KLASIFIKASI BAKTERI

CLASSIFICATION OBSERVATION: Many kinds of organisms: Some similar to each other. wood frog, leopard frog, bull frog 08 June 2009 Classification.ppt 2

CLASSIFICATION Others less similar fish, frogs, snakes 08 June 2009 Classification.ppt 3

CLASSIFICATION Others very dissimilar people, pine trees, protozoans 08 June 2009 Classification.ppt 4

CLASSIFICATION Why are some kinds similar and others NOT similar? Question to be answered later? How can we make sense of (explain) this diversity? How can we organize what we know about these organisms? 08 June 2009 Classification.ppt 5

Answer: CLASSIFY Similar “types” (species) grouped together, separated from other species. Then, group similar groups together, etc. 08 June 2009 Classification.ppt 6

CLASSIFICATION Species = kind of organism fundamental unit in evolution and ecology more precise definition soon 08 June 2009 Classification.ppt 7

CLASSIFICATION Necessary? YES !! ~ 1 million species of plants, 5-10 million species of animals + fungi, protists, bacteria no good estimates of numbers of species Human mind needs to organize information. 08 June 2009 Classification.ppt 8

CLASSIFICATION Classification system organizes biological knowledge. Classification itself is HYPOTHESIS about relationships, similarity because of common ancestry. 08 June 2009 Classification.ppt 9

HYPOTHESIS of relationship 08 June 2009 Classification.ppt 10

CLASSIFICATION = Sequence of levels CLASSIFICATION = Sequence of levels. Linnaean system, from Carolus Linnaeus, 1740's Kingdom Phylum Class Order Family Genus Species King Phil called old fat George stupid. 08 June 2009 Classification.ppt 11

CLASSIFICATION = Linnaean system 08 June 2009 Classification.ppt 12

CLASSIFICATION Whittaker’s Five Kingdoms, 1965 Kingdom Monera (Bacteria) Kingdom Protista Kingdom Fungi Kingdom Plantae Kingdom Animalia 08 June 2009 Classification.ppt 13

CLASSIFICATION Woese, 1985 Prokaryotic organisms are far more diverse than thought previously. Domain Eubacteria (prokaryotic “true bacteria”) Domain Archaea (prokaryotic “archaeans”) Domain Eukarya (eukaryotic organisms) 08 June 2009 Classification.ppt 14

CLASSIFICATION Woese, 1985 Prokaryotic organisms are far more diverse than thought previously. Domain Eubacteria (prokaryotic “true bacteria”) Kingdom Gram-positive bacteria Kingdom Gram-negative bacteria Kingdom Mycoplasmas Kingdom Rickettsias Kingdom purple-sulfur bacteria and more Domain Archaea (prokaryotic “archaeans”) Domain Eukarya (eukaryotic organisms) 08 June 2009 Classification.ppt 15

CLASSIFICATION Woese, 1985 Prokaryotic organisms are far more diverse than thought previously. Domain Eubacteria (prokaryotic “true bacteria”) Domain Archaea (prokaryotic “archaeans”) Kingdom Thermophiles Kingdom Halophiles Kingdom Methanogens Kingdom ARMANS (“Archeal Richmond Mine Acidophilic Nanoorganism” Science vol 314, 22 Dec. 2006.) Domain Eukarya (eukaryotic organisms) 08 June 2009 Classification.ppt 16

CLASSIFICATION Woese, 1985 Prokaryotic organisms are far more diverse than thought previously. Domain Eubacteria (prokaryotic “true bacteria”) Domain Archaea (prokaryotic “archaeans”) Domain Eukarya (eukaryotic organisms) Kingdom Protista Kingdom Fungi Kingdom Plantae Kingdom Animalia 08 June 2009 Classification.ppt 17

CLASSIFICATION Woese, 1985 08 June 2009 Classification.ppt 18

CLASSIFICATION Woese, 1985 Domain Kingdom Phylum Class Order Family Genus Species Did King Phil call old fat George stupid ? 08 June 2009 Classification.ppt 19

Tree of Life

Eukaryote origins:

Scientific Nomenclature: Binomial nomenclature Genus species Bacteria- Journal of Systematic Bacteriology ____________ Manual Latinized names commemorate microbiologists or describe features of the organism

Scientific nomenclature: a hierarchical system

Classification of Bacteria: Bergey’s manual of systematic bacteriology, 2nd edition is being published (What’s in our lab????????) Bacterial species are defined as a population of cells with similar characteristics Strains exist within species

Classification of Bacteria: Fig. 10-6

Methods of Classification and Identification of Microorganisms: Necessary to identify microorganism Bacteria are small and many are similar in shapes so must Test metabolic reactions Identify specific characters to identify

Bergey’s Manual of Determinative Bacteriology Not evolutionary relatedness, but provides identification (determinative) schemes based upon Cell wall composition Differential staining Oxygen requirements Biochemical testing

Morphological Characteristics: Cocci, bacilli, spirilla, spirochetes Position of any flagella Position of developing endospores with in the cell

Differential Staining: Gram Stain Acid Fast Stain Quick and may allow a physician to begin appropriate treatment

Biochemical tests: Enzymatic activities ex.: ability of bacteria to ferment a variety of carbohydrates Ecological roles: nitrogen fixation for example Enteric Bacteria: some are pathogens Escherichia, Enterobacter, Citrobacter ferment glucosa Shigella and Salmonella (PATHOGENS)

Bacteria are identified using a series of physiological, immunological or molecular characteristic

Gram-Negative Rods Enteric Bacteria E. coli Salmonella Shigella Yersinia Pseudomonas Proteus Vibrio cholerae Klebsiella pneumoniae

Gram-Negative Rods Fastidious GNRs Bordetella pertussis Haemophilus influenzae Campylobacter jejuni Helicobacter pylori Legionella pneumophila Anaerobic GNRs Bacteroides fragilis Fusobacterium

Gram-Positive Rods Clostridia Anaerobes C.perfringens C. tetani C. botulinum C. difficile Bacillus cereus Aerobe Listeria monocytogenes Faculative anaerobe

Gram-Negative Cocci Neisseria gonorrhoeae The Gonococcus Neisseria meningitidis The Meningococcus Both Gram-negative intracellular diplococci

Gram-positive Cocci Staphylococci Catalase-positive Gram-positive cocci in clusters Staphylococcus aureus coagulase-positive Staph. epidermidis and other coagulase negative staphylococci

Gram-Positive Cocci Streptococci Catalase-negative Gram-positive cocci in chains or pairs Strep. pyogenes Strep. pneumoniae Viridans-type streps Enterococcus faecalis

Non-Gram-stainable bacteria Unusual gram-positives Spirochaetes Obligate intra-cellular bacteria

Unusual Gram-positives Mycoplasmas Smallest free-living organisms No cell wall M. pneumonia, M. genitalium Mycobacteria Acid-fast bacilli, stained by Ziehl-Neelsen stain M. tuberculosis M. leprae M. avium

Spirochaetes Thin spiral bacteria Viewable by phase-contrast microscopy or silver stain Treponema pallidum Borrelia burgdorferi Leptospira

Obligate intracellular bacteria Rickettsia Coxiella burneti Chlamydias C. trachomatis C. pneumoniae C. psittaci

Identification of Enteric Pathogens:

Enterotube:

Fast Identification Techniques: Serology: antigens on bacteria cause antibodies to be formed, then can be used to id the bacteria, even specific strains! Slide agglutination ELISA – enzyme linked immunosorbent assay Western blotting-Bacterial antigens in serum Phage typing: uses viruses that infect bacteria to identify bacteria

Slide Agglutination:

Other methods: Fatty Acid Profiles: bacteria produce a consistent set Commercial system to separate cellular fatty acids from those of known microorganisms Flow cytometry Cells flow-numbers and shapes-laser Immunoflourescent tags reveal specific organisms

Fatty acid analysis Fatty acid methyl ester (FAME) chromatogram of an unknown species, showing chromatographic column retention times and peak heights. Note: 10:0, 12:0, 16:0, and 19:0 indicate saturated fatty acids with 10, 12, 16, and 19 carbons; 16:1 and 18:1, monounsaturated 16-carbon and 18-carbon fatty acids; omega number, the position of the double bond relative to the omega end—that is the hydrocarbon end (not the carboxyl end)—of the fatty acid chain; cis and trans, the configuration of the double bond. For example, omega 7 cis indicates a cis double bond between the seventh and eighth carbons from the omega end of the fatty acid. Also, 2OH indicates a hydroxyl group at the second carbon from the omega end; cyclo omega 8, a cyclo-carbon at the eighth position from the omega end. The 18:1 omega 7 cis, omega 9 trans, and omega 12 trans peak results from either one fatty acid or a mixture of fatty acids with double bonds at the three positions indicated (the chromatographic column does not separate these three fatty acids). Courtesy of MIDI (Microbial Identification, Incorporated, Delaware).

Identification by DNA based methods: DNA base composition: G-C % ‘ages DNA fingerprinting- specific id rRNA sequencing-phylogenic relationship Polymerase chain reaction(PCR)-increase amount of DNA so it can be studied Hybridization, Southern blotting, and DNA probes are other DNA based id techniques

DNA Chip Technology:

Summary of Classification Methods: Dichotomous keys Widely used, based upon questions each of which has two possible answers, eventually get to identification Cladograms are used to show degrees of evolutionary relationship

Summary of Classification/Identification: