Taxonomy I General Information 1 Definition the study

Taxonomy

I. General Information 1. Definition: the study of classification. 2. Why group things? 1. Makes it easier to find information on an organism. 2. Makes it easier to identify an organism. 3. Shows evolutionary relationships.

Taxonomy Microbiology 2314

Taxonomy The science of biological classification, by grouping organisms with similar characteristics.

Three Interrelated Parts of Taxonomy a. Classification a. Arrangement into groups b. Nomenclature Assignment of Names • Identification Determining Identity

Two Kingdom System (Proposed by Aristotle) a. Plantae Bacteria Fungi Algae Plants

Two Kingdom System a. Animalia Animals Protozoa

Problem with Aristotle’s Classification System: If it was green, it was a plant regardless of other features.

Five Kingdom System a. Animalia b. Plantae c. Fungi d. Protista e. Procaryote/Monera

Animalia 1. Multicellular 2. Heterotrophs

Plantae 1. Multicellular 2. Photoautotrophs

Fungi 1. Absorptive Chemoheterotroph s 2. Decomposers

Protista 1. Unicellular 2. Autotrophic or Heterotrophic

Monera (Bacteria)

Six Kingdom System

Three Domain System (Difference in r. RNA and Cell Wall in Procaryotic Organisms) a. Domain Eukaryae All Eukaryotic Organisms • Domain Eubacteria True Bacteria and Cyanobacteria • Domain Archaea Ancient “Extreme” Bacteria

Taxonomic Hierarchy Domain (Carl Woese 1978) Kingdom Phylum/Division Class Order Family Genus Species

Domains

Carolus Linnaeus 1753 1. Kingdom Through Species 2. Binomial Nomenclature 3. Bacillus subtilis 3. Common/Descriptive Names Tubercule Bacillus Mycobacterium tuberculosis

Dichotomous Keys 1 a. Bean round Garbanzo Bean 1 b Bean elliptical or oblong Go to 2 2 a Bean white White Navy 2 b Bean dark Go to 3 3 a. Bean evenly pigmented Kidney Bean 3 b Bean pigmentation mottled Pinto Bean

Phylogenetic Classification a. Genetic Similarity and Evolutionary Relatedness Reflects Genetic Similarity and Evolutionary Relatedness

Charles Darwin

Protista

Phenetic Classification a. Based on Observable Characteristics.

Species verses Strain a. Species A specific or defined type of organism capable of producing young that can also reproduce. • Strain Variation within a species. § descended from a single organism § different isolates may be same species but are different strains; often have slight differences

Bergey’s Manual of Systematic Bacteriology

a. First edition published in 1923, now in 9 th edition. a. Uses both morphological and Physiological characteristics b. Very practical system. Use successive "key" features to narrow down identification c. Ex. Gram + or -? Then shape? Then motile or not? etc. Eventually only a few organisms match the process of elimination.

a. Second edition now being published, a major reorganization • Primary emphasis is phylogenetic, not phenetic • Example: pathogens are not grouped together, instead they are scattered in different areas • Five volumes have instructive titles: The Archaea, and the Deeply Branching and Phototrophic Bacteria The Proteobacteria The Low G + C Gram-positive Bacteria The High G + C Gram-positive Bacteria The Planctomyces, Spirochaetes, Fibrobacters, Bacterioidetes, and Fusobacteria

American Type Culture Collection a. Algae and Protozoa b. Bacteria and Baceriophages c. Cell Lines d. DNA Materials e. Fungi and Yeasts f. Plant Tissues g. Seeds h. Viruses and Virus Antiserum

Eukaryotic Cells Domain Eukaryae 1. Membrane System 2. Compartmentalization 3. Membrane Enclosed Organelles 4. Nucleus

Prokaryotic Cells Domain Eubacteria & Archaea 1. Few if Any Internal Membranes 2. Plasma Membrane Mediates Internal Processes 3. Nucleoid 4. No Membrane Bound Organelles

Viruses a. Noncellular b. Nonliving c. Either DNA or RNA d. Capsid (Protein Shell) e. Envelope

Viruses a. Virus Species A population of viruses with similar characteristics that occupy a particular ecological niche. • No Independent Metabolism or Replication • Requires a Host (Parasitic)

Viral Replication 1. Attachment 2. Penetration 3. Disassembly 4. Reassembly 5. Release

Major Criteria and Methods Used in the Taxonomy of Microorganisms Classical Approach a. Morphology b. Differential Staining c. Biochemical Tests d. Oxygen Requirements e. Serology f. Phage Typing

Molecular Approach a. Amino Acid Sequencing b. Total Protein Analysis c. Base Composition d. Nucleic Acid Hybridization e. Numerical Taxonomy f. Fatty Acid Profiles

Cladogram

FYI Bacteria Consist of Approximately 12 Distinct

Biologists say greensulfur bacteria are important because they perform photosynthesis in a different way from that of other bacteria and that of plants. Obligately anaerobic photolithoautotrophs that use hydrogen sulfide, elemental sulfur and hydrogen as electron sources; elemental sulfur produced by sulfide oxidation is deposited outside the cell. Have gas vessicles because they lack flagella and are

Merismopedia Cyanobacteria have historically been essential for the developing of more complicated life forms by the production of oxygen in our atmosphere. Largest and most diverse group of photosynthetic bacteria. Photosynthetic system resembles that of eucaryotes, having chlorophyll a and photosystem II; carry out oxygenic

The Gram-positive cocci are the leading pathogens of humans. It is estimated that they produce at least a third of all the bacterial infections of humans, including strep throat, pneumonia, food poisoning, various skin diseases and severe types of septic shock.

a. Purple bacteria (anaerobic) use energy from the sun but extract electrons from substances other than water, and therefore release no oxygen. Most species are strict anaerobes and live in the sediment of ponds and lakes. These bacteria deposit sulfur granules outside their

a. Chlamydiae are tiny bacteria that infect birds and mammals. They may colonize and infect tissues of the eye and urogenital tract in humans. Chlamydia trachomatis causes several important diseases in humans: chlamydia, the most prevalent sexually transmitted disease in the U. S. Chlamydia pneumoniae is a cause of pneumonia and has been recently linked to atherosclerosis.

a. Planctomyces is a marine bacterium that can be found in various habitats around the world. Planctomycetes in general are intriguing because they are the only free living bacteria known to lack peptidoglycan in their cell walls.

Cytophaga is an endotoxin-producing bacteria that can cause respiratory disease if inhaled and is common in soil and both freshwater and marine environments. Cytophaga are unicellular, gram-negative gliding bacteria. Some strains can move at speeds near 10 µm per second. Due to this motility, colonies form spreading swarms on agar and some can cover entire plate in a few days. Cytophaga are chemoheteroorganotrophs, and many of them are able to degrade biomacromolecules such as protein, DNA, RNA, chitin, pectin, agar, starch, or cellulose.

The spirochetes are a phylogenetically distinct group of bacteria which have a unique cell morphology and mode of motility. Spirochetes are very thin, flexible, spiralshaped procaryotes that move by means of structures called axial filaments or endoflagella.

a. Deinococci are extraordinarily resistant to desiccation and radiation: can survive 3 -5 million rad whereas 100 rad can be lethal to humans. An acid producer. Two Chromosomes. b. Can be isolated from ground meat, feces, air, fresh water, and other sources but their natural habitat is not known c. Have an unusual ability to repair chromosomal damage and this probably accounts for their ability to resist radiation

a. Green Nonsulfur Bacteria a. Filamentous, gliding bacteria b. Thermophilic, often isolated from neutral to alkaline hot springs where they grow in the form of orange-reddish mats c. Ultrastructure and photosynthetic pigments are like green bacteria, but their metabolism is similar to that of the purple nonsulfur bacteria

a. Thermotoga - second deepest branch of the bacteria. Hyperthermophiles with an optimum of 80°C and a maximum of 90°C b. Gram-negative rods with an outer sheath-like envelope (like a toga) that can balloon out from the ends of the cell c. Grow in active geothermal areas (e. g. , marine hydrothermal vents and terrestrial sulfur springs)

a. Aquifex are thought to represent the deepest (oldest) branch of bacteria b. Hyperthermophilic c. Chemolithoautotrophic-generate energy by oxidizing electron donors such as hydrogen, thiosulfate, and sulfur with oxygen as the electron acceptor