Certain techniques can be used to determine which pathogen is causing disease. One standard technique for distinguishing strains is microscopy. Under a microscope, "M. pinodes" can be diagnosed by the presence of pseudothecia. "P pinodella" can be diagnosed by the size of conidia produced. "P. pinodella" produces conidia that are smaller than the conidia of "M. pinodes" or "A. pisi". "A. pisi" can be diagnosed by the color of the conidia. In comparison to the light colored, buff spore masses of "M. pinodes" and "P. pinodella" produced on oatmeal agar, "A. pisi" spores masses are carrot red.

Other techniques for diagnosis involve serological assays, isoenzyme analysis, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD) assays, and by using monoclonal antibodies.

There is no resistance to Citrus Black Spot and once a tree has been infected there is no known cure causing tree removal to be the best option. Both Federal and State governments have recommended the following preventative measures.

To control "Guignardia citriparpa" fungicides like copper and/or strobilurins should be applied monthly from early May to the middle of September (in the northern hemisphere). Applications of the fungicides are recommended in early April (northern hemisphere) if that month has experienced more rainfall than usual resulting in the ideal conditions for citrus black spot to form.

Table 1. Recommended Chemical Controls for Citrus Black Spot

1)Lower rates can be used on smaller trees. Do not use less than minimum label rate.

2)Mode of action class for citrus pesticides from the Fungicide Resistance Action Committee (FRAC) 20111. Refer to ENY-624, "Pesticide Resistance and Resistance Management," in the 2012 Florida Citrus Pest Management Guide for more details.

3)Do not use more than 4 applications of strobilurin fungicides/season. Do not make more than 2 sequential applications of strobilurin fungicides.

Another method of control is to accelerate the leaf litter decomposition under the trees in citrus groves. Accelerating this decomposition reduces the chance for ascospore inoculation which generally takes place in the middle of March. There are three possible methods to hasten this decomposition. One method is the increase the mircrosprinkler irrigation in the grove to half an hour for at least five days of the week. This form of control should continue for about a month and a half. The second method is to apply urea or ammonium to the leaf litter. The last and final method to accelerate leaf decomposition is to apply lime or calcium carbonate to the litter. Urea, lime, and calcium carbonate reduce the number of fungal structures and spore production. Since the fungus requires wet conditions to thrive, air flow in the citrus grove should be maximized to reduce leaf wetness.

Along with these methods it is also important to get rid of debris such as fallen fruit or twigs in a manner that reduces the chances of infecting other plants. Citrus Black Spot can colonize and reproduce on dead twigs. To dispose of citrus debris it should either be heated to a minimum of 180℉ for two hours, incinerated, buried in a landfill, or fed to livestock. Plant trash should be moved with caution if at all to avoid spreading the infectious ascospores. Any trees that are infected with citrus black spot should be removed from the grove and disposed of. These trees must be removed because those that are declining and stressed will often have off season bloom. If there is more than one age of fruit present on the tree, it is possible for the asexual spores on the fruit to be transferred to new fruit, intensifying the disease. This off season blooming is often more problematic with Valencia oranges when old and new crops overlap.

Thousand cankers disease can be spread by moving infected black walnut wood. Trees intended for shipment should be inspected for dieback and cankers and galleries after harvest. G. morbidia or the walnut twig beetle ("Pityophthorus juglandis") are not currently known to be moved with walnut seed . There is currently no chemical therapy or prevention available for the disease making it difficult to control the spread of the disease from the west to the eastern united states. Wood from infected trees can still be used for commercial value, but safety measures such as removing the bark, phloem, and cambium to reduce the risk of spreading the disease with shipment. Quarantines have been put in place in some states to reduce the potential movement of fungus or beetle from that region. On May 17th, 2010, the Director of the Michigan Department of Agriculture issued a quarantine from affected states to protect Michigan’s black walnut ecology and production. Contacting the appropriate entities about possible infections is important to stopping or slowing the spread of thousand cankers disease.

This disease is hard to control because plants can carry the pathogen prior to showing any symptoms. It is important to be aware of where new plants are being planted so that they aren't exposed to disease.

The most effective method to avoid disease is to plant resistant cultivars that are specific to the location of planting. Some examples of resistant cultivars include Allstar, Cardinal, Delite, Honeoye, Jewel and Tennessee Beauty. Examples of susceptible cultivars that should be avoided include Sparkle, Sunrise, Raritan and Catskill.

Amongst the many different management strategies, cultural control practices play a significant role in prevention or reduction of disease. Some common cultural practices that have been used are as follows. In order to have more successful yields, strawberry plants should be planted in well-drained soil, in an area exposed to lots of available sunlight and air circulation. Presence of weeds may reduce air circulation for strawberry plants and create a shaded, moist environment, which would make the plants more wet and susceptible to disease. Therefore, weed growth needs to be prevented, either by chemical or cultural control methods. Immediately after harvest, any severely infected plants and plant debris should be raked, removed and burned completely to get rid of any remaining spores and reduce inoculum of the pathogen.

At the beginning of renovation, which occurs after harvest, one application of nitrogen fertilizers should be applied to help with canopy regrowth. About 4–6 weeks later, it is generally a good time to apply another application of nitrogen fertilization to the developing strawberry plants. This will allow for the plants to absorb nutrients provided by the fertilizer. However, applying too much nitrogen fertilizer throughout the spring, may result in an abundance of young foliage tissues that could be susceptible to disease.

Fungicides are not necessarily required, however if the strawberry grower decides to use fungicides, they should be applied during early in the spring and immediately after renovation. A fungicide spray schedule may also be put into place. It is recommended to spray in intervals of about 2 weeks. Examples of some recommended fungicides are Bulletin 506-B2, Midwest Commercial Small Fruit and Grape Spray Guide for commercial growers and Bulletin 780, Controlling Disease and Insects in Home Fruit Plantings for backyard home growers.

The best way to manage SDS is with a resistant variety. One issue is that most resistant varieties are only partially resistant so yield reductions may still occur. Another issue is that the plant needs resistance for SDS and SCN in order to gain true resistance because of their synergistic relationship and most varieties do not have resistance for both. Aside from resistance, the only other ways to control SDS are management practices.

These include:

- Avoid planting in cool, wet conditions

- Plant later when the soil has warmed up

- Try avoiding soil compaction as it creates wet spots in the soil that can increase plant stress and SDS infection rates

- Managing for SCN as this nematode often occurs alongside "F. virguliforme"

- Deep tillage to break up compaction and help the soil warm faster

One common management tactic used in other pathogen management plans is crop rotation. In some cases, disease severity can be reduced but most often it is not effective. This is because of chlamydospores and macroconidia as they can persist in soils for many years.

Fungicides are another common product used to control fungal pathogens. In-furrow applications and seed treatments with fungicides have some effect in decreasing disease instance but in most cases, the timing isn't right and the pathogen can still infect the plants. Foliar applications of fungicides have no effect on disease suppression for SDS because the fungi are found in the soil and mainly the roots of the plants. Most foliar fungicides do not move downward through plants, therefore having no effect on the pathogen.

Bacterial leaf streak of wheat is not easily prevented, but can be controlled with clean seed and resistance. Some foliar products, such as pesticides and antibiotic compounds, have been tested for effectiveness, but have proven to have insignificant outcomes on the bacterial pathogen.

Using clean seed, with little infection, has yielded effective results for researchers and producers. The pathogen, being seed-borne, can be controlled with the elimination of contaminated seed, however, clean seed is not always a sure solution. Because the pathogen may still live in the soil, the use of clean seed is only effective if both the soil and seed are free of the pathogen. Currently, there are no successful seed treatments available for producers to apply to wheat seed for the pathogen.

Variety resistance is another option for control of the disease. Using cultivars such as Blade, Cromwell, Faller, Howard or Knudson, which are resistant to BLS may reduce the impact of the disease and potentially break the disease cycle. Avoiding susceptible cultivars such as Hat Trick, Kelby, and Samson may also reduce the presence of the disease and reduce the amount of bacterial residue in the soil. Using integrated pest management techniques such as tillage to turn over the soil and bury the infection as well as rotating crops may assist with disease management, but are not a definitive control methods. Depending on conditions, the bacteria may survive for up to 81 months. Because the bacteria is moisture driven, irrigation may also increase the risks of BLS infection.

The genus Geosmithia (Ascomycota: Hypocreales) are generally saprophytic fungi affecting hardwoods. As of its identification in 2010, the species G. morbida is the first documented as a plant pathogen. The walnut twig beetle ("Pityophthorus juglandis") carries the mycelium and conidia of the fungus as it burrows into the tree. The beetle is currently only found in warmer climates, allowing for transmission of the fungus throughout the year. Generations of the beetle move to and from black walnut trees carrying the fungus as they create galleries, the adults typically moving horizontally, and the larvae moving vertically with the grain. As they move through the wood, the beetles deposit the fungus, which is then introduced into the phloem; cankers then develop around the galleries, quickly girdling the tree. The fungus has not been found to provide any value to the beetle. A study done by Montecchio and Faccoli in Italy in 2014 found that no fungal fruiting bodies were found around or on the cankers but in the galleries. Mycelium, and sometimes conidiophores and conidia were observed in the galleries as well. No sexual stage of the fungus has currently been found.

Due to the effectiveness of fungicide application and it’s relatively minor damage to crops, there are few cultural controls and no resistant peach variants that have been developed for the current market. For prevention of peach scab, proper pruning of leaves to allow adequate sunlight will drastically reduce the risk of infection and propagation. The primary form of regulation for peach scab requires frequent applications of commercial fungicides. There are three main types of fungicides that are effective against peach scab: captan, chlorothalonil, and demethylation inhibitors. Proper use of chlorothalonil requires application starting from shuck split and reapplication every two weeks. Increased temperature and wet weather will necessitate more frequent applications. Applications are necessary until 4–6 weeks until harvest.

Citrus Black Spot is a fungal disease caused by Guignardia citricarpa. This Ascomycete fungus affects citrus plants throughout subtropical climates, causing a reduction in both fruit quantity and quality. Symptoms include both fruit and leaf lesions, the latter being critical to inter-tree dispersal. Strict regulation and management is necessary to control this disease since there are currently no citrus varieties that are resistant.

Black pod disease is caused by many different "Phytophthora spp." pathogens all expressing the same symptoms in cocoa trees ("Theobroma cacao"). This pathogen if left untreated can destroy all yields; annually the pathogen can cause a yield loss of up to 1/3 and up to 10% of total trees can be lost completely. With the value of the cocoa industry throughout the world being so large there are much research and control efforts that go into these "Phytophthora spp." pathogens.

This pathogen can be located anywhere on the cocoa trees but is most noted for the black mummified look it will give to the fruit of the cocoa tree. Staying ahead of the pathogen is the best means of control, the pathogen can be greatly reduced if leaf litter is not allowed to stay on the ground and if the pathogen gets out of hand chemical control can be used. This pathogen is mostly found in tropical areas where the cocoa trees are located and need rainfall in order to spread its spores.

Peach scab, also known as peach freckles, is a disease of stone fruits caused by the fungi "Cladosporium carpophilum". The disease is most prevalent in wet and warm areas especially southern part of the U.S. as the fungi require rain and wind for dispersal. The fungus causes scabbing, lesions, and defoliating on twig, fruit, and leaf resulting in downgrade of peach quality or loss of fruits due to rotting in severe cases.

Sudden Death Syndrome (SDS) in Soybean plants quickly spread across the southern United States in the 1970s, eventually reaching most agricultural areas of the US. SDS is caused by a Fusarium fungi, more specifically the soil borne root pathogen "Fusarium virguliforme," formerly known as "Fusarium solani" f. sp. "glycines"."." Losses could exceed hundreds of millions of dollars in US soybean markets alone making it one of the most important diseases found in Soybeans across the US

Common spot of strawberry is one of the most common and widespread diseases of strawberry. Common spot of strawberry is caused by the fungus Mycosphaerella fragariae (imperfect stage is "Ramularia tulasnei"). Symptoms of this disease first appear as circular, dark purple spots on the leaf surface. "Mycosphaerella fragariae" is very host specific and only infects strawberry.

Mycosphaerella fragariae is a species from family Mycosphaerellaceae.

The disease can tolerate warm or freezing temperature, but favorable conditions for the disease include wet and humid weather. Irrigated fields provide a favorable environment for the disease. The disease has become quite prevalent in semi-tropical regions, but can found all over the world where wheat is grown. Strong winds that blow soils help contribute to the spread of disease. When the spread is initiated by wind blown soil particles, symptoms will be found most readily towards the edges of the field.

Apple scab is a disease of "Malus" trees, such as apple trees, caused by the ascomycete fungus "Venturia inaequalis". The disease manifests as dull black or grey-brown lesions on the surface of tree leaves, buds or fruits. Lesions may also appear less frequently on the woody tissues of the tree. Fruits and the undersides of leaves are especially susceptible. The disease rarely kills its host, but can significantly reduce fruit yields and fruit quality. Affected fruits are less marketable due to the presence of the black fungal lesions.

Ascochyta blights occur throughout the world and can be of significant economic importance. Three fungi contribute to the ascochyta blight disease complex of pea ("Pisum sativum"). "Ascochyta pinodes" (sexual stage: "Mycosphaerella pinodes") causes Mycosphaerella blight. "Ascochyta pinodella" (synonym: "Phoma medicaginis" var. "pinodella") causes Ascochyta foot rot, and "Ascochyta pisi" causes Ascochyta blight and pod spot. Of the three fungi, "Ascochyta pinodes" is of the most importance. These diseases are conducive under wet and humid conditions and can cause a yield loss of up to fifty percent if left uncontrolled. The best method to control ascochyta blights of pea is to reduce the amount of primary inoculum through sanitation, crop-rotation, and altering the sowing date. Other methods—chemical control, biological control, and development of resistant varieties—may also be used to effectively control ascochyta diseases.

In affected orchards, new infections can be reduced by removing leaf litter and trimmings containing infected tissue from the orchard and incinerating them. This will reduce the amount of new ascospores released in the spring. Additionally, scab lesions on woody tissue can be excised from the tree if possible and similarly destroyed.

Chemical controls can include a variety of compounds. Benzimidazole fungicides, e.g., Benlate (now banned in many countries due to its containing the harmful chemical benzene) work well but resistance can arise quickly. A number of other chemical classes including sterol inhibitors such as Nova 40, and strobilurins such as Sovran are used extensively; however, some of these are slowly being phased out because of resistance problems.

Contact fungicides not prone to resistance, such as Captan, are viable choices. Potassium bicarbonate is an effective fungicide against apple scab, as well as powdery mildew, and is allowed for use in organic farming. Copper and Bordeaux mixture are traditional controls but are less effective than chemical fungicides, and can cause russeting of the fruit. Wettable sulfur also provides some control. Timing of application and concentration varies between compounds.

An apple scab prognostic model called RIMpro was developed by Marc Trapman, which numerically grades infection risk and can serve as a warning system. It allows better targeted spraying. Parameter for calculation are wetness of leaves, amount of rain fall and temperature.

Fifteen genes have been found in apple cultivars that confer resistance against apple scab. Researchers hope to use cisgenic techniques to introduce these genes into commercial cultivars and therefore create new resistant cultivars. This can be done through conventional breeding but would take over 50 years to achieve.

Sugarcane smut or "Ustilago scitaminea Sydow" is caused by the fungus "Sporisorium scitamineum"; smut was previously known as "Ustilago scitaminea". The smut 'whip' is a curved black structure which emerges from the leaf whorl, and which aids in the spreading of the disease. Sugarcane smut causes significant losses to the economic value of a sugarcane crop. Sugarcane smut has recently been found in the eastern seaboard areas of Australia, one of the world's highest-yielding sugar areas.

For the sugarcane crop to be infected by the disease, large spore concentrations are needed. The fungi uses its "smut-whip" to ensure that the disease is spread to other plants, which usually occurs over a time period of three months. As the inoculum is spread, the younger sugarcane buds just coming out of the soil will be the most susceptible. Because water is necessary for spore germination, irrigation has been shown to be a factor in spreading the disease. Therefore, special precautions need to be taken during irrigation to prevent spreading of the smut.

Another way to prevent the disease from occurring in the sugarcane is to use fungicide. This can be done by either pre-plant soaking or post-plant spraying with the specific fungicide. Pre-plant soaking has been proven to give the best results in preventing the disease, but post-plant spraying is a practical option for large sugarcane cultivations.

The smuts are multicellular fungi characterized by their large numbers of teliospores. The smuts get their name from a Germanic word for dirt because of their dark, thick-walled, and dust-like teliospores. They are mostly Ustilaginomycetes (of the class Teliomycetae, subphylum Basidiomycota) and can cause plant disease. The smuts are grouped with the other basidiomycetes because of their commonalities concerning sexual reproduction.

Smuts are cereal and crop pathogens that most notably affect members of the grass family ("Poaceae"). Economically important hosts include maize, barley, wheat, oats, sugarcane, and forage grasses. They eventually hijack the plants' reproductive systems, forming galls which darken and burst, releasing fungal teliospores which infect other plants nearby. Before infection can occur, the smuts need to undergo a successful mating to form dikaryotic hyphae (two haploid cells fuse to form a dikaryon).

Extensive treatments have been used on domestic animals more than on wild animals, probably because infected domestic animals are easier to identify and treat than infected wildlife. Treatment plans and management vary across taxa because this disease tends to affect each species differently. Antifungal drugs are the first line of defense to kill the agents causing phaeohyphomycosis, but despite the significant progress made in the last two decades and a 30% increase in available antifungal drugs since 2000, many drugs are not effective against black fungi. Diseases caused black fungi are hard to treat because the fungi are very difficult to kill. This high resilience may be contributed to the presence of melanin in their cell walls. Current antifungal agents the fungi are not resistant to are posaconazole, voriconazole, and azole isavuconazole.

In 2006, a free-living Eastern box turtle, "Terrapene carolina carolina", was found with a form of phaeohyphomycosis and was brought in the Wildlife Center of Virginia. Its symptom was swelling of the right hindfoot; it was diagnosed as having chromomycosis by histopathology. The center provided a series of antimicrobial treatments and a one-month course of 1 mg itraconazole, administered orally once a day. The eastern box turtle was euthanized due to further complications and the caretakers’ belief that the turtle would not be able to survive if placed back in the wild.

A recent case of a form of phaeohyphomycosis infection was found in a dog in 2011. The Journal of the American Veterinary Medical Association published a case study in which researchers successfully managed an intracranial phaeohyphomycotic fungal granuloma in a one-year-old male Boxer dog. Veterinarians of the Department of Veterinary Clinical Sciences at Tufts University surgically removed the granuloma in the right cerebral hemisphere. The patient was treated with fluconazole for 4 months, and was followed with voriconazole for 10 months. Both are medications used to treat fungal infections. Based on magnetic resonance imaging and cerebrospinal fluid (CSF) analysis 8 months after the surgery, the male Boxer’s outcome was considered excellent.

Emphasis has been placed on how to manage this disease through careful management practices including: proper handling, preventing crowding situation with animals, and transportation. Both the animals and the environment should be treated thoroughly to hinder the spread and control the fungal infection. This is especially important since humans can also contract this disease.

Black band disease is a coral disease in which corals develop a black band. It is characterized by complete tissue degradation due to a pathogenic microbial consortium. The mat is present between apparently healthy coral tissue and freshly exposed coral skeleton.

Black band disease was first observed on reefs in Belize in 1973 by A. Antonius, who described the pathogen he found infecting corals as "Oscillatoria membranacea", one of the cyanobacteria. The band color may be blackish brown to red depending on the vertical position of a cyanobacterial population associated with the band. The vertical position is based on a light intensity-dependent photic response of the cyanobacterial filaments, and the color (due to the cyanobacterial pigment phycoerythrin) is dependent on the thickness of the band. The band is approximately thick and ranges in width from to White specks may be present on surface, at times forming dense white patches. The pathogenic microbial mat moves across coral colonies at rates from to a day. Tissue death is caused by exposure to an hypoxic, sulfide-rich microenvironment associated with the base of the band.

Boric acid (16.5%boron), borax (11.3% boron) or SoluBor (20.5% boron) can be applied to soils to correct boron deficiency. Typical applications of actual boron are about 1.1 kg/hectare or 1.0 lb/acre but optimum levels of boron vary with plant type. Borax, Boric Acid or Solubor can be dissolved in water and sprayed or applied to soil as a dust. Excess boron is toxic to plants so care must be taken to ensure correct application rate and even coverage. Leaves of many plants are damaged by boron; therefore, when in doubt, only apply to soil. Application of boron may not correct boron deficiency in alkaline soils because even with the addition of boron, it may remain unavailable for plant absorption. Continued application of boron may be necessary in soils that are susceptible to leaching such as sandy soils. Flushing soils containing toxic levels of boron with water can remove the boron through leaching.

The application of copper fungicide has been shown to significantly reduce a great number of black pod incidences in Nigeria. Metalaxyl (Ridomil) and cuprous oxide (Perenox) were identified to be successful in increasing the number of harvested healthy pod compared to the application of fosetyl aluminium (Aliete) and control treatment. On top of that, the timing of fungicide application has some positive effect on the final pod yield where this plot produced greater yield than the unsprayed plot. The application was done before August, which is before the main disease epidemic that usually occurs in September and October.

The recommended standard for fungicide application to control black pod disease caused by "P. megakarya" for a season is 6 to 8 times of application in every 3–4 weeks. However, the adoption of recommended application was very low among farmers in Ghana. Therefore, an experiment with a reduced number of fungicide applications demonstrated that there was 25 to 45% reduction in disease incidence. In terms of disease control and yields, sanitation and three applications of Ridomil 72 plus (12% metalaxyl + 60% copper-1-oxide) fungicide showed a better control compared to sanitation alone and sanitation with one or two fungicide applications. However, reduced in fungicide application was shown to be significantly less effective than the recommended standard fungicide application.

It was suggested that the understanding regarding the source of inoculum, the amount of infective inoculum production and how the disease is disseminated is important in order to identify the appropriate and economical method in fungicide application as well as for an effective control of the disease. For example, the application of fungicide on the trunk will help farmers to control the spread of the disease up in the canopy, as it is difficult to reach the canopy during fungicide application. This will eventually save more time, labor and cost for disease management.

Diagnosis of mycetoma is usually established clinically in endemic areas.

X rays and ultrasonography may be employed in evaluating the extent of the disease. X rays findings are extremely variable. The disease is most often observed at an advanced stage that exhibits extensive destruction of all bones of the foot. Rarely, a single lesion may be seen in the tibia where the picture is identical with chronic osteomyelitis. Cytology of fine needle aspirate or pus from the lesion, and tissue biopsy may be undertaken sometimes. Some publications have claimed a "dot in a circle sign" as a characteristic MRI feature for this condition (this feature has also been described on ultrasound).