Tackling plant pathogens with advanced detection methods

Plant pathogens are some of the most significant threats to agriculture worldwide. Organisms like bacteria, fungi, viruses and others can silently devastate entire crops, leading to massive economic losses, food shortages and disruptions across multiple industries.

How do plant pathogens affect crops?

When a plant pathogen infects a crop, the damage may or may not be visible. While some pathogens cause clear signs like wilting, leaf spots or galls, others just weaken the plant from within and reduce the yield without any other outward symptoms. For example, Fusarium graminearum causes Fusarium head blight in wheat, shriveling the grains so they are unusable. On the other hand, Phytophthora infestans, which caused the tragic Irish potato famine, can wipe out entire fields overnight. In both cases, the pathogens lead to reduced food production, lower quality and significant economic losses for farmers.

The impact of plant pathogens on agriculture

Crop damage is one obvious impact of plant pathogens, but the real costs extend much further. Reduced yields, increased management costs and the need to apply more chemical pesticide treatments cost the industry billions of dollars each year. For example, Xylella fastidiosa is a bacterial pathogen responsible for olive quick decline syndrome in Europe. It has destroyed ancient olive groves, some of which have been productive for centuries, leading to staggering financial losses and uprooting the entire way of life for people who depend on olive farming.

The economic burden doesn’t stop at crop losses due to plant diseases. Pathogen outbreaks also drive up the price of food, affect trade agreements and create regulatory challenges as nations try to control the spread of these diseases. In the end, plant pathogens aren’t just a problem for farmers. They affect everyone in the global food chain.

Managing plant pathogens in agriculture

Managing plant pathogens is an ongoing challenge for both researchers and farmers. Traditional methods of plant disease detection often struggle to keep up with the speed and adaptability of these organisms. Pathogens can develop resistance to chemical treatments, and some, like Pseudomonas syringae, can even persist in the soil for long periods, lying dormant until conditions are right to strike again. Early detection is key, but it’s easier said than done. Often, by the time symptoms are visible, the infection has already spread, making control efforts that much harder.

Agrobacterium tumefaciens: This bacterial pathogen causes crown gall disease, where tumor-like growths appear on a variety of plants. It affects apple, peach and cherry trees, as well as grapevines, roses and vegetable crops like tomatoes and peppers. The galls disrupt the plant's ability to transport water and nutrients, stunting grown and even killing the plant in severe cases.

Botrytis cinerea: Known as gray mold, Botrytis cinerea is the bane of fruit growers everywhere. Soft fruits like grapes and strawberries are especially vulnerable, and once Botrytis takes hold, it spreads fast, causing the fruit to rot from the inside out. In winemaking regions, it’s a constant threat, capable of turning an entire season’s crop into a loss if not managed carefully.

Colletotrichum spp.: This group of fungal pathogens causes anthracnose, a disease that hits everything from fruits to vegetables, leaving behind unsightly lesions that worsen post-harvest. Growers might not even realize their crops are infected until they start rotting in storage. Managing Colletotrichum takes vigilance, especially in humid climates.

Curtobacterium flaccumfaciens: This bacterial pathogen causes wilt and blight, and causes the leaves to yellow, wilt and drop from the plant. It spreads through contaminated seed, making it a recurring problem that’s hard to shake season after season.

Erwinia amylovora: This bacterial pathogen causes fire blight, a disease that spreads rapidly in warm, wet weather. Blackened, curling branches can appear overnight, wiping out entire apple and pear orchards in just one season.

Fusarium culmorum: This fungal pathogen hits cereal crops like wheat and barley, causing root rot and Fusarium head blight. It reduces yields and spreads harmful mycotoxins, such as deoxynivalenol (DON), through the grain, risking both human and animal health.

Fusarium graminearum: Another fungal powerhouse, Fusarium graminearum targets wheat and barley, causing Fusarium head blight. This pathogen also produces mycotoxins that can contaminate the grain, making it unsafe for consumption. Farmers dealing with Fusarium graminearum face a double burden: less crop and the risk of dangerous toxins.

Pantoea stewartii: This bacterial pathogen is responsible for Stewart’s wilt in corn, a disease that stunts growth and causes wilting. It's primarily spread by corn flea beetles (Chaetocnema pulicaria), which transmit the bacterium while feeding on the plants. If not caught early, the disease can devastate entire fields, leading to significant losses in yield.

Pepper mild mottle virus (PMMoV): This is a persistent viral pathogen that is known to stick around in the soil and in seeds, long after a grower thinks it’s gone. It reduces both yield and quality in pepper crops, and its ability to linger can cause repeated outbreaks, season after season.

Phytophthora infestans: This fungus-like pathogen, classified as an oomycete, made its mark on history as the cause of the Irish potato famine, and it’s still a menace today. It can ruin potatoes and tomatoes in the blink of an eye, turning leaves and tubers into blackened, decaying masses. It thrives in cool, wet climates, making it a persistent threat in many growing regions.

Plasmodiophora brassicae: Brassica crops like cabbage and broccoli face a unique threat in Plasmodiophora brassicae, the pathogen behind clubroot. The disease causes swelling and deformation of the roots, cutting off nutrient and water flow to the plant. To make matters worse, it sticks around in the soil for years, forcing farmers to adopt long-term strategies to manage it.

Plasmopara viticola: Vineyard owners know this fungus-like pathogen all too well, as it is responsible for downy mildew in grapevines. The oomycete spreads quickly in humid conditions, leaving a white, downy growth, reducing yields and diminishing the fruit quality – a double hit for both growers and winemakers.

Puccinia graminis: This fungal pathogen causes wheat rust and is a long-time adversary for farmers. It releases rust-colored spores that spread easily through the air, infecting wheat plants and reducing their productivity. Adding to the challenge, like many other fungal pathogens, Puccinia graminis can evolve into new strains with increased virulence, making it a moving target for disease management and forcing farmers to continually adapt their strategies to keep wheat rust in check.

Ralstonia solanacearum: This is the bacterium behind bacterial wilt, a disease that devastates potatoes, tomatoes and other crops. What makes this pathogen particularly tricky is that it blocks the plant’s water flow, causing the plant to suddenly wilt and die. Even worse, it can linger in soil and water for extended periods, waiting for the right moment to strike again.

Sclerotinia sclerotiorum: White mold is a disease that hits over 400 plant species, and Sclerotinia sclerotiorum is the pathogen to blame. It thrives in moist environments, causing wilting and stem rot that can lead to complete plant collapse. Once it’s in the soil, this pathogen sticks around for years, making long-term management essential for growers.

Verticillium dahliae: Lurking in the soil, this fungal pathogen causes Verticillium wilt in crops like tomatoes and strawberries. It blocks water and nutrient flow, causing the plant to wither and die. It can also stay dormant in the soil, waiting for the right conditions to strike again. Farmers must be strategic in crop rotation to avoid repeated losses.

Xylella fastidiosa: This bacterial pathogen is behind devastating diseases like Pierce’s disease in grapevines and olive quick decline syndrome. It is spread by insect vectors and often remains hidden until the damage is extensive. Even worse, its ability to infect a wide range of crops makes it a serious threat to global agriculture.

Zymoseptoria tritici: This fungal pathogen is the culprit behind septoria leaf blotch in wheat, reducing photosynthesis as well as yields. This pathogen thrives in cool, wet weather and spreads quickly across the leaves. 

Detecting plant pathogens at different stages of the crop cycle presents numerous challenges, from hidden threats in the soil to asymptomatic infections and post-harvest safety requirements. Understanding these obstacles is essential to developing effective strategies for plant health management.

Testing soil health for threats prior to planting

It all starts with the soil. Before planting anything, farmers and soil scientists need to know what’s lurking beneath the surface. Pathogens like Verticillium dahliae can hide in the soil for years, just waiting for the right conditions to attack. Traditional testing methods are often slow and require separate tests for each pathogen, making these approaches impractical in a time-sensitive planting season. What’s needed is a comprehensive method that is capable of detecting a wide range of pathogens simultaneously, enabling informed crop planning and proactive management.

Field monitoring and detecting pathogens before symptoms show

Once crops are in the ground, the window for effective intervention is often limited. The difficulty lies in the fact that many pathogens remain asymptomatic during the initial stages of infection, allowing them to establish and spread undetected. For instance, Ralstonia solanacearum can invade the plant's vascular system without visible signs, so by the time symptoms like wilting appear, significant internal damage has already occurred. Traditional monitoring methods often lack the sensitivity to detect these low-level, asymptomatic infections, leaving farmers unprepared for sudden disease outbreaks.

Rapid detection of crop diseases in greenhouses and controlled environments

In a greenhouse, there’s literally no room for error – plants are packed closely together and environmental conditions are optimized for growth. However, these same factors can also accelerate pathogen spread. For instance, Botrytis cinerea, commonly known as gray mold, thrives in the humid conditions of greenhouses and can quickly infect multiple plants through airborne spores. Left undetected, it can devastate high-value crops like tomatoes or strawberries within days. The high density of plants and limited space for disease containment mean that even a single missed infection can lead to a significant losses. 

Quality control to ensure healthy crops at harvest time

As harvest approaches, there’s no room for second chances, as the final stages of growth leave little margin for error. Farmers must be certain that their crops are free from pathogens to meet safety standards and market quality. For instance, Aspergillus niger, a common post-harvest fungal pathogen, can infect grapes during the final stages of growth or after harvest, leading to black mold that compromises both yield and quality. This pathogen thrives in warm, humid conditions and can spread rapidly if not detected early. Beyond yield losses, Aspergillus niger poses additional risks by producing mycotoxins that can make grapes unsafe to consume. Traditional testing methods may fail to detect low-level infections or mycotoxin contamination in time, making rapid and highly sensitive diagnostic tools essential to safeguard the harvest, prevent spoilage and protect the farmer's economic interests.

Post-harvest testing to meet trade and safety standards

The crops may be out of the field, but the job is far from over. Post-harvest testing ensures that crops are safe and compliant even after leaving the field. Rigorous testing is mandatory for growers who export their produce, as many countries enforce strict phytosanitary regulations. Detection of pathogens like Puccinia graminis, which causes wheat rust, can lead to the rejection of entire shipments, resulting in significant financial losses, trade restrictions or penalties. With such high stakes, rapid and accurate diagnostic tools are essential to certify that produce meets international safety standards and prevent disruptions to trade.

When it comes to detecting plant pathogens, traditional methods have their limits. Fortunately, advances in technologies like NGS and dPCR are are providing researchers with powerful tools to enhance pathogen detection and management. These tools improve diagnostic precision and enable insights across the crop cycle, though their use often depends on specialized expertise and resources.

Broad-spectrum detection made possible by NGS

NGS is taking plant diagnostics to new heights by offering a comprehensive approach that surpasses traditional methods targeting individual pathogens. Capable of detecting a wide range of organisms simultaneously, NGS enables broad-spectrum monitoring across different crop cycle stages, from testing soil prior to planting to early detection of infections in crops. NGS can identify known pathogens, such as Verticillium dahliae and Ralstonia solanacearum, and even uncover new or emerging threats, all in a single test and even before symptoms appear.

Several factors can make NGS tricky to use routinely in some agricultural settings, like the need for curated databases, bioinformatics tools and substantial resources. Even so, its high throughput and precision make it an incredibly powerful tool for managing evolving pathogenic threats in agriculture.

Precision plant disease testing with dPCR

dPCR delivers exceptional precision in quantifying specific pathogens, allowing farmers to focus on the pathogens relevant to their crops and streamline management efforts. But it doesn’t stop there – dPCR not only confirms the presence of a pathogen but also measures exactly how much of it there is. This level of detail is crucial when managing diseases like Botrytis cinerea, where pathogen load can determine the severity of an outbreak.

Its primary strength lies in targeted applications, such as validating results from broader screening methods like NGS or monitoring specific pathogens over time. This precision is invaluable for tasks like pre-harvest quality control or post-harvest export testing, where accurate pathogen quantification guides critical decisions. In the lab, dPCR further empowers breeders and researchers by providing precise data on how well new crop varieties resist pathogens, enabling them to refine and enhance future crop development.

Integrating NGS and dPCR for comprehensive pathogen detection

Individually, NGS and dPCR are powerful research tools, but together they offer a comprehensive approach for plant pathogen detection and management. NGS provides a broad-spectrum approach, identifying a wide array of pathogens present in soil or plant samples, including novel or emerging threats. Following this, dPCR offers high-precision quantification, allowing for the accurate measurement of specific pathogen loads identified by NGS.

While this combined approach provides valuable insights into pathogen presence and load, it may not yet be feasible for all growers due to cost considerations. However, advancements in automation and cost reduction have the potential to make this integration more accessible in the future. For researchers and exporters, leveraging NGS and dPCR in tandem enables proactive disease management, reduces potential losses and supports compliance with regulatory standards.