Microbio Phylogeny & Diversity

Early Earth was….

anoxic and exclusively anaerobic - chemolithotrophic metabolism

Anaerobic metabolism

obtain carbon from CO2 then obtain energy from H2

Prebiotic Events

prebiotic chemistry: bio building blocks

RNA world: self replicating RNA

protein synthesis: RNA translation

DNA: replication and transcription

lipid bilayers: cellular compartments, high rates horizontal gene transfer

divergence: bacteria and archaea diverge from LUCA

Consequences of Photosynthesis

cyanobacteria were the first to produce oxygen and shift to oxic atmosphere

O2 converts to O3 ozone which absorbs UV radiation from the sun

Oxic atmosphere let to new metabolic pathways that yileded more energy

Consequences of Ozone

UV radiation is super damaging so less UV meant organisms were able to inhabit terrestrial habitats and leave the subsurface and oceans

Endosymbiosis

origins or eukaryotic cells as mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell

Evolution is

a change in allele frequencies in a population over time

Mutations can be

neutral, deleterious, or beneficial

Mutations result from

substitution, deletions, insertions, and duplications

Recombination

segments of DNA snap off and rejoin to create new combinations

Phylogeny is inferred

indirectly from nucleotide sequence data

Molecular clock / chronometers

certain genes and proteins are measures of evolutionary change

rate at which a locus accumulates mutations

Molecular clock assumes

nucleotide changes occur at a constant rate, usually neutral, and random (no they are not)

Most widely used molecular clocks

SSU rRNA genes or small subunit ribosomal RNA genes

SSU rRNA genes

16S rRNA in prokaryotes, mitochondria, and chloroplasts

18S rRNA in eukaryotes

funtionally constant, sufficiently conserved, and long

SSU rRNA genes drawbacks

not good for distinguishing between closely related species

Comparative rRNA sequencing

PCR amplification of SSU rRNA gene

sequencing of amplified gene

analysis in reference to other sequences

Phylogenetic Tree branch length represents

the number of changes that have occurred along that branch

16S rRNA gene sequences are used in

taxonomy and serve as gold standard for identification and description of new species, just need 3% new species and 5% new genus

16S rRNA drawback

lack of divergence is gene limits to poor resolution to species identity

Whole-genome sequence analyses

genome structure, size, number of chromosomes, gene content, and gene order

Phylogenetic diversity

evolutionary relationships between organisms

can be defined on the basis of either genes or organisms

commonly defined by ribosomal RNA phylogeny

Functional diversity

form and function as related to microbial physiology and ecology

ex: organisms not closely related but grouped together because they all eat nitrogen

Reasons why functional traits are seen in different species

gene loss, convergent evolution