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 Taxonomy outline

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PostSubject: Taxonomy outline   Wed Feb 18, 2009 7:18 pm


  1. General Introduction and
    Overview


    1. Taxonomy is the science
      of biological classification



      1. Classification is the
        arrangement of organisms into groups (taxa)
      2. Nomenclature refers to
        the assignment of names to taxonomic groups
      3. Identification refers
        to the determination of the particular taxon to which a particular
        isolate belongs




    1. Importance of microbial
      taxonomy



      1. Allows scientists to
        organize huge amounts of knowledge
      2. Allows scientists to
        make predictions and frame hypotheses about organisms
      3. Places organisms in
        meaningful, useful groups with precise names, thus facilitating
        scientific communication
      4. Essential for accurate
        identification of microorganisms




    1. Systematics is the
      scientific study of organisms with the ultimate object of
      characterizing and arranging them in an orderly manner
    2. Microbial taxonomy is
      going through a period of great change due to the use of new molecular
      techniques



  1. Microbial Evolution and
    Diversity


    1. Earth is about 4.6
      billion years old and fossilized remains of procaryotic cells that are
      3.5 to 3.8 billion years old have been found in stromatolites and
      sedimentary rocks



      1. Stromatolites are
        layered or stratified rocks that are formed by incorporation of
        mineral sediments into microbial mats
      2. The earliest
        procaryotes were probably anaerobic
      3. Aerobic cyanobacteria
        probably developed 2.5 to 3.0 billion years ago




    1. The work of Carl Woese
      and his collaborators suggests that organisms fall into one of three
      domains



      1. Eucarya-contains all
        eucaryotic organisms
      2. Bacteria-contains
        procaryotic organisms with bacterial rRNA and membrane lipids that are
        primarily diacyl glycerol ethers
      3. Archaea-contains
        procaryotic organisms with archaeal rRNA and membrane lipids that are
        primarily isoprenoid glycerol diether or diglycerol tetraether
        derivatives




    1. Modern eucaryotic cells
      appear to have arisen from procaryotes about 1.4 billion years ago



      1. One hypothesis for the
        development of chloroplasts and mitochondria involves invagination of
        the plasma membrane and subsequent compartmentalization of function
      2. The alternative is the
        endosymbiotic hypothesis, which suggests the following:




        1. The first event in
          the development of eucaryotes was the formation of the nucleus
          (possibly by fusion of ancient bacteria and archaea)
        2. Chloroplasts were
          formed from free-living photosynthetic bacteria that entered into a
          symbiotic relationship with the primitive eucaryote (cyanobacteria
          and Prochloron have been suggested as possible candidates)
        3. Mitochondria may have
          arisen by a similar process (ancestors of Agrobacterium, Rhizobium,
          and the rickettsias have been suggested)





      1. The endosymbiotic
        hypothesis has received support from the discovery of an endosymbiotic
        cyanobacterium that inhabits the biflagellate protist Cyanophora
        paradoxa and acts as its chloroplast; the endosymbiont is called a
        cyanelle




  1. Taxonomic Ranks


    1. The taxonomic ranks (in
      ascending order) are: species, genus, family, order, class and kingdom;
      however, microbiologists often use section names (a less formal
      grouping) that are descriptive (e.g., methanogens, purple bacteria,
      lactic acid bacteria, etc.)
    2. The basic taxonomic
      group is the species



      1. Procaryotic species
        are not defined on the basis of sexual reproductive compatibility (as
        for higher organisms) but rather are based on phenotypic and genotypic
        differences; a procaryotic species is a collection of strains that
        share many stable properties and differ significantly from other
        groups of strains
      2. A strain is a
        population of organisms that is distinguishable from at least some
        other populations in a taxonomic category; it is thought to have
        descended from a single organism or pure culture isolate




        1. Biovars-strains that
          differ biochemically or physiologically
        2. Morphovars-strains
          that differ morphologically
        3. Serovars-strains that
          differ in antigenic properties
        4. The type strain is
          usually the first studied (or most fully characterized) strain of a
          species; it does not have to be the most representative member





      1. A genus is a
        well-defined group of one or more species that is clearly separate
        from other genera




    1. In the binomial system
      of nomenclature devised by Carl von Linne (Carolus Linnaeus), the genus
      name is capitalized while the specific epithet is not; both terms are
      italicized (e.g., Escherichia coli); after first usage in a manuscript
      the first name will often be abbreviated to the first letter (e.g., E. coli)



  1. Classification Systems


    1. Natural
      classification-arranges organisms into groups whose members share many
      characteristics and reflects as much as possible the biological nature
      of organisms
    2. Phenetic systems group
      organisms together based on overall similarity



      1. Frequently a natural
        system based on shared characteristics
      2. Not dependent on
        phylogenetic analysis
      3. Use unweighted traits
      4. Best system compares
        as many attributes as possible




    1. Numerical taxonomy
    2. Information about the
      properties of an organism is converted to a form suitable for numerical
      analysis and is compared by means of a computer
    3. The presence or absence
      of at least 50 (preferably several hundred) characters should be
      compared (morphological, biochemical and physiological characters)
    4. An association coefficient
      is determined between characters possessed by two organisms



a.
Simple matching coefficient-proportion that match
whether present or absent

b.
Jaccard coefficient-ignores characters that both
organisms lack

    1. These values are
      arranged to form a similarity matrix; organisms with great similarity
      are grouped together into phenons
    2. A treelike diagram
      called a dendrogram is used to display the results of numerical
      taxonomic analysis
    3. The significance of the
      phenons is not always obvious but phenons with an 80% similarity often
      are equivalent to bacterial species
    4. Phylogenetic (phyletic)
      systems-group organisms together based on probable evolutionary
      relationships



0.
Has been difficult for procaryotes because of the
lack of a good fossil record

1.
Direct comparison of genetic material and gene
products such as rRNA and proteins overcomes this problem
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PostSubject: Re: Taxonomy outline   Wed Feb 18, 2009 7:20 pm


1.


  1. Major Characteristics
    Used in Taxonomy


    1. Classical
      characteristics



0.
Morphological characteristics-easy to analyze,
genetically stable and do not vary greatly with environmental changes; often
are good indications of phylogenetic relatedness

1.
Physiological and metabolic characteristics-directly
related to enzymes and transport proteins (gene products) and therefore
provide an indirect comparison of microbial genomes

2.
Ecological characteristics-include life-cycle
patterns, symbiotic relationships, ability to cause disease, habitat
preferences and growth requirements

3.
Genetic analysis-includes the study of chromosomal
gene exchange through transformation and conjugation; these processes only
rarely cross genera; one must take care to avoid errors that result from
plasmid-borne traits

    1. Molecular
      characteristics



0.
Comparison of proteins-useful because it reflects the
genetic information of the organism; analysis is by:

        1. Determination of the
          amino acid sequence of the protein
        2. Comparison of
          electrophoretic mobility
        3. Determination of
          immunological cross-reactivity
        4. Comparison of
          enzymatic properties





1.
Nucleic acid base composition

        1. G+C content can be
          determined from the melting temperature (Tm-the temperature at which
          the two strands of a DNA molecule separate from one another as the
          temperature is slowly increased)
        2. Taxonomically useful
          because variation within a genus is usually less than 10% but
          variation between genera is quite large, ranging from 25 to 80%





2.
Nucleic acid hybridization

        1. Determines the degree
          of sequence homology
        2. The temperature of
          incubation controls the degree of sequence homology needed to form a
          stable hybrid





3.
Nucleic acid sequencing

        1. rRNA gene sequences
          are most ideal for comparisons because they contain both
          evolutionarily stable and evolutionarily variable sequences
        2. Recently, complete
          procaryotic genomes have been sequenced; direct comparison of
          complete genome sequences undoubtedly will become important in
          procaryotic taxonomy





  1. Assessing Microbial
    Phylogeny


    1. Molecular
      chronometers-based on the assumption of a constant rate of change,
      which is not a correct assumption; however the rate of change may be
      constant within certain genes
    2. Phylogenetic trees



0.
Made of branches that connect nodes, which represent
taxonomic units such as species or genes; rooted trees provide a node that
serves as the common ancestor for the organisms being analyzed

1.
Developed by comparing molecular sequences and
differences are expressed as evolutionary distance; organisms are then
clustered to determine relatedness; alternatively, relatedness can be
estimated by parsimony analysis assuming that evolutionary change occurs
along the shortest pathway with the fewest changes to get from ancestor to
the organism in question

    1. rRNA, DNA, and proteins
      as indicators of phylogeny



0.
Association coefficients from rRNA studies are a
measure of relatedness

1.
Oligonucleotide signature sequences occur in most or
all members of a particular phylogenetic group and are rarely or never
present in other groups even closely related ones; useful at kingdom or
domain levels

2.
DNA similarity studies are more effective at the
species and genus level

3.
Protein sequences are less affected by
organism-specific differences in G+C content

4.
Analyses of the three types of molecules do not
always produce the same evolutionary trees

    1. Polyphasic taxonomy



0.
Uses a wide range of phenotypic and genotypic
information to develop a taxonomic scheme

1.
Techniques and information used depend on level of
taxonomic resolution needed (e.g., serological techniques are good for
identifying strains, but not genera or species)

  1. The Major Divisions of
    Life


    1. Domains



0.
Woese and collaborators used rRNA studies to group
all living organism into three domains

        1. Bacteria-comprise the
          vast majority of procaryotes; cell walls contain muramic acid;
          membrane lipids contain ester-linked straight-chain fatty acids
        2. Archaea-procaryotes
          that: lack muramic acid, have lipids with ether-linked branched
          aliphatic chains, lack thymidine in the T arm of tRNA molecules, have
          distinctive RNA polymerases, and have ribosomes with a different
          composition and shape than those observed in Bacteria
        3. Eucarya-have a more
          complex membrane-delimited organelle structure





1.
Several different phylogenetic trees have been
proposed relating the major domains and some trees do not even support a
three-domain pattern

2.
One of the most important difficulties in
constructing a tree is widespread, frequent horizontal gene transfer; a more
correct tree may resemble a web or network with many lateral branches linking
various trunks

    1. Kingdoms



0.
Whittakerís five-kingdom system was the first to gain
wide acceptance

        1. Animalia-multicellular,
          nonwalled eucaryotes with ingestive nutrition
        2. Plantae-multicellular,
          walled eucaryotes with photoautotrophic nutrition
        3. Fungi-multicellular
          and unicellular, walled eucaryotes with absorptive nutrition
        4. Protista-unicellular
          eucaryotes with various nutritional mechanisms
        5. Monera
          (Procaryotae)-all procaryotic organisms





1.
Many biologists do not accept Whittakerís system,
primarily because it does not distinguish bacteria from archaea

2.
A number of alternatives have been suggested,
including a six-kingdom system and a two-empire, eight-kingdom system

  1. Bergeyís Manual of
    Systematic Bacteriology


    1. The First Edition of
      Bergeyís Manual of Systematic Bacteriology-primarily phenetic



0.
Contains 33 sections in four volumes

1.
Each section contains bacteria that share a few
easily determined characteristics (e.g., morphology, gram reaction, oxygen
relationships) and bears a title that describes these properties or provides
the vernacular names of the bacteria included

    1. The Second Edition of
      Bergeyís Manual of Systematic Bacteriology



0.
Largely phylogenetic rather than phenetic

1.
Consists of five volumes

  1. A Survey of Procaryotic
    Phylogeny and Diversity


    1. Volume 1 (of 2nd
      edition of Bergeyís Manual): The Archaea, and Deeply Branching and
      Phototrophic Genera



0.
Archaea-divided into two phyla

        1. Crenarchaeota-diverse
          phylum that contains thermophilic and hyperthermophilic organisms as
          well as some organisms that grow in oceans at low temperatures as
          picoplankton
        2. Euryarchaeota-contains
          primarily methanogenic and halophilic procaryotes and also
          thermophilic, sulfur-reducing procaryotes





1.
Bacteria

        1. Aquificae-phylum
          containing autotrophic bacteria that use hydrogen as an energy
          source; most are thermophilic
        2. Thermatogae-phylum
          containing anaerobic, thermophilic fermentative, gram-negative
          bacteria; have unusual fatty acids
        3. ìDeinococcus-Thermusî-this
          phylum includes bacteria with extraordinary resistance to radiation
          and thermophilic organisms
        4. Chloroflexi-this
          phylum consists of bacteria often called green nonsulfur bacteria;
          some carry out anoxygenic photosynthesis, while others are
          respiratory, gliding bacteria; have unusual peptidoglycans and lack
          lipopolysaccharides in their outer membranes
        5. Cyanobacteria-a
          phylum consisting of oxygenic photosynthetic bacteria
        6. Chlorobi-this phylum
          contains anoxygenic photosynthetic bacteria known as the green sulfur
          bacteria;





    1. Volume 2: The
      Proteobacteria-devoted to a single phylum called Proteobacteria, which
      consists of a diverse array of gram-negative bacteria
    2. Volume 3: The Low G+C
      Gram-Positive Bacteria-devoted to a single phylum called Firmicutes;
      all have a G+C content 50%; with the exception of the mycoplasmas,
      which lack a cell wall, they are gram positive; most are heterotrophs;
      includes genera that produce endospores
    3. Volume 4: The High G+C
      Gram-Positive Bacteria-describes the phylum Actinobacteria; have G+C
      content 50-55%; includes filamentous bacteria (actinomycetes) and
      bacteria with unusual cell walls (mycobacteria)
    4. Volume 5: The
      Planctomycetes, Spriocheates, Fibrobacteres, Bacteroidetes, and
      Fusobacteria-an assortment of deeply branching phylogenetic groups that
      are not necessarily related to one another although all are Gram
      negative



0.
Planctomycetes-this phylum contains bacteria with
unusual features, including cell walls that lack peptidoglycan and cells with
a membrane-enclosed nucleoid; divide by budding and produce appendages called
stalks

1.
Chlamydiae-this phylum contains
obligate-intracellular pathogens having a unique life cycle; they lack
peptidoglycan

2.
Spirochaetes-a phylum composed of helically shaped
bacteria with unique morphology and motility




Bacteroides-this phylum contains a number of
ecologically significant bacteria
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