Microbial ecology and

classification
jean alamo-sumait
SPUP, 2019
Phylogeny: The Study of Evolutionary
Relationships of Living Organisms
Over 1.5 million different organisms have been identified to
date.
Many similarities among living organisms:
• Made up of cells surrounded by a plasma membrane.
• Use ATP as energy source.
• Store genetic information as DNA.
• Ribosomes are the site of protein synthesis.
Phylogeny: The Study of Evolutionary Relationships of Living Organisms

Both differences and similarities among organisms are

caused by natural selection (Darwin, 1858).
Organisms can be classified into taxonomic categories
(taxa), based on the differences and similarities among
them.
Systematics is the discipline of identifying and classifying
organisms.
Phylogeny: The Study of Evolutionary Relationships of Living Organisms

Ancient Greeks classified all living organisms into two groups

Kingdom Plantae
Kingdom Animalia
In 1850s bacteria and fungi were incorrectly placed in the
Plant Kingdom.
In 1860s Kingdom Protista was proposed to include bacteria,
fungi, algae, and protozoa, but many scientists still classified
bacteria and fungi as plants.
Intense disagreement over classification of bacteria and
fungi persisted over 100 years.
Phylogeny: The Study of Evolutionary Relationships of Living Organisms

In 1930s electron microscopy made it clear that bacterial

cells lacked a nucleus. The term procaryote was
introduced in 1937.
In 1959 Kingdom Fungi was established.
In 1961 the current definition of the term procaryote was
established.
In 1968 the Kingdom Procaryotae was accepted by
biologists.
In 1969 Robert Whittaker proposed a five-kingdom system of
biological classification for all living organisms.
Five-Kingdom System of Biological
Classification
1. Kingdom Prokaryotae (Monera): Oldest known cells. Lived over
3.5 billion years ago. Lack a nucleus and membrane bound
organelles.
The other four kingdoms are eukaryotes. Have a true nucleus and
membrane bound organelles.
2. Kingdom Protista: Mostly unicellular, lack tissue organization.
Most have flagella during life.
3. Kingdom Fungi: May be unicellular (yeasts) or multicellular
(molds). Many are saprotrophs.
4. Kingdom Plantae: Multicellular, photosynthetic.
5. Kingdom Animalia: Multicellular, heterotrophs that ingest food
through a mouth or oral cavity.
Five-Kingdom Classification System
Domains
• The highest – largest category, recent addition
• 3 domains
1. Archaea – ancient “bacteria”, unicellular like bacteria, also
simple cell structure (prokaryote) but have distinct metabolism
(chemistry) allowing them to exist in “extreme” environments
2. Bacteria – unicellular, prokaryote, found everywhere (Old
kingdom name – Monera)
3. Eukarya – unicellular to multicellular, complex and organized
cells with nuclei and organelles (e.g. mitochondria)
Domain Archaea
• Archaea are single-
celled organisms that
lack a membrane-bound
nucleus (Prokaryote)

• Archaea can be found in

environments that are too
hostile for other life forms.
Domain Bacteria
• Bacteria are single- celled
organisms that lack a
membrane-bound
nucleus (Prokaryote)

• Bacteria are found almost

everywhere on the planet
Earth.
Domain Eukarya
• The cells of all eukaryotes have a membrane-bound
nucleus. Members of the Domain Eukarya are further
categorized into one of four Kingdoms
Three Domain Classification Kingdoms

Plantae Animalia Fungi Protista

• Bacteria
• Archaea
Domain Bacteria Domain Archaea Domain Eukarya

Prokaryotes Prokaryotes
Chlamydias Gram-positive Endospore Gram-negative Methane that live in that live in
Cyanobacteria Spirochetes bacteria producers bacteria producers Eukaryotes
extreme salt extreme heat

• Eukarya
• Protista
• Fungi
• Plantae
• Animalia
*
Ancestral Cell Line (first living cells)
Microbiology
• Older 5 kingdom scheme is still widely used
• Monera – bacteria (Prokaryotic)
• Protista – Protozoans (Eukaryotic)
• Fungi - yeast, molds, etc. (Eukaryotic)
• Plant – photosynthetic producers (Eukaryotic)
• Animals – heterotrophic consumers (Eukaryotic)
Categories of Classification
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Categories of Classification
Domain – Did
Kingdom - King
Phylum - Philip
Class – Came
Order – Over
Family - For
Genus – Good
Species – Spaghetti?
Categories of Classification
Domain
Most inclusive
Kingdom
Phylum
Class
Order
Family
Genus
Species Least inclusive
Categories of Classification
Naming and classifying
microorganisms
• Carolus Linnaeus established
the system of scientific
nomenclature in 1739.
• Each organism has two names → Binomial
nomenclature: Genus + specific epithet (species)
• Italicized (or underlined), genus capitalized, “latinized”,
used worldwide.
• May be descriptive or honor a scientist.
Examples

• Staphylococcus aureus (S. aureus) -

Describes the clustered arrangement of the cells
(staphylo-) and the golden color of the colonies (aur-).
1857 –1911
• Escherichia coli (E. coli) - Honors the
discoverer, Theodor Escherich, and describes the
bacterium’s habitat–the large intestine or colon.
 Types of Microorganisms
• Bacteria
• Archaea
• Fungi
• Protozoa
• Algae
• Viruses
• Multicellular animal parasites
• Prions
Bacterium / Bacteria
• Prokaryotic
• Peptidoglycan cell wall
• Reproduction by binary fission

Gain energy from use of

• organic chemicals
• inorganic chemicals or
• photosynthesis
 Archaea
• Prokaryotic
• No peptidoglycan
• Live in extreme environments
• Reproduce asexually by binary or
multiple fission, fragmentation, or
budding
• Include: Methanogens, Extreme
halophiles, Extreme
thermophiles/psychrophiles
Fungus/Fungi
• Eukaryotic
• Chitin cell walls
• Use organic chemicals for energy.
• Molds and mushrooms are multicellular consisting of
masses of mycelia, which are composed of filaments
called hyphae.
• Yeasts are unicellular.
• Reproduce asexually by fragmentation, budding, or
producing spores
Protozoan/
Protozoa

• Eukaryotes
• Absorb or ingest organic chemicals
• May be motile via pseudopods, cilia,
or flagella
• Reproduce both asexually through mitosis and
sexually through meiosis and gamete fusion
Viruses
• Are acellular
• Have either DNA or
RNA in core
• Core is surrounded
by a protein coat.
• Coat may be enclosed in a lipid envelope.
• Viruses only replicate within a living host cell.
Multicellular
Animal Parasites
• Eukaryotes
• Multicellular animals
• Helminths are parasitic
flatworms and round worms
• Microscopic stages in life
cycles
• Reproduce sexually (individuals
can either be monoecious/hermaphrodite
or dioecious)
Prions
• derived from the initial letters of the words proteinaceous
and infectious, with -on added by analogy to the word
virion
• Small infectious proteins that cause fatal neurologic
diseases in animals; contains no nucleic acid, does not
trigger an immune response, and is not destroyed by
extreme heat or cold
examples: Scrapie, Bovine Spongiform Encephalopathy (“Mad
Cow Disease”) and Creutzfeldt-Jacob disease
 Microbes and Human Disease
Most microbes are either beneficial or harmless to humans.
Normal microbiota (flora) in and on the human body
Less than 1% of microbes cause disease.
Pathogens overcome the host’s resistance → infectious disease
In 1962, the surgeon general of the United States stated: “The war
against infectious diseases has been won”.
Today it is clear that this was overly optimistic:
Emerging diseases: New diseases like AIDS, hantavirus, Ebola fever, Lyme disease,
Hepatitis C, and others that did not exist a few years ago.
Antibiotic and Drug Resistance: Many old diseases are becoming resistant to
traditional therapies: Tuberculosis, gonorrhea, malaria, etc.
Today infectious diseases cause 50% of the 52 million worldwide deaths
per year.
West Nile Encephalitis
• Caused by West Nile virus
• First diagnosed in the West Nile region of Uganda
in 1937
• Appeared in New York City in 1999

Avian influenza A
• Influenza A virus (H5N1)
• Primarily in waterfowl and poultry
• Sustained human-to-human transmission has not occurred
yet
MRSA
• Methicillin-resistant Staphylococcus aureus
• 1950s: Penicillin resistance developed
• 1980s: Methicillin resistance
• 1990s: MRSA resistance to vancomycin reported
• VISA: Vancomycin-intermediate-resistant S. aureus
• VRSA: Vancomycin-resistant S. aureus

Bovine Spongiform Encephalopathy

• Caused by a prion
• Also causes Creutzfeldt-Jakob disease (CJD). New variant
CJD in humans is related to beef consumption
 Escherichia coli O157:H7
• Toxin-producing strain
of E. coli
• First seen in 1982
• Leading cause of
diarrhea worldwide

Figure 25.12
Acquired immunodeficiency syndrome (AIDS)

• Caused by human immunodeficiency virus (HIV)

• First identified in 1981
• Worldwide epidemic infecting 30 million people; 14,000 new
infections every day
• Sexually transmitted infection affecting males and females
• HIV/AIDS in the U.S.: 30% are female, and 75% are African
American
Neonatal tetanus kills over 600,000 infants every year.
Source: Tropical Medicine and Parasitology, 1997.
Microbes and Disease in Human History
• Bubonic Plague (Black death): Several devastating
epidemics throughout history.
• High mortality: Up to 80% of those infected die.
• 1347-1351: Over 75 million died in Europe, Asia, and Africa.
• Over 25% of population of Europe died.
• Cause was unknown for over 500 years, leading to superstition,
persecution, and hysteria.
• Bacterial disease transmitted by rat fleas.
• Rare today but still occurs:
• 10-15 cases/year in U.S.
• Last epidemic occurred in India in 1994.
Left: Swollen lymph nodes in bubonic plague infection.
Right: Infected flea bite with eschar and carbuncle.
Source: Tropical Medicine and Parasitology, 1997.
Worldwide Distribution of Plague

++: Frequent transmission

+/-: Infrequent transmission.
Source: Tropical Medicine and Parasitology, 1997.
• Smallpox: One of deadliest human infectious diseases
throughout history.
• Caused by smallpox virus.
• First known case in 1175 B.C.: Egyptian pharaoh Ramses V died from
smallpox.
• Several hundred million deaths through history.
• Up to 90% of Native American population was killed by smallpox and other
diseases (measles and plague) introduced during European conquests.
• Native population of Central and South America dropped from 130 million to about
1.6 million over several decades.
• Smallpox was used as a biological weapon by British colonists in North America.
• 600,000 deaths/year in Europe from 1500-1700.
Smallpox infection in a small child.
Disease was eradicated worldwide by immunization in 1977.
Source: Microbiology Perspectives, 1999.
• Smallpox

• 75% of survivors were severely scarred and/or blinded.

• An effective vaccine was developed in 1870s by Edward Jenner,
using a related virus (cowpox).
• Smallpox was the first and only viral disease to be completely
eradicated (1977).
• Worldwide immunization campaign in 1960s.
• Only infects humans.
•Tuberculosis (TB): Caused by a bacterium that mainly infects
lungs but may spread to other parts of body.
• Leading killer of world’s infectious diseases:
• 3 million die worldwide every year.
• Over 1 million killed in U.S. between 1930-49.
• One out of three people infected worldwide.
• In U.S. 10 million people are presently infected, but only 5% will develop active
disease.
• Most healthy individuals can contain infection.
• Treatment: Antibiotics for up to one year.
• After introduction of antibiotics, TB declined from 1950s to 80s, and then started
to increase again.
• Low patient compliance with treatment has caused antibiotic resistant TB.
• AIDS epidemic has caused an increase in cases.
Tuberculosis is leading killer among infectious diseases
worldwide. Patient with lymph node necrosis.
Photo by Dr. I. Small
• Childbirth Fever: Common nosocomial (hospital acquired)
infection.
• Bacterial infection of the uterus as a result of childbirth or abortion.
• Transmitted by hands and instruments of physicians and midwives.
• Extremely common before the 1900s.
• About 1 in 17 women who gave birth would become infected (fever, chills,
delirium, and death).
• Cause was unknown.
• Austrian doctor Semmelweiss showed that washing hands and instruments with
a disinfectant solution greatly reduced cases.
• Today common in women who have illegal abortions, especially in
third world countries.
 • AIDS: Acquired Immune Deficiency Syndrome.
• First cases reported in 1981 at UCLA.
• Cause: Human Immunodeficiency Virus (HIV)
• Transmitted by sexual contact, blood transfusions, mother-to-child,
and infected needles.
• Destroys an individual’s immune system, making them susceptible
to many infectious diseases and cancer.
• Number of cases has grown rapidly during the last two decades.
As of 2001:
• Over 900,000 infected individuals in the U.S.
• Over 40 million deaths worldwide.
African AIDS patient with slim disease
Source: Tropical Medicine and Parasitology, 1997
Endemic Kaposi’s Sarcoma, nodular form in an AIDS patient.
Source: AIDS, 1997.
Extensive symmetric tumor lesions of Kaposis’s sarcoma in an AIDS patient.
Source: AIDS, 1997
Oral candidiasis (yeast infection) in an AIDS patient
Source: Atlas of Clinical Oral Pathology, 1999
Salamat!