Back to November 2017

Not Just Cotton, Not Just Roots, Cotton Root Rot Affects Pecan Trees

Impacting orchards from Texas to Arizona, cotton root rot is not an epidemic but a risk that should be understood.


Th is tree in New Mexico is infected with cotton root rot and is dying. (Photo by Richard Heerema)

Compared with our pecan-growing friends in the humid central and eastern production areas, we in the western states, fortunately, have very, very few plant disease issues that we struggle with on a regular basis in our pecan orchards. Sometimes I’ll even hear folks say that we don’t have any pecan diseases out here because it’s just too dry. But, in reality, that’s not quite true.

We actually do have a few pecan tree diseases that can give us grief out here in the West, and the worst of these is a fungal disease called cotton root rot. Cotton root rot has a couple of other names. It’s also called Texas Root Rot or, less commonly, Phymatotrichum Root Rot.

The Confusing Names

Unfortunately, all of the names of this disease can create confusion about the disease. The name cotton root rot causes many people to conclude that it is caused by growing cotton in a field prior to planting the orchard there or by planting cotton as an inter-crop after the orchard has been planted. But that name actually comes from the fact that cotton plants are also very susceptible to this disease, and many of the cotton root rot infested fields in the southwestern states are in cotton production areas. Fields that have never had any cotton planted in them are not necessarily any less likely to have cotton root rot present in them than ones that have had many years of cotton planted. And actually, the reverse scenario might be true since cotton farmers may have abandoned highly infested sites decades ago.

The Texas root rot name also creates confusion because it falsely seems to imply that the disease originated in Texas and spread to other states from there or that it is only found in Texas today. Texas root rot has always been present in pecan-producing areas of New Mexico, Arizona, Oklahoma, and Texas (as well as some of the northern Mexican states). It did not come from Texas.

Finally, there’s a problem with the name Phymatotrichum root rot too (and not just the fact that it is just about impossible to pronounce or spell, let alone remember). I think the problem with this name is that if you read it a little too fast it looks a lot like the name of another disease-causing organism, Phytophthora. Phytophthora can also cause root or crown rot diseases on a number of crops—including a number of different fruit and nut tree crops.

One species of Phytophthora has been reported to cause a shuck and kernel rot in pecan, but, to my knowledge, no root rot-type diseases caused by Phytophthora have been reported in pecan.

Making the distinction between Phymatotrichum and Phytophthora may sound trivial (they’re both root rots, right?), but it’s not at all trivial because many of the practices that can be used to manage Phytophthora root and crown rot in other tree crops are not likely to help against Phymatotrichum root rot in pecan.

Description of the Pathogen and Disease

Cotton root rot is caused by the soil fungus Phymatotrichopsis omnivora. That species name “omnivora” should tell you something: this fungus is not a picky eater! There are well over 2000 different broadleaf plant species that are vulnerable to infection by this fungus. Interestingly, however, grasses and other monocots (like palm trees) are completely resistant to cotton root rot and many of the broadleaf plants native to the southwest—like mesquite, creosote, desert willow, and palo verde—seem to be tolerant to cotton root rot.

In the region where it occurs, cotton root rot can be found in field sites below 5,000 feet elevation where soils are calcareous, alkaline pH and contain very little organic matter. Fields infested with the cotton root rot fungus often have a patchy distribution of the fungus throughout the field.

The fungus does not seem to spread much through the soil. If it does spread, it spreads very slowly root to root from infected plants to adjacent uninfected plants, and there is no known mechanism for the above-ground spread of cotton root rot.

In field crops, the patches with cotton root rot show up in the same spot season after season. In pecan orchards, this disease often shows up within a few years of planting, but sometimes it can take many years, even decades, before a pecan tree starts showing any symptoms of cotton root rot. Often, a single pecan tree, or only a few adjacent trees, may exhibit symptoms of the disease with all of the other surrounding trees showing no symptoms at all.

The fact that it doesn’t really seem to spread is the good news. Now the bad news: Cotton root rot kills plants.

When this fungus infects a root system, the roots die, preventing adequate nutrient and water transport to the top of the plant, killing the plant. Cotton root rot usually strikes when both the temperatures and the plant’s water needs are high.

In many instances, infected pecan trees die extremely quickly after any above-ground symptoms start appearing (growers describe it as “overnight”), leaving dark brown, crispy leaves still attached to the tree. In other cases, the leaves turn yellow and then bronze with the trees dying a bit more slowly.

Either way, the tree dies.

Diagnosis and Management of Cotton Root Rot

To determine whether trees in your orchard have cotton root rot, you should sample roots from suspect trees. Collect several root segments of pencil-thickness to send to your state’s plant diagnostic clinic. There is no need to send in any huge scaffold roots, but if the tree is small and has already died, it may be helpful if you sent in the entire root system. Unlike with many other plant diseases, accurate diagnoses may be made from a sample collected from trees that have already died.

Your lab will probably make the diagnosis based on the morphology of fungal strands as they appear under the microscope. Cotton root rot has a unique cross-shaped strand that allows for relatively easy identification (if you have a good compound microscope, you could actually learn to do this diagnosis yourself).

There has been a lot of research on cotton root rot over the years, but there are still few reliable management options available. Chemical management options at this point are very limited and of uncertain value. Pretreating soils with fumigants prior to planting is likely to be ineffective against cotton root rot because the pathogen lives far too deep in the soil. There has recently been a lot of interest in a systemic fungicide that has shown efficacy against cotton root rot in cotton and some other crops. At this point, it is unclear how well this fungicide will work long-term in a pecan orchard, but studies at the University of Arizona are underway to test this question.

Some amendments to acidify the soil or increase the soil have long been tried with limited success in staving off pecan tree death in cotton root rot infested orchards. You may read more about studies that lead these efforts by going online to New Mexico State University’s publication on pecan diseases and disorders and Phymatotrichum root rot.

The best management option right now is to avoid planting pecans in cotton root rot infested sites. For starters, my recommendation is to study historical aerial or satellite images of a planned orchard site before the trees are planted. This approach only works if the field was planted to a susceptible crop in the relatively recent past. Google Earth has a function that allows you to view historical satellite images back to early 2000s or mid-1990s for many locations.

If you look at images of the proposed site over time, you may be able to learn a great deal. Look for patches, often roughly circular in shape, where the color is lighter than the crop being grown or perhaps a different shade of green (grassy type weeds often fill in the bare patches). This could be an indication of cotton root rot in that site. Better yet, grow some alfalfa on your proposed orchard site for a few years before you put trees in. Alfalfa, a perennial, is an especially good “canary in the coal mine,” letting you know if there are problem areas. Very susceptible to cotton root rot, alfalfa has an expansive root system that explores deep and wide in the soil.

At this time, there are no cultivars that are known to be resistant to Cotton Root Rot. At the Texas Pecan Growers Association conference in July, Larry Stein, Ph.D., from Texas A&M University in College Station, Texas presented some very interesting research results from a pecan rootstock cotton root rot tolerance screening study. That study, conducted from 2013-2017 in a field that was severely infested with cotton root rot fungus, showed that certain seedling rootstock selections—such as ‘Riverside’ and ‘Apache’—exhibited greater tolerance for this disease than others.

This is extremely encouraging information, especially as we enter the age of cloned pecan rootstocks in the years to come. I am optimistic that in the future we will have options for resistant or tolerant rootstocks.

Author Photo

Richard Heerema

Richard Heerema is the pecan specialist at New Mexico State University, Las Cruces, New Mexico. rjheerem@nmsu.edu