Microbiology: Classification of Microorganisms PDF

Microbiology an Introduction Thirteenth Edition, Global Edition Chapter 10 Classification of Microorganisms Copyright © 2021 Pearson Education Ltd. All Rights Reserved The Study of P...

Microbiology an Introduction Thirteenth Edition, Global Edition Chapter 10 Classification of Microorganisms Copyright © 2021 Pearson Education Ltd. All Rights Reserved The Study of Phylogenetic Relationships Taxonomy is the science of classifying organisms – Shows degree of similarity among organisms Systematics, or phylogeny, is the study of the evolutionary history of organisms Copyright © 2021 Pearson Education Ltd. All Rights Reserved The Study of Phylogenetic Relationships Prokaryote introduced to Linnaeus—kingdoms distinguish cells without a Whittaker—five-kingdom Plantae and Animalia nucleus system 1800s 1968 1735 1937 1969 Bacteria and fungi put in Murray—kingdom kingdom Plantae (Nägeli); Prokaryotae Kingdom Protista proposed for bacteria, protozoa, algae, and fungi (Haeckel) Copyright © 2021 Pearson Education Ltd. All Rights Reserved The Three Domains (1 of 2) Developed by Woese in 1978; based on sequences of nucleotides in rRNA Eukarya – Animals, plants, fungi Bacteria Archaea – Methanogens – Extreme halophiles – Hyperthermophiles Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.1 Three-Domain System Key Concepts All organisms evolved from cells that formed over 3 billion years ago. The DNA passed on from ancestors is described as conserved. The Domain Eukarya includes the kingdoms Fungi, Plantae, and Animalia, as well as protists. The Domains Bacteria and Archaea are prokaryotes. Copyright © 2021 Pearson Education Ltd. All Rights Reserved TABLE 10.1 Some Characteristics of Archaea, Bacteria, and Eukarya Copyright © 2021 Pearson Education Ltd. All Rights Reserved TABLE 10.2 Prokaryotic Cells and Eukaryotic Organelles Compared Copyright © 2021 Pearson Education Ltd. All Rights Reserved The Three Domains (2 of 2) Eukaryotes originated from infoldings of prokaryotic plasma membranes Endosymbiotic bacteria developed into organelles Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.2 A Model of the Origin of Eukaryotes Early cell Bacteria Chloroplast Archaea Mitochondrion DNA Eukarya Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.3 Cyanophora Paradoxa Bacterium Eukaryotic host cell Copyright © 2021 Pearson Education Ltd. All Rights Reserved A Phylogenetic Tree Grouping organisms according to common properties – Fossils – Genomes ▪ Mutations accumulated in the genomes serve as a molecular clock Groups of organisms evolved from a common ancestor Each species retains some characteristics of its ancestor Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.4a Fossilized Prokaryotes Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.4b Fossilized Prokaryotes Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.4c Fossilized Prokaryotes Copyright © 2021 Pearson Education Ltd. All Rights Reserved Scientific Nomenclature Common names vary with languages and geography Binomial nomenclature is used worldwide to consistently and accurately name organisms – Genus – Specific epithet (species) Copyright © 2021 Pearson Education Ltd. All Rights Reserved Table 1.1 Making Scientific Names Familiar Copyright © 2021 Pearson Education Ltd. All Rights Reserved The Taxonomic Hierarchy A series of subdivisions developed by Linnaeus to classify plants and animals Eukaryotic species: a group of closely related organisms that breed among themselves Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.5 The Taxonomic Hierarchy Copyright © 2021 Pearson Education Ltd. All Rights Reserved Classification of Prokaryotes Prokaryotic species: 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 Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.6 Phylogenetic Relationships of Prokaryotes Copyright © 2021 Pearson Education Ltd. All Rights Reserved Classification of Eukaryotes Protista: a catchall kingdom for a variety of organisms; autotrophic and heterotrophic – Grouped into clades based on rRNA Fungi: chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments Plantae: multicellular; cellulose cell walls; undergo photosynthesis Animalia: multicellular; no cell walls; chemoheterotrophic Copyright © 2021 Pearson Education Ltd. All Rights Reserved Classification of Viruses Not a part of any domain; not composed of cells; require a host cell Viral species: population of viruses with similar characteristics that occupies a particular ecological niche Copyright © 2021 Pearson Education Ltd. All Rights Reserved Methods of Classifying and Identifying Microorganisms Classification: placing organisms in groups of related species – Lists of characteristics of known organisms Identification: matching characteristics of an "unknown" organism to lists of known organisms – Clinical lab identification Copyright © 2021 Pearson Education Ltd. All Rights Reserved Methods of Classifying and Identifying Microorganisms Bergey's Manual of Determinative Bacteriology provides identification schemes for identifying bacteria and archaea Approved Lists of Bacterial Names lists species of known classification Copyright © 2021 Pearson Education Ltd. All Rights Reserved Methods of Classifying and Identifying Microorganisms In clinical microbiology, lab requisition forms are used to note types of specimens collected and tests to be conducted Transport media is used to collect and transport pathogens to a laboratory Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.7 A clinical Microbiology Lab Report Form Copyright © 2021 Pearson Education Ltd. All Rights Reserved Methods of Classifying and Identifying Microorganisms Morphological characteristics: useful for identifying eukaryotes; tell little about phylogenetic relationships Differential staining: Gram staining, acid-fast staining; not useful for bacteria without cell walls Biochemical tests: determine presence of bacterial enzymes Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.8 The Use of Metabolic Characteristics to Identify Selected Genera of Enteric Bacteria Copyright © 2021 Pearson Education Ltd. All Rights Reserved Biochemical Tests (1 of 2) Rapid identification methods perform several biochemical tests simultaneously – Results of each test are assigned a number Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10. 9 One type of Rapid Identification Method for Bacteria: EnteroPluri Test From BD Diagnostics One tube containing media for 15 biochemical tests is inoculated with an unknown enteric bacterium. After incubation, the tube is observed for results. Phenylalanine Arabinose Ornithine Adonitol Glucose Sorbitol Lactose Dulcitol Urease Citrate Lysine Indole V–P Gas H 2S The value for each positive test is circled, and the numbers from each group of tests are added to give the code number. Comparing the resultant code number with a Code Number Microorganism Atypical Test Results computerized listing shows that the organism in the tube is Citrobacter freundii. 62352 Citrobacter freundii Citrate 62353 Citrobacter freundii None Copyright © 2021 Pearson Education Ltd. All Rights Reserved Biochemical Tests (2 of 2) Automated rapid identification system is available for medically important bacteria and yeast – The data from a mass spectrophotometer are compared to a database Copyright © 2021 Pearson Education Ltd. All Rights Reserved Serology (1 of 3) The science that studies serum and immune responses in serum Microorganisms are antigenic—they stimulate the body to form antibodies in the serum In an antiserum, a solution of antibodies is tested against an unknown bacterium Copyright © 2021 Pearson Education Ltd. All Rights Reserved Serology (2 of 3) In the slide agglutination test, bacteria agglutinate when mixed with antibodies produced in response to the bacteria Serological testing can differentiate between species and strains within species Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.11 A Slide Agglutination Test Copyright © 2021 Pearson Education Ltd. All Rights Reserved Serology (3 of 3) Enzyme-linked immunosorbent assay (ELISA) – Known antibodies and an unknown type of bacterium are added to a well; a reaction identifies the bacteria Western blotting – Identifies antibodies in a patient's serum; confirms HIV infection, and Lyme disease Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.12 An ELISA Test Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 18.14a The ELISA Method Copyright © 2021 Pearson Education Ltd. All Rights Reserved  If Lyme disease is suspected in a patient: Electrophoresis is used to separate Borrelia burgdorferi proteins. Proteins move at Lysed Polyacrylamide different rates based on their charge and size bacteria gel Figure 10.13 when the gel is exposed to an electric current. Proteins The Western Larger Blot Smaller The bands are transferred to a nitrocellulose Paper towels filter by blotting. Each band consists of many Salt solution Sponge molecules of a particular protein (antigen). The bands are not visible at this point. Gel Nitrocellulose filter The proteins (antigens) are positioned on the filter exactly as they were on the gel. The filter is then washed with patient’s serum followed by antihuman antibodies tagged with an enzyme. The patient antibodies that combine with their specific antigen are visible (shown here in red) when the enzyme’s substrate is added. The test is read. If the tagged antibodies stick to the filter, evidence of the presence of the microorganism in question—in this case, B. burgdorferi—has been found in the patient’s serum. Copyright © 2021 Pearson Education Ltd. All Rights Reserved Phage Typing Test for determining which phages a bacterium is susceptible to On a plate, clearings called plaques appear where phages infect and lyse bacterial cells Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.14 Phage Typing of a Strain of Salmonella Enterica Copyright © 2021 Pearson Education Ltd. All Rights Reserved Fatty Acid Profiles FAMEs: Fatty acid methyl esters provide profiles that are constant for a particular species Copyright © 2021 Pearson Education Ltd. All Rights Reserved Flow Cytometry Uses differences in electrical conductivity between species or fluorescence Copyright © 2021 Pearson Education Ltd. All Rights Reserved  A mixture of cells is treated to label cells that have certain antigens with Figure 18.12The Fluorescence- fluorescent-antibody markers. Activated Cell Sorter (FACS) Cell mixture leaves Fluorescently nozzle in droplets. labeled cells Laser beam strikes each droplet. Laser beam Detector of Laser scattered light Fluorescence detector Electrode identifies fluorescent cells by fluorescent light emitted by cell. Fluorescence detector Electrode gives positive charge to Electrically charged identified cells. metal plates As cells drop between electrically charged plates, the cells with a positive charge move closer to the negative plate. The separated cells fall into different collection tubes. Collection tubes Copyright © 2021 Pearson Education Ltd. All Rights Reserved DNA Sequencing DNA base composition – Guanine + cytosine % – GC + AT = 100% – Two organisms that are closely related have similar amounts of various bases – Online databases (NCBI Genome Database) Copyright © 2021 Pearson Education Ltd. All Rights Reserved DNA Fingerprinting DNA fingerprint – Electrophoresis of restriction enzyme digests of an organism's DNA – Comparing fragments from different organisms provides information on genetic similarities and differences Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.15 DNA fingerprints Copyright © 2021 Pearson Education Ltd. All Rights Reserved Nucleic Acid Hybridization (1 of 5) Nucleic acid hybridization measures the ability of DNA strands from one organism to hybridize with DNA strands of another organism – Greater degree of hybridization, greater degree of relatedness – Hybridization of >70% indicates same species Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.16 DNA-DNA Hybridization Copyright © 2021 Pearson Education Ltd. All Rights Reserved Nucleic Acid Hybridization (2 of 5) Nucleic Acid Amplification Tests (NAATs) use PCR to amplify DNA of an unknown microorganism that cannot be cultured Copyright © 2021 Pearson Education Ltd. All Rights Reserved Nucleic Acid Hybridization (3 of 5) Southern blotting uses nucleic acid hybridization to identify unknown microorganisms using DNA probes Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.17 A Plasmid DNA Probe Used Salmonella DNA to Identify fragment Bacteria Unknown bacteria A Salmonella DNA are collected fragment is cloned in on a filter. E. coli. The cells are lysed, and the DNA is released. Cloned DNA fragments are marked with fluorescent dye and separated into single strands, forming DNA probes. The DNA is separated into single strands. DNA probes are added to the DNA from the Fluorescent probe unknown bacteria. Salmonella DNA DNA probes hybridize with Salmonella DNA from sample. Then excess probe is washed DNA from off. Fluorescence indicates other bacteria presence of Salmonella. Copyright © 2021 Pearson Education Ltd. All Rights Reserved Nucleic Acid Hybridization (4 of 5) A DNA chip (also known as a microarray) contains DNA probes and detects pathogens by hybridization between the probe and DNA in the sample – Detected by fluorescence Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.18a-b DNA Chip Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.18c-d DNA Chip Copyright © 2021 Pearson Education Ltd. All Rights Reserved Nucleic Acid Hybridization (5 of 5) Ribotyping – rRNA sequencing Fluorescent in situ hybridization (FISH) – Fluorescent DNA or RNA probes stain the microorganisms being targeted – Determines the identity, abundance, and relative activity of microorganisms in an environment Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.19 FISH, or Fluorescent in Situ Hybridization Copyright © 2021 Pearson Education Ltd. All Rights Reserved Putting Classification Methods Together Dichotomous keys – Identification keys based on successive questions Cladograms – Maps that show evolutionary relationships among organisms; based on rRNA sequences Copyright © 2021 Pearson Education Ltd. All Rights Reserved Figure 10.20 Building a Cladogram Copyright © 2021 Pearson Education Ltd. All Rights Reserved Animation: Dichotomous Keys: Overview Copyright © 2021 Pearson Education Ltd. All Rights Reserved Animation: Dichotomous Keys: Sample with Flowchart Copyright © 2021 Pearson Education Ltd. All Rights Reserved Animation: Dichotomous Keys: Practice Copyright © 2021 Pearson Education Ltd. All Rights Reserved