,
Klebsiella pneumoniae, and Pseudomonas aeruginosa.
 Biofilms are very resistant to antibiotics and
disinfectants.
o Antibiotics that are effective against pure cultures of
organisms have been found to be ineffective against
those same organisms within an actual biofilm.
 Bacteria in biofilms produce different types of proteins
that may not be produced by the bacteria in pure
culture.

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Biofilm Development

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Scanning Electron Micrograph of a
Staphylococcus aureus Biofilm

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Synergistic Infections

 When two or more organisms “team up” to produce a

disease that neither could cause by itself; it is referred
to as synergism.
 The diseases are called synergistic infections,
polymicrobial infections, or mixed infections.
o Examples:
 Acute necrotizing ulcerative gingivitis (ANUG,
trench mouth, or Vincent disease).
 Bacterial vaginosis (BV)

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Agricultural Microbiology #1

 There are many uses of microbes in agriculture (e.g., in

genetic engineering).
 Role of microbes in elemental cycles
o Bacteria found within other microorganisms are
known as endosymbionts.
o Microorganisms play an important role in the cycling
of nutrients and elements such as nitrogen, carbon,
oxygen, sulfur, and phosphorus.
 N2 is converted by nitrogen-fixing bacteria and
cyanobacteria into ammonia (NH3) and
ammonium ion (NH4).

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The Nitrogen Cycle

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Agricultural Microbiology #2

 Role of microbes in elemental cycles—(cont.)

o Some nitrogen-fixing bacteria (e.g., Rhizobium and
Bradyrhizobium spp.) live in and near the root
nodules of legumes such as alfalfa, soybeans, and
peanuts.
o Nitrifying bacteria include Nitrosomonas,
Nitrosospira, Nitrosococcus, Nitrosolobus, and
Nitrobacter spp.
o Denitrifying bacteria include some species of
Pseudomonas and Bacillus.

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Root Nodules of Legumes

(A) Soybean root nodules, which contain nitrogen-fixing

Rhizobium bacteria. (B) Nitrogen-fixing bacteria
(arrows) can be seen in this cross section of a soybean
root nodule.

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Agricultural Microbiology #3

 Other soil microbes

o There are a multitude of other microbes in soil—
bacteria, fungi, algae, protozoa, viruses, and
viroids; many are decomposers.
o A variety of human pathogens live in soil, including
Clostridium spp. (such as C. tetani and C.
botulinum) and the spores of Bacillus anthracis.
o The types and amount of microbes living in soil
depend on many factors (e.g., amount of decaying
matter, available nutrients, moisture, amount of
O2, pH, temperature, and the presence of waste
products of other microbes).
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Agricultural Microbiology #4

 Infectious diseases of farm animals

o Diseases of farm animals are caused by a wide
variety of pathogens.
o These diseases can be transmitted to humans.
o These diseases are of economic concern to farmers
and ranchers.
 Microbial diseases of plants
o Microbes cause thousands of different plant diseases!
o Most plant diseases are caused by fungi, viruses,
viroids, and bacteria.
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 Biotechnology

 Defined as “any technological application that uses

biological systems, living organisms, or derivatives
thereof, to make or modify products or processes for
specific use.”
 Microbes are used in a variety of industries, including the
production of certain foods and beverages, food additives,
vaccines, and antibiotics.
 Microbes are used in the production of foods such as
bread, cheeses, olives, pickles, vinegar, and yogurt, as
well as in the production of alcoholic beverages such as
beer and wine.
 Many antibiotics and drugs are produced in pharmaceutical
companies by fungi and bacteria (e.g., penicillin).
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 Bioremediation
 Bioremediation refers to the use of microbes to clean up
various types of wastes, including industrial and toxic
wastes, and environmental pollutants (e.g., herbicides
and pesticides).
 Some microbes are genetically engineered to digest
specific wastes (e.g., petroleum-digesting bacteria to
clean up oil spills).
 Methanotrophs (bacteria that normally consume methane
in the environment) have been used to remove highly
toxic solvents such as trichloroethylene and
tetrachloroethylene from the soil.

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