Microbial Biodiversity Analysis

Methods

The following depicts how we calculated each of the data for the following graphs: 

 Richness (S) = Number of the different carbon sources meeting the biological threshold of 0.25 for that condition. 

Shannon -  The more diverse the carbon sources being utilized by the community, the higher the H value. H is defined as: −1 X Σ [pi × ln(pi)]. 

Evenness - We can calculate Evenness (E) by removing the Richness (S) component from the Shannon Diversity Index (H). Specifically, to calculate E, divide H by ln(S). Note that ln(S) is the theoretically possible maximum value of H given a certain number of carbon sources in the system 

Carbon utilization - This calculation is used to determine the relative carbon source utilization efficiency (%). It is determined by taking the sum of carbon sources being used by bacteria for that specific carbon source group for that condition divided by the total carbon sources used by bacteria for that condition, then multiplied by 100 to convert to a percentage.  

Legend

An EcoPlate was used with a negative control and soil samples from the rain garden and non-rain garden to collect data about the bacteria types present in the samples.

 For figures 3A, 3B, and 3C, the average (mean) of each data set is represented by the X mark on the plots. The line dividing the boxes represents the median. The upper portion of each large rectangle represents the 3rd quartile range for each data set. The lower portion of the large rectangle represents the 1st quartile range for each data set. The upper whisker line represents the maximum value of each data set. The lower whisker line represents the minimum value of each data set. The inner points are used to identify any potential outliers between the box section of the plot, or they may be used to simply determine any differences between data sets. 

An unpaired t-test assuming unequal variance was used to determine the p-value for figures 3A, 3B, and 3C (3A p = 0.87, 3B p = 0.92, 3C p = 0.40) with a critical value of 0.05. For figure 3D, the relative utilization efficiency for different types of macromolecules was calculated using the EcoPlate Data. The graph represents the relative percentage of utilization efficiency for each of the macromolecules listed in both the rain garden and non-rain garden samples. 

Evidence

The mean for the Shannon Diversity index of our non-rain garden was 3.14, and 3.167 for our rain garden samples. We can see that the Shannon Diversity Index was slightly lower for our non-rain garden than our rain garden. The standard deviation for our Shannon Diversity Index of our non-rain garden and rain garden was 0.267 and 0.221 respectively. Our non-rain garden sample has a slightly higher variance (20.81% higher) in the Shannon Diversity Index than our rain garden sample. Our p-value for the Shannon Diversity Index was 0.87. Since this value is not less than 0.05, the difference in the diversity index between our samples is not significant. 

The mean for the Species Richness of our non-rain garden was 25.29, and 25.57 for our rain garden samples. We can see that the Species Richness was slightly higher for our rain garden (1.11%) than our non- rain garden. The standard deviation for our Species Richness of our non-rain garden and rain garden was 5.62 and 4.65 respectively. Our non-rain garden sample has a slightly higher variance (20.86%) in Species Richness than our rain garden sample. The p-value for our species richness was 0.92, and therefore the difference between samples in richness is not significant because the value is not less than 0.05. 

The averages for our Species Evenness for non-rain garden and rain garden, respectively were 0.979 and 0.984, while our standard deviations for non-rain garden and rain garden samples respectively were, 0.0125 and 0.0066. Our average for our rain garden was slightly higher (0.51%) than our non-rain garden sample and our standard deviation was much higher (88.39%) for our non-rain garden (than our rain garden. Our non-rain garden sample likely had more variance in the Species Evenness. Our p-value for evenness is 0.404, and since this is not less than 0.05, we can conclude that the difference between our samples is not significant for species evenness. 

For our carbon utilization efficiency graph, we can see that there were no amines present in our rain garden samples, whereas all four macromolecules that were tested were present in our non-rain garden samples. We can also see that amino acids, carbohydrates, and polymers were measured to be relatively the same in both compounds, but there were significantly more carboxylic acids present in our non-rain garden sample than our rain garden sample.

Conclusion

Primarily, we can conclude that there is no significant difference between the two species for Shannon Diversity Index according to the p-value for our data. The p-value is 0.87 for this data, showing that since it is not below 0.05 there is not a significant difference. We can be quite confident in our conclusion based on our calculations. 

Secondly, based on our evidence for the second chart, we can conclude that there is no significant difference between the species richness between the non-rain garden and the rain garden. By analyzing our p-value for the samples we can determine that since the value was 0.92 it is not below 0.05 therefore not showing any significant difference between the two sites. Based on our calculations we are able to be quite confident in our conclusion. 

For the third set of data we are able to be confident in our conclusion that there is no significant difference between the evenness of the two species based on the p-value being 0.404. Since this value is not below 0.05 we can be confident that there is no significant difference with the non-rain garden and rain garden. 

Finally, based on our data for the last graph we can be confident in our conclusion that for both samples we can see an equivalent amount of amino acids, carbohydrates, and polymers. We can also say confidently based on our data there are more carboxylic acids in our non-rain garden samples than that for the rain garden. To conclude, overall we are not able to see a clear or significant difference between our non-rain garden and rain garden samples.

Explanation

To further explain why there is no significant difference  between the two samples of soil, we can refer to the article (Zhang & Xu, 2017). For the data in the first graph we are measuring the different microbial communities with a combination of analysis of richness and evenness. This means that both of the sites are able to perform the same functional functions such as nutrient cycling, breaking down crop residues, or stimulating plant growth (Bell, 2021) because they contain the same types of bacteria and roughly the same number of the bacteria in each site, meaning the bacteria for the two sites are performing the same functions. 

For the data in the second graph, we are analyzing the richness, also known as the diversity of microorganisms in the soil (Coleman & Whitman, 2017). This means that with different types of microorganisms, some may be better at nitrogen fixation, phosphorus solubilization, or improvement of plant stress, for example (Bell, 2021). Though different types of microorganisms are useful, both of the samples had the same types of bacteria providing the same functions in both sites. 

The data in the last graph is analyzing the species evenness which is how abundant each species in the soil is, compared to the others (Wang & Ge, 2023). Having different abundances of species in our soil we are able to see how certain processes which take place in the soil such as those mentioned like nitrogen fixation, etc, will occur more often or with more efficiency based on the types of species present, though the same processes will take place in each sample due to there not being a significant difference between the two sites. 

With our final graph we are able to see there is an equal number of amino acids, carbohydrates and polymers for the two different species, meaning both of the samples have roughly the same amount of plant nutrition as amino acids source organic nitrogen for the plants (Cao & Ma, 2016). With all of our data, based on the p-values for each, we were able to determine there is no significant difference between the two species for any of the graphs showing both sites performed the same functions rather there being an advantage for either site in any of the analyses.