Fusarium Wilt and Fusarium Bud Rot in Cannabis (Hemp and Marijuana)

Anyone involved in plant pathology can tell you that the genus Fusarium is one of the most damaging group of fungi to crops. There are many species of Fusarium that cause disease on different crops. Some infections can cause devastating root rots and vascular diseases, some can cause cankers on branches and stems, and some can even infect foliage. Yield losses can be dramatic in some circumstances. For instance, in 1999 in northern Great Plains and central USA, Fusarium head blight of winter wheat alone suffered $2.7 billion losses [32]. In tomato, when disease is severe, crop losses can reach 80% [33].

In Cannabis, two formae speciales of F. oxysporum have been described as causing Fusarium wilt: Fusarium oxysporum f. sp. vasinfectum (FOV) and Fusarium oxysporum f. sp. cannabis (FOC) [2, 21]. Furthermore, Fusarium solani has been found to be prevalent in hydroponic Cannabis grown in Canada [21]. Furthermore, F. brachygibbosum and F. equiseti have been isolated (in addition to F. oxysporum and F. solani) from symptomatic field-grown Cannabis plants in Northern CA [23]. F. oxysporum has been isolated from wilted Cannabis plants that does not match with either of the formae speciales cannabis or vasinfectum [21].

Fusarium oxysporum species complex

Fusarium oxysporum is a diverse species; some species are harmless soil inhabitants, while some are plant pathogens. Arguments have been presented that there may be at least two phylogenetically distinct species based on DNA sequencing, and that most plant pathogens belong two one of these groups (PS2) [1].

Forma specialis is not a phylogenetically recognized categorization; it is a way for plant pathologists to discuss particular isolates of Fusarium species that attack particular plant species. A forma specialis is generally named after the diseased plant that it was isolated from, this is why one of the isolate groups that infect Cannabis is called F. oxysporum f. sp. cannabis. The two formae speciales that infect Cannabis can be distinguished by their host range. FOC only infects Cannabis, whereas FOV has a wider host range and can infect cotton, coffee, and other plants. F. oxysporum has at least 100 different species-specific isolates. Sexual reproduction has not been observed in this species, but horizontal gene transfer likely had an important role in the evolution of this organism [1]. all observed spores from F. oxysporum are asexual in nature.

Infections begin with the germination of spores or growth of mycelium into plant roots through injured areas or sites of lateral root emergence. The filamentous mycelium penetrates into the xylem vessels and begins colonizing the plant’s vasculature. It becomes systemic and can form sporulating structures known as sporodochia on aerial parts of the plant. The sporodochia produce conidia (2 types, microconidia and macroconidia [macroconidia is larger, multinucleate, and multiseptate]). The conidia is carried by wind and air. When it comes to overwintering, Fusarium can survive in the infected crop residues, but it can also make overwintering asexual spores known as chlamydospores. Chlamydospores don’t require special structures to form, they can form at the terminal ends of fungal hyphae or within the hyphae (intercalary). They are generally thick walled, melanized, and multicellular spores.

Image from Plant Pathology 5th Edition, Agrios (2005)

This disease of Cannabis has been amplified through human activity. Fusarium oxysporum is a deadly pathogen and it has been foolishly used as a mycoherbicide all over the world in order to try to kill ‘illicit’ Cannabis plants [2, 3]. All cultivars that have been tested are susceptible to the disease. In native ecosystems, F. oxysporum is not known to be a major disease risk. It seems that through intensive agriculture and monocropping, more pathogenic and virulent isolates have been able to evolve and amplify their populations clonally [1].

Fusarium solani species complex [22]

F. solani, much like F. oxysporum, was previously divided into formae speciales based on the host range. However, recent phylogenetic studies have determined that different formae speciales are really unique species, and the F. solani species complex (FSSC) is divided into at least 60 unique species. Some of these species have been renamed, but many are still unnamed and are referred to by ‘haplotype number’, which is basically just a number that represents certain genotypes. The FSSC has a wide host range, and even particular species within the FSSC can have broad host ranges. Unlike in the FOSC, sexual reproduction has been observed in some species in the FSSC.

The life cycles, infection techniques, and symptoms are very similar between FOSC and FSSC, so I when I mention Fusarium from here on out, I will be referring to all Fusarium sepecies capable of causing root rots of Cannabis.

Root Infection

Chlamydospores require a conducive environment to germinate and cause disease. In soil, this generally means the presence of root exudates [34]. Because of this, only spores in very close proximity to roots actually pose a disease risk. The rhizosphere (which I will define as the area of soil directly affected by the root exudates) is generally very small (<1 mm) from the plant root [9, 10]. The actual volume of soil that falls within this distance from roots is typically under 35%, even for plants with extensive roots and highly active exudation [1]. However, evidence of targeted growth of germinated spores towards roots is lacking (i.e. lacking evidence for chemotaxis) [11]. Infections may fail to establish, especially in the case of a rapidly growing root (spore germinates in response to root exudate, if the germ tube reaches the root, chances are the root tip has already advanced and the fungus is now encountering more differentiated plant tissue more capable of defensive responses) [12].

Flower and Seedling Infection

Along with Pythium, Fusarium can cause damping off of seedlings. Infection can begin in roots or the hypocotyl and can quickly invade the vasculature [21].

Fusarium usually begins its infection cycle from chlamydospores in the soil. However, as the infection progresses, sporodochia form on the crown and lower stem that produce conidia. Conidia can become airborne and can infect aerial portions of the plant. In particular, it can readily form flower infections and cause bud rot. Flower-infecting species include F. solaniF. oxysporum and F. equiseti [25]. F. solani appears to be the most aggressive species. It appears that the F. oxysporum that has been isolated from flowers is the same type involved in root infections [25]. These Fusarium species can directly infect the bracts and pistils of flowers.

In hydroponics, Fusarium can be particularly aggressive [13]. In fact, researches generally use aqueous spore suspensions in experiments to guarantee that the plant is inoculated. First of all, the spores are essentially in suspension and circulate around the water, almost guaranteeing that the spores will come in direct contact with the roots. Furthermore, the spores can directly adhere to the root tips, foregoing the need for germ tubes to find their way through soil to the plant roots and decreasing the chance that the plant root can grow faster than it takes for the fungal mycelium to reach the root. This allows easy access for the fungus to susceptible meristematic tissue. Root tip infection does not occur for all plant species, but spore adhesion to roots certainly does raise disease risk for any plant species.

Once the fungal mycelium contacts a root, the fungus proliferates into a hyphal network to maximize points of contact. They likely utilize cell wall degrading enzymes to form an opening, and the mycelium can then penetrate directly through epidermal cells or may grow in between cells [1]. Either way, growth advances towards the root cortex.

Necrotroph or Biotroph?

For those who have read my articles on two other major Cannabis pathogens, bud rot and powdery mildew, you may be aware that pathogenic fungi can have a variety of different strategies. A biotroph requires the host cells to be alive and extracts nutrients from the living host cells (a true parasite, such as PM [manipulates host immune responses]), whereas a necrotroph such as the bud rot pathogen Botrytis cinerea induces or causes cell death to overcome plant resistance responses and have dead organic matter to feed on (it may be argued that there is a brief biotrophic phase in bud rot but in general can be viewed as a necrotroph).

Strictly speaking, Fusarium is necrotrophic because even isolates that do not cause any visible damage to a given plant (nonpathogenic) are observed to grow intracellularly and cause cell death on a microscopic level [14]. However, as mentioned, there are many cases of F. oxysporum isolates not causing any really visible disease or crop losses, or even examples of isolates that cause disease symptoms on some plant species but can colonize the roots of other plant species without causing visible disease symptoms. In these cases, though necrotrophy is visible on a microscopic level, F. oxysporum may be considered an endophyte, and the complexity of the relationship between endophytic Fusarium isolates and their plant hosts are not fully understood [1, 15, 16, 17, 18]. In fact, F. oxysporum can even be isolated as an endophyte from nonsymptomatic Cannabis plants [24].

There have been some conflicting reports as to how the wilt disease progresses (this will mostly focus on studies done with F. oxysporum in flax), but the differences might be attributable to environmental differences between studies, differences in how microscopic images were interpreted, or it may even be evidence that different isolates within a given forma specialis may span a spectrum of necrotrophic and biotrophic lifestyles.

Disease Cycle Proposition 1: The extended biotrophic phase [19]

  1. The fungus has an extended biotrophic phase in which infected cells remain viable and the fungus can continually be isolated from seemingly disease-free root tips.
  2. After entering the xylem vessels, the fungus grows in the vessels and feeds on the nutrients carried within the xylem. It continues to grow until the vessels become occluded (blocked), either through the accumulation of fungal biomass or through plant responses such as forming tyloses.
  3. After xylem occlusion and plant wilting/death, the fungus then grows out of the vasculature and begins a necrotrophic phase in which is begins killing and feeding on all other plant tissues.

Disease cycle proposition 2: The true necrotroph [20]

  1. No biotrophic phase observed, cell death is common among all cells the fungus comes in contact with.
  2. Infection of roots leads to root cell death and necrosis before the fungus even reaches xylem vessels (i.e. root rot can precede systemic vascular infection)
  3. Fungus aggressively colonizes both vasculature and other tissues


  • Initial symptoms can look similar to Nitrogen deficiencies. Chlorosis of lower leaves and slight wilting becomes evident. Plant stunting is common, especially in the case of F. solani infection
Left plant is uninoculated. Middle plant inoculated with F. oxysporum, right plant inoculated with F. solani.
Image adapted from Punja, Z., Scott, C., & Chen, S. (2018). Root and crown rot pathogens causing wilt symptoms on field-grown marijuana ( Cannabis sativa L.) plants.
  • The crown region of the plants become darkly discolored and sunken. Discoloration of the vasculature can extend up to 15cm from the soil surface.
Image adapted from Punja, Z., Scott, C., & Chen, S. (2018). Root and crown rot pathogens causing wilt symptoms on field-grown marijuana ( Cannabis sativa L.) plants.
Showing discolored pith. Image adapted from Image adapted from Punja et al. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
  • In hydroponics, roots become discolored
Image adapted from Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
  • When xylem vessels become occluded, whole plants can begin to wilt.
Image adapted from Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
  • In this hydroponic system, the Fusarium wilt ended up killing the plant.
Image adapted from Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
  • Sporodochia form on the necrotic stem and the spores can become airborne, infecting surrounding plants. In humid conditions, mycelium can grow out of the stem
Image adapted from Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
  • Fusarium can cause damping off in seedlings and clones as seen in the following tray of clones:
Image adapted from Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
  • Fusarium oxysporum can cause bud rot! When inoculated on flowers, they can cause necrosis of the buds very similar to Botrytis cinerea. The mycelium is usually much more white than the mycelium from B. cinerea.
Image adapted from Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.
The Effect Of Fusarium On Marijuana Plants - Grasscity Magazine ...
Image from https://growersnetwork.org/cultivation-resources/growers-networks-disease-profile-fusarium-wilt/
  • Depending on where the infection occurs, wilting can be evident on some branches/colas but not others.
Image from https://www.lahuertagrowshop.com/blog/como-prevenir-y-eliminar-fusarium-en-plantas-de-marihuana/


What Factors Favor Fusarium Development?

For F. oxysporum f. sp. lycopersici (the forma specialis that infects tomato), the following factors favor wilt development (28):

  • Soil and air temperatures of 28°C (Too warm (34°C) or too cool (17-20°C) will inhibit development)
  • Low nitrogen and phosphorus, high potassium
  • Low soil pH
  • Short day day length
  • Low light
  • use of ammonium nitrogen

Root exudates appear to stimulate spore germination and drive plant infection. However, certain techniques based on manipulating the soil microbiome may be beneficial in controlling the severity of Fusarium wilt.

  • Amending soil with organic matter to promote microbial activity may make soils more disease-resistant [4].
  • Soil treatments aimed at reducing the number of viable fungal propagules in the soil such as anaerobic soil disinfestation (ASD) [5] and solarization [6].
    • ASD is a process of flooding a field and covering with a plastic ‘mulch’. Anaerobic bacteria multiply and gasses from these bacteria accumulate under the plastic mulch.
    • Solarization is the process of putting a black plastic over a field during hot seasons in direct sun to raise soil temperatures.
  • Certain bacteria or microbial groups may contribute to how conducive a soil is to disease development
    • For instance, a species of Arthrobacter in suppressive soils was associated with greater levels of lysis of fungal germ tubes from soil chlamydospores [7].
      • Soils that are more disease suppressive are sometimes associated with certain microbial groups in the soil microbiome [8]

Resistant Cultivars

Resistant strains undoubdtedly can be bred for. In hemp, SF and CF cultivars appear to be more resistant than the cultivar Iran [3]. I am not sure what strains are best in regards to marijuana cultivars with resistance to Fusarium, and I am struggling to find information on this. Comments with relevant information on this would be appreciated.

Biocontrol Agents

I will list some approved spray/soil drench control methods, but can not promise the effectiveness of any method, much cannot be found in literature.

  • In Canada, possible biocontrol agents for Fusarium infections in foliage and flowers include Prestop WP (Gliocladium catenulatum strain J1446) and Rootshield WP (Trichoderma harzianum Rifai strain RRL-AG2) [25].
    • These microbes will be counted on CFU testing, so should not be applied late in locations that test using this method.
  • In Canada, approved biocontrol agents for root-infecting pathogens are Rootshield WP (Trichoderma harzianum Rifai strain RRL-AG2) and Prestop WP (Gliocladium catenulatum strain J1446) [21].
  • In California, Gliocladium virens, Trichoderma harzianum, and Bacillus amyloliquefaciens strain D747 are approved biofungicides [26].
  • Other possible biocontrol biocontrol agents include Rhapsody (Bacillus subtilis strain QST 713) and Mycostop (Streptomyces griseoviridis strain K61) [21].

Plant Activators

In California extract of Giant Knotweed (Reynoutria sachalinensis) REGALIA® Rx Biofungicide is an approved fungicide.

Marrone Bio Innovations Regalia Biofungicide Fungicide inhibits fungal and Bacterial Disease Boosting Yield, 0-Day PHI, 4 Hour REI, OMRI Listed (1 Gallon)

Kelp extracts (contain arachadonic acid) and crab meal/insect frass (contain chitin) may be useful soil amendments for priming plant resistance to soil borne fungal pathogens.

Liquid Kelp Extract Seaweed 32 Ounce Fertilizer Concentrate

In Oregon, potassium phosphite such as Agri-Fos, (which happens to also be a good source of potassium and phosphorus in flower) is also approved as a plant protectant and fungicide

Monterey Agri-Fos Disease Control Fungicide – Pint LG3340

Quest Reliant Systemic Fungicide (Agri-Fos/Garden Phos) 1 Gallon

Cultural Methods

  • Control and prevention should include efforts to reduce inoculum loads. For growers using hydroponics (including coco) and/or indoor grows: ultraviolet light in ducting and even the grow area (which also may increase cannabinoid production if used correctly), ozonation of the grow area (too high of a level may have negative effects on plant and human health), chlorination of water used in hydroponics, hydrogen peroxide flushes of the root zone (or products such as Zerotol which also contains peroxyacetic acid), heat pasteurization and/or mechanical filtration of water [21].DPD ZeroTol 2.0 2.5GAL
  • It is a good idea to remove wilted plants to prevent aerial spore transfer and quickly remove any infected flowers or branches, especially in environments of high humidity.
  • In hydroponics, keeping nutrient solution at temperatures between 17℃ and 22℃ is ideal for preventing pathogens, promoting water oxygenation, and preventing growth retardation of the plants. Active Aqua AACH10HP Water Chiller Cooling System, 1/10 HP, Rated per hour: 1,020 BTU, User-Friendly
  • Always sterilize your tools in between cuts, wear proper PPE to avoid introducing inoculum.
  • Despite common conceptions that Fusarium grows best in flooded soils, many Fusarium species actually grow best in aerobic, well-draining soil [30]. Another study similarly found F. oxysporum f. sp. lycopersici to not grow in saturated soils. However, plants were actually resistant to infection at soil moisture contents of 13%-19% [31].
    • In short, it is good to let your soil dry between waterings (not to the point of plant wilting though). Fusarium grows best in aerobic (well-draining), and moist but not flooded soils (i.e. most coir or peat based media).
    • Anaerobic soil disinfestation (ASD) may be a good way to reduce soil inoculum levels between grows in no-till systems.

Foliar/Flower Controls

The most important factor in preventing flower infections from Fusarium is probably humidity [25]. Flower infection relies on airborne conidia released from the sporodochia (spore-bearing structures) on aerial tissue of the plant. Humidity needs to be high in order to successfully form these sporodochia. A different Fusarium species, F. graminearum requires humidity of over 85% RH to form perithecia (sexual spore-bearing structure of this species) [27].

For Fusarium oxysporum f. sp. erythroxyli (this paper is unfortunately discussing the possible use of this Fusarium species to kill the ‘illicit narcotic’ coca plant), the isolate was found to sporulate at relative humidities (RHs) between 75% and 100% [29]. Fusarium‘s primary route of infection is through the roots in soil, and it is a bit easier to control for aerial infections than soil infections in Cannabis.

General humidity control aiming to correlate with vapor pressure deficit conditions or slightly lower for IPM reasons (around 60% RH in veg, 50% in flower down to 40% the last couple weeks of flower) should be good enough to prevent a lot of aerial sporulation. Good airflow and ciculation is definitely recommended to reduce high-humidity microclimates.

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  2. McPartland, J. M., & Hillig, K. W. (2004). CANNABIS CLINIC Fusarium Wilt. Journal of Industrial Hemp, 9(2), 67–77. https://doi.org/10.1300/J237v09n02_07
  3. Council, N. R. (2011). Feasibility of Using Mycoherbicides for Controlling Illicit Drug Crops. The National Academies Press. https://doi.org/10.17226/13278
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  21. Punja, Z. K., & Rodriguez, G. (2018). Fusarium and Pythium species infecting roots of hydroponically grown marijuana (Cannabis sativa L.) plants. Canadian Journal of Plant Pathology, 40(4), 498–513. https://doi.org/10.1080/07060661.2018.1535466
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  24. Punja, Z. K., Collyer, D., Scott, C., Lung, S., Holmes, J., & Sutton, D. (2019). Pathogens and Molds Affecting Production and Quality of Cannabis sativa L. Frontiers in Plant Science, 10, 1120. https://doi.org/10.3389/fpls.2019.01120
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  34. Akhter, A., Hage-Ahmed, K., Soja, G., & Steinkellner, S. (2016). Potential of Fusarium wilt-inducing chlamydospores, in vitro behaviour in root exudates and physiology of tomato in biochar and compost amended soil. Plant and Soil, 406(1), 425–440. https://doi.org/10.1007/s11104-016-2948-4

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