Classification of Organisms Lecture 7 PDF

Classification of Organisms Lecture: 7 All texts and images are subject to copyright The Study of Phylogenetic Relationships ▪ Taxonomy is the study of classification of organisms into categories, or taxa (singular: taxon), to show degrees of similarities among organ...

Classification of Organisms Lecture: 7 All texts and images are subject to copyright The Study of Phylogenetic Relationships ▪ Taxonomy is the study of classification of 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. ▪ Hierarchy of taxa reflects their evolutionary, or phylogenetic, relationships. ▪ From the time of Aristotle, living organisms were categorized in just two ways, as either plants or animals. ▪ In 1735 Carolus Linnaeus introduced a formal system of classification with two kingdoms-Plantae and Animalia. ▪ The term prokaryote was introduced in 1937 to distinguish cells having no nucleus from the nucleated cells of plants and animals. ▪ In 1968, Robert G. E. Murray proposed the Kingdom Prokaryotae. ▪ In 1969, Robert H. Whittaker founded the five-kingdom system in which prokaryotes were placed in the Kingdom Prokaryotae, or Monera, and eukaryotes comprised the other four kingdoms. ▪ The Kingdom Prokaryotae had been based on microscopic observations. The Three Domains Ribosomes are present in all cells. Comparing the sequences of nucleotides in ribosomal RNA from different kinds of cells shows that there are three distinctly different cell groups: the eukaryotes and two different types of prokaryotes—the bacteria and the archaea. In 1978, Carl R. Woese proposed elevating the three cell types, namely Archaea, Bacteria and Eukarya to a level above kingdom, called domain. In addition to differences in rRNA, the three domains differ in membrane lipid structure, transfer RNA molecules, and sensitivity to antibiotics. 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 non-pathogenic prokaryotes found in soil and water. The photoautotrophic prokaryotes are also in this domain. The Domain Archaea includes prokaryotes that do not have peptidoglycan in their cell walls. They often live in extreme environments and carry out unusual metabolic processes. The Three Domains Based on rRNA analysis, three cell lineages clearly emerged as cells were forming 3.5 billion years ago. That led to the Archaea, the Bacteria, and what eventually became the nucleoplasm of the eukaryotes. However, the three cell lines were not isolated from each other; horizontal gene transfer appears to have occurred among them. Analysis of complete genomes shows that each domain shares genes with other domains. Gene transfer also has been seen between eukaryotic hosts and their prokaryote symbionts. The Study of Phylogenetic Relationships Phylogenetic Tree 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. Scientific Nomenclature ▪ Every organism is assigned two names. ▪ These names are the genus name and specific epithet (species), and both names are printed underlined or italicized. ▪ The genus name is always capitalized and is always a noun. ▪ The species name is lowercase and is usually an adjective. ▪ Because this system gives two names to each organism, the system is called binomial nomenclature. Example: Homo sapiens. The Taxonomic Hierarchy ▪ All organisms can be grouped into a series of subdivisions that make up the taxonomic hierarchy.  Figure: The taxonomic hierarchy. Organisms are grouped according to relatedness. Species that are closely related are grouped into a genus. For example, the baker’s yeast, Saccharomyces cerevisiae, belongs to the genus that includes sourdough yeast (S. exiguus). Related genera, such as Saccharomyces and Candida, are placed in a family, and so on. Each group is more comprehensive. The domain Eukarya includes all organisms with eukaryotic cells Classification of Prokaryotes ▪ The taxonomic classification scheme for prokaryotes is found in Bergey’s Manual of Systematics of Archaea and Bacteria. ▪ In Bergey’s Manual, prokaryotes are divided into two domains: Bacteria and Archaea. ▪ Each domain is divided into phyla. ▪ The classification is based on similarities in rRNA nucleotide sequences. ▪ Classes are divided into orders; orders, into families; families, into genera; and genera, into species. ▪ The term prokaryotic species is defined simply as a population of cells with a high degree of genomic similarity. ▪ The members of a bacterial species are nearly indistinguishable from each other but are distinguishable from members of other species, usually on the basis of several features. Classification of Prokaryotes ▪ Bacteria grown in media are called a culture. ▪ 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. ▪ Bergey’s Manual provides a reference for identifying bacteria in the laboratory, as well as a classification scheme for prokaryotes. Figure: Phylogenetic relationships of prokaryotes. Arrows indicate major lines of descent of prokaryotic groups. Selected phyla are indicated. Classification of Viruses Viruses are not classified as part of any of the three domains. They are not composed of cells, and don’t precisely fit a clearcut definition of a living organism because they must take over the anabolic machinery of living host cells to multiply. However, viruses are a major cause of disease, and their classification is important. A viral genome can directly biosynthesize inside a host cell, and some viral genomes can be incorporated into the host genome. The International Committee on Taxonomy of Viruses defines a viral species as a population of viruses with similar characteristics that can be distinguished from other species by multiple methods (including morphology, genes, enzymes, and ecological niche). Classification of Viruses ▪ Viruses are obligatory intracellular parasites. ▪ Viral genes carried in the genomes of other organisms provide a record of viral evolution. ▪ Recent analysis shows that bornavirus and retrovirus genes integrated into mammals, including humans, at least 40 million years ago. ▪ There are three hypotheses on the origin of viruses: 1. They arose from independently replicating strands of nucleic acids (such as plasmids). 2. They developed from degenerative cells that, through many generations, gradually lost the ability to survive independently but could survive when associated with another cell. 3. They coevolved with host cells. Methods of Classifying and Identifying Microorganisms Bergey’s Manual of Determinative Bacteriology has been a widely used reference since the first edition was published in 1923. Bergey’s Manual of Determinative Bacteriology does not classify bacteria according to evolutionary relatedness but instead provides identification schemes based on such criteria as cell wall composition, morphology, differential staining, oxygen requirements, and biochemical testing. The majority of Bacteria and Archaea haven’t been cultured, and scientists estimate that only 1% of these microbes have been discovered. In addition to properties of the organism itself, the source and habitat of a bacterial isolate are part of the identification processes. In clinical microbiology, a physician will swab a patient’s pus or tissue surface. The swab is inserted into a tube of transport medium. Transport media are usually not nutritive and are designed to prolong viability of fastidious pathogens. Conventional Identification ▪ Morphology ▪ Differential Staining Biochemical Tests ▪ Generally, bacteria are grown in culture before identification testing is performed. ▪ Enzymatic activities are widely used to differentiate bacteria. ▪ Even closely related bacteria can usually be separated into distinct species by subjecting them to biochemical tests. ▪ A limitation of biochemical testing is that mutations and plasmid acquisition can result in strains with different characteristics. ▪ Unless a large number of tests is used, an organism could be incorrectly identified. ▪ Therefore, specific series of biochemical tests have been developed for fast identification in hospital laboratories. ▪ Such tools are designed to perform several biochemical tests simultaneously and can identify bacteria within 4 to 24 hours. ▪ This is sometimes called numerical identification because the results of each test are assigned a number. ▪ In the simplest form, a positive test would be assigned a value of 1, and a negative is assigned a value of 0. ▪ In most commercial testing kits, test results are assigned numbers ranging from 1 to 4 that are based on the relative reliability and importance of each test, and the resulting total is compared to a database of known organisms. Figure” One type of rapid identification method for bacteria: EnteroPluri test from BD Diagnostics. Serology Serology is the science that studies serum and immune responses that are evident in serum. Microorganisms that enter an animal’s body stimulate it to form antibodies, which are immune-system proteins that circulate in the blood and combine in a highly specific way with the bacteria that caused their production. For example, the immune system of a rabbit injected with killed typhoid bacteria (antigens) responds by producing antibodies against typhoid bacteria. Solutions of serological testing can differentiate among microbial species as well as strains within species. Strains with different antigens are called serotypes, serovars, or biovars. Phage Typing ▪ Phage typing is a test for determining to which phages a bacterium is susceptible. ▪ Bacteriophages (phages) are bacterial viruses that usually cause lysis of the bacterial cells they infect. ▪ Highly specialized, they usually infect only members of a particular species or even particular strains within a species. ▪ One bacterial strain might be susceptible to two different phages, whereas another strain of the same species might be susceptible to those two phages plus a third phage. ▪ Phage typing is used to trace the spread of infections caused by Mycobacterium tuberculosis, Yersinia pestis, Bacillus anthracis, and S. aureus. Figure: Phage typing of a strain of Salmonella enterica. The tested strain was grown over the entire plate. A different bacteriophage was added to each grid square. Plaques, or areas of lysis, were produced by bacteriophages, indicating that the strain of S. enterica was sensitive to infection by these phages. Molecular Profiles Flow Cytometry Whole Genome Sequencing Nucleic Acid Hybridization Nucleic Acid Amplification Tests (NAATs), e.g. PCR (polymerase chain reaction) Southern Blotting DNA Chips Ribotyping and Ribosomal RNA Sequencing Ribotyping Fluorescent In Situ Hybridization (FISH)  Putting Classification Methods Together Dichotomous Keys ▪ Dichotomous keys are widely used for identification. ▪ In a dichotomous key, identification is based on successive questions, and each question has two possible answers (dichotomous means cut in two). ▪ After answering one question, the investigator is directed to another question until an organism is identified. ▪ Although these keys often have little to do with phylogenetic relationships, they’re invaluable for identification. ▪ For example, a dichotomous key for bacteria could begin with an easily determined characteristic, such as cell shape, and move on to Gram reaction and the ability to ferment a sugar.  Putting Classification Methods Together Cladograms ▪ Cladograms are maps that show evolutionary relationships among organisms (clado-means branch). ▪ Each branch point on the cladogram is defined by a feature shared by various species on that branch. ▪ Historically, cladograms for vertebrates were made using fossil evidence. ▪ As most microorganisms do not leave fossils; therefore, rRNA sequencing is primarily used to make cladograms for microorganisms. ▪ The small rRNA subunit used has 1500 bases, and computer programs do the calculations. ▪ The steps for constructing a cladogram are as follows: 1. Two rRNA sequences are aligned. 2. The percentage of similarity between the sequences is calculated. 3. Then the horizontal branches are drawn in a length proportional to the calculated percent similarity. All species beyond a node (branch point) have similar rRNA sequences, suggesting that they arose from an ancestor at that node. Figure 10.20 Building a cladogram.