Microbiology: Classification of Microorganisms Lecture Notes PDF

Microbiology an Introduction Thirteenth Edition Chapter 10 Classification of Microorganisms Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Study of Phylogenetic Relationships Learning Objecti...

Microbiology an Introduction Thirteenth Edition Chapter 10 Classification of Microorganisms Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Study of Phylogenetic Relationships Learning Objectives 10-1 Define taxonomy, taxon, and phylogeny. 10-3 Identify the contributions of Linnaeus, Whittaker, and Woese. 10-4 Discuss the advantages of the three-domain system. 10-5 List the characteristics of the Bacteria, Archaea, and Eukarya domains. 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 © 2019 Pearson Education, Inc. All Rights Reserved The Study of Phylogenetic Relationships continued 1735: Linnaeus—kingdoms Plantae and Animalia 1800s: Bacteria and fungi put in kingdom Plantae (Nägeli); Kingdom Protista proposed for bacteria, protozoa, algae, and fungi (Haeckel) 1937: Prokaryote introduced to distinguish cells without a nucleus 1968: Murray—kingdom Prokaryotae 1969: Whittaker—five-kingdom system  Prokaryotae (Monera), Protista, Fungi, Plantae, Animalia, Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Three Domains Developed by Woese in 1978; based on sequences of nucleotides in rRNA Eukarya – Animals, plants, fungi Bacteria Archaea – Methanogens – Extreme halophiles – Hyperthermophiles Copyright © 2019 Pearson Education, Inc. All Rights Reserved Three-Domain System continued 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. These similarities are the result of evolution, or descent from a common ancestor Copyright © 2019 Pearson Education, Inc. All Rights Reserved Characteristics of Archaea, Bacteria, and Eukarya Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Three Domains continued Eukaryotes originated from infoldings of prokaryotic plasma membranes Endosymbiotic bacteria developed into organelles Copyright © 2019 Pearson Education, Inc. All Rights Reserved Prokaryotic Cells and Eukaryotic Organelles Compared Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 10.3 Cyanophora Paradoxa Bacterium Eukaryotic host cell Copyright © 2019 Pearson Education, Inc. 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 © 2019 Pearson Education, Inc. All Rights Reserved Diatoms and the White Cliffs of Dover Copyright © 2019 Pearson Education, Inc. All Rights Reserved Fossilized Prokaryotes Stromatolites Oldest fossils on earth formed from layers of colonial cyanobacteria dating back over 3 billion years. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Fossilized Prokaryotes Stromatolites Copyright © 2019 Pearson Education, Inc. All Rights Reserved Scientific Nomenclature Learning Objectives 10-6 Explain why scientific names are used. 10-7 List the major taxa. 10-9 List the major characteristics used to differentiate the three kingdoms of multicellular Eukarya. 10-11 Differentiate eukaryotic, prokaryotic, and viral species. Common names vary with languages and geography Binomial nomenclature is used worldwide to consistently and accurately name organisms – Genus – Specific epithet (species) 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 © 2019 Pearson Education, Inc. All Rights Reserved Copyright © 2019 Pearson Education, Inc. 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 © 2019 Pearson Education, Inc. All Rights Reserved Figure 10.6 Phylogenetic Relationships of Prokaryotes Copyright © 2019 Pearson Education, Inc. 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 © 2019 Pearson Education, Inc. 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 © 2019 Pearson Education, Inc. All Rights Reserved Methods of Classifying and Identifying Microorganisms Learning Objectives 10-13 Explain the purpose of Bergey's Manual. 10-14 Describe how staining and biochemical tests are used to identify bacteria. 10-15 Differentiate Western blotting from Southern blotting. 10-16 Explain how serological tests and phage typing can be used to identify an unknown bacterium. 10-17 Describe how a newly discovered microbe can be classified by DNA sequencing, DNA fingerprinting, and PCR. 10-18 Describe how microorganisms can be identified by nucleic acid hybridization, Southern blotting, DNA chips, ribotyping, and FISH. 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 © 2019 Pearson Education, Inc. All Rights Reserved The Use of Metabolic Characteristics to Identify Selected Genera of Enteric Bacteria Copyright © 2019 Pearson Education, Inc. All Rights Reserved  Methods of Classifying and Identifying Microorganisms continued Bergey's Manual of Determinative Bacteriology provides identification schemes for identifying bacteria and archaea 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 © 2019 Pearson Education, Inc. All Rights Reserved Methods of Classifying and Identifying Microorganisms continued Biochemical Tests Rapid identification methods perform several biochemical tests simultaneously – Results of each test are assigned a number Copyright © 2019 Pearson Education, Inc. All Rights Reserved Methods of Classifying and Identifying Microorganisms continued Serology Studies serum and immune responses (antibodies) 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 Serological testing can differentiate between species and strains within species Copyright © 2019 Pearson Education, Inc. All Rights Reserved Serology continued In the slide agglutination test, bacteria agglutinate when mixed with antibodies produced in response to the bacteria Copyright © 2019 Pearson Education, Inc. All Rights Reserved Serology continued Enzyme-linked immunosorbent assay (ELISA) Known antibodies and an unknown type of bacterium are added to a well; a reaction identifies the bacteria Copyright © 2019 Pearson Education, Inc. All Rights Reserved Serology continued The Western Blot – Identifies antibodies(proteins) in a patient's serum; confirms HIV infection, and Lyme disease Copyright © 2019 Pearson Education, Inc. All Rights Reserved Methods of Classifying and Identifying Microorganisms continued Phage Typing Test for determining which phages (viruses) a bacterium is susceptible to On a plate, clearings called plaques appear where phages infect and lyse bacterial cells Copyright © 2019 Pearson Education, Inc. All Rights Reserved Methods of Classifying and Identifying Microorganisms continued DNA DNA base composition – Guanine + cytosine % – GC + AT = 100% DNA Sequencing – Two organisms that are closely related have similar amounts of various bases and can be found in online databases Copyright © 2019 Pearson Education, Inc. All Rights Reserved  DNA continued DNA fingerprinting – Electrophoresis of restriction enzyme digests of an organism's DNA – Comparing the number and sizes of DNA fragments produced from RE digests identifies genetic similarities – Polymerase Chain Reaction(PCR) can be used to amplify small DNA samples Copyright © 2019 Pearson Education, Inc. All Rights Reserved DNA continued Nucleic Acid Hybridization measures the ability of DNA strands from one organism to hybridize with DNA strands of another organism Copyright © 2019 Pearson Education, Inc. All Rights Reserved DNA continued Nucleic Acid Hybridization – Greater degree of hybridization, greater degree of relatedness – Hybridization of >70% indicates same species Examples include – Southern Blotting – DNA chips – FISH Copyright © 2019 Pearson Education, Inc. All Rights Reserved DNA continued Nucleic Acid Hybridization Copyright © 2019 Pearson Education, Inc. All Rights Reserved DNA continued Nucleic Acid Hybridization 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 © 2019 Pearson Education, Inc. All Rights Reserved Nucleic Acid Hybridization 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 © 2019 Pearson Education, Inc. All Rights Reserved Figure 10.19 FISH, or Fluorescent in Situ Hybridization Copyright © 2019 Pearson Education, Inc. 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 © 2019 Pearson Education, Inc. All Rights Reserved Building a Cladogram Copyright © 2019 Pearson Education, Inc. All Rights Reserved EXPLORING THE MICROBIOME Techniques for Identifying Members of Your Microbiome Copyright © 2019 Pearson Education, Inc. All Rights Reserved