Physiology of Fungi

PHYSIOLOGY OF FUNGI OR MYCETES OR MYCOPHYTES - MYCOLOGY
(see also human diseases caused by fungi

)

taxonomy & features

true Fungi (Kingdom Mycota or Eumycota) with many characteristic biochemical features, showing that they are a monophyletic group of organisms. Click here for a simplified NCBI taxonomy .

genomics :

haploid, whereas the other major groups of eukaryotes are diploid.
synthetise the amino acid lysine by a unique pathway, different from that of other organisms.
characteristic soluble carbohydrates (the disaccharide trehalose and polyhydric alcohols like mannitol and arabitol) and storage compounds (e.g. glycogen), differing from those of most plants and animals.

capsule :

mannan (a a(1->6) D-Man homopolysaccharide with b(1->2) GlcUA and b(1->4) Xil substitutions)
a(1->3) glucan

cell wall :

chitin / mycosin (a b(1->4) D-GlcNAc homopolysaccharide) is a major component of fungal walls (but also found in the exoskeleton of Arthropoda, etc.). The enzyme that synthesizes chitin (chitin synthase) is a target for the polyoxin antibiotics.
zymosan : a mixture of polysaccharides, proteins, and ash, of variable concentration, derived from the cell walls or the entire cell of yeast, commonly Saccharomyces cerevisiae. It is anticomplementary, absorbing the C3 component of complement , and is used in assaying properdin

b-glucans (Betafectin^® PGG-glucan) are glucose polymers (a b(1->3), b(1->6) D-Glc homopolysaccharide) found in the cell walls of plants, fungi, and bacteria and as conserved structures can be considered to be classical PAMPs^ref. These polymers belong to a class of drugs known as biological response modifiers and have a variety of effects on the immune system, including antitumor^ref and anti-infective activities, protecting against fungal^ref, bacterial^ref, viral^ref, and protozoal infections^ref. Both particulate and soluble b-glucans mediate these activities by activating leukocytes and stimulating their phagocytic activity and the production of reactive oxygen intermediates, inflammatory mediators, and cytokines^ref. Despite the wealth of knowledge regarding the effects of b-glucans and their obvious therapeutic potential, the molecular mechanisms that underlie these responses are not well understood. Receptors on leukocytes that recognize b-glucans were originally described over 20 years ago as phagocytic receptors for particulate activators of the alternative complement pathway^ref. It is recognized by :

dendritic cell-associated C-type lectin 1 / dectin 1 / b-glucan receptor (bGR)
neutral glycosphingolipids with a terminal galactose, including galactosylceramide (CDw17, a major glycosphingolipid of polymorphonuclear leukocytes), globotriaosylceramide, gangliotetraosylceramide, lactosylceramide^ref
class C scavenger receptor, Drosophila SR-CI (dSR-CI), a 609-residue type I integral membrane protein containing several well-known sequence motifs, including two complement control protein (CCP) domains and somatomedin B, MAM, and mucin-like domains, whose expression was restricted to macrophages/hemocytes during embryonic developments^ref
CD11bCD18 / a_Mb₂ integrin / Mac1 / CR3 : in addition to the iC3b binding site, CR3 possesses a lectin site for b-glucans that, in combination with iC3b, enhances phagocytic and cytotoxic responses^ref1,
ref2. b-glucans can also prime the receptor for subsequent iC3b-mediated cytotoxic responses, including the iC3b-restricted antitumor activity^ref.
mannose-binding protein or lectin 2 (MBP / MBL2) / protein C (?)

cellulose (a b(1->3), b(1->4) D-Glc homopolysaccharide)
mannan (a a(1->6) D-Man homopolysaccharide with a(1->2) and a(1->3) ramifications)

divisional septum : in yeasts it is made up of chitin.
even a-glucan is secreted in the extracellular medium.

plasma membrane : instead of cholesterol, it contains ergosterol / ergocalcipherol (a.k.a. viosterol, i.e. (ultra)vio(let ergo)sterol : it is the vitamin D₂ precursor).

zymosterol : a mycosterol occurring in yeast as an intermediate in the synthesis of cholesterol

plate-like cristae in the mitochondria (like animals)
tubular unstacked Golgi cisternae (unlike animals or plants).
fungal tubulins bind to the antibiotic griseofulvin (used to treat some fungal infections of humans) and to the benzimidazole fungicides (used widely for control of fungal pathogens of plants).
trichophytin : mixture of soluble antigens from dermatophytes

hypha (plural, hyphae) : ong and often branched tubular filament that constitutes the vegetative body of many fungi and funguslike organisms.

monokaryon : fungal hypha in which compartments contain one nucleus.
haustorium (plural, haustoria) : specialized hypha for necrotrophic feeding in parasitic Fungi.

rhizoid : specialized hypha for anchoring and feeding in Zygomycota

stolon : specialized hypha parallel to invasion surface in Zygomycota
coenocytic hypha : fungal hypha without crosswalls (septa), so that the nuclei present in the cytoplasm are free-floating and mobile. The hyphae of members of the Oomycota and Chytridiomycota are considered coenocytic.
pseudohypha : a string of cells resulting from the building of the blastoconidia, without the cytoplasmic connection of a true hypha; seen in some yeasts

mycelium (plural, mycelia) or tallus : mass of hyphae that form the vegetative body of many fungal organisms.

heterothallic : hyphae that are incompatible with each other each requiring contact with another hypha of compatible mating type.
homothallic : hyphae that are self-compatible in that sexual reproduction occurs in the same organ. Upon fusion they may form ...

diploid (2n)
dikaryon : 2 nuclei present in the same hyphal compartment. n+n

homokaryon : fungal hypha in which all nuclei are genetically identical.
heterokaryon : hypha that contains at least two genetically dissimilar nuclei.

rhizomycelium : indeterminate growth form in zoosporic fungi. Effectively, a mycelium except usually much finer filaments that are closer in size to rhizoids.
fruiting body : the visible (i.e. : over the ground) part of a mycelium (the commonly said fungum), a specialized structure that produces spores;

mushroom : large, sometimes edible, fruiting body produced by some fungi.

dimorphism (transition often occurs between in vivo and in vitro environments) : yeasts or Blastomycetes(unicellular; usually earlier stages in vivo; schizogony or budding => enteroblastic blastospores) <=> pseudomycelium <=> molds (moulds) or filamentous fungi or Hyphomycetes (pluricellular => hyphae & micelia ; usually in vitro and late stages in vivo)

endogenous : a form of thallus development in which the nucleus remains in an encysted zoospore that simply enlarges to form one or more sporangia.
holocarpic : refers to an organism with a thallus that is converted entirely into one or more reproductive structures.

hymenium : layer of hyphae which are fertile in producing asci (fungi in the phylum Ascomycota) or basidia (fungi in the phylum Basidiomycota) from the process of meiosis.
sclerotium : modified fungal hyphae that form a compact, hard vegetative resting structure with a thick pigmented outer rind.
rhizomorph : mass of fungal hyphae organized into long, thick strands usually with a darkly pigmented outer rind and containing specialized tissues for absorption and water transport.
chlamydospore : thick-walled resting structure that forms from the cell wall of a fungal hypha; usually formed under conditions where the hypha is no longer able to function optimally.
conidiophore : aerial hypha bearing conidia.

conidium (plural, conidia) : nonmotile, asexual spore resulting from mitotic nuclear division and formed from the ends or sides of a hypha; produced in abundant numbers by the asexual phase of soil fungi in the phyla Ascomycota and Basidiomycota.

diplanetic : refers to a dimorphic species in which two swarming periods occur (Oomycota).
monoplanetic : refers to zoospores that have only one swarming period.
polyplanetic : refers to a species of Oomycota in which there are several swarming periods and incidentally only one type of zoospore (monomorphic).
reproduction includes ...

... a sexual or perfect stage (teleomorph) in which cells are formed by the process of mitosis (absent in Deuteromycota)

... non specialized hyphae fusion
... gametangia fusion

oogamous : refers to a type of fertilization in which two heterogametangia come in contact, and the contents of one flow into the other through a pore or tube.
gametangium : a structure that contains gametes.

antheridia : male gametangium found in Ascomycota, Oomycota and members of the order Monoblepharidales (Chytridiomycota).
oogonium : female gametangium containing one or more eggs.

oosphere : a large, naked, nonmotile female gamete.

periplasm : a layer of protoplasm surrounding the oosphere in some Oomycota.
oospore : thick-walled spore that develops from an oosphere through either fertilization or parthenogenesis.

ooplast : a membrane-bound cellular incision in the oospore of some Oomycota.

... gametes fusion

planogamete : motile gamete.

antherozoid : motile male gamete of the order Monoblepharidales (Chytridiomycota)

planogametic copulation : fusion of naked gametes, one or both of which are motile.

... and an asexual or imperfect stage (anamorph), through ...

... hyphae fragmentation
... spore formation

sporangiophore : a specialized hypha that bears a sporangium, mantaining it over the micelium, facilitating wind-mediated spore dispersion. Seen in several species of Oomycota (Phytophthora, Peronospora, Albugo)

sporangium : a saclike structure, the entire protoplasmic contents of which become converted into an indefinite number of spores (specialized reproductive cell, referred as sporangiospore in the phylum Zygomycota).

meiosporangium : a sporangium in which meiosis occurs; used in reference to certain Chytridiomycota.

meiospore : a spore formed after meiosis.

mitosporangium : sporangium in which mitosis occurs; used in reference to certain Chytridiomycota.

mitospore : a spore with a nucleus that has been formed by mitosis; an asexual spore.

zoosporangium : a mitosporangium that contains zoospores.

zoospore : a motile mitospore.

dimorphic : producing two morphologically distinct types of zoospores.
monomorphic : producing zoospores of a single morphological type.
nuclear cap : an aggregation of ribosomes that surrounds the nucleus in the zoospores of members of the Blastocladiales. The cap in the Blastocladiales is surrounded by two membranes that are continuous with the outer membrane of the nuclear envelope.
microbody-lipid globule complex : an association of lipid bodies, microbodies, mitochondria and membrane cisternae in zoospores of aerobic Chytridiomycota.

operculum (hinged cap): lid on a zoosporangium that, when popped off, or hinged open as here, allows the zoospores to escape. Sporangia that have this type of release mechanism are said to be operculate, otherwise referred as inoperculate.

asexual spores germinate without union with other cells
sexual spores of opposite mating types unite to form a zygote before germination occurs.

holomorph : whole fungus consisting of all sexual and asexual stages in its life cycle.

brown rot fungus : fungus that attacks cellulose and hemicellulose in wood, leaving dark-colored lignin and phenolic materials behind.
white rot fungus : fungus that attacks lignin, along with cellulose, and hemicellulose, leading to a marked lightening of the infected wood.
mycophagous : organisms that consume fungi, such as mycophagous nematodes.
mycophage or mycovirus : virus that infects fungi.
bothrosome : a cell surface organelle which produces the ectoplasmic network and through which there is continuity from the network matrix to the cell cytoplasm. Also referred to as a sagenogen. Only found in the Labyrinthulomycetes.

ectoplasmic net : a network of branching and anastomosing wall-less filaments which absorb nutrients and attach vegetative cells to the substrate.

endobiotic : reproductive structure is inside of the substrate or host cell.
epibiotic : reproductive structure is on the outside of the substrate or host cell.
heterokont : a biflagellate condition in which the two flagella are unequal in length, movement, or form; especially a cell with one trailing whiplash flagellum and one anteriorly directed flagellum bearing flagellar hairs (tinsel flagellum).
tinsel flagellum : a flagellum that bears hairs (mastigonemes) on the flagellar membrane.
polycentric : having a number of points of growth and development. Usually producing many sporangia (sp) or reproductive units. Polycentric organisms can be propagated by chopping up the vegetative rhizomycelium (rh) and plating the pieces on an appropriate medium.
rootlet or rhizoplast: a system of cytoplasmic microtubules and filaments associated with the kinetosome (basal body) and the nucleus of motile cells.
sclerotic bodies / muriform or sclerotic cells : a type of rounded cells surrounded by thick walls, characteristic of the dematiaceous fungi that cause chromoblastomycosis
zostera : a submersed marine aquatic herb used as a substrate by members of the Labyrinthulida (a.k.a. Labyrinthulomycota). A member of the Eel grass family (Monocot, Zosteraceae), it is found all along the coasts of North America and Europe

2 of the ways in which fungi make a living are as saprophytes , drawing sustenance from decaying matter, and as lichens , in which they form an intimate relationship with green algae or photosynthetic bacteria. Evidently, however, a single fungal species can adopt either lifestyle according to circumstance. Using molecular techniques, Wedin et al. looked at fungi living on different parts of European aspen (Populus tremula) in northern Sweden. On analysing four independent genomic markers, they found that three different species of a fungal genus (Stictis) grew directly on wood without bark as typical saprophytes; but when on the bark of the trunk, the same species associated with green algae to form a whitish, crust-like lichen. In both images the scale bar is 1 mm. The lichens had hitherto been placed in a separate genus, Conotrema. 35 years ago it was realized that the fruit bodies of Stictis and Conotrema are microscopically almost indistinguishable, but Stictis was not previously recognized as a lichen-forming genus. That species classified in separate genera are in fact the same organism exhibiting different biologies is a startling discovery. In all 3 cases, the wood-inhabiting non-lichenized and lichenized specimens were mixed together in phylogenetic trees. The ability of a fungus to opt for different nutritional modes means that individual species can exploit a wider range of habitats. If the spores that are shot from the fruits of these fungi land on wood, they establish themselves as saprophytes; if they land on bark where appropriate algae are present, they form lichens. The frequency of this plasticity in lifestyles is unknown. But it may be common, at least in this group of fungi, as the three species able to become optionally lichenized were found on a single species of tree. The study reinforces the case for never treating lichens as anything other than a lifestyle category among the fungi. It also shows the wisdom of the 1959 decision to restrict the scientific names of lichens to the fungal partners; in consequence, the same names can be used for the fungi regardless of their lifestyle.
5 sub-groups are recognised :

lower Fungi or Phycomycetes

Mastigomycotina or Chytridiomycota. Typically unicellular, or with primitive chains of cells attached to a food base by tapering rhizoids; sexual reproduction is by fusion of motile gametes; asexual reproduction is by cytoplasmic cleavage in a sporangium, producing motile, uniflagellate zoospores. They also have centrioles. Chytrid is a general term used to describe fungal organism in the phylum Chytridiomycota that consists of a spherical cell from which short thin filamentous branches (rhizoids) grow that resemble fine roots; previously restricted to members of the Chytridiales.
Zygomycota or Zygomycotina (conjugating Fungi). > 600 species. Typically grow as coenocytic hyphae; sexual reproduction is by fusion of sex organs (gametangia) leading to thick-walled resting spores (zygospores), with swellings on either side termed suspensors; asexual reproduction is by cytoplasmic cleavage in a sporangium on an aerial hypha termed a sporangiophore, producing non-motile spores. Saprophytes or parasites. The appearance of these structures leads to the common name "pin moulds".

higher Fungi

Ascomycota (sac Fungi). > 30,000 species + > 25,000 species in lichens. Grow as hyphae with cross-walls (septa) or unicellular (yeasts); sexual reproduction is by fusion of modified hyphae (or yeasts), sometimes by fusion of a "male" spore (spermatium) with a "female" receptive hypha (trichogyne), leading to development of one or more asci. Once they fuse and begin to grow as one, the nuclei are shared, but do not fuse (there is no karyogamy). Each pair of nuclei are contained within compartments created by septations - crosswalls with simple pores. So, the new hyphae formed is called dikaryotic (n+n). The dikaryotic nuclei fuse at a special region called a crozier (resembles a fiddlehead) and a sac is formed. Within the sac, the nuclei go through meiosis and form the 4 haploid spores. Usually in these fungi, the spores then go through a round of mitosis and form 8 final ascospores in each ascus. Asexual reproduction as in the Deuteromycota.

Woronin body : spherical structure associated with the simple pore in the septa separating hyphal compartments.
carp : a fruiting body of a fungus

ascocarp / ascoma : the fruiting body of an ascomycetous fungus, including the

ascus : the sporangium or spore case of certain lichens and fungi, consisting of a single terminal cell

paraphysis : a sterile thread alongside the spore sac or sexual organs in the hymenial layer of some fungi, especially ascomycetes; also found in mosses and ferns.

bitunicate ascus : a cylindrical ascus whose wall has two layers; at maturity, the outer layer splits and the inner layer expands during expulsion of spores

Bitunicatae : in fungal taxonomy, a series of the subphylum Ascomycotina, consisting of those having a bitunicate ascus. It includes the orders Dothideales and Erysiphales.

prototunicate ascus : a type of ascus that is more or less spherical (as opposed to cylindrical) and has a thin wall that ruptures or disintegrates at maturity to release spores
unitunicate ascus : a cylindrical ascus whose wall has a single layer. There are two types: the operculate type has a small cap at the end of the ascus, which pops open when the mature organism is ready to eject its spores; and the inoperculate type has no cap and ejects its spores through a pore or slit that momentarily opens.

ascospores (a sexual spore formed within a special sac, or ascus, as in ascomycetous fungi).

apothecium : an open or expanded fruiting body seen in lichens and actinomycetous fungi, having asci contained on its exposed surface.
cleistothecium : the fruiting body (ascocarp) produced by certain ascomycetes, in which there is no pore for the escape of ascospores, the spores being released by rupture or decay of the body.
gymnothecium : a type of fruiting body (ascocarp) composed of a loose network of mycelia through which ascospores filter and are released at maturity; its reproductive organs are in the form of naked asci. Seen in fungi of the family Gymnoascaceae.
perithecium : the flask-shaped fruiting body of certain molds and ascomycetous fungi having a pore for the escape of spores

basidiocarp : the large fruiting body characteristic of the majority of fungi of the subphylum Basidiomycotina; it is composed of masses of intertwined hyphal elements and produces basidia. Mushrooms and toadstools are common examples

Basidiomycota. > 25,000 species. Grow as hyphae divided by perfored septa or yeasts; asexual spores are relatively rare; sexual reproduction is by fusion of compatible hyphae, leading ultimately to production of basidiospores on basidia, sometimes on or in a fruiting body. The basidiomycota include the economically important rust fungi of crop plants and the mushroom- and toadstool-producers.

dolipore septum : specialized crosswall separating compartments of a hypha, consisting of a central pore covered with perforated membranes on both sides (called a parenthosome).
clamp connection : small branch of a fungal hypha that connects two compartments separated by a septum and helps to maintain a dikaryon in each hyphal compartment; characteristic of fungi in the phylum Basidiomycota.
basidioma (plural, basidiomata) / basidiocarp / mushrooms: fruiting body that produces basidia. The mycelium from which it arises may have a diameter up to 35 meters !

Deuteromycota or deuteromycotina (Fungi imperfecti). > 25,000 species. Grow as hyphae (with septa) or unicellular (yeasts); sexual reproduction is absent, rare or unknown; asexual spores (conidia) are formed in various ways from hyphae but never by cytoplasmic cleavage in a sporangium. Once the sexual stage is observed, the species is renamed and placed in the appropriate division.

organisms with a fungal lifestyle (Kingdom Stramenopila)but with cellulose walls and with cellular and biochemical features resembling those of plants, constituting most or marine phytoplankton. The Kingdom Stramenopila contains ...

Phaeophyta or brown algae
Chrysophyta or golden algae
Bacillariophyta or diatoms
Oomycota or water molds. They grow as coenocytic hyphae; asexual reproduction is by formation of motile, biflagellate zoospores (with one tinsel and one whiplash flagella) in a sporangium; sexual reproduction is by fusion of a "male" sex organ (antheridium) with a "female" sex organ (oogonium), leading to production of thick-walled resting spores (oospores).
Labyrinthulomycota : there is little known about this group of organisms. Often they are classified with the slime molds. They possess a structure called a net-plasmodium during the vegetative stage. The asexual cells are motile and fusiform in shape. There does not appear to be a sexual stage.
Hyphochytridiomycota : aquatic, marine or freshwater chytrid-like organisms. They were previously classified as a class containing one order and 15 known species. Members possess motile spores which have an anteriorly, tinsel flagella. They can be parasitic on algae or fungi. The cell wall is made of chitin and the thallus is either holocarpic or eucarpic. The zoosporangia release zoospores through discharge tubes. Little is known about their means of sexual reproduction.

organisms with some fungus-like features, but which grow as wall-less protoplasmic stages. There are several unrelated organisms in this group :

Acrasiomycetes or acrasids and dictyostelids (cellular slime moulds). These are amoeboid organisms that engulf Bacteria and other food particles by phagocytosis; they aggregate to form a fungus-like fruiting body that releases dry, air-borne spores.
Hydromyxomycetes
Myxomycetes (plasmodial slime moulds). Grow as a network of protoplasm (the plasmodium) that engulfs bacteria and other food particles; at the onset of starvation they form fruiting bodies (pseudoplasmodium) that release dry, air-borne spores.
Plasmidiophoromycetes or plasmodiophoromycota or plasmidiophorids. Obligate intracellular parasites of Fungi, Algae and higher plants; they grow as naked plasmodia in the host cells.

general resources

bibliography

Farr, D.G. et al. 1989. Fungi on Plants and Plant Products in the United States. American Phytopathological Society Press.
Hawksworth, D.L.et al. 1995. Ainsworth Bisby's Dictionary of the Fungi (8^th edition). CAB International.
McLaughlin, E.J., McLaughlin, E.G., and P.A. Lemke. 2001. The Mycota. VII. Systematics and Evolution. Springer-Verlag.
Rossman, A.Y., M.E. Palm, and L.J. Spielman. 1987. A Literature Guide for the Identification of Plant Pathogenic Fungi. American Phytopathological Society Press.
Kurtzman, C.P. and J.W. Fell (Eds.). 1998. The Yeasts: A Taxonomic Study (4^th edition). Elsevier.
Alexopoulous, C. J., Mims, C. W., and M. Blackwell. 1996. Introductory Mycology. John Wiley & Sons, New York.

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