Is Biofilm in a Hydroponic System Bad?

By Lynette Morgan
Published: March 1, 2017 | Last updated: April 27, 2021 12:59:05
Key Takeaways

At the first sign of biofilm in a hydroponic system, most gardeners are ready to get out the chemicals and scrubbers. Some biofilms are beneficial, however, and can contribute to healthier plants. Before waging war, it’s best to know which biofilms are friend and which are foe.

Biofilms are often poorly understood by indoor gardeners. While most gardeners are ready to wage war at the first sign of biofilm, these microscopic colonies actually have the potential to be either friend or foe in a hydroponic system.


Just as nutrient solutions and root rhizospheres are colonized by a wide range of different microbes, so too are the biofilms that develop in all systems. While the term ‘biofilm’ has often come to be associated with an evil, pathogen-filled, slimy source of disease-ridden grime clinging to hydroponic system surfaces, this is not always the case.

Healthy biofilms exist everywhere in nature where moisture and nutrients are present, containing a diversity of microbial life—many biofilms associated with colonizing the root system contain important beneficial bacteria.


These include plant growth-promoting rhizobacteria, which can assist with nutrient uptake as well as competitive suppression of pathogens. In aquaponic systems, biofilms (called biofilters) are actively encouraged and inoculated to contain beneficial bacteria such as Nitrosomonas and Nitrobacter, which convert organic material from fish waste into plant-usable nutrients.

Disease control options for commercial hydroponic systems, such as slow sand filtration, are highly reliant on the establishment of large colonies of beneficial bacteria present in biofilms, which actively control and suppress disease pathogens present in the water supply or nutrient solution.

In organic hydroponic systems, the presence of such colony-forming microbes on surfaces carry out a similar, vitally important role. Biofilms can form on both biotic (living) and abiotic (non-living) surfaces, which is why irrigation lines, growing channel surfaces, filters, drippers, reservoirs, pumps, and other hydroponic system components can become coated with rapidly forming biofilms.


When Biofilms Go Bad

While biofilms are often colonized by largely beneficial or benign bacteria, major issues can arise in hydroponic systems that have become infected with root rot pathogens such as Pythium.

The presence of these pathogens in biofilms is frequently responsible for the reoccurrence of outbreaks even after a cleaning process has been completed. A severe outbreak of Pythium or other root disease is usually treated by removal of the infected plants and growing substrate, complete replacement of the nutrient solution in recirculating systems, and often some form of treatment of the water and/or nutrient solution at the reservoir.


Unfortunately, while these steps do help reduce and eliminate many pathogen spores, biofilms that have formed on system surfaces will act as a fresh source of disease inoculant for the new crop. Growers who suffer frequent reoccurring outbreaks of root rot disease often have biofilms harboring these pathogens somewhere in their system.

What is a Biofilm?

Biofilms are not uncommon or unique to hydroponic systems. In fact, biofilms are an important component of many biological systems. Biofilms form in humans and animals, as well as in plant-based production systems.

A common example is dental plaque, a yellowish biofilm that builds up on our teeth. Biofilms are nothing particularly mysterious, they are simply communities or colonies of microorganisms where the cells are attached to a surface and to each other. These cells are embedded in a self-produced matrix of extracellular polymeric substances that provide protection and allow the biofilm to persist and build over time.

Biofilms contain both dead and live microbes and a variety of secreted compounds such as polysaccharides, proteins, DNA, lipids, minerals, and other components from the environment, all of which form complex and resistant layers. Because of this structure, biofilms that have formed on hydroponic system surfaces are protected from many of the low dose disinfection compounds that may be added to the nutrient solution to control root rot pathogens.

Biofilms begin life as free-floating bacteria that are common in most water supplies. These bacteria attach to surfaces and are not particular about where they take up residence. In plant production systems, bacteria are often attracted to the organic material contained in root exudates that act as a food source, thus roots are often rapidly colonized.

However, even the smooth interiors of irrigation pipes are easily colonized. After this initial phase, the microorganisms begin to secrete organic compounds that adhere them firmly to the surface. Water, oxygen, and nutrients are then absorbed from the nutrient solution and the process of colonization then attracts further microbes as the biofilm grows.

While it’s easy to think of such a biofilm matrix to be a thick, visible, crusty layer forming on system surfaces, this is not always the case. Many biofilms are not visible to the human eye, so even a clean looking system can harbor extensive biofilm formations. It is not until biofilms have remained undisturbed for some time and have developed very thick matrix layers that they may appear as brownish or tan deposits.

They may also become visible after being colonized by green or brown algae. Once an established biofilm has a well-formed colony of microbes, individual planktonic microbes will detach from the biofilm surface and move with the water/nutrient solution flow to find new sites for growth.

These detached microbes also make contact with plant root systems, so those that are pathogenic spread the process of infection from biofilm to plant and then from plant to plant within the system. Biofilms may also block system filters and drippers, requiring frequent maintenance to keep the nutrient solution flowing at the correct rate.

The dangers of biofilms harboring unwanted microbial life in a hydroponic system are not limited to the inside surfaces of irrigation lines, reservoirs, or growing channels. Biofilms can form on plants themselves, most commonly on the roots.

However, recent research has identified that some of the food-borne illness causing pathogens can adhere to and form biofilms on fruit and foliage.

This finding is of particular concern for crops that are not cooked before consumption—salad and leafy greens, microgreens, fresh herbs, and berries are higher risk items for food-related illness outbreaks.

While salad greens and other leafy vegetables are often well-washed in chlorinated water after harvest, any food-borne illness pathogens that are protected inside biofilms can persist and be resistant to disinfection treatments.

Salmonella and E. Coli, which have caused a number of food illness outbreaks in fresh produce, have been shown to adhere to and form biofilms on plants. For hydroponic growers and salad green producers, this is an important finding as it places emphasis on crop hygiene and prevention of contamination of the crop with these bacteria, rather than complete reliance on post harvest washing and disinfection processes.

Biofilm Control and Removal

Biofilms that are acting as a reservoir of pathogenic disease spores can be removed due to their sticky and persistent structure. This, however, requires additional effort. If a severe root rot disease outbreak such as Pythium or Fusarium has occurred, the first step is to remove and destroy the infected plants well away from the indoor garden. Substrates should also be discarded and the system completely shut down for disinfection.

The most effective way of removing established biofilms on surfaces such as NFT channels, grow beds, or pots and reservoirs is a good scrub with a hard brush to physically remove the biofilm.

Even if all the biofilm is not physically removed, scrubbing allows sanitation chemicals to more effectively come into contact with the surface beneath. For the interiors of irrigation lines and other hard-to-reach places, running an acidic solution through the system once it is fully shut down helps remove salt build-up, lime scale, and dissolve biofilms, allowing these to be rinsed away with clean water.

As a further step, running an oxidation agent such as hydrogen peroxide at a high rate through the plant-free system also assists to remove pathogen-infested biofilms.

As disinfection agents can cause root damage on sensitive young plants, residue removal then needs to be carried out with several rinses of clean water, before replanting.

Use of disinfection agents at high concentrations provide good control of biofilms in systems shut down for cleaning. These compounds are far less effective when run at lower concentrations when plants are present and run the risk of root damage.

Some research studies have indicated that UV (ultra violet irradiation) and ozone disinfection of the nutrient solution can reduce biofilm growth, but not completely eliminate it. These methods should be used with caution as they can affect the availability of certain nutrient ions in the solution.

In the future, we can expect to see some new and innovative treatments for the root disease pathogens harbored in biofilms. These innovations are likely to center around inoculation with biosurfacant producing and other suppressant microbes, rather than complete elimination of biofilms themselves.

While the prospect of biofilms colonized with disease pathogens that continually reinfect a hydroponic system is frightening, in reality, most soilless systems harbor many beneficial populations of microbes which help suppress pathogens. Many large commercial hydroponic systems exist that have been in operation for years with no regular removal of biofilms or any thorough cleaning of irrigation lines and system surfaces, and root disease is not encountered.

However, other growers both large and small have encountered frequent outbreaks of Pythium and other pathogens known to inhabit biofilms.

If released into the nutrient solution, they carry the potential to cause disease—if conditions are inductive for development. In these cases, where a root rot disease outbreak has occurred, control and elimination of biofilms is an important step in the clean-up process to prevent reinfection.


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Written by Lynette Morgan | Author, Partner at SUNTEC International Hydroponic Consultants

Profile Picture of Lynette Morgan

Dr. Lynette Morgan holds a B. Hort. Tech. degree and a PhD in hydroponic greenhouse production from Massey University, New Zealand. A partner with SUNTEC International Hydroponic Consultants, Lynette is involved in remote and on-site consultancy services for new and existing commercial greenhouse growers worldwide as well as research trials and product development for manufacturers of hydroponic products. Lynette has authored five hydroponic technical books and is working on her sixth.

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