Pruning Wound Cankers Found in Almond Trees

Making pruning cuts on almond trees is risky business. Every cut provides the opportunity for fungal/bacterial pathogens to enter the tree (Think: a cut on you hand can allow bacteria to enter). Once the pathogens enter the tree and successfully colonize, poor tree performance and shortened orchard life can be expected.

Figure 1: Fungal canker associated with a pruning wound on a young tree. Upon bark removal, canker growth and damage is evident.

Fungi are the most commonly found pathogens invading tree wounds. In figure 1, a large pruning cut was made on a super-vigorous first leaf almond. The pruning wound became infected with the fungi Eutypa which grew through the tree causing a large canker. This canker did not become noticeable until the third leaf. Upon bark removal, it is clear that the canker grows outward from the point of origin. As the canker continues to grow, it has the ability to kill branches by girdling (Figure 2), weaken scaffolds which then break (Figure 3), and/or killing the tree by girdling the trunk (Figure 4). Botryosphaeria is another fungi that may cause this problem.

Figure 2: Scaffold killed by fungal canker girdling the vascular tissues of the branch.

Figure 3: Scaffold split caused by weakening of crotch angle by invading fungi.

Figure 4: Tree killed by wood fungal canker girdling the vascular tissue of the tree trunk. Bark removal shows the advancement of the canker.

Irregardless of the possible infection by fungi, trees need to be pruned to shape (young trees), remove unwanted branches, and remove dead/diseased tissue. Knowing this, how can we prune the tree and reduce the chance of fungal infection? Most fungi require moisture/high humidity/rain event to produce spores. These spores are usually transferred by wind-blown rain.

The "window of opportunity" for these fungi to infect almond trees occurs when the tree has an open wound. Large cuts (larger than a quarter) made on an almond tree may take up to 14 days to heal, while smaller cuts can take up to 10 days. This open wound can provide a point of infection for fungi until the cut tissue "heals." At this point it becomes resistant to most infections. To prevent these types of problems, it is advised that growers prune their trees when rain is not forecasted for the foreseeable future (7-10 days). For super-vigorous first/second leaf trees, consideration should be made to prune unwanted branches during a period of low humidity (late summer/early fall). Available pruning wound paints do not appear to be effective in preventing invasion by Eutypa and Botryosphaeria in almond.

Pruning First and Second Leaf Almonds

Written By Brent Holtz, UCCE Madera County Farm Advisor
Pruning after the first growing season is critical in determining the shape and performance of an almond tree. At this time you should select three permanent primary scaffolds that will form the framework of the tree. I have seen quite a few first year trees pruned improperly in Madera County, resulting in premature loss of tree vigor, increased susceptibility to disease, and in some extreme cases the eventual removal of orchards; all because these trees were pruned improperly their first dormant season.

The primary goal of the first dormant pruning is to select three primary branches with as much space as possible between them (fig. 1-A). Wide spacing ensures the best chance of a strong branch attachment that will not split as the tree matures. The three primary scaffolds should be oriented 120 degrees apart when viewed from above (fig. 1-B). Such an arrangement reduces the chance of splitting branches, leaning trunks, and crossing limbs. If possible, one of the three primary scaffolds, preferably the strongest, should grow into the prevailing wind, usually northwest. A strong, vigorous limb on the north side helps keep the tree from being dominated by growth on the sunny south side of the tree.

Pruners should also pay attention to the angle of the primary limbs when selecting them; for the scaffold angle determines whether bark will become embedded between limb and trunk. The ideal primary scaffold grows 45 degrees from the vertical and the horizontal (fig. 1-C). If the ideal limb is not present try to find limbs at least 30 degrees from the vertical or at least 30 degrees from the horizontal. Limbs that grow at too flat an angle tend to lose their vigor and upright orientation. Limbs where the bark becomes embedded will be weak and may split with the first heavy crop.

Why only three primary limbs? No tree needs to have more than three primary limbs. A mature tree with more than three limbs will limit access to limb-shaking equipment. I have seen a few prime orchards in Madera County decline prematurely because they were too large to trunk shake, but because they had more than 3 primary limbs they could not be limb shaken and thus the trees were barked severely while attempting to trunk shake these large trees. Because of tree barking almost every tree had Ceratocystis bark canker, so instead of reaching optimal age and production these orchards were being removed.

What if you can’t find three acceptable primary scaffolds? Selecting two sound scaffolds is better than keeping four poor ones (somebody will probably argue with me here)! After the primary scaffolds have been selected, the next step is to remove all other major limbs that originate from the trunk, and all growth below the lowest primary limb. Pruners should leave small lateral branches on the primaries; this growth promotes scaffold caliper growth and is the first to develop spurs and produce nuts.

Growers can use three methods for pruning the first growing season: short pruning, long pruning, and intermediate pruning. These tree pruning methods do not affect trunk diameter or limb caliper; but production differences related to tree training occur the first few harvests but disappear after trees mature. In choosing the pruning method a grower must decide which is more important, high early production or ease of training during the early growing years, and the grower must also consider the growth habit of the variety and the wind conditions in the orchard. I usually prefer the happy medium-intermediate pruning.

Long pruning
Growers who use long pruning make no major heading cuts on primary on primary scaffolds and retain small lateral branches that will provide leaf surface and early fruiting. This type of pruning allows the tree to develop a natural branching habit. Scaffolds and fruit wood develop quickly, and the canopy, because it is relatively uncontrolled, grows rangy. Long-pruned trees usually need roping or tying (fig. 2-B). Even after being properly tied, limbs may break. If ropes are used, they must be placed as high on the primary scaffolds as possible so that the scaffolds do not bend over them. In this system secondary and tertiary branches are selected from the natural branching of the tree. Long pruning takes time and judgment, and if the pruner is uncomfortable with making second and third level framework decisions, another pruning method other than long pruning may be more appropriate. The main advantage of long pruning is heavy early production. Disadvantages include the need for more work and care the second growing season and greater difficulty in achieving an ideally shaped tree. Willowy growing varieties such as Monterey may be unsuitable for this system of training.

Short Pruning
This type of pruning involves heading each of the three primaries back to 18 -24 inches. Unfortunately I have seen some pruners in Madera County head their primaries back to 12 inches or less--this is much to severe and will lead to “elbow” growths and sharp secondary angle branching. Short pruning done properly (18- 24 inches) stimulates vigorous secondary growth that is largely removed later with thinning cuts. This type of pruning allows growers a large role in shaping trees, because the vigorous regrowth provides many choices for secondary limb selection where you want it. Because short-pruned trees are short in stature, they rarely require roping or tying (fig. 2-D). Keeping trees short is particularly advantageous during the second growing season in areas with strong wind in April and May. Also, in the case of weak trees, short pruning can be a desirable way to stimulate vigorous shoots the next growing season. Although this is an easy pruning method, growers must consider the trade-offs. Heading cuts on vigorous trees can encourage vegetative growth at the expense of early nut production. On short-pruned trees, developing a primary scaffold long enough to limbshake can be difficult.

Intermediate pruning
A compromise between short and long pruning, intermediate pruning contains elements of both. Growers make heading cuts high on the primary scaffolds. These cuts are at 42-48 inches from the trunk, usually at a point just below the closely spaced buds that are common in the last 6 to 12 inches of shoot growth (fig. 2-C). Heading at this distance greatly reduces the number of new shoots that originate near the end of the branch in the second leaf. This reduces the shoot weight at the end of the primary scaffold and makes it less likely to bend in spring winds. As with long pruning, orchardists who practice intermediate pruning keep small lateral branches for their leaf surface and to promote early fruiting. This system of pruning generates fewer undesirable water sprouts than short pruning, but it requires thought when selecting among the relatively few secondary branches in the second dormant season. If intermediate pruned trees are especially vigorous or if the variety is willowy, branches may require roping prior to the second leaf. Overall, this is a successful training system that avoids the worse problems of long pruning but offers advantages in terms of early production.

Second Dormant Pruning
After the second growing season the grower selects the secondary scaffolds--two per each primary limb. A secondary scaffold is a vigorous, upright lateral that forms a “Y” off a primary limb. The secondary branches should be evenly spaced around the canopy (6 branches, 60 degrees apart) and have an upward and outward orientation. The secondaries do not need to be headed unless excessively long, since most almond trees branch sufficiently without heading cuts. Other than pruning limbs that compete with the selected secondaries, removing badly crossing branches, and cutting an excess of internal water sprouts, additional limb removal is usually unnecessary.

Summary of Farm Calls Made in 2009

Written By: David Doll, UCCE Merced County

Below is my submission to the 2009 Proceedings of the Almond Board of California. This information will be presented in a poster at the 2009 Annual Conference of the Almond Board of California. It is important to note that this summary will be used to help re-direct current almond production research to provide future management practices for the problems found.

Survey of diseases associated with decline of almond orchards in Merced County

Objectives: Merced County has been a major producer of almonds for over 60 years, with an estimated 88,000 bearing and 3,500 non-bearing acres. Orchards have been established on a large diversity of soil types, irrigated with varying water quality, and managed with different orchard practices. Many blocks have experienced tree loss from Phyophthora crown rot, Armillaria Root Rot, Almond Leaf Scorch, Silver Leaf, Nematodes (Root-knot, Ring, and Lesion), Crown Gall, and wood decay pathogens. These diseases, in severely affected orchard blocks, have caused the loss of many trees, shortening the production life of those orchards. This survey, which will be conducted through farm visits, will help determine abiotic and biotic causes of orchard problems, while aiding in the extension efforts between the newly hired farm advisor and county growers.

Summary: The survey was conducted during farm visits. Visits made for this projects were requested by the orchard operator in order to help with an identified problem. A survey addressing management practices was developed and used to evaluate each orchard. Diagnoses of disease and tree problems were confirmed through tissue/soil sampling, isolation of pathogens, and discussions with advisors and consultants. In some locations where nematode problems were suspected, soil samples from 3-5 locations in the orchard were submitted to UC labs for nematode population counts.

A total of 52 orchard visits were made during the 2009 growing season and the diagnosis associated with the problems can be seen in table 1. 16 (30.7%) and 36 (69.3%) orchards were diagnosed with abiotic and biotic problems, respectively. Abiotic problems included herbicide drift injury, nutrient uptake toxicity, salt burn, and water stress. Of the biotic diseases, 9 orchards (17.3%) were identified to have root problems, with four orchards being diagnosed with Armillaria mellea (Oak Root Fungus). 17 orchards (32.7%) displayed symptoms of scaffold diseases, which include lower limb dieback and fungal cankers associated with pruning wounds (Eutypa and Botryosphaeria). The high occurrence of scaffold diseases suggests that a review of canopy management practices should be made. Samples collected from this survey have contributed to the first isolation and identification of the fungal disease Eutypa lata in almond. Pathogenicity tests are currently being conducted.

Nematode sampling was performed in 12 orchards, and the population levels detected can be seen in table 2. All 12 orchards were located in sand to loamy sand soils. High counts of Lesion and Ring nematode were found in 7 (58.3%) and 5 (41.6%) orchards, respectively. Orchards infested with lesion nematode often had counts above 1000 nematodes/liter (data not shown). It is important to note that genetic resistance to lesion nematode has not been identified in almond rootstocks, and should be addressed in future development.

Replant Disease of Almond

Written By Greg Browne, USDA-ARS UC Davis

When orchards are replaced, growth and productivity of the succeeding generations of trees are often suppressed by “replant problems” unless precautions are taken. Replant problems can result from interacting physical, chemical, and biological factors, but the biological aspects usually dominate. Growers can minimize physical and chemical contributions to replant problems by pre-plant ripping and other site remediation practices and amendments to insure good soil water drainage, good soil structure, and optimal soil chemical properties (e.g. pH, soil extract electrical conductivity, etc.). Of course, appropriate soil tests are needed to evaluate the latter properties. Dealing with biological contributions to replant problems should also start with some homework—sampling for nematodes. Although plant parasitic nematodes (ring, lesion, and, on some rootstocks, root knot nematodes) probably contribute to replant problems in less than one third of California’s replanted almond and stone fruit orchards (rough estimate), it is important to sample your soil to check for them before replanting. Root damage caused by the ring nematode in sandy soils predisposes almond and other stone fruit trees to bacterial canker disease. In addition, although not common at most sites, Phytophthora species, Armillaria mellea, and Verticillium dahliae infest some orchard soils and can cause tree stunting, decline, and death in young replanted orchards as well as in established ones. It is difficult to detect and assess populations of these pathogens by soil sampling, and therefore a history of disease caused by them in the previous orchard tends to be the best predictor of future replant problems they may incite. Although it varies in severity, the most common replant problem is Prunus replant disease (PRD). In our experience, it occurs nearly universally in replanted almond and stone fruit orchards in California unless precautions are taken.

Figure 1: Almond trees affected by Prunus Replant Disease (Right), compared to a healthy, fumigated almond tree (Left). Pictures were taken in Firebaugh, CA.

PRD causes slight to severe growth suppression in almond and stone fruit orchards planted after one another. Instances of severe PRD can kill or prevent growth in more than half of the trees in a replanted orchard (such cases have occurred repeatedly on some soils in Butte County). More commonly, PRD stunts trees, especially during the first year after planting. In any case, cumulative crop production of trees affected by PRD may never fully catch that of trees planted where PRD prevention practices were used. Although the cause of PRD is still being unraveled, it has been associated with a complex of soilborne fungi, oomycetes, and bacteria left from the preceding crop.

There are not currently soil tests available to predict severity of PRD, but such tests may be useful once validated. In the meanwhile, local experience obtained by growers and from field trials such as those described below can be very useful in predicting risk and severity of PRD on a given soil series with a given crop history.

For the past several years, a team involving the authors, the Pacific Area-Wide Pest Management Program for Integrated MB Alternatives, commercial growers, TriCal, Inc., and others has been testing and optimizing fumigant- and crop-rotation based approaches for preventing PRD. Some key aspects we have examined include:
-- Testing efficacy of chloropicrin (CP), 1,3-dichloropropene (1,3-D, trade formulation Telone II), and iodomethane (IM, trade formulation Midas), and several mixtures these fumigants, as alternatives to methyl bromide (MB)
-- Developing efficient spot fumigation methods with potential to reduce fumigant costs and emissions
-- Examining contributions of a single year of fallow or short-term crop rotations with sudan grass or mustard for management of PRD
-- Testing effects of irrigation intensity (e.g., from 70 to 120% of ET) on severity of PRD in fumigated and non-fumigated soil.

Below, in summary form, we highlight some of the recent results from this work. Key findings to date:
-- In general, chloropicrin (CP) and mixtures of it with IM, 1,3-D, or MB are more effective for preventing PRD than 1,3-D or MB alone. (IM products are not registered in California at this time)
-- Rates of 300 to 400 lb/per treated acre of CP or mixtures of it with 1,3-D or IM appear optimal for prevention of PRD. (See Tables 1,2). (Product labels and Ag Commissioner must be consulted for appropriate rates).
-- GPS-controlled shank-applied spot treatments (applied to tree sites before planting), with CP or Telone C35 (CP:1,3-D) or drip-applied spot treatments (also applied to tree sites before planting) with Inline (drip formulation of CP:1,3-D) appear nearly as effective as strip or broadcast treatments with the same fumigants (See Tables 1-3).
-- Short-term rotations with sudan grass, wheat followed by sudan grass, or mustard, or a single season of fallowing can improve growth or replanted trees, thereby reducing effects of PRD (Table 4).
-- It appears important not to over or under water almond trees replanted without pre-plant soil fumigation after removal of almond on peach rootstock; doing so can make PRD worse.

Fall survey for problematic weeds

Written by David Doll, UCCE Merced County
Monitoring weeds in the fall provides the ability to evaluate the current year's weed control program. By surveying the orchard for areas of weed species that escaped control, control practices can be adjusted to control these weeds in the following year. Fall monitoring also provides the ability to identify emerging winter species and allow for the selection of a pre-emergent herbicide to control spring weeds. (Note: Pre-emergent herbicides are usually applied at a later date - December-February).

Surveying for weeds is relatively simple. After the first rains look for annual weeds in the tree rows to check the effectiveness of any previous pre-emergence herbicide applications. Check the ground cover in the row middles for any perennial seedlings. Record weed infestations and use a map to show areas of escaped weeds.

With the emergence of herbicide resistant weeds in almond orchards (Hairy Fleabane, Pigweed, Horseweed, etc.) control of escaped weeds is critical to an affordable weed management program. For example, controlling glyphosate resistant fleabane with spot treatments of Rely/Gromoxone tank mix that has been found on 3 acres of the orchard block is more affordable than trying to control it over the entire 40 acre block. Only by monitoring can the areas infested by escaped weeds can be identified. It is important to use a different chemistry and address these escaped weeds BEFORE they become to big or go to seed.

Below are some pictures of common weeds to help in identification:
Figure 1: Bermudagrass (Cynodon dactylon). Vigorous spring- and winter-growing perennial. Frequently becomes a problem in mowed orchards. Very competitive for moisture and nutrients. Spot treat with postemergents.


Figure 2: Dallisgrass (Paspalum dilatatum). Perennial commonly found in orchards. Seedlings in spring and summer. Tends to become dominant in mowed areas and standing water.



Figure 3: Field Bindweed (Convolvules arvensis). Vigorous perennial. Seeds can survive for up to 30 years in the soil. Crucial to destroy plants before seeding. Plants may spread from stem or root sections cut during cultivation.


Figure 4: Hairy Fleabane (Conyza bonariensis). Annual plant. Emerges in February and in December if winter temperatures are moderate. It can withstand several mowings and still produce seeds.


Figure 5: Common Purslane (Portulaca oleracea).It is a prostrate summer annual. Germinates in April to early May. It can cause problems with both nut drying and pick-up during harvest operations.


Figure 6: Nutsedge (Cyperus esculentus). It is a perennial weed. It reproduces from tubers that can survive for 2 to 5 years in the ground. Each tuber contains several buds that are capable of producing plants.

Further Resources:
"Weeds of California and Other Western States." Vol. 1 and Vol. 2. J.M. Ditomaso and E.A. Healy. University of California Agriculture and Natural Resources. Publication 3488.

"Integrated Pest Management for Almonds." 2nd edition. Statewide Integrated Pest Management Project. University of California Agriculture and Natural Resources. Publication 3308.

Article was based off of Tulio Macedo's Orchard Weed Notes newsletter article titled "Fall Weed Monitoring."