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 • KingdomPlantae • KingdomAnimalia • In 1850s bacteria and fungi were incorrectly placed in the Plant Kingdom. • In 1860s KingdomProtista 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 KingdomProcaryotae 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 in1969 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

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

9. Taxonomic Categories Division (Bacteria)

10. Bacterial Groups • Most widely accepted taxonomic classification for bacteria is Bergey’s 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. • Bergey’s update currently in progress. Bacteria are divided into 26 phyla according to the characteristics of their ribosomal RNA sequences. • Each phylum is divided into sections according to: • Cell shape, arrangement, and motility • Nutritional and metabolic properties • Each phylum contains one or more genus.

11. Prokaryotic Taxonomy

12. 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 (Thermophilusaquaticus) • 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

13. Four Divisions of Bacteria

14. 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 burgorferi.: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. • GenusAzospirillum fixes nitrogen in soil. • GenusBdellovibrioattacks 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.

19. 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. • GenusPseudomonas: 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. • GenusLegionella: 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. • GenusNeisseria: 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. • GenusMoraxella: Aerobic egg-shaped cocco-bacilli. • Moraxella lacunata: Conjunctivitis. • GenusBrucella: Small nonmotile coccobacilli. All species are obligate parasites of mammals. Cause brucellosis. Can survive phagocytosis. • GenusBordetella: Nonmotile rods. Virulent forms have capsules. • Bordetella pertussis: Whooping cough (P in DPT vaccine). • GenusFrancisella: Small pleomorphic bacteria. • Francisella tularensis: Tularemia • GeneraRhizobium and Bradyrhizobium: Form nodules on legume roots and fix nitrogen in soil.

26. 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), traveler’s 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. • S. 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 causepneumonia and nosocomial infections. • Genus Serratia: Opportunistic respiratory and urinary tract infections. • Serratia marcescens: Produces a red pigment. Important cause of nosocomial infections.

28. 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.

29. 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. vaginaliscauses 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 • GenusStreptococcus: 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, puerperal fever, glomerulonephritis.

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: • Mycobacteriumtuberculosis: Causes tuberculosis. • Mycobacteriumleprae: 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.