Classification of Bacteria Chapter 4 Taxonomy Systematics Identification

Classification of Bacteria Chapter 4

Taxonomy / Systematics • Identification • Distinguishing features • Organization into groups • Engine size • Car • Mileage • Truck • Number of passengers • SUV • Type of transmission • Van • Classification • 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 2

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

Bacteria Archaea Eukarya 3 Carl. Domain System 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. 4

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 5

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

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) 7

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

4 Main Shapes of Bacteria Cocci Bacilli Spirilla Spirochetes 9

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… 10

Four Groups Based on Cell Wall Composition 1. 2. 3. 4. Gram-positive cells Gram-negative cells Bacteria without cell walls Bacteria with chemically unique cell walls 11

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 N-acetylglucosamine (NAG) • Provides strong, flexible support to keep bacteria from bursting or collapsing because of changes in osmotic pressure 12

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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 14

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 15

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

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 17

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 18

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 19

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 20

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

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

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

Bacteria phylogenetic relationships based on r. RNA sequences

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

Gamma Proteobacteria 27

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

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

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.

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Cyanobacteria • Gram negative phototrophs – Oxygenic photosynthesis 12 H 2 O + 6 CO 2 C 6 H 12 O 6 + 6 H 2 O + 6 O 2 – 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 N 2 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 32

Some cyanobacteria can fix nitrogen Internal photosynthetic membrane Heterocysts N 2 fixation 33

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

Spirochetes Borrelia burgdorferi 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 35

www. surrey. ac. uk/SBMS/ACADEMICS_homepage/mcfadden_johnjoe/sbms 243. html 36

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 37

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Magnetotactic • Magnetosome – Crystalline particles of iron oxide or sulfide – Magnetite Fe 3 O 4 – Greigite Fe 3 S 4 • 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 O 2 or anaerobic habitats 39

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

N 2 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 www. tari. gov. tw/ARI_E/E_image/ACD_13. jpg • No eukaryotic organisms fix N 2 41

mdchoice. com/photo/img 0110. jpg Pyogenic cocci • Causes many suppurative infections • Gram + cocci – Staphylococcus aureus, Streptococcus pyogenes & 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 42

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 & CO 2 – Regenerate NAD+ for glycolysis • Species of Streptococcus and Lactobacillus • Dairy industry – Cheese, cottage cheese, yogurt 43

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

Purple and Green Bacteria • Anoxygenic photosynthesis – 12 H 2 S + 6 CO 2 C 6 H 12 O 6 + 12 S° • Colors due to color of slightly different bacteriochlorophylls – Green - deposit S° outside – Purple - S° is inside the cell • Anaerobic H 2 S-containing mud and water 45

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 www. nature. com/. . . /020603/full/020603 -2. html 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 ergo. integratedgenomics. com 46

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

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 48

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 science. nasa. gov – Repair chromosomes that have been broken into 100 fragments 49