Indoor diseases: bud rot, powdery mildew, root rot and HLVd

Seven weeks into flowering, the biggest bud has a dull brown leaf poking out of it, and inside it is grey and soft. Or the fan leaves carry a dusting like flour. Or a plant that was fine on Monday wilts by Thursday, with brown roots. Or a plant never thrives: short, brittle, with small, loose, faint-smelling buds, for no obvious reason.

Small growers' answer to all of this is mostly climate and cleanliness. The grow guide in this app, built from UK small-grow practice, teaches relative humidity (RH) below 50 % in bloom, ideally 40–45 %, with fans running around the clock against bud rot. Many growers also hang sachets of predatory mites against pests and stop spraying anything on flowers after about the third week of bloom. That is practice built on experience, not a tested protocol.

This article looks at what research says about bud rot, powdery mildew, root rot and hop latent viroid (HLVd): how each spreads, what favours it, where the studies were done, and what that tells someone with a 1×1 m tent. It gives no pesticide recommendations or doses. A legal note: in the UK, growing cannabis, even with a prescription, requires a Home Office licence; this article is educational.

Four problems, four kinds of organism

The best single survey for drug-type cannabis is Punja et al. (2019). The team sampled about 220 plants in 2016–2018, roughly 90 from two licensed indoor facilities and 120 from a greenhouse in British Columbia, grown hydroponically in rockwool or coco fibre, plus some field plants. Roots carried Fusarium and Pythium species, which caused browning, stunting, yellowing and sometimes death. On leaves, powdery mildew was "the major pathogen observed". On buds they found Botrytis, Penicillium and Fusarium bud rots. The study was part-funded by a company, alongside a public research grant.

Bud rot: the late-bloom ambush

What it is

Botrytis cinerea attacks more than 1,000 plant species. On cannabis, flowers brown and decay from the inside until the whole cola is consumed. Mahmoud et al. (2023), a review drawing on Canadian greenhouse experience and on other crops, report that bud rot appears "usually in weeks 6 to 8" of flowering, starting deep inside the bud from spores that landed earlier. Infected tissue then releases fresh spores towards neighbouring plants.

What favours it

The review names the conditions: relative humidity above 70 % and moderate temperatures of 17–24 °C. The review stresses moisture on plant surfaces and how long it lasts. When a surface cools to its dew point, water condenses on it and spores can germinate. The review gives an example from greenhouse literature: at 30 °C and RH above 90 %, a drop of just 1.8 °C reaches the dew point.

This is where vapour pressure deficit (VPD) comes in. VPD is the difference between how much water vapour the air could hold at its temperature and how much it actually holds (Grossiord et al., 2020). Because the air's capacity rises steeply with temperature, the same RH means a larger VPD in warm air than in cool air. Mahmoud et al. (2023) note that a VPD below about 0.4 kPa means the air is close to saturation and moisture stays on the leaf, which encourages fungi; that observation comes from tomato and cucumber. They recommend fans and "avoiding sudden changes in temperature and relative humidity".

The shape of the plant matters

In one greenhouse comparison, three genotypes grown side by side from August to October had bud rot on 1 % to 26 % of plants. The most affected had large, dense top buds; and among four genotypes, more small leaves around the flowers went with more infection. The authors avoid calling the less-affected genotypes "resistant": looser buds probably just make a drier microclimate, and no genetic resistance to Botrytis is known in cannabis.

Spacing had the same effect. In a cannabis trial with two genotypes, plants at 1 plant per m² had significantly less bud rot than plants at 2 per m², but flower yield per m² fell by 18–23 % at the lower density. The authors doubted that trade-off made commercial sense; in a home tent the arithmetic differs.

In severe outbreaks, Punja et al. (2019) saw bud rot on up to 50 % of plants in a greenhouse facility, with leaf spots appearing as well. Mahmoud et al. (2023) mention losses of up to 30 % of flower yield in highly susceptible genotypes, but that figure comes from the authors' unpublished observations.

After the chop

Rot does not stop at harvest. Punja et al. (2019) found that mechanical trimming increased the moulds recovered from buds, probably because wounds leak nutrients. Mahmoud et al. (2023) describe drying to below 13 % moisture and spot checks by prying buds open; our post-harvest article covers drying in detail.

Powdery mildew: the white dust

What it is

Powdery mildew starts as sparse white threads on young leaves and ends as a flour-like coat of spores, sometimes on stems and flowers as well (Punja et al., 2019). Under the electron microscope, Punja's team found mildew spores stuck to the glandular trichomes on bracts. Unlike Botrytis, mildew is an obligate biotroph: it can only feed on living tissue. According to Seifi et al. (2025), under high humidity and moderate temperatures the fungus can complete its life cycle in one to two weeks after reaching a susceptible plant.

Spores travel in the air and, importantly, on cuttings: Punja et al. (2019) note that both mildew and Botrytis spread "through vegetative propagation".

Is there resistant genetics?

Pépin et al. (2021) studied MLO genes; in barley, broken copies of one have given durable mildew resistance for decades. Inoculating the drug-type cultivar 'Pineapple Express' in growth chambers, they found two cannabis MLO genes switched on during infection. They then searched 32 cultivars, 31 of them drug types from a Canadian licensed producer, for mutations disabling these genes, found none, and concluded that complete resistance of this kind "might be hard to find among existing commercial cultivars". (We read the preprint version of this paper.)

Seifi et al. (2025), working at a Canadian cannabis company, screened 510 genotypes from its collection, including landraces. Rooted clones were dusted with spores and kept at 23 °C and 70–80 % RH. More than 70 % scored above the midpoint of the disease scale. Only two carried a strong resistance locus, named PM2; the resistant parent lines used to map it were THC-dominant drug types, and the team developed DNA markers to breed it into other cultivars. (Preprint version read.)

So a few resistant lines may appear, but no small grower can assume a cultivar is resistant.

Root rot: trouble you cannot see

What it is

Root rot is caused mainly by Pythium water moulds and Fusarium fungi. Infected roots turn brown and decay, the crown can discolour, and plants yellow, stunt, wilt and sometimes die (Punja et al., 2019). Punja's team found Fusarium spores in recirculating nutrient solution and in rooting cubes, where they killed cuttings through the cut stem ends. Likely sources were contaminated substrates, diseased cuttings, spores in air or water and leftovers from previous crops; unpasteurised coco fibre was flagged as a possible source of moulds.

Coco and rockwool from one facility

McGehee and Raudales (2021) cultured coco coir and rockwool from one commercial facility in Connecticut where plants had root rot and wilting, recovering mostly Pythium myriotylum. Local law barred experiments on drug-type cannabis, so they tested the isolates on hemp seedlings ('Wife') in a greenhouse at about 25 °C. Every isolate caused disease, and inoculated plants were "smaller by 32% or more" than uninfected ones. With P. myriotylum, wilting and yellowing appeared six days after inoculation. The authors stress the small sample from a single facility.

Warm, airless water

What favours Pythium is known mainly from other crops. Sutton et al. (2006) reviewed root rot in hydroponic cucumber, tomato, pepper, lettuce and others. In their own work with peppers, raising the nutrient solution to 28 or 34 °C for a few hours or days before infection made root browning start earlier and spread faster. They conclude that high temperature predisposes plants to root rot and think low dissolved oxygen probably does the same. Warm water holds less oxygen: without any roots or microbes, dissolved oxygen falls from about 9 to 7 mg per litre as temperature rises from 20 to 35 °C. Meanwhile, roots and microbes need more oxygen as they warm. The review also notes that roots can be heavily colonised without showing symptoms, and that 30–70 % of such roots can turn brown within 12 to 24 hours. That is why root rot often seems to arrive overnight.

None of this comes from cannabis, but the message is general: warm, stagnant, oxygen-poor root zones favour Pythium.

HLVd: the disease that hides

What a viroid is

Hop latent viroid is not a fungus or a virus. It is a viroid: a closed circle of RNA only 256 units long, with no protein coat (Adkar-Purushothama et al., 2023). First found in hops, it is widespread and often symptomless there. In cannabis it was linked to "dudding" in 2019, when two independent teams in the United States tied it to stunted plants; the disease was first reported in California. Chiginsky et al. (2021) later found it in outdoor hemp in Colorado, with genomes identical to sequences recorded from hops.

Symptoms and losses

In susceptible cultivars, the review lists shorter internodes, smaller leaves, stunting, an outward-sprawling shape, yellowing, brittle stems and reduced vigour. In flower, plants typically show "smaller and looser buds, weaker flower smell and less trichome production" (Adkar-Purushothama et al., 2023). Torres et al. (2025) add that symptoms may only appear when a stress such as the switch to a flowering photoperiod triggers them. Many cultivars carry the viroid without any obvious signs.

Headline numbers need care: roughly 90 % of Californian facilities infected and up to 50 % less cannabinoid and terpene production come from an industry survey and web reports, not controlled trials.

How it spreads

In hops, HLVd spreads by propagation, grafting, contaminated tools and machinery. Pollen transmission is reported as low, seed transmission has not been found and no insect vector is known (Adkar-Purushothama et al., 2023). Torres et al. (2025) point to contaminated tools during trimming and cloning as a primary driver of spread in cannabis. For a home grower, the danger is a mother plant, a shared clone or a pair of scissors.

Testing and "cleaning"

No chemical cures viroids. Only a laboratory test, such as RT-PCR or RT-qPCR, which detect the viroid's RNA, shows whether a plant is infected. Because the viroid is unevenly spread, the review advises sampling several old and new leaves from low to high on the stem. For incoming plants, it recommends a 30-day quarantine with a test in the third week. For tools, it names a household bleach solution as the most reliable and widely used treatment, with the warning that bleach corrodes equipment and can damage plants.

Infected stock can sometimes be rescued in a laboratory. Torres et al. (2025), at and funded by a US hemp-genetics company, cultured tiny shoot tips (meristems) of 13 hemp cultivars at 30 °C for four to five weeks. Survival was 71–95 %. In the first test, the share of clean plantlets ranged from 0 % to 94 % depending on cultivar, and two cultivars did not clear at all. When plantlets that first tested clean were retested ten weeks later, 93–100 % were still negative, depending on cultivar. The review adds an important caveat: a cleaned plant is viroid-free, "not viroid-resistant", and can be reinfected.

A hierarchy of prevention

Taken together, the research points to an order of priorities, which matches good small-grow practice.

1. Climate, airflow and hygiene

For bud rot, this is the main line of defence: no free water on the plant, moving air, no sudden temperature drops, open plant structure and sanitation (Mahmoud et al., 2023). The review notes that no fungicides were registered for use on cannabis when it was written. For root rot, prevention means clean substrate and water and a cool, well-oxygenated root zone (Punja et al., 2019; Sutton et al., 2006). For HLVd, it means clean starting material and clean tools (Adkar-Purushothama et al., 2023). Punja's air sampling showed hygiene at work: after a thorough clean, airborne moulds were very low when new plants arrived, then rose again.

2. Biological control, used early

Biological control uses living organisms, such as microbes or predatory mites. For cannabis the evidence is thin.

• Mahmoud et al. (2023) report a lab study in which a Bacillus amyloliquefaciens product applied to detached cannabis buds 48 hours before Botrytis spores significantly suppressed rot: a detached-bud test, not a whole-plant trial. Yeasts, promising in other crops, are untested on cannabis and could raise mould and yeast counts.
• Punja et al. (2019) found applied biocontrol fungi (Trichoderma, Beauveria) in the facility air in the weeks after use: beneficials do not stay where they are put.
• Against pests, Messelink et al. (2009) tested the predatory mite Amblyseius swirskii, the one in many growers' sachets, on greenhouse cucumber (18–24 m² compartments, about 22 °C and 74 % RH). When spider mites arrived first, the predators failed, partly because webbing cut predation by 57 % in a lab test. Released a week before the spider mites, with pollen as food, more predators meant fewer spider mites. Once colonies form, a specialised predator is needed.

Biological control works as prevention, established before the problem arrives.

3. Resistant genetics, where they exist

No resistance to bud rot or HLVd is known in cannabis (Mahmoud et al., 2023; Adkar-Purushothama et al., 2023). For powdery mildew, resistance exists but is rare: two genotypes out of 510 in Seifi et al. (2025), and no disabled MLO genes among 32 cultivars in Pépin et al. (2021). Looser-budded cultivars escape bud rot more often (Mahmoud et al., 2023), worth weighing when choosing seeds.

Why the research and the tent do not line up neatly

Almost every number here comes from licensed facilities and greenhouses with hundreds of plants, hemp seedlings, cucumbers, other hydroponic vegetables or company collections, and several studies were done at or funded by companies. The outcomes are commercial: share of plants infected, yield per m², mould counts. Nobody measured what mild Botrytis does to the smell of a home-dried jar. What transfers well is the biology: the same organisms, the same physics of condensation, and HLVd spreading on clones and blades at any scale. A tent differs in having small air volumes that cool quickly at lights-off, but also few plants that can be watched every day.

What this means for a 1×1 tent

These are moderate, educational takeaways, not a protocol.

Keep surfaces dry in late bloom. The research gives a danger zone of RH above 70 % at 17–24 °C (Mahmoud et al., 2023). The tutorial's 40–50 % RH in late bloom gives a wide margin below it. More important than the exact figure is avoiding condensation: watch the first hour after lights-off, when the tent cools, and stay clearly above a VPD of about 0.4 kPa.

Move air through the canopy, not just over it. The point is to keep air moving where condensation forms, between and around the buds, not only across the top.

Think about density. A 1×1 m tent is exactly the scale of the 1 versus 2 plants per m² comparison. Fewer, well-spread plants had less bud rot, at a yield cost of around a fifth in that trial. At home, losing a cola to rot may matter more than a little potential yield. Thinning crowded inner growth helps too.

Inspect from week 5. Bud rot usually appears in weeks 6 to 8. Check the densest buds and small leaves browning for no reason. Bag affected material before cutting well below it, so spores are not shaken loose.

Start the root zone clean. Use fresh or pasteurised substrate rather than last cycle's, clean reservoirs and lines between grows, and keep the root zone from running warm.

Treat every incoming clone as untested. Use few clone sources, or start from seed (hop research found no seed transmission). Disinfect blades between plants. For a long-kept mother, only a laboratory test shows its status; symptoms alone cannot confirm the viroid, and home "cures" do not exist.

Use beneficials early, if at all. They are prevention, not rescue.

Dry properly. Hidden infections at harvest grow during slow, damp drying.

What we know, and what we don't

We know which organisms cause the main indoor diseases of cannabis and how they spread: spores in air and water, contaminated substrate, cuttings, wounds and tools (Punja et al., 2019; McGehee and Raudales, 2021). We know that Botrytis needs high humidity and wet surfaces, that dense buds and crowding favour it, and that no genetic resistance to it is known (Mahmoud et al., 2023). We know that strong mildew resistance exists but is rare (Seifi et al., 2025; Pépin et al., 2021). We know that HLVd spreads mainly through propagation and tools, can only be confirmed by a laboratory test, and can be removed from plants only by laboratory methods, with cultivar-dependent success (Adkar-Purushothama et al., 2023; Torres et al., 2025).

We don't know which RH setting, fan arrangement or spraying cut-off actually prevents bud rot in a small tent; no study has tested them. Many of the humidity and wetness thresholds come from tomatoes, strawberries, grapes and other crops, not from cannabis. We don't know how much yield or quality HLVd costs in a home grow, or how often traded clones carry it. The well-known figures come from industry surveys. We don't know how well biological control products protect whole cannabis plants rather than detached buds or cucumbers.

The research supports what careful growers already do: dry surfaces, moving air, open and spaced plants, clean tools, and suspicion of anything brought in. It adds when to look, what crowding costs, and why a tested clone beats a trusted one.

Sources

Adkar-Purushothama, C.R., Sano, T. and Perreault, J.-P. (2023) 'Hop latent viroid: a hidden threat to the cannabis industry', Viruses, 15(3), 681. doi:10.3390/v15030681.

Chiginsky, J., Langemeier, K., MacWilliams, J., Albrecht, T., Cranshaw, W., Fulladolsa, A.C., Kapuscinski, M., Stenglein, M. and Nachappa, P. (2021) 'First insights into the virus and viroid communities in hemp (Cannabis sativa)', Frontiers in Agronomy, 3, 778433. doi:10.3389/fagro.2021.778433.

Grossiord, C., Buckley, T.N., Cernusak, L.A., Novick, K.A., Poulter, B., Siegwolf, R.T.W., Sperry, J.S. and McDowell, N.G. (2020) 'Plant responses to rising vapor pressure deficit', New Phytologist, 226, pp. 1550–1566. doi:10.1111/nph.16485.

Mahmoud, M., BenRejeb, I., Punja, Z.K., Buirs, L. and Jabaji, S. (2023) 'Understanding bud rot development, caused by Botrytis cinerea, on cannabis (Cannabis sativa L.) plants grown under greenhouse conditions', Botany. doi:10.1139/cjb-2022-0139. (Accepted manuscript consulted.)

McGehee, C.S. and Raudales, R.E. (2021) 'Pathogenicity and mefenoxam sensitivity of Pythium, Globisporangium, and Fusarium isolates from coconut coir and rockwool in marijuana (Cannabis sativa L.) production', Frontiers in Agronomy, 3, 706138. doi:10.3389/fagro.2021.706138.

Messelink, G.J., van Maanen, R., van Holstein-Saj, R., Sabelis, M.W. and Janssen, A. (2009) 'Pest species diversity enhances control of spider mites and whiteflies by a generalist phytoseiid predator', BioControl, 55, pp. 387–398 (published online 2009; issue dated 2010). doi:10.1007/s10526-009-9258-1.

Pépin, N., Hebert, F.O. and Joly, D.L. (2021) 'Genome-wide characterization of the MLO gene family in Cannabis sativa reveals two genes as strong candidates for powdery mildew susceptibility', Frontiers in Plant Science, 12, 729261. doi:10.3389/fpls.2021.729261. (bioRxiv preprint version consulted, doi:10.1101/2021.07.16.452661.)

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