A Comparison of Okra and Native Plant Soil Samples in Relation to pH, Moisture, and Function and Genetic Biodiversity of Bacteria 

By Giovanni Galacio and Yuan Yue

Purdue University

Urban gardens are essential for sustainable food production and green spaces in cities, but their success depends on soil health. By studying bacterial biodiversity, soil pH, and moisture content, we better understood their interaction and influence on plant growth. Soil pH, the "master soil variable" (Neina, 2019), affects key biological and chemical processes essential for plants. Understanding pH's impact on plants and microbes can guide effective regulation techniques for urban environments. Soil moisture directly impacts plant health and microbial activity. Urban gardens often face retention issues, but moisture supports microbial activity and heat evolution (Barros et al., 1995). Investigating moisture can enhance irrigation practices to retain soil moisture.

On the morning of September 4th, we traveled to the Lincoln Sharing Community Garden to collect soil from two conditions, Okra Plants and Native Plants. To collect the soil samples, we dug a soil corer 6 inches into both of the dig sites and collected 3 columns worth of soil from the Okra site and the Native Plant site. These samples were then put into Ziploc bags and stored in a freezer for use in lab.

Figure 1 displays the relationship between the pH of the soil samples compared to the type of soil. The data displayed in the graph is the combination of the measured pH levels of the soil samples. The range of pH for okra soil is 7.58-7.96. The range of pH for native plants is 7.48-8.20. Based on the class data, the average pH for okra soil and native plant soil is 7.78 and 7.87, respectively. The standard deviation for pH of okra soil and native plant soil is 0.13 and 0.30, respectively. When comparing the pH between the two conditions, an unpaired t-test was use through assuming unequal variance. P-value = 0.421. This shows that there is no significant difference in pH between okra and native plant soil because the p-value of 0.421 is significantly greater than 0.05.

We measured the pH of the soil by combing the soil sample with deionized water and used a pH meter to find the pH of the solution, telling us what the pH of the sample was.

Evidence: The data in the graph is that the average pH of the okra plant is 7.78, while the average pH of the native plant is 7.87. The difference between the two is 0.09 in pH, meaning that okra plants require more acidic soil. The standard deviation of the okra plant is 0.13, while the standard deviation of the native plant is 0.30. There is a difference of 0.17 in standard deviation which shows that the native plants can live in a larger range of pH soil compared to okra plants. To compare the data, we performed an unpaired t-test assuming unequal variance. The p-value of the data set is 0.421, which is greater than the critical value of 0.05, showing that there is no significant difference between the data sets. This shows that the pH of the samples is too similar to have a significant difference between them.

Conclusion: Condition 1 (okra soil site) and Condition 2 (native plant soil site) do not provide unique moisture content values. We are confident that there is no difference between the pH of the soil samples because the p-value is larger than the critical value, meaning that values collected were similar for the two conditions. Both average soil pH is similar with 7.78 and 7.87, meaning that if the two plants were put in the other plants soil, it would be able to survive. This is proven by the large p-value, meaning that there is not a large enough difference between the pH values of the soil samples. The bigger noticeable difference would be for the standard deviation which concludes that there is a greater variation of pH for native plants than okra. With slight differences in our group-specific data (0.22 in pH), lower differences in class average (0.09 in pH), and the high p-value of 0.421, we are confident that there is no unique moisture content provided from our two sample conditions.

Explanation: As found in the graph, the pH of the two soil samples is very similar, but the average pH of the okra sample was lower than the native plants. In an article by Oklahoma State University, it was found that okra plants are “tolerant of a wide range of soil pH but prefers soil with a pH between 6.0 and 6.8” (Brandenberger). This explains the lower average pH of the okra plants, while the okra plants also being tolerant to higher pH levels. This explains how it can thrive in pH levels of the sampled community garden which was almost 8. This would lead to a similarity in the garden, because the okra can survive in higher pH, which would lead to a similar pH in the garden, causing the miniscule difference in the pH levels of the samples.

Figure 2 measures the moisture content of the two conditions (okra and native plant). The range for the moisture levels of okra soil is 12.40%–24.69%. The range for the moisture levels of native plant soil is 13.40%–21.95%. Based on the class data, the average moisture content for okra soil and native plant soil is 17.91% and 17.67%, respectively. The standard deviation of the moisture content for okra soil and native plant soil is 0.0366 and 0.0281, respectively. To compare the data, an unpaired t-test was used through assuming unequal variance. P-value = 0.881. This shows that there is no significant difference in moisture content (%) because the p-value of 0.881 is significantly greater than 0.05.

We weighed approximately 1 gram of soil from the two conditions and then put it in the oven.  After all moisture was evaporated, the two conditions were weighed again, and the difference in weight showed the change in moisture. 

Evidence: The average soil moisture recorded from the okra site and native plant site were similar, with only a difference of 0.25 percentage points. The standard deviation for the class data was 0.0366 for the okra site and 0.0281 for the native plant site. This means there was more variation in soil moisture for okra sites, but ultimately the moisture contents were still very similar between the two locations. To compare the data, we performed an unpaired t-test assuming unequal variance and got a p-value of 0.881. Since the p-value of 0.881 is greater than a critical value of 0.05, there is no significant statistical difference in soil moisture content between the two conditions.

Conclusion: Condition 1 (okra soil site) and Condition 2 (native plant soil site) do not provide unique moisture content values. We are certain of this result based on our group-specific data and the overall class data, both having similar values collected for the two conditions. The only noticeable difference would be in standard deviation which concludes that there is a greater variation of moisture content for okra than native plants. With the slight differences in our group-specific data (2.55 percentage points), the lower differences in class average (0.25 percentage points), and the extremely high p-value of 0.881, we are confident that there is no unique moisture content provided from our two sampled conditions. 

Explanation: The significant similarity between the moisture content of the two different soil types (okra and native plants) can be explained by the climate during when the samples were taken. The time that the samples were taken was in the morning, where there was a higher dew point than later during the day. The presence of shade that covered parts of the sites also could have made a difference in soil moisture through water evaporation. From an article that drew the relationship between relative humidity and soil moisture, “soil water content of all the soils increased with increasing relative humidity” (Leelamanie). With a higher dew point during the morning and less time for evaporation, there would have been a higher relative humidity during the time that the samples were collected, leading to a higher soil moisture content. Another reason could be that the garden is watered every so often so both sites could have had the same amount of moisture added to the soil. Both options are possible reasons why the moisture content of both sites are so similar to each other.

Figure 3A: Displays Shannon diversity index (H) of functional biodiversity for okra and native plant soil. The average Shannon diversity index for okra and native plant soil is 3.378 and 3.376, respectively. The p-value of Figure 3A is 0.355. Figure 3B: Displays the richness (S) of functional biodiversity for both samples. The average richness of both the okra and native plant site is 30. The p-value of Figure 3B is 0.346. Figure 3C: Measures the evenness (E) of the functional biodiversity for the okra and native plant sites. The average evenness of the okra and native plant is 0.9932 and 0.9926. The p-value of figure 3C is 0.605. For Figures 3A, 3B, and 3C, n=8. Figure 3D: Displays the relative utilization efficiency of different carbon source in the two different soil conditions. In both conditions, the primary source of carbon is taken from carbohydrates, having a utilization efficiency of 33.33%. Both sites had the same utilization efficiency for all the other sources, with 26.67% carboxylic Acid, 20% amino acids, 13.33% polymers, and 6.67% amines. For Figure 3D, n=1

Figure 3 measures the functional biodiversity of organisms for condition 1 (okra site) and condition 2 (native plant site). In the experiment, we used EcoPlateTM plated with difference carbon sources to examine which are utilized by the microbial community. The wells of the plate would turn into different shades of purple based on the utilization of carbon sources. The change in absorbance is measured at 595 nm after a week of incubation. Data between the two conditions were compared through an unpaired t-test and assuming equal variance.

Evidence: The Shannon value index of the native plant site is 99.9% of the okra site, being only 0.0242 greater, meaning that they are very similar. This is also apparent in the t-test of the Shannon diversity index, which resulted in a p-value of a great than the critical value of 0.05, meaning that the okra and native plant site had nearly the same use of carbon sources found in the soil. The two soil conditions had the same richness values of 30. The p-value associated with richness was less than the critical value of 0.05, meaning that the measure of biodiversity in use of carbon sources in the okra and native plant soil are very similar. The evenness of the okra site is 0.9932, and the evenness of the native plant site is 0.9926, so there was 99.32% evenness in the okra site, and 99.26% evenness in the Native plant site, meaning that there was 0.06 percent point difference in evenness. The p-value for the evenness of the two sites is greater than the critical value, so this means that even though the evenness of the okra site was greater, there is not a significant difference in the data set. The two conditions had the same utilization efficiency for all the carbon sources. Every source was used the same amount, and there was no difference between what the plants preferred to get their carbon from. Both sites had the same utilization efficiency for all the sources, with 33.33% Carbohydrates, 26.67% Carboxylic Acid, 20% Amino Acids, 13.33% Polymers, and 6.67% Amines. 

Conclusion: We are certain that Condition 1 (okra soil site) and Condition 2 (native plant soil site) do not provide unique H, S, E in carbon sources utilized. We are certain of this result based on our group-specific data. The Shannon index values for carbon source utilization are similar between the okra site, with a value of 3.378, and the native plant site, with a value of 3.376. The difference in standard deviation is 0.0035. A p-value greater than 0.05 indicates no significant difference in biodiversity. Both sites have a richness of 30, meaning they utilize the same number of carbon sources, a p-value of 0.346, suggesting similar bacterial communities. Okra site has twice the standard deviation of native plants for evenness. The evenness values are very close to 1, with the okra site at 0.9932 and the native plant site at 0.9926, indicating that bacteria in both conditions process carbon sources in very similar ways. This is confirmed by a p-value of 0.605 and a minimal standard deviation difference of 0.0001. Overall, there is no significant difference in carbon processing or utilization efficiency between the two sites. Both conditions have the same utilization efficiency, showing that the functional biodiversity is the same. Bacteria from one site would function similarly if transferred to the other, requiring the same carbon concentrations. We are confident that the two conditions of soil do not differ in functional diversity.

Explanation: The similarity of the functional bacteria of the Okra Site and the Native Plant site is comparable to another experiment. While studying the difference between garden soil bacteria diversity and skin bacteria diversity, it was found that between garden bed the bacteria in each bed was “[b]acterial community composition was largely similar across different garden beds” (Mhuireach). With similar bacterial communities, an explanation would be given for the same utilization of carbon sources. This supports our findings because we found that across different garden beds and plants, the bacteria that was present in the conditions was similar due to the similar Shannon diversity index, richness, evenness, and breakup of carbon utilization. 

Figure 4A: Displays Shannon diversity index (H) of genetic biodiversity for condition 1 (okra site) and condition 2 (native plant site). The average Shannon diversity index for okra and native plant soil is 4.370 and 4.394, respectively. The p-value of Figure 3A is 0.802. Figure 4B: Displays the richness (S) of genetic biodiversity for both condition sites. The average richness of both the okra and native plant site is 118.5 and 125.75, respectively. The p-value of Figure 3B is 0.464. Figure 4C: Measures the evenness (E) of the okra and native plant site. The average evenness of the okra and native plant is 0.9161 and 0.9091. The p-value of figure 3C is 0.364. Figure 4D: Displays the relative genetic biodiversity frequency of taxonomic phyla for the four samples each for two conditions. In both conditions, the phylum of bacterium is the same with the primary phyla being proteobacteria. The four samples of okra soil have more consistent frequencies than the four samples of native plant soil. For Figure 4A, 4B, 4C, and 4D, n=4

Figure 4 measures the genetic biodiversity of condition 1 (okra site) and condition 2 (native plant site). We isolated and amplified the 16S rRNA gene, which is common in nearly all microorganisms. After PCR, the DNA fragments were run through gel electrophoresis where DNA bands were seen. Samples were also sent to Rush University where a more thorough DNA sequencing and PCR was inputted into a computer detection system for us to analyze; the data is used for figure 4. Data between the two conditions were compared through an unpaired t-test and assuming equal variance.

Evidence: The average of Shannon diversity index (H) between both conditions are similar, having a difference of 0.024. This means that the diversity of species in the two plant communities are similar. Both also have a similar standard deviation meaning that the diversity between the two conditions is within the same range. With a high p-value of 0.802 greater than a critical value of 0.05, there is no difference between the two genetic diversities of the conditions. The average of richness (S) is greater in okra, being 7.25 higher. The standard deviation of richness of native plants is greater than okra with a 2.980 difference. However, with a p-value of 0464, these differences are not significant and show that the number of different species present in the two soil sites are similar. The average of evenness of native plant and okra soil is extremely similar with only a difference of 0.0066. The standard deviation is both extremely small, meaning that there is no spread of abundance in biodiversity. The similarity is also proven with a p-value of 0.364, showing that there is no statistical difference between the evenness of both conditions. Figure 4D visually shows that both conditions have the same taxonomic phylum. The native plants had more consistent frequencies of bacterium phylum than okra. However, this does not mean that the difference between the phylum frequencies is significantly different.

Conclusion: We are certain that Condition 1 (okra soil site) and Condition 2 (native plant soil site) do not provide unique H, S, E phyla taxonomy values. We are certain of this result based on our group-specific data. With similar averages and low standard deviations, the three values analyzed do not differ from each other in range. This is also proven through the unpaired t-test using unequal variance. There is no statistically significant evidence between Shannon diversity index, richness, and evenness between okra and native plant soil because of the high values of 0.802, 0.464, 0.364, respectively. From the high p-values and figure 4D having no visual difference among the relative frequencies of bacterial diversity, we are confident that the two conditions of soil do not differ in genetic diversity.

Explanation: The significant similarity between the genetic diversity of the two different soil types (okra and native plants) can be explained by the limiting factors that contribute to bacterial diversity in soil. According to the article, “The diversity and biogeography of soil bacterial communities,” “soil pH was the best predictor of bacterial richness and diversity, it was also the strongest predictor of overall community composition” (Fierer). As concluded from Figure 1, there was no significant statistical difference in proving that the soil pH of both conditions was different. Therefore, the pH similarity would explain the similarity in genetic diversity. Geographical distance, although reasonable, is also unlikely to affect biodiversity: “soils with similar environmental characteristics have similar bacterial communities regardless of geographic distance” (Fierer). The similar environment conditions and pH of soils would cause the genetic diversity of both soil conditions to be similar.

After comparing our group data with the ones in other groups in our section, as well as other studies, it was determined that there was no significant between the Okra condition and the Native Plant conditions. This means that there is no need for any change in the setup of the garden, as both conditions can survive in either soil. This can lead to a discussion about planting both plants directly next to each other changing the setup of the garden to create more space for different plants. These findings can aid the community garden as it can further their understanding of the bacterial biodiversity of the soil samples and can lead to a more optimal set up for the garden and the plant within. An increased biodiversity can also prevent disease and other issues in the plants, as shown through the USDA, "Lack of biodiversity severely limits the potential of any cropping system and increases disease and pest problems. Biodiversity is ultimately the key to the success of any agricultural system" (USDA, 2024). This shows that planting the two conditions can lead to many benefits. 

We would like to thank Professor Adler and Purdue University for the opportunity to conduct these experiments and lead us in analyzing these results. Thank you to our Teaching Assistant Ayomide for the guidance through the research and analysis of our results and thank you to the teaching interns for helping us and giving advice during the research process. Thank you to Purdue University for funding this project.

Brandenberger, Lynn, Okra Production. Oklahoma State University, Ferguson School of

Agriculture. Jan 2019, Okra Production | Oklahoma State University (okstate.edu).

Fierer, N., & Jackson, R. B. (2006). The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences, 103(3), 626–631. https://doi.org/10.1073/pnas.0507535103

Leelamanie, DAL. “Changes in Soil Water Content with Ambient Relative Humidity in Relation to the Organic Matter and Clay.” Tropical Agricultural Research and Extension, vol. 13, no. 1, 22 June 2011, p. 6, https://doi.org/10.4038/tare.v13i1.3130.

Mhuireach, Gwynne. Encountering Microbiomes in the Garden. Garden Ecology Lab. Oregon State University. July 23, 2021. Encountering Microbiomes in the Garden | Garden Ecology Lab

USDA. (2024). http://www.nrcs.usda.gov/conservation-basics/natural-resource-concerns/soils/soil-health. Natural Resources Conservation Service. https://www.nrcs.usda.gov/conservation-basics/natural-resource-concerns/soils/soil-health