Back to June 2019

Soil Health: Does your orchard need a checkup?

This microscopic view of a Switchgrass root appears like a thick, brown line with tiny blondish root hairs branching off of it. The Serendipita mycorrhiza appear like fuzzy, thin, white lines in the background.

Endomycorrhizae Serendipita vermifera subsp. bescii growing on Switchgrass (Panicum virgotum L.) (Photo by Kelly Craven)

Over the last few months, I have visited many potential pecan orchard sites in several states. As always, one of the first topics discussed is the soil at the proposed site. The importance of a good soil for pecan production cannot be overemphasized. Planting a pecan orchard is not a short-term goal and it often involves not just the current generation but also the next—inherited by children and then grandchildren. For a commercial pecan operation to be successful, selection of a good soil allowing optimum tree growth and nut production is one of the most important decisions you will make.

Pecan trees are not only large above the ground but they also have a massive root system that spreads over large areas and penetrates deeply to obtain moisture and nutrients. We’ve all heard the basics. Soil is comprised of minerals, organic matter, water, air, and microorganisms. Most textbooks will quote a ratio of 50 percent minerals and organic matter, 25 percent air, and 25 percent water. In plain English, good soil sites contain adequate amounts of plant nutrients, good air exchange characteristics, good internal soil drainage, and the ability to store large volumes of water.

Not static, the soil system is an ever-changing, dynamic system that is exceedingly complex to manage correctly. Healthy pecan trees’ growth and development depend on healthy roots. While soil’s role in optimizing pecan production is often ignored or forgotten, the continued stewardship of the soil is necessary for pecans to stay productive, and you must always consider how your cultural management decisions will affect your trees in the future. Last month, someone called my attention to the short overview of the “Underwear Soil Test” on page 252 of the 2019 The Old Farmer’s Almanac. For you neophytes unfamiliar with this test, you bury a pair of new cotton underwear 6 to 8 inches deep in your field and check on its status after two months. The condition of your underwear will give you an indication of your soil’s “Organic Quality,” or the population of earthworms, fungi, bacteria, and other microscopic organisms in your soil. Today, instead of soil quality, we will refer to it as soil health.

Soil health? Some people might question this term and suggest that only living things can have health. Am I suggesting that a soil can get sick and we’ll have to call the “soil doctor” to help it get better? Well, perhaps your orchard does need a checkup. The first thing we have to realize is the soil isn’t an inert growing medium like we use in the greenhouse but rather a home to billions of bacteria, fungi, and other microbes that make up the foundation of a healthy symbiotic ecosystem. Although each one of these organisms brings something unique, this article will explore one of these: fungi. The fungi are typically divided into three functional groups: decomposers, pathogens (parasites), and mutualists.

The first group—decomposers or saprophytic fungi—act as a cleanup crew. Pecan orchards generally have a lot of dead organic matter from several sources. The trees contribute leaves, shucks, and dead limbs. Additionally, mowing the orchard floor results in a lot of organic matter. Some orchard managers will use chicken litter or manure as a fertilizer source in the orchard, while weed control using organic mulch is another common practice in some orchards. In the central pecan growing region, it is a common practice to graze cattle in native groves, which adds to the pile-up of dead organic matter. Fungi play a very important part in the decomposition process because they can break down tough organic materials, such as cellulose and lignin, which invertebrates find difficult to digest. These fungi also release extracellular enzymes that metabolize complex organic compounds into soluble nutrients, such as simple sugars, nitrates, and phosphates. A few fungi are called “sugar fungi” (Saccharomyces) because they use the same simple substrates as do many bacteria. These bacteria and fungi are important for immobilizing, or retaining, nutrients in the soil. In addition, as dead organic matter is converted to fungal biomass, carbon dioxide, and other secondary metabolites, these secondary compounds—such as organic acids—help increase the accumulation of humic-acid rich organic matter that is resistant to degradation and may stay in the soil for many years.

The second group, pathogens or parasites cause reduced production or death when they colonize roots and other organisms. Root-pathogenic fungi, such as Phymatotrichopsis and Phytophthora, cause economic losses in pecans each year. Many fungi help control diseases by keeping pathogenic fungi from reaching and infecting the tree root system. Additionally, nematode-trapping fungi that parasitize disease-causing nematodes and fungi that feed on insects may be useful as biocontrol agents.

The last functional group of fungi, mutualists give just as much as they take. Symbiosis is the ecological interaction between two dissimilar organisms intimately living together with one or both receiving benefits. When both members of the association benefit, the symbiotic relationship is called mutualistic. This concept applies to the mycorrhizal fungi, which colonize plant roots. In exchange for carbon from the plant, mycorrhizal fungi facilitate the transfer of soil nutrients (phosphorus, nitrogen, micronutrients, and perhaps water) from the soil into the plant roots.

Mycorrhizae are divided into several types. The ectomycorrhizae grow on the surface layers of the roots and have a Hartig net of hyphae that physically extends into the root but between the cells. This type is most commonly associated with trees. The second major group of mycorrhizae are the endomycorrhizae that grow within the root cells and are commonly associated with grasses, row crops, vegetables, and shrubs. Arbuscular mycorrhizal (AM) fungi are a type of endomycorrhizal fungi. In these mycorrhizas, the fungi form arbuscules that penetrate root cells and are the site of the metabolic exchanges between the fungus and the host plant.

Mycorrhizal associations may also decrease attack from root pathogens and increase the plant’s tolerance to adverse conditions such as heavy metals, drought, and salinity. In general, mycorrhizas play an important role in sustainable plant productivity and maintenance of soil structure.

Additionally, mycorrhizas can increase plant uptake of phosphorus and trace elements. They do this by extending the volume of soil explored by the plant. Mycorrhizal fungi are characterized by very thin hyphae, which are between 1 and 10 thousandths of a millimeter in width, but these hyphae create vast networks into the soil well beyond the existing tree root system. In fact, the hyphae form networks between neighboring soil particles, between roots and soil particles, between roots on the same plant, and between roots of different plants (even different types of plants). When phosphorus is scarce in soil, plants that have developed mycorrhizas on their root systems have greater access to and take up more phosphorus than others. Trace elements, copper, and zinc behave in a similar way to phosphorus in soil and plant roots must explore the soil to intercept them.

Ectomycorrhizal fungi can change the growth form of plant roots by promoting root branching and restricting root extension. The hyphal mantle over the surface of the roots can provide protection against the entry of pathogenic soil fungi and the hyphal network in soil surrounding roots allows water uptake from more soil. These effects on plant growth combine to make the associated plant more robust and increase its chances of survival.

Most trees will typically only form an association with one type of mycorrhiza, either endomycorrhiza or ectomycorrhiza. However, research has shown that pecan is able to associate with both types. It appears to prefer ectomycorrhiza with colonization by arbuscular mycorrhiza usually only occurring on less than one-third of the root system. A question that still must be answered is “Does this dual association provide pecan trees an advantage in soil exploration for nutrients and is this one of the reasons pecans are able to expand into geographically different environments so easily?”

Knowing the impact mycorrhizal colonization can have on pecan tree health increases the importance of your pecan orchard management decisions. Management choices affect the amount of soil organic matter, soil structure, soil depth, and water and nutrient holding capacity. Should you choose a cover crop that contains a wide range of plant species or is a monoculture of clover acceptable? Should you fertilize the orchard with animal manure or continue to use a synthetic fertilizer? The use of different kinds of organic manure has a strong influence on soil health through indirect effects (i.e., via changes in physicochemical characteristics) and a direct effect on soil fungal communities. Does the use of organic mulch for weed control take on a whole new meaning and importance? One goal of soil health research is to answer these questions and learn how to manage soil in a way that improves soil function. Understanding and selecting the appropriate cultural practices and/or increasing fungal biodiversity can prevent or decrease the damage from root diseases and play a crucial role in the maintenance of soil quality and health.

Soil will work for you if you work for the soil by using management practices that improve soil health and increase productivity and profitability. A fully functioning soil produces the maximum number of products at the least cost; therefore, maximizing soil health is essential to maximizing the profitability of your orchard. In plant productivity, cultivating soil fungal biodiversity through potential application poses a new and promising development to improve your soil quality, increase agricultural ecosystems’ productivity, and most importantly, help your soil pass its checkup.

Author Photo

Charlie Graham

Charles J. Graham is the Senior Pecan Specialist at the Noble Research Institute. Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401; E-MAIL: