Quotes

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

Taxonomy (Classification)

Microbiology 2314

Taxonomy

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

Three Interrelated Parts of Taxonomy

•

Classification

Arrangement into groups •

Nomenclature

Assignment of Names •

Identification

Determining Identity

Classification Versus Identification

• Classification answers questions of the sort:

How is this fungus related to other fungi?

• Identification addresses the more immediate question:

What's the name of the specimen in front of me?

Three Major Domains

• The

three-domain system

is a biological classification introduced by Carl Woese in 1990 that divides cellular life forms into

archaea

,

bacteria

, and

eukaryote

domains.

• In particular, it emphasizes the separation of prokaryotes into two groups, originally called

Eubacteria

(now

Bacteria

) and

Archaebacteria

(now

Archaea

). • Woese argued that, on the basis of differences in 16S rRNA genes, these two groups and the eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms.

Archaea Domain

• Prokaryotic, no nuclear membrane, distinct biochemistry and RNA markers from eubacteria, possess unique ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth; traditionally classified as archaebacteria; often characterized by living in extreme environment.

• Kingdom Archaebacteria Example: • Methanogens – metabolize hydrogen and carbon

Bacteria Domain

•

P

rokaryotic, no nuclear membrane, traditionally classified as bacteria, contain most known pathogenic prokaryotic organisms, studied far more extensively than Archaea • Kingdom Eubacteria Example: • Cyanobacteria – photosynthesizing bacteria

Eukarya Domain

•

E

ukaryotes, nuclear membrane present.

• Kingdom Protista or protists Kingdom Fungi or fungi Kingdom Plantae or plants Kingdom Animalia or animals

Two Kingdom System

(Proposed by Aristotle) •

Plantae

Bacteria Fungi Algae Plants

Two Kingdom System

•

Animalia

Animals Protozoa

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

Five Kingdom System

• Animalia • Plantae • Fungi • Protista • Procaryotae/Monera

Animalia

1. Multicellular 2. Heterotrophs

Plantae

1. Multicellular 2. Photoautotrophs

Fungi

1. Absorptive Chemoheterotrophs 2. Decomposers

Protista

1. Unicellular 2. Autotrophic or Heterotrophic

Monera (Bacteria)

Six Kingdom System

Three Domain System ( Difference in rRNA and Cell Wall in Procaryotic Organisms) •

Domain Eukaryae

All Eukaryotic Organisms •

Domain Bacteria

True Bacteria and Cyanobacteria •

Domain Archaea

Ancient “Extreme” Bacteria

Modern Taxonomic Hierarchy

Domain

(Carl Woese)

Kingdom Phylum/Division Class Order Family Genus Species

Domains

Carolus Linnaeus 1753

1. Kingdom Through Species 2. Binomial Nomenclature 3. Bacillus subtilis

Bacillus subtilis

3. Common/Descriptive Names Tubercule Bacillus

Mycobacterium tuberculosis

Phylogenetic Classification

• Genetic Similarity and Evolutionary Relatedness Reflects Genetic Similarity and Evolutionary Relatedness

Charles Darwin

Protista

Phenetic Classification

• Based on Observable Characteristics.

Species verses Strain

• •

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

• •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 Collection

• Algae and Protozoa • Bacteria and Baceriophages • Cell Lines • DNA Materials • Fungi and Yeasts • Plant Tissues • Seeds • Viruses and Virus Antiserum

Eukaryotic Cells

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

Prokaryotic Cells

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

Viruses

• Noncellular • Nonliving • Either DNA or RNA • Capsid (Protein Shell) • Envelope

Viruses

•

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 Uses These Tools • Morphology • Differential Staining • Biochemical Tests • Oxygen Requirements • Serology • Phage Typing

Molecular Approach Uses These Tools

• Amino Acid Sequencing • Total Protein Analysis • Base Composition • Nucleic Acid Hybridization • Numerical Taxonomy • Fatty Acid Profiles

Describe how staining, biochemical, immunological, and molecular tests are used for identification

Dichotomous Keys

(Always Given Two Choices) 1a. Bean round 1b Bean elliptical or oblong Garbanzo Bean Go to 2 2a Bean white 2b Bean dark White Navy Go to 3 3a. Bean evenly pigmented 3b Bean pigmentation mottled Kidney Bean Pinto Bean

Cladogram

Disease Causing Microorganisms

• Among the almost infinite varieties of microorganisms, relatively few cause disease in otherwise healthy individuals.

Koch’s Postulates

• One way of proving that a given disease is "infectious", is to satisfy Koch's postulates (first proposed by Robert Koch), which demands that the infectious agent be identified only in patients and not in healthy controls, and that patients who contract the agent also develop the disease. These postulates were first used in the discovery that

Mycobacteria

species cause tuberculosis.

Diagnosis

• Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.

Culturing Bacteria

• Microbiological culture is a principal tool used to diagnose infectious disease. • In a microbial culture, a growth medium is provided for a specific agent. • A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium.

Staining Bacteria

• Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. • Microscopy is often also used to observe the reaction of specific bacteria with specific stains or dyes.

Biochemical Tests

• Biochemical tests used in the identification of infectious agents include the detection of metabolic or enzymatic products characteristic of a particular infectious agent. Since bacteria ferment carbohydrates in patterns characteristic of their genus and species.

Immunological Tests

• Immunologic or Serological methods are highly sensitive, specific and often extremely rapid tests used to identify microorganisms. • These tests are based upon the ability of an antibody to bind specifically to an antigen. The antigen, usually a protein or carbohydrate made by an infectious agent, is bound by the antibody.

Molecular Diagnostics

• Technologies based upon the polymerase chain reaction (PCR) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. • First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified.

• Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids in order to cause a disease. • This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. • Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known, if they are not already.