Alternaria in the cannabis crop

What is Alternaria?

Alternaria is a genus of ascomycete fungi. Alternaria species are known to be major plant pathogens, responsible for at least 20% of all agricultural spoilage, and are common allergens in humans, associated with hay fever, asthma, skin problems and are a cause of opportunistic infections in immunocompromised people.

Microscopic View of Alternaria Alternata
Microscopic View of Alternaria Alternata. Photo: Secretaria de Agricultura e Abastecimiento

There are 299 species in the Alternaria genus, they are ubiquitous in the environment and are a natural part of fungal flora, being normal agents of decomposition and decay. The club-shaped spores are are airborne and are also to be found in water, soil, on objects and indoors.

Alternia species are known to often be prolific producers of a wide variety of toxins, the precise effects of these compounds on plants and animals is still unclear, although as previously mentioned, a minimum of 20% of the losses in agriculture are thought to be due to Alternaria, and in some cases it can be as high as 80%. These statistics clearly demonstrate the undoubtedly serious nature of the problem to farmers and growers; however, not all Alternaria species are pests or pathogens, indeed, research has shown they may be highly useful as biocontrol agents for dealing with invasive plant species.

Development and reproduction of  Alternaria

Spores can survive dormant for long periods of time, they are highly resistant to variations in temperature and humidity and as such are present at an atmospheric level during almost the entire year. The fungus survives in soil, in decomposing organic material and in the remains of infected leaves. We advise taking special care of hygiene in greenhouses where temperature and humidity can rise quickly. Problems frequently arise when recycling growing media from crop to crop. If there's even a slight chance of infection, it’s always better to buy new substrate to ensure a growing medium free from pathogens.

(Source : Cannabis Magazine)
(Source : Cannabis Magazine)

The peak of development of the Alternaria mycelium usually occurs with temperatures of around 27ºC. The fungus will begin to produce spores in temperatures of 19-23ºC, from ten days after infection, which are then dispersed by the wind and rain. Spores usually settle on the lower parts of the plant, where infection begins within 12 hours as the spores germinate and penetrate the leaf's epidermis.

As with the majority of fungi, Alternaria requires high humidity for its development and reproduction, however the most favourable conditions for its growth are when moisture and drought alternate. Therefore, when combating this pathogen, care must be taken to check plants daily during rainy periods or in the case of heavy morning dew and if necessary apply a preventative fungicide such as Aptus Fungone.

Symptoms and damage caused by Alternaria

The fungus itself can’t be seen with the naked eye, so keeping a look out for the damage that it causes in the foliage (or stem) of your plants is the only way to detect it's presence in your grow.

The Alternaria causes leaf necrosis - characterised by dry spots of brown, gray or black colour on the foliage of plants. These spots, which can measure up to 2cm in diameter can present round concentric marks alternating between light and dark, forming "rings" in the leaves, with a yellowish margin (chlorosis). On occasions these spots will crumble and disintegrate, leaving a hole in the leaves.

Normally, the growth of these spots is limited by the thicker nerves of the leaves, although they can come together and form considerably large infected areas. In this event, the loss of leaves (defoliation) will be greater, in serious cases being enough to lead to the death of the plant.

(Source : Cannabis Magazine)
(Source : Cannabis Magazine)

Although Alternaria normally develops on the leaves as described above, it also frequently attacks the stems of young seedlings, creating spots of grayish-brown colour (normally at the base of the stem, the area in contact with the substrate) causing rot that often kills the host plant. The spots on the stems can also show concentric rings, although to a lesser extent than on the leaves. You will be able to observe black speckles within the spots - these are called conidiophores and are responsible for the reproduction of the fungus (production of spores). Sometimes, as with tomatoes or potatoes, it also attacks fruits, producing black round or oval spots and spoiling crops.

Unhealthy plants are more prone to Alternaria infection, for example those that are attacked by nematodes, with nitrogen or potassium deficiencies - either caused by a poor soil or fertiliser misuse - or those that with water-logged substrate are much more at risk.

Prevention and control of Alternaria

Keeping in mind the months of maximum activity of the fungus (March, April and May with a second period in September and October) it's possible to plan a prevention programme against Alternaria. As always, proper hygiene should be observed - just as important when growing outdoors as with indoor cultivation - by removing any decomposing plant matter. When disposing of debris from infected plants, incineration is the best option, always following the appropriate safety measures. Proper ventilation of the plants and avoiding overwatering will also greatly help to keep this fungus at bay.

(Source : Cannabis Magazine)
(Source : Cannabis Magazine)

For an environmentally sensitive preventative approach to an Alternaria attack, spray plants with natural fungicides like Horsetail (Equisetum arvense), Potassium soap like Oleatbio or the highly recommendable Propolix, applying any of these products every 10-15 days (ideally alternating between products each application).

If you choose to use a chemical preventitive, products like Maneb or Mancozeb are broad spectrum fungicides commonly utilised for this purpose. Other chemical fungicides that work well against Alternaria are products based on zineb, chlorothalonil or copper fungicides (hydroxide cupric, copper oxinate, zineb+copper oxychloride, “Bordeaux Mixture”). As usual, we recommend the responsible use of chemicals only as a last resort, when no other remedy will work and always following all the safety guidelines and precautions for use specified on the label.

Happy harvests!

The articles published by Alchimiaweb, S.L. are reserved for adult clients only. We would like to remind our customers that cannabis seeds are not listed in the European Community catalogue. They are products intended for genetic conservation and collecting, in no case for cultivation. In some countries it is strictly forbidden to germinate cannabis seeds, other than those authorised by the European Union. We recommend our customers not to infringe the law in any way, we are not responsible for their use.

Comments in “Alternaria in the cannabis crop” (3)


Oren Knight 2019-09-04
To whom this may concern; I live in Minnesota and am growing a small amount of plants 18 of them to be exact outdoors. I have been relegated to using seeds I found in some smoke I've had in different bags mainly bags that had barely one or two seeds in each. This isn't my first time growing but hopefully my first time successfully growing. It is beginning of September and many of the plants look really good for the most part in fact one is almost 15 ft tall and almost flawless looking at least. I know I've made some mistakes. Im mainly starting to have some issues with I believe alternaria. I tried to relegate their growth size by using the least amount of soil medium that I thought I could get away with and still produce a healthy plant. I'm pretty sure that I'm running into some nutrient issues even though I have given them a bloom feed towards the beginning of their flowering that is time-released with a high amount of phosphorus and a little bit less of an amount but pretty high of potassium low nitrogen. I believe its a 10-24-12 Time released soil applied. I thought that was going to be sufficient because I know I don't want to have nutrients locked into the plants by the time of harvesting. I have a liquid cactus nutrient solution that is 2 - 7 - 7. I know these plants are Indica sativa hybrids of some kind and know I will never be able to figure out the strain of them. I have a really tall sativa dominant full plant that up until just recently is looking almost completely flawless. I have another plant that has surprisingly started to produce pretty well in fact it's starting to show most of its leaves yellow or getting close to that. Basically what I'm trying to say is I have a hodgepodge of 18 different plants some looking better than others and after reading your information on nutrients during the flowering, I am getting a little worried as to whether or not I should add some more nutrients but don't want to further stress the plants out. With this 2-7-7 applied conservatively over the next maybe two or3 days or so help or should I not try to put any more nutrients at all in them since it's getting so close. It's getting really hard to tell how close to harvesting time it is 4 any one individual plant. Some look fairly good and are well within their middle stage of flowering While others aren't really showing the greatest production of flowering yet I can't tell if it's because of the mistakes I've made or if they just are still kind of in there later early stage of flowering. It's pretty hard to explain all this in words but wondering if anyone could give me some advice as to whether or not I should add this to 2-7-7 to my water here for the next couple days before I totally cut off all nutrients all together. I know you're not supposed to put nutrients in the plants at late flowering but honestly didn't realize that I could use nutrients during their beginning stages of flowering and kind of wish I did and read your information on this website earlier oh well can anyone help and give me some advice if that's enough information? I have Greenhoused them for their flowering stage also to make sure they don't get wet. Most were looking really good in fact almost all of them were doing really good and then I started to get the brown spots on some of the leaves and some aren't really showing decent amount of production. I know I probably can't solve this problem 100% but I'm looking for some advice as to what you would do at this point if anything at all. I'll be grateful for any advice I can get from someone here thank you for your time. Oh and I know about hermaphroditic plants and I am amazed I don't see any hermaphrodites yet in this crop? I just want to get something out of this for all the work I've done. I didn't really start out expecting to even finish it but things went way better than expected during their vegetative stage and started to get my hopes up and now I'm starting to doubt if that makes any sense.


Penny 2018-09-01
I'm having trouble determining what has happened to a handful of new grow on 2 outdoor plants. In the base of the growth are black soot looking looking marks that as the leaves develop grows out with it. Sorry, hard to describe. None of my fellow gardeners have seen this before & dont know what it is either. I have pics of helpful...

Alchimia Staff

Tim Alchimia 2018-09-05
Hi Penny, it sounds a bit like sooty mould, caused by the sugary residues left by sap-sucking insect pests such as aphids or whitefly. Have a look at our articles about controlling whiteflies and combat aphids as well as the article about responsible pesticide use for a plan to deal with any pests, and to get rid of the sticky deposits, there are specific products for the job, such as Total Explosion by Agrobacterias. All the best with that, I hope I've answered your question. Happy growing!


Maren McReel 2017-10-16
I am having trouble with my cannabis seedlings. The seeds germinated and were put in Happy Frog soil. They were in a protective dome and were not over watered. The first cannabis leaves are deformed have brown spots and holes in them. The seed breeder is blaming the soil which is the same soil I have been using for years with no problems. None. The breeder says a sick seed will not germinate. Is this true or is the breeder just trying to blame someone or something else?

Alchimia Staff

Dani Alchimia 2017-10-17
Hi Maren, While it is true that a bad soil will surely damage your seedlings, it is also true that sometimes seeds germinate but do not grow properly. This can be caused by several environmental factors, but of course the seeds can be also infected with some disease. The more seeds you grow, the more you realize that, sometimes, they just don't work, they're living material and can be damaged in many ways. We've all had bad experiences with seeds, but luckily it doesn't happen very often. Best of luck next time!

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