MBIO 1010 Lecture 2

• First anaerobic life appeared between 3.8 and 3.9 billion years ago before this, anoxygenic phototrophic bacteria were the only life forms
• Earth is 4.6 billion years old
• Photosynthetic bacteria oxygenated the Earth about 2 billion years ago (origin of cyanobacteria), allowed the evolution of modern eukaryotic microorganisms
• First plants and animals appeared about 0.5 billion years ago
• LUCA

  Last Universal Common Ancestor
• Prokaryotes have 70S ribosomes, 16S SSU rRNA
• Eukaryotes have 80S ribosomes, 18S SSU rRNA
• rRNA genes change slowly over time
• SSU rRNA genes examines genetic differences rather than morphological differences
• Viruses don't have rRNA so we can't do this and therefore we can't determine their genetic variation
• Basic steps involved in sequencing rRNA genes

  Step 1. DNA is collected from a pure culture

  Step 2. Amplify (increase number of that section - the SSU rRNA gene) using PCR

  Step 3. The gene is sequence

  Step 4. Align with sequences of other organisms to figure out how similar or different they are by calculating by counting the number of differences and then you're able to plot them onto a phylogenetic tree
• PCR

  Used to make many identical copies of a short sequence of DNA (Like a photocopier)
• Phylogenetic trees are based on 16S or 18S ribosomal DNA sequences
• all organisms can be grouped into 3 distinct domains of life: Bacteria, Archaea and Eukarya
• Microorganisms are far more genetically diverse than plants and animals
• Fundamental unit of biological diversity are the species
• Phylogenetic species concept

  A group of strains that share certain diagnostic traits, are genetically cohesive and have a unique recent common ancestor
• Species of Bacteria and Archaea should have

  • Most (but not all) characteristics in common
  • Greater than 97% sequence similarity in the 16S rRNA gene (3% is where we can get strains)
  • High degree of genome similarity
  • DNA-DNA hybridization
  • In the very near future: whole genome sequences
• Microbiologists use Hierarchical classification

  • Groups of organisms are placed in successively larger groups
  • Species, genus and phylum are commonly used
  • order of taxon: Domain, phylum, class, order, family, genus, species, strain
• Nomenclature

  Binomial species names: Escherichia coli

  Genus (capitalized) Specific epithet (not capitalized)

  Strains can be identified by symbols after the species name

  E. coli K12
• Rules of nomenclature

  1. Names are latinized
  2. everything is italicized or underlined
  3. Genus capitalized, epithet is not
  4. Genus name may be abbreviated the second time it's used: E. coli
  5. Trivial names can be used, but do not follow these rules
• Who is the first to describe microbes?

  Robert Hooke
• Robert Hooke

  • Used a compound microscope - uses 2 lenses to magnify
  • Magnification up to 30x
  • Used it to observe
  • Cells in cork
  • Bread mold filaments - 1st microbe
  • beginning of cell theory - all living things are composed of cells
• First discovery of bacteria was by Antoni van Leeuwenhoek
• Antoni van Leeuwenhoek

  • Built microscopes that magnified specimen by 50-300x
  • observed single celled microorganisms - called them animalcules
• Louis Pasteur

  • Studied beer and wine production
  • Yeasts convert sugar to alcohol in the absence of oxygen - Fermentation (life without air)
  • Bacteria can sour wine by converting alcohols to acid
  • developed a method of gentle heating to kill unwanted bacteria - Pasteurization
• Biogenesis is when living organisms arise from other living organisms
• spontaneity is what was previously thought happens to organisms as they just appear out of thin air... literally
• sterile = no microbes
• Swan neck flasks

  • Prepared meat infusion inside of flask
  • boiled the infusion to sterilize it
  • As long as the flask remains upright, dust and microbes cannot enter and the infusion remains sterile - led to the development of methods for controlling the growth of microorganisms (aseptic techniques)
  • Dust and microorganisms trapped in bend
  • although we don't use swan neck tubes anymore, we still utilize the concept by using test tubes with loosely fitted caps allowing air in the same pathway as the swan neck