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Taking on pests and diseases in cannabis: The propagation stages

January 5, 2021  By Dr. Michael Brownbridge

Photo credit: DoraDalton/Getty Images

The cannabis sector is a young and vibrant part of the horticulture industry. With legalization across Canada, opportunities to grow the crop at scale emerged overnight. This has brought significant challenges as growers adapt from ‘basement grow-ops’ to multi-acre facilities. Because cannabis has some unique features that it shares with many other greenhouse crops, growers can transfer some well-established IPM technology from other horticultural sectors to prevent many of the pests and diseases they have in common.

Scope and purpose

The intent of this two-part article series is to provide information on pest and disease management tools that are currently approved for use in Canada. It does not cover a wish list of products and materials that could be used. Serving as a companion to the Greenhouse Canada webinar presented in September 2020 (, this article series addresses common production issues and available solutions at each stage of crop development, allowing us to consider ways in which they may be prevented or managed at that point in time. This is especially important as the use of a biopesticide/biocontrol agent in one stage may differ from how it can be applied in another. Furthermore, successful use in one stage inevitably impacts what occurs at the next. In this way, I hope to bring more of a ‘whole program’ approach to pest and disease management through the lifecycle of the crop, from propagation to harvest. And last, the methods discussed are essentially for indoor production of cannabis – greenhouse or grow facility – but the methods described for propagation can be applied to production of transplants for either outdoor cannabis or hemp.

Now that that’s out of the way, where to begin? To avoid diluting the information by trying to cover too much, the focus is on implementation of functional IPM programs for cannabis, highlighting use of biopesticides and biological control agents, considering the best fit of the different components, and how they can be integrated into a crop protection scheme.


The importance of plant nutrition in IPM

Let me first digress a little to stress the importance of plant nutrition in IPM, as it has a direct impact on plant health. By optimizing growing practices, we create a more resilient crop that is not only more productive, but inherently less prone to pests and diseases. However, high nitrogen levels in plant tissue can also dramatically increase plant susceptibility to pests and diseases. This has been shown in a variety of other crops ranging from cereals, to flowers, vegetables and fruits, and studies have documented a particularly strong correlation between high levels of applied (synthetic) nitrogen fertilizer and growth of pest populations. Populations of pests such as two-spotted spider mite, green peach aphid and western flower thrips will expand rapidly when high levels of synthetic N are applied. This then raises the question – can fertilizer inputs be reduced without affecting crop quality or production time? Can the type of fertilizer inputs be managed to avoid rapid accumulation of high N levels in plant tissues while ensuring sufficient supply for growth? And is there latitude to reduce fertilizer inputs as a means of slowing pest population growth?

We know that plants require different types and levels of nutrients at different stages of development and growth, and essential nutrients (N, P and K) are manipulated to fulfill those changing requirements. In cannabis, some nutrients (particularly N) are ‘pushed’ at flowering to promote larger blooms. But this can compromise plant tissue formation and increase susceptibility to diseases like powdery mildew and Botrytis. Recent changes to Health Canada regulations on the application of nutrients by foliar spray is a significant development as it may allow reductions in salt-based nutrient inputs without compromising yield. Research has shown that application of foliar nutrients at times of peak nutrient demand and prior to stress events (rapid growth, bloom, and flower development, drought, temperature extremes, major changes in light and humidity) will enhance plant stress tolerance. Use of some sprayable nutrients can also enhance uptake and translocation of elements like calcium (Ca), an essential component of plant cell walls. Stronger cells, especially in flowers, can reduce susceptibility to diseases like Botrytis. This has been demonstrated in petunia where susceptibility is linked to poor movement of Ca into flowers and deficiencies increase susceptibility to the disease. Higher Ca concentrations enable more pectic bonds to be formed in flower cell walls, improving resistance to breakdown by enzymes produced by Botrytis, thereby reducing susceptibility to infection by the fungus. This has yet to be tested in cannabis, but observational evidence suggests that use of such nutritional supplements may help combat Botrytis.

Sanitation and prevention: Creating the right foundations

Sanitation and prevention are at the heart of any IPM program, especially ones utilizing biological inputs. At its core, biocontrol is a preventative strategy and not a curative one. Biocontrol agents and biopesticides should be applied proactively to prevent pest or disease problems from developing, as opposed to controlling them. This is particularly important in cannabis as there are no (legal) rescue products that can save a crop if pests or diseases get the upper hand.

A beneficial fungal product applied during propagation can improve root development in cannabis cuttings and increase yield. (Pictured: trial with Rootshield Plus) Photo credit: BioWorks Inc.

Looking after mother

What is true in life is also true in cannabis, look after your mother! Sanitation starts from the very beginning of a production cycle. If you maintain your own stock plants, the area in which they are kept should be dedicated to keeping plants healthy in a stress-free, clean growing environment, ideally with systems and mechanisms in place to prevent ingress of bacterial and fungal spores and insects.

Limiting access to the room further reduces the risk of pests and diseases being transferred into the area. Pests and diseases readily hitch a ride on crop workers, so restricting plant care to a few individuals will go a long way to reducing risk. Maintain a strict ‘order of entry’ for those workers. In other words, all work on the mother plants and in the propagation space should be done first before they go into the main production areas. Once entering the production area, there should be no return to the stock plants until the following day. In addition, ask staff whether they grow plants at home. This is a tough question, but pests/diseases do not care and can be transferred via those workers from home to the production facility.

The order of entry and movement of workers will be unique to every greenhouse/grow facility. It is well worth the effort to develop a work schedule that eliminates the potential of pest/disease movement around the facility and enforces restrictions on staff movement to avoid spread. Think of the arrows that are prevalent in supermarket aisles these days. They ‘encourage’ a unidirectional flow of customers to reduce close contact and aid in social distancing practices as we all strive to reduce the chances of COVID transmission.

Test plants regularly to ensure they are free from viruses and other diseases. Stay on top of bioprograms and sprays to ensure plant health and prevent diseases and pests on mother plants, as they will transfer with clones. Keep mother healthy and happy, and her offspring will get a much better start in life!


When we say ‘sanitation,’ I’m sure many think about this process being solely applied to the production space. And certainly, growing spaces and rooms should be thoroughly cleaned (removing any and all debris) and sanitized after a crop is harvested, and then again before a new crop is brought in. This reduces the risk of pests and diseases carrying over from one crop cycle to the next. But good sanitation practices should be applied in every stage of production.

Send in the clones

The goal of every grower should be to start clean. This will reduce problems later in production. It starts with the mother plants as discussed and extends into the propagation of clones. Hydrogen peroxide-based materials (e.g. ZeroTol) can be used to sanitize tools and surfaces as well as any flats and trays used for the young plants. Don’t forget to sanitize irrigation lines between crops, as biofilm layers can develop inside them and harbour diseases. Stabilized hydrogen peroxide products are extremely effective at eliminating biofilm build-up. After harvest, charge the lines with a peroxide solution (use label rates), leave them overnight and then flush with clean water before using them again. In addition, peroxide can be drenched onto the rooting medium or cubes the day before sticking to sterilize the medium. The beauty of using peroxide is that it breaks down rapidly and leaves no residues.

If bringing in clones, then assume they will carry something. I have heard many stories of greenhouses claiming to have had “…no root aphid issues until we brought in clones from…” for example. At some point, especially with recent incidents of virus-infected clones arriving from propagators, I’m sure there will be calls for some form of phytosanitary certification to accompany cloned material, but until and even after such time, sanitation is your best friend. Dips in biopesticides (e.g. BotaniGard) or horticultural oils are ways to reduce or eliminate pests (thrips, aphids, whiteflies, mites) coming in on clones. Can you quarantine clones and new plants to avoid transmission should they be infested? Again, limiting access to personnel and having a specific ‘order of entry’ plan in place can go a long way to reducing movement of pests. Consider sending out samples for analysis (e.g. DNA multiscan) to confirm plants are free from disease before transferring to the main production areas. Yes, there is a cost to this service, but it is minor compared to the costs of control or crop loss.


After taking care of mother, you must nurture your babies. Prevention starts here, nipping pest and disease problems in the bud, and taking steps to promote healthy root development. These are important steps to initiate right from the beginning for protecting your investment.

Disease management

Managing root diseases is part of doing business in any greenhouse crop, and cannabis is no exception. Pythium and Fusarium species, for example, are well-known pathogens on other crops and quite happily use cannabis as a host. Unfortunately, they are readily transferred in irrigation water, in soil, and on people, and can easily come in via infected clones. We’ve already touched on some of the sanitation steps that can be taken to reduce inoculum levels on hard surfaces and in propagation media, and it’s also worth testing your water supply to ensure it is free from these diseases. Be sure to test before and after any water sterilization process to ensure it works.

There are also biological tools that can be used to prevent diseases. Beneficial fungi can be used to colonize and grow on developing plant roots, protecting them from many soilborne pathogens. These biocontrol fungi work by bringing several different modes of action to the system. For example, Trichoderma (RootShield) and Gliocladium (Prestop/Lalstop) protect roots through a combination of antagonism, competition, predation/parasitism, and induction of plant resistance. These tools also deliver other plant benefits, including stimulation of root growth and solubilization of nutrients in the soil so they are more accessible to the plant, promoting plant growth and health. In trials conducted on cannabis, Trichoderma applied at sticking (in the form of RootShield PLUS) resulted in improved root development in clones, which ultimately translated to a 4% increase in flower yield at harvest.

Pest management

In terms of pests, those of primary concern in propagation are mites, aphids, thrips and fungus gnats.

Mites: Right now, three species are problematic in cannabis – hemp russet mite, broad mite and two-spotted spider mite (TSSM). And before you ask, yes, all three often come in on clones. All three species share certain characteristics: they have a high capacity for rapid population increase; they are hard to detect owing to their small size, and the first sign of an infestation may be symptoms of damage, and by then it may be too late to effect control. As we only have tools to prevent pests from increasing, we must act early, using biopesticides to provide a relatively quick knock down, supported by early introduction of biological control agents (BCAs).

Of the biopesticides, mineral oils will control several problem pests including mites (all stages, including eggs), thrips, aphids, and whiteflies. Two products approved for use in cannabis are Suffoil-X and PureSpray FX. Both are based on horticultural oils, but their formulations impart slightly different characteristics to each product. As a sidenote, Suffoil-X is also known to suppress powdery mildew and will complement a foliar biofungicide program. Application rates (1 to 2%) are similar for both products, which should be re-applied every 7 to 14 days. Thorough spray coverage is essential to efficacy.

Use caution when applying to newly stuck cuttings; at this stage, we recommend using the 1% rate and ideally waiting until plants have developed roots before spraying (approx. 7 to 10 days after sticking). Be aware that use of spray oils will leave a sheen on the leaves, but this does not interfere with transpiration. Trials have shown that immersion of clones in SuffOil-X at the label rates recommended for ornamental cuttings can eliminate many hitch-hiking pests but this method of application is not yet approved for cannabis.

BCAs for mites include Amblyseius andersoni which is moderately effective against hemp russet mite; Neoseiulus (=Amblyseius) cucumeris, a highly efficacious choice for broad mite; and Amblyseius (=Neoseiulus) fallacis which is a good option at this stage in production for TSSM. For hemp russet mite, early treatment of clones by dipping provides the best knockdown of an incoming or resident population, followed by two to three successive foliar sprays. Although oils will kill predatory mites and other BCAs on contact, they leave no toxic residues when dry; that means they will not harm mites in sachets or BCAs released after the spray program has been completed.

Aphids: Rice root aphids can quickly grow out of hand unless you get on top of things early. Drenching rooting blocks with an approved Beauveria bassiana formulation (e.g. BotaniGard 22WP) is a good tactic in propagation. Make sure cubes are thoroughly wetted so that infective Beauveria spores permeate the entire block and come into contact with aphids on the roots. This must be repeated as aphids multiply rapidly. Later in production, root drenches should be accompanied by foliar sprays to target winged adult aphids.

Thrips: I am convinced that western flower thrips can survive on any plant. It might not be completely true, but they can cause a lot of damage in cannabis and often accompany cuttings. There are two fungal biopesticides registered as foliar sprays: BotaniGard 22WP/ES and BioCeres G WP/EC. Several different predators can also be incorporated into a biocontrol strategy. These include N. cucumeris (sachets on sticks preferred) which feeds on first instar thrips on the foliage, as well as soil-dwelling predators Stratiolaelaps scimitus (formerly Hypoaspis miles) and Dalotia (formerly Atheta) coriaria which feed on pupating thrips. These BCAs provide simultaneous control of other pests, such as cucumeris for broad mites, while Stratiolaelaps and Dalotia feed on fungus gnat larvae. Last, the nematode Steinernema feltiae may be a useful addition to the program if needed, applied as a drench to the rooting cubes every two weeks. It is important to remember that the biopesticides and BCAs are applied to control different life stages of thrips and will remain with the plants when potted up in the main production area.

Fungus gnats: These are perhaps more of a nuisance problem than anything else, but they can passively vector soilborne diseases such as Fusarium, and high numbers of larvae in the growing substrate may cause significant feeding damage to freshly stuck clones. Cultural practices such as not overwatering will help limit populations, and the BCAs used to manage soil-dwelling stages of thrips are equally effective against fungus gnat larvae. Yellow sticky cards used to monitor for flying stages of pests can also make a significant contribution to the overall removal of adult pests, including fungus gnats and thrips.

Stay clean

All being well, investment in good sanitation and prevention practices through propagation will mean that everything is under control as plants move into the vegetative phase of their growth, but you cannot afford to relax. Steps taken in propagation should be maintained.

Click here for cannabis IPM part 2: vegetative growth phase to early flowering.

To watch a recording of the accompanying webinar, click here

Michael Brownbridge, PhD, is a Biological Program Manager at BioWorks Inc. He can be reached at

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