EVSC 5230    Microbial Ecology   Spring 2012

HANDOUTS/ILLUSTRATIONS/ADDITIONAL RESOURCES

This page will contain links to handouts, etc. that are referred to in class. Most of the "overheads" will be placed here.  Items will be in the approximate order that they are used, or referred to, in class, and titles, etc. should be adequately descriptive to allow you to find the material you need.  A large number of the pages are Adobe PDF files, indicated as PDF. If you do not have the Adobe Acrobat Reader, go to www.adobe.com to obtain a free copy.

SUPPLEMENTAL PAPERS  I have placed a series of papers on this page. Some are required, some are not. Because several of the papers are protected by copyright, this page is closed to all except those within the .virginia.edu domain. If you are reading this page from home, and you are a member of the UVa community, go here to learn how to establish a proxy server setting or to use UVA Anywhere to allow access to the materials from off-grounds.

Introductory Material

• Introductory slides - first couple of lectures
• 5-Kingdom (old) phylogenetic tree  The Whittaker-Margulis model   PDF
• Phylogenetic tree based on rRNA  The "3 cell- domain model"   PDF

Energetics

• Fundamental trophic categories
• Energy and material flow in biological systems (aka the World's Greatest Diagram)
• NAD and ATP Diagrams of NAD and ATP molecules showing energy storage and electron transfer (PDF version)
• Carbon and Electron flow in respiration and fermentation - a drawing taken from Brock  PDF
• Energy yields  Amount of energy gained by microbes by oxidizing carbon with different electron acceptors and energy gained from oxidations by various chemoautotrophs.  PDF
• Glycolysis  The reaction sequence without molecular structure  PDF
• Glycolysis II The reaction sequence with the molecular structures PDF
• TCA  PDF
• ETS  PDF
• Amino Acid Structure Molecular structure of the 20 common amino acids  (PDF version)
• Banjo diagram - Glycolysis and TCA showing entry points for important molecules (PDF version)

Genetics

• PCR procedure   diagram showing the amplification process (PDF)
• DNA Sequencing a one page description of how base pair sequences are determined [OFF SITE]
• Community Fingerprinting  Analysis of a gel by hierarchical clustering (PDF)

Microbes in the Environment

• Seasonal distribution of bacteria and phytoplankton (from Overbeek)
• Vertical distribution of bacteria in Lake Pluss (from Overbeek) PDF

Molecular Approaches to Microbial Ecology (note: these pages are links off this site)

• You try it! DNA Workshop. Animated illustrations from PBS that illustrate very well the principles of DNA replication and protein synthesis. NOTE This page requires the Shockwave plug-in.  [OFF SITE]

• DNA Sequencing General information on how DNA sequences are determined - not detailed methods [OFF SITE]

• Gel Electrophoresis  A very basic presentation of the principles and processes that compose electrophoretic separation [OFF SITE]

Carbon Cycle

• Generalized view of the carbon cycle (adapted from Alexander) PDF
• Carbohydrate polymers  PDF
• A list of common cellulolytic organisms
• Structure of hemicellulose monomers  PDF
• Lignin - structure and breakdown  PDF

Nitrogen Cycle

• The complete set of N-cycle handouts and then some  PDF

Public Health

• A Global Decline in Microbiological Safety of Water: A Call for Action   Report from a colloquium of the American Academy of Microbiology (A large PDF file)
• Chuck Gerba Profile of a sanitary microbiologist (gif file) - Definitely worth reading!!!

Other Useful Links (things may just appear here as I find neat sites, tools, etc. for you to use.)

• MPN Calculator