Classification of Bacteria

1. Classification of Bacteria Chapter 4

2. Taxonomy / Systematics • Identification • Distinguishing features • Engine size • Mileage • Number of passengers • Type of transmission • Classification • Organization into groups • Car • Truck • SUV • Van • Nomenclature • Providing a formal name • Genus & species • Ford Crown Victoria • Chevy Impala • Toyota Camry • Honda Civic Consistent rules for all scientist Relevant Meaningful Make biological sense Evolutionary context

3. Five Kingdoms Uni or multicellular Eukaryotic Eukaryotic Unicellular Bacteria Archaea Unicellular Prokaryotic

4. Eukarya Bacteria Archaea 3 Domain System Carl Woese Late 1970’s & early 1980’s Woese, C. R. 2004. A New Biology for a New Century. MMBR. June 68(2):173-86. Woese, C.R. 2002. On the evolution of cells. Proc Natl Acad Sci USA 99(13):8742-7. Woese, C.R. 2000. Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97(15):8392-6.

5. Binomial nomenclature • Genus & species • Escherichia coli • Genus name is always capitalized • Species name is never capitalized coli • Both names are always either italicized or underlined • Abbreviation: E. coli

6. Domains can be Divided into Many Sub-classifications Biological species concept does not apply to prokaryotes!!! • Domain: Bacteria • Phylum: Proteobacteria • Class: Gamma Proteobacteria • Order: Enterobacteriales • Family: Enterobacteriaceae • Genus: Escherichia • Species: Escherichiacoli Species – a collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly

7. 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)

8. Classification of Bacteria Light microscope was the original tool. Initial classification was based on of the shape of the bacterial cells.

9. 4 Main Shapes of Bacteria • Cocci • Bacilli • Spirilla • Spirochetes

10. Medical Microbiologists said… One bacterium = One disease So to these scientists, bacteria were also classified as to the disease they caused… They were also named based on this…

11. Four Groups Based on Cell Wall Composition • Gram-positive cells • Gram-negative cells • Bacteria without cell walls • Bacteria with chemically unique cell walls

12. N-acetylmuramic acid (NAM) Peptidoglycan • Macromolecule composed of a repeating framework of long chains cross-linked by short peptide fragments • Unique to Bacteria • Composed of 2 sugars: NAG & NAM • Sugars alternate in the backbone • Rows linked by polypeptides • Provides strong, flexible support to keep bacteria from bursting or collapsing because of changes in osmotic pressure N-acetylglucosamine (NAG)

14. 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 • Retains crystal violet with iodine as a mordant

15. Gram Negative Cell Wall • Consists of • An outer membrane containing lipopolysaccharide (LPS) • Thin shell of peptidoglycan between inner and outer membranes • Periplasm • Inner membrane • Loses crystal violet-iodine complex when cells are exposed alcohol (decolorization step) and stains red with safranin counterstain

16. Be able to identify all the parts of a Gram + & - cell wall for the next exam.

17. Bacteria with Chemically Unique Cell Walls • Acid-Fast Cells • Mycobacterium species • Gram + type of cell wall • Unique lipid • Mycolic acid – waxy substance • Does not decolorize

18. Rickettsia – Chemically Unique Cell Wall • Stains Gram - • Cell wall contains diaminopimelic acid & lacks teichoic acid • 0.25 m in diameter • Obligate intracellular pathogens • Encapsulated • Enter cell by induced phagocytosis • Divide rapidly once inside • Pathogens that alternate between mammals and fleas, lice or ticks • Rickettsia rickettisii – Rocky Mountain spotted fever • Rickettsia prowazekii – epidemic typhus • Coxiella burnetti – Q fever

19. Chlamydia – Chemically Unique Cell Wall • Obligate intracellular parasites • 0.3 and 1.0 m in diameter • Cell wall contains an outer lipopolysaccharide membrane but lacks peptidoglycan • Contains cysteine-rich proteins that are assumed to be the functional equivalent of peptidoglycan • Stains Gram - • Chlamydia trachomatis • The most common sexually transmitted disease • Chlamydia psittaci • Ornithosis, parrot fever • Chlamydia pneumoniae • Lung infection

20. Bacteria without Cell Walls - Mycoplasma • Lack a rigid cell wall during their entire life cycle • Smallest known organisms – smallest genomes (other than viruses) • Diameter ranges from 0.15 m to 0.30 m • Do not stain with the Gram stain • Pleomorphic • Tiny pleomorphic cocci, short rods, short spirals, and sometimes doughnut shape • Mycoplasma pneumoniae • Atypical pneumonia in humans

21. Numerical Taxonomy Looked at all traits of an organism… every trait had equal importance

22. rRNA Sequence • The greatest advancement in classifying organisms • Differences in the nucleotide sequence are used to classify prokaryotes • 16S rRNA sequences • 23S rRNA sequences Actually look at the DNA that codes for the rRNA

24. How is this accomplished? Extract DNA from a colony, or from an environmental sample without growing the organism. PCR with primers for rRNA sequences Automated DNA sequencer Coefficient of Similarity

25. Bacteria phylogenetic relationships based on rRNA sequences

26. Phylogenetic tree of 16S rDNA sequences Coefficient of Similarity Texas A&M Microbiology www-odp.tamu.edu/.../ 203/images/03_f03b.gif

27. Gamma Proteobacteria

28. Bergey’s Manual of Systematic Bacteriology • Prokaryotes into 25 phyla • Archaea • 2 • Bacteria • 23 • Consensus of experts

29. Relevant Meaningful Make biological sense Evolutionary context rRNA Sequence • The greatest advancement in classifying organisms • Differences in the nucleotide sequence are used to classify prokaryotes • 16S rRNA sequences • 23S rRNA sequences Actually look at the DNA that codes for the rRNA

30. A Selection of Biologically Important Groups of Bacteria These groups have been traditionally defined by cell shape, metabolism, method of motility or type of infection.

32. Cyanobacteria • Gram negative phototrophs • Oxygenic photosynthesis 12H2O + 6CO2 C6H12O6 + 6H2O + 6O2 • Existed for  2.3 bya • Largest and one of the most important groups of bacteria on Earth • Extremely diverse group • Unicellular, colonial & filamentous form • Some species fix N2 in heterocysts • Some species produce akinete • Analogous to a endospore Most species are found in fresh water • Marine • Damp soil • Temporarily moistened desert rocks • Endosymbionts in lichens, plants, various protists or sponges

33. Some cyanobacteria can fix nitrogen Internal photosynthetic membrane Heterocysts N2 fixation

34. Oscillatoria sp. Spirulina sp. Merismopedia sp. vis-pc.plantbio.ohiou.edu/algaeimage/pages/anabaena.html

35. Borrelia burgdorferi Spirochetes www.microbeworld.org • Long, helically coiled cells. • Gram – • Axial filaments • Running lengthwise between the cell membrane and cell wall • Most spirochetes are free-living and anaerobic, but there are exceptions • 3 families • Leptospira spp. • Leptospirosis • Borrelia burgdorferi • Lyme disease • Treponema pallidum • syphilus www.bbc.co.uk/.../stis_syphilis.shtml

36. www.surrey.ac.uk/SBMS/ACADEMICS_homepage/mcfadden_johnjoe/sbms243.htmlwww.surrey.ac.uk/SBMS/ACADEMICS_homepage/mcfadden_johnjoe/sbms243.html

37. Enterics • Gram – rods, facultative anaerobes • Family Enterobacteriaceae • Many are part of the intestinal microflora of mammalian intestines • Infamous pathogens • Salmonella, Escherichia, Klebsiella, Proteus, Enterobacter, Citrobacter • Most ferment glucose, reduce nitrates to nitrites and oxidase negative • Many diagnostic tests to identify these organisms • Page 615 & 616 • Table 20.2

38. page 613

39. Magnetotactic • Magnetosome • Crystalline particles of iron oxide or sulfide • Magnetite Fe3O4 • Greigite Fe3S4 • All are either obligate microaerophiles or strict anaerobes • Motile, aquatic bacteria • Direction of motility is affected by the Earth’s geomagnetic field • Strains are either north- or south-seeking depending upon oxic conditions • North-seekers predominate in the northern hemisphere • South-seekers predominate the southern hemisphere • Exist in equal numbers at the equator • Current hypothesis states that these bacteria use the geomagnetic field to locate lower O2 or anaerobic habitats

40. There are Two Types of Magneto-aerotaxis... Axial Magneto-aerotaxis Polar Magneto-aerotaxis e.g., Magnetospirillum magnetotacticum e.g., strain MC-1, a magnetotactic coccus

41. N2 Fixation • Archaea & Bacteria • Nodules • Rhizobium and Bradyrhizobium form nodules on the roots of legumes • Frankia forms nodules on the roots of alders (Alnus), wax myrtles (Myrica) and mountain lilacs • “pioneer plants” • Free-living • Azospirillum • Azotobacter • Clostridium • Bacillus • Klebsiella • Methanosarcina • Archaea • Cyanobacteria • No eukaryotic organisms fix N2 www.tari.gov.tw/ARI_E/E_image/ACD_13.jpg

42. mdchoice.com/photo/img/img0110.jpg Pyogenic cocci • Causes many suppurative infections • Gram + cocci • Staphylococcus aureus, Streptococcuspyogenes & Streptococcus pneumoniae, • Gram - cocci • Neisseria gonorrhoeae & N. meningitidis • ⅓ of all human bacterial infections • Food poisoning, strep throat, pneumonia, various skin diseases, septic shock, gonorrhea & meningitis • Bacteria in this group are unrelated nova.medicina.cz/files/gonorrhea_01.jpg

43. Lactic Acid Bacteria • Fementative bacteria that produce lactic acid under anaerobic conditions (can be described as oxytolerant anaerobes) • Convert pyruvate to lactic acid • Also produce acetic acid & CO2 • Regenerate NAD+ for glycolysis • Species of Streptococcus and Lactobacillus • Dairy industry • Cheese, cottage cheese, yogurt

44. Endospore-forming Bacteria • Gram + • Bacillus, Clostridium and Sporosarcina • Survival structure • Resistant to heat, UV, desiccation • Pathogen • Bacillus anthracis • Clostridium tetani • C. perfringens • C. botulinum

45. Purple and Green Bacteria • Anoxygenic photosynthesis • 12H2S + 6CO2 C6H12O6 + 12S° • Colors due to color of slightly different bacteriochlorophylls • Green - deposit S° outside • Purple - S° is inside the cell • Anaerobic H2S-containing mud and water

46. Vibrios • Gram -, slightly curved rods, polar flagellum • Estuarine & marine environments • Pathogenic and cooperative interactions with eukaryotic host • Vibrio cholerae • Cholera • Extreme watery diarrhea • Only species that can survive in both fresh and salt water • Potent toxin • Vibrio fischeri • Bacterial bioluminescence • Lives planktonically in seawater but can also colonizes organs of squids and marine fish • Autoinducer • Quorum sensing www.nature.com/.../020603/full/020603-2.html ergo.integratedgenomics.com

47. Myxobacteria • Glide over surface • No flagella • Vegetative cells swarm during nutrient depletion • Fruiting body • Dormant myxospores • Spores “germinate” under favorable conditions www.textbookofbacteriology.net

48. Actinomycetes • Filamentous, Gram + soil bacteria • Aerobic decomposition of organic compounds • Biodegradation • Carbon cycle • Geosmins • Earth odor • Antibiotics • Streptomyces • Tetracyclines, macrolides and aminoglycosides • Pathogens • Mycobacterium tuberculosis • Corynebacterium diphtheriae

49. Radioresistant • Deinococcus radiodurans • Gram + • Survive a dosage of radiation that is 3,000 times greater than what would kill a human • Survive DNA damaging chemicals, and high levels of ionizing and ultraviolet radiation, and dehydration • Able to repair chromosome fragments within 12-24 hours • Repair chromosomes that have been broken into 100 fragments science.nasa.gov