Library › Part E · Article 41 in the series · Level 2 · 11 min read

Pests and diseases in soilless systems

Standfirst: After reading this article you will be able to explain why a shared nutrient solution makes root diseases spread faster than in soil, tell a rotting root from a healthy one, and match the common leaf diseases and insect pests to the conditions that favour them. You will also be able to set up a weekly sticky-card count for a small grow room and work out how much hydrogen peroxide a tank needs for a published treatment dose.

Before you read: Anatomy of a hydroponic system, Dissolved oxygen, Temperature, humidity and VPD.

Soilless culture trades one set of diseases for another

Growing without soil removes many soil-borne organisms. Stanghellini and Rasmussen counted only four viruses, two bacteria and 20 fungal pathogens associated with root diseases of hydroponic vegetables, yet losses to disease are occasionally greater than in soil¹.

Their explanation is the mechanism this article builds on. A pathogen that enters a closed system finds many genetically identical hosts, a steady temperature and moisture regime, and a fast, even route to every root: the recirculating solution¹. Canadian growers report severe root rot more often in troughs shared by hundreds or thousands of plants than in rockwool slabs where a few plants share a root zone². Failing to manage the organisms from even one infected plant puts the whole crop at risk³.

Disease control in hydroponics follows from this. Keep the organism out. Keep the roots in conditions where the organism loses. Keep the solution from carrying it.

Root diseases: the water moulds

Apart from one Fusarium disease of tomato, most destructive root diseases in hydroponics are caused by Pythium, Phytophthora and two other genera that all produce a swimming spore, the zoospore, and are favoured by water¹. Pythium belongs to the oomycetes, once classed as fungi and now described as fungus-like²; growers call this group water moulds. A zoospore is a single cell 3 to 12 µm across that can swim for up to 24 hours; it finds a root by chemical signals and can enter it within 5 minutes under ideal conditions, and in some species a new generation can follow within 12 hours¹. On lettuce roots infected by a related pathogen, about 40 spore cases (sporangia) per centimetre of root each released about 100 zoospores, some 4,000 per centimetre¹.

Two root-zone conditions decide the damage. The first is temperature, and its effect depends on the species. Pythium aphanidermatum causes severe root rot when the root zone is at about 23 to 27 °C or warmer². Pythium dissotocum is most damaging to hydroponic spinach at a cooler 17 to 22 °C⁴. Chilling the solution therefore helps against one species but not against every one. In one Caribbean raft farm, holding the solution at 18 °C under 32 °C air reduced Pythium problems⁵.

The second condition is dissolved oxygen. Root rot generally increases when oxygen is low, and growers have been advised to keep at least 5 mg of oxygen per litre of solution². Cornell grows lettuce at 4 mg/L or more and holds its ponds near 8 mg/L⁶. Warm solutions hurt twice: water holds less oxygen as it warms, about 9 mg/L at 20 °C against 7 mg/L at 35 °C, while roots and microbes use oxygen faster^2,4. Dissolved oxygen explains the physics.

Fusarium, the other common root and crown pathogen, has no swimming spores¹ but still spreads with recirculating water³. In a Cornell study of spinach grown in NFT channels, listed in the handbook’s references, none of several remedies against a Fusarium crown rot, including three biological fungicides and potassium silicate, proved consistently successful⁶.

Reading roots, and what to do when they turn brown

Pythium can live in a root for a while without visible symptoms². When it moves on to killing tissue, the roots turn brown, grey-brown, reddish-brown, yellow-brown or yellow, depending on the crop and the pathogen². In severe cases many roots are brown, decayed and breaking apart², and fragments of the sloughed outer root tissue carry the pathogen into the solution². The shoot can mislead you: in pepper and cucumber, the leaves often stay green until root rot is already severe².

When roots turn brown, measure the solution temperature and dissolved oxygen first, because both are causes you can fix today². Then have the organism identified, since no single control works against every root pathogen¹. If root disease is confirmed in a pond system, the Cornell handbook advises draining ponds and tanks, sacrificing the crop and cleaning with a 2% bleach solution⁶. Cleaning between crops is covered in hygiene and turnover.

Leaf diseases depend on water on the leaf

Leaf diseases are controlled by the air, through humidity, leaf wetness and temperature (see temperature, humidity and VPD).

Powdery mildew shows as white powdery spots that spread and join⁴. Its spores germinate best at very high humidity, 97 to 99% relative humidity (RH) for two rose and cucurbit species, yet free water on the leaf can harm them⁴. The rose species stops germinating below 75% RH, but it can still grow and sporulate at 21 to 22% RH⁴. So powdery mildew needs humid air but not wet leaves (this article’s reading). The Cornell handbook warns that it can be a problem in winter lettuce production⁶.

Downy mildews need wet leaves. Basil downy mildew, caused by Peronospora belbahrii, arrives on seed and on air-blown spores⁷. It needs at least 4 hours of leaf wetness to infect and more than 7.5 hours above 95% RH at night to sporulate⁷. Lettuce downy mildew, Bremia lactucae, also sporulates on wet surfaces⁴. On basil, the first sign is yellowing of upper leaves that can be mistaken for a nutrient problem, followed by grey to purplish-brown growth on the leaf underside⁷.

Grey mould (Botrytis cinerea) is favoured by cool, humid conditions: in one comparison of greenhouse coverings for Douglas fir seedlings, 15 to 20 °C with RH above 90% was the predisposing combination⁴. Most fungi sporulate best in still air at a vapour pressure deficit of 0.6 to 1.2 kPa⁴.

Bacterial soft rots, caused by Erwinia and Pseudomonas species, make the pith of tomato stems turn brown and disintegrate; lush plants grown at high RH are more susceptible⁴. For all of them, avoid long periods of wet leaves and night condensation, and keep air moving.

Algae: not a pathogen, still a problem

Algae grow wherever light reaches the solution. They do not infect plants, but they compete with roots for nutrients and, at night, for dissolved oxygen, and they produce toxic products as they decompose⁵. The Cornell handbook adds that algae can weaken a crop and make it more prone to disease⁶. Algal growth also favours fungus gnats⁵. The control is to exclude light: use opaque or black tanks, pipes and channel covers^5,6.

Insect and mite pests

Soilless culture does not remove soil insects. Fungus gnats, leaf miners and thrips are numerous in rockwool, and shore flies are always present in pools of water on plastic sheets⁴. Fungus gnats and shore flies matter beyond their own damage: Pythium spores have been found in the gut of larvae and adults of both². In fungus gnats the spores survive from larva to adult, and the flying adult can carry them to other plants².

Thrips deserve special care in leafy crops because of the viruses. One western flower thrips adult can infect a plant after feeding for only 30 minutes, and there is no cure for an infected plant⁸.

Integrated pest management

Integrated pest management (IPM) combines exclusion, early detection, unfavourable conditions and natural enemies, with pesticides last.

Exclusion

Screen vents and inlets, start each crop with a clean room and clean plants, and keep doors closed^6,8. Screens with 100 holes per square inch kept out all life stages of thrips in North Carolina trials; because they reduce airflow, some greenhouses fit 4 to 5 square feet of screen per square foot of vent⁸. Remove weeds in and around the room, since they shelter thrips and tospoviruses⁸. Against Pythium, one review adds pathogen-free transplants and media, and a 1 cm layer of sterilised sand on rockwool cubes to stop gnats laying eggs².

Scouting with sticky cards

Yellow cards catch winged aphids, whiteflies and fungus gnats; blue cards catch more thrips⁸. Hang cards just above the canopy and near doors and vents, at one card per 500 square feet⁸ to one per 1,000 square feet^9,10. Count one side of each card weekly, replace cards every 1 to 2 weeks, and graph the counts^8,10.

Action thresholds are not universal. Rutgers offers 15 thrips per yellow card per week, with one card per 1,000 square feet, as an arbitrary starting point, and lists crop-specific values from under 10 for sensitive crops to 40 or more for poinsettia; Purdue used 20 per card per week in an experimental greenhouse^9,10. Where tospoviruses are present, the Rutgers threshold is one thrips⁹. Aphids have no usable threshold, because winged aphids on cards mean the colony is already large⁹. For fungus gnats, potato disks 1 to 2 inches across (2.5 to 5 cm, our conversion) pressed into the medium attract larvae; in propagation areas, 3 to 5 larvae per disk after 48 hours can already cause considerable damage⁹.

Worked example: scouting a 10 m² grow room.

1. One square foot is 0.0929 m², so the published densities are one card per 46.5 m² to one per 92.9 m² (our conversion of^8,9,10).
2. By the densest rule, 10 m² / 46.5 m² = 0.22 cards (our arithmetic). Less than one card, so the near-doors-and-vents rule decides⁸. This article suggests two cards: yellow above the centre of the canopy, blue by the door as an early thrips warning.
3. Count one side of each card every 7 days; replace every 1 to 2 weeks¹⁰.
4. Suppose the yellow card shows 3, 6, then 16 thrips in three successive weeks (invented counts). The third count passes the Rutgers starting threshold of 15⁹, so you act; with tospovirus symptoms, you act at the first thrips⁹.
5. This article’s caution: these thresholds come largely from ornamental greenhouses, so for a leaf crop you may act earlier.

Cultural control

Keep solution temperature and oxygen in range, avoid wet leaves at night, keep media surfaces dry against fungus gnats, and shade wet surfaces against algae^2,5,6,7. Fast growth also makes it hard for pest populations to establish⁶.

Biological control

Natural enemies of insects and mites are sold commercially; for root diseases the evidence is weaker. Follow the supplier’s instructions over general rates, as Resh advises⁵.

Treating the solution

Pathogens can be killed in the solution before it returns to the plants³. Heat at 95 °C killed 99.9% of various pathogens in 10 seconds (30 seconds is recommended commercially), and 60 °C for 2 minutes kills fungi, bacteria and nematodes but not viruses³. Recommended UV doses run from 100 mJ/cm² for bacteria and fungi to 250 mJ/cm² for viruses³. Slow sand filtration removes 99.9% of Pythium and Phytophthora and can be built by the grower³. Ozone at 10 g per hour per cubic metre of drain water for 1 hour eliminates all pathogens, but it breaks down iron chelates, and even brief exposure to ozone venting from the system can irritate mucous membranes³.

There is a limit. Disinfesting the solution outside the crop commonly has a minor effect on Pythium epidemics compared with protecting the roots, because few spores leaving the troughs survive the ride to the UV unit². Resh states that UV sterilisation does not combat Pythium⁵.

Hydrogen peroxide oxidises any organic matter, pathogens included. Recommended doses are 0.005% against Pythium, 0.01% against other fungi and 0.05% against viruses, which also harms roots³. Commercial products carry acid “activators” that lower pH by one to three units at these doses, so pH must be corrected³. The same source calls the method inexpensive but not efficient, and notes that peroxide is now used mainly to clean irrigation lines, other methods having taken over disinfestation³.

Worked example: hydrogen peroxide for a 200 L tank.

1. Target 0.005% against Pythium³, read here as 0.005 g of hydrogen peroxide per 100 mL, or 50 mg/L (our conversion). The source gives this dose for commercial products stabilised with acid activators and does not say whether the percentage refers to the product or to the peroxide itself; plain 3% peroxide has no activator, so treat the result as an estimate, not a tested dose³.
2. Mass needed: 200 L × 50 mg/L = 10,000 mg = 10 g of hydrogen peroxide (our arithmetic).
3. A 3% stock holds 3 g per 100 g; taking 1 L as 1 kg, about 30 g/L (our approximation; the true density is slightly above 1 kg/L, so this errs towards a slight overdose).
4. Stock volume: 10 g / 30 g/L = 0.33 L, about 330 mL (our arithmetic).
5. The root-damaging 0.05%³ is ten times the target, about 3.3 L of the same stock (our arithmetic). Check the strength on your product’s label and redo the sum.

Chemical control

Pesticides come last. Use only products registered for food crops in your country, follow the label, and rotate modes of action, because thrips and whiteflies quickly become resistant^5,8. Few pesticides are labelled for greenhouse vegetables⁶. We do not recommend products.

Key numbers

Common mistakes

1. Treating the shoot instead of the root. Leaves can stay green until root rot is severe, so check roots at every solution change².
2. Chilling the solution and calling it cured. Cooling works against warm-loving Pythium aphanidermatum, but P. dissotocum is most damaging at 17 to 22 °C^2,4. Cooling can also hide an infection: pepper and chrysanthemum roots colonised by Pythium stayed almost symptomless at 16 to 18 °C and developed severe symptoms within hours when warmed to 24 to 28 °C².
3. Relying on a UV lamp alone. The lamp treats the solution passing through it, not the pathogen already in the roots^2,5.
4. Leaving light on the solution. Algae compete for oxygen at night and favour fungus gnats, which carry Pythium^2,5.
5. Waiting for damage before scouting. Thrips damage and virus transmission are usually noticed only after they have happened⁸.
6. Overdosing hydrogen peroxide. Ten times the Pythium dose harms roots³.

Summary

A recirculating solution removes many soil diseases but gives water moulds such as Pythium a fast, even route to every root. Warm solution and low dissolved oxygen favour root rot, although the temperature that matters depends on the species. Brown, soft, sloughing roots call first for a check of temperature and oxygen, then for identification of the organism. Leaf diseases follow leaf wetness and humidity, so night condensation and still air are the main risks. Algae are a competitor and a food source for fungus gnats, and light exclusion controls them. Integrated pest management combines exclusion, weekly sticky-card counts, conditions that favour the crop, natural enemies, and registered pesticides as the last step. Treating the solution helps, but protecting the roots matters more.

Next in the series: Hygiene, cleaning and crop turnover.

References

1. Stanghellini, M. E. and Rasmussen, S. L. (1994). Hydroponics: a solution for zoosporic pathogens. Plant Disease, 78(12), 1129–1138. https://www.apsnet.org/publications/plantdisease/backissues/Documents/1994Articles/PlantDisease78n12_1129.pdf
2. Sutton, J. C., Sopher, C. R., Owen-Going, T. N., Liu, W., Grodzinski, B., Hall, J. C. and Benchimol, R. L. (2006). Etiology and epidemiology of Pythium root rot in hydroponic crops: current knowledge and perspectives. Summa Phytopathologica, 32(4), 307–321. https://www.alice.cnptia.embrapa.br/alice/bitstream/doc/576855/1/a01v32n4.pdf
3. Postma, J., van Os, E. and Bonants, P. J. M. (2008). Pathogen detection and management strategies in soilless plant growing systems. In Raviv, M. and Lieth, J. H. (eds), Soilless Culture: Theory and Practice, chapter 10. Elsevier, Amsterdam.
4. Albajes, R., Gullino, M. L., van Lenteren, J. C. and Elad, Y. (eds) (2000). Integrated Pest and Disease Management in Greenhouse Crops. Developments in Plant Pathology 14. Kluwer Academic Publishers, Dordrecht.
5. Resh, H. M. (2013). Hydroponic Food Production: A Definitive Guidebook for the Advanced Home Gardener and the Commercial Hydroponic Grower, 7th ed. CRC Press, Boca Raton. ISBN 978-1-4398-7869-9.
6. Brechner, M. and Both, A. J. (2013). Cornell University Hydroponic Lettuce Handbook. Cornell University Controlled Environment Agriculture. https://cpb-us-e1.wpmucdn.com/blogs.cornell.edu/dist/8/8824/files/2019/06/Cornell-CEA-Lettuce-Handbook-.pdf
7. Pundt, L. and Allen, J. (2013, revised 2024). Downy mildew on basil in the greenhouse. UConn Extension Integrated Pest Management Program fact sheet. https://ipm-cahnr.media.uconn.edu/wp-content/uploads/sites/3216/2024/06/basildownymildewghs.pdf
8. University of Maryland Extension (2012). Thrips management in greenhouses. Fact Sheet FS-762.
9. Rettke, S. K. (2022). Pest counts and action thresholds in the greenhouse. Rutgers Plant and Pest Advisory, 12 April 2022. https://plant-pest-advisory.rutgers.edu/pest-counts-action-thresholds-in-the-greenhouse
10. Cloyd, R. A. and Sadof, C. S. (2013). Western flower thrips. Purdue University Extension publication E-110-W. https://www.extension.entm.purdue.edu/publications/E-110.pdf
11. Pundt, L. (2013, revised 2024). Managing shore flies in the greenhouse. UConn Extension Integrated Pest Management Program fact sheet. https://ipm-cahnr.media.uconn.edu/wp-content/uploads/sites/3216/2024/03/shorefliesghs.pdf

This article was drafted with the help of AI tools and reviewed and edited by PonicLabs. Sources are listed above; tell us if you find an error.