chapter 12 Brock

Question 1

core genome

Answer 1

those genes found in common in all the genomes of all strains of a species - useful because microbial genomes are dynamic: genome size and gene content can vary considerably between strains of a species.

Question 2

DNA-DNA hybridization

Answer 2

the experimental determination of genomic similarity by measuring the extent of hybridization of DNA from one organism with that of another

Question 3

domain

Answer 3

in a taxonomic sense, the highest level of biological classification

Question 4

endosymbiotic hypothesis

Answer 4

a chemoorganotrophic bacterium and a cyanobacterium were stably incorporated into another cell type to give rise, respectively, to the mitochondria and chloroplasts of modern-day eukaryotes.

Question 5

evolution

Answer 5

a change in allele frequencies over time with new alleles arising due to mutation and recombination

Question 6

FAME - each peak from the gas chromatograph is due to one particular fatty acid methyl ester, and the peak height is proportional to the amount

Answer 6

fatty acid methyl ester - a technique for identifying microorganisms by their fatty acids - more than 200 structurally distinct fatty acids from bacterial sources are known. A methyl ester contains a methyl group in place of the proton on the carboxylic acid group of the fatty acid.

Question 7

fitness

Answer 7

the capacity of an organism to survive and reproduce compared to that of competing organisms

Question 8

genetic drift

Answer 8

a process that results in a change in allele frequencies in a population as a result of random changes in the number of offspring from each individual over time

Question 9

some phenotypic characteristics of taxonomic value
(Taxonomic methods in systematics)

systematics - the study of the diversity and relationships of living organisms.

Answer 9

morphology;
motility;
metabolism;
physiology;
cell lipid chemistry;
cell wall chemistry;
other traits

Question 10

Classification by phenotype - morphology

Answer 10

colony morphology;
Gram reaction;
cell size and shape;
pattern of flagellation;
presence of spores, inclusion bodies (eg PHB, glycogen or polyphosphate granules, gas vesicles, magnetosomes);
capsules, S-layers or slime layers;
stalks or appendages;
fruiting-body formation.

Question 11

Classification by phenotype - motility

Answer 11

Nonmotile;
gliding motility;
swimming (flagellar) motility;
swarming;
motile by gas vesicles

Question 12

Classification by phenotype - metabolism

Answer 12

mechanism of energy conservation (phototroph, chemoorganotroph, chemolithotroph);
utilisation of individual C, N or S compounds;
fermentation of sugars;
nitrogen fixation;
growth factor requirements.

Question 13

Classification by phenotype - physiology

Answer 13

Temperature, pH and salt ranges for growth;
response to oxygen (aerobic, facultative, anaerobic);
presence of catalase or oxidase;
production of extracellular enzymes.

Question 14

Classification by phenotype - cell lipid chemistry

Answer 14

Fatty acids;
polar lipids;
respiratory quinones.

Question 15

Classification by phenotype - cell wall chemistry

Answer 15

Presence or absence of peptidoglycan;
amino acid composition of cross-links;
presence or absence of cross-link interbridge.

Question 16

Classification by phenotype - other traits not mentioned…

Answer 16

pigments;
luminescence;
antibiotic sensitivity;
serotype;
production of unique compounds, eg antibiotics

Question 17

Taxonomic methods in systematics:

Gene sequence analysis

Answer 17

Gene sequence analysis: 16S rRNA gene tree but better resolution from multigene analysis eg 16S rRNA gene and highly conserved genes eg recA and gyrB - good for distinguishing bacteria at species level - how? The DNA sequences of protein-encoding genes accumulate mutations more rapidly than rRNA genes.

Question 18

Taxonomic methods in systematics;

Multilocus sequence typing

Answer 18

MLST is a method in which several different ‘housekeeping’ gense from several related organisms are sequenced and the sequences used collectivley to distinguish the organisms. Housekeeping genes encode essential function in cells - always found on chromosome not plasmids.
First, isolate DNA, amplify 6-7 target genes, sequence, analyse alleles, compare with other strains and generate tree (dendrogram).
V. good for distinguishing between v. closely related strains of a given spp. but not useful for comparing organisms above the spp. level - resolution is too sensitive.

Question 19

Taxonomic methods in systematics:

Genome Fingerprinting

Answer 19

A rapid approach for evaluation polymorphisms between strains. Might be fragments of DNA generated from individual genes or whole genomes
Ribotyping is a method of genome fingerprinting based on the locatlisation of SSU rRNA genes on genome fragments - the number of rRNA operons present in a microbial genome is a conserved feature of all strains of a species - can be 1-15.

Question 20

Taxonomic methods in systematics:

Multigene and whole genome analyses

Answer 20

Increasingly affordable and practicable.
Shared orthologs (homologous genes with same function) can be aligned and phylogenetically examined and average nucleotide identity of genes determined.