Lecture 6: Evolution of Microbial Diversity

Question 1

What is the root?

Answer 1

The last universal common ancestor (LUCA)

Question 2

What does LUCA stand for and what does it mean?

Answer 2

1) Last universal common ancestor
2) Last common ancestry of the 3 domains (bacteria, archaea, and eukarya)

Question 3

How do we know that Eukarya and Archaea had common ancestry at some point?

Answer 3

Eukarya and Archaea share key proteins

Question 4

What 3 things should be considered when looking into microbial genetic diversity?

Answer 4

1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms (mutations and gene transfer)

Question 5

Name 2 microbial mechanisms

Answer 5

1) Mutations
2) Gene transfer

Question 6

What is another word for anagenesis? What does it mean?

Answer 6

1) Genetic drift
2) Defined as small, random genetic changes that occur over generations

Question 7

What 3 things contribute to anagenesis?

Answer 7

1) Extremely fast microbial growth
2) Type of mutation
3) Selection pressure (adaptive mutation)
-ex: pH, oxygen, temp, etc

Question 8

Give 3 examples of selective pressures

Answer 8

pH, oxygen, temp

Question 9

Name 4 mechanisms of genetic variation

Answer 9

1) Gene mutation
2) Gene duplication
3) Gene loss
4) Recombination

Question 10

Name 2 models for evolutionary mechanisms of diversity and briefly describe them

Answer 10

1)Metapopulation model: Small changes (gradual)
2) Stable ecotype model: Rapid bursts of speciation

Question 11

1) Describe the metapopulation model of evolutionary mechanisms of diversity
2) What are the 3 ways niches of microbes can expand?

Answer 11

1) There are small changes in the environment along with small changes in the DNA of the organisms.
2) Patches (niches) of microbes can either expand:
a) Clonally
b) Heterogeneously
c) Migrate when nutrients wane
4) All local populations have a chance of extinction

Question 12

Describe the stable ecotype model of evolutionary mechanisms of genetic diversity

Answer 12

1) Members of microbial population undergo genetic changes
2) So they outcompete the rest, which means that the winners advance and losers go extinct.
3) Results in rapid bursts of speciation.

Question 13

Define ecotype

Answer 13

A population of microbes that’s genetically similar but ecologically distinct

Question 14

Define a core genome (most conserved). Any variation in this genome is based on what?

Answer 14

The set of genes found in all members of a species; any variation in this genome is mutation-based.

Question 15

Define pan-genome and name its 3 parts

Answer 15

1) The complete gene repertoire of taxon (all strains)
2) Core + ‘housekeeping’ + dispensable genes

Question 16

Describe the 3 parts that make up the pan-genome of a species

Answer 16

1) Core: needed genes
2) ‘Housekeeping” genes: genes needed for normal growth and metabolism
3) Dispensable genes: extra genes you don’t need (genes for flagella, virulence factor genes, etc)

Question 17

How is the pan-genome acquired?

Answer 17

By horizontal gene transfer (HGT)

Question 18

1) What does horizontal gene transfer require?
2) What is the rate of transfer like in HGT?
3) What is HGT associated with?

Answer 18

1) Horizontal gene transfer requires a heterogeneous population
2) The rate of transfer is extremely variable
3) Associated with rapid adaptation to new environments

Question 19

List and describe the 3 methods of horizontal gene transfer (HGT)

Answer 19

1) Conjugation: Physical connection between bacteria mediates transfer
2) Transformation: Uptake of naked DNA from the environment
3) Transduction: Viral transfer of DNA into bacteria

Question 20

What 3 things is horizontal gene transfer important for?

Answer 20

1) Evolution
2) Adaptation
3) Pathogenicity

Question 21

What 3 things can result from horizontal gene transfer (HGT)?

Answer 21

Gene acquisition, plasmid acquisition, phage infection

Question 22

Describe the importance of Bergey’s Manual of Systematic Bacteriology

Answer 22

1) Contains descriptions of all known bacterial and archaeal species
2) An extremely valuable reference for microbiologists