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 Homeworks 20% Discussion participation 20% Mid term exam 20% Final Exam 20% Lab/Field Project and Paper 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

Why size is important Food, ‘air’, nutrients diffuse in and out of the cell  smaller size, faster these things move, faster metabolism, faster rate of division… How small can microbes get?  Minimum amount of material to have enough chemical diversity to support basic life functions 0.3 MBp, with cell around 170 mm

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

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