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Plant health, pest and disease control

3 months ago

21 min read

Plant health has a broad meaning that goes far beyond just the absence of illnesses; it is the overall status of well-being that allows a plant to achieve its full productive potential. Plant health, including disease prevention and pest deterrence and removal, is an extremely important aspect of aquaponic food production (Figure 6.8). Although the most important advances in plant health have been achieved through the management of pathogens and pests, optimal nutrition, intelligent planting techniques and proper environmental management are also fundamental to secure healthy plants. In addition, knowledge on the specific plants grown is fundamental to addressing various production issues. Although some basic concepts on plant nutrition have already been described, this section aims to provide a far greater understanding on how to minimize the risks and to address plant diseases and pests in small-scale aquaponics.

For more information on beneficial insects, including insect characteristics and climatic needs, along with general information on pest identification, as well as integrated pest and disease management (including different products available for treatment), see Appendix 2 and the resources listed in the section on Further Reading.

Plant pests, integrated production and pest management

Insect pests are problematic for plant production because they carry diseases that plants can contract. Pests also extract liquids as they bore into plant tissues, leading to stunted growth. Controlled environments, such as greenhouses, can be particularly problematic for pests because the enclosed space provides favourable conditions for insects without rain or wind. Pest management for outdoor conditions also differs from that in protected cultivation (net houses, greenhouses), due to the physical separation of the plants from the surrounding area, which allows the use of beneficial insects indoor to kill/control the insect pests. Insect pest prevalence is also highly dependent on climate and environment. Pest management in temperate or arid zones is easier than in tropical regions, where higher incidence and competition among insects make pest control a far more difficult task.

As aquaponic units maintain an independent ecosystem, it is normal for a host of micro-organisms and small insects and spiders to exist within the media beds. However, other harmful insect pests, such as whiteflies, thrips, aphids, leaf miners, cabbage moths and spider mites feed upon and damage the plants. A common practice for dealing with problematic insect pests in soil vegetable production is to use chemical pesticides or insecticides, but this is impossible in aquaponics. Any strong chemical pesticide could be fatal for fish as well as the beneficial bacteria living in system. Therefore, commercial chemical pesticides must never be used. However, there are other effective physical, environmental and cultural controls to reduce the threat of pests from aquaponics. Insecticides and deterrents should be considered a last resort. Nevertheless, successful management integrates crop and environmental management with the use of organic and biological pest deterrents.

Integrated production and pest management (IPPM) is an ecosystem approach to soil-based and soil-less plant production and protection that combines different management strategies and practices to grow healthy plants and minimize pesticide use. It is a combination of mechanical, physical, chemical, biological and microbial controls along with host-plant resistance and cultural practices. Not all of these controls are applicable for aquaponics as some may be fatal for fish and bacteria (i.e. chemical and some organic pesticides) while others may not be economically justified for small- scale aquaponics (i.e. microbial control agents). Thus, this section concentrates on the most applicable strategies for small-scale aquaponics, including mechanical and physical control, host plant resistance and cultural techniques to prevent the threat of pests and diseases. Some brief comments are given on some aquaponic-safe biological controls (i.e. beneficial insects and microorganisms), and more details are included in Appendix 2. For further information on these methods, see the section on Further Reading.

Physical, mechanical and cultural controls

For pest management in aquaponics, prevention is fundamental. Regular and thorough monitoring for pests is vital, and, ideally, minor infestations can be identified and managed before the insects damage the entire crop. Below is a list of simple inexpensive controls used in organic/conventional agriculture, which are also suitable for small- scale aquaponics, to avoid pest infestations. Physical exclusion refers to keeping the pests away. Mechanical removal is when the farmer actively takes the pests away from the plants. Cultural controls are the choices and management activities that the farmer can undertake to prevent pests. These controls should be used as a first line of defence against insect pests before other methods are considered.


This method is common to prevent pest damage in tropical regions or wherever organic horticulture is practised or pesticides are not effective. Netting mesh size varies depending on the pest targeted; use nets with a mesh size of 0.15 mm to exclude thrips, 0.35 mm to exclude whitefly and aphids, and 0.8 mm to keep out leaf miners. Netting is particularly effective while the seedlings are very young and tender. Screens do not suppress or eradicate pests, they only exclude most of them; therefore, they must be installed prior to pest appearance and care should be taken not to let pests enter into the protected environment.

Physical barriers


Given the limited distances that insects can cover, it is possible to reduce pest prevalence by adding physical barriers between the vegetables and the surrounding vegetation such as paved surfaces or building stories. Rooftop aquaponic production benefits from the natural ventilation, given the higher altitude, and the large physical barrier (distance from the ground) creating ideal conditions for outdoor production relatively free from pests and diseases (Figure 6.9). Greenhouses often have a strong fan blowing out through the entrance way that can help to prevent insects from entering with the farmer.

Another useful technique is to create a barrier on the legs of the hydroponic containers. A ring

of copper flashing can prevent snails and slugs from climbing up the legs, and a coating of petroleum jelly can prevent ants. Placing the bottom of the legs in a container of water can also prevent ants.

Hand inspection and removal


The removal, either by hand or using a high-pressured stream of water, of heavily infested leaves or plants helps to avoid and/or to delay the spread of insects to surrounding plants (Figure 6.10). Larger pests and larvae may also be used as supplementary food for the fish. Water sprayed from a hose directed at the underside of the leaves is an extremely effective management technique on many types of sucking insects. The stream can actually kill some insects, and the others are washed away. This is effective on sucking insects such as aphids and whiteflies. This is one of the most effective methods on small-scale systems, but it can be just a temporary remedy as the displaced pests can return to the plants. It can use significant volumes of water and become too labour-intensive with larger systems.


Sticky traps positioned slightly above the canopy of plants are effective in protected environments (e.g. net houses, greenhouses). Blue sticky cards trap adult stages of thrips while yellow sticky cards trap whiteflies and microlepidoptera (Figure 6.11). Sticky traps are less effective in outdoor conditions as new insects can easily come from the surrounding areas. The continuous monitoring of insects being captured by the traps can help a farmer to adopt specific measures to reduce the occurrence of certain pests. Another effective way of dealing with pests is to use pheromone-baited traps. These attract males of specific pests, thereby reducing the mating population in the area.

Environmental management

Maintain optimal light, temperature and humidity conditions, which can be easily changed in protected cultivation, to favour healthier plant growth and to build unfavourable conditions for pests. For example, spider mites do not tolerate wet and humid conditions, so timed misters directed on the plant leaves can deter infestations.

Plant choice

Some pests are more attracted to specific plant species than others. Similarly, different plant varieties from the same species have different resistance/tolerance to pests. This is one reason that polyculture can often prevent large infestations because some plants remain unaffected. Moreover, some plants attract and retain more beneficial insects to help manage pest populations (discussed in more detail below). Choose resistant varieties from local suppliers and agriculture extension agents to help reduce diseases and infestations.

Indicator plants and sacrificial/catch/trap crops

Some plants, such as cucumber and legumes, are more prone to aphids or red mite infestations and thus can be used to detect pest prevalence early. Often, indicator plants are planted along the exterior edge of larger gardens. Another strategy that can be adopted in aquaponics is the use of biological insecticides on sacrificial or "catch plants" planted near to, but not within, the aquaponic system. Catch plants (i.e. fava beans) attract pests. These plants can be grown in pots beside the aquaponic unit, attracting the pests away from the unit, which are then treated with insecticides (see below). This strategy would not affect the aquaponic ecosystem or beneficial insects present around the unit. Although not purely organic, catch plants can even be treated with commercial synthetic insecticides if large infestations are present. Fava beans and petunias (flowers) can be used to catch thrips, aphids and mites. Cucumbers are also used to catch aphids and hoppers while succulent lettuce seedlings are used to capture other leaf-eating insects.

Companion planting

Companion planting is the constructive use of plant relationships by growers. For example, all plants produce natural chemicals that they release from their leaves, flowers and roots. These chemicals may attract or repel certain insects and can enhance or limit the growth rate and yield of neighbouring plants. It is therefore important to be aware of which plants benefit from each other when planted together, and which plant combinations are best avoided. Appendix 2 provides a companion planting table to use when choosing crops. When using the companion table, concentrate on avoiding the bad companions rather than planning for good ones. Some plants release chemicals from their roots or leaves that either suppress or repel pests, which can serve to protect other neighbouring plants.


As mentioned above, excessive nitrogen makes plants more prone to pest attack because they have more succulent tissues. A correct balance of nutrients using the feed rate ratio (see Chapters 2 and 8) helps plants to grow stronger in order to withstand pest attacks. Some water should be exchanged when nitrate levels are greater than 120 mg/litre for this reason.


High planting density and/or inadequate pruning increases competition for light, encouraging insect pests. This competition eventually makes plant tissue more succulent for pests to bore through or for pathogens to penetrate, and the cramped conditions offer shelter to the pests. Be sure that there is adequate ventilation and sunlight penetration through the canopy. As previously discussed, many plants have special needs for sunlight or a lack of it. By combining full-sun with shade-tolerant plants, it is possible to intensify the production without the risk of raising competition and weakening the plants. In this case shade-tolerant plants can grow under the canopy of sun-loving ones. In this way, the plants are healthier and more resistant to pests and disease.

Crop rotation

Although aquaponic units can be managed as monoculture without facing problems of soil tiredness (depletion of nutrients naturally present in soil), growing the same species continuously over multiple seasons can have a selective effect on the surrounding pests. Thus, a change in crop, even for a short period, may cause a drastic reduction of pests specifically targeting the monoculture crop.


The removal of all plant debris, including all roots, at the end of each harvest helps to reduce the incidence of pests and diseases. Dead leaves and diseased branches should be removed consistently. In outdoor conditions without nets, it is advisable to reduce the surrounding vegetation to a minimum in order to prevent pests spreading to the aquaponic unit. Diseased plants and compost piles should be kept far from the system to prevent contamination.

Chemical controls

If pests remain a problem after using the above physical, mechanical and cultural controls, it may be necessary to use chemical control. Synthetic pesticides and insecticides must never be used in aquaponics because they will kill the fish. Many biological controls are also deadly to fish. All chemicals controls are to be considered a last resort in aquaponic systems and only used sparingly. If possible, such as for DWC systems, it is better to remove and treat the plants away from the system and allow the chemicals to dry completely. Appendix 2 contains a list of common insecticides and repellents, their indications and their relative toxicity to fish.

Biological controls

As for botanical pesticides, some extracts obtained from micro-organisms are safe for aquatic animals because they act specifically on insect structures and do not harm mammals or fish. Two organisms widely used in aquaponics and organic agriculture are Bacillus thuringiensis and Beauveria bassiana. The former is a toxin extract from a bacterium that damages the insect's digestive tract and kills it. It can be sprayed on leaves and specifically targets caterpillars, leaf rollers, moth or butterfly larvae without damaging other beneficial insects. B. bassiana is a fungus that germinates and penetrates the insect's skin (chitin), killing the pest through dehydration. The efficacy of the fungus depends on the number of spores sprayed and on the optimal humidity and temperature conditions, ideally a good agent for humid tropics.

Beneficial insects - pest predators

Finally, beneficial insects are another effective method to control pests, particularly in controlled environments such as greenhouses or nethouses. Beneficial or predator insects such as lacewings are introduced into the plant growing space in order to control any further infestation. Some of the advantages of using beneficial insects include: the absence of pesticide residue or pesticide-induced resistance in pests, economically feasible (in the long run for large-scale operations only), and ecologically sound. However, successful pest control using this method depends on detailed knowledge of each beneficial insect along with the constant monitoring of pests to time correctly the introduction of beneficial insects. Moreover, beneficial insects can be attracted naturally to outdoor systems. Many of these beneficial insects feed on nectar in their adult stages, so a selection of flowers near the aquaponic unit can maintain a population that can keep pests in balance.

It is important to underline that this method of control never fully eradicates the pests. Instead, pests are suppressed under a tight prey-predator relationship. This method has already been used with positive results for large-scale aquaponics, yet for small-scale aquaponics there may not be enough pests for the beneficial insects to predate, which may lead them to fly away. The choice of beneficial insects to use (see Appendix 2) should take into account the environmental conditions where they are going to operate.

Plant diseases and integrated disease management

Unlike hydroponics, which is mostly managed under sterile conditions, aquaponics takes advantage of a complex microscopic ecosystem that includes bacteria, fungi and other micro-organisms. The presence of these well adapted micro-organisms makes each system more resilient in the event of attack by pests or diseases. Nevertheless, successful plant production is the result of management strategies to avoid disease outbreaks that mainly focus on the environmental conditions, pest deterrence (pests such as whitefly may carry lethal viruses) on plant management as well as the use of organic remedies that help to prevent or to cure the plants. Similar to IPPM, integrated disease management relies on prevention, plant choice, and monitoring as a first line of defence against disease, and uses targeted treatment only when necessary.

Environmental controls

Temperature and humidity play an important role in the health management of plants. Each plant pathogen (i.e. bacteria, fungi or parasites; Figure 6.8) has optimal growth temperatures that can be different to those of plants. Thus, diseases occur in certain areas and periods during the year when conditions are more favourable to the pathogen than to its host. Moreover, moisture plays a key role for the germination of fungal spores, which require a thin film of water covering the plant tissues. Similarly, the activation of some bacterial and fungal diseases is strictly correlated with the presence of surface water. Therefore, the control of relative humidity and moisture are essential in order to reduce the risks of disease outbreaks. Appendix 2 contains detailed environmental conditions that encourage several common fungal diseases.

Control of relative humidity, especially in greenhouse aquaponics, is particularly important. This can be achieved through dynamic or forced ventilation by means of windows and fans creating horizontal airflow helping to minimize temperature differentials and cold spots where condensation occurs. Moving air is continually mixed, which prevents the temperature dropping below the dew point; therefore, water does not condense on the vegetables.

Evaporation from fish tanks and/or aerated DWC canals housed in greenhouses should also be avoided by physically covering the water surfaces, as evaporated water can dramatically increase the indoor humidity. Pipes in NFT units are prone to high water temperatures in hot seasons because of the continuous exposure to the sun on the pipes. Media bed systems are an optimal compromise, given the right choice of medium, because the top surfaces of the beds are always kept dry (see Chapter 4). Finally, systems built on rooftops have the advantage of a drier microclimate and good ventilation compared with ground level, which facilitates environmental management of plants.

Control of water temperature plays a key role in avoiding fungal outbreaks. A very common disease in aquaponics is root rot caused by Pythium spp., a soil-borne pathogen that can be accidentally introduced into the system from contaminated materials (soil, peat, seedlings from nurseries). Unlike in hydroponics, in aquaponics this fungus does not cause damage below certain temperatures because of the competitive presence of other micro-organisms. The maintenance of temperatures below 28-30 °C is thus essential in order to avoid the exponential germination of spores that would eventually cause an outbreak.

Attention should also be given to planting densities. Very high densities reduce the internal ventilation and increase the humidity among the plants. The risk of diseases for densely planted crops is also enhanced as, under intense light competition, plants grow without consolidating their cells, leading to softer and more succulent tissues walls. Tender tissues are more prone to disease because of their limited resistance to pest and/or pathogen penetration.

Plant choice

Plant varieties have different levels of resistances to pathogens. In some cases, using known resistant cultivars is the most successful method of avoiding disease. Thus, it is vital to select plant varieties that are more adapted to grow in certain environments or have a higher degree of resistance against a particular pathogen. Moreover, many seed companies offer a wide selection of plants that have different responses against pathogens. The use of local varieties that are naturally selected for a specific environment can ensure healthy plant growth.

If it is not possible to control certain diseases with resistant varieties, it is wise to shift to other crops during the critical season. In the case of Pythium spp. if resistant varieties of lettuce and beneficial micro-organisms are not able to control the infestation, it is opportune to shift to other species, such as basil, that are more tolerant to the pathogen and to high water temperatures.

Seeds and/or seedlings must be bought from a reputable nursery that employs effective disease prevention strategies and can secure disease-free products. Moreover, avoid injury to plants, as broken branches, cracks, cuts and pest damage often lead to diseases breaking out in the same area.

Plant nutrition

Nutrition greatly affects a plant's susceptibility to disease. It also affects a plant's ability to respond against disease using different mechanisms, including antixenosis (processes to deter colonization by herbivores) or antibiosis (processes to kill or reduce herbivores after landing or during eating). A correct balance of nutrients not only provides optimal growth but also makes plants less susceptible to diseases. Although the description of nutritional disorders has been discussed above, Table 6.2 outlines how some nutrients can play a major role in disease occurrence.

Effect of nutrients on fungal disease prevention
Nutrient Effect
Nitrogen Overfertilization makes more succulent tissues that are more prone to fungal attack. Nitrogen starvation makes stunted plants more prone to attacks from opportunistic micro-organisms.
Potassium Accelerates wound healing and reduces the effect of frost damage. Delays maturity and senescence of plants.
Phosphorus Improves nutrient balances and accelerates the maturity of the plants.
Calcium Reduces the severity of some root and stem fungal diseases. Affects the cell wall composition in plants that resists fungal penetration.
Silicon Helps plants to produce specific defence reactions, including the release of phenolic compounds against pathogens.

Source: Agrios (2004).

Monitoring - inspection and exclusion

Early detection and intervention is the foundation of disease and pest management. Thus, plants should be inspected regularly for early signs of infection or pest presence that may result in infection. Whenever plants show signs of damage or initial stages of disease (wilt, blight or root rot), it is vital to remove the infected branches, leaves or the whole plant to avoid the disease spreading throughout the entire crop. Moreover, regarding exclusion, it is important to enforce the control of potential vectors (sources) of viruses, such as whiteflies, by growing plants in insect-proof structures (see Section 6.5.1). In addition, the avoidance of soil contamination as well as the use of disinfected tools (e.g. shears used for pruning/harvesting) would help to avoid the transmission of potential pathogens into the system. Finally, it is good practice to monitor and record all symptoms and the progression of each disease in order to determine the best prevention and treatment methods in the future.

Treatment - inorganic or chemical

As mentioned above, aquaponics is a complex ecosystem that is more resilient than hydroponics to soil-borne disease. However, some disease outbreaks may still occur in the case of unfavourable environmental conditions, such as higher relative humidity in greenhouses or in tropical climates, and need to be controlled. As aquaponics is an integrated system containing fish, plants and beneficial micro-organisms, it is not possible to use the standard disease treatments of conventional agriculture (i.e. chemical fungicides) as they are toxic to fish. However, common practices used for organic agriculture are possible, provided that they do not harm fish and/or the bacteria or do not accumulate in the system leading to higher than accepted thresholds. Appendix 2 indicates elements and methods of application used in organic agriculture that can also be used for aquaponics to fight and stave off different diseases. In general, successful treatment using the methods relies on the combination of a few strategies that can have synergic effect against specific pathogens.

Treatment - biological

Some biological control agents can be used for aquaponics such as Thricoderma spp., Ampelomices spp. and Bacillus subtilis, which are cultured micro-organisms used to fight against specific diseases. These biological agents can be applied either on leaves or at the root zone. They provide protection against the most common soil-borne diseases including downy mildew, powdery mildew and some bacteria. In particular, Thricoderma spp. have proved effective in controlling Pythium spp. and most of the soil-borne pathogens, while Ampelomices spp. could offset any need for inorganic or chemical treatments against powdery mildew. In the case of Thricoderma spp., the spores can be distributed on substrate when seeding, to let the beneficial fungus protect plants starting at their seedling stage. Product information, producers and distributors should be consulted before use in order to identify the best treatment methods for specific diseases.

For more detailed information on specific vegetable diseases including identification, susceptibility and prevalence, see recommended texts in the section on Further Reading.

Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, Reproduced with permission.

Food and Agriculture Organization of the United Nations