Lecture 10: Taxonomy of Bacteria & Archaea

Question 1

What are the two ways to classify bacteria?

Answer 1

• Overall similarity (phenetic)

- Evolutionary relationships (Phylogenetics)

Question 2

How long ago was the first evidence of microbial life?

Answer 2

3.5 by ago. (Earth is 4.5byo)

Question 3

What is the best evidence we have of early life?

Answer 3

Stromatolites

Question 4

What are stromatolites?

Answer 4

Microbial mats, layers of filamentous prokaryotes, sediments, and extracellular matrix.

Question 5

True or false? Early earth was anoxic and hot.

Answer 5

True

Question 6

What are ancient stromatolites?

Answer 6

Anoxygenic phototrophic filamentous bacteria.

Question 7

What are moderm stromatolites?

Answer 7

Oxygenic phototrophic cyanobacteria

Question 8

True or false? The 18s ribosomal subunit is found in prokaryotes.

Answer 8

False. Eukaryotes

Question 9

What is the surface origin hypothesis?

Answer 9

1st membrane enclosed self repilcating cells arose out of primondial soup rich in organic/inorganic compounds on earths surface

Question 10

What is the problem with the surface origin hypothesis?

Answer 10

Earth’s surface was not hospitable. Dramatic temp fluctuations (day/night), meteor impacts, dust clouds, UV, storms

Question 11

What is the subsurface origin hypothesis?

Answer 11

• life originated in hydrothermal vents on ocean floor
• more stable conditions
• steady and abundant supply of energy

Question 12

True or false. Archaea are often extremophiles.

Answer 12

True

Question 13

What role did hydrothermal vents play in the origin of life?

Answer 13

• Nutrients in hot hydrothermal H20 flow up through mound
• mineral pores form compartments=first cells=RNA
• Compartments allow for coupling of energetic rxns to molecular replication
• eventually lipid bilayers took place of mineral compartments

Question 14

What is the RNA world theory?

Answer 14

• First self-replication system may have been RNA based
• RNA can bind small molecules (ATP)
• RNA has catalytic activity, may have catalyzed it’s own synthesis (can be copied like DNA)

Question 15

How did the great oxidation event occur?

Answer 15

In Archaen eon-origin of cyanobacteria creates so much O2 that it created possibility for eukaryotic life

Question 16

What is phylogenetic classification?

Answer 16

Evolutionary relationships.

-Mutations, gene duplication, gene loss, HGT

Question 17

What is an adaptive mutation?

Answer 17

Improve fitness of organism, increases survival

Question 18

what is an deleterious mutation?

Answer 18

Decrease fitness of organism, decreases survival

Question 19

What did Carl Woese do?

Answer 19

• RNA sequencing if SSU RNA (16s in prokaryotes, 18s in eukaryotes)
• Established presence of 3 domains of life
• Provided unified phylogenetic framework for bacteria
• Came up with RNA world theory
• Comparative rRNA sequencing

Question 20

What is comparative rRNA sequencing?

Answer 20

1. Amplification of gene encoding SSU rRNA
2. Sequencing of amplified gene
3. Analysis of sequence in reference to other sequences

Question 21

What is SSU rRNA?

Answer 21

Conserved and highly variable region, accumulates neutral mutations over time (genetic drift)
-Few ssu rRNA differences=closely related

Question 22

How do you sequence rRNA?

Answer 22

1. Sequence 16s rRNA (Isolate DNA, amplify by PCR)
2. Align sequences (take into acct. insertion/deletion)
3. Look for similarities, count up base changes
4. 5.

Question 23

True or false. Eukaryotic cells are chimeric.

Answer 23

True (formed from various parts)

Question 24

How do you sequence rRNA?

Answer 24

1. Sequence 16s rRNA (Isolate DNA, amplify by PCR)
2. Align sequences (take into acct. insertion/deletion)
3. Look for similarities, count up base changes
4. Construct phylogenetic tree

Question 25

How do you construct a phylogenetic tree?

Answer 25

``` (Branch length represents # of changes) (Nodes = common ancestor) 1. Align sequences 2. calculate difference graph from # of sequence differences 3. Construct forked tree ```

Question 26

What is the hypothesis of the endosybiotic origin of eukaryotes?

Answer 26

Mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell=primitive eukaryote

Question 27

What are the two different hypotheses on how eukaryotes gained mitochondria and chloroplasts?

Answer 27

1. Eukaryotes began as a nucleus bearing lineage that later acquired mitochondria & chloroplasts by endosymbiosis 2. Eukaryotic cells arose from intracellular association between a H2 producing bacterium (symbiot) and that later became a mitochondria. Host later developed nucleus

Question 28

What are filamentous actinobacteria? (Streptomyces)

Answer 28

- Filaments elongate from their ends and form branching hyphae - Cytoplasm separated by cross walls - produce desiccation resistant spores @ tip of sporophore when nutrients depleted

Question 29

What are predatory bacteria? (Bdellovibrio)

Answer 29

- Infect other bacterial cells, acquire nutrients from host | - doesn't grow on agar, gram + bact. not affected

Question 30

What are stalked bacteria? (Caulobacter)

Answer 30

- Found in aquatic environments - chemoorganotroph - undergoes unequal binary fission - sedentary stalked mother cell and motile flagellated daughter cell (swarmer cell)

Question 31

What are obligate intracellular bacteria? (Chlamydia)

Answer 31

- Parasites, grow only inside host cells - start as elementary body (infectious) - Host takes in elementary body thru phagocytosis - inside Host=reticulate body, non infectious - Reticulate body converts to elementary=lysis

Question 32

What is the polyphasic approach to taxonomy?

Answer 32

Phylogenetic analysis+phenotypic analysis+genotypic analysis

Question 33

What is multilocus sequence typing?

Answer 33

- Type of phylogenetic analysis - looks at housekeeping genes - sequence and align different housekeeping genes from same species - sufficient resolving power to distinguish between closely related strains - identify new strains this way

Question 34

How do you identify an unknown organism?

Answer 34

``` Look at: Morphology Biochemical properties 16s gene MLST ```

Question 35

What is a dichotomous key?

Answer 35

Graph that you can follow to see what characteristics an organism has: 1. Gram stain 2. glucose fermentation/morphology 3. Motile @ 37C? 4. Urea hydrolyzed? 5. Indole produced/citrate utilized

Question 36

What are 2 differential and selective methods to identify organisms?

Answer 36

Glucose fermentation and API strips

Question 37

How can glucose fermentation be used to identify an organism?

Answer 37

If organism can ferment glucose, media will change from red to yellow

Question 38

How can API strips be used to identify an organism?

Answer 38

Analytical profile index, fast identification through a series of small reaction tubes with indicators.

Question 39

What is serotyping?

Answer 39

Based on binding of specific antibody to surface structure | Antibodies recognize and bind to molc on surface of microorganism/secreted proteins

Question 40

What is a serotype?

Answer 40

Separate groups within a species that share similar characteristics (ie Same # of antigens on surface) - LPS: O serotypes - Capsule: K serotypes - Flagella: H serotypes