Chapter 11: Characterizing and Classifying Prokaryotes

1

• Chapter 11 Characterizing and Classifying
  Prokaryotes

2

• 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.
• 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.

3

• 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.

4

• 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 five-kingdom
  system of biological classification for all
  living organisms.

5

• 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.

6
Five-Kingdom Classification System
7

• Classification of Organisms
• Scientific Nomenclature
• Scientific nomenclature Universal system for
  naming and classifying living organisms.
  Initially developed in the 18th century by Carl
  Linnaeus.
• Binomial nomenclature Each organism (species)
  has a two part name. Names are either italicized
  or underlined.
• Genus name Always capitalized, always a noun.
  May use initial.
• species name Always lower case, usually an
  adjective.
• Names are usually derived from Latin (or Greek)
  or may have latinized endings. Examples
• Homo sapiens (H. sapiens) Human
• Penicillium notatum (P. notatum) Mold that
  produces penicillin
• Canis familiaris (C. familiaris) Domestic dog

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• Classification of Organisms
• Hierarchy of Taxonomic Categories
• DOMAIN
• Kingdom
• Phylum or Division (Bacteria)
• Class
• Order
• Family
• Genus
• species

9
Taxonomic Categories
Division (Bacteria)
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• Bacterial Groups
• The most widely accepted taxonomic classification
  for bacteria is in Bergeys Manual of Systematic
  Bacteriology
• Close to 5000 bacterial species identified and
  classified
• Millions of bacterial species have not been
  isolated or cultured (up to 99.5 of existing
  species)
• Bergeys Manual is updated regularly. Prokaryotes
  are grouped into 27 phyla based on ribosomal RNA
  sequence
• 24 Bacteria phyla
• 3 Archaea phyla
• Each phylum is divided into sections according
  to
• Cell shape, arrangement, and motility
• Nutritional and metabolic properties
• Each phylum contains one or more Genus (plural
  Genera)

11
Prokaryotic Taxonomy
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• Survey of Archaea
• Have features that distinguish them from most
  bacteria
• Unique ribosomal RNA (rRNA) sequences
• No peptidoglycan in cell walls
• Membrane lipids have branched hydrocarbon chains
• Initial amino acid in proteins is Methionine
  (versus N-formylmethionine )
• Extremophiles Require extreme conditions to
  survive
• Thermophiles Only grow at temperatures above
  45oC
• 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
• Obligate anaerobes that generate methane gas from
  CO2, H2, and acids
• Significant environmental impact by converting
  waste into methane
• Live in ponds, lakes, swamps (swamp gas),
  ocean sediments, and intestinal tract of cows
• Methane is a greenhouse gas which contributes to
  global warming

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Four Divisions of Bacteria
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• 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

15
Gram Negative BacteriaSpirochetes
16
Syphilis is Caused by a Spirochete
Primary syphilitic chancre and secondary
rash. Source Tropical Medicine and
Parasitology, 1997
17
Lyme Disease is Caused by a Spirochete
Lyme Disease early lesion at tick bite
site. Source Medical Microbiology, 1998
18

• 2. Aerobic, Motile, Helical/Vibroid
  Gram-Negative 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
  food-borne 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.

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Gram Negative BacteriaAerobic, Motile,
Helical/Vibroid Gram-Negative Bacteria
20
Helicobacter pylori causes Gastric Ulcers
21

• 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.

22
Neisseria gonorrhea Diplococci
23
Neisseria gonorrhea Causes Salpingitis
24
Neisseria gonorrhea Causes Neonatal Blindness
Ophtalmia neonatorum caused by Neisseria
gonorrheae Source Microbiology Perspectives,
1999
25

• 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.
• Genus Moraxella Aerobic egg-shaped
  cocco-bacilli.
• Moraxella lacunata Conjunctivitis.
• 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).
• Genus Francisella Small pleomorphic bacteria.
• Francisella tularensis Tularemia
• Genera Rhizobium and Bradyrhizobium Form
  nodules on legume roots and fix nitrogen in soil.

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• 5. Facultative Anaerobic Gram-Negative Rods
• Many cause diseases of gastrointestinal tract.
• Contains three medically significant families.
• I. Family Enterobacteriaceae (Enterics)
• 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), travelers diarrhea, and
  food-borne disease.

27

• 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 travelers 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.

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• 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.

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• 5. Facultative Anaerobic Gram-Negative Rods
• II. Family Vibrionaceae
• Found in aquatic habitats.
• Straight or slightly curved rods
• Genus Vibrio Slightly curved rods.
• Vibrio cholerae Cholera, profuse watery
  diarrhea.
• Vibrio parahaemolyticus Gastroenteritis.
  Shellfish.

30
Cholera is Caused by Vibrio cholerae
Rice-water stool of cholera. Source Tropical
Medicine and Parasitology, 1995
31

• 5. Facultative Anaerobic Gram-Negative Rods
• III. Family Pasterellaceae
• 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.

32

• 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.

33

• 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).

34
Rickettsias are Intracellular Parasites
35

• 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.

36

• 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.
• 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.

37
Diseases Caused by Staphylococcus aureus
Scalded Sty Toxic Shock Skin
Syndrome Syndrome
38

• 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.
• 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.

39
Scarlet Fever is Caused by a Strain of
Streptococcus pyogenes
40
Flesh-Eating Streptococcus pyogenes
Necrotizing fasciitis with blood filled
vesicles. Source Perspectives in Microbiology,
1995
41
Erysipelas is Caused by Strep. pyogenes
Erysipelas on face due to S. pyogenes infection
Source Color Guide to Infectious Diseases, 1992
42

• 18. Endospore-Forming Gram-Positive Rods and
  Cocci
• Aerobic to strictly anaerobic.
• Motile and nonmotile.
• Survive harsh environmental conditions.
• Genus Bacillus Rod shaped bacteria.
• Bacillus anthracis Causes anthrax a disease of
  cattle. Large (4-8 um) nonmotile facultative
  anaerobe.
• Bacillus thuringiensis Kills insects, used by
  gardeners.
• Genus Clostridium Rod shaped bacteria, obligate
  anaerobes.
• 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.

43
Tetanus is Caused by Clostridium tetani
Neonatal Tetanus (Wrinkled brow and risus
sardonicus) Source Color Guide to Infectious
Diseases, 1992
44
Gangrene Caused by Clostridium perfringens
Severe gangrene caused by Clostridium
perfringens. Source Tropical Medicine and
Parasitology, 1997
45

• 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.
• Listeria monocytogenes Survives in phagocytic
  cells and grows in refrigerators.
• Causes listeriosis.
• Infection of pregnant women can cause stillbirth
  or severe damage to fetus.

46

• 20. Irregular Nonsporing Gram-Positive Rods
• Club shaped (Corynebacteria), pleomorphic.
• May be anaerobic or aerobic.
• Important pathogens
• Corynebacterium diphtheriae Cause diphtheria (D
  in DPT vaccine).
• Propionibacterium acnes Causes acne.

47

• 21. Mycobacteria
• 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
• Mycobacterium tuberculosis Causes tuberculosis.
• Mycobacterium leprae Causes leprosy.

48
Mycobacterium leprae Causes Leprosy
Source Tropical Medicine and Parasitology, 1995
49
Mycobacterium leprae Causes Leprosy
Severe bone destruction in advanced
leprosy Source Diagnostic Pictures in
Infectious Diseases, 1995
50

• 22. Nocardioforms
• Gram-positive, filamentous, aerobic.
• Many are acid fast.
• Common in soil.
• Genus Nocardia Form filaments which fragment
  into short rods to reproduce.
• 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.

51

• Division III. Wall-Less Bacteria
• 30. Mycoplasmas
• 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.