Chapter 10 Environmental and Applied Microbiology

Chapter 10.
Microbial Ecology
and Microbial Biotechnology
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Chapter 10 Outline
• Introduction
• Symbiotic Relationships Involving Microorganisms
• Indigenous Microflora of Humans
• Beneficial and Harmful Roles of Indigenous Microflora
• Microbial Communities (Biofilms)
• Agricultural Microbiology
• Microbial Biotechnology

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
microflora (older term = normal flora).

Symbiotic Relationships Involving
Microorganisms
• Symbiosis
– Defined as two dissimilar organisms living together in
a close association.
– The organisms in the relationship are referred to as
symbionts.
– Many microorganisms participate in symbiotic
relationships.
• Neutralism
– Refers to a symbiotic relationship in which neither
symbiont is affected by the relationship.
Microorganisms, cont.
• Commensalism
– A symbiotic relationship that is beneficial to one
symbiont and of no consequence to the other.
– Many organisms in the indigenous microflora of
humans are considered to be commensals.
• Mutualism
– A symbiotic relationship that is beneficial to both
symbionts; examples include lichens (an alga and a
fungus) and the relationship humans have with the
intestinal bacterium, Escherichia coli).

Microorganisms, cont.
• Parasitism
– 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.

• For example, conditions can cause a mutualistic or commensalistic relationship
between humans and their indigenous microflora to shift to a parasitic,
disease-causing (pathogenic) relationship.
• Recall that many of the microbes of our indigenous microflora are
opportunistic pathogens (opportunists), awaiting the opportunity to cause
disease.
Conditions that may enable an opportunist to cause disease include

1. burns,
2. lacerations,
3. surgical procedures, or
4. diseases that debilitate (weaken) the host or interfere with host defense
mechanisms
 Immunosuppressed individuals are especially susceptible to opportunistic
pathogens.
Opportunists can also cause disease in otherwise healthy persons if they gain
access to the blood, urinary bladder, lungs, or other organs and tissues of those
individuals.

Various Symbiotic Relationships
Lichen (a mutualistic Demodex mites in Cause of African

relationship) human hair follicles sleeping sickness (a
(a commensalistic parasitic relation-
relationship) ship)
Indigenous Microflora of Humans
• Includes all the microbes (bacteria, fungi, protozoa and viruses)

that reside on and within a person; sometimes referred to as our
“normal flora”
• Our indigenous microflora is composed of between 500 and 1,000
different species!
• Blood, lymph, spinal fluid, and most internal tissues and organs
are normally free of microorganisms (i.e., they are sterile).
• A fetus has no indigenous microflora. But during and after
delivery, a newborn is exposed to many microorganisms from its
mother, food, air, and virtually everything that touches the infant.
Both harmless and helpful microbes take up residence on the
baby’s skin, at all body openings, and on mucous membranes that
line the digestive tract (mouth to anus) and the genitourinary
tract. These moist, warm environments provide excellent
conditions for growth.
 Destruction of resident microflora disturbs the delicate balance between host and
microorganisms.
- prolonged therapy with certain antibiotics often destroys many of the intestinal
microflora. Diarrhea is usually the result of such an imbalance, which in turn leaves
the body more susceptible to secondary invaders.
- When the number of usual resident microbes is greatly reduced, opportunistic
invaders can more easily establish themselves within those areas.
One important opportunist usually found in small numbers near body

openings is the yeast, Candida albicans, which, in the absence of
sufficient numbers of other resident microflora, may grow unchecked
in the mouth, vagina, or lower intestine, causing the disease
candidiasis (also known as moniliasis). Such an overgrowth or
population explosion of an organism that is usually present in low
numbers is referred to as a superinfection.

• Transient microflora take up temporary residence on and
within humans.
 only temporary for many reasons:
1. they may be washed from external areas by bathing; they
2. may not be able to compete with the resident microflora;
3. they may fail to survive in the acidic or alkaline environment of
the site;
4. they may be killed by substances produced by resident
microflora; or
5. they may be flushed away by bodily excretions or secretions
(such as urine, feces, tears, and perspiration).

Areas of the body where
most of the indigenous
microflora reside.

Indigenous Microflora of Humans, cont.
MICROFLORA OF THE SKIN
– Primarily bacteria and fungi – about 30 different types; most common =
Staphylococcus spp., Corynebacterium & Propionibacterium
– Number and variety of microorganisms depend on:

• Amount of moisture present
- Moist, warm conditions in hairy areas of the body where there are many sweat
and oil glands, such as under the arms and in the groin area, stimulate the growth of
many different microorganisms.
- Dry, calloused areas of skin have few bacteria, whereas moist folds
between the toes and fingers support many bacteria and fungi.
- The surface of the skin near mucosal openings of the body

(the mouth, eyes, nose, anus, and genitalia) is inhabited
by bacteria present in various excretions and secretions.
SEM of Penile Bacteria
SEM of E. Coli on skin and

hair follicle
SEM of Staphylococcus aureus
on skin
SEM of belly button bacteria

Other factors are:
 pH
 Temperature
•Salinity
•Presence of chemical wastes and other microbes
 Frequent washing with soap and water removes most of

the potentially harmful transient microorganisms harbored
in sweat, oil, and other secretions from moist body parts,
as well as the dead epithelial cells on which they feed.
 Healthcare professionals must be particularly careful to keep their
skin and clothing as free of transient microbes as possible to help
prevent personal infections and to avoid transferring pathogens to
patients.
• Microflora of the Ears and Eyes

– Middle ear and inner ear are usually sterile; outer ear
and auditory canal contain the same microorganisms
as on the skin
– Eye is lubricated and cleansed by tears, mucus and
sebum – few microorganisms present
• Microflora of the Respiratory Tract
– Divided into upper respiratory tract (nasal passages
and throat) and lower respiratory tract (larynx,
trachea, bronchi and lungs)

• Microflora of the Respiratory Tract, cont.
– Upper respiratory tract (nasal passages and throat)
has an abundance of microorganisms; many are
harmless, some are opportunistic pathogens
– Carriers harbor virulent pathogens in their nasal
passages or throats, but do not have the diseases
usually caused by these pathogens
• Examples: people harboring the bacteria that
cause diphtheria, pneumonia, meningitis, and
whooping cough
– Lower respiratory tract is usually free of microbes
• Microflora of the Oral Cavity (Mouth)
– A shelter for numerous anaerobic and aerobic
bacteria; remaining food particles provide a rich
nutrient medium for bacteria
– Careless dental hygiene may cause:
• Dental caries (tooth decay)
• Gingivitis (gum disease)
• Periodontitis
– The most common organisms within the indigenous
microflora of the mouth are various species of alpha-
hemolytic streptococci

SEM of Streptococcus
mutans
SEM of tongue bacteria

• Microflora of the Gastrointestinal (GI) Tract
- The GI tract is designed for digestion of food, absorption of nutrients, and
elimination of undigested materials
- Gastric enzymes and the extremely acidic pH (approximately
pH 1.5) of the stomach usually prevent growth of indigenous
microflora, and most transient microbes (i.e., microbes consumed in
foods and beverages) are killed as they pass through the stomach.
- There is one bacterium though —a Gram-negative bacillus named

Helicobacter pylori—that lives in some people’s stomachs and is a
common cause of ulcers.
- when the amount of acid is reduced in the course of diseases such as
stomach cancer, certain bacteria may be found in the stomach.

SEM of
Helicobacter pylori

The colon (large intestine) contains the largest number and
variety of microorganisms of any colonized area of the
body; an estimated 500-600 different species - primarily
bacteria.
Colon is anaerobic; bacteria in colon are mostly obligate-,
aerotolerant-, and facultative anaerobes.
Many of the microflora of the colon are opportunists, causing
disease only when they gain access to other areas of the
body ( e.g. urinary bladder, bloodstream r lesions), or when
the usual balance of microorganisms is upset.
Example: E, coli may cause UTI when they gain access to the
urinary bladder.

Indigenous Microflora of Humans (cont.)
• Microflora of the Genitourinary (GU) Tract
– The GU tract consists of the kidneys, ureters, urinary
bladder, urethra, and parts of the female/male
reproductive systems
– Kidney, ureters and urinary bladder are usually sterile; the
distal urethra and its external opening harbor many
microbes including bacteria, yeasts and viruses
– Most frequent causes of urethral infections include
Chlamydia trachomatis, Neisseria gonorrhoeae, and
mycoplasmas
– The male and female reproductive systems are usually
sterile, with the exception of the vagina

In the vagina, the microflora varies with the stage of sexual
development.
* During puberty and after menopause, vaginal secretions

are alkaline, supporting the growth of various diphtheroids,
streptococci, staphylococci, and coliforms (E. coli and closely
related enteric Gram-negative bacilli).
* Through the childbearing years, vaginal secretions are acidic (pH
4.0–5.0), encouraging the growth mainly of lactobacilli, along with a
few a-hemolytic streptococci, staphylococci, diphtheroids, and
yeasts.
* The metabolic byproducts of lactobacilli, especially lactic acid,
inhibit growth of the bacteria associated with bacterial vaginosis
(BV). A decrease may also lead to the overgrowth of yeast that may
lead to yeast vaginitis.

“Vaginitis” versus “Vaginosis”
- The similarly sounding terms vaginitis and vaginosis both
refer to vaginal infections. The suffix “-itis” refers to
inflammation, and inflammation usually involves the influx
of white blood cells known as polymorphonuclear cells
(PMNs).
- Thus, a vaginal infection involving inflammation and the
influx of PMNs is referred to as vaginitis.
- In bacterial vaginosis (BV), there is a watery,
noninflammatory discharge, lacking white blood cells
(WBCs).
- Thus, the difference between vaginitis and vaginosis boils
down to the presence or absence of WBCs. Whereas
vaginitis is usually caused by one particular pathogen, BV
is a synergistic infection.
SEM of vaginal bacteria
SEM of cells from a urine

infection
Beneficial and Harmful Roles of
Indigenous Microflora
Humans derive many benefits from their indigenous microflora

1. Some nutrients, particularly vitamins K and B12, pantothenic
acid, pyridoxine, and biotin, are obtained from secretions of
certain intestinal bacteria.
2. Evidence also indicates that indigenous microbes provide a
constant source of irritants and antigens to stimulate the
immune system. This causes the immune system to respond
more readily by producing antibodies to foreign invaders and
substances, which in turn enhances the body’s protection against
pathogens.
3. Mere presence of large numbers of microorganisms at certain
anatomic locations is beneficial, in that they prevent pathogens
from colonizing those locations. This is called Microbial
antagonism

Beneficial and Harmful Roles of
Indigenous Microflora, cont.
When the delicate balance among the various species in the population of
indigenous microflora is upset by antibiotics, other types of chemotherapy, or
changes in pH, many complications may result.
- Certain microorganisms may flourish out of control, such as C. albicans in
the vagina, leading to yeast vaginitis.
- diarrhea and pseudomembranous colitis may occur as a result of
overgrowth of Clostridium difficile in the colon.
Cultures of Lactobacillus in yogurt or in medications may be prescribed to
reestablish and stabilize the microbial balance. Bacteria and yeasts used in this
manner are called biotherapeutic agents (or probiotics). Other microorganisms
that have been used as biotherapeutic agents include Bifidobacterium spp.,
nonpathogenic Enterococcus spp., and Saccharomyces spp. (yeasts).

Microbial Communities
• It is rare to find an ecologic niche in which only one type
of microorganism is causing a particular effect
• Microorganisms are often organized into biofilms –
complex communities of assorted organisms. Biofilms are
everywhere; example – 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 and medical equipment and can cause diseases
like endocarditis

Microbial Communities, cont.
• Microbes commonly associated with biofilms on medical

devices include the yeast, Candida albicans, and bacteria
like Staphylococcus aureus, Enterococcus spp., Klebsiella
pneumoniae, and Pseudomonas aeruginosa.
• Biofilms are very resistant to antibiotics and disinfectants
– 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.

Synergistic Infections
• When 2 or more organisms “team up” to produce a

disease that neither could cause by itself, the diseases
are called synergistic infections, polymicrobial infections,
or mixed infections
– Examples:
• Acute necrotizing ulcerative gingivitis (ANUG,
trench mouth, or Vincent’s disease).
• Bacterial vaginosis (BV)

Agricultural Microbiology
• There are many uses for microorganisms in agriculture
(e.g., their use in genetic engineering).
• Role of Microbes in Elemental Cycles
– Bacteria found within other microorganisms are
known as endosymbionts.
– Microorganisms play an important role in the cycling
of nutrients and elements like nitrogen, carbon,
oxygen, sulfur, and phosphorus.
• N2 is converted by nitrogen-fixing bacteria and
cyanobacteria into ammonia (NH3) and ammonium
ion (NH4).
The Nitrogen Cycle

Agricultural Microbiology, cont.
• Role of Microbes in Elemental Cycles, cont.

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

(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.

• Other Soil Microorganisms

– There are a multitude of other microorganisms in
soil – bacteria, fungi, algae, protozoa, viruses, and
viroids; many are decomposers.
– A variety of human pathogens live in soil including
Clostridium spp. (such as C. tetani and C.
botulinum) and the spores of Bacillus anthracis.
– The types and amount of microorganisms 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).

• Infectious Diseases of Farm Animals
– Diseases of farm animals are caused by a wide
variety of pathogens
– These diseases can be transmitted to humans
– These diseases are of economic concern to farmers
and ranchers
• Microbial Diseases of Plants
– Microbes cause thousands of different plant diseases!
– Most plant diseases are caused by fungi, viruses,
viroids, and bacteria
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”
The following are some of the uses of microorganisms in
biotechnology:
1. Production of therapeutic proteins such as human
insulin, human growth hormone, human tissue
plasminogen activator, interferon, and hepatitis B
vaccine;
2. Production of DNA vaccines.
3. Production of vitamins such as B2 (riboflavin), B7
(biotin), B9 (folic acid), B12, and K2.

4. Use of microbial metabolites as antimicrobial agents and
other types of therapeutic agents.
 Penicillins and cephalosporins are examples of
antibiotics produced by fungi. Bacitracin,
chloramphenicol, erythromycin, polymyxin B,
streptomycin, tetracycline, and vancomycin are examples
of antibiotics produced by bacteria.
5. Agricultural applications.
Example:
 Bt corn and Bt. talong
 Certain microbial metabolites have microbicidal, herbicidal,
insecticidal, or nematocidal activities. For example, a soil
bacterium named Bacillus subtilis secretes compounds with
antifungal, antibacterial, and insecticidal activities.
6. Food technology
Example:
 Microbes are used in the commercial production of amino acids
(e.g., alanine, aspartate, cysteine, glutamate, glycine, histidine,
lysine, methionine, phenylalanine, tryptophan) for use in the food
industry. •
 Algae and fungi are used as a source of single-cell protein for
animal and human consumption.
7. Production of chemicals.
 Microbes can be used in the large-scale production of acetic acid,
acetone, butanol, citric acid, ethanol, formic acid, glycerol,
isopropanol, and lactic acid, as well as biofuels such as hydrogen
and methane.

8. Biomining.
 Microbes have been used in the mining of
arsenic, cadmium, cobalt, copper, nickel,
uranium, zinc, and other metals by a process
known as leaching or bioleaching.
9. Bioremediation.
- The term bioremediation refers to the use of
microorganisms to clean up various types of wastes,
including industrial wastes and other pollutants
Example: microbes are used extensively in composting,
sewage treatment, and water purification

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Chapter 10.

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

• Ecology is the systematic study of the interrelationships

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Conditions that may enable an opportunist to cause disease include

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Lichen (a mutualistic Demodex mites in Cause of African

• Includes all the microbes (bacteria, fungi, protozoa and viruses)

One important opportunist usually found in small numbers near body

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

– Number and variety of microorganisms depend on:

- The surface of the skin near mucosal openings of the body

SEM of E. Coli on skin and

SEM of belly button bacteria

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

 Frequent washing with soap and water removes most of

• Microflora of the Ears and Eyes

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

SEM of tongue bacteria

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

- There is one bacterium though —a Gram-negative bacillus named

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

* During puberty and after menopause, vaginal secretions

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

SEM of cells from a urine

Humans derive many benefits from their indigenous microflora

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

• Microbes commonly associated with biofilms on medical

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

• When 2 or more organisms “team up” to produce a

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

• Role of Microbes in Elemental Cycles, cont.

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

• Other Soil Microorganisms

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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