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Eumycota: mushrooms, sac fungi, yeast, molds, rusts, smuts, etc.

Meredith Blackwell, Rytas Vilgalys, and John W. Taylor
Chytridium growing on a single pine pollen grain. Successive photos show zoospore release from the sporangium, and the arrow points to a flagellum.Black sporangium atop swollen Pilobolus sporangiophoreMassed fruiting bodies of the chicken-of-the-woodsFruiting body of the scarlet cup fungus
taxon links [down<--]Eukaryotes [up-->]Basidiomycota [up-->]Ascomycota [up-->]Glomeromycota Not Monophyletic [up-->]Chytridiomycota Not Monophyletic [up-->]Zygomycota Interpreting the tree
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This tree diagram shows the relationships between several groups of organisms.

The root of the current tree connects the organisms featured in this tree to their containing group and the rest of the Tree of Life. The basal branching point in the tree represents the ancestor of the other groups in the tree. This ancestor diversified over time into several descendent subgroups, which are represented as internal nodes and terminal taxa to the right.

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Phylogeny modified from Bruns et al. 1991, 1993

Containing group: Eukaryotes


The organisms of the fungal lineage include mushrooms, rusts, smuts, puffballs, truffles, morels, molds, and yeasts, as well as many less well-known organisms (Alexopoulos et al., 1996). About 70,000 species of fungi have been described; however, some estimates of total numbers suggest that 1.5 million species may exist (Hawksworth, 1991; Hawksworth et al., 1995).

As the sister group of animals and part of the eukaryotic crown group that radiated about a billion years ago, the fungi constitute an independent group equal in rank to that of plants and animals. They share with animals the ability to export hydrolytic enzymes that break down biopolymers, which can be absorbed for nutrition. Rather than requiring a stomach to accomplish digestion, fungi live in their own food supply and simply grow into new food as the local environment becomes nutrient depleted.

Most biologists have seen dense filamentous fungal colonies growing on rich nutrient agar plates, but in nature the filaments can be much longer and the colonies less dense. When one of the filaments contacts a food supply, the entire colony mobilizes and reallocates resources to exploit the new food. Should all food become depleted, sporulation is triggered. Although the fungal filaments and spores are microscopic, the colony can be very large with individuals of some species rivaling the mass of the largest animals or plants.

hyphaeimage info

Figure 1: Hyphae of a wood-decaying fungus found growing on the underside of a fallen log. The metabolically active hyphae have secreted droplets on their surfaces. Copyright ? M. Blackwell 1996.

Prior to mating in sexual reproduction, individual fungi communicate with other individuals chemically via pheromones. In every phylum at least one pheromone has been characterized, and they range from sesquiterpines and derivatives of the carotenoid pathway in chytridiomycetes and zygomycetes to oligopeptides in ascomycetes and basidiomycetes.

Within their varied natural habitats fungi usually are the primary decomposer organisms present. Many species are free-living saprobes (users of carbon fixed by other organisms) in woody substrates, soils, leaf litter, dead animals, and animal exudates. The large cavities eaten out of living trees by wood-decaying fungi provide nest holes for a variety of animals, and extinction of the ivory billed woodpecker was due in large part to loss, through human activity, of nesting trees in bottom land hardwoods. In some low nitrogen environments several independent groups of fungi have adaptations such as nooses and sticky knobs with which to trap and degrade nematodes and other small animals. A number of references on fungal ecology are available (Carroll and Wicklow, 1992; Cooke and Whipps, 1993; Dix and Webster, 1995).

However, many other fungi are biotrophs, and in this role a number of successful groups form symbiotic associations with plants (including algae), animals (especially arthropods), and prokaryotes. Examples are lichens, mycorrhizae, and leaf and stem endophytes. Although lichens may seem infrequent in polluted cities, they can form the dominant vegetation in nordic environments, and there is a better than 80% chance that any plant you find is mycorrhizal. Leaf and stem endophytes are a more recent discovery, and some of these fungi can protect the plants they inhabit from herbivory and even influence flowering and other aspects of plant reproductive biology. Fungi are our most important plant pathogens, and include rusts, smuts, and many ascomycetes such as the agents of Dutch elm disease and chestnut blight. Among the other well known associations are fungal parasites of animals. Humans, for example, may succumb to diseases caused by Pneumocystis (a type of pneumonia that affects individuals with supressed immune systems), Coccidioides (valley fever), Ajellomyces (blastomycosis and histoplasmosis), and Cryptococcus (cryptococcosis) (Kwon-Chung and Bennett, 1992).

Rhizopogon rubescensimage info

Figure 2: The fluffy white hyphae of the mycorrhizal fungus Rhizopogon rubescens has enveloped the smaller roots of a Virginia pine seedling. Note that some of the mycelium extends out into the surrounding environment. Copyright ? J. B. Anderson 1996.

Entomophthoraimage info

Figure 3: Entomophthora, "destroyer of insects", is the agent of a fungual infection that kills flies. After their death the fungal growth erupts through the fly cuticle, and dispersal by forcible spore discharge is a source of inoculum for infection of new flies. Copyright ? G. L. Barron 1996.

Fungal spores may be actively or passively released for dispersal by several effective methods. The air we breathe is filled with spores of species that are air dispersed. These usually are species that produce large numbers of spores, and examples include many species pathogenic on agricultural crops and trees. Other species are adapted for dispersal within or on the surfaces of animals (particularly arthropods). Some fungi are rain splash or flowing water dispersed. In a few cases the forcible release of spores is sufficient to serve as the dispersal method as well. The function of some spores is not primarily for dispersal, but to allow the organisms to survive as resistant cells during periods when the conditions of the environment are not conducive to growth.

Fungi are vital for their ecosystem functions, some of which we have reviewed in the previous paragraphs. In addition a number of fungi are used in the processing and flavoring of foods (baker's and brewer's yeasts, Penicillia in cheese-making) and in production of antibiotics and organic acids. Other fungi produce secondary metabolites such as aflatoxins that may be potent toxins and carcinogens in food of birds, fish, humans, and other mammals.

A few species are studied as model organisms that can be used to gain knowledge of basic processes such as genetics, physiology, biochemistry, and molecular biology with results that are applicable to many organisms (Taylor et al., 1993). Some of the fungi that have been intensively studied in this way include Saccharomyces cereviseae, Neurospora crassa, and Ustilago maydis.

Most phyla appear to be terrestrial in origin, although all major groups have invaded marine and freshwater habitats. An exception to this generality is the flagellum-bearing phylum Chytridiomycota, which probably had an aquatic origin; however, some chytrid species do occur in terrestrial environments, primarily as plant pathogenic fungi.


Fungi are characterized by non-motile bodies (thalli) constructed of apically elongating walled filaments (hyphae), a life cycle with sexual and asexual reproduction, usually from a common thallus, haploid thalli resulting from zygotic meiosis, and heterotrophic nutrition. Spindle pole bodies, not centrioles, usually are associated with the nuclear envelope during cell division. The characteristic wall components are chitin (beta-1,4-linked homopolymers of N-acetylglucosamine in microcrystalline state) and glucans primarily alpha-glucans (alpha-1,3- and alpha-1,6- linkages) (Griffin, 1994).

Aspergillus flavusimage info

Figure 4: Portion of a hypha of a zygomycete stained with a blue dye to show the many nuclei present. Many other fungi have septations that devide the hyphae into compartments that usually contain one to several nuclei per compartment. Copyright ? M. Blackwell 1996.

zygomyceteimage info

Figure 5: Transmission electron micrograph showing duplicated spindle pole body of a prophase I meiotic nucleus of a basidiomycete Exobasidium. Only chytrids among fungi have centrioles and lack spindle pole bodies. Copyright ? Beth Richardson 1996.

Exceptions to this characterization of fungi are well known, and include the following: Most species of Chytridiomycota have cells with a single, smooth, posteriorly inserted flagellum at some stage in the life cycle, and centrioles are associated with nuclear division. The life cycles of most Chytridiomycota are poorly studied, but some (Blastocladiales) are known to have zygotic meiosis (therefore, alternation between haploid and diploid generations). Certain members of Zygomycota, Ascomycota, and Basidiomycota may lack hyphal growth during part or all of their life cycles, and, instead, produce budding yeast cells. Most fungal species with yeast growth forms contain only minute amounts of chitin in the walls of the yeast cells. A few species of Ascomycota (Ophiostomataceae) have cellulose in their walls, and certain members of Chytridiomycota (Coelomomycetales) lack walls (Alexopoulos et al., 1996).

Fossil Record

Based on the available fossil record, fungi are presumed to have been present in Late Proterozoic (900-570 mya). Terrestrial forms of purported ascomycetes are reported in associations with microarthropods in the Silurian Period (438-408 mya) (Sherwood-Pike and Gray, 1985). Fossil hyphae in association with wood decay and fossil chytrids and Glomales-Endogenales representatives associated with plants of the Rhynie Chert are reported from the Devonian Period (408-360 mya) (Hass et al., 1994; Remy et al., 1994a, 1994b; Taylor et al., 1994a, 1995b). Fungal fossil diversity increased throughout the Paleozoic Era (Taylor et al., 1994b) with all modern classes reported in the Pennsylvanian Epoch (320-286 mya).

A first attempt to match molecular data on fungal phylogeny to the geological record shows general agreement, but does point out some conflicts between the two types of data (Berbee and Taylor 1993).


Wherever adequate moisture, temperature, and organic substrates are available, fungi are present. Although we normally think of fungi as growing in warm, moist forests, many species occur in habitats that are cold, periodically arid, or otherwise seemingly inhospitable. It is important to recognize that optimum conditions for growth and reproduction vary widely with fungal species. Diversity of most groups of fungi tends to increase in tropical regions, but detailed studies are only in their infancy (Isaac et al., 1993).

Although many saprobic and plant pathogenic species with low substrate specificity and effective dispersal systems have broad distributions, gene flow appears to be restricted in many fungi. For these species large bodies of water such as the Atlantic and Pacific Oceans create barriers to gene exchange. Some distributions are limited by substrate availability, and dramatic examples come from parasites of Gondowanan plants; one of these is the Southern Hemisphere distribution of the ascomycete Cyttaria, corresponding with part of the distribution of its host plant Nothofagus. The fossil record shows that fungi were present in Antarctica, as is the case for other organisms with Gondwanan distributions. Arthropod associates also may show distributions throughout part or all of a host range, and some fungal species (ex. wood wasp associates) occur outside the range of the associated arthropod.

Notable Fungi

Discussion of Phylogenetic Relationships

As presently delimited, the kingdom Fungi is believed to constitute a monophyletic group that shares some characters with animals such as chitinous structures, storage of glycogen, and mitochondrial UGA coding for tryptophan. Only species of the basal Chytridiomycota possess the primitive character of a single smooth, posteriorly inserted flagellum (Barr, 1992; Cavalier-Smith, 1987, 1995).

The branch uniting the fungi and animals is well-supported from nuclear small subunit ribosomal RNA gene (SSU rDNA, or 18S rDNA) sequence analysis, and also has been supported with studies of elongation factor and three other proteins: alpha- and beta-tubulin and actin (Baldauf and Palmer, 1993; Bruns et al., 1991; Wainright et al., 1993). However, the hypothesis has been challenged by comparison of RNA polymerase gene sequences and reanalysis of SSU rDNA data (Rodrigo et al., 1994; Sidow and Thomas, 1994).

In the absence of many derived morphological (other than hyphal growth in some species) and biochemical characters, Chytridiomycota (previously characterized by the presence of a flagellate cell in the life cycle) now has been redefined by SSU rDNA sequence analysis. The study also has shown that some non-flagellate species traditionally placed in Zygomycota actually are chytrids (ex. Basidiobolus ranarum) (Nagahama et al., 1995).

Zygomycota as traditionally delimited on the basis of often non-septate hyphae and production of zygospores is not monophyletic. The position of some lineages such as that of Glomales and of Engodonales-Mortierellales is unclear, but they too may lie outside Zygomycota as independent lineages basal to the Ascomycota-Basidiomycota lineage (Bruns et al., 1993; K. O'Donnell, personal communication, 1996).

Evidence from shared morphological characters such as regularly septate hyphae and a dikaryotic stage (two separate and different nuclei in a single hyphal segment) in the life cycle, usually has been interpreted as support for a close relationship between Basidiomycota and Ascomycota. SSU rDNA adds support for this hypothesis (Berbee and Taylor, 1992).

Molecular characters have been essential for phylogenetic analysis in cases when morphological characters are convergent, reduced, or missing among the taxa considered. This is especially true of species that never reproduce sexually, because characters of sexual reproduction traditionally have been the basis for classification of Fungi. Use of molecular characters allows asexual fungi to be placed among their closest relatives. Excluded groups previously considered to be Fungi are stramenopiles (Oomycota, Hyphochytriomycota, and Labyrinthulomycota) and slime molds (Myxomycota, Plasmodiomycota, Dictyosteliomycota, Acrasiomycota) (Bhattacharya et al., 1992; Leipe et al., 1994; Van der Auwera et al., 1995).


Alexopoulos, C. J., C. W. Mims, and M. Blackwell. 1996. Introductory Mycology (4th Ed.). John Wiley and Sons, New York, USA. 868p.

Baldauf, S. L., and J. D. Palmer. 1993. Animals and fungi are each other's closest relatives: congruent evidence form multiple proteins. Proceedings of the National Academy of Sciences (USA) 90:11558-11562.

Barr, D. J. S. 1992. Evolution and kingdoms of organisms from the perspective of a mycologist. Mycologia 84:1-11.

Berbee, M. L., and J. W. Taylor. 1992. Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequence. Molecular Biology and Evolution 9:278-284.

Berbee, M. L., and J. W. Taylor. 1993. Dating the evolutionary radiations of the true fungi. Canadian Journal of Botany 71:1114-1127.

Bhattacharya, D., L. Medlin, P. O. Wainright, E. V. Ariztia, C. Bibeau, S. K. Stickel, and M. L. Sogin. 1992. Algae containing chlorophylls a +c are paraphyletic: molecular evolutionary analysis of the Chromophyta. Evolution 46:801-1817.

Bruns, T. D., T. J. White, and J. W. Taylor. 1991. Fungal molecular systematics. Annual Review of Ecology and Systematics 22:525-564.

Bruns, T. D., R. Vilgalys, S. M. Barns, D. Gonzalez, D. S. Hibbett, D. J. Lane, L. Simon, S. Stickel, T. M. Szaro, W. G. Weisburg, and M. L. Sogin. 1993. Evolutionary relationships within the fungi: analysis of nuclear small subunit rRNA sequences. Molecular Phylogenetics and Evolution 1:231 241.

Carroll, G.C., and D.T. Wicklow. 1992. The Fungal Community: Its Organization and Role in the Ecosystem. Marcel Deker, Inc., New York.

Cavalier-Smith, T. 1987. The origin of Fungi and Pseudofungi. Pp. 339-353. In: Evolutionary Biology of the Fungi. Eds. A. D. M. Rayner, C. M. Brasier, and D. Moore. Cambridge University Press, Cambridge, United Kingdom.

Cooke, R.C., and J.M. Whipps. 1993. Ecophysiology of Fungi. Blackwell Scientific Pub., London, U.K.

Dix, N.J., and J.W. Webster. 1995. Fungal Ecology. Capman and Hall. London, U.K.

Griffin, D. 1993. Fungal Physiology (2nd Ed.). Wiley-Liss. New York.

Hasegawa, M., T. Hashimoto, J. Adachi, N. Iwabe, and T. Miyata. 1993. Early branchings in the evolution of eukaryotes: ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. Journal of Molecular Evolution 36:380-388.

Hass, H., T. N. Taylor, and W. Remy. 1994. Fungi from the Lower Devonian Rhynie Chert - mycoparasitism. American Journal of Botany 81:29-37.

Hawksworth, D. L. 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycological Research 95:641-655.

Hawksworth, D. L., P. M. Kirk, B. C. Sutton, and D. N. Pegler. 1995. Ainsworth and Bisby's Dictionary of the Fungi (8th Ed.). CAB International, Wallingford, United Kingdom. 616p.

Isaac, S., J. C. Frankland, R. Watling, and A. J. S. Whalley. 1993. Aspects of Tropical Mycology. Cambridge University Press, Cambridge, U.K.

Kwon-Chung, K.J., and J.E. Bennett. 1992. Medical Mycology. Lea and Febiger, Philadelphia.

Leipe, D. D., P. O. Wainright, J. H. Gunderson, D. Porter, D. J. Patterson, F. Valois, S. Himmerich, and M. L. Sogin. 1994. The straminopiles from a molecular perspective: 16S-like rRNA sequences from Labyrinthula minuta and Cafeteria roenbergensis. Phycologia 33:369-377.

Nagahama, T., H. Sato, M. Shimazu, and J. Sugiyama. 1995. Phylogenetic divergence of the entomophthoralean fungi: evidence from nuclear 18S ribosomal RNA gene sequences. Mycologia 87:203-209.

Matthews, P. (Ed.). 1994. Guinness Book of Records. Bantum Books, New York. 819p.

Remy, W., T. N. Taylor, and H. Hass. 1994a. Early Devonian fungi - a blastocladalean fungus with sexual reproduction. American Journal of Botany 81:690-702.

Remy, W., T. N. Taylor, H. Hass, and H. Kerp. 1994b. Four hundred-million-year-old vesicular arbuscular mycorrhizae. Proceedings of the National Academy of Sciences (USA) 91:11841-11843.

Rodrigo, A. G., P. R. Bergquist, and P. I. Bergquist. 1994. Inadequate support for an evolutionary link between the metazoa and the fungi. Systematic Biology 43:578-584.

Sherwood-Pike, M. A., and J. Gray. 1985. Silurian fungal remains: probable records of the class Ascomycota. Lethaia 18:1-20.

Sidow, A., and W. K. Thomas. 1994. A molecular evolutionary framework for eukaryotic model organisms. Current Biology 4:596-603.

Taylor, J. W., B. Bowman, M. L. Berbee, and T. J. White. 1993. Fungal model organisms: phylogenetics of Saccharomyces, Aspergillus and Neurospora.. Systematic Biology 42:440-457.

Taylor, T. N., W. Remy, H. Hass 1994a. Allomyces in the Devonian. Nature 367:601-601.

Taylor, T. N., J. Galtier, B. J. Axsmith. 1994b. Fungi from the Lower Carboniferous of central France. Review of Palaeobotany and Palynology 83:253-260.

Taylor, T. N., W. Remy, H. Hass, H. Kerp. 1995a. Fossil arbuscular mycorrhizae from the Early Devonian. Mycologia 87:560-573.

Van der Auwera, G., R. De Baere, Y. Van de Peer, P. De Rijk, I. Van den Broeck, and R. De Wachter. 1995. The phylogeny of Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. Molecular Biology and Evolution 12:671-678.

Wainright, P. O., G. Hinkle, M. L. Sogin, and S. K. Stickel. 1993. Monophyletic origins of the Metazoa: an evolutionary link with fungi. Science 260:340-342.

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Title Illustrations
Scientific Name Chytridium (Chytridiomycota)
Comments Individual growing on a single pine pollen grain. Successive photos show zoospore release from the sporangium, and the arrow points to a flagellum.
Copyright © 1996 H. Whisler, M. Fuller
Scientific Name Pilobolus (Zygomycota)
Comments Black sporangium atop swollen sporangiophore. Shortly, the swollen subsporangial vesicle will burst to send the sporangium flying. Herbivores eat the sporangium, and the enclosed mitospores germinate in the dung. The bright yellow carotenoid pigment enables the sporangium to orient to light (phototropism). If you look closely, you can see masses of nematodes on the vesicle; probably herbivore pathogens hoping to hitch a ride.
Specimen Condition Live Specimen
Copyright © 1996 Meredith Blackwell
Scientific Name Laetiporus sulphureus (Basidiomycota)
Comments Massed fruiting bodies of the chicken-of-the-woods. The tiny tubular filaments (hyphae) that make the body of this fungus (mycelium) are growing in the old, dead wood of a large cherry tree. Laetiporus is not a parasite, but the decay may weaken the tree so much that wind or ice storms can topple it.
Specimen Condition Live Specimen
Copyright © 1996 Meredith Blackwell
Scientific Name Scarcoscypha coccinea (Ascomycota)
Comments Fruiting body of the scarlet cup fungus. Hundreds of millions of meiospores (ascospores) are discharged from this cup, usually in puffs that produce visible clouds of spores.
Specimen Condition Live Specimen
Copyright © 1996 Joey Spatafora
About This Page

Many thanks to Soren Rosendahl and Atul Batra for scanning photos and David Maddison and Atul Batra for page design advice.

Meredith Blackwell

Department of Plant Biology
Louisiana State University
Baton Rouge
Louisiana 70803, USA

Rytas Vilgalys

Department of Botany
Duke University
Durham, NC 27708-0338

John W. Taylor

Department of Plant and Microbial Biology
321 Koshland Hall
University of California
Berkeley, CA 94720-3120

Correspondence regarding this page should be directed to Meredith Blackwell at

Citing this page:

Blackwell, Meredith, Vilgalys, Rytas, and Taylor, John W. 2005. Fungi. Eumycota: mushrooms, sac fungi, yeast, molds, rusts, smuts, etc.. Version 14 February 2005 (under construction). http://tolweb.org/Fungi/2377/2005.02.14 in The Tree of Life Web Project, http://tolweb.org/

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