Citrus Diseases

Black Rot (fungus – Alternaria citri): The infection starts while the fruit is still on the tree. The fruit is infected through cracks or openings on the stylar end of fruit. The fruit colors prematurely and drops.

Brown Rot (fungus – Phytophthora spp.): The same species of Phytophthora that causes foot rot can infect fruit, commonly those close to the ground. Fruit are infected during periods of excessive rain, resulting in decayed areas that are brown, firm and leathery. Later, a white, velvety growth is seen on the surface of the fruit (See Photo), accompanied by a strong fermenting odor. The best control for brown rot is sanitation during transit and in the packing house. Disinfecting the boxes is important. Treatment with disinfectant solutions and refrigeration are effective for prevention.

Cachexia (viroid – Xyloporosis): This pathogen makes the inner bark surface bumpy (See Photo). The bark projections are smooth, in contrast to the sharp projections produced by the citrus tristeza virus. Cachexia affects certain mandarins and tangelos, particularly Orlando tangelo. Sour orange is tolerant to the virus.

Citrus Tatter Leaf (tatter leaf-citrange stunt virus): This virus causes a bud union crease. It can be detected using certain indicator plants (e.g. swingle citromelo citrus)(See Photo). It is serious on rootstocks of Troyer and Carrizo.

Cotton Root Rot (fungus – Phymatotrichopsis omnivora): This is a minor disease of citrus and it rarely appears on trees that are more than three years old. The fungus kills trees quickly; most of the dried leaves remain attached to the branches. (See Section on Cotton Root Rot)

Diplodia Stem-End Rot (fungus – Diplodia natalensis, also known as Physalospora rhodina): Fruit are contaminated with the fungus in the field, but the disease commonly occurs at the packing house or in transit. Decay occurs around the stem end (See Photo) and advances in streaks down the side of the fruit. There is no fungal growth on the surface of the fruit. Decay is reduced by dipping the fruit in fungicide solutions before placement in de-greening rooms. Promptness in handling and shipping, as well as refrigeration during transit, will minimize losses.

Exocortis (citrus exocortis viroid): This pathogen causes bark-shelling and stunting of trees on trifoliate orange, trifoliate hybrids, and Rangpur lime rootstocks. Sour orange rootstock is tolerant. In the early stages of the disease, gum exudes from pustules at the base of the trunk and may extend from below the soil line to the bud union. New bark forms beneath the pustules, and the outer bark sloughs off forming the characteristic bark-shelling (See Photo). The tree eventually declines. The pathogen is spread via grafts and also via pruning tools. The pathogen can be detected following grafting on Etrog citron. Symptoms on this indicator plant include stunting and leaf deformation and necrosis of the leaf midrib.

Feeder Root Rot (fungi – Phytophthora spp.): The fungus infects the cortex of feeder roots, giving the root system a stringy appearance. This can lead to yield loss and a general prolonged tree decline. Sour orange rootstock is relatively resistant. This disease can be controlled with fungicides (See Table 1 at Bottom). Soil solarization may also be an effective treatment.

Firing (physiological – wind dessication): The injury (See Photo) is usually limited to late growth flush (September or October) which has not matured prior to the arrival of a dry cool front in October or November.

Flyspeck (fungus – Leptothyrium pomi): This is caused by a fungus that keeps citrus fruit from turning yellow in the infected spots. Small black specks are formed on the rind in areas immediately surrounding the oil glands (See Photo). The contrast between green and yellow color lowers fruit grade, even though there is no effect on fruit or juice quality.

Green Mold (fungus – Penicillium digitatum): The fungus causes a rapid breakdown of fruit punctured or bruised during harvesting and packing operations. The fungus enters the fruit only through wounds. A white mold that later turns green is seen growing on the skin (See Photo). The decayed fruit becomes soft and shrinks in size. Losses from green mold can be reduced by preventing injury during harvest and transit. The fruit is treated in the packing shed with a fungicide solution.

Greasy Spot (fungus – Mycosphaerella citri): This is a very common disease in Texas. The fungus is primarily a leaf pathogen, but it can also infect fruit. Yellow spots are seen at first on the upper surface of the leaf (See Photo). The corresponding areas on the undersides of the leaves turn dark and appear slightly raised and greasy. With severe infection, leaves may turn yellow and drop prematurely. The infection is favored by rust mite injury and humid weather. Yellowing caused by scale insects may be mistaken for early symptoms of greasy spot. Either citrus oils or fungicides (See Table 1 Below) can be applied during the summer for control. Heavy infections occurring in wet years may require 2 to 3 fungicide treatments. Since infection occurs on the lower leaf surface, thorough spray coverage is essential for effective control. The spores of the fungus originate in the leaf litter on the orchard floor and are released following rainfall or irrigation. Thus, removing litter will reduce the amount of spores present.

Heart Rot / Wood Rot (various fungi): The visible external symptom is the fruiting structures (“conks”) of the fungus projecting from the trunk (See Photo). Eventually, the tree declines. Species documented on citrus in Texas include Ganoderma lucidum, which has a shiny, brown appearance on the upper surface of the conk, and Phellinus robustus, which appears flat on the bark surface. These fungi, and other species, cause decay of internal wood. The fungi enter the tree through injuries to the roots or scaffold limbs or improper pruning cuts. Growth of the pathogen is favored when the tree is under environmental stress. Once infected, the tree can not be treated. Proper pruning practices, which promote rapid wound healing, will minimize the risk of infection.

Leaf Miner (insect): The larvae tunnel within the leaf, leaving snaking trails of dead tissue (See Photo).

Leaf Yellowing (physiological – various causes): Injury by the herbicides Krovar (a mixture of diuron and bromacil) or Hyvar (bromacil) can cause yellowing. Magnesium deficiency causes yellowing of the leaf, except for a lanceolate area along the petiole (See Photo). However, this type of yellowing can also be caused by iron or zinc deficiency, or it may be a consequence of foot or root rot.

Melanose (fungus – Diaporthe citri): This is primarily a disease of grapefruit. The first symptoms on leaves are small, circular, dark depressions with a yellow margin. Later, the spots become raised and turn dark brown (See Photo). Leaves turn yellow and may drop prematurely. Raised spots are also found on twigs, which may be killed. Fruit can also become infected. The disease can be severe following rainy periods in the spring, particularly when such periods follow a freeze that has left an abundance of dead twigs. Melanose is usually controlled by a single fungicide application (See Table 1 Below) after bloom or petal fall and before the fruit averages one-half inch in diameter. With a particularly wet spring, a second application may be needed. Citrus should be sprayed for melanose control in the spring following a freeze. Chemical control efforts in heavily infected orchards may need to be combined with supplemental pruning to reduce the quantity of the pathogen. This fungus also infects fruits. Spots on the fruit are at first small, light brown, and sunken; later they become dark and raised. When several spots are close together, the surface has a rough feeling to the touch, hence the name “sandpaper” melanose. Spots sometimes develop in a tear-streaked pattern (See Photo), resulting from infection caused by spores which wash down over the fruit surface during heavy dews or light rains. In other cases, large areas of the fruit surface crack in irregular patterns, resulting in the “mud cake” type of melanose.

Oleocellosis (physiological): The damage is caused to rind cells by peel oil release as a result of abrasion, rough handling or other injuries. Foggy and wet weather predispose rind to oleocellosis by making the fruit more turgid. The first symptoms are spots, which later become sunken (See Photo). The damage can be minimized by harvesting later in the day on days with cool, foggy mornings.

Phytophthora Foot Rot / Gummosis (fungus – Phytophthora spp.): This is one of the more important pathogens of citrus in Texas. It primarily infects the roots and the trunk (See Photo). Infection of the trunk results in a dark, water-soaked areas, often with profuse exudation of a dark resin from the lesion. The dead bark frequently sloughs off the wood in vertical strips. If the lesion encircles the trunk, girdling occurs, leading to the death of the tree. Trees killed by this fungus are defoliated and show an abundance of fruit. Trees with the bud union beneath or close to the soil and trees in poorly drained locations are especially susceptible to infection. Phytophthora foot rot can be prevented through the use of resistant sour orange rootstock, budded 4 to 6 inches high, and planting at the proper depth in well-drained soil. Flood irrigation water must be kept below the scion and micro-irrigation emitters should be placed so that the trunk is not left wet for prolonged periods. Soil banks should be removed as soon as the danger of frost has passed. When tree wraps are used on young trees, trunks should be treated with a recommended fungicide and they should be inspected for bark damage or gumming if there has been fire ant activity. Pruning and sprout removal are best done only in dry weather. Cultural activities that result in occasional trunk injury, such as disking or boom spray applications should be done at least 2 days in advance of irrigation. Trunk lesions can be treated with fungicides (See Table 1 Below). Severely damaged or unproductive trees should be removed from the orchard.

Rio Grande Gummosis (fungus – Physalospora rhodina, also known as Diplodia natalensis, possibly other fungi involved): This is not a common disease. Narrow cracks appear in the bark which exude a pale yellow gum. Symptoms are usually found in association with injured or dead branches. The wood beneath infected tissue is pink to orange in color. Later, gum pockets develop beneath the bark. Stressful growing conditions, such as freeze damage, high water table, salt accumulation, and poor cultural practices predispose trees to the disease. Removal of dead wood and pruning which promotes quick healing is recommended as a preventative measure.

Rust mite (insect): The fruit can be scarred as a result of mite feeding (See Photo). Early infestation results in a sharkskinned fruit texture of tan color, and fruit size is reduced. Later infestation causes russetting or bronzing of the rind.

Psorosis (Scaly Bark) (virus): Sweet orange, grapefruit, and tangerine are severely affected. The pathogen is spread by budding nursery stock with budwood from infected trees. Variable symptoms can be produced on young leaves and can include pale flecks or mottling. The earliest bark symptom is scaling (See Photo). Bark scaling of the trunk and larger branches is typical of psorosis symptoms in citrus trees eight to 12 years or older. As the disease progresses, the tree declines rapidly and eventually becomes unproductive.

Slow Decline (nematode – Tylenchulus semipenetrans): The nematode causing this disease attacks the roots. Symptoms associated with the presence of nematodes are wilting, lack of vigor, poor fruit production, small fruit size, and poor response to watering and fertilization. Poor drainage, excess salt, improper watering and damage caused by other soilborne organisms will affect trees in much the same way as the citrus nematode. Positive diagnosis requires laboratory analysis of root and soil samples, which are obtained following specific sampling guidelines. Proper sampling is important to obtain an accurate assessment of the problem. Collect soil samples at a time when soil moisture is neither excessive nor very low. The best period for sampling is during the second week following an irrigation or a rain. Collect samples under the drip line of the tree. After removing surface debris, use a shovel to cut a slice of soil from the surface to about 8-10 inches deep from the four sides of a tree. Place soil and feeder roots in a clean plastic bucket and mix well with soil and roots from other trees. Then place a composite sample from these in a plastic bag and label for laboratory examination. One laboratory sample should represent at least five trees sampled at random diagonally across rows for every 5 acres. Losses caused by the citrus nematode in heavily infected orchards can be reduced by applying nematicides (See Table 2 Below) to the soil. The table of citrus nematode action thresholds (See Table 3 Below) can be used as a guide to determine whether nematode populations warrant chemical controls. When establishing a new orchard, avoid old sites known to be infested. Soil should be sampled before establishing a new orchard to determine if parasitic nematodes are present in damaging numbers. Ideally, nematode-free plants should be used when establishing new orchards, i.e. grown in containers or in fumigated nursery soil.

Table 2: Citrus Diseases – Nematicides

Metam sodium Oxamyl Aldicarb Fenamiphos
Vapam, Soil Prep,
Pre-plant treatment only
Vydate L,
Do not apply more than 4 qt/acre
in any 30-day period,
7-day pre-harvest interval,
Restricted use
chemical – permit required
Temik 15G,
Apply just before or
during spring flush of growth,
Restricted use
chemical – permit required
Nemacur 3:
Limit of 3.33 gal/acre/season,
Nemacur 15G:
Limit of 67 lb/acre/season,
Do not apply within
30 days of harvest,
Restricted use
chemical – permit required

Table 3: Citrus Nematode Action Thresholds

Number of juvenile nematodes in 100cc of soil and 3 grams of feed roots
Sampling Time Low Population Medium Population High Population
February – May 500 – 1,500 3,000 – 6,000 10,000+
June – September 100 – 200 400 – 600 750 – 5,000
October – January 200 – 500 1,000 – 3,000 5,000 – 10,000

Citrus Nematode counts considered low, medium, or high at different sampling times during the growing season.

Factors to consider before applying nematicides include:

  • What is potential orchard production with and without treatment?
  • Will treatment increase yields, fruit grade, or fruit size?
  • Will treatment control other pests, such as mites?
  • How will the treatment affect beneficial organisms in the orchard?
  • Can soil incorporation, activation, or other application requirements be satisfied under existing water limitations, soil, and climactic conditions?

Sooty Mold (fungi – Capnodium spp.): Leaves, fruit and sometimes branches have a black, moldy appearance. The fungi causing sooty mold do not actually infect the plant, instead they grow on the sugary exudates of insects such as aphids, brown soft scale, blackflies and whiteflies. The amount of sooty mold found is directly proportional to the number of honeydew-secreting insects present. A heavy sooty mold coating on the fruit can result in a lower grade of fruit, while a heavy coating of fungi on the leaves could retard growth, causing lighter flowering and reduced yields. Insect control will prevent sooty mold development. Heavy sooty mold can be treated by adding one-half percent oil to the insecticide spray.

Spray Burn (physiological): The fruit has a dry, brown sunken spot. (See Photo)

Sunscald (physiological – strong sunlight): Irregular, brown pustules are found on the underside of leaves (See Photo). This occurs when the undersides of leaves are suddenly exposed to direct sunlight, for example, after harvest because of repositioning of limbs and leaves after removal of the fruit that had bent them downward.

Tristeza (virus – citrus tristeza): The virus infects most types of citrus and it is transmitted by certain aphids or by the use infected budwood. The symptoms produced depend upon the variety, environmental conditions, and the virus strain. The virus can cause a decline or death of the tree (See Photo). Mild strains were identified in Texas in 1991, although tristeza was also detected in the 1950′s. There are several serious strains that are not known to occur in Texas. Three strains are of particular concern: one causes the decline of sweet orange on sour orange by killing phloem, resulting in girdling at the bud union; and the stem pitting strains (one on grapefruit, the other on sweet orange). The stem pitting strains causes limbs of trees to become brittle, forms deep pits on the underside of bark, and a roping appearance of the trunk that results in a decline of the tree. Although the tree doesn’t die, there is reduced set, size and quality of fruit. The virus is inefficiently vectored by three species of aphids present in Texas: Aphis gossypii, A. spiraeola, and Toxoptera aurantii. It is very efficiently vectored by the brown citrus aphid, Toxoptera citricida, which is present in Florida, but not in Texas. If the brown citrus aphid arrives in Texas, it could move severe strains of tristeza suspected to be present on symptomless hosts in dooryard (i.e. non-commercial) trees to commercial orchards, potentially destroying the Texas industry. This is because sour orange rootstock, which is predominantly used in Texas, is susceptible to severe strains. Control efforts in Texas are mainly directed toward keeping infected budwood out of the Lower Rio Grande Valley by quarantine measures and a shoot tip grafting and budwood certification program to clean up infected material already in Texas and place it in commercial orchards. Should these measures fail, a proposed alternative control is cross-protection of trees with mild strains of the virus and/or alternative rootstocks which may tolerate the disease.

Twig Dieback (various fungi): Twig dieback can be caused by several fungi, as well as by other factors. Fungal infection often occurs following a freeze or mechanical or chemical injury. Affected young branches die back from the tip, sometimes producing gum exudation. Wood is discolored underneath the bark (See Photo). Damage by twig dieback usually is not severe.

Wind Scar (physiological): This damage occurs as the result of twigs or leaves rubbing against young fruit (See Photo). The injury develops early, i.e. within the first couple of months post-bloom.

Table 1: Fungicides for Treatment of Citrus Diseases

Phytophthora Foot Rot/
Feeder Root Rot Melanose Greasy Spot
Copper hydroxide,
Metalaxyl, Fosetyl-Al
Metalaxyl, Fosetyl-Al Copper ammonium complex,
Copper hydroxide,
Copper oxychloride,
Copper resinate,
Copper sulfate,
Sulfur + copper sulfate
Copper ammonium complex,
Copper hydroxide,
Copper oxychloride,
Copper resinate,
Copper sulfate
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