Supplemental Material to Lamb, Kennedy, and Siciliano
Relationships between community composition and experimentally varied species richness, evenness, and density
Initial community composition (presence or absence of plant species) was described using a non-metric multidimensional scaling (NMS) ordination fit using PC-ORD v5.19 (McCune and Mefford, 2006, McCune and Grace, 2002). The Jaccard distance measure was used and a three-axis solution with a final stress of 24.976 and final instability <0.00001 was obtained. The ordination axes accounted for 9.6, 16.5, and 17.0% of the variation in the distance matrix respectively for a total r2=0.431.
The low variance explained and our inability to obtain a useful one- or two-axis solution stem from the inherent difficulties in producing a sensible ordination from randomly assembled communities. The primary purpose of this ordination was to display how the composition of the randomly assembled communities related to experimentally imposed variation in species richness, evenness, and density. In general the ordinations resulted in a broad scatter of pots along all three axes with monoculture pots at the margins and more species rich pots toward the center (Supp. Figure 2). There is a general trend for more species rich pots to be in the center of the ordination. This trend is an expected product of the ordination since the monocultures are arrayed around the edges of the ordination. Pots containing multiple species will be placed between the positions of the monoculture pots with species represented in the pot. There were no patterns in the relationship between initial community composition and initial evenness (Supp. Figure 3). There was a weak negative relationship between axis 1 and initial density (Supp. Figure 4). This relationship suggests that pots including species such as Agropyron smithii, Penstemon procerus, and Horedum jubatum had lower overall germination rates and hence lower average densities than other pots.
Supplemental Figure 1. Relationship between plant community composition and initial species richness. Larger symbols indicate pots with higher species richness.
Supplemental Figure 2. Relationship between plant community composition and initial evenness. Larger symbols indicate pots with higher evenness.
Supplemental Figure 3. Relationship between plant community composition and initial density. Larger symbols indicate pots with higher initial density.
Supplemental Figure 4. Relationship between plant community composition and functional group composition. With the exception of 3 pots that contained two grasses each, all multispecies pots contained at least one grass and at least one forb species.
Supplemental Figure 5. Relationship between initial plant community composition and harvest plant community evenness. Larger symbols indicate higher evenness. There was no consistent relationship between initial plant community composition and plant community evenness at harvest. This indicates that the negative initial species richness – harvest evenness relationship observed in this study was not due to a single aggressive plant species, but due to many species which are capable, under the right conditions, of achieving dominance.
Supplementary Table 1. Means (±1 SD) and ranges for all variables included in the structural equation models.
Variable / mean / sd / min / max / Transformation used in SEMInitial Species Richness / 2.606 / 1.994 / 1 / 8 / Square Root
Initial Evenness / 0.833 / 0.22 / 0.259 / 1 / None
Initial Density (plants pot-1) / 17.219 / 11.062 / 1 / 50 / Square Root
Root Biomass (g) / 3.459 / 2.136 / 0.210 / 9.47 / Ln
Harvest Plant Species Richness / 2.321 / 1.649 / 1 / 7 / Square Root
Harvest Plant Evenness / 0.704 / 0.350 / 0.047 / 1 / None
Bacterial OTU Evenness / 0.620 / 0.069 / 0.425 / 0.996 / None
Bacterial OTU Relative Richness / 14.299 / 4.711 / 4 / 28 / Square Root
Bacterial Abundance (log copy number) / 8.742 / 0.387 / 7.869 / 9.688 / None
Archaeal Abundance (log copy number) / 8.760 / 0.62 / 6.598 / 9.891 / None
Dissolved Organic Carbon DOC (mg L-1) / 65.994 / 42.191 / 24.343 / 405.869 / Ln
Total Dissolved Nitrogen TDN (mg L-1) / 18.184 / 10.244 / 1.863 / 48.967 / Ln
AmoA prevalence (log copy number) / 6.880 / 1.056 / 3.466 / 9.055 / None
AamoA prevalence (log copy number) / 5.989 / 2.164 / 2.803 / 9.423 / None
Supplementary Table 2.Raw variance-covariance matrix for the bacterial SEM.
Initial Even / Initial Density / Initial Rich / Harvest Even / Root Biomass / Harvest rich / TDN / DOC / Bacteria Abund / Bacteria Even / Bacteria Rich / amoAInitial Even / 0.049
Initial Density / -0.135 / 2.012
Initial Rich / -0.075 / 0.477 / 0.333
Harvest Even / 0.045 / -0.239 / -0.169 / 0.123
Root Biomass / -0.031 / 0.282 / 0.081 / -0.049 / 0.243
Harvest richness / -0.197 / 1.225 / 0.904 / -0.45 / 0.227 / 2.74
TDN / 0.045 / -0.373 / -0.174 / 0.097 / -0.149 / -0.43 / 0.367
DOC / 0.001 / 0.063 / 0.004 / 0 / 0.06 / 0.008 / 0.034 / 0.158
Bacterial Abund / 0.007 / -0.104 / -0.068 / 0.044 / -0.032 / -0.197 / 0.03 / -0.004 / 0.142
Bacterial Even / 0 / 0.007 / 0 / 0 / 0.004 / -0.007 / -0.007 / 0 / 0.004 / 0.005
Bacterial Rich / -0.005 / -0.084 / -0.011 / -0.002 / 0.052 / 0.017 / -0.032 / -0.011 / 0.029 / 0.013 / 0.377
AmoA / 0.049 / -0.626 / -0.243 / 0.136 / -0.079 / -0.662 / 0.169 / -0.005 / 0.201 / 0.009 / 0.099 / 1.107
Supplementary Table 3. Raw variance-covariance matrix for the archaeal SEM.
Initial Evenness / Initial Density / Initial Richness / Harvest Evenness / Root Biomass / Harvest richness / TDN / DOC / Archaeal Abund / Archaeal amoAInitial Evenness / 0.049
Initial Density / -0.14 / 2.125
Initial Eichness / -0.076 / 0.496 / 0.34
Harvest Evenness / 0.047 / -0.254 / -0.173 / 0.118
Root Biomass / -0.034 / 0.359 / 0.089 / -0.053 / 0.248
Harvest richness / -0.2 / 1.272 / 0.919 / -0.459 / 0.244 / 2.773
TDN / 0.045 / -0.422 / -0.178 / 0.095 / -0.156 / -0.431 / 0.359
DOC / -0.001 / 0.069 / 0.008 / -0.004 / 0.059 / 0.021 / 0.025 / 0.15
Archaeal Abundance / 0.006 / -0.103 / -0.045 / 0.03 / -0.03 / -0.141 / 0.028 / 0.013 / 0.396
Archaeal amoA / -0.205 / 1.118 / 0.82 / -0.418 / 0.302 / 2.216 / -0.628 / 0.026 / 0.054 / 4.649
Supplementary Table 4. Full SEM results for each path in the final bacterial community model. UnStd Est = unstandardized path coefficient estimates, SE = standard error of the unstandardized path estimate, C.R. = Critical ratio for regression weight (UnStd Est/SE), p = test of significance of path estimate, Std = Standardized path coefficient estimates.
Path / UnStd Est / SE / C.R. / p / StdInital Species Richness to Harvest Species Richness / 2.753 / 0.1 / 27.549 / <0.001 / 0.959
Initial Density to Root Biomass / 0.119 / 0.034 / 3.463 / <0.001 / 0.342
Initial Evenness to Harvest Evenness / 0.204 / 0.092 / 2.213 / 0.027 / 0.129
Initial Species Richness to Root Biomass / 0.007 / 0.094 / 0.073 / 0.942 / 0.008
Initial Species Richness to Harvest Evenness / -0.463 / 0.035 / -13.053 / <0.001 / -0.76
Initial Evenness to Root Biomass / -0.291 / 0.22 / -1.321 / 0.186 / -0.131
Initial Evenness to Harvest Species Richness / 0.167 / 0.26 / 0.64 / 0.522 / 0.022
Harvest Species Richness to DOC / -0.003 / 0.033 / -0.081 / 0.936 / -0.011
Root Biomass to DOC / 0.271 / 0.07 / 3.877 / <0.001 / 0.335
Harvest Species Richness to TDN / -0.05 / 0.042 / -1.182 / 0.237 / -0.136
Root Biomass to TDN / -0.485 / 0.089 / -5.42 / <0.001 / -0.396
Harvest Evenness to TDN / 0.409 / 0.197 / 2.076 / 0.038 / 0.238
Harvest Evenness to DOC / 0.102 / 0.154 / 0.664 / 0.506 / 0.09
DOC to Bacterial Abundance / -0.024 / 0.079 / -0.305 / 0.761 / -0.025
TDN to Bacterial Abundance / -0.013 / 0.058 / -0.226 / 0.821 / -0.021
Harvest Evenness to Bacterial Abundance / 0.37 / 0.099 / 3.733 / <0.001 / 0.345
Bacterial Abundance to Bacterial Richness / 0.274 / 0.14 / 1.955 / 0.051 / 0.168
Bacterial Abundance to Bacterial Evenness / 0.029 / 0.016 / 1.742 / 0.081 / 0.157
Harvest Evenness to Bacterial Evenness / 0.008 / 0.019 / 0.44 / 0.66 / 0.043
Harvest Species Richness to Bacterial Richness / 0.053 / 0.039 / 1.37 / 0.171 / 0.142
DOC to Bacterial Richness / -0.157 / 0.143 / -1.098 / 0.272 / -0.102
TDN to Bacterial Evenness / -0.025 / 0.011 / -2.319 / 0.02 / -0.222
TDN to Bacterial Richness / 0.002 / 0.11 / 0.019 / 0.985 / 0.002
DOC to Bacterial Evenness / 0.009 / 0.015 / 0.587 / 0.558 / 0.05
Root Biomass to Bacterial Richness / 0.353 / 0.131 / 2.684 / 0.007 / 0.282
Initial Density to Bacterial Richness / -0.107 / 0.044 / -2.444 / 0.015 / -0.245
Bacterial Richness to AmoA / 0.094 / 0.126 / 0.745 / 0.456 / 0.055
Bacterial Abundance to AmoA / 1.164 / 0.199 / 5.837 / <0.001 / 0.419
Bacterial Evenness to AmoA / 1.368 / 1.13 / 1.211 / 0.226 / 0.09
DOC to AmoA / 0.054 / 0.186 / 0.29 / 0.772 / 0.021
TDN to AmoA / 0.17 / 0.134 / 1.265 / 0.206 / 0.098
Initial Density to AmoA / -0.222 / 0.056 / -3.967 / <0.001 / -0.301
Initial Evenness with Initial Species Richness / -0.075 / 0.013 / -5.75 / <0.001 / -0.584
Initial Evenness with Initial Density / -0.135 / 0.03 / -4.505 / <0.001 / -0.43
Initial Density with Initial Species Richness / 0.477 / 0.083 / 5.746 / <0.001 / 0.583
DOC with TDN / 0.063 / 0.017 / 3.744 / <0.001 / 0.348
Bacterial Richness with Bacterial Evenness / 0.011 / 0.004 / 3.173 / 0.002 / 0.29
Supplementary Table 5.Full SEM results for each path in the final bacterial community model. UnStd Est = unstandardized path coefficient estimates, SE = standard error of the unstandardized path estimate, C.R. = Critical ratio for regression weight (UnStd Est/SE), p = test of significance of path estimate, Std = Standardized path coefficient estimates.
Path / UnStd Est / SE / C.R. / p / StdInitial Species Richness to Harvest Species Richness / 2.748 / 0.1 / 27.547 / <0.001 / 0.962
Initial Density to Root Biomass / 0.158 / 0.032 / 4.904 / <0.001 / 0.463
Initial Evenness to Harvest Evenness / 0.251 / 0.082 / 3.052 / 0.002 / 0.162
Initial Evenness to Root Biomass / -0.285 / 0.213 / -1.335 / 0.182 / -0.127
Initial Evenness to Harvest Species Richness / 0.194 / 0.263 / 0.74 / 0.459 / 0.026
Initial Species Richness to Root Biomass / -0.032 / 0.09 / -0.36 / 0.719 / -0.038
Initial Species Richness to Harvest Evenness / -0.453 / 0.031 / -14.469 / <0.001 / -0.768
Harvest Species Richness to DOC / -0.005 / 0.034 / -0.161 / 0.872 / -0.023
Root Biomass to DOC / 0.256 / 0.068 / 3.762 / <0.001 / 0.329
Harvest Species Richness to TDN / -0.042 / 0.043 / -0.962 / 0.336 / -0.116
Root Biomass to TDN / -0.498 / 0.088 / -5.685 / <0.001 / -0.415
Harvest Evenness to TDN / 0.423 / 0.21 / 2.018 / 0.044 / 0.243
Harvest Evenness to DOC / 0.057 / 0.163 / 0.348 / 0.728 / 0.05
DOC to Archaea / 0.073 / 0.143 / 0.512 / 0.609 / 0.045
TDN to Archaea / 0.074 / 0.093 / 0.8 / 0.424 / 0.071
Archaea to Archaeal amoA / 0.44 / 0.223 / 1.974 / 0.048 / 0.128
DOC to Archaeal amoA / 0.204 / 0.365 / 0.558 / 0.577 / 0.036
TDN to Archaeal amoA / -0.999 / 0.262 / -3.807 / <0.001 / -0.275
Harvest Species Richness to Archaeal amoA / 0.665 / 0.093 / 7.113 / <0.001 / 0.51
Initial Evenness with Initial Species Richness / -0.076 / 0.013 / -5.769 / <0.001 / -0.59
Initial Evenness with Initial Density / -0.14 / 0.031 / -4.509 / <0.001 / -0.433
Initial Density with Initial Species Richness / 0.496 / 0.087 / 5.724 / <0.001 / 0.583
DOC with TDN / 0.057 / 0.016 / 3.547 / <0.001 / 0.329
References
McCune, B. & Grace, J.B. (2002) Analysis of ecological communities. MjM Software Design, Gleneden Beach, Oregon.
McCune, B. & Mefford, M.J. (2006) PC-ORD: Multivariate analysis of ecological data. MjM Software Design, Gleneden Beach, Oregon, USA.