Overview

-       Taxonomy & Systematics (phylogeny)

-       Three domains

-       Origin of Eukaryotes

-       Classification

-       Phylogenetics, nomenclature, & hierarchy

-       Prokaryotes, Eukaryotes, Viruses

-       Methods

-       Classification vs. Identification

-       Morphological

-       Staining

-       Biochemical

-       Serology (ELISA, Western Blot)

-       Phage typing

-       Flow cytometry

-       DNA (PCR, fingerprinting, hybridization)

-       Keys (dichotomous, cladograms)

 

Taxonomy

-       The science of classifying organisms

-       Provides universal names for organisms

-       Provides a reference for identifying organisms

 

Systematics, or Phylogeny

-       The study of the evolutionary history of organisms

-       All Species Inventory (2001–2025)

-       To identify all species of life on Earth

 

Placing Bacteria

-       1735  Kingdoms Plantae and Animalia

-       1857  Bacteria and fungi put in the Kingdom Plantae  – “Flora”

-       1866  Kingdom Protista proposed for bacteria, protozoa, algae, and fungi

-       1937  Prokaryote introduced for cells "without a nucleus"

-       1961  Prokaryote defined as cell in which nucleoplasm is not surrounded by a nuclear membrane

-       1959  Kingdom Fungi

-       1968  Kingdom Prokaryotae proposed

-       1978  Two types of prokaryotic cells found

 

The Three-Domain System

 

A Model of the Origin of Eukaryotes

 

Endosymbiotic Theory

 

Fossilized Prokaryotes

 

Phylogenetics

-       Each species retains some characteristics of its ancestor

-       Grouping organisms according to common properties implies that a group of organisms evolved from a common ancestor

-       Anatomy

-       Fossils

-       rRNA

 

Scientific Nomenclature

-       Common names

-       Vary with languages

-       Vary with geography

-       Binomial Nomenclature (genus + specific epithet)

-       Used worldwide

-       Escherichia coli

-       Homo sapiens

 

Scientific Names

 

Taxonomic Hierarchy

-       Domain

-       Kingdom

-       Phylum

-       Class

-       Order

-       Family

-       Genus

-       Species

 

Classification of Prokaryotes

-       Prokaryotic species: A population of cells with similar characteristics

-       Culture: Grown in laboratory media

-       Clone: Population of cells derived from a single cell

-       Strain: Genetically different cells within a clone

 

Phylogenetic Relationships of Prokaryotes

 

Classification of Eukaryotes

-       Eukaryotic species: A group of closely related organisms that breed among themselves

 

Classification of Eukaryotes

-       Animalia: Multicellular; no cell walls; chemoheterotrophic

-       Plantae: Multicellular; cellulose cell walls; usually photoautotrophic

-       Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments

-       Protista: A catchall kingdom for eukaryotic organisms that do not fit other kingdoms

-       Grouped into clades based on rRNA

 

Classification of Viruses

-       Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche

-       Non-living, acellular

 

Classification and Identification

-       Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.

-       Identification: Matching characteristics of an “unknown” organism to lists of known organisms.

-       Clinical lab identification

 

-       Identifying Klebsiella doesn’t tell you it’s classified as gammaproteobacteria

 

Identification Methods

-       Morphological characteristics: Useful for identifying eukaryotes

-       Differential staining: Gram staining, acid-fast staining

-       Biochemical tests: Determines presence of bacterial enzymes

 

Biochemical - Numerical Identification

 

Serology

-       Combine known antiserum plus unknown bacterium

-       Slide agglutination test

 

Serology - ELISA

-       Enzyme-linked immunosorbent assay

-       Known antibodies

-       Unknown type of bacterium

-       Antibodies linked to enzyme

-       Enzyme substrate

 

Serology - The Western Blot

 

Phage Typing of Salmonella enterica

 

Flow Cytometry

-       Uses differences in electrical conductivity between species

-       Fluorescence of some species

-       Cells selectively stained with antibody plus fluorescent dye            

 

DNA - Genetics

-       DNA base composition

-       Guanine + cytosine content

-       DNA fingerprinting

-       Electrophoresis of restriction enzyme digests

-       rRNA sequencing

-       Polymerase chain reaction (PCR)

 

DNA - Nucleic Acid Hybridization

 

DNA - Identifying Bacteria with a probe

 

DNA - DNA Chip Technology

 

DNA - FISH

-       Fluorescent in situ hybridization

-       Add DNA probe for S. aureus

 

Keys - Dichotomous Key

 

Keys - Building a Cladogram