life history
- life evolved between 4.5-3.5 bya
- initial life was likely RNA based
- anaerobic metabolism evolved first
- aerobic metabolism evolved once O2 was present
- eukaryotes appeared 2.5-2 bya
- cyanobacteria lead to the accumulation of oxygen
- 2.4-2.7bya great oxidation event
endosymbiotic theory
- the eukaryote organelles mitochondria and chloroplasts are derived from bacteria
-phagocytosis by a protist like proto-eukaryote - development of symbiosis
- selection and genome reduction by microbe
- became an obligate relationship
- cyanobacterium gained protection from eukaryote - chloroplast
- organism lived inside another organism
prokaryote classification
phenetic classification - groups organisms together based on phenotypic similarity
- can reveal evolutionary relationships (not always correct)
-> individual characteristics are not weighed
- > best systems compare as many attributes as possible
phylogenetic classification - groups organisms based on evolutionary relationships
- based on direct comparison of genetic material and gene products
genetic classification - based on genetic similarity
polyphasic classification - uses combination of the 3 above (best one)
-> is used to determine genus and species of a newly discovered prokaryote
species definition for prokaryotes
- collection of strains that share many stable properties and differ significantly from other groups of strains
- genetic similarity have been defined in several ways
phylogenetic diversity
- study of evolutionary relationship among organisms
- analyzed based on genomes and specific genes
- 16s rRNA gene used to differentiate (highly conserved)
-> stems have more variability
-> loops is where rRNA molecules interacts with other (conserved)
molecular methods for classification
- FAME - lipids analysis
- MALDI-TOF - proteins analysis
DNA based for genetic classification
- GC content
- DNA -DNA hybridization -> ANI analysis (AAI)
- SSU rRNA gene sequencing (16s)
- MLST -> SNP analysis to classify strain
-> single nucleotide polymorphisms
-> classify outbreaks
-> looks at specific sequence changes (small scale)
MALDI-TOF-MS advantages vs disadvantages
- newer method to identify microbes based on protein composition
advantages
- relatively low cost per sample
- little training required
- very quick
disadvantage
- high cost for instrument
- requires pure culture
- cant be used to identify non cultivatable microbes
- not reliable for mixed
- dependence on database, and presence of similar organisms in the database
16S rRNA analysis procedure
- amplify gene
- purify using universal primers
- analyze on agarose gel
- DNA sequence PCR product
- compare and align sequence data
- does rely on database - if microbe not well known might not be identified
- need pure culture, if contaminated = not accurate
how do the molecular methods compare
- cost of sequencing whole genomes is going down rapidly bit is still not accessible to everyone
-> also requires a database for comparison - 16S rRNA gene lacks resolution at species/strain level
- important in phylogeny
- %G+C and DNA hybridization are more useful at species/ subspecies level
family - genus -species- subspecies- strain
why phylogenetic and phenetic don’t always match
gene loss
-> a trait present in a common ancestor of several lineages is lost in some but retained in others due to loss of genetic info related to the trait
convergent evolution
-> independent evolution of the same trait in 2 unrelated lineages, the genes encoding the trait are usually dissimilar
horizontal gene transfer
-> genes encoding a specific trait are transferred between 2 unrelated lineages, the genes encoding the trait share evolutionary history
