BISC209/S11: Assignment 209 Lab9

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Wellesley College-BISC 209 Microbiology -Spring 2011

Discussion and Graphical abstract:

See the definition for a graphical abstract and find examples from published research reports at | Pay particular attention to examples 1,4,5 and #15 (those that are less molecular and more topically ecological).

A graphical abstract is a visual representation of the main point of a research report. Because the graphical abstract you will compose for this homework assignment is a visualization of the main take home message of the paper you will write on this semester long project, you must be pretty clear about where you are going in your paper. It's time to think about the discussion section of your paper. You know the investigative goals of this project: how many microbes comprise your soil community; which ones are there; do they work as community? You can use the evidence you have collected from the work you have done to answer these experimental questions in the RESULTS SECTION of your paper. So what will you discuss in your discussion? The discussion section of a research report addresses one or more of the following general ideas: what's the larger context for the findings; why are the findings important; what other research helps explain the findings in this study; or have the authors been able to answer their basic questions or do they feel that there is some limitation to their ability to answer the question(s) completely?

Although you could go in any of these directions for your discussion, the direction we suggest is the last one. Do you think we (meaning not just you but ANY investigator in 2011) can know the full extent of the diversity and abundance of a soil community? To discuss this fully, bring in comparative studies on soil samples from other research that come up with similar or different number estimates using other methods to compare to your findings. Bring in both the technological advances as well as any limitations on our ability to know how much and what's there. This is the time to bring in some pyrosequencing studies that did high throughput sequencing and compare the diversity obtained through pyrosequencing to your random sampling of the bacteria by a different culture independent method. Take a look at the paper by Pexito and colleagues using the rpoB gene rather than the 16srRNA gene and include a comparison of other ways of determining phylogenetic diversity. Leave your reader with the sense that although the field has come along way from the recognition of the great plate count anomaly, there is always more to know and discover about the full range of abundance and richness in soil communities. Make this discussion POSITIVE. DO NOT TRASH YOUR METHODS OR YOUR FINDINGS!!!!!! Start your discussion with a summary of what you are sure of: that you do have conclusive evidence for mind-boggling abundance and significant phylogenetic and metabolic diversity in this soil community and that there is clear evidence for community behavior (co-operation and competition). Do not turn a discussion of the advances and limitations of technology in 2011 into a negative discussion about lack of confidence in your findings. This is NOT about "sources of error" but about where we are (we being science not Wellesley's BISC209 class) in being able to assess diversity and abundance and how soil communities work as communities.

Now that you have most of the evidence for answering your experimental questions and you know the direction of your discussion of those findings, you will be able to compose the basic structure of a graphical abstract. Although you have most of the test results that you will use to address our investigative goals, you don't yet have your evidence for phylogenetic diversity back from the sequencing facility. You won't make the "tree" that will be the main visualization of that important aspect of your findings until after we analyze the sequencing data in LAB 9, you may leave a place holder for such an image (if you want to use it in your graphical abstract) and indicate that you will add it later. As you consider possible visualizations of SOME of the data that make your main points, keep in mind that simplicity is important. Do not try to use everything. Do step back and stress the big picture. There is a folder in Resources in Sakai, called Images. Your instructor has uploaded images of the Wellesley Greenhouses including the Tropical room that you may use if you wish. NOTE that these images are available as an OPTION. It is not required to use them or even suggested that anything specific be part of your graphical abstract!

You may work alone or as a team on the graphical abstract assignment. You may submit it either individually or as one abstract for your soil sample group of three or four teamates.

Links to Labs

Lab 1
Lab 2
Lab 3
Lab 4
Lab 5
Lab 6
Lab 7
Lab 8
Lab 9
Lab 10
Lab 12