lecture 6: microbial diversity Flashcards
evolution
the change in species or populations overtime
how did we go from one organism to the diversity we now have?
gradients, niches and speciation
gradients
= gradual changes in traits, environments, or conditions across space, time, or populations that influence evolutionary processes
- the world is full of gradients
- as microbes grow, they also create gradients
- gradients create diversity of habitats
- they are driven from the environment and by other microbes
- different traits are optimal for different conditions = diverse microbes across different species
niche
- combination of the roles that an organism plays
- role and position within an ecosystem including relationships with abiotic and biotic features
speciation
- the evolutionary process by which new biological species arise from a pre existing species, typically through reproductive isolation and genetic divergence
experimental evidence of evolution
Eg 1:
- single E.coli clone inoculated and grown in glucose limited media in a chemostat
- resulted in 3 clones with differences in maximum specific growth rates and in the uptake rates for different carbon sources, including glucose, acetate and glycerol
Eg 2:
- added cells to growth media
- over 80,000 generations
how do we measure diversity in microbial communities?
- metabolism = metabolic pathway
- function = types of processes and activities they can carry out
- taxonomy = determining which microbes are present and classifying them
classification of microbial diversity
- biological
- phenetic
- cladistic (phylogenetic)
biological classification system
group based on ability to breed and create fertile offspring
biological limitation
invalid for microbes because they reproduce asexually not sexually
phenetic classification system
- grouped based on overall physical similarity (analogous)
- no account of evolutionary history (measures the end product only)
phenetic limitation
- convergent evolution can lead to same phenotypes with no shared recent ancestry = liable to make errors
eg: goes through different pathways to get to the same phenotype
cladistic (phylogenetic) classification system
- grouping based on evolution from a shared ancestor (clade) as determined from a shared trait
- evolutionary history of groups of species can be deduced by comparing their nucleotide or amino acid sequences
cladistic (phylogenetic) limitations
liable to ignore useful descriptive traits by being too focused on one evolutionary trait or gene
molecular clock
a gene whose sequence (DNA or amino acid) can be used as a comparative temporal measure of evolutionary divergence
what gene is most commonly used as a molecular clock
16s rRNA gene (encodes the RNA sequence within the small subunit of the ribosome)
why is the 16S gene a good molecular clock?
- found in all living organisms
- maintains its function amongst all organisms
- highly conserved with multiple hypervariable regions (areas that can change overtime)
- sufficient length
three domains of life tree
- 3 domains instead of 5 kingdoms
- eubacteria, eukaryotes, archaebacteria
- archaea are distinct from eubacteria
- validated by different RNA polymerase structure in the three domains of life
- uses 16s rRNA
the two domain of life
- competing hypothesis for the origin of the eukaryotic host cell
- eocyte hypothesis (2) implies that the closest relative to eukaryotes is one, or all of the ‘TACK’ archaea
- suggests eukaryotes descended from archaea
- ‘TACK’ archaea and eukaryotes share genes not found in other archaea
2 domains = bacteria and archaea
current view of the tree of life
- total diversity represented by available sequenced genomes
- 92 bacterial phyla
- 26 archaeal phyla
- all five of the eukaryotic supergroups
what creates niches
gradients
