DNA Sequencing

Method: Measured by extracting bacteria DNA from apple and peach soil. DNA (specifically the 16s gene) was then pipetted into an EcoPlate. DNA (16s gene) was sent to Nephele (the software program which was used for analyzing our results) where they performed PCR testing to evaluate our samples. We used Nephele to analyze our group's Paired-End Quality Control of Sequencing Results, as well as DADA2  and QIIME  pipelines.

The DNA was extracted from the soil by using by ZymoBIOMICS technology. The soil was vortexed with DI water and bashing beads. The DNA separated in the solution and was removed by a micropipette. The DNA was filtered many times and put through a vortex.

The 16s was isolated by separating the double helix using primer reverse and primer forward. When the double helix was separated you can read the DNA for sequecing.

The mapping file given by the TA (Ayomide) was used to analyze the Paired-End Quality Control by putting the mapping file into the Nephele system and determining if the data was of good quality. The DADA2 and QIIME mapping files were given to us by the TA (Ayomide). These files were put into the Nephele system and gave us biodiversity results.

Data Analysis

Evidence:

The difference between richness of apple and peach soil is not statistically different because the p-value calculated by the t-test is 0.67 which is higher than 0.05. The difference of evenness between apple and peach soil is not statistically different because the p-value calculated by the t-test is 0.20 which is higher than 0.05. The Shannon diversity index is not statistically different between apple soil and peach soil because the t-test value of 0.32 is higher than 0.05. This is consistent with the above data in Figure 1 because pH can affect the bacteria in the soil and apple and peach soil have statistically similar pH (Dupont, 2018).

Because the differences between our soil samples for condition one [apple] and condition two [peach] vary so little, we know that there is no unique data within our t-test or Shannon Diversity Index. We also know that the bacterial biodiversity within our samples is consistent to each other because our Shannon Diversity Indexes for condition one and two didn’t have a large difference and they were greater than 0.05. This means that the biodiversity is evenly spread through the soil of each, however their frequencies measure both samples to have a relatively low biodiversity due to their values being less than 1.0. The carbon utilization of both of our conditions were relative to each other because the carboxylic acids, amino acids, carbohydrates, polymers, and amines cycled through the same amount of carbon.

Conclusion:

Condition had lower richness concentration than the peach tree. However, this data is moderate, as there is no significant change between the richness values of our conditions. Condition 1 had a richness average of 29.625, while condition 2 has an average value of 29.375. This means that there is only a 0.25 difference. Based on these calculations, we can confidently conclude that this data is not unique. We are also able to conclude that the biodiversity is evenly spread throughout the samples. There is a relatively low biodiversity in both condition 1 and condition 2. We were able to conclude this piece of information by performing a t-test and Shannon Diversity Index and analyzing both values.

Explanation:

The average richness, evenness, and Shannon diversity of peach tree soil and apple tree soil is not statistically different. This could be due to the apple and peach tree being near each other. The apple and peach trees were both towards the edge of the garden and closer to the road. The condition of the soil was similar from each condition. Soil biodiversity is linked to soil pH (Wu et al., 2017). Since soil pH for apple and peach soil is not statistically different this could be an explanation as to why the soil biodiversity is not significantly different between apple and peach soil.