Sunday, June 18, 2023

New for 2023: Prairie Soil Moisture Maps


June is an important month in terms of field crop pathogen and disease development for Prairie farmers.  For cereals and pulses initial leaf disease infections occur and with favourable weather conditions secondary development and spread takes place.  Fungicide use decisions for these leaf diseases can be based partly on disease symptoms, but also consideration of weather and host factors.  Key weather and host considerations include the occurrence of frequent rainfall, moderate temperatures (15-25oC), level of disease resistance, crop yield potential/canopy density, and commodity prices.  Previous PCDMN posts discussed scouting for leaf disease in cereals and fungicide use decisions.  See:


For diseases such as sclerotinia stem rot of canola and ergot of small grain cereals, suitable pathogen development must occur to produce spores before host infection can take place.  The pathogens associated with both diseases overwinter as resting bodies known as sclerotia, which are compact masses of hyphae (Figure 1).  Germination of stem rot sclerotia to produce the golf-tee shaped apothecia, aka carpogenic germination, requires sufficient soil moisture and moderate temperatures.  Typically, germination takes up to three weeks with the occurrence of temperatures that range from 10 to 20oC with soil water potentials of about 0 to 500 kPa, although germination is reduced as kPa increases to >=300-500 kPa (Abawi and Grogan 1975; Boland 1984; Boland and Hall 1988; Clarkson et al. 2004; Hao et al. 203; Teo and Morrall 1985a,b).  These conditions typically occur for Prairie crops with adequate rainfall following canopy closure over the soil surface, which helps to buffer temperature and moisture fluctuations. 


Soil water (matric) potential is a measure of how closely water is held by soil particles and pores (Datta et al. 2017; Irmak 2019).  Soil volumetric water content (VWC) is related to the ratio of soil water volume and the volume of the soil and is expressed in percentages.  The relationship between VMC and soil matric potential varies depending on soil texture and is expressed through a soil water characteristic curve for each soil type .  When soils approach saturation (0 kPa) the VMC will be up to 45% for clay textured soil, while for sandy soils this value is 30%.  Once soil water potential increases above 300 kPa plant root access to water will be increasingly difficult, while for soils overall the permanent wilting point of a plant is generally considered to be reached around 1,500 kPa (Datta et al. 2017).


PCDMN weekly soil moisture maps

 Starting in mid to late June in 2023 the PCDMN will be posting weekly soil moisture maps to help farmers and consultants identify regions where rainfall has occurred, and soil moisture levels are potentially favourable for germination of sclerotia and production of apothecia of the stem rot pathogen.  For regions with favourable soil moisture conditions, farmers and consultants are encouraged to scout for apothecia and also use in-field sclerotinia stem rot risk assessment tools including the checklist, as well as measures of aerial spore load via petal testing or spore trapping (  Fungicide use and timing decisions can be improved by using these sources of information. 


PCDMN related information for sclerotinia stem rot can be found here:


The PCDMN has been working with Agriculture and Agri-Food Canada (AAFC) to obtain maps showing surface soil moisture based on satellite observations.  These soil moisture values are in VMC and usually range from 5- 45% by volume and the relationship between this value and the plant available water are affected by soil texture.  For example, a dry sandy soil may have a volumetric moisture content as low as 5% when dry, whereas the lower bounds for a clay textured soil may be closer to 20% VMC.  Soils with a VMC of 40-60% would be wet/saturated, although the level of saturation would vary based on soil texture, where a sandy soil may be saturated at 30% compared to 40-60% for heavier textured or organic soils.


In addition to total soil moisture (i.e., VMC), AAFC also provides maps showing the % difference from average over a specified period. Here +ve values indicates the moisture is wetter than normal, while a –ve value indicates it is dryer than normal.  When you have a high percentage difference, this would indicate the soil is either much wetter or much drier than normal.


Prairie soil moisture levels and need to scout for apothecia of the sclerotinia stem rot pathogen, June 12, 2023


As June 12, 2023 most Prairie regions have well below normal soil moisture levels with large areas with <40 to 60% of normal (Figure 2).  Based on satellite data from June 5-11, 2023, large areas of the Prairies would only have <5 to 20% surface soil moisture (VMC) and as Figure 3 indicates, the corresponding satellite image shows well below long term average soil moisture levels for large areas of the Prairies including regions where sclerotinia stem rot can occur (Figure 4). 


As of June 12, the need to scout fields for apothecia of the stem rot fungus and/or to assess in-field risk is low.  This is based on soil moisture maps (Figures 2-4) and that flowering in most canola crops is still 2-3 weeks away.  




Information related to soil moisture is OFFERED TO THE PUBLIC FOR INFORMATIONAL PURPOSES ONLY. Agriculture and Agri-Food Canada, and their employees assume no liability from the use of this information.  Soil moisture conditions will vary depending on soil texture, and localized rainfall and temperature conditions.  Sclerotinia stem rot risk will vary depending on host, pathogen and weather factors, and farmers and consultants are encouraged to use currently available risk assessment tools (




Abawi, G.S., and R.G. Grogan. 1975. Source of primary inoculum and effects of temperature and moisture on infection of beans by Whetzelinia sclerotiorum. Phytopathology 65: 300-309.

Boland, G.J. 1984. Epidemiology and management of diseases caused by Sclerotinia sclerotiorum in whitebean and soybean. Ph. D. thesis, Univ. of Guelph, Guelph, Ontario. 245 pp.

Boland, G. J., and Hall, R. 1988. Epidemiology of Sclerotinia stem rot of soybean in Ontario. Phytopathology 78:1241-1245.

Clarkson, J. P., Phelps, K., Whipps, J. M., Young, C. S., Smith, J. A., and Watling, M. 2004. Forecasting Sclerotinia disease on lettuce: Toward developing a prediction model for carpogenic germination of sclerotia.  Phytopathology 94:268-279.

Datta, S., Taghvaeian, S., and Stivers, J.  2017.  Understanding Soil Water Content and Thresholds for Irrigation Management.  Oklahoma Cooperative Extension Service, BAE-1537, June 2017.  Division of Agricultural Sciences and Natural Resources, Oklahoma State University. 

Grogan, R.G., and Abawi, G.S. 1975.  Influence of water potential on growth and survival of Whetzelinia sclerotiorum. Phytopathology 65: 122-128.

Hao, J. J., Subbarao, K. V., and Duniway, J. M. 2003. Germination of Sclerotinia minor and S. sclerotiorum sclerotia under various soil moisture and temperature combinations. Phytopathology 93:443-450.

Irmak, S. 2019.  Soil water content – and soil matric potential-based irrigation trigger values for different soil types.  Institute of Agriculture and Natural Resources, CropWatch, University of Nebraska-Lincoln.

Teo, B. K., and Morrall, R. A. A. 1985a. Influence of matric potentials on carpogenic germination of sclerotia of Sclerotinia sclerotiorum. 1. Development of an inclined box technique to observe apothecium production. Can. J. Plant Pathol. 7:359-364.

Teo, B.K., and R.A.A. Morrall. 1985b. Influence of matric potentials on carpogenic germination of sclerotia of Sclerotinia sclerotiorum. II. A comparison of results obtained with different techniques. Can. J. Plant Pathol. 7: 365-369.

Figure 1.  Disease cycle of sclerotinia stem rot of canola.  Courtesy of Taryn Dickson, Resource Manager, Crop Production and Innovation and the Canola Council of Canada (

Figure 2.  Percentage of normal soil moisture (drought model) as of June 12, 2023.  Courtesy of Agriculture and Agri-Food Canada's Science and Technology Branch, AAFC Geomatics.  

Figure 3.  Percent saturated surface soil moisture from SMOS satellite data, June 5-11, 2023.  Courtesy of Agriculture and Agri-Food Canada's Science and Technology Branch, AAFC Geomatics.

Figure 4.  Difference from long term average, percent saturated surface soil moisture from the Soil Moisture and Ocean Salinity (SMOS) data, June 5-11, 2023.  Courtesy of Agriculture and Agri-Food Canada's Agroclimate Geomatics and Earth Observation Division.