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Study Outline
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  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
    2. 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
    3. Systematics is the scientific study of organisms with the ultimate object of characterizing and arranging them in an orderly manner
    4. Microbial taxonomy is going through a period of great change due to the use of new molecular techniques
  2. 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
    2. 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
    3. 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)
      3. 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
  3. 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
      3. A genus is a well-defined group of one or more species that is clearly separate from other genera
    3. 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)
  4. 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
    3. Numerical taxonomy
    4. Information about the properties of an organism is converted to a form suitable for numerical analysis and is compared by means of a computer
    5. The presence or absence of at least 50 (preferably several hundred) characters should be compared (morphological, biochemical and physiological characters)
    6. An association coefficient is determined between characters possessed by two organisms
      1. Simple matching coefficient-proportion that match whether present or absent
      2. Jaccard coefficient-ignores characters that both organisms lack
    7. These values are arranged to form a similarity matrix; organisms with great similarity are grouped together into phenons
    8. A treelike diagram called a dendrogram is used to display the results of numerical taxonomic analysis
    9. The significance of the phenons is not always obvious but phenons with an 80% similarity often are equivalent to bacterial species
    10. Phylogenetic (phyletic) systems-group organisms together based on probable evolutionary relationships
      1. Has been difficult for procaryotes because of the lack of a good fossil record
      2. Direct comparison of genetic material and gene products such as rRNA and proteins overcomes this problem
  5. Major Characteristics Used in Taxonomy
    1. Classical characteristics
      1. Morphological characteristics-easy to analyze, genetically stable and do not vary greatly with environmental changes; often are good indications of phylogenetic relatedness
      2. Physiological and metabolic characteristics-directly related to enzymes and transport proteins (gene products) and therefore provide an indirect comparison of microbial genomes
      3. Ecological characteristics-include life-cycle patterns, symbiotic relationships, ability to cause disease, habitat preferences and growth requirements
      4. 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
    2. Molecular characteristics
      1. 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
      2. 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%
      3. 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
      4. 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
  6. 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
      1. 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
      2. 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
    3. rRNA, DNA, and proteins as indicators of phylogeny
      1. Association coefficients from rRNA studies are a measure of relatedness
      2. 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
      3. DNA similarity studies are more effective at the species and genus level
      4. Protein sequences are less affected by organism-specific differences in G+C content
      5. Analyses of the three types of molecules do not always produce the same evolutionary trees
    4. Polyphasic taxonomy
      1. Uses a wide range of phenotypic and genotypic information to develop a taxonomic scheme
      2. 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)
  7. The Major Divisions of Life
    1. Domains
      1. 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
      2. Several different phylogenetic trees have been proposed relating the major domains and some trees do not even support a three-domain pattern
      3. 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
    2. Kingdoms
      1. 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
      2. Many biologists do not accept Whittakerís system, primarily because it does not distinguish bacteria from archaea
      3. A number of alternatives have been suggested, including a six-kingdom system and a two-empire, eight-kingdom system
  8. Bergeyís Manual of Systematic Bacteriology
    1. The First Edition of Bergeyís Manual of Systematic Bacteriology-primarily phenetic
      1. Contains 33 sections in four volumes
      2. 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
    2. The Second Edition of Bergeyís Manual of Systematic Bacteriology
      1. Largely phylogenetic rather than phenetic
      2. Consists of five volumes
  9. A Survey of Procaryotic Phylogeny and Diversity
    1. Volume 1 (of 2nd edition of Bergeyís Manual): The Archaea, and Deeply Branching and Phototrophic Genera
      1. 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
      2. 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;
    2. Volume 2: The Proteobacteria-devoted to a single phylum called Proteobacteria, which consists of a diverse array of gram-negative bacteria
    3. 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
    4. 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)
    5. 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
      1. 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
      2. Chlamydiae-this phylum contains obligate-intracellular pathogens having a unique life cycle; they lack peptidoglycan
      3. Spirochaetes-a phylum composed of helically shaped bacteria with unique morphology and motility
      4. Bacteroides-this phylum contains a number of ecologically significant bacteria

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