At Hydroponic Systems, we have spent years developing solutions that help growers protect the roots of their crops and optimise water management in greenhouses. We know that one of the main threats to productivity is root disease, which can cause significant losses if not detected early.
Our team of hydroponics experts has proven that early diagnosis is the most effective tool for preventing irreversible root damage and reducing dependence on corrective fungicides.
In this blog, we will share with you a practical guide to
- Recognising the initial symptoms
- Differentiating between problems caused by pathogens and abiotic factors
- Learning about the most effective methods of diagnosis and prevention
Our goal is that, by the end of this post, you will have a clear understanding of how to identify, diagnose, and manage root diseases in greenhouses, with technical solutions adapted to different crops and production systems.
Why is early diagnosis of root diseases so important?
In our experience, early diagnosis makes the difference between a healthy crop and a loss that is difficult to recover from. Root diseases progress silently: by the time symptoms are visible above ground, the roots are usually already severely compromised. That is why early detection is the best strategy for protecting the production system and ensuring the profitability of the season.
Economic impact of late diagnosis
When diagnosis is delayed, the economic effects are immediate. An attack by Pythium, Fusarium or Phytophthora can drastically reduce plant vigour, limit water and nutrient uptake and, as a result, decrease crop quality and volume.
In many cases, growers are forced to invest in expensive fungicides, replace substrates, or even replant, resulting in a cumulative economic impact that is difficult to recover in a single cycle. Conversely, identifying root symptoms in the early stages allows for quick action, reducing corrective treatments and avoiding millions in losses.
Differentiating pathogens from abiotic problems (pH, salts, excessive irrigation)
One of the great challenges for agricultural technicians is distinguishing between root disease and an abiotic problem. Excessive salts, inadequate pH, or excessive irrigation can cause symptoms very similar to those of a pathogen: yellowing leaves, wilting, or loss of vigour.
At Hydroponic Systems, we have often seen that this confusion leads to incorrect treatments being applied, increasing costs without solving the real cause of the problem. That is why we insist on the importance of combining field observation with diagnostic tools that allow us to differentiate between an environmental factor and a fungal or bacterial attack. Only in this way can an effective response be achieved that is adapted to the real needs of the crop.
Visible symptoms and hidden signs in the roots
Detecting root disease early requires observing both the above-ground and underground parts of the plant. In many cases, the first signs appear on the leaves and stems, but the real source of the problem is in the roots. That is why we always recommend a complete inspection that includes the substrate and root system.
Initial symptoms on leaves and stems
In our experience, the first signs usually appear on the above-ground part of the plant, even though the real problem is underground. Some of the most common are:
- Sudden wilting, even with sufficient moisture in the substrate.
- Yellowing of lower leaves.
- Slowed growth and loss of vigour.
- Thinner and weaker stems than normal.
These symptoms are an early warning sign, but should not be confused with nutritional deficiencies. To confirm this, it is essential to check the condition of the roots.
Specific damage to roots: rot, colour and texture
When we examine the roots directly, it is possible to identify clearer signs of disease. Among the most common are:
- Soft, dark roots, indicating rot.
- Colour changes: from healthy white to brown or black.
- Bad smell in the substrate, caused by decomposition.
- Absence of fine roots or capillaries, which are essential for the absorption of water and nutrients.
These indicators are key to differentiating between a healthy crop and one that already has an active infection.
Confusing signs: nutritional deficiencies vs pathogens
One of the biggest challenges facing growers is that root symptoms can be confused with nutritional deficiencies. For example:
- Yellowing may appear to be a lack of nitrogen.
- Necrosis in young leaves can be confused with calcium deficiency.
- Wilting can be attributed to insufficient watering.
At Hydroponic Systems, we know that this type of confusion delays response and increases management costs. That is why we always recommend combining visual observation with substrate, water, and root analysis to confirm whether it is a nutritional imbalance or an active pathogen.
Main root pathogens in greenhouse crops
In protected crops, root problems are usually dominated by a small group of pathogens that recur in different production systems. Knowing what they are and how to identify them is key to taking timely action and avoiding losses. At Hydroponic Systems, we have worked closely with growers facing these challenges, and here we share the most common cases.
Pythium: the most common pathogen in hydroponic systems
Pythium is undoubtedly the most common root pathogen in hydroponic and water recirculation systems. Its presence is favoured by high humidity and moderate temperatures.
The symptoms we observe in the field include:
- Rot of fine roots.
- Plants with sudden wilting, despite having water available.
- Delayed growth and loss of uniformity in the crop.
An important characteristic is that Pythium spreads easily through irrigation water, making soilless systems particularly vulnerable environments.
Fusarium: symptoms and differential diagnosis
Fusarium oxysporum is a vascular pathogen that affects both the roots and the plant’s conduction system. Unlike Pythium, its symptoms are more progressive:
- Yellowing of the lower leaves, progressing towards the top.
- Necrosis in stems and blockage of sap flow.
- Partial or total wilting, difficult to reverse.
In our experience, differentiating Fusarium from abiotic problems (such as excess salts) requires internal observation of the stem: when a cut is made, brown discolouration can be seen in the conducting vessels, an unmistakable sign of infection.
Phytophthora and Rhizoctonia: risks and detection
Two other common pathogens in greenhouses are Phytophthora spp. and Rhizoctonia solani. Although less common than Pythium or Fusarium, their impact can be just as severe if they are not detected in time.
- Phytophthora: causes root and collar rot, with progressive darkening and collapse of the plant. Early detection is difficult, as the initial symptoms are confused with wilting due to water stress.
- Rhizoctonia: causes brown lesions at the base of the stem and necrosis in young roots. It is especially dangerous in seedbeds and seedlings, where it can cause the loss of entire trays.
At Hydroponic Systems, we insist that these pathogens should not be addressed with corrective treatments alone. The key is prevention, monitoring and early diagnosis, integrated into a greenhouse health management plan.
Methods for diagnosing root diseases
An accurate diagnosis requires combining different approaches. At Hydroponic Systems, we always recommend starting with direct observation in the greenhouse and supplementing this with more advanced tests when necessary. This combination reduces errors, avoids confusion and allows quick decisions to be made to protect crop health.
Visual assessment and field sampling
The first step is a visual assessment. To do this, we observe both the aerial part and the roots: wilted leaves, weakened stems, and roots with changes in colour or texture are the first signs that something is wrong.
Field sampling is essential: we collect representative plants (healthy and diseased), along with a sample of the substrate and irrigation water. These materials allow us to confirm whether the damage is uniform or localised, and facilitate a more accurate diagnosis in later stages.
Laboratory tests to identify pathogens
When visual analysis is not sufficient, we resort to laboratory tests, which allow us to accurately identify the pathogen involved. Among the most commonly used are:
- Isolation in culture media to detect Pythium, Fusarium, Phytophthora or Rhizoctonia.
- Molecular tests (PCR, qPCR) to confirm the species and quantify the presence of the pathogen.
- Microscopy to observe characteristic structures such as hyphae and spores.
In our experience, combining field observation with molecular testing speeds up decision-making and reduces the margin of error.
Emerging technologies: sensors, AI and digital diagnostics
Technological innovation is transforming diagnostics in greenhouses. Today, we already have sensors for humidity, dissolved oxygen and ORP, which help identify risk conditions before visible symptoms appear.
In addition, tools based on artificial intelligence (AI) and digital image diagnostics are beginning to be adopted. These tools make it possible to analyse photos of roots or plants and obtain an automatic prediction of the type of disease. Combined with international databases, these technologies represent a major step forward in early detection and predictive management.
At Hydroponic Systems, we are closely following these trends because we believe that the future of root diagnostics lies in the integration of real-time monitoring, AI and sustainable agronomic practices.
Prevention strategies and integrated managemento
At Hydroponic Systems, we believe that the best defence against root diseases is prevention. Over the years, we have found that the key lies not only in subsequent treatments, but also in designing a growing system that prevents conditions conducive to the proliferation of pathogens.
Good irrigation and drainage practices
Inefficient irrigation and poor drainage are the main causes of waterlogging, which creates an environment conducive to the development of fungi such as Pythium or Phytophthora.
That is why we insist on the importance of adjusting the frequency and intensity of irrigation according to the needs of the crop, and of having systems in place that ensure effective drainage of excess water.
Use of channel systems with spacers to prevent waterlogging
Our line of spacers has been developed precisely to ensure effective drainage and keep grow bags elevated, preventing contact with standing water and reducing pathogen pressure on the roots.
- Premium Spacer: creates a stable separation space between plants and the drainage channel, improving overall crop yield.
Ideal for strawberries, tomatoes, peppers, medical cannabis, leafy greens and flowers. - Eco Spacer: thanks to its lightweight construction, it is a practical solution that facilitates installation and daily handling.
Designed for tomatoes, peppers, leafy greens, and flowers, with a lighter and easier-to-handle structure. - Spacer Hydropot: specially designed for greenhouse blueberry cultivation, it ensures adequate aeration over the drainage flow.
Perfect for blueberries, medical cannabis, and flowers, providing optimal aeration for sensitive crops. - Spacer Elevated: a key complement to the HS Evolution system, providing greater functionality and efficiency in crop management.
Recommended for strawberries, tomatoes, peppers, cucumbers, courgettes, aubergines…
Thanks to these solutions, growers can prevent waterlogging, improve root oxygenation and reduce the risk of diseases associated with root rot.
Complement with good integrated management practices
Although the spacer channel is the basis for prevention, we recommend integrating it with a management plan that includes:
- Constant monitoring of root condition.
- Periodic review of parameters such as pH and electrical conductivity.
- Sanitisation of the irrigation system and proper maintenance of equipment.
In this way, we not only prevent the spread of root diseases, but also ensure a healthier, more uniform and productive crop.
Cases and experiences in international horticultural crops
At Hydroponic Systems, we have assisted producers from different countries in implementing strategies to prevent and manage root diseases. Each crop and each production system has taught us valuable lessons that we now share with you.
Tomatoes and peppers: Pythium control in hydroponics
Tomatoes and peppers are two of the crops most susceptible to Pythium attack, especially in recirculating hydroponic systems. In international experiences, we have seen how the combination of early diagnosis, irrigation water disinfection, and precise adjustment of oxygenation parameters can contain the spread of the pathogen.
Thanks to these measures, growers not only reduced the incidence of the disease, but also extended the useful life of the irrigation system and improved crop uniformity.
Strawberries and lettuce: root rot prevention
In strawberry and lettuce crops, root rot is a constant risk due to high humidity and prolonged contact with moist substrates. In this context, we have implemented systems that combine:
- Monitoring of drainage and substrate moisture.
- Use of safe disinfectants in irrigation water.
- Preventive application of biological agents such as Trichoderma.
The results have been consistent: reduced root rot, more vigorous plants and better quality crops, with less need for chemical treatments.
Lessons learned in high-tech greenhouses
In high-tech greenhouses, where production is intensive and the margin for error is minimal, we have confirmed that success depends on the integration of tools. Isolated actions are not enough: diagnosis, digital monitoring, water disinfection and good irrigation practices must work together.
Our main lesson is clear: root health is not achieved with one-off solutions, but with systems designed to prevent, control and sustain long-term productivity. And that is the philosophy that guides all our solutions.
Final recommendations for producers and agricultural technicians
At Hydroponic Systems, we know that dealing with root diseases is one of the biggest challenges in greenhouse production. That is why we want to conclude this guide with practical recommendations that can help you protect your crops and make safer decisions.
Early diagnosis checklist
To facilitate timely detection, we propose a simple checklist that we use in our field evaluations:
- Check the condition of the roots weekly (colour, texture and smell).
- Observe initial symptoms on leaves and stems (yellowing, wilting, loss of vigour).
- Verify irrigation parameters: frequency, drainage, EC, and pH..
- Compare symptoms with possible nutritional deficiencies before applying treatment.
- Take plant and water samples if pathogens are suspected.
With this basic protocol, it is possible to anticipate serious problems and avoid hasty decisions that increase costs.
Decision-making tools and support services
In addition to field observation, we recommend using tools that increase diagnostic accuracy:
- Humidity, dissolved oxygen, and ORP sensors, which allow you to identify risk conditions.
- Laboratory analysis, useful for confirming the presence of pathogens such as Pythium, Fusarium, or Phytophthora.
- Digital monitoring solutions, which integrate real-time data and facilitate the traceability of health management.
At Hydroponic Systems, we support producers in the implementation of these technologies, offering technical support and personalised advice. Our goal is for every decision to be backed by reliable information tailored to the specific needs of your crop.
Strengthen the root health of your crop with accurate diagnosis
At Hydroponic Systems, we believe that early diagnosis and comprehensive management are the basis for ensuring more productive, sustainable, and profitable crops. Our solutions are designed to help you prevent root diseases, optimise water use, and maintain the stability of your production system throughout the entire cycle.
If you want to implement reliable strategies to protect your plants’ roots, our team of specialists is ready to assist you with technical advice, diagnostic tools, and innovative systems.
Contact us today and discover how we can help you strengthen the health of your crops from the roots up.
