Lecture 2 Microbial Communities

Question 1

what are archaea

Answer 1

single celled prokaryotes which have no cell nucleus or organelles - most have never been studied in labs, only detected via analysis of nucleic acids in environmental samples

Question 2

where can archaean fossils be found

Answer 2

in stromatolites

Question 3

what is the theory of endosymbiosis

Answer 3

says that eukaryotic life evolved from archaea, and that organelles evolved from bacteria that prokaryotes engulfed, and subsequently had a symbiotic relationship

Question 4

what is the process of FISH (fluorescent in situ hybridisation)

Answer 4

DNA is labelled directly and indirectly
- directly : modified nucleotides with fluorophore
- indirectly: probes with modified with hapten
the labelled probe and target DNA are denatured, and combining of the two allow annealing of complimentary DNA sequences

for indirect labelling- extra step needed via use of enzymes to detect nonfluorescent hapten

Question 5

is directly labelling or indirect labelling quicker in FISH

Answer 5

direct is quicker but indirectly uses many layers of antibodies that give a brighter signal

Question 6

which two types of staining use nucleic acid probes

Answer 6

phylogenetic staining and FISH

Question 7

What can be detected via use of PCR

Answer 7

Beta lactamase gene (enzymatic drug modification)
- tetracycline resistance genes (efflux of drug, enzymatic drug modification

vancomycin resistance (target modification)

antibiotic resistance genes

Question 8

explain the community sampling approach of metagenomics

Answer 8

1. extract total community DNA
2. amplify a single gene i.e gene for 16S rRNA
3. sequence and generate tree
4. outcome is a single gene phylogenetic tree: gives a phylogenetic snapshot of most members of community + identification of novel phylotypes (new types)

Question 9

describe environmental genomic approach

Answer 9

1. extract total community DNA
2. restriction digest total DNA and then shotgun sequence, OR sequence directly using a high throughout DNA sequencer
3. assemble and annotation
4. outcome is a lot of partial genomes, where total gene pool of the community is discovered. can discover new genes, and can link genes to phylotypes

Question 10

metagenomics definition

Answer 10

analysis of DNA/ genetic sequences in a community where a representation of the DNA is provided

Question 11

metatranscriptomics

Answer 11

analyses sequences of total mRNA in a community - gene expressione

Question 12

metaproteomics

Answer 12

measures diversity and the abundance of different proteins in commuity

Question 13

metabolomics

Answer 13

measures diversity of molecules or compounds produced