Writing Assignment

Directions: The goal of this writing assignment is to compare genetic biodiversity of your designated plant (either Lemonadeberry or California sage), in two soil samples (Marsh vs. Coastal soil). Specifically, we asked: Does phylum abundance and Shannon diversity differ between the soil samples? And therefore, are the soil samples different in their genetic diversity? Well use the class bacterial phyla data to determine the phylum abundance, richness, evenness, and Shannon diversity in the two soil samples. If the abundance of phyla and the Shannon diversity are different between the samples, then we can say the genetic diversity is probably different between the samples (and vice versa).

Your assignment will consist of six components that are explained in detail below: figure, evidence, conclusion, explanation, references and collaboration notes. The entire assignment should be no more than one page of written content (1.5-spaced, 1-inch margins, 12-point font), but its okay if you go a little over with figures, references, and collaboration notes. Please let us know if you have any questions.

Figure

The dataset that all groups will use is posted on CANVAS under the Week 10 module. In order to graph and analyze the dataset properly, look at the example dataset analysis posted on CANVAS. Follow along with the posted lab manual. These are the figures you’ll need:

1. A 100% stacked bar graph representing the distributions of the 10 most common bacterial phyla for both soil types
2. A single indices table showing richness, evenness, and Shannon diversity for both soil types
3. The PCoA plots (F24/F25 comparison, all quarters, seasonal)
4. The heatmap

Evidence

1. Describe the data in paragraph-form and state what samples are being examined.

2. For the stacked bar graph, make observations. For example, state which soil had more of certain bacterial phyla or less of certain bacterial phyla.

3. For the diversity indices table, state which soil type had more phyla richness, evenness, and Shannon diversity.

4. Read through the provided Microbiome Analysis of our sequenced data across a span of several quarters. Make observations about any patterns you might see for two of the three PCoA plots and the heatmap. Address the concept questions.

5. In your own words, what is the analysis showing you? Based on all these analyses, what are your thoughts regarding the microbial diversity in both soils?

6. This section should also include necessary interpretation to lead directly to the conclusion.

Hint: what do your results mean?

The bar graph tells you the proportion or abundance of different phyla between the soil types. For example, there is more of phylum X in one soil.

• The indices table (S, E, and H) tells you the richness, evenness, and overall Shannon diversity of phyla in the two soil types

Conclusion

Taking into account all your data including phylum abundance, Shannon diversity, the PCoA plots, and heatmap results propose an explanation for how plant species AND/OR soil site influence microbial community structure in the soil. Using the evidence, draw a conclusion that best addresses the research question. This section should also include an assessment of how confident you are of the conclusion based on the available evidence.

Explanation

The explanation should include a reasonable proposed mechanism for the results you found, this mechanism needs to be supported by peer-reviewed literature. This means you should not be guessing at the reasons behind your results, rather you should find research papers to back up and explain your findings. Think about what might have caused your results and then find a paper to back up your explanation. For this assignment, it means explaining why the soil of different native plants may have similar (if thats what you found) or different (if thats what you found):

1. Abundance of their top ranked phyla

2. Phylum Shannon diversity

You dont need to restrict yourself to literature sources that compared these two plant species specifically. Instead you could find papers that show differences or similarities in bacterial phyla, species, genes, etc. in soils under native and invasive plants in general. For example, if you find a paper that says bacterial species are different between native and invasive soil, that’s one piece of evidence that the phyla is different between native and invasive soil. Google scholar is your friend in order to read the whole article, make sure you are connected to the campus vpn if you are off campus.

Citations and references

For this assignment, identify and incorporate at least two peer-reviewed resources. Please include both in-text citations (where the information appears in the assignment) and references (at the end of the assignment). You may use any standard citation and reference format. For example:

In-text citation: “This invasive grass is a type of Bromus (Robertson et al. 2020)” Reference:Robertson R, Smith S, Gollakota L (2020) Invasive grasses affect soil pH concentration. Journal of Microbiology 45:90-99.

+0.5: in-text citation of peer-reviewed resource #1

+0.5: citation of peer-reviewed resource #1 in “Works Cited” section

+0.5: in-text citation of peer-reviewed resource #2

+0.5: citation of peer-reviewed resource #2 in “Works Cited” section

2 pts

Full Marks

1.5 pts

Developing

1 pts

Developing

0.5 pts

Not sufficient

0 pts

No Marks

2 pts

This criterion is linked to a Learning Outcome

Collaboration

Explain how the team collaborated on the assignment and describe how each member

contributed.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Explanation

included a reasonable proposed mechanism for the results found, supported by peer-reviewed literature.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Explanation

explained why the native plant and invasive plant soil may have similar (if thats what you found) or different (if thats what you found) abundance of top 10 phyla

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Explanation

explained why the native plant and invasive plant soil may have similar (if thats what you found) or different (if thats what you found) Phylum Shannon Diversity

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Figures

A 100% stacked bar graph representing the distributions of the 10 most common bacterial phyla for both soil types

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Figures

The PCoA plots

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Figures

A single indices table showing richness, evenness, and Shannon diversity for both soil types

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Conclusion

drew a conclusion that best addresses the research question

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Conclusion

assessment of how confident you are of the conclusion based on the available evidence

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

described the data in paragraph-form

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

Stated what samples are being examined.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

For the stacked bar graph, made observations. For example, stated which soil had more of certain bacterial phyla or less of certain bacterial phyla.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

Addressed the concept questions.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

Explained what the p-value means about the phyla abundance data.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

For the diversity indices table, stated which soil type had more phyla richness.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

For the diversity indices table, stated which soil type had more phyla evenness.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

For the diversity indices table, stated which soil type had more phyla Shannon diversity.

1 pts

Full Marks

0.5 pts

Developing

0 pts

No Marks

1 pts

This criterion is linked to a Learning Outcome

Evidence

Included necessary interpretation to lead directly to the

conclusion