Question

Microbiology Tutorial - Phylogeny and Evolution

Answer 1

Note: This is a reference for educational/studying purposes, not a question, please save all comments or questions for the end.

Answer 2

\({\bf{Important~People}}\)

1923: Bergey publishes Manual of Determinative Bacteriology which gives species descriptions of bacteria
1977: Carl Woese: describes new kingdom Archaebacteria and determines that a universal phylogeny for bacteria is possible; bases on the semantide 16S rRNA

\({\bf{Phylogenetic~Trees}}\)

internal nodes: ancestor species
external nodes: species that still exist
branch length: evolutionary distance between species

monophyletic clade: includes ancestral species and all of its descendants (only valid calde)
paraphyletic clade: includes ancestral species but not all of its descendants
polyphyletic clade: includes ancestral species but also descendants of other ancestral species

\({\bf{Principle~of~Parsimony}}\)
cladogram with the fewest # of evolutionary changes is the accepted one

Answer 3

Predominant view of evolution: all organisms continue to evolve/diverge (contrast to the historical view that microbes were evolutionary dead-ends)

\({\bf{Species~Concept~(Prokaryotes)}}\)
- must have similar G/C molar content
- DNA must have 70% + reassociation

\({\bf{Endosymbiosis}}\)
- Mitochondria: derived from alpha purple bacteria
- Chloroplasts: derived from cyanobacteria

Answer 4

\({\bf{Archaea}}\)
- originally grouped w/ bacteria, determined to be distinct after Woese and Fox's research
- original ancestor proposed to be prokaryotic
- can assume a variety of shapes: spherical, rod, lobed, filamentous, rectangular
- single circular DNA
- no organelles
- may have flagella
- extremophiles
- methanogens
- have some similarities to eukarya: tRNA, ribosomes, TATA binding promoters, initiation/elongation factors, DNA polymerase
- phyletic groups:
crenarchaeota
euryarchaeota
korarychaeota
- membranes with ether linkages
- resistant to lysozyme; beta-lactam antibiotics
- no peptidoglycan in cell wall

Answer 5

\({\bf{Vocabulary}}\)
- microbiome: a microbial population characterized by a habitat and particular biochemical properties
- microbiota: the microorganisms that inhabit a particular habitat
- metagenome: the collective genome of a microbial population
- functional metagenomics: analytical method that seeks specific functions in the metagenome; metagenome is cloned into a vector then analyzed within a test microbe and screened for specific functions
- metabolome: total # of small metabolites in a microbial population

- prebiotic: nutrients that favor growth of microbes
- probiotic: microorganisms that confer benefits to host when consumed

- transcriptome: transcriptionally active genes of a microbiota

\({\bf{Classification~Units}}\)
- OTU (operational taxonomic unit): classification unit based on marker gene like 16S rRNA
- phylotype: classification unit based on comparing a query sequence to a given databse

Answer 6

probably going to add to this later

Answer 7

going to add a few blurbs about Lokiarchaota

-may be the origin of complex multicellular life
-monophyletic with eukarya
-small gtpases of Lokiarchaeota share sequence domains w/ eukaryotic gtpases
- has primiordial ESCRT complex (involved in complex vessicle transport which is associated with eukaryotes not prokaryotes)
- has eukaryotic signature proteins (ESPs)