Organic Pest & Disease Control

   We like to think of an organic orchard as utilizing the natural elements of the farm to grow a robust yield, instead of relying on imported synthetics to sustain our trees. We hope to boost our soil productivity by simply applying an abundance of compost and mulch throughout the orchard. These two ingredients in coordination with appropriate soil moisture should keep your trees healthy and nourished throughout the seasons. A well nourished tree should avoid many of the challenges we have described below.  When we encounter challenges our solution often requires a modest adjustment such as broadcasting an organic fertilizer around the trees, a foliar application of fish emulsion, lime/sulfur or neem oil if necessary.   If pests become a problem, you can use a variety of methods that don't involve spraying pesticides or other chemicals. If you run across a problem in your garden, there is a good chance an organic method can help fix the problem. 

Apple Borer

apple borer

   Flatheaded apple borers are serious pests of newly planted fruit trees. Apple trees are desired, but they damage many other deciduous trees. Damage is caused by the larvae, which tunnels beneath the bark, creating winding, frass-filled tunnels resulting in sunken lesions that scar and weaken trunks, slow tree growth and can even kill trees young fruit trees.
   Fully-grown larvae are about one inch long and have a creamy-white, segmented body. The segments just behind the head are wider than the others, giving the grub a “flatheaded” or cobra-like appearance. These are big larvae that produce large feeding galleries, which means even a single larva can cause significant damage to a tree that is only a few inches in diameter. Trees are most susceptible during the first few years after planting, especially if injured or stressed. Healthy, well-established trees are much less likely to be damaged.
   There is only one generation per year, with adults beginning to emerge in mid-spring and continuing to be active into late summer. Although these are day-flying insects, they are rarely seen. Female beetles can sometimes be seen crawling about on the sunny sides of tree trunks as they search for egg-laying sites. Egg-laying is focused on the sunny sides of trunks because these areas are most likely to suffer sunscald, a.k.a. southwest injury, which can occur during winter, but eggs are also laid around other points of injury, such as pruning scars and graft unions.
   Cultural practices that prevent sunscald and bark damage and encourage vigor make trees much less susceptible and help trees grow out of the susceptible stage faster. This can include things like proper planting depth, proper mulching,  proper use of trunk wraps, and/or painting the trunk. Keep trees adequately watered and use mulch, but not too deep, and not too high around the trunk. Drought stress and/or clay soils are two recipes for borer damage.  If discovered we'll go after the larvae with a sharp knife and paperclip to poke up the tunnels. It's fine to carve away at the tree in pursuit of the larvae. The larvae needs to be removed. The wound will heal. 

Brown Rot


    Brown Rot is a fungal disease that affects stone fruit, especially peaches and cherries. At first (commonly seen in spring), the symptoms of the disease are dying blossoms that turn to mush and form a grayish fuzzy spore mass on the branch. Then it may enter the twig and cankers form. When maturing fruit is infected, the signs begin with a small brown rotted spot and rapid spore growth. The entire fruit may be consumed in a matter of days. Like most fungal diseases, it thrives in humid weather. A  season with long, warm wet spells perfectly suit the development of the fungus, and it's not uncommon for an entire crop to be infected. If this is common for your area earlier ripening stone fruits may be best. 

  When the trees become dormant spray them with lime Sulphur, then follow up a month later with a second spray. To really provide the best chance of clean fruit. If you have high pressure for brown a third application on the fruit when it's about the size of a thumb nail. 

Cedar Apple Rust


   If your apple trees (Malus spp.) develop cedar apple rust, there's not much you can do this season. In future years, however, knowing how to keep the disease from gaining a foothold on new crops may reduce or eliminate the amount of ruined fruit you harvest. As the name suggests, cedar apple rust most often develops on apple trees growing in the vicinity of cedar trees (Juniperus spp).

   Cedar apple rust first appears as shiny orange spots on apple tree foliage. Young fruit have raised orange spots, which turn brown as the disease progresses. By the time harvest time approaches, the fruit lesions are larger and cracked. If your cedar trees are infected, you'll notice golf ball-sized brownish growth that develop spikes in the spring.

    It is important to remove any possible host plants growing within 300 yards of your apple trees. Red cedar (Juniperus virginia) is a common host. Additionally, any members of the juniper family are capable of spreading the disease. Other potential culprits that can "catch" the disorder and spread it to apple trees include hawthorn trees (Crataegus spp.) and flowering crabapples (Malus spp.).

   Sulfur treatment is considered an organically acceptable preventable treatment for cedar rust disease. Apply it three times during the growing season. The most effective periods to spray are when trees form flower buds, 10 days after the first spray and 10 days after the flowers fall from the trees. Coat upper and lower surfaces of the apple tree's foliage. Spray in the early evening to avoid disturbing beneficial pollinating birds and insects. If you have only a few trees, the sulfur is usually diluted at a rate of 3 tablespoons per gallon If cedar apple rust is a continuing problem, organic fungicides can be applied weekly starting with bud break on apples and crabapples. Fungicide applications are used to protect the tree from spores being released by the juniper host in mid-spring. This occurs only once a year, so additional applications after this springtime spread are not necessary. Rake up and dispose of fallen leaves and other debris from under apple trees. Remove galls from infected junipers. In some cases, juniper plants should be removed entirely.

   Organic Orchardist and author, Michael Phillips, advises that bolstering the health of apple trees helps them resist diseases like cedar apple rust. He suggests making sprays from garlic (Allium sativum), stinging nettle (Urtica dioica) or horsetail (Equisetum arvense). All are traditional treatments in the garden and orchard to fight off bacterial and fungal diseases, based on their pathogen-fighting isoflavonoid and terpene content. Garlic sprays may be made by blending cloves with water, straining and decanting in a spray bottle or orchard sprayer. Stinging nettle and horsetail involves filling a 5-gallon bucket with either botanical, covering with water and leaving to steep for at least 24 hours. The resulting solution, once strained, can be applied to apple foliage either full strength or diluted with plain water.



   Fire blight is considered the most devastating bacterial disease of apples and pears. The fire blight bacterium is native to eastern North America, but since the mid-1900s has spread to regions across the world. In western US, infections commonly occur in May and June on the second flush of flowers, but occasionally, infections can wreak havoc during the primary bloom. It is caused by a bacterium (Erwinia amylovora) that enters the plant through susceptible tissue, such as flowers, wounds or young growing tips, and the disease cycle starts from there. Insects and rain transfer the bacteria from old cankers to new flowers, where they multiply rapidly, and later between infested flowers. In wet weather, the bacteria are washed into the nectar-producing region of the flower, where they enter the tree’s vascular system. The bacteria move through the tree, killing tissues as the infection spreads. Twigs on infected trees develop a characteristic charred appearance. The first symptoms of fire blight occur in early spring.

   Infected blooms will appear water-soaked and discolored, and it rapidly turns black. If the disease enters twigs, it will move from the tip down, with stem and leaves looking water-soaked then turning brown. The leaves will remain attached to the stem as the stem shrivels and bends at the tip, resembling a shepherd’s crook. The disease moves from the tips into main branches, causing cankers that ooze bacteria. As mentioned the splashing rain or insects can move the bacterial ooze to new places. It is most active when temperatures are above 60 degrees Fahrenheit, and the weather is wet or humid.

   The moment we see slight wilting of a limb we'll remove the shoot by cutting back at least 8 inches beyond the appearance of infection. This can make some difficult pruning cuts, but it must be done or the infection will continue to spread into the heart of the tree.  We'll dispose of the cutting in the trash or buried in the earth of the orchard.  If you're in a location where fireblight is a annual concern there are some well timed sprays that will limit exposure to the bacterium. A benign alternative method is to use 2 cups of white vinegar with one gallon of water in a sprayer applied prior, during and after the blossom times.  A product called Blossom Protect made from a naturally occurring yeast, shows promise  against fire blight. Best applied after the traditional lime sulfur application in the early spring since the lime sulfur can kill the yeast in Blossom Protect. But when sprayed after the lime sulfur, they each inhibit the growth of the fire blight bacteria.

Deer and Roaming Ungulates  

   Deer prefer to browse the new growth on most fruit trees. The deterrents with noxious solutions to spray on leaves is often a temporary fix, but once new growth emerges reapplication is required. Fencing is often best. A few affordable and  temporary fencing options for deer are using 5' concrete mesh ( 6" squares, 5' tall, a 150' roll goes for about $100 at home improvement center) formed into an 8' circular cage.  Two or three 5' pieces of 1/2" Re-bar are driven into the ground and used to anchor the cages so the deer can't push them over.  Alternatively, we'll place four stakes in a four 4 ft. square enclosure with 4' to 5' fencing. Deer are unwilling to hop into this tight of an enclosure so trees are protected. Once trees grow beyond the enclosure the deer become your summer pruning experts or they'll have moved on to greener pasture. 

Gnawing Rodents 

   It is essential to protect your newly planted young trees from rodents seen and unseen. If you observe small mounds of fresh soil in random places throughout your yard, you probably have gophers. Below-ground dwellers, such as gophers and moles/voles, can be deterred by planting trees in gopher baskets, or wire mesh enclosures. These will protect the young roots without inhibiting root growth as most are made with wire material that will break down over time or break open as the roots expand. You can make your own baskets with hardware cloth found at your local hardware store (there are several how-to videos on the internet) or by purchasing pre-made gopher baskets. Gopher baskets come in several sizes to accommodate young shrubs (blueberry bushes) to fruit trees. If you are planting fruit trees, the 5 gallon size is sufficient, but the 15 gallon size will allow for plenty of root growth.  

   The other necessity is a tree guard or wrap. We like the spiral tree guards that expand with the tree's growth, such as the vinyl guards found at A.M. Leonard. These feature pre-cut ventilation holes to aid in air circulation to prevent mold and mildew and are a good alternative to rodenticides. They also protect against nicks or wounds caused by manual weed removal like hoes or weed whackers. Many of our customers have also had luck with squirrel baffles (upside down metal or plastic cones) to prevent squirrels from climbing up fruit trees. There are many sources on the internet as well as some DIY videos using sheet metal or plastic buckets.

Leaf Mosaic 

   Leaf Mosaic is generally any plant disease characterized by mottled discoloration of leaves. Discoloration is very common under environmental stress or on young trees; just about all fig trees in the United States have fig mosaic. Thankfully, it doesn't have any detrimental impact on the fruit of the tree and most trees outgrow it with maturity. Often, the discoloration is due to a mild nutrient deficiency. If you foliar feed (spray the leaves and trunk) with a liquid fertilizer, such as fish emulsion and kelp, you should see the coloring improve. Please note this is most often visible in young figs or fig trees under some degree of water stress. 

Peach Leaf Curl

   Leaf curl is a disease affecting the genus Prunus, notably peach, nectarine, and almond and rare occasion apricots. The fungus is called Taphrina deformans. Infected trees exhibit leaves which are puckered and distorted, before ultimately curling downwards and becoming discolored. The first symptoms of leaf curl typically arise in spring, with affected leaves developing reddish patches. These areas thicken and pucker, eventually causing leaves to curl and distort. The early stages of the disease can look similar to the consequences of aphid infection in fruit trees.

   As the disease progresses, symptoms become more obvious and distinctive. Leaves will experience chlorosis, while the initially puckered patches can become almost tumorous looking, with extremely severe infections turning red and purple.  The fungal pathogen responsible for the disease produces spores on leaf surfaces, causing them to take on a dusty, velvety appearance as they develop. These spores can be blown onto the leaves of other branches or nearby trees, spreading the disease.  

   It's too late to treat the infection when symptoms are visible, but we suggest foliar feeding (spraying the leaves and bark) with liquid fish emulsion and kelp extract. This will provide an infusion of nutrients to aide in the new growth which will push through the infection.  Best prevention is spraying the trees just prior to bud swell in late winter with liquid sulfur or fixed copper solution when tree is dormant.                                                                          

Perennial Canker  

   A canker is an infectious disease of the phloem and cambium on stems, branches or twigs of trees. A patch of phloem and cambium is killed, the underlying wood dies as a result, and the killing often progresses over time. Cankers are often sunken if they grow slowly because the shoot continues to grow around it. Also, callus may be produced around the canker that makes it appear more sunken.

    There are some diseases usually considered with other groups that are cankers, as well as injuries that can be confused with cankers: Bacterial cankers: These are covered with bacterial diseases. Canker rots: Some basidiomycetes that decay wood in the stem may also kill patches of sapwood and bark. We consider most of them along with stem-decay fungi.stem rusts: These cause cankers, but we consider them separately with the rusts. Foliage diseases, shoot and tip blights: Some of these kinds of diseases also can involve small cankers of twigs, branches, and even main stems; they are considered under foliage diseases. Winter injury or sunscald. These kill patches of bark, and can be confused with cankers. Also, canker pathogens can infect living tissues at the margins, so they can become cankers.

   We suggest immediately pruning back any limbs or trunk that display a visible canker infection. In some situations we have removed a canker with a sharp by carving around the discolored bark. 

Powdery Mildew

   Fungal disease that affects plants and crop yield. Powdery mildew is one of the easier plant diseases to identify as its white powdery spots on the leaves and stems will be a sure giveaway in vegetables, but with fruit trees it's not always so obvious. Often it's discovered after the infection has run its course. The mid summer discovery of leaves half baked brown is a sign of mildew infection that's now passed. Foliar spray of Lime sulfur or baking soda  is fine prevention in spring. Not a significant concern. 


   Apple scab is the most important disease of apple trees in the world. All parts of the tree are attacked. Scab infection of fruit is most obvious to spot. The scab fungus overwinters mainly as the sexual state (pseudothecia) on leaves on the orchard floor. It can also survive as mycelium in lesions on the tree as wood scab, bud scale scab or shoot base scab. The importance of this source of inoculum varies with variety, region and season. In spring spores either ascospores released in rain from overwintering leaves or conidia from tree sources infect developing leaves and fruit to initiate the new scab epidemic.

   Wet leaves or fruit are essential for infection. Once new infections are established, conidia are produced and these spread in wind and rain to infect other new leaves and fruit. Infection of fruit near harvest can lead to the development of storage scab on fruit in store. In late summer/fall older leaves which had become resistant to scab with maturity become susceptible to scab again as the cuticle cracks with age. This diffuse late scab developing on leaves contributes most to the overwintering scab on the orchard floor. Apple scab infects most parts of the tree including leaves, petioles, blossoms, sepals, fruits, pedicels, shoots, bud scales. Symptoms are most easily observed on leaves and fruit.

   Where susceptible varieties are used, it's important to work on the eradication of overwintering scab and maintaining trees with good air circulation to encourage rapid drying of leaves and fruit after rain and dew. Spray a copper fungicide and or lime/sulfur  prior to bud break. Reapplication will be necessary after spring rains in locations with heavy scab pressure. 

Shot Hole

   The exact cause of shot-hole disease (Wilsonomyces carpophilus) is thought to be a combination of a bacterium and a fungus that attacks peaches, plums, cherries, apricots, and nectarines, which are all closely related. The shot-hole appearance of the leaves is where the disease-infected tissue dries up and falls out of the center of the leaf spot, leaving a hole about 1/8” inch in diameter. This disease literally appears as though someone were shooting a shotgun at the leaves of your tree, creating a random pattern of small shot-holes.

   The good news is that this disease is not lethal to fruit trees. However, it does make the appearance of the tree look bad and sometimes can cause some of the leaves to drop in mid-summer. This premature leaf drop can be stressful, but is tolerated quite well by trees that are otherwise healthy. Some years will be worse than others, depending on the weather. This disease favors warm, wet spring weather. Cleaning up and removing dead leaves can help break the cycle of this disease from carrying over one year to the next. Vigilant leaf removal may not totally eliminate the disease, but can definitely help cut down on the severity of it next year.

Spider mites

   Its innumerable hosts include many weeds, field crops, ornamental and house plants, vegetables, forage crops, small fruits and tree fruits. Among the tree fruits, apple, pear, peach, nectarine, apricot, cherry (sweet and sour), plum, and prune are suitable hosts. High mite populations encountered on pear are likely to be either two spotted or McDaniel spider mite. Two spotted spider mite used to be rare on apple, but has become more common in recent years, greatly surpassing McDaniel spider mite as a problem. In pears, leaves turn dark brown or black, especially if intense feeding occurs over a relatively short period. A serious infestation can delay tree growth, reduce fruit size and cause premature drop.


   Often the first major heat spike of the season will burn tender new leaves. This can be mistaken for disease or nutritional disorder. 

Herbicide damage

   Each year in early summer, many home orchardist as well as commercial fruit  growers begin to notice distorted leaf growth on their fruit trees, berries and grapes. Commonly, the cause of the distortion is due to herbicide application to a nearby field, lawn, road bank, or other area, that has drifted to these very susceptible crops.

   Phenoxy-type herbicides, such as ones containing 2,4-D, are most often the culprit. These herbicides are absorbed by the plant and transported to its growing points, and can cause damage at just 1/100 of the label rate. Unfortunately, they are quite volatile (especially the ester types), and can drift up to a mile or more, especially with relatively light (10 mph) winds, and some formulations can even re-volatilize for days after spraying, when temperatures are over 80 to 90 F degrees. Because air currents are usually quite variable, damage can be spotty, and may even “skip” over one portion of a field, making it more difficult to determine the source.

Is it a nutrient deficiency? 

Symptoms generally appear by early July in the leaf of the fruit tree.


   If calcium is lacking, you’ll noticed newer leaves at the top looking distorted or odd-shaped. It can also cause premature rotting of fruits. Apple trees nearly always obtain enough Calcium from soils if pH is maintained above
6.0 with appropriate liming. Apple fruit, however, often obtain inadequate Ca even when the trees are adequately supplied. This results from the limited mobility of Calcium in trees and causes bitter pit, internal breakdown, or premature softening. Calcium very important addition to fruit tree orchards. It's also critical to success in clay soils. 


    Leaf margins first affected, showing discoloration near upper or lower lateral edges; leaves laterally curling upward, smaller than normal. Marginal necrosis may be preceded by slight chlorosis. Marginal scorch. If soil test indicate a need for Mg in your orchard, soil pH is nearly always too low, and dolomitic lime is the best treatment. Clay soils are high in magnesium. Calcium needs to be added. 


    Potassium deficiency is commonly noted in most deciduous fruit trees by curling up of the leaves' margins, which is also ubiquitous in drought situation. This symptom may be linked to the fact that potassium shortage may interfere with the closure of the stomata and reduce their dehydration control of the plant. Older leaves may appear bronze and fall easily. Orchards on sandy soils are most prone to potassium deficiency. Clay soils due to high magnesium levels can tie up potassium as well. 


    Internodes not markedly shortened near tip. Fine lace-like network of leaf veins green. Youngest expanding leaf may be devoid of green color. Leaves acquire some green color with increasing age. Orchards and gardens do not respond consistently to ground applications of Zinc on high pH soils. Foliar sprays of Zinc chelates at recommended rates and timing are the best,


    Iron chlorosis is a yellowing of plant leaves while the tissue close to the leaf veins remains green. Typically, it is caused by an iron deficiency, usually due to a high soil pH (pH above 7.0).Tip leaves chlorotic, main veins green, shoot tips frequently die back and new shoots grow out from lower buds producing dieback and witches‘-broom. Incorporate organic compost into the soil with iron sulfate.


   Young leaves not chlorotic or only slightly so. Young leaves may be curved boat-like; shoot tips may be curved; terminal buds aborted and new shoots die back.


   Midribs of leaflets shortened, tips rounded, wrinkled, and cupped. Only apply Boron if leaf analysis results indicate a need. The difference between deficient
& excessive Boron levels is small, and Boron toxicity is very damaging.


   Phosphorus deficiency is more difficult to diagnose than a deficiency of nitrogen or potassium. Crops usually display no obvious symptoms of phosphorus deficiency other than a general stunting of the plant during early growth. By the time a visual deficiency is recognized, it may be too late to correct in the current growing season. Soils high in organic matter contain considerable amounts of organic phosphorus that are mineralized (similar to organic nitrogen), and provide available phosphorus for plant growth. In addition to supplying phosphorus, organic matter also acts as a chelating agent and combines with iron, thereby preventing the formation of insoluble iron phosphates. Heavy applications of organic materials such as compost, manure, plant residues or green manure crops to soils with high pH values not only supply phosphorus, but upon decomposition, provide acidic compounds, which increase the availability of mineral forms of phosphorus in the soil. Often characterized by some bronze to purple leaf margin with cupping and undulating leaf. 


   Pale green or yellow leaves, as well as poor growth, are common symptoms of nitrogen-deficient plants. The poor growth is a function of the yellow and pale leaves. These lead to a reduced ability to produce chlorophyll. Be conservative with Nitrogen rates until you are familiar with the planting. It is easier to
apply more Nitrogen than to manage excessive vigor caused by too high rates. Adjust rates according to leaf Nitrogen concentrations, orchard vigor, fruit quality, and productivity. Three factors that have the greatest effect on Nitrogen requirements are soil type, orchard floor management and pruning.
Orchards on fertile loam soils may require Nitrogen at only half the recommended rates, whereas those on very sandy soils may require 50 percent more Nitrogen. 


   Symptoms principally on fruit. Young fruit show corky lesions. Frequently internal necrotic spots in fruit or internal cork. Deep cracking of fruit may develop as they mature.