BISC209/F13: Assignment 209 BIOLOG: Difference between revisions
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Due prior to Lab 5. | Due prior to Lab 5. | ||
Your assignment is to create | Your assignment is to create the results section (including a narrative and tables/figures from the data collected for your community functional metabolic diversity testing [carbon source utilization] and in exo-enzyme prevalence assays) and the discussion section of a scientific research report.<BR> | ||
<BR> | <BR> | ||
One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community each finds a niche to survive and thrive. Our working hypothesis is that the microbial population must be highly diverse, particularly functionally diverse. We propose that they work as a community-- co-operating as well as competing for resources and space. There is evidence that soil community members are not unaware of the other microbes they live among. There is also evidence that bacteria sometimes aid other members of the community by secreting digestive enzymes into the environment that digest or process nutrients into a form usable by themselves and by members of the community that lack the ability to process those nutrients without help. Altruistic intent is hard to establish, but the result of metabolic diversity in community level exoenzyme prevalence is a community benefit: a richer, more diverse community means that not every member has to have the all the metabolic machinery to break down the wide variety of nutrients that may be available. | One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community each finds a niche to survive and thrive. Our working hypothesis is that the microbial population must be highly diverse, particularly functionally metabolically diverse. We propose that they work as a community-- co-operating as well as competing for resources and space. There is evidence that soil community members are not unaware of the other microbes they live among. There is also evidence that bacteria sometimes aid other members of the community by secreting digestive enzymes into the environment that digest or process nutrients into a form usable by themselves and by members of the community that lack the ability to process those nutrients without help. Altruistic intent is hard to establish, but the result of metabolic diversity in community level exoenzyme prevalence is a community benefit: a richer, more diverse community means that not every member has to have the all the metabolic machinery to break down the wide variety of nutrients that may be available. | ||
'''How can you effectively present our evidence for functional metabolic diversity and co-operative behavior among the microbes in the soil community?''' <BR> | '''How can you effectively present our evidence for functional metabolic diversity and co-operative behavior among the microbes in the soil community?''' <BR> | ||
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<UL> | <UL> | ||
<li>Be sure you calculate the prevalence (the percentage of microbes that can process each of the nutrients for which we tested compared to the total number detected in your assays). Compare those prevelances and think about what differences might suggest or mean. What is the best way to show these prevalence data in a table or in graphic form | <li>Be sure you calculate the prevalence (the percentage of microbes that can process each of the nutrients for which we tested compared to the total number detected in your assays). Compare those prevelances and think about what differences might suggest or mean. What is the best way to show these prevalence data in a table or in graphic form? The goal is to provide visual information that allows your reader to visualize easily the relevant processed data and understand the evidence for the main conclusion(s) you make in the narrative.</ul><BR> | ||
What to do with the DATA you have collected and processed (A<sub>590nm</sub>) from your BIOLOG™ plate?<BR> | What to do with the DATA you have collected and processed (A<sub>590nm</sub>) from your BIOLOG™ plate?<BR> | ||
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Because relative number of carbon sources used by a community does not provide information about the pattern of carbon substrates useable, you must think about a different way to display these complex data. For example, you could plot on the y axis the A<sub>590nm</sub> absorbance on the final day of testing or on the peak day of metabolic activity versus the 31 different carbon sources on the x axis. Should you arrange the substrates on the x axis in a different order than in the random order on the Biolog plate? Yes. What should be the criterion for an alternative organization? What arrangement of substrates would best show your reader your main point(s)? The main point you want to make from looking at the pattern of utilization is what? Note that there is no such thing as negative absorbance; therefore, any negative values should be graphed as zero. Are there other or better ways to organize and display these data to make your main point than the graph just described? What are your conclusions about soil community microbial metabolic diversity or about co-operation/competition? Your goal is to design a graph that visually shows those conclusions. | Because relative number of carbon sources used by a community does not provide information about the pattern of carbon substrates useable, you must think about a different way to display these complex data. For example, you could plot on the y axis the A<sub>590nm</sub> absorbance on the final day of testing or on the peak day of metabolic activity versus the 31 different carbon sources on the x axis. Should you arrange the substrates on the x axis in a different order than in the random order on the Biolog plate? Yes. What should be the criterion for an alternative organization? What arrangement of substrates would best show your reader your main point(s)? The main point you want to make from looking at the pattern of utilization is what? Note that there is no such thing as negative absorbance; therefore, any negative values should be graphed as zero. Are there other or better ways to organize and display these data to make your main point than the graph just described? What are your conclusions about soil community microbial metabolic diversity or about co-operation/competition? Your goal is to design a graph that visually shows those conclusions. | ||
</LI></UL> | </LI></UL> | ||
What is there to "discuss"<BR> | |||
Coming up with a quantitative measurement of diversity as CMD as a number and inferring great or little functional metabolic diversity from that measurement is difficult without comparisions to other microbial communities and a plausible reason for diversity based on evidence. There are many other tools that we could have used to measure functional metabolic diversity. In your discussion use outside sources to strengthen your conclusions, validate your tools or the converse. Remember that the discussion can't leave your data behind after the initial summary paragraph but must always be centered around your findings and use outside sources as a comparison. Don't trash your tools but help your reader understand their limitations if that's important. Always end with a concluding paragraph that sums up where your findings fit in the body of knowledge on our question(s). | |||
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Revision as of 04:56, 25 September 2013
Assignment:Evidence for Functional Metabolic Diversity in a Soil Community
Due prior to Lab 5.
Your assignment is to create the results section (including a narrative and tables/figures from the data collected for your community functional metabolic diversity testing [carbon source utilization] and in exo-enzyme prevalence assays) and the discussion section of a scientific research report.
One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community each finds a niche to survive and thrive. Our working hypothesis is that the microbial population must be highly diverse, particularly functionally metabolically diverse. We propose that they work as a community-- co-operating as well as competing for resources and space. There is evidence that soil community members are not unaware of the other microbes they live among. There is also evidence that bacteria sometimes aid other members of the community by secreting digestive enzymes into the environment that digest or process nutrients into a form usable by themselves and by members of the community that lack the ability to process those nutrients without help. Altruistic intent is hard to establish, but the result of metabolic diversity in community level exoenzyme prevalence is a community benefit: a richer, more diverse community means that not every member has to have the all the metabolic machinery to break down the wide variety of nutrients that may be available.
How can you effectively present our evidence for functional metabolic diversity and co-operative behavior among the microbes in the soil community?
What to do with the DATA you have collected from your community exoenzyme assays?
- Be sure you calculate the prevalence (the percentage of microbes that can process each of the nutrients for which we tested compared to the total number detected in your assays). Compare those prevelances and think about what differences might suggest or mean. What is the best way to show these prevalence data in a table or in graphic form? The goal is to provide visual information that allows your reader to visualize easily the relevant processed data and understand the evidence for the main conclusion(s) you make in the narrative.
What to do with the DATA you have collected and processed (A590nm) from your BIOLOG™ plate?
- Measuring Community Metabolic diversity
A quantitative measurement of metabolic diversity can be calculated from figuring out the proportion of carbon sources available (offered to your microbial community) that were useable by microbes in your soil. There were 31 carbon sources available on the 96 well plate (remember there were replicates and controls)? You calculated the proportion that were able to be used. Therefore, the closer the number is to 100%, (31) the more functionally diverse the community is. However, we are unlikely to have offered the community the full range of carbon sources found in your soil. That is a shortcoming in this measuring tool, but the 31 sources offered include a broad range of substrates. This assay is evidence for functional metabolic diversity but it has the shortcoming of not being a complete test. - Showing Carbon source utilization patterning:
Because relative number of carbon sources used by a community does not provide information about the pattern of carbon substrates useable, you must think about a different way to display these complex data. For example, you could plot on the y axis the A590nm absorbance on the final day of testing or on the peak day of metabolic activity versus the 31 different carbon sources on the x axis. Should you arrange the substrates on the x axis in a different order than in the random order on the Biolog plate? Yes. What should be the criterion for an alternative organization? What arrangement of substrates would best show your reader your main point(s)? The main point you want to make from looking at the pattern of utilization is what? Note that there is no such thing as negative absorbance; therefore, any negative values should be graphed as zero. Are there other or better ways to organize and display these data to make your main point than the graph just described? What are your conclusions about soil community microbial metabolic diversity or about co-operation/competition? Your goal is to design a graph that visually shows those conclusions.
What is there to "discuss"
Coming up with a quantitative measurement of diversity as CMD as a number and inferring great or little functional metabolic diversity from that measurement is difficult without comparisions to other microbial communities and a plausible reason for diversity based on evidence. There are many other tools that we could have used to measure functional metabolic diversity. In your discussion use outside sources to strengthen your conclusions, validate your tools or the converse. Remember that the discussion can't leave your data behind after the initial summary paragraph but must always be centered around your findings and use outside sources as a comparison. Don't trash your tools but help your reader understand their limitations if that's important. Always end with a concluding paragraph that sums up where your findings fit in the body of knowledge on our question(s).
