Soil Microbiome Benefits for Tree Nuts

Figure 1: How soil microbes (fungi and bacteria) improve tree nut soils and crop performance4 (courtesy K. Wyant.)

Without a doubt, West Coast growers are exceptional at producing a wide variety of nuts, including almonds, walnuts and pistachios, that are enjoyed across the globe. Furthermore, progress in advancing best practices in nut crop production, plant breeding programs, nutrient and pest management, and using the latest in agricultural technologies are widely recognized. The next frontier for tree nut growers and their crop advisor partners is to promote new practices that encourage the long-term sustainability of farms for future generations.

Two important components of on-farm sustainability programs are soil health and soil quality. Soil health refers to the biological integrity of a field and includes practices that optimize the living, biological components of a soil6. Soil quality refers to how well an agricultural soil does its “job”, and we often use measurements of soil structure and water storage along with typical measurements of crop yield and quality to keep track of this.

Researchers recognize a strong link between soil health and quality and crop performance. A recent article demonstrates this connection quite clearly and shows the power of committing to a program that builds soil health and quality on the farm3. For example, when California almond growers adapted soil health management practices into their operation, nut yields increased by 10% to 20% over time. These practices include upgrading the irrigation system to double line drip, laying down mulch made from pruned branches, using compost and building out a custom fertilizer program that includes products that help optimize the biological components of a soil. Another important research study shows that practices that help improve soil health and quality, such as reducing tillage, are critical for the long term sustainability of tree nut production2.

The remainder of this article will focus on the key connection between soil microbes and tree nuts and how a grower can optimize the living component of their soil by incorporating several practices into their operation (Table 1) to help drive soil health and soil quality improvement programs. But first, some agronomy basics on soil microbes and how they positively impact your trees.

Table 1: A brief listing of soil health and quality practices that can be deployed in the field5 (courtesy K. Wyant.)


Importance of Soil Microbial Activity

Although soil microbes, including bacteria and fungi, are microscopically small, they can have an enormous impact on the performance of your nut crop and are critical indicators of overall soil health and quality. According to a recent study, soil microbial communities associated with tree crops are critical for their long-term growth and development, particularly under challenging soil conditions1,4 (Fig. 1). Healthy soil microbial communities are known to help optimize above ground plant productivity, improve the availability of nutrients and water, and mitigate the negative impacts of abiotic stressors (e.g. heat/cold, low/high soil moisture, excess salinity, etc.) and toxic compounds for the associated crop4,5. With this agronomic underpinning, I will outline several key practices a grower can use to improve the soil microbiome.


Feed the Soil Biology

There are billions of bacteria and fungi in your soil that are waiting to be put to work. All they need is a food source to help jumpstart their activity, particularly in the cooler months when root exudate supply from trees is at a minimum. Root exudates act as a food source but are most available during the warmer months when plant growth rates peak (e.g. June to August). Microbes, on the other hand, can be put to work year-round if given the right food source. Microbial food choices include products derived from microalgae, molasses, grocery store waste, worms and compost teas, among others. Focus on providing the soil microbiome a balanced food source (carbohydrate %, protein %, lipids %, ash %) to help optimize both below ground abundance and species diversity.


Cover Cropping

This practice helps keep living roots in the soil, which can have a positive impact on microbial populations and other measures of soil health and quality. As mentioned above, living roots provide a food source for microbes via carbon ‘leaked’ from the roots (exudates), and will help maintain the biological component of your soil in the off-season. Keeping the soil covered can also help reduce wind and water erosion and can also reverse the impacts of soil compaction.


Reduce Tillage

Tillage is a critical tool for growers, but it can slice and dice soil microorganisms and their soil habitat, thereby reducing the biological component of your soil over time. No-till or reduced tillage practices helps to keep soil structure and microbial communities intact. By reducing the physical disturbance to the soil habitat, you can promote more biological activity over the long term.


Incorporate Mulches and Compost

These materials provide a bulk carbon and nutrient source to the soil. If your soil samples tend to come back with a Soil Organic Matter (SOM) reading of less than 3%, consider adding more bulk carbon to the soil to help boost this number over time. Soils with a higher SOM% tend to have better aggregate structure, improved water holding capacity and optimized cation exchange holding capacity. This soil carbon building practice takes commitment as increasing the SOM% is a slow process, especially in the warm, dry areas we produce nut crops in. The mulch and compost will not only improve your soil habitat and provide nutrients to the plants, it will also provide a slower release food source for the microbes.


Irrigation Management

This point may seem out of place, but hear me out. Like human beings, microbes have a certain comfort zone for soil moisture. Too dry, they dehydrate and go dormant. Too wet and they will drown. If you want to optimize your soil microbial community and their potential impact on crop growth, then good irrigation management is crucial. By correcting issues with distribution uniformity and matching irrigation run times to plant demand and soil type, your microbes will benefit along with your trees. Best practices in irrigation and nutrient management also help keep materials on the field and out of local waterways and the groundwater, which is a win/win for everybody.



Tree nut crops have a clear connection to important soil health and soil quality metrics, including a robust and healthy soil microbiome (bacteria and fungi), good soil structure and the soil’s ability to store moisture for crop use during periods of stress (e.g. peak summer irrigation and harvest dry down). Practices that help improve belowground microbial abundance and diversity (Table 1, see page 67) should be considered for optimizing the biological components of a soil and their known positive impact on crop growth and production. Furthermore, an improved soil microbiome can influence soil moisture characteristics, which can help push the crop through periods of abiotic stress. Please take a look at the reference section for some key resources on the connection between tree nut crops and the soil microbiome if you would like to read more.
Dr. Karl Wyant currently oversees the internal and external PhycoTerra® trials, assists with building regenerative agriculture implementation and oversees agronomy training at Heliae Agriculture. To learn more about the future of soil health and regenerative agriculture, you can follow his webinar and blog series at



1. Hollingsworth, Joy. “Overview of Biostimulants in Permanent Crops.” West Coast Nut, JCS Marketing Inc., 2 Nov. 2020,
2. Korzekwa, Kaine. “Keeping California a Powerhouse of Almond Production.” Soil Science Society of America, 30 Nov. 2020,
3. Magnuson, Mary. “Almond Growers Adapt Soil Health Management, Increase Yield 10 to 20%.” The Packer, Farm Journal, Inc., 5 Jan. 2021,
4. Mercado-Blanco, Jesús, et al. “Belowground Microbiota and the Health of Tree Crops.” Frontiers, Frontiers, 30 Apr. 2018,
5. Weil, Raymond R, and Nyle C Brady. The Nature and Properties of Soils. 15th ed., Pearson, 2017.
6.Wyant, Karl A. “Making Sense of Biostimulants for Improving Your Soil.” Progressive Crop Consultant, JCS Marketing Inc., 5 Oct. 2020,