Fungi

1.1. Fungi are neither plants nor animals

For a long time in the history of biology, fungi were regarded as part of the plant kingdom. The grounds for this were: they are immobile, have a cell wall, grow apically, and reproduce by spores. However, already in the second half of the 20th century, with the development of electron microscopy, biochemistry, and molecular biology, it became obvious that this similarity is superficial, and in a number of key features fungi fundamentally differ from plants (Alexopoulos et al., 1996).

According to modern concepts, fungi are heterotrophic eukaryotic organisms that feed by absorption (osmotrophy), have chitinous cell walls (in most groups), store glycogen (not starch, as plants do), and do not contain chlorophyll (Alexopoulos et al., 1996; Webster & Weber, 2007).

Let us examine these features sequentially.

Heterotrophy. Fungi are incapable of photosynthesis. They obtain carbon and energy by decomposing ready-made organic substances. This is why fungi are so important as decomposers and so dangerous as pathogens. Unlike animals, which ingest food (ingestion), fungi secrete hydrolytic enzymes outward that break down complex polymers (cellulose, lignin, proteins, chitin) into soluble monomers, which are then absorbed by the entire surface of the mycelium (Webster & Weber, 2007). This mode of nutrition is called osmotrophic (from Greek osmos — push, pressure, and trophe — nutrition). Osmotrophy determines everything: the filamentous body form (an enormous surface-to-volume ratio), powerful enzyme systems, and the need for close contact with the substrate.

Cell wall. In true fungi (Eumycota), the cell wall is built on the basis of chitin — a polymer of N-acetylglucosamine (Webster & Weber, 2007; Raven et al., 2013). Chitin is a nitrogen-containing polysaccharide that does not occur in plants (they have cellulose) and only rarely in animals (in the exoskeleton of arthropods). This is a biochemical marker that clearly delimits fungi from plants. An important exception is oomycetes (Oomycota), whose cell wall contains cellulose and glucans, but not chitin. This is precisely why oomycetes, including the causative agent of late blight Phytophthora infestans, are today considered not fungi, but a separate group within the kingdom Chromista (Stramenopila) (Agrios, 2005; Sokirko, 2019).

Storage substances. Fungi store glycogen, like animals, and not starch, like plants. This is another feature that brings them closer to animals at the biochemical level (Alexopoulos et al., 1996).

Absence of chlorophyll and plastids. Fungi have no chloroplasts or photosynthetic pigments. Even if some fungi are colored (orange, red, purple), this is due not to chlorophyll but to carotenoids, melanins, or other secondary metabolites.

1.2. Molecular data and relationships

Molecular phylogenetic studies based on comparison of 18S and 28S rRNA gene sequences, as well as other conserved genes, have shown that fungi are closer to animals than to plants (Raven et al., 2013; Webster & Weber, 2007). Fungi and animals together form the supergroup Opisthokonta (posterior-flagellate organisms), characterized by a single posterior flagellum in motile cells (in fungi it is preserved only in chytrids). Plants belong to another supergroup — Archaeplastida.

It is believed that fungi diverged from the common ancestor with animals approximately 900–1500 million years ago (Webster & Weber, 2007; Raven et al., 2013). The oldest fossil remains resembling fungi date to the Lower Cambrian (about 544 million years ago), and well-preserved fungi close to modern chytrids and glomeromycetes have been found in Devonian deposits (about 400 million years ago) (Raven et al., 2013; Webster & Weber, 2007).

Thus, fungi are a separate kingdom (Fungi, or Mycota), equal in rank to the kingdoms Plantae (plants), Animalia (animals), Chromista (chromists, including oomycetes), and Protozoa (protozoans, including slime molds) (Sokirko, 2019; Webster & Weber, 2007).

It should be emphasized that in a broad sense, “fungi” often refers to all heterotrophic osmotrophic organisms with a mycelial structure, including oomycetes. However, from the standpoint of modern systematics, this is an assemblage ecological group, not a natural taxon. In our course we will adhere to a strict phylogenetic approach: oomycetes are considered separately, in the kingdom Chromista, although they are studied in the same module as fungi because of their enormous importance for the agrosphere (Sokirko, 2019).

1.3. Diversity and ecological role of fungi

Fungi are one of the most numerous groups of living organisms. It is estimated that there are from 1.5 to 5 million species of fungi on Earth, of which only about 100–120 thousand have been described (Webster & Weber, 2007; Alexopoulos et al., 1996). This means that we know only a small part of fungal diversity. About 1200 new species are described annually (Raven et al., 2013).

The ecological importance of fungi is enormous. Together with heterotrophic bacteria, they are the main decomposers of the biosphere. They decompose organic remains — fallen leaves, wood, animal corpses — and return carbon, nitrogen, phosphorus, and other elements to the soil, making them available to plants. Without fungi, the cycling of substances in nature would be impossible (Raven et al., 2013; Webster & Weber, 2007).

The role of fungi in the decomposition of wood is especially important. Neither animals nor most bacteria are capable of effectively destroying lignin and cellulose. Fungi are the only organisms that largely carry out this process, secreting powerful oxidative enzymes (laccases, peroxidases). This is why fungi determine the rate of decomposition of forest litter and the release of carbon in forest ecosystems (Raven et al., 2013; Lambers & Oliveira, 2019).

Fungi also form symbiotic associations with plants — mycorrhiza (from Greek mykes — fungus and rhiza — root). About 85–90% of all vascular plants form mycorrhiza with fungi (Lambers & Oliveira, 2019; Raven et al., 2013). Mycorrhizal fungi increase the absorbing surface of roots, supply plants with phosphorus, nitrogen, and other poorly available elements, and also protect against pathogens. In return, they receive carbohydrates from the plant. We will discuss this in detail in a separate lecture.

Finally, fungi can be parasites of plants, animals, and humans. More than 10,000 species of fungi cause plant diseases (Agrios, 2005). Among them are the causative agents of rust, smut, scab, fusarioses, late blight (the latter is an oomycete), powdery mildew, and many other diseases. Pathogenic fungi annually destroy a significant part of the world harvest of agricultural crops, and some of them (for example, ergot) can also be dangerous to humans because of mycotoxins.

1.4. Importance of fungi for the agrosphere

For an agronomist, the importance of fungi is multifaceted. Five main aspects can be distinguished.

1. Phytopathogens. Fungi and fungus-like organisms (oomycetes) are the main causative agents of diseases of agricultural crops. It is estimated that crop losses from fungal diseases reach 10–20% of world food production, and in some years and regions — significantly more (Agrios, 2005). Examples include potato late blight (Phytophthora infestans — an oomycete), which caused the Irish famine of the 1840s; rice blast (Magnaporthe oryzae); Fusarium wilt (Fusarium oxysporum); gray mold (Botrytis cinerea); apple scab (Venturia inaequalis); ergot of cereals (Claviceps purpurea) (Agrios, 2005; Campos & Ortiz, 2020). In addition to direct crop losses, phytopathogenic fungi produce mycotoxins — poisonous secondary metabolites dangerous to humans and animals. Aflatoxins (Aspergillus flavus), fumonisins (Fusarium moniliforme), deoxynivalenol (Fusarium graminearum) are only some of them (Agrios, 2005; Raven et al., 2013).

2. Mycorrhizal symbionts. As already mentioned, mycorrhiza plays a key role in plant nutrition. For an agronomist, this means that mycorrhizal fungi can increase crop productivity, improve phosphorus and other element uptake, and increase resistance to drought and pathogens. Inoculation with mycorrhizal preparations (for example, based on Glomus intraradices) is increasingly used in organic farming and nursery management (Lambers & Oliveira, 2019). We will return to this in the lecture on Glomeromycota.

3. Decomposers and biodegradation. Fungi decompose plant residues, straw, manure, promoting humus formation and increasing soil fertility. Some fungi (for example, Trichoderma) are used for bioremediation of contaminated soils, decomposition of xenobiotics and pesticides (Webster & Weber, 2007; Agrios, 2005).

4. Biocontrol. Many fungi are antagonists of phytopathogens or entomopathogens. Trichoderma harzianum suppresses the growth of root rot pathogens; Beauveria bassiana and Metarhizium anisopliae infect insect pests and are used as biological insecticides; Entomophthora muscae destroys flies (Webster & Weber, 2007; Raven et al., 2013). Fungus-based biocontrol is a rapidly developing area of plant protection.

5. Food and medicinal species. Fungi have long been used by humans. Yeast Saccharomyces cerevisiae is the basis of baking, winemaking, and brewing. Penicillium roqueforti and P. camemberti give cheeses their characteristic taste and aroma. Aspergillus oryzae is used for fermentation of soy (soy sauce, miso). Many cap mushrooms (button mushroom, oyster mushroom, shiitake) are cultivated on an industrial scale. Antibiotics (penicillin from Penicillium chrysogenum), immunosuppressants (cyclosporine from Tolypocladium inflatum), statins, and other medicinal preparations are obtained from fungi (Raven et al., 2013; Alexopoulos et al., 1996).

1.5. Key concepts and terms

Before moving on to systematics, let us fix the basic terms that will be used throughout the course.

Mycelium — the aggregate of hyphae (filaments) of a fungus. Hypha — an individual filament. Hyphae can be septate (with cross walls) or aseptate (without cross walls, coenocytic). In most true fungi (Ascomycota, Basidiomycota), hyphae are septate, but the septa have a central pore through which organelles and even nuclei can pass (Webster & Weber, 2007).

Plasmodium — a multinucleate mass of protoplasm without cell walls, characteristic of slime molds and some chytrids (Raven et al., 2013).

Spore — a specialized cell for reproduction and dispersal. Spores can be asexual (mitotic) and sexual (formed as a result of meiosis). In fungi, zoospores (motile, with flagella), sporangiospores (in sporangia), conidia (exogenous, on conidiophores), ascospores (in asci), basidiospores (on basidia), zygospores, and oospores (resting sexual spores) are distinguished (Alexopoulos et al., 1996; Webster & Weber, 2007).

Teleomorph — the sexual stage (the set of features of sexual reproduction). Anamorph — the asexual stage. Holomorph — the aggregate of all stages of the life cycle (Webster & Weber, 2007; Sokirko, 2019). In older literature, the teleomorph was called the “perfect” stage, and the anamorph — the “imperfect” stage. Hence the historical name Deuteromycota (Fungi Imperfecti) — fungi in which the sexual stage is unknown. Today it has been proven that most deuteromycetes are anamorphs of ascomycetes or basidiomycetes (Webster & Weber, 2007; Alexopoulos et al., 1996).

Septum — a cross wall in a hypha. In ascomycetes the septum is simple, with a central pore; in basidiomycetes it is dolipore (with a barrel-shaped swelling and parenthesomes) (Webster & Weber, 2007; Raven et al., 2013).

Haustorium — a specialized hypha of a parasitic fungus that penetrates the host cell to absorb nutrients (Agrios, 2005; Raven et al., 2013).

Appressorium — a flattened enlargement of a hypha used for attachment to the host surface and penetration inside (Agrios, 2005).

Sclerotium — a hard resting structure consisting of a plexus of hyphae, serving to survive unfavorable conditions (Webster & Weber, 2007; Agrios, 2005).

1.6. Modern phylogeny of fungi: general overview

In the next lecture we will examine the modern system of fungi in detail, but already now let us outline its contours. Until the 1990s, fungi were divided into four main classes: Chytridiomycetes, Zygomycetes, Ascomycetes, Basidiomycetes, and also the artificial group Deuteromycetes (imperfect fungi). This classification was based predominantly on the morphology of sexual structures (Alexopoulos et al., 1996).

Molecular data of the late 20th and early 21st centuries radically changed our understanding. It turned out that:

— Zygomycota is an assemblage group, including several independent evolutionary lineages that are now separated into distinct phyla: Mucoromycota, Glomeromycota, Entomophthoromycota, and others (Webster & Weber, 2007; Spatafora et al., 2016).

— Chytridiomycota is a basal group of fungi that has retained flagellate stages. Together with Blastocladiomycota and Neocallimastigomycota, they form the early branches of the fungal tree (Webster & Weber, 2007; Raven et al., 2013).

— Microsporidia — intracellular parasites of animals, previously considered protozoans, are now regarded as extremely reduced fungi close to chytrids or zygomycetes (Raven et al., 2013; Webster & Weber, 2007).

— Glomeromycota — a separate phylum including all arbuscular mycorrhizal fungi (Lambers & Oliveira, 2019; Webster & Weber, 2007).

— Ascomycota and Basidiomycota — the largest phyla, united in the subkingdom Dikarya (dikaryotic fungi), characterized by a long dikaryotic phase in the life cycle (Webster & Weber, 2007; Raven et al., 2013).

Thus, the modern phylogeny of fungi looks approximately as follows (simplified):

Fungi (Mycota)

• Chytridiomycota
• Blastocladiomycota
• Neocallimastigomycota
• Microsporidia
• Glomeromycota
• Mucoromycota (including Mucorales, Umbelopsidales, Mortierellales)
• Ascomycota
• Basidiomycota

We will follow this scheme in our course, with necessary caveats and simplifications for agricultural specialties (Webster & Weber, 2007; Sokirko, 2019).

Introduction

In the previous chapter we established that fungi are a separate kingdom of living nature, fundamentally differing from plants and animals in type of nutrition, cell wall composition, and molecular-genetic characteristics. Now we face the task of understanding how this enormous diversity is organized into a system. What groups of fungi exist, how are they related to each other, and what place do they occupy in modern phylogenetic classification?

Without understanding the modern system of fungi, it is impossible to speak meaningfully about disease diagnostics, biocontrol, or mycorrhiza. We must clearly grasp: the traditional classification of fungi based only on morphology has become a thing of the past. It has been replaced by genosystematics (molecular systematics), which has radically restructured our ideas about the relationships of fungi (Sokirko, 2019; Webster & Weber, 2007).

2.1. Traditional classification and its limitations

Until the end of the 20th century, fungi were classified predominantly on the basis of morphological features: structure of the mycelium (septate or aseptate), type of sexual spores (zygospores, ascospores, basidiospores), and features of asexual reproduction (Sokirko, 2019; Alexopoulos et al., 1996).

In the classical system, going back to works of the late 19th and early 20th centuries, the kingdom Fungi was divided into several large groups:

• Chytridiomycetes — fungi with flagellate zoospores;
• Zygomycetes — fungi with zygospores (mucoraceous);
• Ascomycetes — sac fungi with ascospores;
• Basidiomycetes — basidial fungi with basidiospores;
• Deuteromycetes (Fungi Imperfecti) — “imperfect” fungi in which the sexual stage is unknown (Alexopoulos et al., 1996).

This system was convenient for identification, but did not reflect evolutionary relationships. Molecular studies showed that many traditional groups are polyphyletic — that is, they unite organisms that descended from different ancestors but are outwardly similar as a result of convergent evolution (Webster & Weber, 2007; Sokirko, 2019).

The most striking example is Zygomycota. Traditionally, this group included all fungi with aseptate mycelium and zygospores: mucoraceous, entomophthoraceous, glomeraceous (arbuscular mycorrhizal fungi), endogonaceous, and others. However, molecular phylogenetic data showed that this is an assemblage group consisting of several independent evolutionary lineages that diverged very long ago and are not close relatives (Webster & Weber, 2007; Spatafora et al., 2016; Sokirko, 2019).

This is precisely why modern systematics abandoned Zygomycota as a single taxon and divided it into several independent phyla: Mucoromycota, Glomeromycota, Entomophthoromycota, and others (Webster & Weber, 2007; Spatafora et al., 2016).

2.2. Molecular revolution in fungal systematics

Since the 1990s, molecular methods based on analysis of DNA, RNA, and protein sequences began to be actively used in mycology. This approach is called genosystematics or molecular systematics (Sokirko, 2019).

The main molecular markers used for phylogenetic analysis of fungi:

• 18S rRNA (small subunit ribosomal RNA) — used for comparing distantly related groups, at the level of kingdoms and phyla;
• 28S rRNA (large subunit) — for comparing groups at the level of phyla, classes, and orders;
• ITS regions (internal transcribed spacers) — for distinguishing closely related species and strains;
• Genes of β-tubulin, actin, elongation factor 1α (TEF1), RNA polymerase II (RPB2) — additional markers for refining phylogeny (Webster & Weber, 2007; Sokirko, 2019).

These methods allow:

1. Determining nucleotide sequences of individual genes or DNA regions;

2. Evaluating phylogenetic relationships of taxa of any level;

3. Testing monophyly (origin from one ancestor) or polyphyly (origin from several ancestors) of groups;

4. Estimating the age of taxa using the “molecular clock” principle (Sokirko, 2019).

According to modern data, the oldest group of fungi is chytrids. Approximately 100 million years after their appearance, zygomycetes arose. Ascomycetes and basidiomycetes appeared later — in the Devonian period, about 400 million years ago (Sokirko, 2019; Webster & Weber, 2007).

It is important to understand that molecular methods also have limitations. Gene sequences can evolve at different rates, and phylogenetic trees constructed from different genes may not coincide. Therefore, modern systematics strives to integrate molecular, morphological, ultrastructural, and biochemical data (Sokirko, 2019; Webster & Weber, 2007).

2.3. Modern system of the kingdom Fungi

According to modern concepts based on molecular phylogenetic data, the kingdom Fungi (Mycota) includes the following main phyla (divisions):

1. Chytridiomycota — chytrids;

2. Blastocladiomycota — blastoclads;

3. Neocallimastigomycota — neocallimastigomycetes;

4. Microsporidia — microsporidia;

5. Glomeromycota — glomeromycetes;

6. Mucoromycota — mucoromycetes;

7. Ascomycota — ascomycetes (sac fungi);

8. Basidiomycota — basidiomycetes.

At the same time, Ascomycota and Basidiomycota are united in the subkingdom Dikarya (dikaryotic fungi), characterized by a long dikaryotic phase in the life cycle (Webster & Weber, 2007; Raven et al., 2013).

Let us briefly consider each of these groups to obtain a general idea. We will examine them in more detail in subsequent lectures.

2.4. “Fungi” in the broad sense: oomycetes and other pseudofungi

Until now we have spoken about true fungi (Eumycota), which constitute the kingdom Fungi. However, in agronomic practice and in phytopathology, “fungi” often means a broader group of organisms, including also oomycetes (Oomycota) and some other fungus-like protists (Sokirko, 2019).

Oomycetes are a separate group in the kingdom Chromista (Stramenopila). They are outwardly similar to fungi: they have mycelium, absorb nutrients, and reproduce by spores. However, their cell wall contains cellulose, not chitin; the flagella of zoospores are heterokont (one smooth, one feathery); mitochondrial cristae are tubular, not plate-like (Sokirko, 2019; Webster & Weber, 2007).

Oomycetes include:

• Phytophthora infestans — causative agent of late blight of potato and tomato;
• Pythium — causative agent of root rots, blackleg, damping-off;
• Plasmopara viticola — downy mildew of grapevine;
• Peronospora — downy mildew (of tobacco, onion, soybean);
• Albugo candida — white rust of crucifers (Sokirko, 2019; Agrios, 2005).

Oomycetes are not fungi in the strict phylogenetic sense, but they are studied together with them because of their ecological and agronomic similarity. In our course we will consider them separately, but within the general module “Microorganisms of the Agrosphere” (Sokirko, 2019).

Besides oomycetes, “fungus-like” organisms include:

• Myxomycota (slime molds) — saprotrophs, not plant pathogens;
• Plasmodiophoromycota — intracellular parasites of plants, including Plasmodiophora brassicae — causative agent of clubroot of crucifers (Sokirko, 2019; Webster & Weber, 2007).

These groups are also considered in our course, since they cause diseases of agricultural crops.

2.5. Dikarya: union of ascomycetes and basidiomycetes

An important stage in modern fungal systematics was the separation of the subkingdom Dikarya (dikaryotic fungi), which unites Ascomycota and Basidiomycota (Webster & Weber, 2007; Raven et al., 2013).

Common features of Dikarya:

• Septate mycelium with pores;
• Long dikaryotic phase — a stage when two genetically different nuclei are present in the cell, dividing synchronously but not fusing;
• Clamp connections in basidiomycetes and crozers in ascomycetes — structures ensuring correct nuclear distribution during division;
• Ascocarps and basidiocarps — complex fruiting bodies;
• Conidia — asexual spores formed exogenously (Webster & Weber, 2007; Alexopoulos et al., 1996).

It is believed that Dikarya originated from a common ancestor approximately 400–600 million years ago (Webster & Weber, 2007). This is the youngest and most evolutionarily advanced group of fungi.

2.6. Importance of modern classification for the agronomist

Why is it important for an agronomist to know the modern classification of fungi? There are several reasons.

1. Accurate diagnosis. Determining the systematic position of the pathogen is an obligatory stage of disease diagnosis. Different groups of fungi require different approaches to protection. For example, oomycetes (Phytophthora, Pythium) are not sensitive to most azoles and strobilurins, which are effective against true fungi. To combat them, special fungicides are needed (metalaxyl, mancozeb) (Agrios, 2005; Campos & Ortiz, 2020).

2. Forecasting disease development. Knowledge of the pathogen’s life cycle (presence of resting stages, sources of infection, conditions for sporulation) allows forecasting epiphytotics. For example, Sclerotinia sclerotiorum forms sclerotia that persist in soil for up to 7 years; Claviceps purpurea — sclerotia, which germinate in spring into stromata with perithecia (Agrios, 2005; Webster & Weber, 2007).

3. Choice of protection strategy. Different groups of fungi have different sensitivity to fungicides, different resistance mechanisms, and different ecological niches. For example, Botrytis cinerea rapidly develops resistance to systemic fungicides, so rotation of preparations with different mechanisms of action is required (Agrios, 2005).

4. Use of beneficial fungi. Knowledge of systematics allows identification of mycorrhizal fungi (Glomeromycota, Basidiomycota), entomopathogens (Beauveria, Metarhizium — Ascomycota), antagonists (Trichoderma — Ascomycota) and their use in biocontrol and biofertilizers (Lambers & Oliveira, 2019; Webster & Weber, 2007).

5. Understanding mycotoxins. Different groups of fungi produce different mycotoxins. Aspergillus flavus — aflatoxins; Fusarium — fumonisins, deoxynivalenol (DON), zearalenone; Claviceps purpurea — ergot alkaloids; Penicillium — patulin, ochratoxin (Agrios, 2005; Raven et al., 2013). Knowledge of systematics helps predict the risk of product contamination.

2.7. Conclusion

Let us summarize the second lecture.

Modern classification of fungi is based on molecular phylogenetic data, which have radically restructured the traditional system. The abandonment of Zygomycota as a single group and the separation of Mucoromycota, Glomeromycota, Entomophthoromycota, and other phyla is a most important step toward a natural system.

Main phyla of the kingdom Fungi:

• Chytridiomycota, Blastocladiomycota, Neocallimastigomycota — basal groups that have retained flagellate stages (except Neocallimastigomycota, which have multiple flagella);
• Microsporidia — parasites of animals, including bees;
• Glomeromycota — arbuscular mycorrhizal fungi;
• Mucoromycota — mucoraceous fungi, saprotrophs and pathogens;
• Ascomycota and Basidiomycota — the largest phyla, united in Dikarya.

Oomycetes (Oomycota) are not fungi, but a separate group in the kingdom Chromista, yet they are studied together with fungi because of ecological and agronomic similarity.

Knowledge of systematics is necessary for an agronomist for accurate diagnosis of diseases, choice of plant protection strategy, use of beneficial fungi, and forecasting mycotoxin risks.

3.1. Key features of Ascomycota

The name “Ascomycota” comes from the Greek words askos (sac, bag) and mykes (fungus). The main distinguishing feature of this group is the ascus (sac) — a specialized cell in which ascospores are formed as a result of meiosis (Webster & Weber, 2007; Alexopoulos et al., 1996).

Let us examine the main features of ascomycetes in more detail.

Ascus and ascospores. The ascus is a cell inside which, after nuclear fusion (karyogamy), meiosis occurs, followed by mitosis, resulting in usually eight haploid ascospores (Webster & Weber, 2007; Alexopoulos et al., 1996). The number of ascospores can vary: in some species there are four (Neurospora tetrasperma), in others — more than eight (up to several hundred in some tropical species). Asci can be naked (in yeasts) or enclosed in ascocarps (fruiting bodies) (Webster & Weber, 2007).

Ascocarps. Four main types of ascocarps are distinguished (Webster & Weber, 2007; Alexopoulos et al., 1996):

• Gymnothecium — an open plexus of hyphae not completely enclosing the asci (for example, in Gymnoascus);
• Cleistothecium — a completely closed spherical fruiting body (for example, in Erysiphe, Aspergillus);
• Perithecium — a flask-shaped fruiting body with an opening (ostiole) for release of ascospores (for example, in Sordaria, Neurospora, Claviceps);
• Apothecium — an open cup-shaped or saucer-shaped fruiting body (for example, in Morchella, Peziza, Sclerotinia).

Mycelium. The mycelium of ascomycetes is septate, with simple pores in the septa. Organelles and even nuclei can pass through the pores. A characteristic feature is the presence of Woronin bodies (Woronin bodies) — protein organelles that plug the pores when a hypha is damaged (Webster & Weber, 2007; Alexopoulos et al., 1996).

Conidia. Asexual reproduction in most ascomycetes is carried out by conidia — exogenous spores that are formed on specialized hyphae — conidiophores. Conidia can be formed:

• Freely on the mycelium (for example, in Alternaria, Cladosporium);
• In sporangia (for example, in Aspergillus, Penicillium — phialides);
• In pycnidia — flask-shaped fruiting bodies (for example, in Septoria, Phoma);
• In acervuli — flat cushions (for example, in Colletotrichum).

Yeasts. Some ascomycetes (Saccharomyces, Candida) exist in a unicellular yeast form, reproducing by budding or fission. Yeasts do not form mycelium, but under certain conditions can form pseudohyphae (Webster & Weber, 2007; Raven et al., 2013).

Dikaryotic phase. Ascomycota, like Basidiomycota, are characterized by a dikaryotic phase — a stage when two genetically different nuclei are present in the cell, dividing synchronously but not fusing. In ascomycetes this phase is short and associated with the formation of ascogenous hyphae inside the ascocarp (Webster & Weber, 2007; Alexopoulos et al., 1996).

3.2. Life cycle of Ascomycota

The life cycle of ascomycetes includes sexual and asexual stages. Let us consider it using a typical representative — Pyronema omphaloides (Webster & Weber, 2007; Alexopoulos et al., 1996).

Asexual stage (anamorph). The ascospore germinates, forming a haploid mycelium. On the mycelium, conidiophores with conidia are formed, which are spread by air currents, rain, or insects. Conidia, landing on a suitable substrate, germinate and give rise to a new mycelium. The asexual stage can be repeated many times during the growing season, ensuring rapid accumulation of infection (Webster & Weber, 2007).

Sexual process. When certain conditions occur (nutrient depletion, changes in temperature, humidity), the mycelium switches to sexual reproduction. Gametangia are formed:

• Ascogonium — female gametangium, often with a trichogyne (outgrowth for receiving male nuclei);
• Antheridium — male gametangium.

Nuclei from the antheridium migrate through the trichogyne into the ascogonium. Plasmogamy occurs (fusion of cytoplasm), but not karyogamy (fusion of nuclei). The ascogonium forms ascogenous hyphae, whose cells contain dikaryons (pairs of nuclei). At the ends of ascogenous hyphae, crozers are formed, ensuring correct nuclear distribution during division. The terminal cell of the crozer becomes the ascus (Webster & Weber, 2007; Alexopoulos et al., 1996).

In the ascus, karyogamy occurs — fusion of two nuclei with formation of a diploid nucleus. Then follows meiosis, giving four haploid nuclei, and mitosis, resulting in eight haploid nuclei. Each nucleus is surrounded by cytoplasm and covered by a wall — ascospores are formed (Webster & Weber, 2007; Alexopoulos et al., 1996).

Ascospores are released from the ascus (actively ejected or passively released upon destruction of the ascocarp) and, landing in suitable conditions, germinate, giving rise to a new haploid mycelium. The cycle closes.

3.3. Pathogenic Ascomycota

Ascomycota include an enormous number of phytopathogens causing serious damage to agriculture. Let us consider the most important representatives.

3.4. Beneficial Ascomycota

Ascomycota are not only pathogens, but also the most important beneficial fungi used in the food, pharmaceutical, and biotechnological industries.

3.5. Entomopathogenic Ascomycota

Some ascomycetes are pathogens of insects and are used for biological control of pests.

3.6. Practical importance of Ascomycota for the agronomist

Ascomycota are of enormous importance for agriculture. Their role is multifaceted:

1. Phytopathogens. Ascomycota are the main causative agents of plant diseases. They cause fusarioses, scab, ergot, sclerotinia, gray mold, alternarioses, anthracnoses, rice blast, and many other diseases. Crop losses from these diseases reach 10–30%, and in some years — 50–90% (Agrios, 2005).

2. Mycotoxins. Many ascomycetes produce mycotoxins dangerous to humans and animals:

• Aflatoxins (Aspergillus flavus) — carcinogens;
• Fumonisins (Fusarium moniliforme) — neurotoxins;
• Deoxynivalenol (DON) (Fusarium graminearum) — immunosuppressant;
• Ergot alkaloids (Claviceps purpurea) — gangrene, hallucinations (Agrios, 2005; Raven et al., 2013).

3. Biocontrol. Trichoderma (Ascomycota) — antagonist of phytopathogens, used for biocontrol of root rots. Beauveria, Metarhizium — entomopathogens, used for biocontrol of insects (Webster & Weber, 2007; Raven et al., 2013).

4. Food industry. Saccharomyces (bread, wine, beer), Penicillium (cheeses), Aspergillus (soy sauce, citric acid), Morchella, Tuber (delicacies) (Raven et al., 2013).

5. Pharmaceuticals. Penicillium (penicillin), Tolypocladium inflatum (cyclosporine — immunosuppressant for organ transplantation) (Raven et al., 2013).

6. Scientific research. Saccharomyces cerevisiae, Neurospora crassa, Aspergillus nidulans — model objects of genetics, molecular biology, cell biology (Raven et al., 2013; Alexopoulos et al., 1996).

3.7. Conclusion

Ascomycota is the largest and most diverse phylum of the kingdom Fungi. Their key feature is the ascus with ascospores formed as a result of meiosis. Ascomycetes have septate mycelium with simple pores and Woronin bodies, reproduce by conidia, and form ascocarps of four types.

Among Ascomycota are the most important phytopathogens (Fusarium, Venturia, Claviceps, Sclerotinia, Botrytis, Alternaria, Colletotrichum, Magnaporthe), beneficial species (Saccharomyces, Penicillium, Aspergillus, morels, truffles), and entomopathogens (Beauveria, Metarhizium).

For an agronomist, knowledge of Ascomycota is necessary for diagnosis of diseases, choice of protection strategy, forecasting mycotoxin risks, and use of beneficial fungi in biocontrol and biotechnology.

In the next lecture we will examine Basidiomycota — the second largest phylum of fungi, including rust, smut, cap mushrooms, ectomycorrhizal symbionts, and wood decomposers.

Introduction

Basidiomycota is the second largest phylum of the kingdom Fungi, including, by various estimates, from 22,300 to 30,000 described species (Webster & Weber, 2007; Raven et al., 2013). If Ascomycota are primarily “pathogenic fungi” and “mold fungi,” then Basidiomycota are primarily cap mushrooms, polypores, rust and smut fungi, and also the most important ectomycorrhizal symbionts.

For an agronomist, Basidiomycota are of enormous importance for several reasons. On the one hand, among them are destroyers of the harvest (rust, smut, Rhizoctonia, honey fungus); on the other — indispensable symbionts, without which normal development of many woody species is impossible, and decomposers that break down wood and plant residues. In addition, Basidiomycota are a source of food products (button mushrooms, oyster mushrooms, shiitake) and biologically active compounds (Webster & Weber, 2007; Agrios, 2005).

In this lecture we will examine in detail the morphology, life cycles, and practical importance of the most important representatives of Basidiomycota.

4.1. Key features of Basidiomycota

The name “Basidiomycota” comes from the Greek words basis (base, pedestal) and mykes (fungus). The main distinguishing feature of this group is the basidium — a specialized cell on which basidiospores are formed exogenously as a result of meiosis (Webster & Weber, 2007; Alexopoulos et al., 1996).

Let us examine the main features of basidiomycetes in more detail.

Basidium and basidiospores. The basidium is a cell in which karyogamy (nuclear fusion) and meiosis occur, after which usually four haploid basidiospores are formed (Webster & Weber, 2007; Alexopoulos et al., 1996). Basidiospores are located on sterigmata — thin outgrowths of the basidium, and are actively discharged by a surface-tension catapult mechanism (Buller’s drop mechanism). Basidia can be:

• Holobasidia — not divided by septa (in cap mushrooms, polypores);
• Phragmobasidia — divided by transverse or longitudinal septa (in rust, smut, jelly fungi) (Webster & Weber, 2007).

Dolipore septa. The mycelium of basidiomycetes is septate, but the septa have a dolipore structure — a central pore surrounded by a barrel-shaped swelling, covered on both sides by parenthesomes (membrane caps). This is the most characteristic feature of Basidiomycota, distinguishing them from Ascomycota with simple pores (Webster & Weber, 2007; Raven et al., 2013).

Clamp connections. In many basidiomycetes, clamp connections are formed on the dikaryotic mycelium — special structures ensuring correct distribution of two genetically different nuclei during cell division. The clamp connection is formed as a lateral outgrowth of the hypha, into which one of the nuclei migrates; then synchronous division of both nuclei occurs, and the daughter nuclei are distributed into the daughter cells. Clamp connections are homologous to crozers of ascomycetes (Webster & Weber, 2007; Alexopoulos et al., 1996).

Dikaryotic phase. Basidiomycota are characterized by a long dikaryotic phase — a stage when two genetically different nuclei are present in the cell, dividing synchronously but not fusing. In basidiomycetes this phase dominates in the life cycle: it is the dikaryotic mycelium that forms fruiting bodies (Webster & Weber, 2007; Raven et al., 2013).

Fruiting bodies (basidiocarps). Basidiomycetes form basidiocarps — complexly organized fruiting bodies consisting of plectenchyma (false tissue). Basidiocarps can be:

• Gymenial — with an open hymenium (cap mushrooms, polypores);
• Gasteroid — with a closed hymenium (puffballs, stinkhorns, bird’s-nest fungi) (Webster & Weber, 2007; Raven et al., 2013).

Hymenium. The hymenium is the spore-bearing layer consisting of basidia and cystidia (sterile elements). In cap mushrooms the hymenium lines plates (agaricoid), tubes (polypore), spines (hydnoid), or folds (cantharelloid) (Webster & Weber, 2007).

4.2. Life cycle of Basidiomycota

The life cycle of basidiomycetes includes haploid, dikaryotic, and diploid stages, with the dikaryotic stage dominating (Webster & Weber, 2007; Alexopoulos et al., 1996).

Haploid stage. The basidiospore germinates, forming a haploid mycelium (primary mycelium). In most basidiomycetes the haploid mycelium is short-lived and does not form fruiting bodies. In some species (for example, smut fungi), the haploid stage can exist as yeast-like cells (sporidia) capable of saprotrophic growth (Webster & Weber, 2007).

Plasmogamy and dikaryotization. When two compatible haploid mycelia meet, plasmogamy occurs (fusion of cytoplasm), but not karyogamy. A dikaryotic mycelium (secondary mycelium) is formed, whose cells contain pairs of nuclei (dikaryons). The dikaryotic mycelium grows and forms fruiting bodies (Webster & Weber, 2007; Alexopoulos et al., 1996).

Karyogamy and meiosis. In the basidia formed on the dikaryotic mycelium, karyogamy occurs — fusion of two nuclei with formation of a diploid nucleus. Then follows meiosis, giving four haploid nuclei, which migrate into basidiospores (Webster & Weber, 2007; Alexopoulos et al., 1996).

Dispersal of basidiospores. Basidiospores are actively discharged from the basidium over a distance of up to 0.1–0.2 mm by the surface-tension catapult mechanism (Buller’s drop). Then they are picked up by air currents and spread over long distances. Landing in suitable conditions, basidiospores germinate, and the cycle closes (Webster & Weber, 2007; Raven et al., 2013).

4.3. Pathogenic Basidiomycota

Basidiomycota include a number of dangerous phytopathogens causing enormous damage to agriculture. Let us consider the most important representatives.

4.4. Symbiotic Basidiomycota: ectomycorrhiza

Many Basidiomycota form ectomycorrhiza (ectotrophic mycorrhiza) with roots of woody species — oak, beech, birch, pine, spruce, larch, willow, poplar, eucalyptus (Lambers & Oliveira, 2019; Raven et al., 2013).

Structure of ectomycorrhiza. The fungus forms a mantle (sheath) of hyphae around the root and a Hartig net (Hartig net) between cells of the cortex. Hyphae do not penetrate inside cells (unlike arbuscular mycorrhiza). Ectomycorrhiza changes root morphology: it thickens, branches, and loses root hairs (Lambers & Oliveira, 2019; Raven et al., 2013).

Functions of ectomycorrhiza:

• Improved nutrition: hyphae increase the absorbing surface, secrete enzymes (proteases, phosphatases) that break down organic compounds, and carboxylates that mobilize phosphorus from minerals (Lambers & Oliveira, 2019);
• Protection from pathogens: the mantle is a physical barrier; the fungus secretes antibiotics (Lambers & Oliveira, 2019);
• Resistance to stresses: increases drought resistance and salt tolerance (Lambers & Oliveira, 2019).

Most important ectomycorrhizal Basidiomycota:

• Boletus (porcini, bolete);
• Leccinum (birch bolete, orange birch bolete);
• Suillus (slippery jack);
• Cantharellus (chanterelle);
• Lactarius (milk cap, saffron milk cap);
• Russula (russula);
• Amanita (fly agaric, death cap);
• Tricholoma (tricholoma, green cavalier);
• Cortinarius (webcap) (Webster & Weber, 2007; Raven et al., 2013).

Practical use. Inoculation with ectomycorrhizal fungi is used in forest nurseries to improve survival and growth of pine, spruce, and oak seedlings. Mycorrhizal preparations based on Boletus edulis, Suillus luteus, Pisolithus tinctorius are used in reforestation and landscaping (Lambers & Oliveira, 2019; Raven et al., 2013).

4.5. Decomposers: cap mushrooms and polypores

Basidiomycota are the main decomposers of wood in forest ecosystems. They break down lignin, cellulose, hemicellulose using oxidases (laccase, peroxidase) and hydrolases (cellulase, xylanase) (Raven et al., 2013; Webster & Weber, 2007).

Types of rot:

• Brown rot — cellulose is destroyed, lignin remains (brown, brittle). Caused by polypores (Serpula lacrymans, Laetiporus sulphureus) (Webster & Weber, 2007);
• White rot — lignin and cellulose are destroyed (white, fibrous). Caused by polypores (Trametes versicolor, Pleurotus ostreatus) (Webster & Weber, 2007).

Most important decomposers:

• Trametes versicolor — turkey tail, destroyer of dead wood;
• Fomes fomentarius — tinder fungus, parasite and saprotroph of birch;
• Ganoderma applanatum — artist’s conk, wood destroyer;
• Serpula lacrymans — dry rot fungus, destroyer of wood in buildings (Webster & Weber, 2007);
• Pleurotus ostreatus — oyster mushroom, wood destroyer, edible fungus (Webster & Weber, 2007).

Ecological importance. Basidiomycota decomposers return carbon and mineral elements to the soil and maintain the cycling of substances in forest ecosystems. Without them, forest litter would not decompose, and carbon would not return to the atmosphere (Raven et al., 2013).

4.6. Edible Basidiomycota

Many Basidiomycota are edible mushrooms cultivated on an industrial scale.

Agaricus bisporus — button mushroom. The most cultivated mushroom in the world. Production — more than 3.7 million tons per year (Raven et al., 2013). Grown on compost of straw and manure.

Pleurotus ostreatus — oyster mushroom. Cultivated on straw, sawdust, corn cobs. Contains much protein, is low-calorie (Raven et al., 2013).

Lentinula edodes — shiitake. Traditional Japanese mushroom, cultivated on oak wood. Has medicinal properties (antitumor, immunomodulatory) (Raven et al., 2013).

Other cultivated species:

• Flammulina velutipes — winter mushroom (enokitake);
• Volvariella volvacea — straw mushroom;
• Grifola frondosa — maitake (Raven et al., 2013).

Nutritional value. Mushrooms are rich in protein (20–40% dry mass), vitamins (B, D), minerals (K, P, Se), dietary fiber. They are low-calorie and contain chitin, which is not digested by humans but stimulates peristalsis (Raven et al., 2013).

4.7. Practical importance of Basidiomycota for the agronomist

Basidiomycota are of enormous importance for agriculture. Their role is multifaceted:

1. Phytopathogens. Basidiomycota are causative agents of the most dangerous diseases:

• Rusts — stem rust of wheat, soybean rust, coffee rust. Yield losses reach 10–80% (Agrios, 2005);
• Smuts — maize smut, common smut of wheat, loose smut of barley. Losses — 10–50% (Agrios, 2005);
• Rhizoctonia — black scurf of potato, root rots (Agrios, 2005; Campos & Ortiz, 2020);
• Honey fungus — root rots of fruit and forest trees (Agrios, 2005).

2. Ectomycorrhizal symbionts. Basidiomycota form ectomycorrhiza with woody species, improving their nutrition, growth, and resistance to stresses. Inoculation with mycorrhizal fungi is used in forest nurseries and landscaping (Lambers & Oliveira, 2019).

3. Decomposers. Basidiomycota decompose wood and leaf litter, returning carbon and mineral elements to the soil. They are the basis of the cycling of substances in forest ecosystems (Raven et al., 2013).

4. Food products. Button mushrooms, oyster mushrooms, shiitake are valuable food products rich in protein, vitamins, and minerals. World production — more than 3.7 million tons per year (Raven et al., 2013).

5. Biocontrol. Some Basidiomycota (Pleurotus ostreatus) are nematode predators, used for biocontrol (Webster & Weber, 2007).

6. Bioremediation. White rots (Trametes versicolor, Pleurotus ostreatus) decompose xenobiotics, pesticides, petroleum products, and are used for cleaning contaminated soils (Raven et al., 2013).

4.8. Conclusion

Basidiomycota is the second largest phylum of the kingdom Fungi, including cap mushrooms, polypores, rust, smut, jelly fungi, gasteromycetes. Their key feature is the basidium with exogenous basidiospores formed as a result of meiosis. The mycelium is septate, with dolipore septa, and in many — clamp connections. The dikaryotic stage dominates.

Among Basidiomycota are the most dangerous phytopathogens (Puccinia, Ustilago, Tilletia, Rhizoctonia, Armillaria), indispensable ectomycorrhizal symbionts (Boletus, Suillus, Cantharellus, Lactarius), wood decomposers (Trametes, Fomes, Ganoderma), and food mushrooms (Agaricus, Pleurotus, Lentinula).

For an agronomist, knowledge of Basidiomycota is necessary for diagnosis of diseases, choice of protection strategy, use of mycorrhizal preparations, and understanding the ecological functions of fungi in agrocenoses.

Introduction

In previous lectures we became acquainted with the two largest phyla of the kingdom Fungi — Ascomycota and Basidiomycota. However, there is another group of fungi that in importance for the agrosphere is not inferior to them, and in scale of influence on plant productivity perhaps surpasses them. This is Glomeromycota — a phylum of fungi all representatives of which form arbuscular mycorrhiza (AM) with the roots of the vast majority of agricultural crops (Lambers & Oliveira, 2019; Webster & Weber, 2007).

Mycorrhiza (from Greek mykes — fungus and rhiza — root) is a symbiotic association between a fungus and a plant root. The term was introduced in 1885 by the German botanist Albert Bernhard Frank to describe the mutually beneficial cohabitation of a fungus and a root. Today we know that mycorrhiza is not an exception but the rule in the plant world: about 85–90% of all vascular plants form mycorrhiza with fungi (Lambers & Oliveira, 2019; Raven et al., 2013).

For an agronomist, knowledge of mycorrhiza is necessary for several reasons. First, mycorrhizal fungi improve plant nutrition, especially phosphorus, which allows reducing fertilizer doses. Second, they increase plant resistance to drought, salinity, and pathogens. Third, mycorrhiza affects soil structure and nutrient cycling in agrocenoses. Fourth, mycorrhizal preparations are becoming increasingly demanded in organic farming and nursery management (Lambers & Oliveira, 2019; Sokirko, 2019).

In this lecture we will examine in detail Glomeromycota as a separate phylum of fungi, arbuscular mycorrhiza and other types of mycorrhizas, their functions, and practical application in agriculture.

5.1. Glomeromycota: general characteristics

Glomeromycota is a phylum of fungi separated in 2001 on the basis of molecular phylogenetic data. Previously its representatives were included in Zygomycota (order Glomales), but molecular studies showed that this is a separate evolutionary lineage that diverged from other fungi very long ago — probably more than 400 million years ago (Webster & Weber, 2007; Lambers & Oliveira, 2019).

Key features of Glomeromycota:

• Obligate symbiosis with plant roots — unable to grow without a host;
• Aseptate (coenocytic) mycelium — hyphae without cross walls;
• Arbuscular mycorrhiza (AM) — characteristic type of symbiosis;
• Large multinucleate spores (glomerospores, chlamydospores) — formed in soil or in roots;
• Absence of sexual reproduction — reproduce only asexually (Webster & Weber, 2007; Raven et al., 2013).

Taxonomy. According to modern concepts, Glomeromycota includes one class — Glomeromycetes — and four orders: Glomerales, Diversisporales, Paraglomerales, and Archaeosporales. Most important genera: Glomus, Rhizophagus (syn. Glomus intraradices), Funneliformis, Gigaspora, Scutellospora, Acaulospora, Entrophospora (Webster & Weber, 2007; Lambers & Oliveira, 2019).

Distribution. Glomeromycota occur everywhere — from tropical forests to Arctic tundra, from arable lands to natural meadows. They are found in 72% of all vascular plants and 92% of families (Lambers & Oliveira, 2019; Wang & Qiu, 2006). Arbuscular mycorrhiza is the most widespread type of mycorrhiza on Earth.

Evolutionary importance. Fossil remains resembling Glomeromycota have been found in Devonian deposits (about 400 million years ago) together with remains of the first land plants. It is believed that mycorrhiza played a key role in the emergence of plants onto land — it helped the first land plants obtain water and mineral substances from poor soils (Raven et al., 2013; Lambers & Oliveira, 2019).

5.2. Arbuscular mycorrhiza (AM): structure and development

Arbuscular mycorrhiza (AM) is the most widespread type of mycorrhiza, characteristic of Glomeromycota. The name comes from arbuscules (from Latin arbusculum — small tree) — tree-like branches of hyphae inside root cells (Lambers & Oliveira, 2019; Webster & Weber, 2007).

5.3. Ectomycorrhiza (ECM): structure and functions

Ectomycorrhiza (ECM) is the second most widespread type of mycorrhiza, characteristic of woody species of temperate and boreal forests. Ectomycorrhiza is formed by Basidiomycota (most) and Ascomycota (minority) (Lambers & Oliveira, 2019; Raven et al., 2013).

5.4. Other types of mycorrhizas

5.5. Mycorrhizal networks and nutrient transfer

An important discovery of recent decades is common mycelial networks (CMNs). Hyphae of one mycorrhizal fungus can connect roots of different plants, forming an underground network for transfer of water, nutrients, and signaling molecules (Lambers & Oliveira, 2019; van der Heijden et al., 2015).

Experimental evidence. In an experiment with Linum usitatissimum (flax) and Sorghum bicolor (sorghum) connected by a common mycorrhizal network (Glomus intraradices), it was shown that flax receives up to 94% of nitrogen and phosphorus through the network, investing little carbon, whereas sorghum invests much carbon but receives little in return (Walder et al., 2012). This demonstrates asymmetry in the trade relationship between plants and fungus.

Practical importance. CMNs promote:

• Transfer of nutrients from legumes (nitrogen-fixing) to cereals;
• Signaling about pathogens between plants;
• Survival of young plants in the community (Lambers & Oliveira, 2019).

5.6. Role of mycorrhiza in plant nutrition and resistance to stresses

1. Phosphorus nutrition. Mycorrhiza increases phosphorus uptake by 2–10 times. Hyphae obtain phosphorus from soil pores inaccessible to the root and transport it into the plant (Lambers & Oliveira, 2019).

2. Nitrogen nutrition. ECM and ericoid mycorrhiza give access to organic nitrogen; AM — to ammonium. Mycorrhizal fungi transport nitrogen into the plant in the form of amino acids (arginine, glutamine) (Lambers & Oliveira, 2019).

3. Water regime. Mycorrhiza improves the water regime of plants, especially under arid conditions. Hyphae increase the absorbing surface and improve soil structure (Lambers & Oliveira, 2019).

4. Resistance to pathogens. Mycorrhiza protects plants from soil pathogens (Phytophthora, Pythium, Fusarium, nematodes) through competition, antibiotics, and induction of systemic resistance (Lambers & Oliveira, 2019; Jacott et al., 2017).

5. Resistance to abiotic stresses. Mycorrhiza increases salt tolerance, heavy metal tolerance, and resistance to organic pollutants (Lambers & Oliveira, 2019).

5.7. Practical use of mycorrhizal preparations

1. Mycorrhizal inoculants. Preparations based on Glomus intraradices (syn. Rhizophagus irregularis), Gigaspora margarita, Funneliformis mosseae are used for inoculation of agricultural crops, vegetables, fruit, and ornamental plants (Lambers & Oliveira, 2019).

2. Forest nurseries. Inoculation with ectomycorrhizal fungi (Boletus edulis, Suillus luteus, Pisolithus tinctorius) improves survival and growth of pine, spruce, and oak seedlings (Raven et al., 2013).

3. Organic farming. Mycorrhizal preparations reduce the need for phosphorus fertilizers, increase yield, and improve product quality (Lambers & Oliveira, 2019).

4. Recultivation. Mycorrhizal fungi are used for restoration of disturbed lands, contaminated soils, and mine spoils (Lambers & Oliveira, 2019).

5. Limitations. The effectiveness of mycorrhizal preparations depends on:

• Soil type (pH, phosphorus content, organic matter);
• Crop (not all plants are responsive to mycorrhiza);
• Competition with native fungi;
• Application conditions (humidity, temperature) (Lambers & Oliveira, 2019).

5.8. Conclusion

Glomeromycota is a separate phylum of fungi, all representatives of which form arbuscular mycorrhiza (AM) with most agricultural crops. They are obligately symbiotic, have aseptate mycelium, large spores, and do not reproduce sexually.

Arbuscular mycorrhiza is the most widespread type of mycorrhiza (72% of vascular plants). It improves phosphorus and nitrogen nutrition, water regime, protects from pathogens, increases resistance to stresses, and improves soil structure.

Ectomycorrhiza is the second most widespread type, characteristic of woody species. It gives access to organic nitrogen and phosphorus, protects from pathogens, and increases resistance to stresses.

Other types of mycorrhizas — ericoid, orchid — are specialized to certain plant groups.

Mycorrhizal networks (CMNs) connect plants underground, ensuring transfer of nutrients and signaling.

Practical use of mycorrhizal preparations is growing in organic farming, forest nurseries, and recultivation. However, effectiveness depends on application conditions.

For an agronomist, knowledge of mycorrhiza is necessary for understanding plant nutrition, reducing fertilizer doses, increasing crop resistance, and sustainable agriculture.

6.1. Mucoromycota: general characteristics

Mucoromycota is a phylum of fungi separated in 2016 on the basis of molecular phylogenetic data. Previously its representatives were included in Zygomycota — an assemblage group that turned out to be polyphyletic (Webster & Weber, 2007; Spatafora et al., 2016).

Key features of Mucoromycota:

• Aseptate (coenocytic) mycelium — hyphae without cross walls (septa are formed only to separate reproductive structures);
• Cell wall contains chitin and chitosan (partially deacetylated chitin);
• Asexual reproduction — by sporangiospores (immobile spores formed in sporangia);
• Sexual reproduction — by zygospores, formed by fusion of gametangia (Webster & Weber, 2007; Alexopoulos et al., 1996);
• Saprotrophs or weak parasites of plants, animals, and fungi.

Taxonomy. Mucoromycota includes three orders: Mucorales, Umbelopsidales, and Mortierellales. Most important genera: Mucor, Rhizopus, Absidia, Choanephora, Mortierella (Webster & Weber, 2007; Spatafora et al., 2016).

Distribution. Mucoromycetes are ubiquitously distributed in soil, on plant residues, food products, and animal feces. They are among the fastest-growing fungi, capable of colonizing a substrate within several days (Webster & Weber, 2007).

Ecological role. Mucoromycetes are active saprotrophs that decompose simple sugars, starch, and pectin, but are not capable of effectively destroying cellulose and lignin. They are the first to colonize carbohydrate-rich substrates (fruits, vegetables, bread), but then give way to other fungi (Webster & Weber, 2007; Alexopoulos et al., 1996).

6.2. Mucorales: Mucor and Rhizopus

Mucorales is the largest order of Mucoromycota, including more than 300 species. The most important genera — Mucor and Rhizopus — are saprotrophs causing product spoilage and soft rots (Webster & Weber, 2007; Agrios, 2005).

6.3. Entomophthoromycota: entomophthoraceous fungi

Entomophthoromycota is a phylum of fungi formerly included in Zygomycota (order Entomophthorales). Molecular data showed that this is a separate evolutionary lineage that is, however, close to Mucoromycota (Webster & Weber, 2007; Spatafora et al., 2016).

Key features of Entomophthoromycota:

• Mycelium aseptate or septate (septa form during aging);
• Cell wall contains chitin and chitosan;
• Asexual reproduction — by conidia (not sporangiospores!), which are actively discharged;
• Sexual reproduction — by zygospores;
• Obligate or facultative parasites of insects, mites, nematodes (Webster & Weber, 2007; Raven et al., 2013).

Ecological role. Entomophthoromycota are specialized pathogens of insects. They cause epizootics (mass diseases) among insects, regulating their numbers in nature. Some species are narrowly specialized (parasitize one species), others are polyphagous (Webster & Weber, 2007; Raven et al., 2013).

6.4. Chytridiomycota: chytrids

Chytridiomycota is a basal phylum of the kingdom Fungi, including about 1000 species. This is the only group of true fungi that has retained flagellate stages — zoospores and plasmogametes (Webster & Weber, 2007; Sokirko, 2019).

Key features of Chytridiomycota:

• Flagellate zoospores with a single smooth posterior flagellum;
• Cell wall contains chitin;
• Thallus — unicellular or rhizomycelium (rudimentary mycelium without septa);
• Asexual reproduction — by zoospores in zoosporangia;
• Sexual reproduction — isogamy, heterogamy, oogamy, somatogamy (Webster & Weber, 2007; Sokirko, 2019).

Ecological role. Chytrids are aquatic and soil saprotrophs and parasites. They destroy cellulose, chitin, and keratin. Some are parasites of algae, plants, fungi, and insects (Webster & Weber, 2007; Sokirko, 2019).

Importance for the agrosphere. The most important representative is Synchytrium endobioticum, the causative agent of potato wart disease (Sokirko, 2019; Campos & Ortiz, 2020).

6.5. Microsporidia: microsporidia

Microsporidia is a phylum of fungi including about 1,500 species. For a long time they were considered protozoa, but molecular data showed that they are extremely reduced fungi close to chytrids or zygomycetes (Raven et al., 2013; Webster & Weber, 2007).

Key features of Microsporidia:

• Unicellular parasites of animals;
• Absence of mitochondria (rudiments remain — mitosomes);
• Polar tube — a unique structure for injecting the contents of the spore into the host cell;
• Cell wall contains chitin;
• Spores resistant to unfavorable conditions (Raven et al., 2013; Webster & Weber, 2007).

Ecological role. Microsporidia are intracellular parasites of insects, fish, crustaceans, and mammals. They are widespread in nature and can cause epizootics among insects (Raven et al., 2013).

Importance for the agrosphere. The most important are Nosema apis and Nosema ceranae — parasites of honey bees (Raven et al., 2013).

6.6. Practical importance of the considered groups for the agronomist

1. Mucoromycota — spoilage of products. Rhizopus and Mucor cause soft rots of fruits, vegetables, and root crops during storage and transport. Losses reach 30–50% (Agrios, 2005). Prevention — rapid cooling, low humidity, avoiding wounds.

2. Entomophthoromycota — biocontrol. Entomophthora, Pandora, Zoophthora are used for biocontrol of insect pests (aphids, flies, cutworms, silkworm). Preparations are effective but require high humidity and are difficult to produce (Raven et al., 2013; Webster & Weber, 2007).

3. Chytridiomycota — potato wart. Synchytrium endobioticum is a dangerous quarantine pathogen of potato. Yield losses up to 100%. Control — quarantine, resistant varieties, crop rotation (Campos & Ortiz, 2020; Sokirko, 2019).

4. Microsporidia — nosemosis of bees. Nosema apis and N. ceranae cause significant damage to beekeeping, reducing honey productivity and contributing to colony death. Given the role of bees as pollinators, nosemosis poses a threat to crop production (Raven et al., 2013).

5. Biotechnological potential. Some Mucorales (Rhizopus, Mucor) are used for the production of organic acids (fumaric, lactic, citric), enzymes (amylases, proteases), and steroids. Entomophthoromycota are promising biocontrol agents (Webster & Weber, 2007; Raven et al., 2013).

6.7. Conclusion

In this lecture we examined four groups of fungi that are phylogenetically distant from one another but united by their practical importance for the agrosphere:

Mucoromycota — mucoraceous fungi (Mucor, Rhizopus), causing soft rots of fruits, vegetables, and root crops during storage and transport. Losses reach 30–50%. Prevention — rapid cooling, low humidity, avoiding wounds.

Entomophthoromycota — entomophthoraceous fungi (Entomophthora, Pandora, Zoophthora), used for biocontrol of insect pests. Preparations are effective but require high humidity and are difficult to produce.

Chytridiomycota — chytrids (Synchytrium endobioticum), causing potato wart — a dangerous quarantine disease. Yield losses up to 100%. Control — quarantine, resistant varieties, crop rotation.

Microsporidia — microsporidia (Nosema apis, N. ceranae), parasitizing honey bees and causing nosemosis. They cause significant damage to beekeeping and pose a threat to crop production because of the role of bees as pollinators.

For the agronomist, knowledge of these groups is necessary for diagnosing diseases, protecting the harvest, biocontrol of pests, and conserving populations of beneficial insects.

7.1. Phytopathogens: yield losses and mycotoxins

7.2. Mycorrhizal symbionts: increasing plant productivity

7.3. Biocontrol: antagonists and entomopathogens

7.4. Biodegradation: decomposition of plant residues and bioremediation

7.5. Food and pharmaceutical industry

7.6. Conclusion

Fungi are a unique group of organisms whose importance for the agrosphere is difficult to overestimate. They are simultaneously:

• Enemies — phytopathogens destroy 10–40% of the world harvest and produce dangerous mycotoxins;
• Friends — mycorrhizal symbionts increase plant productivity by 10–30% and reduce the need for fertilizers;
• Defenders — biocontrol based on antagonistic fungi and entomopathogens replaces chemical pesticides;
• Sanitizers — biodegradation of plant residues and bioremediation of contaminated soils;
• Producers — the food and pharmaceutical industry uses fungi to produce bread, wine, cheese, antibiotics, enzymes, and vitamins.

For the modern agronomist, knowledge of mycology is not simply a theoretical background but a necessary tool for diagnosing diseases, protecting the harvest, increasing plant productivity, sustainable farming, and producing quality products.

8.1. What we have learned: a brief overview of the module

Let us recall the main milestones of our course.

Chapter 1 laid the foundation. We established that fungi are a separate kingdom (Fungi, or Mycota), fundamentally different from plants and animals in the type of nutrition (osmotrophy — absorption, not ingestion), cell wall composition (chitin, not cellulose), storage substances (glycogen, not starch), and molecular genetic characteristics. We found that fungi are closer to animals than to plants and together with them form the supergroup Opisthokonta (Raven et al., 2013; Webster & Weber, 2007). We also outlined the diversity of ecological roles of fungi — from decomposers and symbionts to pathogens and producers of biologically active compounds.

Chapter 2 was devoted to modern classification. We saw how the molecular revolution of the late 20th and early 21st centuries radically restructured the traditional system. The rejection of Zygomycota as a single group and the recognition of Mucoromycota, Glomeromycota, Entomophthoromycota, and other phyla became an important step toward a natural system reflecting evolutionary relationships. We became acquainted with the main phyla of the kingdom Fungi: Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Microsporidia, Glomeromycota, Mucoromycota, Ascomycota, and Basidiomycota (Spatafora et al., 2016; Webster & Weber, 2007). We also discussed oomycetes — not fungi but a separate group in the kingdom Chromista, which, however, are studied together with fungi because of ecological and agronomic similarity (Sokirko, 2019).

Chapter 3 was devoted to Ascomycota — the largest phylum of fungi. We analyzed their key features (ascus, ascospores, conidia), types of ascocarps (cleistothecia, perithecia, apothecia), and life cycle. We examined in detail the most important phytopathogens — Fusarium (Fusarium diseases), Venturia (apple scab), Claviceps (ergot), Sclerotinia (sclerotiniosis), Botrytis (gray mold), Alternaria (Alternaria blights), Colletotrichum (anthracnoses), Magnaporthe (rice blast) — and beneficial species — Saccharomyces (yeast), Penicillium (penicillin, cheeses), Aspergillus (enzymes, aflatoxins), morels, truffles, as well as entomopathogens — Beauveria, Metarhizium (Agrios, 2005; Webster & Weber, 2007).

Chapter 4 introduced us to Basidiomycota — the second largest phylum. We studied their key features (basidium, basidiospores, dolipore septa, clamp connections) and life cycle with a dominant dikaryotic stage. We examined the most dangerous phytopathogens — rust fungi (Puccinia, Phakopsora, Hemileia), smut fungi (Ustilago, Tilletia), Rhizoctonia (Rhizoctonia disease), Armillaria (honey fungus) — and indispensable symbionts — ectomycorrhizal fungi (Boletus, Suillus, Lactarius, Cantharellus), wood decomposers (Trametes, Fomes, Ganoderma), and edible species (Agaricus, Pleurotus, Lentinula) (Agrios, 2005; Webster & Weber, 2007).

Chapter 5 was devoted to Glomeromycota and mycorrhiza. We found that arbuscular mycorrhiza (AM) is the most widespread type of mycorrhiza (72% of vascular plants), formed by Glomeromycota (Glomus, Rhizophagus, Funneliformis). We analyzed the structure of AM (arbuscules, vesicles, external and internal mycelium), the infection process, and functions — improvement of phosphorus and nitrogen nutrition, water regime, and protection against pathogens. We also examined ectomycorrhiza (ECM), ericoid and orchid mycorrhiza, common mycorrhizal networks (CMNs), and the practical use of mycorrhizal preparations (Lambers & Oliveira, 2019; Raven et al., 2013).

Chapter 6 completed the review of phylogenetic diversity by examining Mucoromycota (Mucor, Rhizopus — soft rots, product spoilage), Entomophthoromycota (Entomophthora, Pandora — biocontrol of insects), Chytridiomycota (Synchytrium endobioticum — potato wart), and Microsporidia (Nosema — nosemosis of bees). We saw that even phylogenetically distant and poorly studied groups can have enormous economic importance (Sokirko, 2019; Webster & Weber, 2007; Campos & Ortiz, 2020).

Chapter 7 systematized the practical importance of fungi for agricultural specialists according to five key aspects: phytopathogens (yield losses, mycotoxins), mycorrhizal symbionts (increasing productivity), biocontrol (antagonists, entomopathogens), biodegradation (decomposition of residues, bioremediation), and the food and pharmaceutical industry (Agrios, 2005; Raven et al., 2013).

8.2. Main conclusions: what the agronomist should learn

The path we have traveled allows us to formulate several key conclusions that should remain with you after completing the module.

First conclusion: fungi are a separate kingdom, not “lower plants.” Understanding the phylogenetic independence of fungi is not an abstract theoretical detail but practically important knowledge. It explains why fungicides effective against true fungi (Ascomycota, Basidiomycota) do not act on oomycetes (Phytophthora, Pythium), and vice versa. The chitinous cell walls of true fungi and the cellulose walls of oomycetes require different approaches to plant protection (Agrios, 2005; Sokirko, 2019).

Second conclusion: modern systematics is based on molecular data. Traditional morphological classification is outdated. Molecular phylogenetic methods have made it possible to reveal true relationships between groups and abandon artificial taxa (for example, Zygomycota). Knowledge of modern phylogeny is necessary for accurate diagnosis of disease agents and prediction of their properties (Spatafora et al., 2016; Webster & Weber, 2007).

Third conclusion: fungi are not only enemies but also friends. Phytopathogenic fungi cause enormous damage to agriculture, destroying 10–40% of the world harvest and producing dangerous mycotoxins. However, mycorrhizal fungi increase plant productivity by 10–30%, biocontrol fungi replace chemical pesticides, and food and pharmaceutical species provide humanity with bread, wine, cheese, antibiotics, and enzymes (Agrios, 2005; Lambers & Oliveira, 2019; Raven et al., 2013).

Fourth conclusion: fungi are key players in ecosystems. As decomposers, fungi break down plant residues and return carbon and mineral elements to the soil. As symbionts, they provide plants with phosphorus, nitrogen, and water. As pathogens, they regulate the population sizes of plants and insects. Without fungi, the normal functioning of agrocenoses and natural ecosystems is impossible (Raven et al., 2013; Webster & Weber, 2007).

Fifth conclusion: knowledge of mycology is a necessary condition for sustainable agriculture. Modern agriculture faces challenges: climate change, pathogen resistance to fungicides, and the need to reduce the chemical burden on the environment. Answers to these challenges are impossible without a deep understanding of the biology and ecology of fungi (Agrios, 2005; Lambers & Oliveira, 2019).

8.3. Connection between systematics and practice: from taxon to protection strategy

Let us show with concrete examples how knowledge of fungal systematics directly influences practical decisions of the agronomist.

Example 1: Potato late blight. The causative agent — Phytophthora infestans — is an oomycete, not a true fungus. Its cell wall contains cellulose, not chitin. Mitochondrial cristae are tubular. This means that fungicides acting on chitin synthesis or ergosterol (azoles, strobilurins) will not be effective. Special preparations are needed to control late blight — metalaxyl, mancozeb, cymoxanil (Agrios, 2005; Campos & Ortiz, 2020).

Example 2: Rust and smut. The causative agents are Basidiomycota (Puccinia, Ustilago, Tilletia). These are true fungi with chitinous walls. Triazoles (tebuconazole, propiconazole), strobilurins (azoxystrobin), and carboxamides (carboxin) are effective against them. Knowledge of life cycles (heteroecious rusts require destruction of intermediate hosts — barberry) makes it possible to develop integrated protection strategies (Agrios, 2005; Webster & Weber, 2007).

Example 3: Mycorrhiza and fertilizers. Arbuscular mycorrhiza (Glomeromycota) improves phosphorus nutrition of plants. Inoculation with mycorrhizal preparations makes it possible to reduce phosphorus fertilizer doses by 20–50% without yield loss. Knowledge that mycorrhiza is suppressed at high phosphorus content in soil helps the agronomist properly plan the fertilization system (Lambers & Oliveira, 2019).

Example 4: Biocontrol. Trichoderma (Ascomycota) is an antagonist of Rhizoctonia, Pythium, Fusarium. Knowledge that Trichoderma acts through mycoparasitism, competition, and antibiotics makes it possible to effectively use its preparations for treating seeds and soil. Beauveria bassiana (Ascomycota) is an entomopathogen acting on a broad spectrum of insects. Knowledge of its biology makes it possible to use it against the Colorado potato beetle, aphids, and whiteflies (Raven et al., 2013; Webster & Weber, 2007).

Example 5: Mycotoxins. Fusarium graminearum (Ascomycota) affects wheat and produces deoxynivalenol (DON). Knowledge that DON accumulates at high humidity during flowering and ripening makes it possible for the agronomist to plan harvesting at optimal times and avoid grain contamination. Knowledge that Aspergillus flavus produces aflatoxins in maize and peanut at high temperature and humidity makes it possible to apply drying and proper storage (Agrios, 2005; Campos & Ortiz, 2020).

8.4. Prospects: what awaits us in the future

Mycology is a rapidly developing science. New research methods (metagenomics, next-generation sequencing, CRISPR-Cas9) open new horizons in the study of fungi. What awaits us in the coming decades?

1. Discovery of new species. According to estimates, only 5–10% of existing fungal species have been described. Tropical forests, soils, and animal intestines contain millions of unknown species. New species may become a source of new antibiotics, enzymes, and bioactive compounds (Webster & Weber, 2007; Raven et al., 2013).

2. Genetic engineering of fungi. Genome editing makes it possible to create strains with improved properties: increased enzyme production, resistance to pathogens, and ability for bioremediation. Genetically modified mycorrhizal fungi may become more effective symbionts (Raven et al., 2013).

3. New biopreparations. The development of new formulations of mycoinsecticides and mycofungicides based on entomopathogens (Beauveria, Metarhizium, Entomophthora) and antagonists (Trichoderma, Gliocladium) will reduce dependence on chemical pesticides (Raven et al., 2013).

4. Mycoremediation. White rots (Trametes, Pleurotus, Phanerochaete) will be increasingly used to clean soils from petroleum products, pesticides, and heavy metals (Raven et al., 2013).

5. Sustainable agriculture. The integration of mycorrhizal preparations, biocontrol, and resistant varieties will make it possible to create farming systems that produce enough food without harming the environment (Lambers & Oliveira, 2019).