Data exploration

During 2022, we carried out 26 plant transects. The soil protocol was employed three times in each plant transect location. So we have three replicates by transect. Here we present an average (in the case of ph, bulk.density, depth, om, N, C) or the median (in the case of hcl.test, chroma, value) of the replicates by transect. In brief, in the dataset we have 26 values of each soil variable.

Dataset features explained

  • ph

  • bulk.density : Soil bulk density (\(\frac{g}{cm^{3}}\))

  • depth : Soil depth (cm)

  • HCL Test :

    • Limestone : In cold condition, generalized effervescence under HCl

    • Dolomite : In cold condition, little or non effervescence under HCL

      • Four categories from 0 to 3 indicating effervescence under HCL

        • 0 : No detectable reaction

        • 1 : Weak, a few bubbles or murmur of effervescence

        • 2 : Medium, bubbles in continuous layer

        • 3 : Vivid, several superimposed layers of bubbles

  • Munsell soil colour :

    • Chroma i.e. the strength or weakness of a colour

    • Value i.e. the lightness or the darkness of the colour

  • om : Percentage (%) of organic matter calculated after being in muffle furnace at 550 °C during 4 hours.

  • N : Percentage (%) of nitrogen in a sample weighing ~ 35 mg. CHN analysis.

  • C : Percentage (%) of carbon (organic + inorganic) in a sample weighing ~ 35 mg. CHN analysis.

Data summary by variable

##        ph         bulk.density        depth          hcl.test     chroma     
##  Min.   :6.537   Min.   :0.8197   Min.   : 8.00   Min.   :0   Min.   :1.000  
##  1st Qu.:6.963   1st Qu.:0.9802   1st Qu.:10.92   1st Qu.:1   1st Qu.:2.000  
##  Median :7.070   Median :1.1615   Median :18.33   Median :1   Median :3.000  
##  Mean   :7.189   Mean   :1.1147   Mean   :21.21   Mean   :1   Mean   :2.846  
##  3rd Qu.:7.543   3rd Qu.:1.2255   3rd Qu.:23.46   3rd Qu.:1   3rd Qu.:3.000  
##  Max.   :7.710   Max.   :1.6278   Max.   :84.17   Max.   :3   Max.   :4.000  
##      value             om               N                C         
##  Min.   :2.000   Min.   : 5.711   Min.   :0.2067   Min.   : 2.383  
##  1st Qu.:3.000   1st Qu.: 8.674   1st Qu.:0.3419   1st Qu.: 4.226  
##  Median :3.000   Median :11.664   Median :0.4877   Median : 7.606  
##  Mean   :3.442   Mean   :12.907   Mean   :0.5138   Mean   : 7.105  
##  3rd Qu.:4.000   3rd Qu.:17.685   3rd Qu.:0.7045   3rd Qu.: 8.680  
##  Max.   :6.000   Max.   :22.736   Max.   :0.8810   Max.   :13.369

Data visualization

Correlation matrix

Spearman correlation

##                 ph bulk.density depth hcl.test chroma value   om    N C
## ph               1                                                     
## bulk.density   0.1            1                                        
## depth         0.05         0.17     1                                  
## hcl.test      0.53         0.09 -0.11        1                         
## chroma        0.14         0.38   0.5     0.15      1                  
## value         0.45         0.44  0.27     0.38    0.4     1            
## om           -0.18        -0.69 -0.35    -0.17  -0.49 -0.62    1       
## N            -0.22        -0.66 -0.39    -0.22  -0.51 -0.62 0.98    1  
## C             0.44        -0.46 -0.28      0.1  -0.41  0.01 0.47 0.48 1

Correlation between Soil organic matter and Total nitrogen

Total nitrogen is highly related to soil organic matter. Also these two variables are slightly and negatively associated with soil bulk density.

PCA of the soil and environmental variables

## $importance
## Importance of components:
##                          PC1    PC2    PC3    PC4    PC5     PC6     PC7
## Eigenvalue            4.3827 2.5593 1.9906 1.5279 1.4704 0.99391 0.75276
## Proportion Explained  0.2739 0.1600 0.1244 0.0955 0.0919 0.06212 0.04705
## Cumulative Proportion 0.2739 0.4339 0.5583 0.6538 0.7457 0.80781 0.85486
##                           PC8     PC9    PC10    PC11    PC12     PC13     PC14
## Eigenvalue            0.65078 0.47767 0.41039 0.28449 0.23767 0.137653 0.088923
## Proportion Explained  0.04067 0.02985 0.02565 0.01778 0.01485 0.008603 0.005558
## Cumulative Proportion 0.89553 0.92538 0.95103 0.96881 0.98367 0.992271 0.997828
##                           PC15      PC16
## Eigenvalue            0.027800 0.0069478
## Proportion Explained  0.001738 0.0004342
## Cumulative Proportion 0.999566 1.0000000

Principal component one explains 27%, component two explains 16%, and component three explains 12% of the variance.

Principal Components 1-2

Principal Components 1-2

Principal Components 1-3

Principal Components 1-3

Plant transect ordination

library(vegan)
bray_dist_sqrt = vegdist(sqrt(community_data_density_22_23), method="bray", binary=FALSE, diag=FALSE, upper=FALSE,na.rm = FALSE)
nmds_density_22_23 <- metaMDS(comm = bray_dist_sqrt, autotransform = FALSE, k=3,weakties = TRUE, model = "global", maxit = 300, try = 40,trymax = 100)
# change to sqrt(community_data_density_22_23) ass Li 2021 does 
nmds_density_22_23$stress
## [1] 0.162594

Dimensions one and two of the NMDS

Site ordination

Site ordination

To remember the coding, the initial letter C,S and P represent Castril, Santiago and Pontones, respectively. The following number (01 up to 12) is the pastoral zones in each common. The letters A, B and C are the replicate in each pastoral zones. Replicates A were carried out during the spring 2022. Replicates B and C were carried out in 2023.

In the plant transects done in 2022 (highlighted in blue in the above figure) we did the soil sampling. In contrast, in the plant transect done in 2023 (highlighted in red), we did not do the soil sampling.

Species ordination

Significant Species

Species ordination

Species ordination

Dimensions one and three of the NMDS

Site ordination

Site ordination

Species ordination

Species ordination