Oomycetes (Pseudofungi) — the “non-fungi” in plant pathology

A historical excursus: how a “fungus” broke the familiar picture of the world

The paradox is that the first to notice this was not a mycologist but a botanist. As early as 1858, the German botanist Nathaniel Pringsheim, studying aquatic organisms, drew attention to the fact that oomycetes (in particular Saprolegnia) in a number of traits resemble not fungi but certain algae, in particular brown algae (Pringsheim, 1858; Alexopoulos et al., 1996). This observation remained in the shadows for many years, but it was the first “warning bell.”

The situation changed in the mid-20th century, when the development of electron microscopy and biochemistry made it possible to look inside the cell. And here researchers were shocked. It turned out that organisms that everyone considered fungi have fundamental differences from them at the cellular and molecular level. As Agrios writes in his textbook (Agrios, 2005), since the 1990s oomycetes have ceased to be regarded as true fungi. And Alexopoulos and co-authors (Alexopoulos et al., 1996) in their fundamental work Introductory Mycology state directly that oomycetes do not have a close phylogenetic relationship with fungi, and their similarity is the result of convergent evolution.

Three “pillars” of difference: why oomycetes are not fungi

To understand why systematics placed oomycetes in a completely different corner of the tree of life, let us identify three key differences. They concern the cell wall, the organization of hereditary material, and the structure of locomotor organelles.

1. Cell wall: cellulose versus chitin.

This is perhaps the best-known and most easily remembered difference. The cell wall of true fungi consists mainly of chitin—the same material from which the exoskeleton of insects and crustaceans is made. In oomycetes, however, the main structural component of the wall is cellulose (Agrios, 2005; Alexopoulos et al., 1996). Cellulose is a polymer of glucose, which we are accustomed to seeing in plant cell walls. Because of this, oomycetes are sometimes called “cellulose fungi.” The presence of cellulose instead of chitin is a fundamental biochemical difference that indicates a different origin. Some oomycetes, for example from the order Leptomitales, may contain small amounts of chitin, but this is rather the exception that proves the rule (Alexopoulos et al., 1996).

2. Nuclear cycle: diploid vegetative mycelium.

The second important difference concerns genetics. In most true fungi, the vegetative (that is, growing and feeding) mycelium is haploid. This means that each cell contains one set of chromosomes. The diploid stage in them is usually represented only by the zygote, which quickly divides by meiosis. In oomycetes, the opposite is true. Their vegetative mycelium is diploid. Each cell contains a double set of chromosomes. Meiosis in them occurs not immediately after zygote formation but in specialized organs—gametangia—before gamete formation (Alexopoulos et al., 1996). This brings them closer to animals and some other eukaryotes, but not to fungi.

3. Zoospores: two flagella of different types.

The third difference is the structure of the organs of movement. Oomycetes produce zoospores—motile cells that can swim in water. Each zoospore has two flagella located at the anterior end (apically). One of them is long, feathery, the so-called “tinsel” flagellum, covered with fine hairs. It is directed forward. The second is short, smooth, the “whiplash” flagellum, directed backward. This heterokont (different-flagella) structure is unique and is a key feature for the entire large group of organisms (Alexopoulos et al., 1996; Mauseth, 2017).

It was precisely this feature—heterokonty—that gave the name to the entire supergroup to which oomycetes belong.

Modern phylogenetic position: from fungi to stramenopiles

So where is the place of oomycetes in the modern system of the organic world? Thanks to DNA sequence analysis, primarily ribosomal RNA genes, scientists were able to construct an objective phylogenetic tree.

The result was stunning for traditional mycology. Oomycetes are not merely not fungi. They belong to a completely different branch of eukaryotes called SAR (Stramenopiles + Alveolata + Rhizaria) and, specifically, to the supergroup Stramenopiles or Heterokonta (Mauseth, 2017). This same group includes brown algae, diatoms, golden algae, and other organisms, most of which are photosynthetic. Oomycetes are a heterotrophic branch of this group that has lost chloroplasts (Alexopoulos et al., 1996; Mauseth, 2017).

Imagine: the closest relatives of Phytophthora are not button mushrooms or yeast but giant brown algae—kelps—and microscopic diatoms. That is why the name Pseudofungi—“false fungi”—was proposed for oomycetes, to emphasize their external similarity to fungi while completely lacking kinship.

Summary

Let us sum up the first chapter. We have established that:

1. Oomycetes were historically considered fungi because of mycelium-like growth and heterotrophic nutrition.

2. Modern science has proven that they are an independent evolutionary lineage belonging to Stramenopiles (Heterokonta).

3. The key differences between oomycetes and true fungi are:

• A cellulose cell wall instead of a chitinous one.
• A diploid vegetative mycelium.
• The presence of two heterokont zoospores.
• The closest relatives of oomycetes are brown and diatom algae, not fungi.

Understanding this fundamental fact is the key to all the subsequent material. It explains why oomycetes are so dangerous for plants and why they are so difficult to control with chemical methods that work against true fungi. In the next chapter we will examine in detail their systematics and phylogeny in order to see the full diversity of these “false fungi.”

2.1. Place in the system of eukaryotes: from kingdoms to supergroups

Traditional systematics, which you may have encountered in school, divided all living things into five kingdoms: Prokaryotes, Protists, Fungi, Plants, and Animals. In this scheme, oomycetes were placed in the kingdom Fungi or, in older works, in the kingdom Protists as “fungus-like protists” (Alexopoulos et al., 1996). However, modern phylogenetics, based on comparison of DNA sequences, has completely revised these ideas.

Today we use a system in which all eukaryotic organisms are divided into several large supergroups. Oomycetes belong to the supergroup SAR, whose name is formed from the first letters of the three groups included in it: Stramenopiles (or Heterokonta), Alveolata, and Rhizaria (Mauseth, 2017). Within SAR, oomycetes belong to Stramenopiles—a group also called Heterokonta because of the heterokont (different-flagella) structure of the zoospores.

Stramenopiles is a huge and diverse group. Besides oomycetes, it includes:

• Brown algae (Phaeophyceae)—giant marine plants such as kelp and Macrocystis.
• Diatoms (Bacillariophyta)—microscopic algae with a silica shell.
• Golden algae (Chrysophyceae).
• Yellow-green algae (Xanthophyceae).
• Hyphochytriomycetes (Hyphochytriomycota)—close relatives of oomycetes, also heterotrophs.

All these organisms are united by common origin and a number of key features, the main one being the presence of two different flagella in motile cells (Mauseth, 2017). Oomycetes are the only large group of Stramenopiles that has completely lost the ability to photosynthesize and switched to a heterotrophic way of life, becoming parasites and saprotrophs.

2.2. Superkingdom Pseudofungi: “false fungi”

For the group uniting oomycetes and hyphochytriomycetes, the name Pseudofungi—“false fungi”—was proposed (Alexopoulos et al., 1996). This name emphasizes their external similarity to true fungi while completely lacking phylogenetic kinship. Within this lecture we will focus on the phylum Oomycota (or simply Oomycetes), which includes all the main phytopathogenic representatives.

2.3. Classification of Oomycota: orders and genera

The class Oomycetes is divided into several orders. In the context of plant pathology, four of them are most important (Alexopoulos et al., 1996; Agrios, 2005):

1. Saprolegniales—saprolegnialean oomycetes. Mainly aquatic saprotrophs, but there are also parasites of animals. A typical representative is Saprolegnia.

2. Pythiales—pythialean oomycetes. They include soil saprotrophs and facultative plant parasites. The main genus is Pythium. Modern systematics often also places the genus Phytophthora here.

3. Peronosporales—peronosporalean oomycetes. Obligate plant parasites causing downy mildews. The main genera are Plasmopara, Peronospora, Pseudoperonospora, Bremia.

4. Albuginales—albuginalean oomycetes. Obligate parasites causing white rust. The main genus is Albugo.

Below is a brief characterization of the main genera that we will examine in detail in the following chapters.

• Saprolegnia. An aquatic oomycete, a saprotroph, but it can parasitize fish and eggs. A model object for studying the biology of oomycetes (Alexopoulos et al., 1996).
• Pythium. A soil organism. It causes blackleg, root rots, and damping-off of seedlings of many crops. It has a well-developed aseptate mycelium. Zoospores are formed in vesicles (Agrios, 2005).
• Phytophthora. “Plant destroyer”—that is how the name of this genus is translated. It includes more than 100 species, many of which are extremely dangerous pathogens. Phytophthora infestans causes late blight of potato and tomato. Other species affect soybean, cacao, fruit trees, causing root and stem rots (Agrios, 2005; Campos and Ortiz, 2020).
• Plasmopara. An obligate parasite. Plasmopara viticola is the causal agent of grape downy mildew, one of the most destructive diseases of this crop (Agrios, 2005).
• Peronospora and Pseudoperonospora. Obligate parasites causing downy mildews. Peronospora tabacina affects tobacco (blue mold), Pseudoperonospora cubensis affects cucumber and other cucurbits (Agrios, 2005).
• Bremia. Bremia lactucae is the causal agent of lettuce downy mildew (Agrios, 2005).
• Albugo. Albugo candida causes white rust of crucifers (cabbage, radish, mustard) (Agrios, 2005).

2.4. Molecular and biochemical differences from true fungi

The external similarity of oomycetes to fungi is limited to the morphology of the mycelium. At the molecular and biochemical level, the differences are fundamental. These differences are important to know because they explain why many antifungal drugs do not act on oomycetes.

1. Cell wall. As already mentioned, in oomycetes it consists of cellulose and β-glucans, while in true fungi it consists of chitin. This difference underlies the action of many fungicides. For example, preparations inhibiting chitin synthesis (chitin synthase) are absolutely useless against oomycetes, since they do not have this enzyme. Instead, they use cellulose synthase (Agrios, 2005; Alexopoulos et al., 1996).

2. Lysine synthesis pathway. The amino acid lysine is synthesized in fungi via the α-aminoadipic acid pathway, while in oomycetes it is synthesized via the diaminopimelic acid pathway, which is characteristic of plants and some bacteria (Alexopoulos et al., 1996). This is another proof of their evolutionary closeness to stramenopiles rather than to fungi.

3. Sterols. True fungi use ergosterol to build membranes. Most fungicides from the azole group (triazoles, imidazoles) inhibit ergosterol synthesis. Oomycetes either do not synthesize sterols at all or use other sterols, for example fucosterol. Therefore, azole fungicides are ineffective against them (Agrios, 2005; Alexopoulos et al., 1996).

4. Storage nutrients. Fungi store glycogen, while oomycetes store mycolaminarin (a water-soluble β-1,3-glucan), which is close to laminarin of brown algae (Alexopoulos et al., 1996).

5. Mitochondrial cristae. In oomycetes, mitochondrial cristae are tubular, while in true fungi they are plate-like (Alexopoulos et al., 1996).

6. Composition of cell walls. Besides cellulose, the walls of oomycetes contain the amino acid hydroxyproline, which also distinguishes them from fungi (Alexopoulos et al., 1996).

These biochemical and molecular features convincingly prove that oomycetes are an independent branch of evolution, and their unification with fungi was artificial, based only on external similarity.

2.5. Significance for practice

Understanding the phylogenetic position and systematics of oomycetes has direct practical significance.

First, diagnostics. Knowing that oomycetes have a cellulose wall, we can use specific staining methods or molecular probes to detect them, distinguishing them from true fungi.

Second, choice of fungicides. As we have already noted, most classical fungicides do not work against oomycetes. Special preparations have been developed to control them: metalaxyl, mancozeb, cymoxanil, fosetyl aluminum. Their action is based on inhibiting RNA synthesis, cellular respiration, or cellulose synthase (Agrios, 2005). For example, metalaxyl suppresses ribosomal RNA synthesis, while cymoxanil disrupts cellulose synthesis.

Third, quarantine. Many oomycete species, such as Phytophthora ramorum (the causal agent of sudden oak death) and P. kernoviae, are quarantine objects. Their accurate identification is critically important for preventing introduction into new regions (Campos and Ortiz, 2020).

Summary

Thus, we have established:

1. Oomycetes belong to the supergroup SAR, group Stramenopiles (Heterokonta), and are “false fungi” (Pseudofungi).

2. Their closest relatives are brown and diatom algae, not fungi.

3. The class Oomycetes includes the orders Saprolegniales, Pythiales, Peronosporales, and Albuginales. The most important phytopathogenic genera are Phytophthora, Pythium, Plasmopara, Peronospora, Pseudoperonospora, Bremia, Albugo.

4. Molecular-biochemical differences from fungi (cellulose wall, diaminopimelic acid pathway of lysine synthesis, absence of ergosterol, mycolaminarin, tubular mitochondrial cristae) explain why many antifungal preparations do not work against oomycetes.

5. Knowledge of oomycete systematics is necessary for correct diagnostics, choice of specific fungicides, and quarantine measures.

3.1. Vegetative body: aseptate multinucleate mycelium

The basis of the vegetative body of oomycetes, as in true fungi, is the mycelium—a system of branching filaments called hyphae. However, the structure of this mycelium has fundamental differences.

In most true fungi, hyphae are divided by transverse septa into individual cells, each containing one or several nuclei. In oomycetes, hyphae are aseptate. This means that they are long, continuous tubes within which cytoplasm with numerous nuclei moves freely. This type of mycelium is called coenocytic (from Greek koinos—common, kytos—cell) (Alexopoulos et al., 1996). Septa in oomycetes are formed only to separate reproductive organs (sporangia, gametangia) from the rest of the mycelium or to plug old, emptied sections of hyphae.

This structure ensures rapid growth and efficient distribution of nutrients along the entire length of the mycelium. It is precisely the coenocytic mycelium that allows Phytophthora infestans to fill the entire intercellular space of a potato leaf within a few days.

Hyphae of oomycetes usually grow apically (at the tip), branch at right angles, and have a diameter of 2 to 10 micrometers, although in some species they can reach 100 micrometers (Alexopoulos et al., 1996). The cell wall, as we remember, consists of cellulose and β-glucans.

3.2. Reproduction: asexual and sexual

Oomycetes reproduce both asexually and sexually. The ratio of these methods and their role in the life cycle differ among orders, but the general principles are the same.

3.3. Ecological groups of oomycetes

Oomycetes have mastered a wide range of ecological niches. They can be divided into three main groups:

1. Aquatic saprotrophs. They inhabit freshwater bodies and feed on remains of plants and animals. Typical representatives are Saprolegnia, Achlya. They play an important role in the decomposition of organic matter in aquatic ecosystems (Alexopoulos et al., 1996).

2. Soil saprotrophs and facultative parasites. They live in soil, feeding on dead plant remains. Upon contact with a weakened or young plant, they can switch to parasitism. This group includes Pythium and some species of Phytophthora (Agrios, 2005).

3. Obligate plant parasites. They are unable to grow on artificial media and are completely dependent on a living host. These are all representatives of the order Peronosporales (Plasmopara, Peronospora, Pseudoperonospora, Bremia) and Albuginales (Albugo) (Agrios, 2005).

3.4. Conditions favorable for development

The development of oomycetes, like that of any organisms, depends on environmental factors. The key ones for them are:

1. Humidity. Oomycetes are aquatic organisms by nature. Even terrestrial forms require droplet moisture on the plant surface for infection. Zoospores can move only in a water film. Therefore, late blight, downy mildew, and downy mildews are most rampant during rainy, humid periods (Agrios, 2005).

2. Temperature. Optimal temperatures vary among species. Phytophthora infestans is most active at 15–22 °C. Pythium prefers cooler soils (Agrios, 2005).

3. Presence of a host. For obligate parasites this is a mandatory condition. For facultative ones it is desirable but not strictly mandatory.

4. Soil acidity. Some species, for example Pythium, develop better in acidic soils.

3.5. Significance for practice

Understanding the biology and ecology of oomycetes gives us keys to managing them.

First, forecasting epidemics. Knowing that droplet moisture and a certain temperature are needed for infection, we can use weather data to predict outbreaks of late blight and other diseases. Forecast systems such as Blitecast are based on this (Agrios, 2005).

Second, agronomic practices. Soil drainage, avoiding overhead irrigation, and correct choice of sowing dates all reduce humidity and hinder the spread of zoospores.

Third, breeding. Knowing that the sexual process leads to the appearance of new races forces breeders to seek resistant varieties that do not lose resistance quickly.

Fourth, control of aquatic oomycetes. In aquaculture, antiseptics are used against saprolegniosis and water cleanliness is maintained.

Summary

Thus, in this chapter we have examined:

1. The vegetative body of oomycetes—aseptate coenocytic mycelium growing apically.

2. Asexual reproduction—by zoospores (in aquatic and some terrestrial forms) or conidia (in specialized terrestrial forms).

3. Sexual reproduction—with the formation of oospores, resting stages capable of surviving for years. The sexual process can be homothallic or heterothallic.

4. Ecological groups: aquatic saprotrophs, soil saprotrophs and facultative parasites, obligate plant parasites.

5. Aquatic oomycetes can be pathogens of animals (fish, crayfish).

6. Humidity and temperature are critically important for the development of oomycetes.

In the next chapter we will move on to specific representatives of phytopathogenic oomycetes and examine their role in diseases of agricultural crops.

4.1. Phytophthora infestans—late blight of potato and tomato

Phytophthora infestans is the best-known and perhaps the most dangerous phytopathogenic oomycete. Its name translates as “plant destroyer,” and this is no exaggeration. This pathogen causes late blight (or late rot) of potato and tomato, a disease that became the cause of one of the largest humanitarian catastrophes in history—the Irish potato famine of 1845–1849 (Agrios, 2005; Campos and Ortiz, 2020).

4.2. Other species of Phytophthora

The genus Phytophthora includes more than 100 species, many of which are dangerous pathogens. Besides P. infestans, the most significant are:

Phytophthora capsici—affects pepper, tomato, eggplant, cucurbits. It causes root and stem rots and fruit blight. It is especially dangerous under conditions of high humidity and temperature (Coyotl-Pérez et al., 2025).

Phytophthora nicotianae (syn. P. parasitica)—causes root and stem rots, as well as fruit rot in tomato, tobacco, and citrus. It affects plants in the field and in greenhouses (Blancard, 2012).

Phytophthora cinnamomi—one of the most dangerous pathogens in the world. It affects more than 1000 plant species, including avocado, pineapple, eucalyptus, oak. It causes root rot and death of trees. In Australia it destroyed significant areas of eucalyptus forests (Agrios, 2005).

Phytophthora ramorum—the causal agent of “sudden oak death.” It was first detected in California and Oregon in the 1990s. It affects oaks, rhododendrons, and other plants. It causes cankers on trunks that exude a dark liquid. The disease leads to rapid death of trees. It is a quarantine object (Agrios, 2005; Campos and Ortiz, 2020).

Phytophthora fragariae—the causal agent of red stele root rot of strawberry. It affects roots and causes reddening of the stele (central cylinder). It leads to stunting and death of plants (Agrios, 2005).

Phytophthora cactorum—causes root and crown rot of fruit trees (apple, pear, stone fruits). It also affects strawberry and other crops (Grove et al., 2003; Gull, 2023).

4.3. Pythium—blackleg and root rots

The genus Pythium includes more than 120 species inhabiting soil and water. Most of them are saprotrophs, but many are facultative plant parasites (Agrios, 2005; Alexopoulos et al., 1996).

4.4. Plasmopara viticola—grape downy mildew

Plasmopara viticola is an obligate parasite causing downy mildew of grape. It is one of the most destructive diseases of viticulture (Agrios, 2005).

4.5. Peronospora and Pseudoperonospora—downy mildews

These genera include obligate parasites causing downy mildews on various crops.

Peronospora tabacina—the causal agent of blue mold of tobacco. It affects leaves, causing yellowish spots that are then covered with a gray-blue coating. The disease can destroy the tobacco harvest. In 1979, an epidemic of blue mold in the USA and Canada led to losses of hundreds of millions of dollars (Agrios, 2005).

Pseudoperonospora cubensis—the causal agent of downy mildew of cucurbits (cucumbers, melons, pumpkins). It affects leaves, causing angular yellow spots limited by veins. On the lower side a gray-violet coating forms. The disease leads to rapid drying of leaves and reduced yield (Agrios, 2005; Blancard, 2012).

Peronospora destructor—the causal agent of downy mildew of onion. It affects leaves, causing yellowing and death. It can lead to significant losses in onion yield (Agrios, 2005).

4.6. Bremia lactucae—lettuce downy mildew

Bremia lactucae is an obligate parasite causing lettuce downy mildew. The disease manifests as yellow spots on the upper side of the leaf and a white coating on the lower side. Affected leaves become unsuitable for sale. The disease is especially dangerous under conditions of high humidity and moderate temperature (Agrios, 2005).

Sporangiophores of Bremia have characteristic dichotomous branching ending in cup-shaped expansions (apophyses), on which sporangia form. This is an important diagnostic feature (Agrios, 2005; Alexopoulos et al., 1996).

4.7. Albugo candida—white rust of crucifers

Albugo candida is an obligate parasite causing white rust of crucifers (cabbage, radish, mustard, rapeseed). The disease manifests as white, shiny pustules on leaves, stems, and flower stalks. Chains of sporangia form under the epidermis. Upon maturation the epidermis ruptures, and the sporangia are released. Affected organs are deformed, and flowers are sterile (Agrios, 2005; Alexopoulos et al., 1996).

Albugo is an obligate parasite. It overwinters in the form of oospores in plant tissues. In spring the oospores germinate, forming zoospores that infect young plants. During summer it spreads by means of sporangia carried by wind (Agrios, 2005).

Control measures include crop rotation, destruction of plant residues, use of resistant varieties, and fungicides (Agrios, 2005).

4.8. Significance for practice

The diversity of phytopathogenic oomycetes is enormous, but all of them are united by common features of biology:

• Droplet moisture is necessary for infection.
• They are not sensitive to most classical fungicides that act on true fungi.
• Specific preparations have been developed to control them (metalaxyl, cymoxanil, fosetyl aluminum, mancozeb).
• Resistance to systemic fungicides develops quickly, requiring rotation of preparations.
• Resistant varieties are the most promising and ecologically friendly path of protection.

Understanding the biology and ecology of each specific pathogen allows choosing the correct protection strategy and minimizing crop losses.

Summary

In this chapter we examined:

1. Phytophthora infestans—the causal agent of late blight of potato and tomato. History, symptoms, biology, epidemiology, control measures.

2. Other species of Phytophthora—P. capsici, P. nicotianae, P. cinnamomi, P. ramorum, P. fragariae, P. cactorum.

3. Pythium spp.—causal agents of damping-off, root rots, and soft rots.

4. Plasmopara viticola—the causal agent of grape downy mildew. History of the discovery of Bordeaux mixture.

5. Peronospora and Pseudoperonospora—downy mildews of tobacco, cucurbits, onion.

6. Bremia lactucae—lettuce downy mildew.

7. Albugo candida—white rust of crucifers.

In the next chapter we will examine in detail why knowledge of oomycete systematics is critically important for choosing fungicides and plant protection strategy.

5.1. Fundamental cause: different targets

Let us recall the key biochemical difference between oomycetes and true fungi. The cell wall of fungi consists of chitin, while the cell wall of oomycetes consists of cellulose (Agrios, 2005; Alexopoulos et al., 1996). This difference underlies the action of an entire class of fungicides.

Many modern fungicides, especially systemic ones, act on chitin synthase—the enzyme that builds chitin microfibrils. For example, preparations such as polyoxins and some others inhibit this enzyme. Against true fungi they are highly effective. But oomycetes do not have chitin synthase. They have cellulose synthase. Therefore, all preparations targeting chitin are absolutely useless against them (Agrios, 2005).

This is not merely a theoretical consideration. It is a practical rule: if you see angular yellow spots on cucumber leaves and a gray-violet coating on the lower side, and you know that this is downy mildew caused by Pseudoperonospora cubensis, you should not spend money on a fungicide that works only against true powdery mildews (for example, sulfur or azoles). You must use a preparation active against oomycetes (Blancard, 2012).

5.2. Second fundamental difference: sterols

Another important class of fungicides is sterol synthesis inhibitors (DMI fungicides, or azoles). These include triazoles (difenoconazole, tebuconazole, miconazole) and imidazoles. These preparations block the enzyme C14-demethylase, which participates in the synthesis of ergosterol—the main sterol of cell membranes of true fungi. Without ergosterol, the fungal membrane loses integrity, and the cell dies (Agrios, 2005; Alexopoulos et al., 1996).

Oomycetes either do not synthesize sterols at all or use other sterols, for example fucosterol. They do not have ergosterol and, consequently, do not have a target for azole action. Therefore, all azole fungicides—among the most popular and effective against true fungi—do not work against oomycetes (Agrios, 2005; Alexopoulos et al., 1996).

This is another practical conclusion: if you see late blight on tomatoes caused by Phytophthora infestans, and you treat the plants with difenoconazole (Score) or tebuconazole (Folicur), you will not only fail to stop the disease but also lose the time during which the pathogen will destroy the harvest.

5.3. Specific preparations against oomycetes

Because oomycetes differ so greatly from fungi, a separate group of fungicides has been developed to control them, sometimes called anti-oomycete or anti-downy mildew preparations. Their targets are unique to oomycetes.

1. Metalaxyl (and its analogs, for example mefenoxam). This is a systemic fungicide from the group of phenylamides. Its mechanism of action consists in inhibiting the synthesis of ribosomal RNA. It suppresses mycelial growth and sporulation. However, resistance to it arises very quickly. In the 1980s and 1990s, resistant strains of Phytophthora infestans and Plasmopara viticola appeared in many regions. Therefore, metalaxyl is recommended for use only in mixtures with contact preparations (Agrios, 2005; Campos and Ortiz, 2020).

2. Cymoxanil. This is also a systemic preparation, but with a different mechanism of action. It disrupts the synthesis of cellulose in the cell wall of oomycetes. Since fungi do not have cellulose, this preparation is highly specific against oomycetes. It is effective against Phytophthora, Pythium, Plasmopara (Agrios, 2005).

3. Fosetyl aluminum. This is a systemic fungicide that acts on oomycetes, but its exact mechanism is not fully understood. It is assumed to inhibit the synthesis of phospholipids and glucans in the cell wall and also induces plant defense reactions. It is effective against Phytophthora and Pythium (Agrios, 2005; Campos and Ortiz, 2020).

4. Mancozeb, maneb, chlorothalonil, copper preparations. These are contact broad-spectrum fungicides. They do not penetrate the plant but protect its surface. They are effective against many fungi and oomycetes, but their action is nonspecific. They are used in mixtures with systemic preparations to broaden the spectrum and prevent resistance (Agrios, 2005).

5. Cyazofamid, fenamidone, famoxadone. These are more modern systemic preparations that act on mitochondrial respiration (complex III inhibitors). They are effective against oomycetes, but are also subject to the risk of resistance (Campos and Ortiz, 2020).

5.4. The problem of resistance and the need for rotation

Resistance is the evolutionary response of a pathogen to the use of a fungicide. Oomycetes, especially Phytophthora and Plasmopara, possess high variability and a short life cycle, which accelerates the appearance of resistant strains (Campos and Ortiz, 2020).

Example with metalaxyl. When metalaxyl was first introduced in the 1970s, it seemed a miracle preparation. But already in the 1980s resistant strains of Phytophthora infestans appeared in Europe. This happened because metalaxyl has a single-site mechanism of action—it blocks one specific enzyme. A single point mutation in the gene encoding this enzyme is enough for the pathogen to become insensitive. In contrast, multi-site preparations (mancozeb, copper) act on several targets simultaneously, and the probability of resistance appearing to them is much lower (Agrios, 2005).

Rotation strategy. To slow the appearance of resistance, it is necessary to alternate preparations with different mechanisms of action. The same systemic fungicide must not be used several times in a row. It is recommended to alternate systemic preparations with contact ones and also to use mixtures (Agrios, 2005; Campos and Ortiz, 2020).

5.5. Biological control: limitations and possibilities

Biological control is the use of living organisms or their products to suppress pathogens. In the case of oomycetes there are both successes and limitations.

Trichoderma spp. These antagonistic fungi are widely used against soil pathogens, including Pythium and Rhizoctonia. They act through mycoparasitism (parasitizing the pathogen’s hyphae), antibiosis (releasing antibiotics), and competition for nutrients and space (Carbu et al., 2016). However, Trichoderma is ineffective against Phytophthora, since Phytophthora is an obligate or facultative parasite that quickly colonizes plant tissues, and Trichoderma does not manage to suppress it. In addition, Trichoderma is sensitive to UV radiation and requires certain humidity conditions (Carbu et al., 2016).

Bacillus spp. Some species of Bacillus (for example, B. subtilis) show antagonism against Pythium and Phytophthora. They release lipopeptides that destroy the cell walls of pathogens and induce systemic resistance of the plant (Coyotl-Pérez et al., 2025). However, their effectiveness in the field is often lower than that of chemical fungicides and strongly depends on environmental conditions.

Pseudomonas spp. Fluorescent pseudomonads are also used for biocontrol. They compete for iron (release siderophores) and release antibiotics. But their effectiveness against oomycetes varies (Carbu et al., 2016).

Limitations of biocontrol. Biological control is a prophylactic method. It works when the pathogen has not yet penetrated the plant. If the disease is already developing, biopreparations cannot stop the epidemic. In addition, they are less effective than chemical fungicides and require strict adherence to application conditions (Carbu et al., 2016).

5.6. Diagnostics: the key to the right choice

Before choosing a fungicide, it is necessary to accurately identify the pathogen. An error in diagnostics leads to the wrong choice of preparation and loss of harvest.

Morphological features. For oomycetes, important diagnostic features are:

• Shape of sporangia: lemon-shaped in Phytophthora, filamentous in Pythium, dichotomously branching with apophyses in Bremia (Agrios, 2005).
• Structure of zoospores: two flagella, heterokont structure (Alexopoulos et al., 1996).
• Oospores: thick-walled, spherical, often ornamented (Agrios, 2005).

Molecular methods. For accurate identification the following are used:

• Sequencing of the ITS region of ribosomal DNA. This is a standard method for distinguishing closely related species (Campos and Ortiz, 2020).
• Sequencing of COX1 and COX2 genes (mitochondrial genes). Used for phylogenetic analysis and species identification (Campos and Ortiz, 2020).
• PCR with species-specific primers. Allows rapid detection of a specific pathogen in a sample (Campos and Ortiz, 2020).

Problems of diagnostics. Oomycetes possess high variability. There are hybrids between species, for example Phytophthora × alni, which arose as a result of crossing P. cambivora and P. fragariae. Such hybrids may have intermediate features and be resistant to those preparations that work against the parental species (Campos and Ortiz, 2020). Therefore, accurate diagnostics often requires a combination of morphological and molecular methods.

5.7. Quarantine objects: special importance of systematics

Some oomycetes are quarantine objects. This means that their introduction and spread into new regions are strictly prohibited, since they can cause catastrophic damage to agriculture and natural ecosystems.

Phytophthora ramorum—the causal agent of “sudden oak death.” It was first detected in California in the 1990s. It affects oaks, rhododendrons, chestnuts, and other plants. It causes cankers on trunks that exude a dark liquid. It leads to rapid death of trees. It is a quarantine object in Europe and North America (Campos and Ortiz, 2020; Agrios, 2005).

Phytophthora kernoviae—another quarantine species detected in Great Britain. It affects rhododendrons and beeches. It also causes cankers and death of plants (Campos and Ortiz, 2020).

Phytophthora infestans—although this species is widespread, its new, more aggressive strains (for example, the A2 type) are also the object of close attention and control (Campos and Ortiz, 2020).

Importance of systematics for quarantine. Accurate species identification is critically important for quarantine services. If a sample of an infected plant arrives at a laboratory, it is necessary to determine quickly and accurately whether the pathogen is a quarantine species. An error can lead to a dangerous pathogen being missed across the border or, conversely, to a healthy consignment being detained. Molecular methods (PCR, sequencing) allow identification within several hours (Campos and Ortiz, 2020).

5.8. Practical recommendations for the agronomist

Summing up, let us formulate practical recommendations arising from knowledge of the systematics and biology of oomycetes:

1. Know your enemy. Before choosing a fungicide, accurately identify the pathogen. Use visual diagnostics and, if in doubt, molecular methods.

2. Do not use preparations targeting chitin. Chitin synthase is a target for fungicides against true fungi. Oomycetes do not have it. Use cymoxanil (an inhibitor of cellulose synthesis).

3. Do not use azoles. Oomycetes do not synthesize ergosterol. Use metalaxyl, fosetyl aluminum, cyazofamid.

4. Rotate preparations. To slow the appearance of resistance, alternate systemic preparations with different mechanisms of action and contact fungicides. Do not use the same systemic preparation several times in a row.

5. Use forecasting. Forecast systems (Blitecast, Hyre) based on temperature and humidity allow determining optimal treatment timing and avoiding unnecessary treatments.

6. Combine methods. Chemical protection must be combined with agronomic practices (drainage, crop rotation, destruction of residues), resistant varieties, and, where possible, biocontrol.

7. Remember quarantine. If you suspect a quarantine object, immediately inform the quarantine service. Do not attempt to control it yourself.

Summary

In this chapter we answered the question of why knowledge of oomycete systematics is critically important for choosing fungicides:

1. Oomycetes are not sensitive to fungicides acting on chitin (chitin synthase) and ergosterol (azoles), due to fundamental biochemical differences.

2. Specific preparations have been developed to control them: metalaxyl (RNA synthesis inhibitor), cymoxanil (cellulose synthesis inhibitor), fosetyl aluminum (phospholipid synthesis inhibitor), cyazofamid (respiration inhibitor).

3. Resistance to systemic preparations develops quickly, which requires rotation of preparations with different mechanisms of action.

4. Biological control (Trichoderma, Bacillus) is effective against some oomycetes (Pythium) but not against Phytophthora, and works only prophylactically.

5. Accurate diagnostics (morphological and molecular) is necessary for the correct choice of preparation and quarantine measures.

6. Quarantine objects (P. ramorum, P. kernoviae) require special attention and accurate identification.

In the final chapter we will summarize everything said and once again emphasize that oomycetes are an independent evolutionary lineage, understanding of which is the basis of effective plant protection.

6.1. Introduction: why is diagnostics of oomycetes difficult?

Diagnostics of oomycetes involves a number of difficulties that distinguish it from diagnostics of true fungi.

First, many oomycetes are obligate parasites. They do not grow on artificial nutrient media, which makes it impossible to isolate them in pure culture and study them by standard mycological methods (Agrios, 2005; Alexopoulos et al., 1996). They can be studied only on a living host plant or under special conditions.

Second, oomycetes possess high morphological plasticity. The shape and size of sporangia, the length of sporangiophores, and the number and arrangement of zoospores can vary depending on environmental conditions, culture age, and host plant species (Campos and Ortiz, 2020). This complicates identification by morphological features.

Third, there are many closely related species that are almost morphologically indistinguishable but differ in pathogenicity, host range, and sensitivity to fungicides. For example, species of Phytophthora from the P. citricola complex or P. cactorum can be identified only with molecular methods (Campos and Ortiz, 2020).

Fourth, hybrids between oomycete species occur in nature. For example, Phytophthora × alni is a hybrid between P. cambivora and P. fragariae. Such hybrids may possess intermediate morphological features and be resistant to those fungicides that work against the parental species (Campos and Ortiz, 2020).

Therefore, modern diagnostics of oomycetes is built on an integrated approach including:

1. Visual diagnostics of symptoms on the plant.

2. Microscopic examination of morphological structures.

3. Molecular-genetic methods for accurate species identification.

4. Biological tests (inoculation of indicator plants) to confirm pathogenicity.

6.2. Morphological diagnostics: classical methods

Despite the development of molecular methods, morphological diagnostics remains the basis of primary identification. It allows rapid determination that we are dealing with an oomycete rather than a true fungus and to suggest its genus affiliation.

6.3. Molecular-genetic methods

Morphological diagnostics is often insufficient for accurate species identification. Molecular methods come to the rescue, allowing analysis of the pathogen’s DNA.

6.4. Problems of diagnostics of oomycetes

6.5. Quarantine objects and their identification

Some oomycetes are quarantine objects. Their introduction and spread into new regions are strictly prohibited, since they can cause catastrophic damage to agriculture and natural ecosystems.

Phytophthora ramorum—the causal agent of “sudden oak death.” It was first detected in California in the 1990s. It affects oaks, rhododendrons, chestnuts, and other plants. It causes cankers on trunks that exude a dark liquid. It leads to rapid death of trees. It is a quarantine object in Europe and North America (Campos and Ortiz, 2020; Agrios, 2005).

Phytophthora kernoviae—another quarantine species detected in Great Britain. It affects rhododendrons and beeches. It also causes cankers and death of plants (Campos and Ortiz, 2020).

Importance of systematics for quarantine. Accurate species identification is critically important for quarantine services. If a sample of an infected plant arrives at a laboratory, it is necessary to determine quickly and accurately whether the pathogen is a quarantine species. An error can lead to a dangerous pathogen being missed across the border or, conversely, to a healthy consignment being detained. Molecular methods (PCR, sequencing) allow identification within several hours (Campos and Ortiz, 2020).

6.6. Example: diagnostics of Phytophthora infestans—the causal agent of potato late blight

Let us consider the diagnostics of Phytophthora infestans as an example of an integrated approach.

6.7. Practical recommendations for diagnostics

Summing up, let us formulate practical recommendations for diagnostics of oomycetes:

1. Start with visual diagnostics. Pay attention to symptoms: watery spots, white coating, brown rots. This will help suggest the genus of oomycete.

2. Use microscopy. Examine the mycelium (aseptate), sporangia (shape, mode of formation), zoospores (heterokont), oospores (ornamentation).

3. Apply molecular methods. For accurate species identification, use sequencing of ITS, COX1, COX2 or species-specific PCR.

4. Consider the possibility of hybrids. If morphological and molecular data are contradictory, check for hybrids.

5. Remember quarantine. If a quarantine object is suspected, immediately inform the quarantine service.

6. Combine methods. Only an integrated approach (visual, microscopic, molecular, biological) ensures accurate diagnostics.

Summary

In this chapter we examined:

1. Difficulties of diagnostics of oomycetes: obligate parasitism, morphological plasticity, closely related species, hybrids.

2. Morphological methods: examination of mycelium (aseptate), sporangia (shape, mode of germination), zoospores (heterokont), oospores (ornamentation), symptoms on the plant.

3. Molecular-genetic methods: sequencing of ITS, COX1, COX2, PCR with species-specific primers, RFLP, AFLP, microsatellites.

4. Problems of diagnostics: closely related species, hybrids, latent infection, misdiagnoses.

5. Quarantine objects: Phytophthora ramorum, P. kernoviae—the need for accurate identification.

6. Example of diagnostics of Phytophthora infestans: an integrated approach including visual, microscopic, and molecular methods.

7. Practical recommendations: combination of visual diagnostics, microscopy, and molecular methods for accurate identification of oomycetes.

In the final chapter we will summarize everything said and once again emphasize that oomycetes are an independent evolutionary lineage, understanding of which is the basis of effective plant protection.

7.1. Oomycetes are an independent evolutionary lineage

The main conclusion we must draw: oomycetes are not fungi. They are an independent, ancient evolutionary lineage that only externally, convergently, came to resemble fungi. Their true place in the system of the organic world is the supergroup SAR, group Stramenopiles (or Heterokonta), where their closest relatives are brown algae, diatoms, and golden algae (Alexopoulos et al., 1996; Mauseth, 2017). The name Pseudofungi—“false fungi”—was proposed to designate this group (Alexopoulos et al., 1996).

This conclusion is based on three fundamental differences:

1. Cell wall: cellulose instead of chitin.

2. Nuclear cycle: diploid vegetative mycelium.

3. Zoospores: two heterokont flagella.

These differences are not merely academic. They underlie the practical decisions that you will make every day.

7.2. Systematics and diversity

Oomycetes include several orders, of which the most important for plant pathology are Saprolegniales, Pythiales, Peronosporales, and Albuginales (Agrios, 2005; Alexopoulos et al., 1996). We examined the most important representatives:

• Phytophthora infestans—late blight of potato and tomato, the cause of the Irish famine.
• Phytophthora spp.—root and stem rots, late blights of fruit crops, soybean, cacao, sudden oak death.
• Pythium spp.—blackleg, root rots, damping-off of seedlings.
• Plasmopara viticola—grape downy mildew, the history of the discovery of Bordeaux mixture.
• Peronospora and *Pseudoperonospora*—downy mildews of tobacco, cucurbits, onion.
• Bremia lactucae—lettuce downy mildew.
• Albugo candida—white rust of crucifers.

Each of these pathogens has its own features of biology, ecology, and epidemiology. But all of them are united by one thing: they need droplet moisture for infection, and all of them are not sensitive to most classical fungicides.

7.3. Why systematics is important for choosing fungicides

This is perhaps the most important practical conclusion of our course. Knowledge of oomycete systematics directly determines the choice of plant protection strategy.

Fundamental rule: oomycetes are not sensitive to fungicides acting on chitin (chitin synthase) and ergosterol (azoles). Therefore:

• Do not use against oomycetes preparations targeting chitin (polyoxins) and azoles (difenoconazole, tebuconazole).
• Use specific preparations: metalaxyl (RNA synthesis inhibitor), cymoxanil (cellulose synthesis inhibitor), fosetyl aluminum (phospholipid synthesis inhibitor), cyazofamid (respiration inhibitor) (Agrios, 2005; Campos and Ortiz, 2020).
• Rotate preparations with different mechanisms of action to slow the appearance of resistance. Resistance to systemic preparations, especially to metalaxyl, develops very quickly (Agrios, 2005; Campos and Ortiz, 2020).
• Combine chemical protection with agronomic practices (drainage, crop rotation, destruction of plant residues), resistant varieties, and, where possible, biocontrol.
• Remember quarantine. Phytophthora ramorum and P. kernoviae are quarantine objects. If you suspect them, immediately inform the quarantine service (Campos and Ortiz, 2020).

7.4. Diagnostics is the key to the right decision

We examined that diagnostics of oomycetes is complex and requires an integrated approach:

1. Visual diagnostics of symptoms on the plant.

2. Microscopic examination of morphological structures (mycelium, sporangia, zoospores, oospores).

3. Molecular-genetic methods (sequencing of ITS, COX1, COX2, PCR with species-specific primers) for accurate species identification.

4. Biological tests (inoculation of indicator plants) to confirm pathogenicity.

Only a combination of these methods allows accurate determination of the pathogen and choice of the correct protection strategy. An error in diagnostics can lead to loss of harvest, wasted funds, and harm to the environment.

7.5. Practical significance for the agronomist

Summing up, let us formulate practical recommendations that you must remember:

1. Know your enemy. Before choosing a fungicide, accurately identify the pathogen. Use visual diagnostics and, if in doubt, molecular methods.

2. Do not use preparations targeting chitin and ergosterol. They are useless against oomycetes.

3. Use specific anti-oomycete preparations: metalaxyl, cymoxanil, fosetyl aluminum, cyazofamid.

4. Rotate preparations. Alternate systemic preparations with different mechanisms of action and contact fungicides.

5. Use forecasting. Forecast systems (Blitecast, Hyre) based on temperature and humidity allow determination of optimal treatment timing.

6. Combine methods. Chemical protection must be combined with agronomic practices, resistant varieties, and biocontrol.

7. Remember quarantine. If you suspect a quarantine object, immediately inform the quarantine service.

7.6. Prospects

Science does not stand still. Modern research on oomycetes is aimed at:

• Studying pathogen genomes to identify new targets for fungicides.
• Developing rapid diagnostic methods based on PCR and sequencing.
• Creating resistant varieties using genes from wild plant species.
• Developing biological control using antagonists and inducers of systemic resistance.
• Studying interactions of oomycetes with other microorganisms in agrocoenoses.

These studies open new possibilities for effective and ecologically safe plant protection.

7.7. Conclusion

Oomycetes are a unique group of organisms that, despite external similarity to fungi, have a completely different evolutionary history, biochemistry, and genetics. Understanding this fact is the basis for correct diagnostics and choice of plant protection strategy. Knowledge of the systematics, biology, and ecology of oomycetes allows one to:

• Accurately diagnose diseases.
• Correctly choose fungicides.
• Effectively protect the harvest.
• Minimize harm to the environment.
• Prevent the introduction of quarantine objects.