Taxonomy II:

Applied systems

Modern Classification Systems

Robert Whittaker (1969)• Five Kingdom System

– Monera

– Protista

– Fungi

– Plantae

– Animalia

Modern Classification Systems

Carl Woese

Three domain system » Archea

» Eubacteria

» Eukarya

Fig. 14-2

stromatolites

Fig. 14-9

Archaea may be closer to Eukarya than Eubacteria.

Phenotypes

Replica plating (lederberg)All colonies grow Mutants do not grow

Pressplate ontovelveteen

Velveteen withimprint of allcolonies

Completemedium

Incubate

All colonies grow Mutants do not grow

Minimalmedium

Transfer imprintof colonies tofresh media

Master plate;growth oncompletemedium

Velveteen;sterilized

Plastic hoop

Wooden block

Testing phenotypes

Complementation via recombination

DNA fromTrp+ cells

Agar lackingtryptophan

Trp– cells No growth Trp– cells Recombinantsform colonies

Agar lackingtryptophan

“Trp auxotroph”

16s RNA map

Basic Local Alignment Search Tool BLAST

Number ofsequence ofmatches

Afteralignment

Beforealignment

Species 1

Species 2

Species 1

Species 2

9

15

Nonidentities

Gaps

More distant = more differences

Making a phylogenetic tree

node 1

node 2node 3

node 4

Hybridization analysiis

Hybridizationexperiment:

Same genus,but differentspecies

Organisms tobe compared:

Genomic DNA

Heat todenature

Mix DNA from two organisms—unlabeledDNA is added in excess:

DNApreparation

Genomic DNA

Results andinterpretation:

Same species

Differentgenera 100% < 25%

100 75 50 25 0 Same strain(control)

1 and 2 are likelydifferent generaPercent hybridization

Unhybridized Organism 2 DNAHybridized DNA

Shear and label ( )

Hybridized DNA

Shear DNA

Organism 1 Organism 2

Fig. 14-21

Genomic DNA–DNA hybridization (%)16S

rR

NA

gen

e se

qu

ence

sim

ilari

ty (

%)

0 20 40 60 70 80 100

100

98

96

94

92

90

88

GC content

Thermophiles have higher GC content, why?

B. Applied Taxonomic Systems

3. Bacterial taxonomy• Bergey's Manual

• Criteria for identification and classification

3a. Bacterial taxonomy - Bergey's

Manual• Criteria for identification and classification

• Morphology– Cell Shape & Arrangement

– Cell Size

– Staining Reactions

3b. Bacterial taxonomy - Bergey's

Manual• Criteria for identification and classification

• Chemical– Chemical Composition

» Teichoic acid

» LPS

3c. Bacterial taxonomy - Bergey's

Manual• Criteria for identification and classification

• Cultural– Nutritional Requirements

– Living Host Requirement

– Physical Conditions

» Temperature, Light, Gas

3d. Bacterial taxonomy - Bergey's

Manual• Criteria for identification and classification

• Metabolic– Energy Yielding Processes - Fermentation

– Energy Utilizing Processes - Nutrient transport

– Motility

– Enzymes

3e. Bacterial taxonomy - Bergey's

Manual• Criteria for identification and classification

• Antigens– Stimulate the immune system -antigens

• Genetics– G-C ratio

– Plasmids

3f. Bacterial taxonomy - Bergey's

Manual• Criteria for identification and classification

• Pathogenic– Cause disease

– Host - plant, animal

• Ecological least reliable– Habitat

C. Nomenclature

1a. Nomenclature• Sample First Words

» Latin Root

Bacillus - Small Rod » Greek Root

Clostridium - small spindle

Corynebacterium - club

bacterium» Personal Names

Erwinia

1b. Nomenclature• Sample Second Words

– Albus - White

– Aureus - Gold

– Lutea - Yellow

– Meningitis - inflammation of meninges

2. Nomenclature• Writing technical names

– First word - always capitalized & in italics

– Second word - never capitalized & in italics

Bacillus subtilis

B. subtilis