introduction to microbial diversity

timeline

• 400-200 BC: aristotle and theophrasus, history of animals

• 1674: antonnie van leeuwenhock, 1st observation of single cell using a microscope

• 1735: carl linnaeus, systema naturae

• 1866: ernst haeckel, 3 kingdoms

• 1937: edouard chatton, suggests to divide living organisms into 2 categories

• 1938: herbert copeland, 4 kingdoms

• 1959: robert whittaker, 5 kingdoms

• 1990: carl woese, 3 domains

genetic plassticity drives microbial diversity

• bacteria are often haploid, meaning that a mutation will be passed onto the next generation

• bacteria divide rapidly

• horizontal gene transfer- impacts the rate of evolution (different types: transformation, transduction and conjugation)

taxonomy

• the discipline that deals with the classification of organisms

• species are defined according to a taxonomic hierarchy

classification

• involves the definition of taxonomic subdivisions and names using a binomial nomenclature

morphology/ differential staining

• allows you to stain bacteria differently based on its composition

metabolic properties

inoculate all compartments with the same media and define the composition based on the change in colours

phage typing

• spread bacteria on agar plate and helps to distinguish which grow faster using phages

fatty acid profiles

• uses gas chromatography and compares patterns of peaks with database

phenotypic analysis

• morphology/ differential staining

• metabolic properties

• phage typing

• fatty acid profiles

• mass spectrometry

genotypic analysis

• DNA/ DNA hybridisation: cells can adapt to the environment

• fluorescence in situ hybridisation (FISH): taking a piece of DNA and label it and can see the population

• rDNA (16S) sequencing

• multi locus sequencing typing (MLST)/ fingerprinting

• whole genome sequencing

phylogeny

• studies evolutionary history of organisms

• evolutionary relationships are measures comparing DNA uses sequences called molecular clocks

• encoding conserved proteins with similar functions

• undergoing randoms and neutral mutations (steady states)

phylogenetic genes

• based on a comparative analysis of rRNA gene sequence

• some domains can have overlapping qualities