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Good plant health is not only the absence of diseases and pests. Good cultivation techniques with adequate nutrition, water quality, climate conditions and production hygiene are required for healthy growth. To achieve sustainable plant protection management, it is essential to understand how to minimize the risk of plant diseases and pests. Prevention is the most important part of integrated pest management (Table 2).

Table 2: Plant disease prevention measures in aquaponics

Control measureExamples of actionsHygiene of cultivatingconditionsRespecting sanitation rules, specific clothes, separate room for plantgermination, avoiding algae developmentPhysical water treatmentUV treatmentsHeat treatmentPhysical barriers againstinsect vectorsNettingTrappingRespect of good agricultural practicesUse of tolerant and resistant crop varietiesAdequate supply of nutrientsCorrect plant spacingRegular monitoringManagement of environmental conditionsThe regulation of humidity and temperature is central to the prevention of fungal and bacterial diseases in covered crops. Manipulate the heating, the ventilation, the shading, the supplement of lights, the cooling and the fogging tofind the optimal conditions allowing both plant production and disease controlSupport the natural community of diseasesuppressing organismsBeneficial microorganismsBeneficial insectsCompost extracts

Hygiene of cultivation conditions

Before starting aquaponics (or any other cultivation) in a greenhouse it is necessary to clean and disinfect the interior and all the tools. First, all plant material, slabs, floor covers etc. should be removed. Greenhouse plastic cover films older than 3-4 years tend to be dirty and less translucent, and therefore suboptimal for plant growth. Every year the exterior of the greenhouse should be washed to improve the light level for the crops. Before disinfecting a greenhouse, all surfaces need to be clean and free from organic matter. Sustainable disinfectants are water, water damp, alcohol (70%), peroxide, organic acids etc. It is also recommended that working tools such as knives be disinfected. A clean greenhouse provides the best starting conditions for healthy and strong seedlings. Disinfection before entering a greenhouse, such as using hand-washing techniques and disinfection of shoes with disinfectant foot mats, is indispensable. Cleaning empty greenhouses, irrigation systems, plant containers and harvesting equipment with a sanitizing solution are also important factors to ensure food safety. Protective clothing and shoe covers should also be used.

Tolerant and resistant crop varieties

Plant resistance to insects is one of several cultural control methods. Cultural control methods involve the use of agronomic practices to reduce insect pest abundance and damage below that which would have occurred if the practice had not been used. In IPM, plant resistance to insects refers to the use of resistant crop varieties to suppress insect pest damage. Plant resistance is intended to be used in conjunction with other direct control tactics. The development of tolerant and resistant crop varieties is remarkable, and seed catalogues should be studied carefully in order to choose varieties that are resistant against diseases. In some crops, like tomatoes, cucumbers, peppers or aubergines (Figure 3 and 4), grafting allows for very good results. With some practice, it is possible to do grafting by oneself. Manuals, such as Kleinhenz et al. (2011), and tutorials describing the grafting technique, are available on the internet.

image-20210212142509298 image-20210212142516903
Figure 3: Grafted tomato seedlings (Photo ZHAW) Figure 4: Botrytis infection on lettuce stem (Photo ZHAW)

Appropriate plant spacing

Appropriate plant spacing is a challenge in any greenhouse cultivation, for all crops start very small and grow and develop extensively. High planting density increases competition for light, weakens plant vigour, and invites pest and diseases to settle. Periodic pruning is essential.

Adequate supply of nutrients

Different crops require different fertilisation regimes. A famous example is the tomato crop in conventional hydroponics with more than five different nutrition recipes (Raviv & Lieth 2007); however, this cannot be done in aquaponics, because of recirculation. On the other hand, crops with short cultivation periods and less dependence on vegetative and generative phases usually receive a uniform supply of nutrients during the entire growth cycle. Incorrect nutrient supply encourages pest infestation and disease. For example, too high nitrogen levels make plant tissues more succulent, and easier for pests to penetrate. There are two main ways of regulating the nutrient levels in aquaponics:

  • adding soluble fertilizer according to the nutrient requirements of the crop (Resh 2013, see also Chapters 5, 6, and 9)

  • regulating the nutrition according to the salt concentration in the water (EC level). This method assumes that the ratio between different nutrients (salts) is stable.

EC levels between 0.5 – 1.5 mS/cm are usually applied in aquaponics (Vermeulen & Kamstra 2012). If the salt concentration exceeds 2.5 mS/cm, fresh water should be added. Too high salt concentrations in the water cause physiological disorders, resulting in necrosis on the leaf surface or the leaf margins. Such damage creates access for secondary plant diseases. More information is included in Chapters 5 and 6.


IPM programs work to monitor for pests and diseases and identify them accurately, so that appropriate control decisions can be made in conjunction with action thresholds. Monitoring and identification remove the possibility that pesticides will be used when they are not really needed, or that the wrong kind of pesticide will be used. Regular monitoring of pest and diseases is therefore fundamental. Any discolouring or deformations of leaves and the occurrence of mould fungus on the leaves or fruit should be recorded (see also below). As it is challenging to diagnose fungal diseases or pests, we recommend contacting plant protection consultants.

Physical defence

Plant health can benefit greatly from preventing or limiting injury by arthropod pests from the start. Physical control strategies include methods for excluding pests or limiting their access to crops, disrupting pest behavior, or causing direct mortality (Vincent et al. 2009). Physical control methods can be categorized as active and passive (Vincent et al. 2009). Active methods involve the removal of individual pests by hand, pruning out infested plant tissues, and removing heavily infested plants. Passive methods usually include the use of a device or tool for excluding or removing pests from a crop. Typically, these devices serve as barriers between the plants and the insect pests, thus protecting plants from injury and damage. Other passive tools include repellents and traps. While traps are often used for monitoring pest abundance and distribution, many are designed as ‘attract and kill’ technologies, which attract insect pests through colour, light, shape, texture or scent, or a combination of these.


Use of netting is a simple way of preventing pests from coming into contact with the crop. The mesh size depends on the pest targeted:

  • 0.15 mm against thrips

  • 0.35 mm to exclude whitefly and aphids

  • 0.8 mm to exclude leaf miners and beetles

  • 20 mm against birds

However, netting also has a negative side: it reduces light and raises humidity, and therefore increases the risk of fungal diseases. This is especially true for nets with a mesh size of < 2 mm.


Traps may be used to monitor or detect a pest population, to catch and identify the pest, and to reduce local pest density. Commercial traps are available for controlling or detecting various moth species (pheromone traps), whiteflies and thrips (sticky traps), flies and yellowjackets, snails and slugs, bed bugs, spiders, cockroaches and many other pests. Coloured sticky traps attract different pests. They should be positioned slightly above the canopy of plants. Blue sticky cards trap adult stages of thrips. Yellow sticky cards are used for whiteflies and harmful butterflies. When applying beneficial organisms for pest control, it is best to consult an expert first.

Support the natural community of disease suppressing organisms

Controlled environments include both risks and opportunities for integrated pest management. Greenhouse conditions promote organisms with increased temperature and air moisture requirements, such as fungal diseases. But these climate factors also stimulate the development of many beneficial insects. The use of beneficials is well established in greenhouse farming. Pests and disease can appear even with the best prevention. One of principles of integrated and organic farming is for plants to thrive in the presence of pathogens or pests. This is only possible if beneficial macro- or microorganisms support the control of pests and diseases. A natural community of disease suppressing organisms can be supported by adding biological agents to the water as a stimulant for plant resistance.

Beneficial microorganisms

Important beneficial microorganisms are:

  • Bacillus amyloliquefaciens or Trichoderma harzianum as prevention against root diseases (e.g. Pythium) in early stages of the crop (e.g. seedling stage)

  • Bacillus subtilis against Rhizoctonia

  • Gliocladum catenulatum against Fusarium, Phytophthora, Pythium, Rhizoctonia on cucumber, tomato, pepper, and culinary herbs

Products are commercially available in online shops or garden centres.

Beneficial insects and banker plants

Beneficial insects (or natural enemies) are normally used in organic and conventional vegetable greenhouse production. Widespread and commercially available types are:

  • Ichneumonids against aphids, whitefly and similar

  • Gall midges (Aphidoletes aphidimyza) against aphids

  • Predator mites against spider mites

  • Mirid bugs (Macrolophus pygmaeus) against whitefly

With this kind of pest control, pesticide residues as well as pesticide-induced resistance can be avoided. However, successful pest control using beneficials can be challenging. Each beneficial insect has its own individual needs. Specific attracting flowers (so-called banker plants) planted near or in the greenhouse can support beneficials (Conte et al. 2000). Examples of such plants are buckwheat (Fagopyrum esculentum), cornflower (Centaurea cyanus) and corncockle (Agrostemma githago).

Compost extracts

These are also known as ‘compost tea’ and contain many beneficial microorganisms. They are made by brewing and aerating compost in water (normally for 24 hours) in order to extract the beneficial organisms. Compost tea has to be applied immediately, either directly on the root zone or on the leaves. A first application can be made just after seeding, and a second before planting. Recipes and brewing methods can be found on the internet, for example here:

If all else fails …

Sometimes interventions with chemical products can be justified, but in that case stringent regulations have to be considered. Whenever possible botanical pesticides should be used first, because they are of biological origin. Some extracts from microorganisms are safe for fish and can be used in aquaponics. One is a toxin from Bacillus thuringiensis, which can be used against caterpillars, leaf rollers or other butterfly larvae. The other is Beauveria bassiana, a fungus that enters the insect’s skin, and is effective against a number of pests such as termites, thrips, whiteflies, aphids and beetles. Most of the chemical synthetic fungicides and insecticides, but also some products permitted in organic farming, are toxic and harm aquatic organisms. An application is only worth considering in young plants before being transplanted into the aquaponic system. If chemical control is the last resort, the specific fish toxicity of the product has to be considered very carefully. Appendix 2 of ‘Small-scale aquaponic food production’ (Somerville et al. 2014) lists a selection of possible insecticides with indications of their relative toxicity to fish. Aquaponics is a complex ecosystem composed of different kind of bacteria, fungi and higher organisms with high potential in natural power resistance. It is important to maintain the ecological balance of this ecosystem by proper prevention measures, as described above. This should help to reduce the necessity of implementing direct methods of pest management to a minimum.

Copyright © Partners of the [email protected] Project. [email protected] is an Erasmus+ Strategic Partnership in Higher Education (2017-2020) led by the University of Greenwich, in collaboration with the Zurich University of Applied Sciences (Switzerland), the Technical University of Madrid (Spain), the University of Ljubljana and the Biotechnical Centre Naklo (Slovenia).

Please see the table of contents for more topics.

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