Transcript Chapter 11: Characterizing and Classifying Prokaryotes

Chapter 11: Characterizing and
Classifying Prokaryotes
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:
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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.
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.

Phylogeny: The Study of Evolutionary
Relationships of Living Organisms
 Ancient Greeks classified all living organisms
into two groups
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 In
Kingdom Plantae
Kingdom Animalia
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 Whitaker proposed a fivekingdom system of biological classification for
all living organisms.
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Five-Kingdom System of Biological
Classification
Proposed in 1969 by Robert Whitaker :
1. Kingdom Procaryotae (Monera): Oldest known cells.
Lived over 3.5 billion years ago. Lack a nucleus and
membrane bound organelles.
The other four kingdoms are eucaryotes. 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
Classification of Organisms
Scientific Nomenclature
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Scientific nomenclature: Universal system for naming
and classifying living organisms. Initially developed in the
18th century by Carl Linnaeus.
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Binomial nomenclature: Each organism (species) has a
two part name. Names are either italicized or underlined.
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Genus name: Always capitalized, always a noun. May use initial.
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species name: Always lower case, usually an adjective.
Names are usually derived from Latin (or Greek) or may
have latinized endings. Examples:
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Homo sapiens (H. sapiens): Human
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Penicillium notatum (P. notatum): Mold that produces penicillin
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Canis familiaris (C. familiaris): Domestic dog
Classification of Organisms
Hierarchy of Taxonomic Categories
DOMAIN
Kingdom
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Phylum or Division (Bacteria)
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Class
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Order
 Family
 Genus
species
Taxonomic Categories
Division
(Bacteria)
Bacterial Groups
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The most widely accepted taxonomic classification for
bacteria is in Bergey’s Manual of Systematic Bacteriology
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Close to 5000 bacterial species identified and classified
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Millions of bacterial species have not been isolated or
cultured (up to 99.5% of existing species)
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Bergey’s Manual is updated regularly. Prokaryotes are
grouped into 27 phyla based on ribosomal RNA sequence:
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24 Bacteria phyla
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3 Archaea phyla
Each phylum is divided into sections according to:
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Cell shape, arrangement, and motility
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Nutritional and metabolic properties
Each phylum contains one or more Genus (plural Genera)
Prokaryotic Taxonomy
Survey of Archaea
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Have features that distinguish them from most bacteria:
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Unique ribosomal RNA (rRNA) sequences
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No peptidoglycan in cell walls
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Membrane lipids have branched hydrocarbon chains
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Initial amino acid in proteins is Methionine (versus N-formylmethionine )
Extremophiles: Require extreme conditions to survive
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Thermophiles: Only grow at temperatures above 45oC
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Hyperthermophiles: Require temperatures over 80oC (Thermophilus aquaticus)
Halophiles: Need NaCl concentration greater then 9%. Many have red to
orange pigments. Live in Dead Sea, Salt Lake, brine vats, salted fish, etc.
Methanogens: Largest group of archaea
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Obligate anaerobes that generate methane gas from CO2, H2, and acids
Significant environmental impact by converting waste into methane
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Live in ponds, lakes, swamps (“swamp gas”), ocean sediments, and
intestinal tract of cows
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Methane is a greenhouse gas which contributes to global warming
Four Divisions of Bacteria
Division I. Gram-Negative Bacteria
1. Spirochetes
 Helical
shape. Flexible.
 Contain two or more axial filaments
(endoflagella).
 Move in corkscrew pattern.
 Medically important members:
 Treponema
pallidum: Syphilis
 Borrelia burgdorferi.: Lyme disease, relapsing fever
 Leptospira: Leptospirosis
Gram Negative Bacteria
Spirochetes
Syphilis is Caused by a Spirochete
Primary syphilitic chancre and secondary rash.
Source: Tropical Medicine and Parasitology, 1997
Lyme Disease is Caused by a Spirochete
Lyme Disease early lesion at tick bite site.
Source: Medical Microbiology, 1998
2. Aerobic, Motile, Helical/Vibroid GramNegative Bacteria
 Rigid
helical shape or curved rods.
 Lack axial filaments (endoflagella); have polar
flagella instead.
 Most are harmless aquatic organisms.
 Genus Azospirillum fixes nitrogen in soil.
 Genus Bdellovibrio attacks other bacteria.
 Important pathogens include:
 Campylobacter
jejuni: Most common bacterial foodborne intestinal disease in the United States (2 million
cases/year). Associated with undercooked chicken.
 Helicobacter pylori: Causes most gastric ulcers in
humans.
 Campylobacter fetus: Abortions in domestic animals.
Gram Negative Bacteria
Aerobic, Motile, Helical/Vibroid
Gram-Negative Bacteria
Helicobacter pylori causes Gastric Ulcers
4. Gram-Negative Aerobic Rods and Cocci
Contains many medically significant groups.
 Genus
Pseudomonas: Rods with polar flagella.
Many secrete pigments in media.
• Pseudomonas aeruginosa: Urinary tract infections (UTIs),
septicemia, abcesses, burns, pulmonary infections in cystic
fibrosis patients, and meningitis.
 Genus
Legionella: Rods that live in natural waters.
Frequently found in air conditioning systems,
humidifiers, showers, spas, and fountains.
• Legionella pneumophila: Legionnaires’ disease
(pneumonia, 1976) and Pontiac fever.
 Genus
Neisseria: Diplococci. Frequently found on
human mucous membranes. Only grow well around
body temperature.
• Neisseria gonorrhea: Gonorrhea.
• Neisseria meningitidis: Meningitis.
Neisseria gonorrhea Diplococci
Neisseria gonorrhea Causes Salpingitis
Neisseria gonorrhea Causes Neonatal Blindness
Ophtalmia neonatorum caused by Neisseria gonorrheae
Source: Microbiology Perspectives, 1999
4. Gram-Negative Aerobic Rods and Cocci
(Continued)
 Genus Acinetobacter: Plump rods or coccbacilli, nonmotile.
• Acinetobacter baumannii: Infections (Bone, lung, blood, CSF) in
Iraq war veterans, ICU patients. Multiple drug resistance.
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Genus Moraxella: Aerobic egg-shaped cocco-bacilli.
• Moraxella lacunata: Conjunctivitis.
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Genus Brucella: Small nonmotile coccobacilli.
All species are obligate parasites of mammals.
Cause brucellosis. Can survive phagocytosis.
Genus Bordetella: Nonmotile rods. Virulent forms have
capsules.
• Bordetella pertussis: Whooping cough (P in DPT vaccine).
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Genus Francisella: Small pleomorphic bacteria.
• Francisella tularensis: Tularemia
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Genera Rhizobium and Bradyrhizobium: Form nodules on
legume roots and fix nitrogen in soil.
5. Facultative Anaerobic Gram-Negative
Rods
Many cause diseases of gastrointestinal tract.
Contains three medically significant families.
I. Family Enterobacteriaceae (Enterics)
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Inhabit intestinal tracts of animals.
Motile bacteria with peritrichous flagella or nonmotile.
Many have fimbriae for attachment to mucous membranes
and sex pili for exchange of DNA (antibiotic resistance
genes)
Most ferment glucose and other sugars.
 Genus Escherichia: E. coli is common inhabitant of
human intestinal tract. Most strains are not pathogenic,
but others can cause UTIs (urinary tract infections),
traveler’s diarrhea, and food-borne disease.
I. Family Enterobacteriaceae (Continued)
 Genus
Salmonella: Almost all members are potential
pathogens. Common inhabitants of animal GI tract. Can
contaminate food (eggs, meat).
• Salmonella typhi: Typhoid fever, severe illness.
• Salmonella enteritidis: Causes salmonellosis, the second most
common bacterial food-borne disease.
Over 1.3 million cases/year in the U.S.
 Genus
Shigella: Only found in humans. Second most
common cause of traveler’s diarrhea.
 Genus Klebsiella: Cause respiratory and UTIs.
• Klebsiella pneumoniae: Antibiotic resistant strains cause
pneumonia and nosocomial infections.
 Genus
Serratia: Opportunistic respiratory and urinary
tract infections.
• Serratia marcescens: Produces a red pigment. Important
cause of nosocomial infections.
I. Family Enterobacteriaceae (Continued)
 Genus
Proteus: Actively motile. Cause UTIs, wound
infections, and infant diarrhea (nosocomial).
 Genus Yersinia:
• Yersinia pestis: Causes bubonic plague (black death).
Transmitted by fleas, respiratory droplet, and contact with
animals.
 Genus
Erwinia: Important plant pathogens.
 Genus Enterobacter: Cause UTIs and nosocomial
infections.
5. Facultative Anaerobic Gram-Negative
Rods
II. Family Vibrionaceae
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Found in aquatic habitats.
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Straight or slightly curved rods
 Genus
Vibrio: Slightly curved rods.
• Vibrio cholerae: Cholera, profuse & watery diarrhea.
• Vibrio parahaemolyticus: Gastroenteritis. Shellfish.
Cholera is Caused by Vibrio cholerae
Rice-water stool of cholera.
Source: Tropical Medicine and Parasitology, 1995
5. Facultative Anaerobic Gram-Negative
Rods
III. Family Pasterellaceae
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Found in aquatic habitats.
Straight or slightly curved rods
 Genus Pasteurella: Pathogens of domestic animals.
 Genus Hemophilus: Important pathogens that inhabit
mucous membranes of upper respiratory tract, mouth,
vagina, and intestinal tract. Require blood in culture.
• Hemophilus influenzae: Causes meningitis, ear infections,
bronchitis, arthritis, and pneumonia in children.
• H. ducreyi: Cause of sexually transmitted chancroid.
 Genus
Gardnerella: Not assigned to any family.
• G. vaginalis causes common form of vaginitis.
6. Anaerobic Gram-Negative Rods
May be straight, helical, or curved.
 Genus
Bacteroides: Nonmotile. Live in human intestinal
tract (1 billion/gram of feces) and gum crevices. Cause
peritonitis, abscesses, and deep tissue infections.
 Genus Fusobacterium: Long slender rods with pointed
tips. Found in gingival crevices, cause dental abscesses.
7. Sulfur-Reducing Bacteria
Obligate anaerobes that release H2S into the
atmosphere.
Found in soil and intestinal tract of animals.
Ecologically important.
8. Anaerobic Gram-Negative Cocci
Nonmotile cocci typically found in pairs.
 Genus Veillonella: Cause dental plaque.
9. Rickettsias and Chlamydias
Gram negative bacteria.
Obligate intracellular parasites.
Rickettsias: Rod shaped bacteria or coccobacilli,
highly pleomorphic. Transmitted to humans by
insects and ticks (except for Coxiella burnetti which
causes Q fever).
 Genus
Ehrlichiae: Live in white blood cells.
 Genus Rickettsia: Cause spotted group fevers (Rocky
mountain spotted fever, endemic typhus).
Rickettsias are Intracellular Parasites
Chlamydias: Cocci shaped bacteria. Transmitted to
humans by interpersonal contact or by airborne
respiratory routes.
Unique life cycle: Form a reticulate and elementary
bodies in infected cells.
Three species:
 Chlamydia
trachomatis: Causes blindness in humans and
nongonococcal urethritis (most common STD in U.S.).
 C. psittaci: Parrot fever.
 C. pneumoniae: Mild pneumonia.
Division II. Gram-Positive Bacteria
17. Gram-Positive Cocci
Non-spore forming cocci.
 Aerobic to strictly anaerobic.
 Pyogenic (pus-forming)
 Genus Staphylococcus: Tend to form grape-like clusters.
Grow well under high osmotic pressure and low moisture.
Very common infections, because almost always found on
skin and in nasal mucous membranes.
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Staphylococcus aureus: (aureus = golden) Yellow pigmented
colonies. Produce several toxins. Cause pimples, sties, skin
abscesses, toxic shock syndrome, food poisoning, and nosocomial
infections.
MRSA (Methicillin Resistant S. aureus): Antibiotic resistant S.
aureus is a growing problem.
Vancomycin is last line of defense against antibiotic resistant
strains.
Diseases Caused by Staphylococcus
aureus
Scalded
Skin Syndrome
Sty
Toxic Shock
Syndrome
17. Gram-Positive Cocci
 Genus
Streptococcus: Most are pathogens. Tend to
appear in chains or pairs. Do not use oxygen, but most
are aerotolerant. Classified based on their effect on red
blood cells (hemolysis).
Cause a wide range of diseases: Strep throat, respiratory
infections, abscesses, puerperal fever, and opportunistic
infections.
A flesh eating Streptococcus strain emerged in 1994 and
1998. After initial infection, bacteria live on dead flesh,
produce toxins, and are not treatable by antibiotics.
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Streptococcus pneumoniae: Bacterial pneumonia, ear infections,
meningitis, and sinus infections.
Streptococcus pyogenes: Strep throat, scarlet fever, rheumatic
fever, impetigo, skin infections, erysipelas, childbirth (puerperal)
fever, glomerulonephritis, and flesh eating infections.
Scarlet Fever is Caused by a Strain of
Streptococcus pyogenes
Flesh-Eating Streptococcus pyogenes
Necrotizing fasciitis with blood filled vesicles.
Source: Perspectives in Microbiology, 1995
Erysipelas is Caused by Strep. pyogenes
Erysipelas on face due to S. pyogenes infection
Source: Color Guide to Infectious Diseases, 1992
18. Endospore-Forming Gram-Positive Rods
and Cocci
Aerobic to strictly anaerobic.
 Motile and nonmotile.
 Survive harsh environmental conditions.
 Genus Bacillus: Rod shaped bacteria.
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Bacillus anthracis: Causes anthrax a disease of cattle. Large (48 um) nonmotile facultative anaerobe.
Bacillus thuringiensis: Kills insects, used by gardeners.
 Genus
Clostridium: Rod shaped bacteria, obligate
anaerobes.
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Clostridium tetani: Causes tetanus (T in DPT vaccine).
Clostridium botulinum: Causes botulism (source of Botox).
Clostridium perfringens: Causes gas gangrene and foodborne
diarrhea.
Clostridium dificile: Causes diarrhea, especially after antibiotics.
Tetanus is Caused by Clostridium tetani
Neonatal Tetanus (Wrinkled brow and risus sardonicus)
Source: Color Guide to Infectious Diseases, 1992
Gangrene Caused by Clostridium perfringens
Severe gangrene caused by Clostridium perfringens.
Source: Tropical Medicine and Parasitology, 1997
19. Regular Nonsporing Gram-Positive Rods
 Genus
Lactobacillus: Produce lactic acid which inhibits
the growth of other bacteria. In humans live in vagina,
intestinal tract, and mouth. Used commercially to make
yogurt, pickles, sauerkraut, and buttermilk.
 Genus Listeria: Contaminates dairy products.
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Listeria monocytogenes: Survives in phagocytic cells and grows
in refrigerators.
Causes listeriosis.
Infection of pregnant women can cause stillbirth or severe
damage to fetus.
20. Irregular Nonsporing Gram-Positive
Rods
Club shaped (Corynebacteria), pleomorphic.
May be anaerobic or aerobic.
Important pathogens:
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Corynebacterium diphtheriae: Cause diphtheria (D in DPT
vaccine).
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Propionibacterium acnes: Causes acne.
21. Mycobacteria
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Aerobic, non-spore-forming rods.
Stain Gram-positive, but cell wall structure is more similar to
Gram-negative bacteria.
Waxy cell wall with mycolic acids (instead of
peptidoglycan).
Acid-fast, drug resistant, resistant to drying, and pathogenic
due to waxy cell wall.
Grow very slowly.
Tend to cause chronic infections.
Important pathogens:
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Mycobacterium tuberculosis: Causes tuberculosis.
Mycobacterium leprae: Causes leprosy.
Mycobacterium leprae Causes Leprosy
Source: Tropical Medicine and Parasitology, 1995
Mycobacterium leprae Causes Leprosy
Severe bone destruction in advanced leprosy
Source: Diagnostic Pictures in Infectious Diseases, 1995
22. Nocardioforms
Gram-positive, filamentous, aerobic.
 Many are acid fast.
 Common in soil.
 Genus Nocardia: Form filaments which fragment into
short rods to reproduce.
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Nocardia asteroides: Pulmonary infections, mycetoma,
abscesses.
25. Actinomycetes
Gram-positive, filamentous, resemble molds.
 Common in soil.
 Genus Streptomyces: Live in soil. Give soil its musty
odor. Produce hundreds of antibiotics.
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Division III. Wall-Less Bacteria
30. Mycoplasmas
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Do not form cell walls.
Most are aerobes or facultative anaerobes.
Highly pleomorphic.
Can produce filaments that resemble fungi.
Produce very small colonies (1 nm in diameter).
Smallest free-living cells: 0.1 to 0.25 mm in
diameter.
Can pass through bacterial filters.
Most important human pathogen:
Mycoplasma pneumoniae: Walking pneumonia.