BISC209/S12: Assignment 209 BIOLOG

Assignment: Community Physiological Profiling of a Soil Community by Carbon Source Utilization
What to do with the DATA you have collected (A590nm) from your BIOLOG™ plate? Your group should have about a week and a half of daily measurements recorded on the Excel workbook we provided as a template. This template is pre-formatted for the calculations you will do from these data. It includes the formulas to average replicate measurements each day and it will automatically subtract the background (readings in the water wells). There is a normalization for background that will be subtracted automatically (this threshold absorbance is provided by the manufacturer and was determined to be 0.25 absorbance units for each carbon source). These calculations are the first step in figuring out what you can learn from these data that provides evidence for one or more of our investigative goals. You have been asked to calculate Community Metabolic Diversity (CMD). How does CMD provide evidence for functional metabolic diversity in your soil community? Clearly a quantitative evaluation of CMD is more meaningful in relationship to other soil communities or when compared to some standard or reference point. If you are only analyzing your soil community, what might be such a reference comparison to make this quantitative evidence meaningful? 

We ask you to calculate CMD, but that parameter is certainly not the only way to use the data collected for the information you seek. Keep in mind that CMD does not show the carbon source utilization pattern in your community. Is that something that would be useful to look at? How can you use the carbon utilization pattern you obtained to provide evidence that microorganisms in a community both compete and co-operate to fulfill metabolic needs of the community? Please think about additional or alternate ways to use your data to provide evidence for any of the questions we are exploring in this investigation. You should also keep in mind the limitations of this test in providing the answers you seek. Make sure to discuss (briefly) those limitations WITHOUT completely undermining all your reader's confidence that the data is pertinent to the issues you address. 

Calculating Community Metabolic Diversity (CMD) CMD is a simple way to represent the total number of substrates able to be effectively metabolized by the microbial community. It's a measure of diversity in use of carbon sources. CMD is calculated by summing the number of positive responses (wells with a positive A590nm value after all the corrections) at each incubation time. Any negative values are considered 0 absorbance. On your worksheet enter either a 0 or a 1. Zero indicates that there was a negative value or 0 for corrected A590nm. A 1 indicates a positive value of greater than zero. Once you have entered a 1 or a 0 as the "corrected" absorbance for all the cells, the template will calculate the CMD for that day. Complete the final CMD table on the next to the last page of the template workbook.

GRAPHING THE DATA: Please make figures from your data showing AMR, CMD, and Carbon Utilization patterns.

To graph AMR: You will plot your soil sample's AMR values on the y axis against time on the x to provide a quick comparison of metabolic response. 

To graph CMD: Plot the calculated soil sample's CMD values on the y axis versus time on the x to get a sense of community functional metabolic richness.

Showing Carbon source utilization patterning: Because CMD analysis does not provide information about the pattern of carbon substrates used in each soil community, you must think about a different way to display these complex data. You could plot on the y axis the A590nmabsorbance on the final day or on what appears to be the peak day of data collection versus the 31 different carbon sources on the x axis. Note that there is no such thing as negative absorbance; therefore, any negative values should be graphed as zero. Are there better ways to organize and display these data to make your main point. What is you main conclusion about diversity of microbial metabolism in your soil community? How can you show that most effectively?

