QuotesQuotes

• "When written in Chinese the word 'crisis' is composed of two characters. One represents danger, and the other represents opportunity.“

John Kennedy

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

• Procaryotae/Monera

AnimaliaAnimalia

1. Multicellular

2. Heterotrophs

PlantaePlantae

1. Multicellular

2. Photoautotrophs

http://www.acclaimimages.com/usepolicy.html

http://www.acclaimimages.com/usepolicy.html

FungiFungi

1. Absorptive Chemoheterotrophs

2. Decomposers

http://www.acclaimimages.com/usepolicy.html

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

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

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

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