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					Week 3 Monera, Protista, Fungi and Classification                                                                              1

Ch 10 Classification of Microorganisms
1. Taxonomy- the science of classification
                   1) naming helps us to understand our world and to communicate with others about it
        A. Linnaeus- the father of taxonomy
                              a. SCIENCE of classification
                   1. Binomial nomenclature (Rules for bacterial names are established by the International Committee on
                   Systematic Bacteriology.
                              a. Genus: general name of an organism
                              b. species or specific epithet: generally have several common characteristics that distinguish that
                              species from all other species, In a eukaryote it is describes as an organism that does not breed
                              with other species.
                              c. Strain: subgroup of a species with one or more characteristics that distinguish it from other
                              subgroups of the same species
                              d. species<genus<family<order<class<division (phyla)<kingdom<Domain
        B. A scientist will name a previously described organism using a taxonomic key
                   1. dichotomous key: paired statements allowing an either or method of determine the name of an
                   organism defined by certain characteristics
        C. Problems in taxonomy
                   1. It is hard to study taxonomy in bacteria because they have no morphology
                   2. Very rarely do they have an organized DNA exchange in nature (they don't mate)
        D. Developments since Linnaeus's time
                   1. Contributions by Haeckel
                              a. the three kingdoms including the protista
                   2. Bergey 's Manual of Determinative Bacteriology
                              a.The actual book that tells what is what in bacteria
                   3. Contributions by Margulis and Copeland
                              a. They developed the idea that prokaryotes with no nucleus were uniquely different
                   4. Contributions by Whittaker
                              a. thought that nutrition should be the method to determine different kingdoms. Was the start of
                              the 5 kingdom system

2. The Five-Kingdom Classification System by Whittaker
        A. General features: Living organisms can be divided into 5 kingdoms depending on their nutritional needs
                1) This system is useful because everyone and all texts use it, However it is in the process of being replaced
                in the near future.
        B. Kingdom Monera
                          a. Prokaryote: True bacteria: true bacteria lack cell wall
                1. Cyanobacteria: blue green algae: are photosynthetic
                2. Archaebacteria: primitive proks that have adapted to extreme environments
                4. A group of bacteria derived frrm a single cell is called a strain, related strains make a species.
        C. Kingdom Protista
                1. Eukaryotes, majority are unicellular.
                2. do not develop embryo
                3. developed the 3 major types of nutrition seen in the next 3 kingdoms
                4. International code of Zoological Nomenclature
        D. Kingdom Fungi
                1. obtain nutrients solely by absorption of organic matter form dead organisms.
                2. yeast, molds, mushrooms
                3. International Code for Botanical Nomenclature
        E. Kingdom Plantae




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                 1. macroscopic green plants, moss, weeds, trees
       F. Kingdom Animalia
                 1.all animals derived from zygotes, sponges to man
       G Classification of Viruses
                 1) acellular infectious agents
                 2) contain nucleic acid and are coated with protein
                 3) not assigned a kingdom
                 4) a viral species is a population of viruses with similar characteristics that occupies a particular
                 ecological niche
3. The Three Domains: modern classification techniques have placed life into 3 groups above kingdoms
1) Bacteria – true bacteria have cell walls made of peptidoglycans
   a) Membrane is straight carbon chains attached to glycerol by ester linkage
   b) First aminoacid is formylmethionine
   c) Sensitive to antibiotics
2) Eucarya – Eukaryotes, animals, plants, fungi and protists.
   a) Straight carbon chains attachd to glycerol by ester linkage
   b) First amino acid is methionine
   c) Not sensitive to antibiotics
3) Archaea- ancient bacteria have different cell membranes and live in unusual and extreme habitats
   a) Membrane lipids are composed of branchd carbon chains attached to glycerol by ether linkage. Has not
       peptidoglycan

4. Bacterial classification
   A. The standard reference is Bergey’s Manual of Systematic Bacteriology
   B. The usual search for Evolutionary Relationships does not work well with bacteria
       1) microorganisms live few if any fossils
       2) scientists need to develop other methods to determine evolutionary relationships
            a) Morphological Characteristics
                   Differential stains
                   Presence of spores, flagella, and other structures
            b) biochemical tests: certain enzymes can be used in the identification of microorganisms
            c) Serology: microorganisms can be characterized according to their antigenic properties
            d) Phage typing: the sensitivity to bacteria can indicate related ness by surface and DNA structures
            e) Amino Acid Sequencing: the more similar the proteins the more similar the species
            f) Fatty Acid Profiles: different species of bacteria will have different lipid contents
            g) Flow cytometery: does not require culturing, can use stains and antibodies for determination
            h) DNA base composition: probably all the above tests in some way measure the difference in the DNA
                  sequence in microorganisms.
                   Sequencing
                   Hybridization
                   Polymerase chain reaction
       C. Numerical taxonomy: probably the best way to determine relationships with microbes
                   assigning characteristics a value and the more values two organisms share the more closely related
                       they are
                   Cladograms are maps that show evolutionary relationships. Each branch point is defined by some
                       feature. In bacteria rRNA sequences are used to make such maps
Chapter 11 The Prokaryotes and bacteria in general.

1.   Bacterial nomenclature: the naming of species according to internationally agreed upon rules set by the International
     committee on Systematic Bacteriology




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2.   Classification according to Bergey's Manual of Systematic Bacteriology
     A. History and significance of Bergey: provides a working guide for the microbiologist
     B. In B’s Manual organisms are arranged in sections in this book. Provides data on the original strains of bacteria. The
         following are the medically important classifications.
                   1. spirochetes ( sec1)
                             a. distinguishing characteristics
                                        helical motile bacteria
                                        Gram -
                                        multilayered, membranous outer sheath that surrounds the cells wall, inside of
                                            which is the coiled protoplasmic cylinder
                             b. important genera
                                        treponema: pathogenic, syphilis and yaws
                                        Borrelia: carried by ticks cause relapsing fever, lime disease
                                        Leptospira: cause fever and liver and kidney damage, infection by digesting
                                            contaminated food and water
                   2. Aerobic/ microaerophilic, motile, helical/ vibrioid, gram- negative bacteria (sec 2)
                                       (1) have flagella and swim in a straight line
                                       (2) all are gram negative
                                        Most are non pathogenic
                             a. distinguishing characteristics: helical morphology, no axial filaments
                             b. important genera
                                        Spirillum: adapted to low concentrations of organic matter
                                        Aquasprillium:
                                        Azospirillum: fixes nitrogen in association with grasses
                                        Camphylobacter: present in cats and dogs can infect and cause miscarriage in
                                            humans and other mammals
                                        Helicobacter pylori: causes stomach ulcers
                   3. Gram-negative aerobic rods and cocci ( section 4)
                             a. distinguishing characteristics: Polar flagellum, produce pigments
                                       (1)many significant human pathogens
                             b. important genera
                                       (1) Pseudomonas
                                                   aerobic motile rods with polar flagella
                                                   many synth a yellow-green pigment that fluoresces under UV light
                                                   resistant to many chemicals and antibiotics
                                       (2) leginella
                                                  (a) legionnaires disease
                                                  (b) fastidious organisms found in many environments
                                       (3) Neisseria
                                                  (a) mostly mucous membranes of humans and animals
                                       (4) Brucella
                                                  (a) obligate intracellular parasites
                                       (5) Bordetella
                                                  (a) whooping cough
                                       (6) Francisella
                                                  (a) tularemia in rabbits etc
                                                  (b) requires cysteine
                                       (7) agrobacterium: used to introduce DNA into plants.
                                       (8) Azotobacter is a nitrogen fixing soil bacterium
                   4. Facultatively anaerobic gram-negative rods (sec 5)




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                            a. distinguishing characteristics
                                      (1) basically oxidase test and a requirement for organic nitrogen
                            b. Important genera of the enterics ( oxidase -)
                                      (1) Escherichia( inhabit intestine of animals)

                                      (2) Shigella
                                                 (a) bacillary dysentery
                                      (3) Salmonella
                                                 (a) cannot produce acid or gas during lactose fermentation
                                                 (b) typhoid fever, enteritis and food poisoning
                                      (4) Klebsiella cause enteric diseases
                                      (5)Enterobacter opportunistic pathogen
                                      (6) Proteus
                                                 (a) phenylalanine deaminase and urease
                                                 (b) INFECTS burns and wounds
                                      (7) Providencia lacks urease
                                                 (a) infects burns and wounds
                                      (8) Yersinia
                                                 (a) lacks deaminase
                                                 (b) plague organism
                                      (9) Serratia
                                                 (a) opportunistic pathogen
                                                 (b) room temp has a red pigment
                            c. Important genera of the vibrios
(1) Vibrio: curved or comma shaped facultative anaerobes with polar flagella
                                                  causes cholera
                                      (2) Photobacteriuim: luminescent marine bacteria
                            d. Important genera of the Pasteurella-Hemophilus group
                                                 (a) gram negative bacilli or coccobacilli
                                                 (b) lack flagella and are nutritionally fastidious
                                                 (c) parasites of animals and few are pathogens
                                                 (d) attack mucus membranes and respiratory tract
                                      (1) Pasteurella
                                                 (a) can infect humans, but mostly animals
                                      (2) Hemophilus
                                                 (a) blood loving will only grow on media supplemented with blood
                   5. Anaerobic gram-negative straight, curved, and helical rods ( section 6)
                            a. Distinguishing characteristics
                                      (1) stringently anaerobic
                                      (2) in intestinal and respiratory tracts of humans, may cause dental abscesses
                            b. Important genera
                                      (1) Bacteroides
                                      (2) Fusobacterium, may cause dental abscesses
                                      (3) Leptotrichia

                   6. Anaerobic gram- negative cocci (section 8)
                            a. Distinguishing characteristics
                                      (1) are capnophilic (CO 2 loving)
                            b. Important genera
                                      (1) Veillonells
                                                (a) cause tooth abscesses and gum disease



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Week 3 Monera, Protista, Fungi and Classification                                                                       5


                 7. Rickettsias and chlamydias (sec 9)
                          a. Distinguishing characteristics
                                    (1) obligate intracellular parasites
                          b. Important genera
                                    (1) rickettsia
                                              (b) small rods, gram negative passed by insects or ticks
                                    (2) coxiella: Q fever
                                    (3) Bartonella: cat scratch diseases
                                    (4) Chlamydia
                                              (a) rod shaped or coccoid bacteria that invade host cells
                                              (b) cause pneumonia in humans
                                              (c) respiratory infections
                                              (d) non gonococcal urethritis
                 8. Mycoplasmas ( sec 10)
                          a. Distinguishing characteristics
                                    (1) gram negative staining
                                    (2) lack a cell wall
                                    (3) have gliding movement and cholesterol in their cell walls
                                     requires sterols in culture media
                          b. important genera
                                    (1) mycoplasma: primary atypical pneumonia
                                    (2) Ureaplasma: urinary tract infections
                 9. Gram positive cocci (section 12)
                          a. Distinguishing characteristics: medically and industrially important
                          b. Important genera
                                    (1) Micrococcus
                                     aerobes or facultative anaerobes that form irregular clusters by dividing in two or
                                         mare planes
                                    (2) Streptococcus
                                     aerotolerant anaerobes that obtain energy from fermenting sugars to lactic acid
                                     form chains by dividing in one or two planes
                                     lack catalase
                                     can cause extensive tissue destruction by the release of enzymes that degrade fibrin
                                    (3) Staphylococcus
                                     common human pathogen
                                     responsible for skin abscesses or boils
                                     will tolerate and grow in high salt concentrations
                                     will rapidly develop antibiotic resistance
                                    (4) Peptococcus
                                              (a) obligate anaerobes lack both catalase and enzymes to ferment lactic acid
                                              (b) form pairs or irregular clusters
                                              (c) can cause many infections
                                    (5) Peptostereptococcus
                 10. Endospore-forming gram-positive rods and cocci (section 13)
                          a. distinguishing characteristics
                          b. important genera
                                    (1) Bacillus
                                              (a) include many aerobes
                                              (b) can cause anthrax




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Week 3 Monera, Protista, Fungi and Classification                                                                6

                                               (c) produce antibiotics
                                     (2) Clostridium
                                               (a) strict anaerobes
                                               (b)motile rods found in soil, water and the intestinal tract
                                               (c) cause disease mostly through their toxins
                 11. Regular nonsporing gram-positive rods (section 14)
                           a. distinguishing characteristics
                                     (1) stain evenly and have characteristic shapes
                           b. Important genera
                                     (1) lactobacillus ( fig 10.15)
                                               (a) foods and cheeses
                                     (2) Listeria
                                               (a) infection of brain and its membranes, will damage fetus
                                     (3) erysipelothrix
                                               (a) red sores in human
                 12. Irregular nonsporing gram-positive rods (sect 15)
                           a. distinguishing characteristics
                                     (1) irregular shape and uneven staining
                           b. important genera
                                     (1) Corynebacterium
                                               (a) can cause diphtheria
                                     (2) Propionibacterium: anaerobic causes acne
                                     (3) Eubacterium
                                     (4) Actinomyces:
                                               (a) branching filamentous soil microbes
                 13. Mycobacteria ( section 16)
                           a. Distinguishing characteristics
                                     (1)cell walls contain large amounts of lipids
                                     (2) can be stained with carbolfuschin in hot phenol
                                     (3) most are soil saphrophyes
                           b. Important genera tuberculosis, leprosy and many infections in aides individuals
                 14. Nocardioforms ( section 17)
                           a. Distinguishing characteristics
                                      gram positive, nonmotile pleomorphic aerobic and generally acid fast and
                                          filamentous.
                           b. Important genera
                                     (1) Nocardia: pulmonary nocardiosis
                                     (2) some pathogens
                 15. Gliding, Sheathed, and budding and/or Appendaged Bacteria
                      Appendaged Bacteria: Caulobacter produce stalks and swarmer cells
                  Gliding, Nonfruiting Bacteria: Cytophaga: cellulose degraders in the soil
                  Gliding, fruiting Bacteria: myxobacteria: cells congregate to form large fruiting body
                  Budding Bacteria: Hyphomicrobium: produces buds like yeast, with an intact parent.
                  Sheathed Bacteria: Sphaerotilus forms a sheath that surrounds bacteria. Found in fresh water and
                      sewage
                 16. Chemoautotrophic Bacteria
                  Use inorganic chemicals as energy sources and carbon dioxide as the only source of carbon.
                  Nitrobacter and Nitrosomonas are a tandem pair that oxidizes ammonium to nitrate
                  Thiobacillus can oxidize reduced forms of sulfur into elemental forms or sulfates (acids)
                 17. Archaea




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Week 3 Monera, Protista, Fungi and Classification                                                                        7

                       Halophiles and methane producing bacteria
                  16.   Phototropic bacteria
                       Purple or green sulfur bacteria, anoxygenic
                       Purple nonsulfur use organic compounds for the photosynthetic reduction of carbon dioxide
                       cyanobacteria carry out oxygen producing photosynthesis

                  16. Actinomycetes: and related genera ( section 29)
                           a. Distinguishing characteristics
                                     (1)resemble fungi
                                     (2)develop extensive branching filaments with spores of many different shapes
                                     (3) produce many antibiotics
                                      Produce geosmin a gas that gives soil its odor.

These are the major types of bacteria that can cause disease in man and his livestock. Have a general idea of the different
types, get a feeling for the bacteria and the diseases it causes.


http://www-cyanosite.bio.purdue.edu/index.html sites for cyanobacteria.


www.portone.com/rlfaef/mark/als/als.html            LYMPHATIC                  FILARIASIS               see            also
http://www.cdc.gov/ncidod/dpd/parasites/lymphaticfilariasis/default.htm




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