Digging Deeper Case #09 Almond Alternaria & Standing Water

Jun 20, 2020 | Blog

Here’s what the scene lookEd like: 


  • Necrotic spots on leaves, primarily on lower leaves anthose near the outside of tree
  • Moderate leaf drop
  • Spots were noticed mid-May and continued to worsen for several weeks
  • Areas of standing water were present throughout the field; trees nearer to standing water showed worse symptoms (photo below shows an extreme case of the standing water; tree symptoms go beyond those considered in this case)
  •  Digging around the wet pattern showed that water was penetrating to 8″, but not to16″ in most places 
  • Symptoms spanned approx. 40 acres and affected all varieties
  • Neighboring almond fields (other farming companies) did not show symptoms; however, about 6 miles away another almond ranch (same farming company) showed similar symptoms.


  • Monterey, Nonpareil and Wood Colony almonds, 5th year, Kern county CA 
  • Drip irrigation, medium-textured soil 
  • No history of Alternaria 
  • Field spread gypsum had been banded in previous fall to address water infiltration issues (6-8 months prior)
  • Irrigation water is known to have water chemistry issues that result in reduced infiltration
  • Field is located in an area known to have low wind speed


Here’s what we know about Alternaria, standing water & almonds: 

  • “Alternaria” or “Alternatia Leaf Spot” are common names for a disease that affects multiple crops, including almonds. In almonds the disease can be caused by various pathogens, including Alternaria alternata, Alternaria arborescensAlternaria tenuissima 
  • Alternaria primarily affects the leaves and can be identified by a spot on the leaf that has a yellow/brown/dead ring around a black center that can be up to the size of a pencil eraser.  
  • In order for a pathogen to take hold in a plant, three factors must be present:
    1. Virulent pathogen
      Like many pathogens, this one can typically be found in any almond field in this area. It sits and waits for the right opportunity. [Alternaria Study]
    2. Susceptible host
      The Monterey variety is known to be particularly susceptible to this type of fungus.
    3. Suitable environment
      The Alternaria pathogen requires a warm, damp environment, or “leaf wetness”. Suitable conditions can be achieved during summer if there is limited airflow and sufficient humidity. A dense canopy can increase humidity and reduce airflow.

[Alternaria Growth & Temperature] 

 [Alternaria Growth & Humidity]


  • Common causes of standing water or poor water infiltration include deflocculated soil due to poor soil/water chemistry, mechanical compaction and over-irrigation. 


Connecting the Dots: 

  • An in-field humidity sensor shows periods of increased humidity around the same time the symptoms appeared.
  • There isn’t a dedicated weather station in this particular field so we don’t have the specific temperature or wind speed, but data from a local CIMIS weather station confirms that symptoms appeared during a time of relatively high temperatures with very little wind.
    • Around the time of infection the canopy was dense and the standing water made for a pretty muggy experience. (note: photo taken in section where alternaria had progressed to defoliating the trees)



    While poor infiltration does not directly result in a flare-up of Alternaria, it can help create the right field conditions for it. Standing water + summer heat + dense canopy creates the nice, damp, relax-in-the-sauna environment that Alternaria is just waiting for, and you can count on a pathogen to make the most of an opportunity!

    Based on their findings, the agronomists recommended that the grower modify the environment to be less-suitable for the pathogen; specifically, reduce the humidity by getting rid of the standing water. Since the standing water was likely due to imbalanced soil chemistry, they recommended the following:

    “Apply gypsum to the affected field. Ideally amend the irrigation water so that the gypsum is exactly where the water is, with every irrigation. This will improve soil flocculation and allow for better water infiltration.”

    The grower did not have the ability to amend the water, but applied field spread gypsum in tight bands following irrigation lines. Shortly after applying the gypsum, the soil moisture sensor data at 16″ and 24″ showed the water infiltrating noticeably deeper into the soil for about 3 weeks.

    Agronomists returned for a follow-up visit and noted that the standing water was greatly reduced.  The spread of Alternaria symptoms was noticeably slowed following the gypsum application. 


    What the field really needed was to have the water amended with gypsum.

    The field-spread application of gypsum was a good short-term solution, but infiltration problems  re-appeared (and possibly Alternaria symptoms) due to the effect of poor water chemistry on the soil. 

    At harvest the infiltration issues had returned, causing very wet drive rows. To prepare for harvest  the rows had to be dried out, causing excessive stress on the trees.

    The drip irrigation line in the field processed some of the applied gypsum, however most of what was applied never made it into the soil. Due to the small footprint of drip irrigation the majority of the applied gypsum was never activated and incorporated into the soil. It is estimated that of the 1 ton per acre application of gypsum that went on the field, only about 10-15% of it was actually activated. Leaving the majority of it sitting on the surface.


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