Geomicrobiology

1. Geomicrobiology

2. 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

3. Grading • Crib Sheets 20% • Discussion participation 20% • Mid term exam 20% • Final Exam 20% • Poster 20%

4. 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

5. 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

6. 100 µm 20 µm 0.5 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

7. Figure 27.3 The most common shapes of prokaryotes http://people.westminstercollege.edu/faculty/jrogers/V%20prokaryotes.ppt#298,3,Slide

8. 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

9. 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)

10. Tree of life

11. 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

12. 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 ?

13. Tree of life

14. 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???

15. 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

16. 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?