Greenhouse Canada

There’s something in the water

Filtering and disinfecting recirculated irrigation in controlled environment agriculture

September 8, 2022  By Dr. Fadi Al-Daoud and Dr. Thomas Graham

UV system in a pepper greenhouse. Photo courtesy of Ontario Ministry of Agriculture, Food, and Rural Affairs

Most greenhouse and vertical farm producers use hydroponic growing systems to grow vegetables, cannabis, and other crops in controlled environment agriculture (CEA). This allows for great control and consistency in fertilizer delivery. To reduce wastewater, the root zone effluent (leachate) is collected and recirculated back to the crops. This results in significant savings for the producer through reduced water consumption and nutrient recovery. Greenhouse producers typically aim for approximately 25% of the applied fertilizer and irrigation (fertigation) solution to leach out of the root zone. This ensures adequate watering and avoids drought stress. Although an efficient use of resources, there are points of concern that must be taken into account. As the nutrient solution passes through the root zone, the plant takes up nutrients and excretes chemicals which change the composition of the nutrient solution. In order to recirculate the leachate, the nutrient levels, electrical conductivity (EC), and pH of the leachate must be readjusted before being fed back to the crop.

Another concern with recirculating nutrient solution is the potential for pathogen proliferation via the watering system. Over time, microbes can build up in recirculated water, including fungi, oomycetes, bacteria, and viruses. This can lead to development of root diseases caused by, but not limited to, Phytophthora and Pythium species. But not all microbes that live in recirculated water system are bad. Many are not pathogenic to the crop and can in fact be beneficial by competing with pathogens (microbes that cause disease) for nutrients and living space. Further, there is emerging research to suggest that some beneficial microorganisms may also directly improve plant health and productivity (e.g., Rhizobacteria).

To avoid disease development, it is recommended that greenhouse and vertical farm producers install filtration and sterilization equipment to reduce the pathogen load of the recycled water. This article aims to provide an overview of filtration and sterilization technologies that are being used in greenhouse and vertical farming production systems. It will discuss benefits and drawbacks of the most popular systems currently used in CEA, including physical filtration, biofiltration, heat treatment (pasteurization), ultraviolet (UV) light and ozone treatment. Special attention is paid to whether a system encourages beneficial microbe growth while reducing pathogen levels. Chemical and biocontrol management options are not discussed here.


Membrane filters
The ability of membrane filters to remove pathogens from recirculated water depends on the size of their pores. As the size of the pores decreases, so too does the size of microbes that are able to pass through the filter. The size of most fungi is 3–50 µm, bacteria are around 0.6–3.5 µm and viruses are the smallest at around 0.03–0.3 µm. The size of Phytophthora particles ranges from 5–171 µm. Filters suitable for removal of microbes have a pore size of < 10 µm. Microfilters remove particles ≥ 50 µm, ultrafilters remove particles ≥ 0.02 µm (20 nm), nanofilters remove particles > 0.01 µm (10 nm) and hyperfilters (those used in reverse osmosis (RO)) remove particles ≥ 0.0001 µm (0.1 nm). Filters with larger pores (5–7 µm) are effective at removing the oomycetes Phytophthora and Pythium.

Membrane filtration is most effective at controlling pathogens when combined in a series of multi-stage filters (large to small pore size). Producers should start with a coarse screen filter to remove debris followed by a series of decreasing pore size filters. One thing to keep in mind is that the size of the filter pores not only restricts microbe passage but also water passage, resulting in backpressure on the system. As the filter pore size gets smaller, the flow rate of water decreases or greater pressure is needed to maintain flow. Depending on the filter pore size, the flow rate can vary between 20–60 L per minute. Therefore, filters with small pores that reduce the flow rate may not be ideal for operations that require large volumes of water. Alternatively, the configuration of the filters can be modified (e.g., multiple polishing filters on distribution lines) but capital and maintenance cost need to be factored into this added complexity.


  • Membrane screen filters are recommended as a basic first step in a water treatment system to reduce the amount of debris and organic matter in the water such as soil, plant tissue and precipitated nutrients. Debris and organic matter can reduce the efficacy of other treatments such as heat (pasteurization), UV light and ozone, as discussed below.
  • Using filters in a multi-step manner such that filters with large pore sizes are followed by filters with smaller pore sizes reduces the occurrence of clogging.
  • Filters do not require chemicals, hence, there is no concern of phytotoxicity (crop damage due to chemicals).
  • Hyperfilters used in RO can be used to not only remove pathogens, but also remove excess salts such as sodium and chloride. This can be used to improve the quality of some water sources. For example, wells that may have high levels of salt.


  • Filters do not discriminate between beneficial and pathogenic microbes. All microbes are filtered depending on their size.
  • Filters have higher installation costs than some other sterilization systems.
  • The smaller the pore size, the lower the flow rate of water. If the operation’s water requirement is high, then it may require a high flow rate of water offered by filters with larger pore sizes, or multiple distributed smaller pore size filters. If larger pore size filters are used, then there is a greater chance for microbes to pass through the filtration system and back to the crop.
  • Filters can be clogged by suspended solids (sand, silt, organic matter), chemical precipitates (Fe, Mn, carbonates, pesticides), biofilms and algae.
  • Filters will not work properly if they are damaged. They need to be replaced and/or maintained on a regular basis to reduce the risk of leakage or breakthrough. Small scale leaks are not easily detected and there is no warning system to let producers know that a filter is damaged or that breakthrough is occurring.
  • RO removes nutrients so it should only be used if filtering external water sources such as wells.

Slow sand filtration, also known as biofiltration

Recirculated drip irrigation in a cucumber greenhouse.

Slow sand filters (biofilters) consist of a sand-based (or similar) filter bed that allows the slow passage of water through the media, and supports the growth of beneficial microbes that consume the organic material entering the filter. The filter material is usually sand, but it can also be granulated rockwool, lava grain, pumice, or anthracite. It is recommended to have a minimum filter bed thickness of between 50–80 cm, and sand grain size of less than 2 mm. The filter is typically supported by layers of gravel underneath. Water typically passes very slowly through the filter material at a rate of 100–300 L per m^2 per hour. The force of gravity is used to push/pull water through the system. A water layer above the filter of about 80–150 cm is required to generate enough hydrostatic pressure on the column to facilitate adequate flow. After some time a biologically active layer forms on the top of the filter with a population of algae, bacteria, fungi, and other microbes that form biofilms. This layer is called the Schmutzdecke and it is key to reducing pathogens. The filter material physically traps inorganic and organic particles including pathogens. The biological and chemical activity of the Schmutzdecke breaks down the trapped particles and kills pathogens.

The maintenance of the biologically active Schmutzdecke is very important to the success of slow sand filters. It is recommended that the water flow gently onto the filter so not to damage the Schmutzdecke at the top layers. A flow rate of 10–30 cm per hour would allow a filter capacity of 100–300 L per m^2 per hour. These systems are thought of as ecosystems that need nutrients and the proper environment to survive and thrive. The slow flow rate of these systems is intentional to give enough time for the biological and chemical processes to happen. These reactions also require adequate oxygen levels (> 3 mg per L), and optimal temperature (10–20 °C). While reducing pathogens, these systems promote the growth of beneficial microbes in the recycled water. Irrigation recirculation systems that use slow sand filtration are typically rich with bacteria (10^3–10^4 colony forming units per mL). This population of bacteria is thought to be beneficial for plants and reduces the ability of pathogens to colonize roots. However, a complete understanding of how these filters work is lacking.

Another important aspect of slow sand filters is the size of the sand grain. Filtration is improved by using smaller grain sizes, similar to filter pore size mentioned in the previous section. Smaller grains have more surface area per unit volume of the filter bed which allows them to filter more water. The smaller the grain size, the better it is at trapping organic and inorganic matter. High filtration efficacy occurs when using a fine and medium sand grain size between 0.15–0.8 mm. However, the smaller the grain size, the lower the flow rate of water (again, similar to filter pore size mentioned in the previous section).

The biological and chemical activity of the Schmutzdecke in combination with the physical filtration of the grains has proven to be very effective at reducing pathogen loads in recycled irrigation solutions. Studies have shown a reduction of Phytophthora, Pythium and viruses by 95–100% using this system.


  • The main benefit of slow sand filters is their ability to maintain natural beneficial microbes in the recirculated water.
  • Their low tech nature allows slow sand filters to be cheaper than other filtration and sterilization systems because they don’t require as much energy to run or specialized training to maintain.
  • No phytotoxic side effects have been observed when using slow sand filters.


  • Their slow rate of water flow does not allow slow sand filters to be used in operations that require large volumes of water.
  • Slow sand filters require a significant amount of space to set up and this is accompanied by a large set-up cost.
  • To prevent clogging, the Schmutzdecke needs to be partially removed every few weeks by scraping off the uppermost layers.
  • Oxygen may be reduced in the solution due to consumption in the Schmutzdecke. Oxygen needs to be supplemented through aeration or active gas supplementation in the nutrient solution.
  • Fluctuating temperatures may adversely affect a biofilter as discussed above.

Heat (Pasteurization)

Reverse osmosis filtration system in a tomato greenhouse.
Photos courtesy of Ontario Ministry of Agriculture, Food, and Rural Affairs

High temperatures disrupt cell integrity and interrupt metabolic processes in microorganisms.

That basically means that if you apply enough heat to something for long enough then you’re able to kill it. Both temperature and contact time (intensity and duration) is important for this process. The more heat you apply in a given period of time the less contact time you need to kill pathogens. Conversely, if you reduce the heat applied in a given period of time, generally it will take longer to kill the pathogens. That is the premise behind using heat (pasteurization) to sterilize recycled nutrient solution in CEA. These types of systems pass water through a series of heat exchangers until the target temperature and desired contact time is reached. The heat is then recovered from the water and the water is cooled before being applied to the crop.

The quickest way to kill most microbes is to heat water to
95°C for 30 seconds. This is effective for controlling Pythium and Phytophthora, as well as some viruses. To reduce energy costs heat levels can be reduced to 60°C but the exposure time must be increased to 2 min to eliminate fungi, bacteria and nematodes. To kill viruses, water needs to be heated to at least 85°C for 3 min. It is recommended that water pH be reduced to 4.5 before heating to reduce calcium precipitation on metal heat exchange plates. Using corrosion-free materials (ex. stainless steel) is also recommended.


  • High temperatures are effective at controlling many pathogens.


  • Heat, like most sterilization techniques, does not discriminate between beneficial microbes and pathogenic ones.
  • High temperatures have some undesired effects such as the precipitation of some salts. These precipitates may cause clogging of the irrigation system and reduce the availability of these chemicals to the crop.
  • Heat reduces the amount of dissolved oxygen in the water, so oxygen supplementation through aeration or active injection may be necessary after heat treatment.

Ultraviolet (UV) light
UV light is electromagnetic radiation with a wavelength between 100–400 nm. Germicidal UV lamps emit radiation that causes a photochemical reaction: this damages the genetic material of microorganisms (DNA and RNA), reducing their ability to reproduce and grow. The optimum UV wavelength to kill microbes is around 254 nm. High pressure lamps emit UV-C radiation with a wavelength between 200–280 nm, whereas, low pressure lamps emit around 254 nm. High pressure lamps are less energy efficient than low pressure lamps, but both lamps are effective at controlling pathogens in recirculated nutrient solution, as long as the proper dose is reached.

Similar to heat treatment, the efficacy of disinfection depends on the duration and intensity (dose) of the UV treatment. This is measured in mJ per cm^2. The effective dose of UV-C can range from 28–850 mJ per cm^2. A UV dose of 100 mJ per cm^2 is sufficient to eliminate pathogenic fungi, while a higher dose of 250 mJ per cm^2 is recommended to remove all organisms including viruses, and an even higher dose of 500 mJ per cm^2 is required to achieve 96% mortality of some nematodes (but 100 mJ per cm^2 prevented reproduction of some nematodes and reduced infection of plant roots). Some Phytophthora and Pythium species can be controlled with UV-C doses of as little as 17–88 mJ per cm^2. In addition to dose, disinfection efficacy is also dependent on the flow rate of water past the UV source. The slower the water flow rate, the more exposure microbes have to the UV light which increases mortality. But the most important factor affecting efficacy is water clarity. UV light is reflected off or absorbed by any material in the water such as suspended solids or plant debris. These particles may shield microbes from the UV light and reduce mortality. Recycled water must be filtered prior to UV light treatment in order to remove suspended particles from the water. This increases UV light penetration and transmission. For UV light to effectively disinfect recycled irrigation water, a minimum UV transmission rate of 60% is essential. That means the water needs to be clear enough so that at least 60% of the UV light emitted by the lamp passes through the water and is not absorbed or reflected by particles. Iron (Fe) also absorbs in the UV waveband. Given iron’s necessity as a micronutrient it is often present or added to fertigation solutions and will impact the efficacy of UV treatments.


  • UV light is not corrosive, does not depend on the pH of the solution and does not require additional chemicals.


  • UV light, like heat treatment, does not discriminate between beneficial microbes and pathogens.
  • Treating recycled nutrient solutions with high intensity UV has been shown to inhibit growth of lettuce plants downstream of the treatment, potentially due to generation of ozone and/or free radicals (bad stuff that hurts plants).
  • UV light can destroy some iron chelates which can cause iron to precipitate out of solution and coat the UV lamp, which will reduce the effective lamp output. Further, iron itself absorbs UV light, thereby reducing the number of photons available to inactivate pathogens. The lack of iron in solution may result in iron chlorosis if iron levels are not amended after treatment. However, some chelates perform better under UV treatment, preventing the negative effects of UV-induced iron deficiency.
  • UV light treatment is costly and requires high maintenance levels because UV lamps degrade with time, which results in reduced dose (up to 10% loss after 1,000 hours of operation, and 35% loss after continuous operation for a year). UV lamps need to be monitored and changed as required.

Ozone (O3)
Ozone is a strong oxidizing agent. More than 1.5 times stronger than chlorine. It acts by direct oxidation or through the production of short-lived hydroxyl free radicals and superoxide ions (bad stuff that can hurt living things). Ozone is generated by combining an oxygen atom (O-) with an oxygen (O2) molecule to form ozone (O3). As stated in the previous section, UV light can be used to generate ozone, but much higher concentrations are produced if electricity is used as the source of energy for this reaction. For example, corona discharge ozone generators use electricity to produce ozone from air, whereas electrolytic discharge ozone generators use electricity to produce ozone directly in the water. Once ozone is generated it is relatively unstable and decomposes back to oxygen, or reacts with other materials, in a short period of time. It has a half-life of less than 20 minutes when dissolved in clean water. This instability can be a good thing and a bad thing. On the positive side, once ozone is produced in the recycled water it kills microbes and quickly breaks down. It is recommended to treat solutions until a minimum residual ozone concentration is achieved (~0.5 mg per L). Prior to distribution to the crop this residual will automatically degrade or can be easily stripped out with an ozone destruct filter. This said, there is evidence that suggests a small residual could be maintained during distribution to help keep pipes and emitters clean without any crop damage. Also, because ozone breaks down into oxygen it has the potential to dramatically increase dissolved oxygen levels. One negative aspect of ozone’s short half-life is that it must be produced at the point of use and immediately dissolved in the solution.

Similar to heat and UV light treatment, the efficacy of ozone depends on the target microbe you’re trying to kill and the dose of ozone (concentration and contact time). Most microorganisms of concern to growers are controlled if ozone is applied until a residual of ~0.5 mg per L can be maintained for 5 minutes in the bulk solution (i.e., in tank). Achieving this residual will require dramatically different amounts of ozone depending on the initial contamination level of the water.

Manganese, iron and micronutrient chelates can be oxidized by ozone, and therefore compete with other contaminants/pathogens for applied ozone. This increases the ozone demand in the solution resulting in longer processing times.


  • Ozone degrades pesticides and other contaminants in the solution.
  • Ozone has a low environmental hazard due to its very short half-life in water.
  • Ozone can increase overall dissolved oxygen levels as it reacts or reverts to diatomic oxygen.


  • Ozone treatment systems have a high cost of installation and maintenance.
  • High levels of ozone can be phytotoxic if the ozone does not break down fast enough before the recycled solution is reapplied to the crop.
  • Ozone demand can be very high in water with a high pH, high organic matter, nitrite, manganese, iron or bicarbonate concentrations.
  • Gaseous ozone is hazardous and proper training, handling and safety measures must be in place.
  • Ozone is an aggressive oxidant and as such system components must be compatible (e.g., rubber fittings will rapidly disintegrate).

There is no single solution for CEA water treatment; rather, a systems approach should be taken that deploys the appropriate water treatment technologies for the specific water quality needs of the operation. Many greenhouse and vertical farm producers install multiple filtration and sterilization systems that work in series. This ensures redundancy in their operations and give them peace of mind that their recycled water is not harboring high levels of pathogens that can cause disease. It is recommended that producers check the quality of their source water and recycled water on a regular basis. Water samples can be sent to a number of accredited and certified laboratories in Ontario that offer identification and quantification services. These services may include molecular techniques that can identify a plethora of pathogens at once, like a DNA multiscan or sequencing. However, positive results from molecular tests should be interpreted with caution because they mean that the genetic material (DNA or RNA) of a pathogen is present, but they cannot tell if that pathogen is alive or dead. If a pathogen is detected with a molecular test it should be verified with bioassays (culturing or inoculation of test plants) to confirm the pathogen is alive. 

Dr. Fadi Al-Daoud is a greenhouse vegetable specialist for the Ontario Ministry of Agriculture, Food and Rural Affairs. Dr. Thomas Graham is an assistant professor at the School of Environmental Sciences, University of Guelph.

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