Microbiology: Chapter 10 - Phylogenetic Relationships

Study of Phylogenetic Relationships

• Taxonomy is the science of classifying organisms
• Organisms are classified based on degree of similarity and categorization by Taxon/Taxa
• Systematics, or Phylogeny, studies the evolutionary history of organisms
• Taxonomic hierarchy shows phylogenetic (evolutionary) relationships among organisms
• In 1735, Linnaeus described the kingdoms Plantae and Animalia
• In the 1800s, Bacteria and fungi were placed in kingdom Plantae (Nägeli)
• Kingdom Protista was proposed for bacteria, protozoa, algae, and fungi by Haeckel
• In 1937, the term Prokaryote was introduced to distinguish cells without a nucleus
• In 1968, Murray described Kingdom Prokaryotae
• In 1969, Whittaker described the five-kingdom system
• In 1978, Two types of prokaryotic cells were found, and prokaryotic relationships are determined by rRNA sequencing
• All Species Inventory was cataloged from 2001-2025

The Three Domains

• Woese developed the three domains in 1978 considering nucleotide sequences in rRNA
• Eukarya includes animals, plants, and fungi
• Bacteria are a domain
• Archaea are a domain characterized by Methanogens, Extreme halophiles, and Hyperthermophiles
• All organisms evolved from cells that formed over 3 billion years ago
• DNA passed on from ancestors is conserved
• The Domain Eukarya includes kingdoms Fungi, Plantae, and Animalia, as well as protists
• The Domains Bacteria and Archaea are prokaryotes
• Eukaryotes originated from infoldings of prokaryotic plasma membranes
• Endosymbiotic bacteria developed into organelles

Phylogenetic Tree Notes

• Grouping organisms is achieved according to common properties like fossils and genomes
• Groups of organisms evolved from a common ancestor
• Each species retains some characteristics of its ancestor

Scientific Nomenclature

• Common names vary with languages and geography
• Binomial nomenclature is used worldwide to consistently and accurately name organisms
• A genus is described
• A specific epithet, or species, is described
• Escherichia coli and Homo sapiens are examples

Characteristics of Archaea, Bacteria, and Eukarya

• Archaea, Bacteria, and Eukarya have different characteristics
• Under the scanning electron microscope, Sulfolobus appears as a dimpled yellow globule of 2.5 micrometers in diameter
• Under the scanning microscope, E Coli appears has a blue rod of length 1.5 to 6 micrometers and diameters 0.5 micrometers, with rounded ends.
• Under the scanning microscope, Amoeba is pale pink with an irregular central mass of diameter 10 to 15 micrometers, with tendrils of diameter 1 micrometer extending 5 to 20 micrometers from the central body.
• Cell types can be prokaryotic or eukaryotic
• Cell walls can be varied
• Membrane Lipids can be varied
• First Amino Acid in Protein Synthesis can be Methionine and/or Formylmethionine
• Antibiotic Sensitivity can be variable
• rRNA loop and Common Arm of tRNA can be present or lacking
• Prokaryotic cells, Eukaryotic cells, and Eukaryotic Organelles have different characteristics

Table 10.2 Prokaryotic Cells and Eukaryotic Organelles Compared

• DNA in Prokaryotic cells is one circular, some two circular; some linear
• DNA in Eukaryotic cells is Linear
• DNA in Eukaryotic Organelles is Circular
• Histones are in archaea
• Histones are in Eukaryotic cells
• Histones are not in Eukaryotic Organelles
• First Amino Acid in Protein Synthesis for Prokaryotic Cells is Formylmethionine (bacteria) Methionine (archaea)
• First Amino Acid in Protein Synthesis for Eukaryotic Cells is Methionine
• First Amino Acid in Protein Synthesis for Eukaryotic Organelles is Formylmethionine
• Ribosomes for Prokaryotic Cells are 70S
• Ribosomes for Eukaryotic Cells are 80S
• Ribosomes for Eukaryotic Organelles are 70S
• Growth for Prokaryotic Cells is Binary fission
• Growth for Eukaryotic Cells is Mitosis
• Growth for Eukaryotic Organelles is Binary fission
• The prokaryotic cell has loose chromosomal material
• Hair-like extensions project outward from the cell membrane, and longer flagella spiral from one end of the cell
• The eukaryotic cell contains chromosomal material concentrated in the nucleus, as well as additional internal structures, or organelles, including mitochondria
• Eukaryotic cells can contain chloroplasts consisting of a network of globular masses connected by tendrils

Taxonomic Hierarchy Notes

• The taxonomic hierarchy is a series of subdivisions
• Linnaeus' taxonomy hierarchy classifies plants and animals
• Similar species are grouped into a genus
• Similar genera are grouped into a family
• Families are grouped into an order
• Orders are grouped into a class
• Classes are grouped into a phylum
• Phyla are grouped into a kingdom
• Kingdoms are grouped into a domain

Classification

• Prokaryotic species are a population of cells with similar characteristics
• Culture: bacteria grown in laboratory media
• Clone: population of cells derived from a single parent cell
• Strain: genetically different cells within a clone
• Eukaryotic species are a group of closely related organisms that breed among themselves
• Protista: a catchall kingdom for a variety of organisms that are autotrophic and heterotrophic
• Protista are grouped into clades based on rRNA
• Fungi are chemoheterotrophic; can be unicellular or multicellular with cell walls of chitin; develop from spores or hyphal fragments
• Plantae are multicellular; have cellulose cell walls; undergo photosynthesis
• Animalia are multicellular; have no cell walls; and are chemoheterotrophic
• Viruses are not a part of any domain, are not composed of cells, and require a host cell
• A viral species is a population of viruses with similar characteristics that occupies a particular ecological niche
• Classification places organisms in groups of related species by listing of characteristics of known organisms
• Identification matches characteristics of an "unknown" organism to lists of known organisms
• Clinical lab identification is identification

Methods of Classification

• Bergey's Manual of Determinative Bacteriology provides identification schemes for identifying bacteria and archaea: morphology, differential staining, biochemical tests
• Bergey's Manual of Systematic Bacteriology provides phylogenetic information on bacteria and archaea based on rRNA sequencing
• Approved Lists of Bacterial Names lists species of known classification
• Morphological characteristics are useful for identifying eukaryotes; and tell little about phylogenetic relationships
• Differential staining tests use Gram staining or acid-fast staining, however is not useful for bacteria without cell walls
• Biochemical tests determine presence of bacterial enzymes

Identification Methods

• Rapid identification methods can perform several biochemical tests simultaneously
• Results of each test are assigned a number
• Identification keys use successive questions
• Maps that show evolutionary relationships among organisms, cladograms, are based on rRNA sequences
• Serology studies serum and immune responses in serum
• Microorganisms are antigenic and stimulate the body to form antibodies in the serum
• Serology involves reactions of microorganisms with specific antibodies by combining known anti-serum with unknown bacterium
• Serology is useful in determining the identity of strains and species, as well as relationships among organisms
• In an antiserum, a solution of antibodies is tested against an unknown bacterium
• Serological testing can differentiate between species and strains within species
• In the slide agglutination test, bacteria agglutinate when mixed with antibodies produced in response to the bacteria
• Enzyme-linked immunosorbent assay (ELISA) utilizes known antibodies and an unknown type of bacterium added to a well; a reaction identifies the bacteria
• Western blotting identifies antibodies in a patient's serum

Diagnostics

• The Western blot confirms HIV infection
• Phage Typing can test bacterial species and strains by determining which phages a bacterium is susceptible to
• Clearings called plaques appear where phages infect and lyse bacterial cells on a plate
• Flow Cytometry uses differences in electrical conductivity between species or fluorescence
• The Fluorescence-Activated Cell Sorter (FACS) uses fluorescent dye antibodies

Genetic Tests

• DNA base composition considers guanine + cytosine %
• Two organisms that are closely related will have similar amounts of various bases
• For Example, 40% GC sample 1 and 60% GC sample 2 are not related because of greater than 10% difference
• DNA fingerprinting characterizes the number and sizes of DNA fragments (fingerprints) produced by RE digests and are used to determine genetic similarities
• Electrophoresis of restriction enzyme digests of an organism's DNA
• Comparing fragments from different organisms provides information on genetic similarities and differences
• Nucleic Acid Amplification Tests, or NAATs, use of PCR (Polymerase chain reaction) to amplify DNA of an unknown microorganism that cannot be cultured
• A specific primer is used for the known microorganism
• Amplified DNA after PCR and a specific primer confirms the unknown microorganism
• Nucleic acid hybridization measures the ability of DNA strands from one organism to hybridize with DNA strands of another organism
• a Greater degree of hybridization indicates a greater degree of relatedness
• Single strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule
• This bonding is called nucleic acid hybridization
• Southern blotting uses nucleic acid hybridization to identify unknown microorganisms using DNA probes
• A DNA chip, also known as a microarray, contains DNA probes and detects pathogens by hybridization between the probe and DNA in the sample
• Detection is by Fluorescence
• Ribotyping characterizes rRNA sequencing
• Fluorescent in situ hybridization or FISH utilizes Fluorescent DNA or RNA probes stain the microorganisms being targeted, and In situ means it will enter the live cells
• This will determines the identity, abundance, and relative activity of microorganisms in an environmental sample