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
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 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.
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).