Part II: diversity and ecology in relation to environmental and edaphic factors

Figures and analyses

Figure 1. Relative abundance of OTUs summarized by clade or genera and state for 2011 and 2012. The clades or genera are color coded according to the legend from top to bottom

Figure 2. Oomycete community structure of species recovered from soybean seedling evaluated by (A) cluster analysis based on Bray-Curtis distance by state surveyed. Dendrogram was constructed using hierarchical clustering with complete linkage; (B) diversity of oomycete communities expressed as Shannon index across the latitudes of the fields sampled; (C) diversity of oomycete communities expressed as Shannon index across longitudes of the fields sampled.

Figure 3. Principal coordinate analysis (PCoA) of oomycete communities collected from soybean seedling in the US based on a Bray-Curtis distance computed from taxon counts. Environmental and edaphic factors are plotted as vectors based on correlations with community distance. Only vectors with significant correlations are represented and the length of the vector represents the strength of the correlation. (CEC = Cation Exchange Capacity, Season: corresponds to April, May and June where most planting and or sampling was conducted).

Figure 4. Representation of the correlation of among community similarity (PCoA ordination axis) and four environmental factors: (A) seasonal precipitation (mm, from April - June) with samples colored by latitude; (B) seasonal minimum temperature (ºC, April - June) with samples colored by latitude; (C) clay content (%) with samples colored by volumetric water content (%); and (D) bulk density of the soil (gm/cm3) with samples colored by volumetric water content (%). Spearman correlation values (rho) and P-value are presented for each comparison. Season refers to the planting and or sampling period which ranged from April to June.

Figure 5. Distribution and abundance of the top 8 pathogenic oomycete species across the states sampled in 2011 and 2012.

For detailed analyses, please go to Ecology_analyses_oomycetes

Tables

Table 1. Oomycete community diversity and evenness by state and year. Data represents state-year average and standard deviation of soybean seedlings sampled by field.

St_Yr N Isolates mean.Observed sd.Observed mean.Shannon sd.Shannon mean.Simpson sd.Simpson mean.Evenness sd.Evenness
Arkansas 2011 1 320 14.000 NA 1.191 NA 0.597 NA 0.451 NA
Arkansas 2012 5 74 8.600 3.050 1.886 0.247 0.809 0.027 0.908 0.064
Illinois 2011 6 243 9.000 3.225 1.663 0.403 0.730 0.119 0.771 0.136
Illinois 2012 6 147 7.167 1.472 1.621 0.188 0.745 0.094 0.838 0.117
Indiana 2011 5 398 10.200 1.789 1.562 0.136 0.688 0.059 0.680 0.087
Indiana 2012 4 30 4.750 1.893 1.349 0.464 0.688 0.137 0.927 0.070
Iowa 2011 9 398 6.889 3.257 1.092 0.627 0.482 0.269 0.572 0.259
Iowa 2012 4 19 2.750 0.957 0.828 0.209 0.514 0.105 0.889 0.171
Kansas 2011 7 213 7.429 2.760 1.363 0.550 0.615 0.261 0.701 0.283
Kansas 2012 6 93 6.667 2.658 1.591 0.513 0.729 0.137 0.870 0.114
Michigan 2011 9 188 5.889 2.804 1.404 0.437 0.695 0.117 0.884 0.096
Michigan 2012 7 134 8.286 3.729 1.752 0.486 0.761 0.125 0.866 0.113
Minnesota 2011 6 185 10.667 6.186 1.859 0.537 0.774 0.104 0.827 0.102
Minnesota 2012 6 130 8.167 4.070 1.762 0.487 0.776 0.113 0.888 0.033
N Dakota 2011 9 210 9.556 5.637 1.784 0.635 0.758 0.162 0.874 0.168
N Dakota 2012 6 162 10.667 2.875 1.916 0.281 0.793 0.065 0.823 0.094
Nebraska 2011 4 75 7.750 3.686 1.654 0.457 0.750 0.102 0.865 0.076
Nebraska 2012 3 49 6.667 4.041 1.638 0.612 0.764 0.131 0.930 0.027
Ontario 2012 1 64 9.000 NA 0.854 NA 0.334 NA 0.389 NA
S Dakota 2011 5 23 2.800 1.304 0.901 0.359 0.559 0.116 0.953 0.078
S Dakota 2012 5 114 13.000 3.808 2.385 0.295 0.889 0.038 0.942 0.035
Wisconsin 2011 6 51 4.667 1.966 1.241 0.532 0.619 0.205 0.846 0.174

Table 2. Comparison of oomycete community structure (beta diversity) by state and year using Bray-Curtis distances.

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
State2 11 9.576 0.871 2.908 0.207 0.001
Year 1 0.702 0.702 2.346 0.015 0.002
State2:Year 9 5.259 0.584 1.952 0.113 0.001
Residuals 103 30.835 0.299 NA 0.665 NA
Total 124 46.371 NA NA 1.000 NA

Table 3. Significance of factors affecting oomycete communites associated with soybean seedlings, based on using ‘envfit’ function form vegan.

Env.var Axis.1.x Axis.2.x Axis.1.y Axis.2.y R2 P.value Env.var2
Lat 0.308 -0.053 0.308 -0.053 0.097 0.005 Latitude
Long -0.025 0.401 -0.025 0.401 0.161 0.001 Longitude
Precip_AMJ -0.405 -0.024 -0.405 -0.024 0.165 0.001 Precip. Season
CEC7 -0.116 -0.234 -0.116 -0.234 0.068 0.020 CEC
Clay -0.066 -0.259 -0.066 -0.259 0.072 0.019 Clay (%)
Db3rdbar 0.016 0.307 0.016 0.307 0.095 0.004 Bulk density
pHwater 0.251 -0.084 0.251 -0.084 0.070 0.020 Soil pH
WC3rdbar -0.131 -0.222 -0.131 -0.222 0.066 0.028 Water content
Precip -0.279 0.275 -0.279 0.275 0.154 0.001 Annual Total Precip.
TMax_30yr_avg -0.284 0.037 -0.284 0.037 0.082 0.012 Max. Temp 30yr
TMean_30yr_avg -0.286 0.069 -0.286 0.069 0.087 0.008 Mean Temp 30yr
TMin_30yr_avg -0.284 0.102 -0.284 0.102 0.091 0.006 Min. Temp 30yr
TMin_yr -0.198 0.160 -0.198 0.160 0.065 0.023 Annual Min. Temp
Precip_30yr_avg -0.279 0.189 -0.279 0.189 0.113 0.002 Precip. 30yr
Tmin_AMJ -0.241 0.029 -0.241 0.029 0.059 0.030 Min. Temp Season

Supplementary figures

Supplementary Table 1. Significance and correlation of environmental and edaphic factors using ‘envfit’ function form vegan that affect oomycete community associated with soybean seedlings.

Env.var Axis.1 Axis.2 R2 P.value
Long -0.025 0.401 0.161 0.001
Precip -0.279 0.275 0.154 0.001
Precip_AMJ_12 -0.101 -0.349 0.132 0.001
Precip_AMJ_11 -0.303 0.278 0.169 0.001
Precip_AMJ -0.405 -0.024 0.165 0.001
Precip_30yr_avg -0.279 0.189 0.113 0.002
Tmin_AMJ_11 -0.290 0.109 0.096 0.002
Db3rdbar 0.016 0.307 0.095 0.004
Tmean_AMJ_12 -0.295 -0.057 0.090 0.004
Lat 0.308 -0.053 0.097 0.005
Tmean_AMJ_11 -0.296 0.061 0.091 0.005
TMin_30yr_avg -0.284 0.102 0.091 0.006
Tmax_AMJ_12 -0.296 -0.047 0.090 0.006
Tmin_AMJ_12 -0.283 -0.066 0.084 0.007
TMean_30yr_avg -0.286 0.069 0.087 0.008
Tmax_AMJ_11 -0.289 0.019 0.084 0.008
TMax_30yr_avg -0.284 0.037 0.082 0.012
Clay -0.066 -0.259 0.072 0.019
CEC7 -0.116 -0.234 0.068 0.020
pHwater 0.251 -0.084 0.070 0.020
TMin_yr -0.198 0.160 0.065 0.023
WC3rdbar -0.131 -0.222 0.066 0.028
Tmin_AMJ -0.241 0.029 0.059 0.030
EC 0.196 -0.119 0.053 0.046
Sand 0.153 0.167 0.051 0.048
TMean_yr -0.188 0.093 0.044 0.084
OrgMatter 0.181 -0.077 0.038 0.096
Silt -0.190 -0.031 0.037 0.120
Tmean_AMJ -0.188 0.013 0.036 0.133
Tmax_yr -0.171 0.028 0.030 0.173
ECEC -0.088 0.138 0.027 0.226
Tmax_AMJ -0.140 0.001 0.020 0.336
Slope_Avg -0.053 0.096 0.012 0.520
Shape_Area -0.103 -0.011 0.011 0.562
Shape_Length -0.079 -0.051 0.009 0.602
AWC -0.034 -0.077 0.007 0.659
Aspect 0.003 0.055 0.003 0.850

Supplementary Figure 1. Map of sampled soybean fields in 2011 and 2012, and intensity of planted soybean acres demonstrated by color intensity at the county/parish level.

Supplementary Figure 2. Climate conditions across soybean fields sampled in the US from May to June (A) mean temperature 2011, (B) mean temperature 2012, (C) mean precipitation 2011, and (D) mean precipitation 2012.

fig2

Supplementary Figure 3. Abundance of designated pathogenic oomycete species Py. sylvaticum, Py. heterothallicum, Py. oopapillum, Py. ultimum var. ultimum, Py. aff. dissotocum and Py. aff. torulosum by different environmental factors: (a) soil pH, (b) clay percent (%), (c) seasonal precipitation (April – June), (d) season minimum temperature (April – June) and, (e) cation exchange capacity (CEC).