CHAPTER 10

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.
• 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).
• 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.
•
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).
• Transient microflora take up temporary residence on and within humans.
• Destruction of resident microflora disturbs the delicate balance between host and microorganisms.
Two types of Microflora
• Resident Flora- are organisms that are relatively of fixed types and are regularly found in a given area
of the body at a given age.
• Transient flora-are those that inhibit the skin and mucous membrane temporarily for hours,days or
weeks and are derived from the environment.
 Microflora of the Skin
• Primarily bacteria and fungi – about 30 different types; most common = Staphylococcus spp (
Staphylococcus epidermidis and Staphylococcus hominis)
• Number and variety of microorganisms depend on:
• Amount of moisture present
• pH
• Temperature
• Salinity
• Presence of chemical wastes and other microbes
•
• Three regions of the skin
1. Axilla,perineum,toe webs- higher moisture levels,body temperature and higher levels of lipids
surface. More microorganism compared to other parts and inhabited by gram-negative bacilli.
2. hands, face and trunk
3. upper arm and legs

• 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
• Microflora of the Gastrointestinal (GI) Tract
– The GI tract is designed for digestion of food, absorption of nutrients, and elimination of
undigested materials
 – 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.
• 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

Beneficial and Harmful Roles of Indigenous Microflora

• Humans derive many benefits from their indigenous microflora; examples - vitamins K and B12.
• Microbial Antagonism
– Means “microbes versus microbes”
– Many members of our indigenous microflora are beneficial in that they prevent other microbes
from becoming established
– Other examples of microbial antagonism involve:
• Production of antibiotics and bacteriocins (antibacterial proteins); an example is colicin,
produced by E. coli
• Opportunistic Pathogens and Biotherapeutic Agents
– Opportunistic pathogens are those microorganisms that “hang around,” waiting for the
opportunity to cause infection
• Examples: E. coli, other members of the family Enterobacteriaceae, S. aureus, and
Enterococcus spp.
– The delicate balance of the indigenous microflora can be upset by antibiotics, other types of
chemotherapy, and changes in pH
– Bacteria and yeasts used to stabilize the microbial balance are called biotherapeutic agents or
probiotics

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
• 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

• 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
• 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”
• 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 like bread, cheeses, olives, pickles, vinegar and yogurt, as
well as in the production of alcoholic beverages like beer and wine.
• Many antibiotics and drugs are produced in pharmaceutical companies by fungi and bacteria (penicillin
for example).

Bioremediation
• Bioremediation refers to the use of microorganisms 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 like trichloroethylene and tetra-chloroethylene from the soil.