BISC209/S13: Assignment 209 Lab1

Assignment Due at the beginning Lab2: Discussion of Enrichment of Culturable Bacteria of Specific Groups

Turn in at the beginning of Lab 2 an Analysis 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 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.

Please write this as a discussion, which means that it should not be in discreet bulleted 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.

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.

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.

Things to Consider When Using Selective or Enrichment Media"

• What are the ingredients in the medium used or in the culture conditions imposed that exploit a desired group of bacteria's growth restrictions or preferences (nutritional needs, concentration of oxygen, light, pH, temperature)? Are there ingredients that inhibit the growth of competitors?
• What are the sources of C,N,S, P (carbon, nitrogen, sulfur, phosphorus)? If these compounds are not found in a useable form in the medium or from the culture conditions or if the microbe doesn't have the metabolic capability to process available nutrients into a useable form, that microorganism will not thrive while those that can use or process these nutrients will.
  

It's fine to start with web based sources of general information such as Wikipedia and this wiki but you can't formally cite either. You will need to consult 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 and discussion section and References page and use those examples as models for how to format both in-text and full citations.

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.

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.

There is an extensive handout about writing each section of a scientific research report found in the Resources section of this wiki under "Guidelines to Scientific Writing" and other helpful information can be found in the Science Writing folder of the Resources tool in Sakai. In addition, please feel free to meet with your instructor to discuss any aspect of this or other assignments that is confusing to you. Struggling with scientific writing is expected and, unfortunately, necessary to achieve the proficiency desired; however, we do not want that struggle to turn into frustration. Please seek help from your instructor or from one of the Science Writing Peer-Mentors. More information on how to schedule a meeting with a writing tutor can be found at: http://www.wellesley.edu/Writing/Program/tutors.html. Good luck!

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10