Geomicrobiology
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
Grading
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Crib Sheets
Discussion participation
Mid term exam
Final Exam
Poster
20%
20%
20%
20%
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
diameter
• 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
Microbes on the head of a pin, false color SEM images, from j. Rogers,
http://people.westminstercollege.edu/faculty/jrogers/V%20prokaryotes.ppt#298,3,Slide 3
0.5 µm
Figure 27.3 The most common shapes of prokaryotes
http://people.westminstercollege.edu/faculty/jrogers/V%20prokaryotes.ppt#298,3,Slide
Diversity
• 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
(Stromatolites)
• Evidence for microbial activity argued for
deposits > 3.7 g.a.
• Couple fossil evidence with genomic
information (analysis of function from genetic
info)
• Put against backdrop of early earth
conditions
– 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
identification
• 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
water
• 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
function
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?