Microbiology--Prokaryotic Taxonomy

Why is taxonomy important?

Provides universal names for all biological organisms

provides a reference for identification

allows for international communication

Identification

matching characteristics of an “unknown” organism to list of known organisms

Taxonomy

The science of categorizing organisms

Systematics (aka phylogeny)

Study of evolutionary history of organisms

demonstrates relatedness among organisms and evolutionary history of organisms

Carolus Linnaeus

Botantist

proposed a formal system for naming organisms

divided all organisms into Plantae and Animalia

Phylogenetics in practice

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

Each species retains some characteristics of its ancestor

Three domain system

Bacteria (oldest)

Archaea

Eukarya (newest)

Archaea

Prokaryotic

varies in cell wall composition

contains no peptidoglycan in cell wall

composed of branched carbon chains attached to glycerol by ether linkage

first AA in protein synthesis is Methionine

Bacteria

Prokaryotic

contains peptidoglycan in cell wall

Composed of straight carbon chains attached to glycerol by ester linkage

first AA in protein synthesis is Formylmethionine

Eukarya

Eukaryotic

Cell wall varies in composition, contains carbohydrates

composed of straight carbon chains attached to glycerol by ester linkage

first AA in protein synthesis is Methionine

What taxonomic hierarchy was just recently added for bacterium?

Kingdom

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

Eukaryotics are grouped into clades based on

rRNA

Viral Species

population of viruses with similar characteristics that occupies a particular ecological niche

Strain

Genetically different cells within a clone

Requirements for naming a species

Pure cultures

~1400 bp of rRNA gene sequence

International Journal of Systematic of Evolutionary Microbiology

Articles with evidence of new species or classification

Approved Lists of Bacterial Names

Lists species of known prokaryotes based on published articles

List of Prokaryotic Names with Standing in Literature

List of species of known prokaryotes based on published articles

Bergey’s Manual of Systematic Bacteriology

Provides phylogenetic and identification information on bacteria and archaea

Names of Prokaryotes

are always changing based on new findings

Historic methods of identification of bacterium

morphology

differential staining

biochemical testing

“Modern” methods of identification of bacterium

High-throughput biochemical testing

Antibody-antigen reactions

DNA sequencing

API strips by Bio Merieux

Tube containing media of 15 biochemical tests is inoculated with unknown

Positive results are circled and are compared to a computerized listing to figure out what the organism is

BIOLOG 96

A plate of a bunch of different carbon utilization tests

Blue color shows if it’s positive, meaning C source was utilized

Antigen-antibody tests

Used for very specific pathogens

fast positive or negative

How ever, if it comes out negative, you have no idea what it could be

Enzyme-linked immunosorbent assay (ELISA)

antibodies linked to a surface

bacteria added to wells

if antigen is recognized, cell binds to antibody

antibody linked covalently to enzyme is mixed in

excess washed away

substrate for enzyme added

if bacterium is present, color changes

Antigen

any molecule on a surface you can detect

16s rRNA gene

1500 bp long

certain regions are more variable than others

PCR primers can be made of all bacteria or certain species

can sequence from pure cultures

can sequence millions from environment simultaneously