Chapter 19 Microbial Taxonomy 2

1. Chapter 19 Microbial Taxonomy

2. General Introduction and Overview • Taxonomy • science of biological classification • consists of three separate but interrelated parts • classification – arrangement of organisms into groups (taxa; s.,taxon) • nomenclature – assignment of names to taxa • identification – determination of taxon to which an isolate belongs

3. Importance of taxonomy • allows scientists to organize huge amounts of knowledge about organisms • allows scientists to make predictions and frame hypotheses about organisms • places organisms into meaningful, useful groups, with precise names, thus facilitating scientific communication • essential for accurate identification of organisms

4. Systematics • Study of organisms with the ultimate object of characterizing and arranging them in an orderly manner

5. Phylogenetic Tree

6. Taxonomic Ranks • microbiologists often use informal names • e.g., purple bacteria, spirochetes, methane-oxidizing bacteria

7. genus – well defined group of one or more species that is clearly separate from other genera

8. Hierarchical arrangement in Taxonomy • Species • Genus • Family • Order • Class • Phylum • Domain Species is the basic taxonomic group in microbial taxonomy

9. Defining procaryotic species • two definitions suggested • collection of strains that share many stable properties and differ significantly from other groups of strains • collection of strains with similar G + C composition and  70% sequence similarity

10. Strains • Strain within a species is a population of organisms that is distinguishable from others within a taxon • descended from a single organism or pure culture isolate • vary from each other in many ways – differ biochemically and physiologically - Biovars – differ morphologically - Morphovars – differ in antigenic properties – Serovars

11. Binomial System of Nomenclature • devised by Carl von Linné (Carolus Linnaeus) • each organism has two names • genus name – italicized and capitalized (e.g., Escherichia) • species epithet – italicized but not capitalized (e.g., coli) • can be abbreviated after first use (e.g., E. coli)

12. Major Characteristics Used in Taxonomy • two major types • Classical characteristics • molecular characteristics

13. Classical Characteristics • Morphological • Physiological and metabolic • Ecological • life-cycle patterns • symbiotic relationships • ability to cause disease • habitat preferences • growth requirements • Genetic analysis • study of chromosomal gene exchange by transformation and conjugation

16. Molecular Characteristics • Comparison of proteins • determination of amino acid sequence • comparison of electrophoretic mobility • Nucleic acid base composition • G + C content • Mol% G + C = (G + C/G + C + A + T)100 • variation within a genus usually < 10% • Nucleic acid hybridization

18. Nucleic acid hybridization • measure of sequence homology • common procedure • bind nonradioactive DNA to nitrocellulose filter • incubate filter with radioactive single-stranded DNA • measure amount of radioactive DNA attached to filter

21. The Major Divisions of Life • Based on rRNA analysis • Proposed by Carl Woese in 1978 • currently held that there are three domains of life • Bacteria • Archaea • Eucarya

23. Bergey’s Manual of Systematic Bacteriology • Published in 1923 by Bergey • detailed work containing descriptions of all procaryotic species currently identified

24. The First Edition of Bergey’s Manual of Systematic Bacteriology • primarily phenetic • cell wall characteristics play important role • Emphasis on • Shape and morphology • Gram staining properties • Oxygen relationships • Motility • Presence of endospores • Mode of energy production

25. First Edition • Procaryotes are divided into • Gram-negative • Gram-positive • Gram-negative with distinctive properties such as cyanobacteria and archaea • Actinomycetes = gram-positive filamentous bacteria

26. The Second Edition of Bergey’s Manual of Systematic Bacteriology • largely phylogenetic rather than phenetic • Contains 5 volumes

27. The Second Edition of Bergey’s Manual of Systematic Bacteriology • Volume 1 – Archeae and branching phototrophic bacteria • Volume 2 – Proteobacteria Gram-negative • Volume 3 – low G+C Gram-positive • Volume 4 – high G+C Gram-positive • Volume 5 – Spirochetes, Planctomycetes, Fusobacteria, Fibrobacteres, Bacteroidetes

29. Volume 1 • Two domains • Archaea • Phylum Crenarchaeota • Phylum Eucaryochaeota • Bacteria

30. Domain Archaea

31. Domain Bacteria

32. Phylum Crenarchaeta

33. Phylum Crenarchaeta • Most are extremely thermophilic • Many are acidophiles • Many are sulfur-dependent • Almost all are strict anaerobes • Contains 69 genera • two best studied are Sulfolobus and Thermoproteus

34. Phylum Crenarchaeta • grow in geothermally heated water or soils that contain elemental sulfur

35. Phylum Encaryochaeta • Consists of many classes, orders, and families • Often divided informally into five major groups • methanogens • halobacteria • extremely thermophilic S0-metabolizers • sulfate-reducers

36. Phylum Encaryochaeta • Methanogens • important in wastewater treatment • can produce significant amounts of methane • Extreme halophiles or Halobacteria • Dependence on high concentration of NaCl • Grow in high salinity habitats such as in dead sea and great lake in Uttah • Have red to yellow pigmentation • Extremely thermophilic S metabolizers • 2 genera Thermococcus and Pyrococcus

37. Volume 2 – Phylum Proteobacteria • Contains Gram-negative Proteobacteria or purple bacteria • Important genera • Escherichia • Neisseria • Pseudomonas • Ricketssia • Salmonella • Vibrio

38. Volume 3 • Gram-positive with low G+C content in their DNA placed in phylum Firmicutes • Some are rods, cocci while Mycoplasma are pleomorphic • Endospores may be present • Phylum Firmicutes is divided into 3 classes • Class Mollicutes (Mycoplasma) – no cell wall • Class Clostridia • Class Bacilli

40. Class Mollicutes (The Mycoplasmas) • Lack cell wall • Penicillin-resistant • Pleomorphic, most are nonmotile • Most are facultative anaerobes, few are obligate anaerobes • Colonies with fried egg appearance

41. Class Clostridia • Obligate anaerobes, Gram-positive • Form endospores • Important species of Clostridium • C. botulinum – food spoilage (especially canned foods); botulism • C. tetani – tetanus • C. perfringens – gas gangrene • C. acetobutylicum – manufacture of butanol

42. Class Bacilli

43. Class Bacilli • Genus Bacillus • Genus Staphylococcus • Genus Listeria • Genera Lactobacillus, Streptococcus, Enterococcus, Lactococcus

44. Genus Bacillus • Contains Gram-positive, endospore forming bacteria • Rods, motile and peritrichously flagellated • Aerobic and catalase positive • various species produce antibiotics • Important species of Bacillus • B. subtilis • B. cereus • B. anthracis • B. Thuringiensis

45. Important species of Bacillus • B. subtilis – important experimental organism • genome recently sequenced • B. cereus – food poisoning • B. anthracis – anthrax • B. thuringiensis and B. sphaericus – used as insecticide

46. Genus Staphylococcus • Facultative anaerobes, nonmotile, Gram-positive cocci • Ferment glucose and have techoic acid in their cell wall • Associated with skin and mucous membranes • Important species • S. aureus • S. epidermidis

47. Genus Listeria • Short rods • motile by peritrichous flagella • Aerobic or facultative • Catalase positive • Important species is Listeria monocytogenes – listeriosis • food-borne disease

48. Genus Lactobacillus • Nonsporing rods, facultative or microaerophilic • Produces lactic acid as their fermentation product • Grow under acidic conditions • widely distributed in nature • on plant surfaces • in dairy products, meat, water, sewage, beer, fruits, and other materials • normal flora of mouth, intestinal tract, and vagina • usually not pathogenic

49. Genus Streptococcus • Facultative anaerobes • do not form endospore, and nonmotile • Homolactic fermentation – ferment sugars but no gas production • Important species • Streptococcus pyogenes – streptococcal sore throat, acute glomerulonephritis, and rheumatic fever • Streptococcus pneumoniae – pneumonia and otitis media • Streptococcus mutans – dental caries

50. Genus Enterococcus • Enterococcus faecalis • Normal residents of intestinal tracts of humans and other animals • Opportunistic pathogen that can cause urinary tract infections and endocarditis • Grow in 6.5% NaCl unlike streptococci