BISC209/S13: Assignment 209 Lab2

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Wellesley College-BISC 209 Microbiology -Spring 2013

Graded Assignment: Great Plate Count Anomaly

Due prior to Lab 3. Please submit an electronic copy to your dropbox and bring a hard copy to class.

This assignment will be incorporated into the Introduction section of your final paper.
Read over the Introduction to the Project page in the wiki to identify the topic and experimental questions addressed. Include the history of the "Great Plate Count Anomaly" (the disparity between enumerating culturable and unculturable soil community microorganisms). Two references that you need to skim for this assignment are:  : | THE UNCULTURED MICROBIAL MAJORITY. Rappe & Giovannoni. 2003. Annual Review of Microbiology. Vol. 57: 369-394. First published online as a Review available through the Wellesley College Library and | Uncultivated Microorganisms by Slava Epstein in Microbiology Monographs Vol. 10, 2009 DOI: 10.1007/978-3-540-85465-4 available as an e-book through Springerlink at the Wellesley College Library or as a pdf file in the Resources section of the lab Sakai site.

The Introduction section of a scientific research report has an expected structure. The writer must keep in mind that the target audience is not just your instructor, but it includes a general readership who needs to be convinced that reading this paper is a worthwhile use of time. The first few sentences must "sell" the importance of the broad topic and your research goals. The reader also expects to find out quickly, exactly what the paper is about. Remember that the story is about what shows up first; therefore, choose your first sentence and first words carefully. You should include "diversity and abundance of bacteria in a soil community" in this first sentence. It is helpful to read other introduction sections of published papers and to note "hyperbole" words in the first few sentences. They are there to heighten the sense of significance of the topic and of the investigation. Follow that model. Since information should move from broad to narrow, you should address the larger general topic before introducing your specific investigative goals. In our case, we will attempt experimentally to discover the abundance and richness of a microbial soil community and investigate some of the ways that a community of soil bacteria behaves like a community. We will also address, specifically and generally, how the community of microorganisms and individuals in it function cooperatively and competitively to exploit resources to maintain a niche and to provide resources that allow other community members to thrive. The first paragraph is called the topic paragraph; therefore, don't begin a new paragraph without fulfilling the reader's expectation to find out your topic and experimental goals before she or he reads further.

The rest of the introduction serves several functions, the most important of which is to get your general audience familiar with previous important findings that led you to want to attempt this investigation. This information should move from oldest to newest, or hierarchically by importance, with most important first. What are the previous findings that led to our understanding that microbial soil communities are much richer, more varied, and more complex than we previously recognized? How do we know that individual members of soil communities have crucial roles in maintaining the health and viability of the whole micro or macro-habitat? Part of that awakening of understanding of richness and abundance comes from the genomic age. We are now able to identify, quantify, and compare individuals and communities of microorganisms using their genes. We can assess evolutionary and functional relatedness using public databases of published gene sequences of identified species. We never knew what was really there in microbial soil communities until the advent of large scale identification of microbes through culture independent tools such as "next generation high throughput DNA sequencing" that allowed more than a glimpse at a skewed sample of members gleaned from traditional, labor-intensive culture techniques. Our investigation will not use all the molecular tools available today (no expensive high throughput sequencing sadly), but we will use chain termination (Sanger) gene sequencing and a public database to identify a few members of your soil community that you have selected and isolated in culture.

Background information includes specific, seminal findings published by previous investigators, therefor you must include properly formatted, in-text citations to give credit to these investigators. A references page with the full citation information is required. We are using the journal Cell's references-citation format. Model it exactly. Attention to detail matters. Students are often unsure where in the paragraph or sentence the (Name, year) citation goes. Look at other introduction sections of published research reports to get the feel for positioning citations properly. It is not acceptable to report several important findings in different sentences and have one citation at the end of the paragraph. The citation appears at the end of the sentence where you describe the finding or, if you have mentioned the investigators in the text, you put only the year in parenthesis directly after the investigators' names. If you go on, in the following sentence to mention more about that study of a different finding published in the same paper, write the sentence in such a way that it is clear to the reader than you are continuing to elaborate on the investigation just cited. Sometimes you may mention several findings in a single sentence, requiring more than one citation per sentence. In that case, each citation comes directly after the phrase that mentions that investigator's contribution. Try not to cite authors of review articles; instead, site the original investigators. Your goal is to give credit to the team or person who made important breakthroughs rather than the author of the review article where you learned about the history of investigations in a topic. Sometimes you will see review articles cited as (Blah, 2010 review) to differentiate discoverer and reporter but, where possible, give credit to those who did the original work when you site a contribution to the field.

Sometimes introductions end with a summary of the investigative findings and conclusions. More commonly, and in this assignment, your introduction to the Great Plate Anomaly should end with a GENERAL overview of the relevant experimental design that will address this concept in our work. No methods detail should be included, but you reader wants to know how you will experimentally achieve your investigative goals. Satisfy that curiosity without overwhelming the reader with too much information. The schematic on the Introduction to the Project page provides a brief, hierarchial, narrative description of our semester's work.

The Lab WIKI will provide you with links or pdf files of some published research reports and review articles on your general topic. You may use these references or find your own as models of how to structure an introduction and where and when to cite. As always, see your instructor for guidance if you have questions or problems. Good luck.