L9: Microbial Diversity

Question 1

Translate the central dogma into microbial ecology

Answer 1

DNA => RNA => protein
genetics => physiology => ecological niche => genetics

Question 2

What is an ecological niche what does it lead to, what happens

Answer 2

site of competition and change in conditions of natural selection = microbial evolution
*mutants evolve to the point where they are no longer same species leading to microbial diversity

Question 3

What is a species, describe their genome

Answer 3

organisms that are able to interbreed and produce a fertile offspring

*genome is different than parents because of meiosis

Question 4

How is the species concept adopted to fit bacterial and archeal species

Answer 4

• no affirmative definition
  *individuals are clones not because of sex
  *not limited to members of same species

Question 5

What does bacterial sex involve

Answer 5

1. tranformation with naked DNA
   2.transfection/transduction using a virus
2. conjugation with sex pilus

Question 6

What does bacterial and archeal species systematics break down into

Answer 6

1. Classical bacterial taxonomy
2. DNA-DNA hybdrisation
3. 16S rRNA sequence comparisions
4. Polyphasic taxonomy and new species
5. Whole genome sequencing

1 CD P W (1cldpropWe)

Question 7

What is involved in classical bacterial taxonomy,tests?

Answer 7

aka determinitive bacteriology defined by pyysiological and cytological tests for classifications purposes

species are defined by phenotypic clustering

eg:
1.gram stains
2. biochemical tests
3. serological antibodies
4. phage typing

Question 8

What is DNA DNA hybridization

Answer 8

calculate the homology between two organisms by comparing the melting points of pure vs hybrid cultures

*correlate melting temperatures with homology, less homology less tightly duplex will bind and make a lower melting temp of hybrid

*minimum 70% homolgy but some species are very similar like Brucella

Question 9

What is 16S rRNA sequence comparisons, requirements

Answer 9

*minimum 98.7% identity
*can distinguish species but better for higher level classifications
*can’t just use environmental sample, must use sequence from cell could be Chimera, requiring a pure culture
[PCR can also amplify chimeras]

Question 10

Compare DDH and 16S rRNA

Answer 10

• different minimum standard for species determiniation >98.7% vs 70%
  *no intraspecies below the requirements
  *some interspecies have 100% for both

Question 11

What are polyphasic taxonomy and new species

Answer 11

*combination of molecular and classicial determinitive data to characterise isolated strains from pure cultures
*used in Bergeys Manual of systematic Bacteriology
*even after molecular tests must do polyphasic approach and accepted into International Jounral of Systematic and Evolutionary Microbiology

Question 12

What are required polyphasic taxonomy tests

Answer 12

*Urea Test
*Gram Stain
*Growth rate

Question 13

What is whole genome sequencing, support

Answer 13

compare 50-500 genes via amino acid idenity and average nucleotide identity
supported by correlation between 16S and AAI identities

Question 14

What genes to compare in whole genome sequencing

Answer 14

• DNA polymerase, 16S rRNA, other homologous genes

Question 15

What is the current state of bacterial diversity

Answer 15

*number of phyla increases as new discoveies are made with many canidate phyla with no cultures epcies
*hard to estimate number of phyla.