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Taxonomy
I. General Information
A. Definition: the study of classification.
B. 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.
TaxonomyTaxonomyMicrobiology 2314
TaxonomyTaxonomyThe science of biological classification, by grouping organisms with similar characteristics.
Three Interrelated Parts of Three Interrelated Parts of TaxonomyTaxonomy
• Classification
Arrangement into groups
• Nomenclature
Assignment of Names
• Identification
Determining Identity
Two Kingdom Two Kingdom SystemSystem
(Proposed by Aristotle)(Proposed by Aristotle)
• PlantaeBacteria
Fungi
Algae
Plants
Two Kingdom Two Kingdom SystemSystem
• AnimaliaAnimals
Protozoa
Problem with Aristotle’s Classification System:
If it was green, it was a plant regardless of other features.
Five Kingdom SystemFive Kingdom System
• Animalia
• Plantae
• Fungi
• Protista
• Procaryote/Monera
AnimaliaAnimalia
1. Multicellular
2. Heterotrophs
PlantaePlantae
1. Multicellular
2. Photoautotrophs
FungiFungi
1. Absorptive Chemoheterotrophs
2. Decomposers
ProtistaProtista
1. Unicellular
2. Autotrophic or Heterotrophic
MoneraMonera(Bacteria)(Bacteria)
Six Kingdom SystemSix Kingdom System
Three Domain SystemThree Domain System((Difference in rRNA and Cell Wall in Procaryotic Organisms)Difference in rRNA and Cell Wall in Procaryotic Organisms)
• Domain Eukaryae
All Eukaryotic Organisms
• Domain Eubacteria
True Bacteria and Cyanobacteria
• Domain Archaea
Ancient “Extreme” Bacteria
Taxonomic HierarchyTaxonomic HierarchyDomain
(Carl Woese 1978)
KingdomPhylum/Division
Class OrderFamilyGenusSpecies
DomainsDomains
Carolus Linnaeus Carolus Linnaeus 17531753
1. Kingdom Through Species
2. Binomial Nomenclature
3. Bacillus subtilis
Bacillus subtilis
3. Common/Descriptive Names
Tubercule Bacillus
Mycobacterium tuberculosis
Dichotomous KeysDichotomous Keys
1a. Bean round Garbanzo Bean
1b Bean elliptical or oblong Go to 2
2a Bean white White Navy
2b Bean dark Go to 3
3a. Bean evenly pigmented Kidney Bean
3b Bean pigmentation mottled Pinto Bean
Phylogenetic ClassificationPhylogenetic Classification
• Genetic Similarity and Evolutionary Relatedness
Reflects Genetic Similarity and Evolutionary Relatedness
Charles DarwinCharles Darwin
Protista
Phenetic ClassificationPhenetic Classification• Based on Observable Characteristics.
Species verses StrainSpecies verses Strain
• SpeciesA specific or defined type of organism capable of producing young that can also reproduce.
• StrainVariation 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 Bergey’s Manual of Systematic BacteriologyBacteriology
•First edition published in 1923, now in 9th edition.•
•Uses both morphological and Physiological characteristics
•Very practical system. Use successive "key" features to narrow down identification
•Ex. Gram + or -? Then shape? Then motile or not? etc. Eventually only a few organisms match the process of elimination.
•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 American Type Culture CollectionCollection
• Algae and Protozoa• Bacteria and Baceriophages• Cell Lines• DNA Materials• Fungi and Yeasts• Plant Tissues• Seeds• Viruses and Virus Antiserum
Eukaryotic Eukaryotic CellsCells
Domain EukaryaeDomain Eukaryae
1. Membrane System
2. Compartmentalization
3. Membrane Enclosed Organelles
4. Nucleus
Prokaryotic Prokaryotic CellsCellsDomain Eubacteria Domain Eubacteria & Archaea& Archaea
1. Few if Any Internal Membranes
2. Plasma Membrane Mediates Internal Processes
3. Nucleoid
4. No Membrane Bound Organelles
VirusesViruses
• Noncellular
• Nonliving
• Either DNA or RNA
• Capsid (Protein Shell)
• Envelope
VirusesViruses
• 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 ReplicationViral Replication
1. Attachment2. Penetration3. Disassembly4. Reassembly5. Release
Major Criteria and Methods Major Criteria and Methods Used in the Taxonomy of Used in the Taxonomy of
MicroorganismsMicroorganisms
• Morphology• Differential Staining• Biochemical Tests• Oxygen Requirements• Serology• Phage Typing
Classical ApproachClassical Approach
Molecular ApproachMolecular Approach
• Amino Acid Sequencing
• Total Protein Analysis
• Base Composition
• Nucleic Acid Hybridization
• Numerical Taxonomy
• Fatty Acid Profiles
CladogramCladogram
Bacteria Consist of Approximately 12 Distinct Groups
FYI
Biologists say green-sulfur 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 nonmotile unless moved by environment.
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 photosynthesis
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.
• 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 cells.
• 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.
• 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, spiral-shaped procaryotes that move by means of structures called axial filaments or endoflagella.
• 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.
• Can be isolated from ground meat, feces, air, fresh water, and other sources but their natural habitat is not known
• Have an unusual ability to repair chromosomal damage and this probably accounts for their ability to resist radiation
• Green Nonsulfur Bacteria – Filamentous, gliding bacteria – Thermophilic, often isolated from neutral to
alkaline hot springs where they grow in the form of orange-reddish mats
– Ultrastructure and photosynthetic pigments are like green bacteria, but their metabolism is similar to that of the purple nonsulfur bacteria
• Thermotoga - second deepest branch of the bacteria. Hyperthermophiles with an optimum of 80°C and a maximum of 90°C
• Gram-negative rods with an outer sheath-like envelope (like a toga) that can balloon out from the ends of the cell
• Grow in active geothermal areas (e.g., marine hydrothermal vents and terrestrial sulfur springs)
• Aquifex are thought to represent the deepest (oldest) branch of bacteria
• Hyperthermophilic
• Chemolithoautotrophic-generate energy by oxidizing electron donors such as hydrogen, thiosulfate, and sulfur with oxygen as the electron acceptor
