==Assignment Due at the beginning Lab2: Discussion of Enrichment of Culturable Bacteria of Specific Groups==
Turn in at the beginning of Lab 2 a '''Discussion with References''' of how the culture techniques and media you will use will select and/or differentiate soil bacteria of the specific groups we seek. Explain how use of these media will allow us to isolate or differentiate microbes with particular metabolic or structural characteristics from other microbes in the community. You will find descriptions of all of the culture media we will use this semester and general information about the differences and definitions of categories of media in the Protocols section of the wiki in the section [http://www.openwetware.org/wiki/BISC209/S12:_Culture_Media Culture Media]. The media you should include in this discussion are: Simmons Citrate, Azotobacter, Glycerol Yeast Extract (GYE), PEA, EMB, Starch, Cellulose Congo Red, Pidovskaya medium (PVK)and Mannitol Nitrate Motility (MNM). To find out how and why we are using them, you will need to read all the background information about this semester's project and skim the protocols. Doing this will help you to do a good job on this assignment, but more importantly, reading ahead in the lab manual wiki will give you a better sense of the "big picture": how we will address our overall experimental questions with specific tools. <BR><BR>
Please write this as a discussion, which means that it should not be in discreet points, but instead must be organized around a main idea. You should organize your information in categories and cite reference information formally in a specific requested style (journal ''Cell''). Start with a topic paragraph that, first, gets your reader interested in the context and significance of the idea of using specific culture conditions and media to find and isolate specific types of bacteria from a source that contains a mind boggling number of other microorganisms. Remember that information in a discussion should move from broad to narrow and old to new and that you are writing for a reader who doesn't know anything about microbiology or about soil. Don't end the topic paragraph without giving your reader a clear sense of what the rest of the discussion will address: targeted culture to select/enrich for specific groups of culturable microorganisms and/or provide information about them that shows or differentiates their structure or metabolic capabilities as evidence for their ability to be co-operative or competitive members of a community. Start generally but include specific analysis of the media that you will use this semester. Why you are using it and how it works to accomplish your goals of elucidating structure and/or metabolic function in targeted bacteria. <BR><BR>
Be sure to incorporate into your discussion clear definitions and examples of general purpose, minimal, selective, differential, enrichment, and defined media. Include an explanation of how the presence or absence of specific ingredients or nutrients exploits some metabolic or physical characteristic common to the group of organisms that will grow on that medium. Include other culture conditions (such as culture in aerobic or anaerobic conditions or heat and dehydration) that are important in selection.<BR><BR>
This discussion will require some outside research into culture media, soil community microorganisms in general, and about the microorganisms that you seek or are likely to find. Among the soil bacteria that we seek to isolate are endospore formers, nitrogen cyclers, and exoenzyme producers. We will use many of the same tools and techniques invented by the fathers and mothers of microbiology. Look carefully at the recipes for the enrichment/selection media we will use to culture bacteria from our soil community. The use of specific types of media has been carefully thought out by your instructors to maximize the chance that you will culture bacteria from specific desired groups with the physical or metabolic characteristics that we seek.