Microorganism taxonomy

Question 1

What method discovered recently has evolutionised taxonomic identificaion of bacteria?

Answer 1

Polymerase Chain Reaction

Question 2

Phenetic Species Concept

Answer 2

Concept of species as groups which members descend from common ancestor showing evidence of defining and derived traits inherited from common ancestor

Question 3

Issues with Phenetic Species Concept

Answer 3

Physiological features may vary with environmental change for microbes.
Homoplasy features
The concept has therefore caused underestimation of actual biodiversity of a microbial ecosystem.

Question 4

Homoplasy definition

Answer 4

Characters which 2 organisms have inherited which are similar/identical but did not inherit from a common ancestor.

Question 5

Homologous definition

Answer 5

Characters inherited from common ancestor

Question 6

Reference for Homoplasy and Homologous features

Answer 6

Wake, 2003

Question 7

Definition of Genospecies concept?

Answer 7

Species can produce fertile offspring and exchange genetic material=Species

Question 8

Issues with genospecies concept?

Answer 8

Microbes can exchange plasmids (containing genetic material) between different phyla. Hybrids exist between species (even in more complex larger organisms such as Anseriformes (Gonzalez et al. 2009).

Question 9

Definition of Genotypical Species Concept

Answer 9

Species/individuals which form genetic/morphological clusters (Mallet, 1995). Relates to DNA homology: Same SPP DNA HOMOLOGY: over 70%, Same genus: DNA HOMOLOGY: over 30%.

Question 10

Issues with genotypical species concept

Answer 10

Variations in the rule of DNA homology: need other definitions to determine a species.

Question 11

Reference for Dideoxy sequencing and definition?

Answer 11

Sanger et al. 1977.
The method of DNA sequencing based on selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during Vitro DNA replication (Sanger et al. 1977).

Question 12

One phylogenetic trait which separates organisms?

Answer 12

Metabolism (i.e. SRB in a different group to the methane reducing bacteria).

Question 13

How can you use 16S rRNA to tell how closely related organisms are from each other?

Answer 13

High degree of 16S rRNA homology may reflect recent separation between organisms-BUT doesn’t reflect genomic similarity.

Question 14

What are the primary issues with evolutionary research in microorganisms?

Answer 14

No fossil record
Variation in evolution speed for differet taxons in microbiology
Genetic transfer breaks rules for a number of species concepts-genospecies concepts

Question 15

Natural Species Concept

Answer 15

Species occupy similar phylogenetic traits but occupy different habitat-thermophiles have identical 16S rRNA composition but are different due to their temperature preference in Yellowstone hot springs.

Question 16

The method of identifying prokaryotes from environmental samples?

Answer 16

Insert DNA extracted from an environmental source into a Polymerase Chain Reaction sequence. This is a fast way to determine diversity/species richness of a microbial habitat (Wintzinerode et al. 1997).

Question 17

How do you separate genes in a polymerase chain reaction?

Answer 17

Use denaturing gradient gel for electrophoresis (Mayzer et al. 1993)

Question 18

How to clone a gene

Answer 18

Include gene in vector (E. coli cell) and allow to grow.