Basik Goobers 

Soil Characteristics as Indicators for Plant Community Species Composition
Biol 471 Lab Report
Dawood Ayub, Amanda Fitch, Lucas Larson, Julia Olson

June 7, 2013


Species in plant communities can be seen to change between various locations. The underlying factors influencing these changes are less clear, however. In order to address these issues we looked at the soil characteristics that may act as indicators for plant community species composition. The characteristics chosen, with the goal of correlating species composition and environmental gradients, for this research were water, light, and essential nutrients. Our methods for this research include sampling locations at the Foege Lawn, Burke-Gilman Trail, and Pinetum. In recording the data we measured pH with a pH meter, moisture with soil moisture probes, color with soil color charts, and radiation was calculated from slope and aspect. From these measurements statistical analysis was performed including CCA and PERMANOVA. Through our analysis we have found that our hypotheses for soil moisture and fertility have been falsified, while our hypotheses for radiation and pH have not been proven false.


Basik Goobers 

Soils are fine layers of rock particles that cover the Earth’s surface resulting from many biotic and abiotic processes, which over time, accumulate in layers. Soils can differ in physical, chemical and biological properties. These properties result from various processes (such as weathering, decomposition, or climate) occurring in the soil at different rates and coincidence with other processes. Washington is comprised of an array of soils primarily due to glaciations and climate. Recently, anthropogenic impacts are altering the surface of our planet. Urban landscaping has become an increasingly predominant part of society with vast lawns and manicured hedges adorning most of our cities. While above ground characteristics can be designed for aesthetics of function and beauty, below ground characteristics will often have adverse effects on species establishment and composition long term. Urban soil differs from natural soil and can be defined as soils that have been disturbed or manipulated by human activity. The manipulation and disturbance to urban soils by various construction and restoration activities cause compaction of at least the surface layer and, in many cases, the lower portions of the soil profile as well (Alberty et

al., 1984). Compaction affects the soil by reducing the ease of root penetration, decreasing the movement of water, and causes a reduction in its water-holding capacity. Compaction also reduces the movement of gases into and out of the soil, particularly the inflow of oxygen, which roots require to function properly, and the outflow of carbon dioxide, which must be removed (Hillel, 1980). By reducing effective soil depth, compaction forces roots to grow close to or on the soil surface (Gilman et al., 1987). This, in effect, can limit a plants access to essential nutrients. Most plants require a similar balance of basic resources to maintain optimal growth—water, light and essential nutrients. Access to these resources is not uniform across landscapes and soil characteristics occur in gradients. Sites with poor below ground characteristics will differ in species composition than sites with more suitable below ground characteristics. As a part of the University of the University of Washington’s biology department we are exploring three study sites Our study across Seattle: a portion of the Burt-Gilman trail, Foege lawn, and Pinetum lawn. The objectives of this study were to evaluate plant community species

Basik Goobers  composition in relation to environmental gradients. Figure 1: PCA of all_plots_spp and soil characteristics

Question & Hypothesis
Our group’s main interest over the course of the quarter continuously lined up with soil characteristics, so we wanted to explore how soil characteristics affected species composition. A PCA was done with the environmental soil characteristics of soil radiation, soil chroma, soil moisture, and soil pH as the highlighted vectors (Fig. 1). We were curious about the observation that there was a large variation between the four soil vectors, and so we decided to independently study each soil characteristics’ influence on species composition to see which of the characteristics mattered for our data’s species composition. In seeking to answer the question, what soil properties best explain variation in lawn vegetation, we came up with a group hypothesis that plant community species composition will vary according to levels of the soil characteristics slope/aspect, pH, soil moisture, and observed color spectrum. Recording of data The students collected data during labs for Biology 471 in the spring of 2013 at three locations in Seattle, WA.

Sampling sites The sampling sites were located in the Foege Lawn (near Hitchcock building), Burke Gilman Trail (on UW campus) and Pinetum (south of UW campus). Soil samples from Foege Lawn were taken on separate days, whereas for the other two locations, they were sampled on the same day. Each of the three sampling sites consisted of slope angles needed.


Basik Goobers  To record the relevant data needed, we used four different techniques. In order to for us to record pH, we added approximately 10 ml of H20 to each sample of soil, and later recorded the pH using an Ecotester2 portable pH meter. We recorded soil chroma by matching our soil samples to a standard Munsell soil color chart. Soil moisture was recorded using Time-doamin Refractometry. Since we had three different plots, we recorded the average. Last but not least, soil radiation was recorded based on potential clear-sky radiation, which was calculated from slope and aspect. Statistical data analysis To analyze Longitude_DD, light, and slope distance, CCA analysis was performed on the three different locations. Furthermore, a PERMANOVA was then completed to relate the species with the environment factors. When analyzing the effects of soil fertility on vegetation, CCA analysis was again performed to show the similarities between the different variables. To find the relationship between soil radiation and species composition, a CCA statistical analysis was ran. After limiting the variables to soil value, slope and soil pH on the second CCA analysis, PERMANOVA helped us test When it comes to soil pH, we used our statistical data from CCA to help us find the significant variables needed to notice a relationship between soil pH and species composition. Using the limiting variables, we ran PERMANOVA analysis to help us reach our conclusion. After determining the most significant environmental factors from the CCA and which factors was closely correlated with chroma, PERMANOVA analysis was done to see the relationship between soil chroma and species composition. our hypothesis regarding the effect of soil radiation on species composition.

Soil Radiation: Dawood Ayub The hypothesis tested in this section is to further examine the effect soil radiation has on total plant community species composition. Soil radiation was calculated according to the slope and aspect of the environment. At first, CCA analysis was done on all variables of the environment to find any correlation with the species in the community matrix. Figure 2 shows the first CCA and the three different variables, which showed strong


Basik Goobers  correlation to soil radiation. These included soil pH, soil value, and slope. Figure 2: CCA of all environmental factors linear relationships within the two data sets, a PERMANOVA analysis was done to show the influence of soil radiation on plant composition alongside the other three factors listed above. Starting with 1000 permutations yielded, an F value of 3.1611 was found. The R2 value was 0.01483, which explains the total percentage of variations affected by soil radiation. Finally, the p value was recorded as 0.091908. Having such a low p value indicates that there is indeed a strong correlation between soil radiation and total plant community species compositions. Soil Oxidation: Julia Olson Using these three variables along with soil radiation, a second CCA was performed on the 4 variables (Figure 3). Figure 3: Modified CCA The hypothesis tested in this section to further examine the effect of soil properties on vegetation is that soil fertility (as explained by the Munsell color notation system) influences plant community species composition such that soil composition will vary according to an oxidation spectrum. Soil chroma and soil value will be analyzed to understand soil fertility. Soil chroma is the best indicator for the oxidation status of the soil. A high chroma value can be attributed to presence of hydrated iron (III) oxides while a lower chroma value indicate the presence of clay minerals, calcium and magnesium Next, to find a stronger correlation without


Basik Goobers  carbonates (limestone), and reduced iron compounds. Figure 4: CCA of all environmental factors As the PERMNANOVA analysis does not account for non-linear associations, PERMANOVA analysis was done next to evaluate the influence of chroma on species composition by how they are modified with respect to the CCA significant factors, soil moisture and soil value. When PERMANOVA is conducted with chroma listed last, the p-value is 0.056. Synthesizing these results from CCA and PERMANOVA of examining the influence of chroma upon species composition while incorporating soil moisture, pH and value, the p-values for chroma do not provide enough confidence Figure 4 shows the same CCA analysis of all quantitative variables that was used for this hypothesis testing. The biplot shows the most similarities between chroma, value, aspect, slope, pH and radiation. While it seems that chroma is related to most of the environmental factors in the CCA biplot, the p-value for the CCA analysis associated with chroma is 0.838, indicating that such a relationship is due to an artifact of sampling. The significant factors for the CCA biplot are soil moisture (p-value – 0.001), soil pH (pvalue – 0.038) and soil value (p-value – 0.007), so when conducting the PERMANOVA, I will account for those in the Adonis function. Soil Moisture: Lucas Larson The hypothesis being tested here is that varying levels of soil moisture will influence plant community species composition. In order to test this hypothesis a CCA was performed on each of the three locations where data was collected. From this analysis the most influencing factors on species composition were represented. As shown in Figures 5-7, the CCA graphs and p-values represent which environmental factors are that the presumed influence of soil oxidation on species composition was not due to random sampling chance, and my hypothesis is falsified.


Basik Goobers  most influencing for each location. For the Pinetum in figure 5, Stratum, Longitude_DD, light, and slope distance were most influencing. In order to test the hypothesis in question, a PERMANOVA was completed in order to partition the variation in the species data in order to relate to the environmental factors that were significant in the CCA test with soil moisture last. The p-value shown for soil moisture of 0.125 suggests that there’s really no relationship between plant communities and soil moisture. Figure 5 "#$%&'!(!

A similar argument can be made for the location data at the Burke-Gilman site and the Foege Lawn site. Using the same methods as previously described a p-value for a compounded PERMANOVA test of 0.228 for Foege lawn soil moisture in figure 6, and 0.342 for Burke-Gilman soil moisture in figure 7 suggests that the relationship shown is probably due to an artifact of the sampling process. Figure 6 "#$%&'!(! !


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Stratum[T.PH] Stratum[T.PE] x Slope_dist Longitude_DD x x x Light[T.PS] x x x xx Stratum[T.PJ] Slope x x + GRASS Light[T.SH] x x




Stratum[T.PI] Stratum[T.PD] Stratum[T.PC]




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Basik Goobers  Although these tests suggest that this hypothesis is false, there are other variables that come into play that could affect the outcomes. These variables include the size of the data collected and the fact that this was experimentation in a controlled setting would help to solidify these findings.
CCA2 1 1
+ + + +

Figure 8: CCA analysis of three lawn species data across Seattle plotted against their environmental with emphasis on soil pH, soil moisture, aspect, and soil chroma.
+ +

not a controlled experiment. Further

Burke- Gilman Foege Pinetum





Soil_Moist +

The soil pH of Pinetum from Washington park arboretum 4.3 to 6.9, but values ranging from 5.1 to 6.4 were most frequent. The pH from the section of Burke- Gilman trail ranged from 5.0 to 8.0 with the highest frequency recorded between 5.4 and 6.9. The pH of the soils from Foege lawn ranged from 5.8 to 7.3 with the highest frequency recorded between 6.1 and 7.2. The pH values from Pinetum and sections of the Burt- Gilman had lower average pH values than that of Foege lawn. Foege lawn also had an average pH value of 6.7 indicating relatively neutral soil and in general, showed more soil pH stability with a narrower range of most frequently recorded pH values. Canonical Correspondence Analysis (CCA) is a multivariate analysis showed which shows that pH has a real correlation with species abundances in the community matrix.






0 CCA1



The pr(>F) value was equal to 0.0105 and indicates that this finding is significant and that the probability that the observed relationship being due to an artifact of the sampling process is small. This suggests a significant correlation between soil pH and species abundance and distribution is likely. PERMANOVA is another multivariate analysis of variance, which doesn’t assume linear relationships between species data and environmental data. It was the second test performed. The results from this test with 999 permutations yielded: an F value of 3.1535, indicating that the variation between the three




Soil pH: Amanda Fitch


Basik Goobers  universes is large The R2 value was 0.01501. This is low and indicates that less than 1% of the total variations in the data are being explained by pH. Last, the p-value for this data is p-value= 0.003. This result indicates a high confidence that a relationship is real and suggests that soil pH is correlated to species abundance and distribution. (0.058) and value (0.292) show that there is not a strong enough statistical significance to explain the community species composition. Due to this fact, the hypothesis that soil fertility influences plant community species composition is rejected for this data.   Soil Moisture  Through the CCA and PERMANOVA tests completed during this research for the data collection sites of the Pinetum, Burke-Gilman trail, and Foege Lawn it is suggested that soil moisture levels doesn’t have an affect on plant community species composition. Further research in a controlled situation would provide much stronger data for either confirming or refuting the findings of the tests performed here. Soil pH Soil pH varies with hydorgen ion concentration and is heterogeneous across landscapes. This environmental variable was analyzed using CCA and PERMANOVA while taking into account other moderating effects of the environment such as aspect, soil chroma, and soil moisture. The PERMANOVA values (p-value= 0.003) show that there is a strong statistical significance which is in support of the original hypothesis that pH affects species distribution and abundance and therefore we can conclude that

Soil Radiation   Soil radiation is measured through clear sky radiation from slope and aspect. Taking other environmental factors such as soil pH, soil value and slope into consideration, a CCA and PERMANOVA analysis were completed. The p value from the PERMANOVA test (pvalue= 0.091908) proved there was a strong correlation between soil radiation levels and species abundance, furthermore verifying our hypothesis that species composition will vary according to different levels of soil radiation. Soil Fertility  Soil fertility as measured by chroma and value to indicate the presence of oxidized minerals such as iron (III) was analyzed using CCA and PERMANOVA taking into account the moderating effects of the environmental factors aspect, slope, pH and radiation. The PERMANOVA p-values for both chroma


Basik Goobers  the hypothesis is verified. Additional studies should take place. Conclusion  The importance of this work is that we have a starting point (as emerging plant ecologists) to begin to understand what soil environmental factors have the most significance on the species composition, especially with regard to Foege Lawn, Burke Gilman Trail, and Pinetum. The limitations of our study were that we didn’t have systematic sampling of our data and every student had different subtle methods of how to account for species cover and classification. We were not able to account for anything that we did not measure in our environmental factors, so we could be missing out on some insightful data in that regard. Also, we did not examine the effect of the overall environment on species composition, which may have a greater role than any one specific factor (for example, frequency of animal trampling and fertilization). As two of our hypotheses on plant community species composition were not falsified, further research needs to be done to assess the importance of soil pH and soil radiation on species composition, as well to examine if they work together in any way. Ideally the next step would be to expand work on our three sites and take in more plots, and from there expand to other locations.

Alberty, C. A., H. M. Pellett, and D. H. Taylor. 1984. Characterization of soil compaction at construction sites and woody plant response. J. Environ. Hort. 2(2): 48-53 Gilman, E. F., I. A. Leone, and F. B. Flower. 1987. Effect of soil compaction and oxygen content on vertical and horizontal root distribution. J. Environ. Hort. 5(1): 33-36 Hillel, D. 1980. Fundamentals of Soil Physics. New York: Wiley



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