Comparing the Bacteria Community Composition of Macatawa Watershed Samples

Introduction

In this assignment you will explore whether certain environmental variables explain some of the variation in the composition of bacterial communities in the Macatawa watershed. Some of the analysis is covered in Tutorial 9, and the first part of the assignment is to read that tutorial and run the code on HPC. You will not turn anything in from this part of the assignment.

The second part of the assignment is to do your own comparison of two groups of samples. The comparison you choose must be related to the questions/topics you are exploring in your final project. In fact, your group will present some of the plots and your analysis results from this assignment in your proposal presentation (PA2). These results may also be included in your final project presentation.

Meet with your project group to determine appropriate two-group comparisons. Each group member must do something different. For example, if you are exploring the relationship between phosphate levels and microbial communities, then you might define a new variable that indicates whether phosphate levels are “high” or “low” in a sample. You could compare the communities between “high” and “low” phosphate samples at lake sites in the summer, while another member of your group might make the same comparison but using lake samples from the winter. A third group member might look at stream sites. You should think carefully about choosing comparisons that will give you the most useful information for your project.

In the next assignment you will conduct an analysis of differential gene expression (DESeq2) that will help you to determine which specific taxa are different between the two groups. In that assignment you will compare the same two groups of samples that you are exploring in this assignment, so you will be learning even more about the questions/topics you are exploring in your final project.

Your two-group comparison

To compare the communities between your groups of samples you will write code similar to the code in the second analysis conducted in Tutorial 9 (with different groups of samples). Your analysis will involve conducting a PERMANOVA to compare communities between your two groups and PERMDISP to test for homogeneous dispersion between the groups (an assumption of the PERMANOVA), and you will create an NMDS plot that only shows the points relevant to your two-group comparison. You should use point shapes and colors to distinguish the groups.

You may need to create a new composite variable and do some filtering to reduce the data set so that it only includes points from your two groups. There is an example of this in Tutorial 9, but talk to an instructor or TA if you have trouble figuring out how to do this.

As usual, you should create a Quarto file to conduct your analyses. It should include a brief introduction, explanatory text for each code chunk, discussion of your statistical results and conclusions you can make based on the tests, and interpretation of your plot. As part of your conclusions based on your statistical analyses, discuss how the results of the PERMDISP test relate to the reliability of the PERMANOVA results. What are the conclusions you can make based on your PERMNAOVA and PERMDISP tests? Make sure you cite relevant statistics (p-values and \(R^2\) values) in your conclusions. For your interpretation, discuss whether your NMDS plot provides evidence of a difference in community composition between your two groups. Discuss whether the NMDS results are consistent with your statistical results (PERMANOVA and PERMDISP). How do your results relate to the questions/topics you are exploring in your final project?

What you need to turn in

For this assignment, you need to turn in 2 files:

• A Quarto (.qmd) file with your code and output and your introduction, explanatory text, conclusions, and interpretation
• The rendered report (.html) that was generated using the Quarto file you created