taxonomy and phylogeny

Question 1

Bacteria

Answer 1

prokaryote (no nucleus) cells; bacterial ribosomal RNA (rRNA); diacyl glycerol diesters major membrane lipids

Question 2

Archaea

Answer 2

archaeal rRNA; isoprenoid glycerol diether or diglycerol tetraether lipids in membrane

Question 3

Eukaryotes

Answer 3

contain nucleus; eukaryotic rRNA; glycerol fatty acyl diester membrane lipids

Question 4

Taxonomic ranks

Answer 4

Domain		Bacteria
Phylum		Proteobacteria
Class		g-proteobacteria
Order		Pseudomonadales
Family		Pseudomonadaceae
Genus		Pseudomonas
Species		Pseudomonas syringae

Question 5

microbial species

Answer 5

a collection of strains that share many stable properties and differ significantly from other groups

Collection of strains with similar G+C composition and >70% similarity using DNA-DNA hybridization experiments

Question 6

divisions within species

Answer 6

strains exhibit some distinct difference to other strains within a species:

Biovars, biochemical/morphological variants
Morphovars, morphological variants
Serovars, serogenic (antigenic) variants
Pathovars, pathogenic variants

Question 7

Classification systems

Answer 7

Natural classification / Phylogenetic classification

Question 8

Natural classification

Answer 8

Arranges groups whose members share many characteristics and reflects biological nature of organisms - E.g. Carolus Linnaeus and anatomical characteristics

= Phenetic classification- Arranges groups based on mutual similarity of phenotypic characteristics

= Numerical taxonomy - Grouping of organisms into taxa based on character states ie morphological, biochemical and physiological characters given values; organisms classified via the designated coefficients

Question 9

Phylogenetic classification

Answer 9

• Greek, phylon, tribe/race, genesis, generation/origin
• Based on evolutionary relationships
• Poor fossil record, but DNA and protein sequences used

Question 10

Phylogenetic classification

Answer 10

Molecular chronometers:

• Nucleic acid (DNA/RNA) and protein change over time
• Assumes there is an evolutionary clock
• Gradual change over time without alteration of function
• Assumes changes are selectively neutral, occur randomly and increase linearly over time
• Highly different sequences indicate divergence long ago

Question 11

Phylogenetic trees

Answer 11

• Nodes may represent species or genes
• Tree may have time scale (eg experimental evolution) or length of branch represents number of molecular changes occurring between 2 nodes
• Unrooted trees – no indication of evolutionary path

Question 12

Indicators of phylogeny

Answer 12

Can use full gene/protein sequence or fragments:

• Ribosomal RNA (rRNA)
• DNA
• Protein

16S rRNA commonly used

Question 13

Assessing similarity

Answer 13

• Make alignments of sequences, 2 or more
• Computer programs determine the level of diversity
• Make phylogenetic tree – similar organisms cluster tightly together, then get larger groupings

Question 14

16S rRNA signature sequences

Answer 14

• Many 16S rRNA molecules have 1 or more “signature sequence” that is unique to particular bacteria
• Can be useful in assigning the specific Class of bacteria

Question 15

Why study taxonomy

Answer 15

Important that we understand differences between organisms

Four practical reasons:

• Cataloguing, future knowledge base
• Allows predictions/hypotheses to be set for research
• Grouping organisms helps scientists to work with them and related organisms
• Essential for accurate identification of microbes

Question 16

taxonomy

Answer 16

Systematics

Greek: Taxis, arrangement/order; nomos, law

Three parts:
~ Classification, arranging groups into taxa (based on similarity or evolutionary relatedness)
~ Nomenclature, assignment of names to taxonomic groups, following published rules
~ Identification, process of defining that a particular isolate belongs to a taxon