==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). <BR><BR>Please write this as a discussion, which means that it should not be in discreet or bulleted points, but instead must be organized hierarchially. Be sure to organize information around a main idea and make specific main points using your experimental design and cited reference information. Start with a topic paragraph that, first, gets your reader interested in the context and significance of your semester long project: Investigating the Abundance and Richness and Community Behavior of Microorganisms in a Soil Community. Remember that information should move from broad to narrow. Don't end the topic paragraph without giving your reader a clear sense of what the rest of the discussion will address: culture techniques that 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. <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 the specific ingredients (or omission of common ingredient)that and how that formula 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 of a soil sample BEFORE microbes are cultured) that are important in selection.<BR><BR>
This discussion will require some outside research into culture media, soil community microorganisms in general, and
those microorganisms more specific to your habitat or particular eco-system or rhizosphere. Start doing research on the soil bacteria that we seek to isolate (endospore formers, nitrogen cyclers, and exoenzyme producers ) in culture this semester using many of the same tools and techniques of the fathers and mothers of microbiology. Look carefully at the recipes for the enrichment/selection media on which we have begun to culture bacteria from a 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.
Things to Consider When Using Selective or Enrichment Media" <BR>
<ul><li>What are the ingredients in the medium used or in the culture conditions imposed that allow a desired group of bacteria's growth restrictions or preferences (nutritional needs, concentration of oxygen, light, pH, temperature) to be exploited? Are there antibiotics or other ingredients that inhibit the growth of competitors?
<LI>What are sources of C,N,S, P (carbon, nitrogen, sulfur, phosphorus)in the
media? <BR> </LI></UL> <BR><BR>
It's fine to start with web based sources of general information such as Wikipedia but you should also
include scholarly sources. You must give credit to the discoverers of information that comes from research. Give this credit through in text citations to the original article where such findings were published. You will also need a References page with full citation information. In BISC209 we will use the Name/Year citation style of the journal ''Cell''. Attention to following EXACTLY this citation style is expected and required. The best way to make sure you are formatting your citations appropriately is to go the Wellesley library's electronic subscription to ''Cell'' and look at research articles' introduction section and References page and use those examples as models for how to format both in-text and full citations. <BR><BR>
Students are often confused about how to differentiate information that needs citation from "common knowledge" that does not require citation. Remember that "common knowledge" is NOT defined as "information that the average person knows". Common knowledge is information that is widely used and generally accepted. Sometimes it so old as to pre-date published citation or it may be so non-specific that it's impossible to be sure who made the original discovery. In general, information that is written without a reference citation in textbooks is common knowledge. You should not cite textbooks or other secondary sources like Wikipedia or internet sites that compile information. For more help in locating the source of information that needs citation, use introduction sections from published research on your topic or from relevant review articles. Remember that you must cite the original, published investigation, not the review article or secondary source that informed you about it.<BR><BR>
One of the focuses of the lab component of BISC209 is learning the structure of scientific writing through writing a scientific style research report on this semester long project. This is an ambitious goal and it could be overwhelmingly difficult without the series of skill-building assignments that we have designed. These weekly assignments are worth few points towards your overall lab grade, but they are crucially important in giving you practice and feedback on the structure of science writing and, specifically, on content aspects of your final paper. Please make sure that you follow directions and give sufficient time and attention to this and other graded assignments this semester. Your hard work during the semester should make your final paper much easier to write and should reward you with a more accomplished and successful final product.