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Pecan bacterial leaf scorch is transmitted from pecan nuts to rootstock

A green bunch of pecan leaves with brown and shriveling edges. This leaflet shows symptoms of the emerging disease Pecan Bacterial Leaf Scorch, or Xylella fastidiosa.

Pecan bacterial leaf scorch symptoms on leaves. (Photo by Dr. Young-Ki Jo)

Pecan bacterial leaf scorch is caused by the bacteria, Xylella fastidiosa, a plant pathogen that can infect at least 655 different plant species. Pecan bacterial leaf scorch (PBLS) is a chronic disease that can occur year after year and cause significant disease symptoms in susceptible cultivars. The disease is widespread across the southern pecan-growing region of the United States, including Arizona, New Mexico, Texas, Louisiana, and Georgia [1-3].

PBLS symptoms include tan to brown leaf tips and edges, which spread toward the base of the leaf and eventually lead to defoliation. Symptoms can occur on individual branches or across the entire canopy. Severe PBLS disease symptoms have been reported to result in up to 58% premature defoliation of the canopy by the end of the growing season, as well as a 10 to 13% reduction of inshell nut weight and a 14 to 19% reduction in kernel weight in the susceptible cultivar ‘Cape Fear’ [4].

Xylella can be transmitted in pecan by insect vectors, such as pecan spittlebug and sharpshooters, and through the grafting of scions onto seedling rootstock [5]. Previous scientific reports have found graft transmission rates of Xylella from uninfected scions onto PBLS-infected rootstocks to be up to 85% [6]. Improved pecan cultivars are produced by grafting clonal scions from a known cultivar onto genetically diverse rootstock seedlings. The rootstock is cultivated from seedlings sprouted or germinated from open-pollinated nuts before grafting.

PBLS symptoms on rootstock versus in the canopy (scions).

Pecan bacterial leaf scorch symptoms on rootstock versus in the canopy (scions).

Xylella had been previously detected in developing nuts. Yet, it was unknown if the bacteria could also infect mature nuts (after shuck split) and be transmitted from the nut to germinated seedling rootstock. The presence of Xylella in nuts could have consequential impacts on the horticultural practices of the industry, particularly given the high rates of transmission from grafting uninfected scions onto PBLSinfected rootstocks.

In a recent study, scientists from USDA-ARS, Texas A&M AgriLife, and New Mexico State University sought to determine whether Xylella was indeed being transmitted from nuts to seedling rootstock [7]. They started by confirming the presence of the bacteria in the nut sap—otherwise known as liquid endosperm—of developing pecan nuts undergoing water stage during late nut sizing. The timing of the water stage is dependent on the cultivar, but in the United States, it most commonly occurs from July to early August. A total of 180 nuts at the water stage were collected from ‘Bradley,’ ‘Wichita,’ ‘Mandan,’ ‘Lakota,’ and ‘Nacono’ (18 pecan trees total, with 10 nuts sampled from each tree). A sterile syringe was used to extract the liquid endosperm from the developing integument, where the nut kernels would eventually form. The endosperm was then diluted in water and diagnosed for Xylella.

 Figure 2 compares the number of positive versus negative samples with Xylella found in various cultivars. The proportion of developing nuts sampled from 18 trees that were diagnosed positive for Xylella.

Figure 2—The proportion of developing nuts sampled from 18 trees that were diagnosed positive for Xylella.

The researchers used a diagnostic technique known as polymerase chain reaction (PCR). PCR allows for making billions of ‘copies’ of the target DNA, in this case Xylella, and allows scientists to determine the presence and amount of bacteria within a sample. They found that 14 out of 18 trees had nuts that were diagnosed positive for this pathogen. A high percentage of nuts were contaminated, with as much as 60% of the nuts collected from a ‘Wichita’ tree testing positive.

Next, the scientists wanted to know if Xylella could be found in mature pecan nuts following shuck split. A total of 72 mature nuts from six PBLS-infected trees were tested by PCR. The pecan nuts diagnosed positive for Xylella ranged from 50 to 90%.

To determine where the bacteria were located within the nut, mature nuts were harvested from a ‘Cape Fear’ tree at the USDA ARS National Collection of Genetic Resources for Pecans and Hickories (USDA ARS NCGR-Carya) in College Station, Texas. The nuts were dissected into four anatomical parts: the embryo, outer integument, vascular integument, and the hilum. The embryo is where the earliest forms of the seedling’s roots, stems, and leaves originate, where germination occurs. The integument is the kernel’s skin, and part of it serves as a vascular structure where sap, endosperm, and nutrients can travel during the nut’s development. The hilum is a scar that marks where the nut was originally attached to the stem of the mother tree. Xylella concentrations were detected by PCR and compared to determine where it predominately resides within these different parts of the nut. They found that the bacteria was most present in the hilum and vascular integument.

With new evidence to show that Xylella is found in both developing and mature pecan nuts, the scientists then needed to determine whether the bacteria was moving into germinated seedlings. They planted 114 nuts into a potting soil mixture to determine the presence of Xylella in germinated pecan seedlings. Thirty seedlings successfully germinated, with nine exhibiting classic PBLS symptoms that included tan to brown lesions on leaves and leaf defoliation. Of the 30 seedlings tested by PCR, 27 were diagnosed as positive for Xylella. It is important to note that 18 seedlings tested positive for the bacteria but did not display PBLS symptoms. This confirms that PBLS-infected seedlings may not always show symptoms of the disease.

Figure 3 maps out the different parts of the kernel and where in the anatomical structure the most Xylella was found. The average amount of Xylella in different parts of mature nuts (2^-(ΔΔCt) indicates the amount of Xylella DNA present in comparison to the total amount of pecan DNA).

Figure 3—The average amount of Xylella in different parts of mature nuts (2^-(ΔΔCt) indicates the amount of Xylella DNA present in comparison to the total amount of pecan DNA).

Like the nut study, the scientists also wanted to know where Xylella predominately resides within different parts of the seedling. Scientists dissected eight ‘Cape Fear’ seedlings into four anatomical parts: stems (shoots), leaves (leaflets), petioles (which connect the leaf to the stem), and roots. All of these seedlings had symptoms of PBLS, and all tested positive. The highest Xylella concentrations were in the petioles, but bacteria were also found in the stem, leaves, and roots.

High-quality nuts with high inshell kernel weight are important for guaranteeing good nut germination. PBLS symptoms in the tree canopy, such as early or premature defoliation, can negatively affect inshell nut and kernel weight. Therefore, it was critical to determine how Xylella infection of the nut influences quality indicators, such as nut fill.

A total of 150 nuts were collected from a ‘Cape Fear’ tree in College Station, Texas. The nut fill (density) was estimated, and the nuts were separated into three groups: high nut fill, medium nut fill, and low nut fill. The nuts were then cut into halves, and the half containing the embryo was planted into potting soil for germination. The remaining half of the nut was tested by PCR to diagnose Xylella. Germination rates of nuts with a high nut fill were higher than medium- and low-filled nuts. The seedlings that germinated from high and medium-filled nuts also grew at a faster rate than seedlings originating from low-filled nuts. Yet surprisingly, the high nut fill group had a significantly greater number of nuts that tested positive for Xylella by PCR than the low-filled nut group. This finding would indicate that the presence of Xylella in nuts does not necessarily equate to poor nut fill.

The amount of the pathogen in different parts of ‘Cape Fear’ seedlings (2^-(ΔΔCt) indicates the amount of Xylella DNA present in comparison to the total amount of pecan DNA).

Figure 4—The amount of Xyllela in different parts of ‘Cape Fear’ seedlings (2^-(ΔΔCt) indicates the amount of Xylella DNA present in comparison to the total amount of pecan DNA).

In summary, the USDA, Texas A&M AgriLife, and New Mexico State University scientists found Xylella in developing nuts, mature nuts, and seedling rootstock. Not all of the seedlings that were diagnosed had disease symptoms of PBLS. Xylella is a diverse pathogen, and not all individuals may be capable of causing disease in the plant. There are different subspecies (types) of Xylella. Previous research on the bacteria seems to indicate that specific Xylella types produce disease in specific plant hosts compared to others. Thus, although Xylella may be transmitted from nut to seedling rootstock, there are several instances where this may not result in ‘disease.’ It may be due to the type and amount of Xylella within the nut or seedling.

The impact of nut fill on the germination and growth rate of ‘Cape Fear’ seedlings.

Figure 5—The impact of nut fill on the germination and growth rate of ‘Cape Fear’ seedlings.

Certain cultivars are more susceptible to infection by Xylella and, therefore, may be more likely to show symptoms of the disease. For example, ‘Cape Fear’ and ‘Cheyenne’ have been found to be severely affected by PBLS and consistently show disease symptoms, whereas ‘Pawnee’ and ‘Stuart’ are thought to be only moderately or minimally affected by the disease. No cultivars have been found to be completely resistant to PBLS. Environmental conditions also likely play a strong role in whether or not PBLS symptoms develop in seedling rootstock or mature grafted trees. Therefore, symptomatic infections can depend heavily on the type and amount of Xylella bacteria involved, the host cultivar, and the environmental conditions of the region in which the tree is planted.

Scientists still do not know how Xylella enters the nut during nut development. High concentrations of the bacteria found in the hilum would indicate that it is entering the nut from the mother tree. During pecan nut development, a vascular system exists, which allows water and nutrients to travel from the mother tree into the nut. The pathogen may be able to travel through this vascular system from a PBLS-infected mother tree into the nut.

Figure 6 shows two charts that compare the nut fill to the percentage of nuts tested positive for Xylella and also the amount of pathogen found in the nut.

Figure 6—The relationship between nut fill and the presence and amount of Xylella. (2^-(ΔΔCt) indicates the amount of Xylella DNA present in comparison to the total amount of pecan DNA).

It is also possible that Xylella is being transmitted into the nuts through insect vectors, including spittlebugs and sharpshooters, feeding on the nut shucks during development. For example, pecan spittlebugs are known to gather in colonies on pecan stems bearing nut clusters in the tree canopy during the early period of the growing season. It is recommended that chemical control methods be used to kill pecan spittlebugs, or other pests, feeding heavily on developing nuts to protect the crop and ensure high yields at harvest time. Imidacloprid is one such pesticide that has been approved for use in controlling pecan spittlebug populations.

Pecan production has expanded to South Africa, Australia, China, Uruguay, Argentina, and Brazil, and production is expected to increase over the next 30 years. Nut to seedling rootstock transmission increases the likelihood that Xylella will spread to pecan-producing countries outside the United States that were previously free of the pathogen.

Xylella is able to easily adapt to new environments and can jump from one plant species to another through mixing with other types of Xylella bacteria or by overcoming the defense strategies of susceptible hosts. For example, Xylella was recently introduced to Italy through infected coffee plants. The pathogen was able to jump from coffee plants to olive trees, causing a disease known as Olive Quick Decline Syndrome (OQDS), which has led to severe infection and the death of over a million olive trees. Xylella is also responsible for causing significant yield reductions in other host crops, such as grapes and citrus, where industry losses are estimated to be over $100 million annually.

The International Plant Protection Convention, governed by the Commission on Phytosanitary Measures (CPM), recognizes Xylella as one of six major international pests. They have adopted and implemented over 100 international standards for diagnostics and phytosanitation to control the spread. Hot-water treatment of scions and other graftwood has been developed but is not completely effective in eliminating this pathogen, and no treatment is currently available for nuts or seedling rootstock [8]. Experiments looking into potential nut treatments are underway. Phytosanitary distribution requirements have not yet been evaluated for pecan nuts but are expected given this new evidence for the nut to seedling rootstock transmission.

It should be mentioned that Xylella is not a human pathogen. The distribution of nuts for human consumption will not be threatened by this new evidence of nut to seedling transmission of PBLS. This is a horticultural issue that will affect the transport and distribution of nuts used as seed stock for growing seedling rootstock. The industry’s global export of nuts as a food source will remain unaffected.

Due to the increasing global movement of plant material and the great demand for pecans worldwide, major challenges include disease surveillance, detection, and diagnosis. Understanding how pathogens spread, especially Xylella fastidiosa, are critical to gauging risks and developing mitigation and phytosanitary protocols and regulation.

Disclaimer: Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture (USDA). The USDA is an equal opportunity provider and employer. 

  1. Sanderlin, R. and K. Heyderich-Alger, Evidence that Xylella fastidiosa can cause leaf scorch disease of pecan. Plant Disease, 2000. 84(12): p. 1282-1286.
  2. Bock, C.H., et al., Pecan bacterial leaf scorch, caused by Xylella fastidiosa, is endemic in Georgia pecan orchards. Plant Health Progress, 2018. 19(4): p. 284-287.
  3. Hilton, A., et al., First report of pecan bacterial leaf scorch caused by Xylella fastidiosa in pecan (Carya illinoinensis) in Arizona, New Mexico, California, and Texas. Plant Disease, 2017. 101(11): p. 1949.
  4. Sanderlin, R. and K. Heyderich-Alger, Effects of pecan bacterial leaf scorch on growth and yield components of cultivar Cape Fear. Plant Disease, 2003. 87(3): p. 259-262.
  5. Sanderlin, R. and R. Melanson, Insect transmission of Xylella fastidiosa to pecan. Plant Disease, 2010. 94(4): p. 465-470.
  6. Sanderlin, R. and R. Melanson, Transmission of Xylella fastidiosa through pecan rootstock. HortScience, 2006. 41(6): p. 1455-1456.
  7. Cervantes, K., et al., Evidence for Seed Transmission of Xylella fastidiosa in Pecan (Carya illinoinensis). Frontiers in Plant Science, 2022. 13.
  8. Sanderlin, R. and R. Melanson, Reduction of Xylella fastidiosa transmission through pecan scion wood by hot-water treatment. Plant Disease, 2008. 92(7): p. 1124-1126.
Author Photo

Drs. Angelyn Hilton, Kimberly Cervantes, and Jennifer Randall

Dr. Angelyn E. Hilton is a Research Geneticist with the USDA ARS Crop Germplasm Unit at the USDA Pecan Breeding Program and Germplasm Repository in College Station, Texas. Dr. Kimberly Cervantes, Research Associate, Department of Entomology, Plant Pathology, and Weed Science, New Mexico State University. Dr. Jennifer J. Randall is a Professor within the Department of Entomology, Plant Pathology, and Weed Science at New Mexico State University and the current director of the Molecular Biology and Interdisciplinary Life Sciences Graduate Program.