Chapter 10: Classification of Microorganisms

10.1 The Study of Phylogenetic Relationships

• Taxonomy is where we put organisms into categories, or taxa (singular: taxon), to show degrees of similarities among organisms.
• Systematics, or phylogeny, is the study of the evolutionary history of organisms, and the hierarchy of taxa reflects their evolutionary, or phylogenetic, relationships.
• In this widely accepted scheme, animals, plants, and fungi are kingdoms in the Domain Eukarya.
• The Domain Bacteria includes all of the pathogenic prokaryotes as well as many of the nonpathogenic prokaryotes found in soil and water.
• The Domain Archaea includes prokaryotes that do not have peptidoglycan in their cell walls.
• ==According to the endosymbiotic theory, eukaryotic cells evolved from prokaryotic cells living inside one another, as endosymbionts.==
• In a phylogenetic tree, grouping organisms according to common properties implies that a group of organisms evolved from a common ancestor; each species retains some of the characteristics of the ancestor.
  • ==Some of the information used to classify and determine phylogenetic relationships in higher organisms comes from fossils.==
• A molecular clock for evolution is based on nucleotide sequences in the genomes of organisms.

10.2 Classification of Organisms

• Every organism is assigned two names, or a binomial.
  • These names are the genus name and specific epithet (species), and both names are printed underlined or italicized.
  • Because this system gives two names to each organism, the system is called binomial nomenclature.
• A eukaryotic species is a group of closely related organisms that breed among themselves.
• Just as a number of species make up a genus, related genera make up a family.
• A group of similar families constitutes an order, and a group of similar orders makes up a class.
• Related classes, in turn, make up a phylum.
• All phyla that are related to each other make up a kingdom, and related kingdoms are grouped into a domain.
• A prokaryotic species is defined simply as a population of cells with similar characteristics.
• A pure culture is  often a clone, a population of cells derived from a single parent cell.
  • ==All cells in the clone should be identical, but in some cases, pure cultures of the same species are not identical in all ways.==
  • Each such group is called a strain. Strains are identified by numbers, letters, or names that follow the specific epithet.
• Consequently, the organisms once classified as protists are being divided into clades, or genetically related groups.
• The Kingdom Fungi includes the unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms.
• The Kingdom Plantae (plants) includes mosses, ferns, conifers, and flowering plants.
• The kingdom of multicellular organisms called Animalia (animals) includes sponges, various worms, insects, and animals with backbones (vertebrates).
• The International Committee on Taxonomy of Viruses defines a viral species as a population of viruses with similar characteristics (including morphology, genes, and enzymes) that occupies a particular ecological niche.

10.3 Methods of Classifying and Identifying Microorganisms

• Transport media are usually not nutritive and are designed to prolong viability of fastidious pathogens.
• Rapid identification methods are manufactured for groups of medically important bacteria, such as the enterics.
• Serology is the science that studies serum and immune responses that are evident in serum.
• Solutions of such antibodies used in the identification of many medically important microorganisms are commercially available; such a solution is called an antiserum.
• In a procedure called a slide agglutination test, samples of an unknown bacterium are placed in a drop of saline on each of several slides.
• Serological testing can differentiate not only among microbial species, but also among strains within species.
  • Strains with different antigens are called serotypes, serovars, or biovars.
• A test called the enzyme-linked immunosorbent assay (ELISA) is widely used because it is fast and can be read by a computer scanner.
• Another serological test, Western blotting, is also used to identify antibodies in a patient’s serum.
• Phage typing is a test for determining to which phages a bacterium is susceptible.
• Flow cytometry can be used to identify bacteria in a sample without culturing the bacteria.
• Taxonomists can use an organism’s DNA base composition to draw conclusions about relatedness.
• Nucleic acid amplification tests (NAATs) can be used to increase the amount of microbial DNA to levels that can be tested by gel electrophoresis.
• Cladograms are maps that show evolutionary relationships among organisms.

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