Fungi 3218

The Linnaean Hierarchy (acronym)

Dumb King Phillip Came Over For Good Soup

Domain, Kingdom, Phylum, Class, Order, Family, Genus, species [subspecies/variety, f.sp.]

Taxon Names for Fungi

Phylum = -mycota

subphylum = -mycotina

class = -mycetes

order = -ales

family = -aceae

The Five* Phyla of Fungi

A,B,C,G,Z: Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Zygomycota

Fungal Phylogeny

• Ascomycota, Basidiomycota, and Glomeromycota are generally considered monophyletic (one common ancestor and all descendants)

• Zygomycota is NON-monophyletic

  • it is paraphyletic (one common ancestor but excludes decendants ABG)

  • it is polyphyletic (multiple evolutionary roots, grouped based on similartraits not ancestry)

• Chytridiomycota is NON-monophyletic

  • may be paraphyletic

Kingdom Fungi - 5 overall characteristics

• A KINGDOM of eukaryotic¹ organisms most closely related to ANIMALS

• Heterotrophic², with extracellular digestion³ and absorptive nutrition⁴, and with cell walls containing chitin, glucans and mannans⁵ [There are exceptions]

Fungi Charactieristics - Growth

• The characteristic feature of most fungi is filamentous growth

  • The fungal body (thallus) is composed of microscopic threads called hyphae

  • Hyphae are tube-like and branching

  • This tube-like branching pattern defines filamentous growth

• The collective, growing mass of hyphae is called the mycelium

  • Mycelium makes up the main vegetative body of a fungus

• Yeasts do not show filamentous growth

  • They grow as single cells (cellular growth)

• Yeasts reproduce by:

  • Budding

    • Typical of Saccharomyces

    • A small daughter cell forms and pinches off from the parent

  • Fission

    • Cell divides into two equal cells

    • Cells split apart after division

Fungi Charactieristics - Nutrition

• Fungi are heterotrophic

  • Obtain carbon and energy from organic matter

  • Do extracellular digestion followed by absorptive nutrition

• Fungi produce a wide array of lytic (digestive) enzymes

  • Enzymes are made inside the cell and secreted outside (exoenzymes)

  • Examples:

    • Cellulase → breaks down cellulose

    • Laccase

    • Chitinase

    • Pectinase → breaks down pectin (the “glue” holding plant cell walls together)

• Hyphal growth allows fungi to penetrate solid substrates

  • Hyphae grow directly through the material being digested

  • This allows access to nutrients unavailable to many other organisms

• Large substrates (e.g., starch grains) are too big to cross membranes

  • Fungi secrete enzymes to digest polymers into small, soluble molecules

  • Starch is broken down into simple sugars

  • Simple sugars are then absorbed across the fungal membrane

Fungi Charactieristics - Nutrition - Competition Problem

• Competition problem

  • Bacteria grow faster than most fungi

  • Bacteria readily consume free sugars

  • Digesting polymers in a mixed environment can “give away” nutrients to competitors

• Fungal solution to competition

  • Some fungi produce antibiotic compounds

  • Antibiotics are released into the environment

  • This reduces bacterial growth so fungi can retain access to liberated sugars

• Filamentous fungi vs bacteria

  • Fungi: penetrate solid substrates via hyphae

  • Bacteria: generally remain in solution and cannot penetrate solids effectively

Fungi Charactieristics - Nutrition - Why Produce Chitinase?

Why fungi produce chitinase (despite having chitin cell walls)

• Chitin is rigid and inflexible

• For hyphae to grow:

  • The cell wall must be temporarily flexible

  • Chitin is partially digested before being re-laid and hardened

• Chitinase allows:

  • Hyphal extension

  • Branch formation toward nutrient sources

  • Remodeling of the fungal cell wall

• Chitinase is also needed because:

  • Fungi can digest other fungi, which also have chitin cell walls

“Fungi” and Fungi with flagella

• “Fungi” (broadly defined) include some organisms with flagellated stages

  • A flagellum (plural flagella) is a motile, whip-like structure used for movement, typically in water

• “Water moulds”

  • Aquatic or water-associated organisms

  • Many produce flagellated spores or cells

  • Examples include:

    • Oomycota

      • Belong to the kingdom Chromista

      • Not true fungi, despite similar growth forms

    • Chytridiomycota

      • Belong to the kingdom Fungi

      • The only true fungi with flagellated cells

• Slime moulds

  • Not fungi

  • Have amoeboid (amoeba-like) stages

  • Will be covered later in the course

Fungi Charactieristics - Cell Walls

Fungal cells have cell walls

• Unlike animal cells, which lack cell walls

• True fungi cell walls are composed mainly of:

  • Chitin

  • Glucans

  • Mannans

  • This combination is characteristic of Kingdom Fungi

• Oomycota cell walls are composed mainly of:

  • Cellulose

  • This distinguishes them from true fungi despite similar growth forms

• Outside the cell wall, fungi have microscopic proteinaceous fimbriae

  • Fine, protein-based surface structures

  • Involved in managing the immediate environment around the cell

• Proposed functions of fimbriae (not fully understood):

  • Help control release of extracellular enzymes

  • Help capture and retrieve digestion products

  • May regulate interactions between the hypha and surrounding substrate

Fungi Charactieristics - Nutrition/Physiology

• Can live in high acid (pH 1) or alkaline (pH 9) environments

• tolerate cold or heat (-5 to 60 C) or low O₂

• tolerate low water availability (.65 vs plants 0.98)

• Most strains can make many compounds directly from simple or complex sources (source of C, N, inorganic ions = prototrophs

• Some strains/mutants have lost ability to make a growth factor (eg vitamin B1) = auxotrophic - so need this factor as a food source

Fungal Numbers

• 97k accepted in DictFun10 (64k A, 32k B, 700 C, 150 G, 1k Z), plus 1k ea Slime moulds & Oomycota

• >350k described species including synonyms (Saccardo, Index of Fungi)

• 1.5M estimated by Hawksworth (1991), based in part on estimate of 5:1 fungi to plant species in the UK [updated to 2.5 M]

• For comparison, there are an estimated 500k species of vascular plants, 55k vertebrates, 30M insects

Group Based on Life Style

• Filamentous fungi (most) vs Yeasts (2k spp)

• Sexual (meiosporic; ~77k spp) vs asexual (mitosporic; ~20k spp)

• Aerobic (almost all?) vs anaerobic (a few chytrids)

• Microfungi (individuals measured in micrometers, fruiting bodies usually lacking) vs macrofungi (individuals may occupy hectares, fruiting bodies > 1 cm)

Groups (Guilds) Based on Nutritional Modes

• Fungi can be grouped into nutritional guilds based on how they obtain nutrients

  • Two broad categories: saprotrophs and symbionts

• Saprotrophs

  • Obtain nutrients from dead organic matter

  • Secrete enzymes to decompose tissues and absorb released nutrients

• Symbionts

  • Live in close association with another organism

• Types of symbiotic fungi:

  • Mutualistic symbionts

    • Both partners benefit

    • Examples:

      • Mycorrhizae

        • Fungus associated with plant roots

        • Fungus receives carbon; plant gains nutrients and water

      • Lichens

        • Fungus partnered with a photoautotroph (alga or cyanobacterium)

        • Fungus provides protection and structure; photosynthetic partner provides carbon

      • Ant–fungus associations

        • Ants cultivate fungi for food

        • Fungi receive substrate and protection

  • Parasitic symbionts

    • Fungus benefits while the host is harmed

    • Include pathogens of:

      • Plants

      • Animals

      • Other fungi

      • Virtually all major groups of living organisms

  • Endophytes (do not fit neatly into one category)

    • Live inside plant tissues

    • Obtain nutrients from the plant

    • Effects on the host can vary:

      • Sometimes beneficial

      • Sometimes detrimental

    • When plant tissue dies:

      • Endophytes often switch to saprotrophic nutrition

      • Decompose dead leaves or stems

Chytridiomycota* = chytrid

• Chytridiomycota (chytrids)

  • True fungi

  • Depend on free water for reproduction

  • Produce flagellated cells

• Flagella

  • Most chytrids have one posterior flagellum

  • Similar in form to animal sperm flagella

  • Presence of a single flagellum is a key feature used to recognize chytrids

• Exceptions

  • Some chytrids (e.g., rumen fungi in herbivore guts) have multiple flagella

  • These were historically misclassified as protozoa because of their motility

• Ecological and applied importance

  • Synchytrium endobioticum

    • Causes potato wart disease

    • Serious agricultural pathogen

    • Led to restrictions on potato movement (e.g., U.S. bans on PEI potatoes in 2000–2001 and again in 2021)

• Related or formerly included groups

  • Blastocladiomycota

  • Sanchytriomycota

  • These groups were once lumped with chytrids but are now recognized as distinct lineages

Glomeromycota

• Glomeromycota

  • Formerly included within Zygomycetes as the group “Glomales”

  • Correct name of the order is Glomerales

  • Later shown to be distinct and elevated to their own phylum

• All known members of this group form symbioses with photoautotrophs

• One exception:

  • Geosiphon

    • Forms an endosymbiosis with a cyanobacterium

    • The cyanobacterium lives inside fungal cells

    • Cyanobacterium performs photosynthesis

    • Fungus takes up the sugars produced

• The majority of species (~200 species):

  • Form mycorrhizal associations with plants

  • Occur in >80% of green plant species

  • This symbiosis is called:

    • Endomycorrhizae

    • Or Arbuscular Mycorrhizae (AM)

• In arbuscular mycorrhizal (AM) relationships:

  • Fungus associates with roots of grasses, trees, and many other plants

  • Fungus receives sugars (carbon) from the plant

  • Fungus supplies the plant with:

    • Water

    • Mineral nutrients (especially phosphorus) from the soil

Zygomycota*

• Zygomycota*

  • Not monophyletic

  • Traditional grouping rather than a natural evolutionary lineage

  • Contains ~1200 species

• Best-known members are the “bread moulds”

  • Includes Rhizopus and relatives

  • Part of the order Mucorales

  • Commonly grow on bread, fruit, pumpkins

• Hyphae

  • Hyphae are tubular fungal cells

  • In most fungi:

    • Diameter ~2–5 µm

  • In zygomycete-type fungi:

    • Diameter ~20–50 µm

    • ~10× wider than typical fungal hyphae

  • Appear:

    • Tall, Broad, Glassy

  • Often visible to the naked eye

• Modern view:

  • Zygomycota has been split into:

    • Mucoromycota

    • Zoopagomycota

• Typical morphology:

  • Tall, glassy hyphae

  • Hyphae often topped with spore-producing structures

Ascomycota

• Largest phylum of fungi

  • ~64,000 described species

• Divided into three subphyla

  • Taphrinomycotina

  • Saccharomycotina

  • Pezizomycotina

• Includes most of the ~20,000 “mitosporic fungi”

  • Reproduce by mitosis only

  • No observed sexual stage

  • Do not form asci

  • DNA sequence data shows they are ascomycetes

• Includes ~20,000 species of lichens

  • Lichens are a symbiosis between:

    • A fungus (usually an ascomycete)

    • A photoautotroph (green alga or cyanobacterium)

  • Commonly grow on:

    • Rocks

    • Tree trunks

    • Soil

• Extremely diverse

  • Wide range of:

    • Nutritional modes

    • Ecological roles

    • Morphologies

  • Common examples include green moulds (e.g., mould on food like pasta sauce)

The Ascus (pl. asci) defines the Ascomycota

• Ascus (plural asci)

  • A sac-like, balloon-shaped cell

  • Spores develop inside the ascus

• Ascospore development

  • Immature spores are pale

  • Mature spores develop thicker walls and often become darker/brown

• Nuclear events inside the ascus

  • A cell initially contains a dikaryon

    • Two haploid nuclei

    • Genetically different

  • Karyogamy

    • Fusion of the two haploid nuclei

    • Forms a diploid nucleus

  • Diploid stage is very short

    • Occurs only inside the ascus

• Meiosis and spore formation

  • Diploid nucleus undergoes meiosis

  • Produces 4 haploid nuclei

  • Often followed by mitosis

    • Doubles the number to 8 haploid ascospores

• Variation among ascomycetes

  • Many species produce 8 ascospores per ascus

  • Some produce 4 spores (no post-meiotic mitosis)

  • Others produce 16, 64, or more spores via multiple mitotic divisions

Basidiomycota

• ~32,000 species

• Divided into three subphyla

  • Agaricomycotina (~22,000 spp.)

    • Includes most mushrooms

    • Mostly mycorrhizal fungi and decomposers

  • Pucciniomycotina (~8,000 spp.)

    • The rust fungi

    • Major plant pathogens

  • Ustilaginomycotina (~1,500 spp.)

    • The smut fungi

    • Major plant pathogens

• Overall includes fungi with diverse ecologies, but rusts and smuts are especially important agriculturally

The Basdium (pl. basdia) defines the basidiomycota

• Basidium (plural basidia) is the spore-producing cell

• Similar to an ascus in function, but:

  • Spores are produced on the outside

  • Spores sit on small projections (sterigmata)

• Typically produces 4 spores

  • Some species undergo mitosis after meiosis and produce 8 spores

• Basidium begins as a dikaryotic cell

  • Contains two haploid nuclei

  • Genetically different (often shown as black vs white nuclei)

• Karyogamy

  • Two haploid nuclei fuse

  • Form a diploid nucleus

• Meiosis

  • Diploid nucleus undergoes meiosis

  • Produces haploid nuclei

  • These migrate into the externally formed basidiospores

Agaricomycetes* - a class within basidiomycota

• Are the dominant decomposers of lignocellulose

  • Especially effective at breaking down lignin

  • Equipped with powerful lignin-modifying enzymes, including:

    • Laccases, Lignin peroxidases, Manganese-dependent peroxidases

• Lignin

  • Acts as the rigid “glue” that holds cellulose fibers together in plant cell walls

  • When lignin is chemically removed (e.g., with sulphuric acid), cellulose becomes soft

    • Example: cellulose processed into Kleenex-like tissue

• Comprise the majority of ectomycorrhizal fungi

  • Associated with most Canadian trees

  • Ecto = outside, Myco = fungus, Rhizal = root

• Ectomycorrhizal relationship

  • Fungi form a sheath or “mitten” around the outside of plant roots

  • Fungal hyphae:

    • Transport water and mineral nutrients from soil to the tree

    • Receive sugars (carbon) from the tree

• Fungi are often better at soil exploration than plant roots

  • Hyphae are:

    • Extremely thin

    • Energetically inexpensive to build and maintain

  • Can explore a much larger soil volume than thick plant roots at lower cost

• Public interest in Agaricomycetes has increased recently

  • Especially after the documentary “Fantastic Fungi”