LECTURE 1 - MICROBIAL EVOLUTION

Phylogenetic Tree of Life labelled

Diagram.

Shows/proves what? 

BY Carl Woese with George Fox

Diverged bacteria and archaea.

Euk cells diverge from archaeal cells, evidence theory at one point archaeal diverge from bacteria etc?

If not animal fungi or plant, often just

Said to be protist. 

Has a list of all the phyla = phylogenetic tree

 

16S rRNA gene sequencing

 Endosymbiosis?

ne cell engulfs another leading to symbiotic relationship, benefits both organisms. = how prokaryotes gave rise to first eukaryotic cells. BY LYNN MARGULIS in 19060s

 stages/evolution of life on earth. (from 4.5bya)

Proof cyanobacteria responsible for production of oxygen

Stromatolites - IN AUSTRALIA/ SOUTH AFRICA. microbial mats from 2.5bya. Layers cyanobacteria cover w sedimentation. Cyanobacteria grow, metabolise the CO2, use for photo to fix the carbon from CO2.

SO pH increases = precipitation of calcium carbonate, w sediment

Layer cyanobacteria grow, cover w sedimentation, form new layer

 

DATE the bacteria inside the rock = see when occured

Prokaryotes main inhabitor for how long?

WHY microbes important?

From 1.6-4bya sole inhabitant of earth. = lots time to evolve/ diversify.

SO microbes improtant for earth survival/ major oxidation event/ formation rocks/ recycle of all elements- due to limited elements at beginning of earth. Elements needed to be recycled by microbes!!!

Microbes biomass on earth?

15% biomass on earth. (Water is 75%. Humans 0.01%)

 Hypothesis on the origin of cellular life? n.o 1

HYPOTHESIS 1:

• Submarine Mound Hypothesis

• First cells formed in hydrothermal vent, between tectonic plates.

• Form compartments, where chem reactions happened, protect from outside env.

• All elements needed for life (essential biomolecules) were present in this vent:

• Carbon provided by methan, cyanoxide?. Polysaccharide chain of hydrocarbon.

• Phosphate from hydrogen sulfate from waters

• Nitrogen from ammonium etc

• Phospholipid

• React w eachother to from a cell.

 

 Hypothesis on the origin of cellular life? n.o. 2

Why do we think genetic info

Start w RNA not DNA

• RNA more active. Due to extra oxygen/ hydroxyl group. And oxygen is very reactive

• FOR EXAMPLE Ribozyme born from RNA folding around other RNA molecules

STRUCTURE OF RIBOSOMES.

EUKARYOTIC vs PROKARYOTIC

 

SSU = small SUBUNIT ribosomal RNA/ key for RNA molecule forming

PROKARYOTIC: 16S rRNA SSU

70S Ribosome size

EUKARYOTIC: 18S rRNA SSU

80S Ribosome size

Subunit role

For binding. / formation new amino acids

Fold into complex secondary/ tertiary struc w multiple domains. Domains facilitate mRNA decoding and tRNA positioning at ribosomal A P E sites for accurate TRANSLATION.

Which subunit rRNA Is used in

Phylogenetic studies? How?

16S rRNA. Due to being highly conserved between diff species bacteria/ archaea. ALSO:

• All cells have ribosome

• All perform same role, so evolution rate slow

• Ribosomal RNA conserved binding sites/ funct

How to identify bacteria?

 

• Isolate DNA

• Amplify 16S RNA gene

• Gel make sure amplify right product

• Sequencing

• Computer power, align all sequences from isolate

• Computer build distance matrix/ compare alignments = see differences in nucleotide

• SO COMPUTER builds phylogenetic tree.

In the example picture, 1 2 3 4 have common ancestors

Unrooted phylogenetic tree?

Shows relationship but not evolutionary path

 

Internal nodes represent?

Ancestors and where diverged into two entities

House keeping genes?

Important for function of cell to evolve very SLOWLY.

i.e. 16S rRNA

MLST?

Multiple housekeeping genes can be targeted to identify bacteria = MULTILOCUS SEQUENCE TYPING (MLST)

Shotgun Metagenomics?

Shotgun Metagenomics = instead of PCR, sequence whole genome = more information instead of just use 16S gene.

 

Genotypic classification?

Entire genome sequence, instead one gene.= longer analysis. More expensive. Not commonly used in diagnosis labs

Phenoytpic classification

• Used around the 19th century. Didn’t extract DNA/ PCR.

• Grow microbes on plate, classify based on morphology/ physiology/ biochemical/ metabolism = what sugar they eat. (Change of colour = metabolise that certain sugar.)

• Bergey's Manual of Systematic Bacteriology - published 1923. charactersie bact by observable traits.

How do we name Microbes?

Don’t

Keep

Ponds

Clean

Or

Frogs

Get

Sick

Write scientific name:

	Genus species