taxonomy n.
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Taxonomy
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  1. Taxonomy http://www.linnean.org/html/history/linnaeus_biography.htm http://www.nhm.ac.uk/library/linn/

  2. www.amazon.com Taxonomy

  3. Plantae Animalia Fungi Protista Monera Five kingdom system

  4. Encephalitozoan EUBACTERIA EUKARYA Hexamita Valrimorpha Cytophaga Giardia Chlorobium Epulopiscium Bacillus Trichomonas Agrobacterium Synechococcus Physarum E. coli Thermus Trypanosoma Thermomicrobium Riftia Chromatium Thermotoga Euglena Aquifex ARCHAEA Naegleria Entamoeba Haloferax Dictylostelium Methanobacterium Methanospirillum Porphyra Methanococcus Methanosarcina Organisms visible to human eye Thermococcus Paramecium Methanopyros Plants Sulfolobus Fungi Animals Thermoproteus Thermofilum pSL50 pSL4 pSL22 pSL12 pJP78 pJP27 Marine group 1 Three Domain System Black, J.G. (2002) Fig. 9.13

  5. Taxonomical “ranks” after Alcamo Fig. 3.4

  6. OR, underline if handwritten: Enterococcus faecalis • strains? (subspecies) Bacterial nomenclature • Genus + species • e.g.: • Escherichia (genus) coli (species) • Bacillus subtilis • Enterococcus faecalis

  7. Prokaryotic Profiles: the Bacteria and the Archaea

  8. Fig. 4.1

  9. flagella • 3 parts - filament – long, thin, helical structure composed of proteins - hook- curved sheath - basal body – stack of rings firmly anchored in cell wall • rotates 360o • 1-2 or many distributed over entire cell • functions in motility

  10. Fig 4.2b

  11. Flagellar arrangements • monotrichous – single flagellum at one end • lophotrichous – small bunches arising from one end of cell • amphitrichous – flagella at both ends of cell • peritrichous – flagella dispersed over surface of cell, slowest

  12. monotrichous lophotrichous amphitrichous pheritrichous

  13. Fig 4.5

  14. Chemotaxis Fig 4.6

  15. axial filaments • periplasmic, internal flagella, enclosed between cell wall and cell membrane of spirochetes • motility

  16. Fig 4.7a b

  17. fimbrae • fine hairlike bristles from the cell surface • function in adhesion to other cells and surfaces

  18. pili • rigid tubular structure made of pilin protein • found only in Gram negative cells • Functions • joins bacterial cells for DNA transfer (conjugation) • adhesion

  19. Conjugation

  20. glycocalyx • Coating of molecules external to the cell wall, made of sugars and/or proteins • 2 types • capsule - highly organized, tightly attached • slime layer - loosely organized and attached • functions • attachment • inhibits killing by white blood cells • receptor

  21. Fig 4.10

  22. 2 Types of Glycocalyx

  23. Biofilms

  24. Peptidoglycan • unique macromolecule composed of a repeating framework of long glycan chains cross-linked by short peptide fragments • provides strong, flexible support to keep bacteria from bursting or collapsing because of changes in osmotic pressure

  25. Peptidoglycan

  26. 4 groups based on cell wall composition • Gram positive cells • Gram negative cells • Bacteria without cell walls • Bacteria with chemically unique cell walls

  27. Gram positiveGram negative Fig 4.16

  28. Gram positive cell wall • Consists of - a thick, homogenous sheath of peptidoglycan 20-80 nm thick - tightly bound acidic polysaccharides, including teichoic acid and lipoteichoic acid • cell membrane • Retain crystal violet and stain purple

  29. Gram positive wall

  30. Gram negative cell wall • Consists of - an outer membrane containing lipopolysaccharide (LPS) - thin shell of peptidoglycan - periplasmic space • inner membrane • Lose crystal violet and stain red from safranin counterstain

  31. Gram negative cell wall

  32. Cytoplasm • dense gelatinous solution of sugars, amino acids, & salts • 70-80% water • serves as solvent for materials used in all cell functions

  33. Chromosome • single, circular, double-stranded DNA molecule that contains all the genetic information required by a cell • DNA is tightly coiled around a protein, aggregated in a dense area called the nucleoid

  34. plasmids • small circular, double-stranded DNA • free or integrated into the chromosome • duplicated and passed on to offspring • not essential to bacterial growth & metabolism • may encode antibiotic resistance, tolerance to toxic metals, enzymes & toxins • used in genetic engineering- readily manipulated & transferred from cell to cell

  35. ribosomes • made of 60% ribosomal RNA & 40% protein • consist of 2 subunits: large & small • procaryotic differ from eucaryotic ribosomes in size & number of proteins • site of protein synthesis • All cells have ribosomes.

  36. ribosomes

  37. Inclusions, granules • intracellular storage bodies • vary in size, number & content • bacterial cell can use them when environmental sources are depleted • Examples: glycogen, poly-b-hydroxybutyrate, gas vesicles for floating, sulfur and polyphosphate granules

  38. Inclusions

  39. endospores • Resting, dormant cells • produced by some G+ genera: Clostridium, Bacillus & Sporosarcina • Have a 2-phase life cycle – vegetative cell & an endospore • sporulation -formation of endospores • germination- return to vegetative growth • hardiest of all life forms • withstand extremes in heat, drying, freezing, radiation & chemicals not a means of reproduction

  40. endospores • resistance linked to high levels of calcium & dipicolinic acid • dehydrated, metabolically inactive • thick coat • longevity verges on immortality 25, 250 million years. • pressurized steam at 120oC for 20-30 minutes will destroy.

  41. endospores

  42. 3 shapes of bacteria • cocci - spherical • bacilli - rod • spiral - helical, comma, twisted rod, spirochete

  43. Methods in bacterial identification • Microscopic morphology • Macroscopic morphology – colony appearance • Physiological / biochemical characteristics • Chemical analysis • Serological analysis • Genetic & molecular analysis • G + C base composition • DNA analysis using genetic probes • Nucleic acid sequencing & rRNA analysis

  44. Major Taxonomic Groups of Bacteria per Bergey’s manual • Gracilicutes – gram-negative cell walls, thin-skinned • Firmicutes – gram-positive cell walls, thick skinned • Tenericutes – lack a cell wall & are soft • Mendosicutes – archaea, primitive procaryotes with unusual cell walls & nutritional habits

  45. species –a collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly • strain or variety – a culture derived from a single parent that differs in structure or metabolism from other cultures of that species (biovars, morphovars) • type – a subspecies that can show differences in antigenic makeup (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype).

  46. Procaryotes with unusual characteristics

  47. Rickettsias • very tiny, gram-negative bacteria • most are pathogens that alternate between mammals and fleas, lice or ticks • obligate intracellular pathogens • cannot survive or multiply outside of a host cell • cannot carry out metabolism on their own • Rickettsia rickettisii – Rocky Mountain spotted fever • Rickettsia prowazekii – epidemic typhus • Coxiella burnetti – Q fever

  48. Chlamydias • tiny • obligate intracellular parasites • not transmitted by arthropods • Chlamydia trachomatis – severe eye infection and one of the most common sexually transmitted diseases • Chlamydia psittaci – ornithosis, parrot fever • Chlamydia pneumoniae – lung infections