Unit 5: Applied Mycology

1. Role of fungi in biotechnology

Fungi are "workhorses" in biotechnology due to their diverse metabolic capabilities and ease of growth in large-scale fermenters.

• Industrial Fermentation: Fungi are used to produce a vast range of products in bioreactors, including enzymes, antibiotics, organic acids, and alcohol.
• Recombinant Protein Production: Yeasts (like *Saccharomyces cerevisiae* and *Pichia pastoris*) are simple eukaryotes, making them ideal hosts for producing complex *eukaryotic* proteins (which bacteria cannot properly fold).
  • Example: Production of human insulin, Hepatitis B vaccine, and other biopharmaceuticals.
• Model Organisms: Yeasts (*S. cerevisiae*) are used as model organisms for genetic research. Because they are eukaryotes, studying their cell cycle, genetics, and gene expression provides direct insights into human biology.
• Bioconversion: Using fungal enzymes to convert low-value substrates into high-value products (e.g., converting steroids).
• Bioremediation: Using fungi (mycoremediation) to break down toxic pollutants like pesticides, industrial dyes, and oil.

2. Application of fungi in food industry

Fungi are central to the production and processing of many foods.

Flavour & texture

• Cheese: Fungi are essential for ripening and flavoring.
  • Blue Cheese (e.g., Roquefort, Stilton): Ripened by Penicillium roqueforti, which grows inside the cheese, creating blue veins and a sharp flavour.
  • Soft-Ripened Cheese (e.g., Brie, Camembert): Ripened by Penicillium camemberti, which grows on the surface, creating a soft rind and creamy texture.
• Soy Products:
  • Soy Sauce: Fermentation of soybeans and wheat by Aspergillus oryzae.
  • Tempeh: Fermentation of soybeans by Rhizopus oligosporus, which binds the beans together into a solid cake.

Fermentation

• Alcoholic Beverages: The yeast Saccharomyces cerevisiae ferments sugars (from grapes for wine, from barley for beer) into ethanol and CO2.
• Industrial Ethanol: Yeasts are also used to produce ethanol for biofuels.

Baking

• Bread: Baker's yeast (Saccharomyces cerevisiae) is used to leaven bread. It ferments sugars in the dough, producing carbon dioxide (CO2). The CO2 gas gets trapped, causing the dough to rise and giving bread its light, airy texture.

Organic acids

Fungi are cultured on an industrial scale to produce organic acids used as food additives.

• Citric Acid: Produced by Aspergillus niger. Used as a flavouring and preservative in soft drinks, jams, and candies.
• Gluconic Acid: Also produced by Aspergillus niger. Used as a food acidulant.

Enzymes

Fungi are a major source of industrial enzymes, which are "green" catalysts for food processing.

• Amylase: (from Aspergillus oryzae) Breaks down starch. Used in baking to improve dough and in brewing to convert starch to sugar.
• Pectinase: (from Aspergillus niger) Breaks down pectin. Used to clarify fruit juices and wine.
• Rennin (Chymosin): (from Mucor) Curdles milk to make cheese. (Recombinant chymosin from engineered yeast is now more common).

Mycoproteins

• Definition: Mycoprotein ("fungus protein") is a protein-rich food product made from fungal mycelium.
• Organism: Fusarium venenatum (an Ascomycota).
• Process: The fungus is grown in large fermenters on a glucose substrate. The mycelium (biomass) is harvested, heat-treated, and processed.
• Product: Sold as Quorn™, a meat substitute high in protein and fiber, and low in fat.

3. Secondary metabolites

These are complex organic compounds produced by the fungus that are *not* essential for its primary growth (like reproduction or defense). They are often of great medical and economic value.

Antibiotics

• Definition: Substances produced by one microbe that inhibit or kill other microbes (especially bacteria).
• Penicillin: The first major antibiotic, discovered by Alexander Fleming. Produced by the mold Penicillium chrysogenum (formerly *P. notatum*).
• Cephalosporin: Another major class of antibiotics, produced by the fungus Acremonium (formerly *Cephalosporium*).

Alkaloids

• Definition: Nitrogen-containing compounds that have potent physiological effects on animals.
• Ergot Alkaloids: Produced by the fungus Claviceps purpurea, which infects rye and other grasses (causing "ergotism").
  • Negative: Highly toxic, causing hallucinations, gangrene, and convulsions.
  • Positive: Purified ergot alkaloids (like ergotamine) are used in medicine to treat migraines and control bleeding after childbirth.
• Statins: (e.g., Lovastatin) are fungal metabolites (from Aspergillus terreus) that are used as a major class of cholesterol-lowering drugs.

Pigments

• Fungi produce a wide array of stable pigments that can be used as natural food colorants.
• Example: Pigments from Monascus purpureus (red yeast rice) are used as a red food coloring in Asia.

4. Biological control

Biological control (or biopesticides) is the use of one living organism (or its products) to suppress or kill another organism (a pest). Fungi are excellent candidates for this.

Biofungicides (Mycofungicides)

• Definition: Using one fungus to control another, plant-pathogenic fungus.
• Mechanism: Usually mycoparasitism (one fungus preys on the other).
• Example: Trichoderma spp. This "friendly" fungus is a common biofungicide. It aggressively colonizes the root zone, attacks pathogenic fungi (like *Rhizoctonia*, *Pythium*), and also promotes plant growth.

Mycoherbicides

• Definition: Using a plant-pathogenic fungus to target and kill a specific weed, without harming the main crop.
• Example: *Colletotrichum gloeosporioides* has been used to control northern jointvetch, a weed in rice and soybean fields.

Mycoinsecticides

• Definition: Using an "entomopathogenic" (insect-killing) fungus to control insect pests.
• Mechanism: The fungal spore lands on the insect's cuticle, germinates, and penetrates the body. The fungus grows inside the insect, killing it, and then sporulates on the outside of the corpse.
• Examples:
  • Beauveria bassiana (causes "white muscardine" disease). Used against whiteflies, aphids, and thrips.
  • Metarhizium anisopliae (causes "green muscardine" disease). Used against ticks, termites, and beetles.

Myconematicides

• Definition: Using a "nematophagous" (nematode-eating) fungus to control plant-parasitic nematodes in the soil.
• Mechanism:
  • Nematode-trapping fungi: These fungi form "traps" in their mycelium, such as sticky nets or constricting rings, to capture nematodes (e.g., *Arthrobotrys*).
  • Endoparasitic fungi: Produce spores that stick to or are eaten by the nematode, then germinate and kill it from within.

5. Medical mycology (Mycoses)

Mycology is the study of fungi, and Medical Mycology is the study of fungal diseases in humans, called mycoses (singular: mycosis).

Mycoses are classified based on the tissue level they infect:

1. Superficial Mycoses:
   • Infect the outermost layers of skin and hair. Non-destructive, purely cosmetic.
   • Example: *Pityriasis versicolor* (discolored skin patches).
2. Cutaneous Mycoses (Dermatophytoses):
   • Infect the keratinized layers of the skin, hair, and nails.
   • Caused by dermatophytes (e.g., *Trichophyton*, *Microsporum*).
   • Example: Ringworm (Tinea), Athlete's Foot.
3. Subcutaneous Mycoses:
   • Infect the dermis, subcutaneous tissue, and muscle.
   • Caused by fungi from soil that enter through a puncture wound.
   • Example: *Sporotrichosis* ("rose-gardener's disease").
4. Systemic (or Deep) Mycoses:
   • The most serious fungal infections.
   • Infection starts in the lungs (by inhaling spores) and spreads (disseminates) to other internal organs.
   • Often caused by dimorphic fungi.
   • Example: *Histoplasmosis*, *Coccidioidomycosis* ("valley fever").
5. Opportunistic Mycoses:
   • Caused by common fungi that are normally harmless but become pathogenic in an immunocompromised host (e.g., AIDS patients, transplant recipients, cancer patients).
   • Example: Candida albicans (causes "thrush," yeast infections), Aspergillus fumigatus (causes Aspergillosis).

6. Mushroom cultivation

Mushroom cultivation is the technology of growing mushrooms (the basidiocarps of certain fungi) for food. It is a major global industry.

Commonly Cultivated Species:

• Button Mushroom: Agaricus bisporus (This is the most common mushroom: white, cremini, and portobello are all the same species).
• Oyster Mushroom: Pleurotus ostreatus.
• Paddy Straw Mushroom: Volvariella volvacea (common in Asia).
• Shiitake Mushroom: Lentinula edodes.

General Steps for *Agaricus* (Button Mushroom) Cultivation:

1. Phase 1: Compost Preparation
   • This is the most critical step. A nutrient-rich substrate is made, usually from wheat straw, horse manure, and supplements.
   • The mixture is composted (allowed to ferment) in large piles, reaching high temperatures (70-80°C). This pasteurizes the substrate, killing pests and "bad" microbes, while encouraging "good" thermophilic microbes.
2. Phase 2: Spawning
   • The compost is cooled and "spawn" is added.
   • Spawn is the fungal mycelium (of *Agaricus*) growing on a substrate, usually sterilized grain. It is the equivalent of "seeds."
   • The spawned compost is placed in trays or bags and kept in a dark, humid room for the mycelium to grow and colonize the compost (this is the "spawn run").
3. Phase 3: Casing
   • After the mycelium fully colonizes the compost, a "casing layer" (a moist mixture of peat moss and chalk) is spread on top.
   • This layer is low in nutrients and helps to induce the formation of fruiting bodies (mushrooms).
4. Phase 4: Pinning and Harvesting
   • The trays are moved to a "fruiting room" with high humidity, fresh air, and a specific temperature.
   • Tiny "pinheads" (primordia) form on the casing surface.
   • These pins develop into mature mushrooms, which are harvested by hand in cycles called "flushes."