Due prior to Lab 5. Please submit an electronic copy to your dropbox and bring a hard copy to class.
Your assignment is to create a results narrative with tables/figures from the data collected for your community metabolic diversity testing (carbon source utilization) and for co-operative behavior shown in exo-enzyme prevalence assays.
One of our main experimental questions is to investigate how the dizzying number of microbial members of a soil community work as a community: implying that individuals in this community must co-operate as well as compete for a viable niche. There is evidence in the literature that shows that soil community members are not unaware of the other microbes they live among. Does your data suggest that our soil community is interacting also? 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 metabolic diversity and co-operative behavior?
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? Would photos of the assay plates be useful or TMI? The goal is to provide visual information that allows your reader to see and compare the relevant processed data and understand the evidence for the conclusion(s) you describe in the narrative.
<LI< Conduct an ANOVA using JMP (or a statistical program familiar to you) on the 3 exoenzymes in your population. Be sure to incorporate the stats into your narrative results section in the appropriate fashion (see writing guide).
What to do with the DATA you have collected and processed (A590nm) from your BIOLOG™ plate?
- Measuring Community Metabolic diversity
Another way of measuring community metabolic diversity was in establishing a quantitative measurement of % carbon source utilization by exposing your soil extract to a variety of carbon sources. There were 31 carbon sources tested on your 96 well plate (remember there were replicates and controls)? Is this number likely to comprise the full range of carbon sources found in the habitat from which your soil community came? No, but the assay tests for wide variety of metabolic machinery needed to process a broad range of substrates. Therefore, this assay is evidence for answering one of your basic questions.
- 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.
The results narrative should be limited to conclusions that can be made to our experimental questions from the data you collected and present in accompanying figures/tables. You can make some conclusions about one soil community from this evidence about metabolic diversity and co-operative behavior using these exozyme prevalence data, but the place to apply these conclusions more broadly is not in results. A discussion of what differences might mean to the soil community or might say about the community would have to be conjecture on your part; therefore, save those ideas for the discussion section of your final paper when you can augment your conjectures with outside evidence from other studies.