Lecture 5 cycles fall 2010

Lecture 5 cycles fall 2010 - Metagenomics How can we study...

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Metagenomics How can we study all the organisms in a sample without culturing them? Extract DNA. Using PCR, clone then sequence molecular phylogeny marker (i.e. 16S rRNA genes). Clone larger pieces of DNA directly from the environment and sequence.
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Metagenomic technique Harvest DNA from sample Shear DNA Clone into vector: Sequence many fragments Assemble with computer
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“Whole-genome shotgun sequencing” Venter’s group samples the Sargasso Sea in Bermuda Identified1800 species 148 previously unknown Venter et. al. Science 2 April 2004: Vol. 304. no. 5667, pp. 66 - 74 http://www.richardcorfield.com/pages/books/silent_landscape/ archives/silent_landscape_extracts_06.htm http://www.sargasso.com/cgi-bin/ccp51/cp-app.cgi?usr=51F499&rnd=19292
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Microbes and the global environment
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Microbes balance and maintain Earth’s environment Ubiquitous Abundant Metabolic diversity and power
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Everywhere and abundant 10 30 prokaryotes on earth Are we more microbe than human? There are more microbes in our intestines than human cells in our bodies A 10-g sample of soil contains more microbes than humans on the planet
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Microbes are able to squeeze every bit of energy from a chemical compound With a little help from their friends Community members scavenge reaction products which shifts the reaction equilibrium and makes it favorable i.e., butyrate-degrading bacteria when co-cultured with a methanogen can grow with a reaction that yields only -4.5 kilojoules per mole of free energy, takes 33 kilojoules per mole to convert ADP to ATP Squeeze and save Expel protons to create gradient sufficient to generate ATP
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Earth’s garbage disposals Degrade plants and animals; otherwise, carbon and bioelements would be sequestered and make life impossible
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Biogeochemical cycles Major bioelements Carbon, nitrogen, oxygen, sulfur, phosphorus Interconversions are in balance Total amounts of the various forms remain relatively constant Almost all cycles are comprised of oxidation and reduction reactions
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Carbon cycle methane Anaerobic sediments
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There are no naturally occurring organic compounds that cannot be broken down by microbes Some are slow to break down, like lignin-rich humus Man made compounds that are resistant to microbial attack are accumulating
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Lecture 5 cycles fall 2010 - Metagenomics How can we study...

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