Lecture 1 - Microbiology Intro

Document Sample
Lecture 1 - Microbiology Intro Powered By Docstoc
                Course Goals
• At the end of this course you will be able to…
  – Intelligently converse with microbiologists, geologists,
    environmental scientists and engineers about the role
    microorganisms play in the cycling of elements
  – Use several techniques to identify and characterize
    microorganisms in any environment
  – Relate microbial physiology, genetics, cell structure,
    and metabolism to the effect, role, or signature that
    microbes uniquely imprint on their surroundings
•   Crib Sheets                20%
•   Discussion participation   20%
•   Mid term exam              20%
•   Final Exam                 20%
•   Poster                     20%
    Basic Microbiology Primer
• Microorganisms exist as single cells or cell
  clusters – almost all of them are invisible
  to the naked eye as individuals but can be
  readily seen as communities
• As opposed to most ‘higher order’ life om
  earth, microbes can eat and breathe
  things besides organic carbon and oxygen
   this makes them critical to cycling of
  compounds that are able to be oxidized or
  reduced in water
        Cell sizes and shape
• Most cells are between 0.1 and 5 mm in
• Several shapes are common:
  – Rod or bacilli
  – Spherical or cocci
  – Spiral
  – Other forms – including square, sheathed,
    stalked, filamentous, star, spindle, lobed,
    pleomorphic forms
      100 µm                                     20 µm                                   0.5 µm

         Microbes on the head of a pin, false color SEM images, from j. Rogers,,3,Slide 3
          Figure 27.3 The most common shapes of prokaryotes,3,Slide
• There are likely millions of different
  microbial species
• Scientists have identified and
  characterized ~10,000 of these
• Typical soils contain hundreds- thousands
  of different species
• Very extreme environments contain as
  little as a few different microbes
           Microbial evolution
• Oldest fossil evidence - ~3.5 g.a
• Evidence for microbial activity argued for
  deposits > 3.7 g.a.
• Couple fossil evidence with genomic
  information (analysis of function from genetic
• Put against backdrop of early earth
  – Significant atmospheric O2 after 2.0 g.a.
• Look at most ‘primitive’ microbes in selected
  environments (similar to early earth)
Tree of life
      Characterizing microbes
• Morphological and functional – what they
  look like and what they eat/breathe
  – Based primarily on culturing – grow microbes
    on specific media – trying to get ‘pure’ culture
• Genetic – Determine sequence of the DNA
  or RNA – only need a part of this for good
• Probes – Based on genetic info, design
  molecule to stick to the DNA/RNA and be
  visible in a microscope
• Classification of life forms:
  – Eukaryotic = Plants, animals, fungus, algae,
    and even protozoa
  – Prokaryotic = archaea and bacteria
• Living cells can:
  – Self-feed
  – Replicate (grow)
  – Differentiate (change in form/function)
  – Communicate
  – Evolve
  Can purely chemical systems do these things?
    All of these things? Why do we care to go
    through this ?
Tree of life
 New perspectives on ‘the tree of life’
• Recently suggested (Norm Pace, 2006) that the word
  prokaryote be thrown out – archea and bacteria are as
  different from one another as they are from eukayotes
• Most trees are constructed from 16S rRNA sections – 1500
  base pairs out of 1 million serves to decipher all differences
  – what about coding in other areas?? – starting to see
  distinct differences in exact 16S genotypes suggesting
  whole genome comparison needed – problem is that
  currently requires cultures for most samples
• Strain level differences – how do we decide what is really in
  the same species yet may be slightly different – how do we
  do this for eukaryotic organisms? How might we do this for
  archaea and bacteria???
     Environmental limits on life
• Liquid H2O – life as we know it requires liquid
• Redox gradient – conditions which limit this?
• Range of conditions for prokaryotes much
  more than that of eukaryotes – inactive stasis
• Spores can take a lot of abuse and last very
  long times
• Tougher living = less diversity
     • Closer to the limits of life – Fewer microbes able to
Microbes and Thermodynamics
• First and foremost, the basic tenet relating
  microbial activity with thermodynamic
  descriptions of physical and chemical
  systems is:
           Equilibrium = Death
• Why then are microbes on seemingly every
  corner of the planet’s surface? Why might
  we expect to find them on other planets?