A number of unrelated organisms share some of the characteristic features of fungi: they are eukaryotic, nonphotosynthetic chemoheterotrophs that reproduce by spores, many have extracellular digestion and absorptive nutrition, and most have a filamentous growth form. True fungi are further characterized by cell walls containing a mixture of glucan, mannan, and chitin, but not cellulose, and by production
FIGURE 6.2 (Continued)
named sequences. The tree includes only the names of environmental sequences. Major clade names follow Hibbett and Thorn (2001), plus the Ceratobasidiales and Heterobasidiomycetes (Russ, russu-loid; G/P, gomphoid/phalloid; Heterobasids, Heterobasidiomycetes). Minor clade names (approximately generic names) follow Moncalvo et al. (2002). Occurrence of minor clades in four treatments is shown at right: T1, corn-soybean-wheat rotation with regular tillage and inputs; T2, no-till corn-soybean-wheat rotation with regular inputs; T7, successional site, burned every spring since tillage ceased in 1989; T8, never-tilled native meadow, mown in fall.
of the membrane sterol ergosterol (Alexopoulos et al., 1996). Molecular phyloge-netic studies are gradually piecing together the relationships of some of these groups, about which we know very little compared to vascular plants or metazoan animals. Early studies were limited by the small number of representatives in culture, but the growing "Tree of Life" project (e.g., Lutzoni et al., 2004) and broad-scale sequencing of environmental DNA (e.g., Venter et al., 2004) are obtaining sequences for novel taxa and discovering many previous unknown lineages among fungi and basal eukaryotes (e.g., Vandenkoornhuyse et al., 2002; Schadt et al., 2003). Funguslike members of the "protist" Phylum Cercozoa are represented in soil by soil-borne plant pathogens Plasmodiophora and Spongospora (Plasmodiophoromycetes), which infect roots via biflagellate zoospores and then form a multinucleate plasmodium within their hosts (Braselton, 2001). Diverse unrecognized lineages of this phylum are apparently widespread (Bass and Cavalier-Smith, 2004). The Oomycota (Heterokonta) include Pythium and Phytophthora, two genera of important soil-borne plant pathogens with broad host ranges (Erwin et al., 1983; Martin, 1992; Levesque and de Cock, 2004). Infection is via biflagellate zoospores that germinate to form broad, rapidly growing tubular hyphae. Oomycotans differ substantially from true fungi in the chemistry of their cell walls and membranes, particularly the presence of cellulose in cell walls and the absence of ergosterol in membranes and also in ploidy, being diploid rather than haploid or dikaryotic (Fuller and Jaworski, 1987; Dick, 2001). Their flagella include a posterior whiplash flagellum and an anterior tinsel flagellum. The Hyphochytriomycota are a small group of little or no known economic importance; their zoospores have a single anterior tinsel flagellum, but molecular and ultrastructural evidence places them together with the biflagellate heterokont organisms such as Oomycota and chromistan algae (Fuller, 2001). Hyphochytrium and Rhizidiomyces may be sapro-trophs or parasites of fungi or other soil organisms. Molecular evidence places the Labyrinthulomycota together with heterokont protists such as Oomycota (Cavalier-Smith, 2004). Labyrinthula have fusoid cells that glide in an extracellular, netlike slime; they are pathogens of marine plants and algae and of vascular plants in saline soils (Bigelow et al., 2005). The Phylum Mycetozoa (=Myxomycota, or slime molds) includes organisms with a mixture of characters resembling fungi and animals: reproduction by spores and ingestion of food by phagocytosis (Baldauf and Doolittle, 1997). Spores of slime molds germinate to form amoebae, which aggregate to form a slime phase that eventually differentiates to form fruiting bodies with spores. In the Class Dictyosteliomycetes (Raper, 1984), the slime phase (pseudoplasmodium) consists of cells that maintain their separate membranes, whereas in the Myxomycetes, the plasmodium is a coenocytic mass of nuclei in a slimy matrix. Both amoeboid and plasmodial phases are phagotrophic on bacteria, spores, and detritus and are probably very important in releasing nutrients that are immobilized in these cells and substrates. Approximately 1000 species in 80 genera are known. Plasmodia and fruiting bodies of some Myxomycetes can be quite conspicuous in lawns and gardens during the summer months (Martin and Alexopoulos, 1969; Stephenson and Stempen, 1994).
FUNGI (CHYTRIDIOMYCOTA, GLOMEROMYCOTA, ZYGOMYCOTA, ASCOMYCOTA, AND BASIDIOMYCOTA)
The chytrids are a relatively small group of approximately 1000 species in 120 genera (Kirk et al., 2001). Soil chytrids include plant pathogens such as Synchytrium and Olpidium, nematode parasites such as Catenaria, parasites of algae such as Chytridium, and saprobes such as Allomyces and Chytriomyces. The soil chytrids possess motile zoospores powered by a single, posterior flagellum and are thought to be close to the common ancestor of fungi and animals (Mendoza et al., 2002; James et al., 2006). Recognition of the Phylum Glomeromycota (Schuessler et al., 2001) resolves some of the problems seen in earlier phylogenetic analyses in which chytrids formed a monophyletic group that divided the zygomycetes or found that both groups were paraphyletic with respect to the other. Gomeromycota and chytrids share ancient sequences for tubulin genes, remarkably conserved despite the age of their divergence (Corradi et al., 2004). Together, the chytrids, Glomeromycota, and Zygomycota differ from the Ascomycota and Basidiomycota in that they have broad, coenocytic hyphae, with multiple haploid nuclei per cell, whereas the Ascomycota and Basidiomycota typically have uninucleate haploid primary mycelia and binucleate (di-haploid) secondary mycelia. The name Phyco-mycetes was formerly used to refer to the coenocytic fungi (sometimes together with the unrelated Oomycota). Regrettably, the best general references to these fungi are quite old (e.g., Sparrow, 1960; Karling, 1977), although there has been a resurgence in research on this group (Barr, 2001).
The Glomales (Phylum Glomeromycota) are the fungal symbionts of arbuscular mycorrhizas (also known as endomycorrhizas). They were recently transferred from the Zygomycota to a new phylum on the basis of molecular phylogenetic information, which is supported by their great age (at least 500 My) and unique biology (Schuessler et al., 2001). Broad, multinucleate hyphae extend from plant roots into soil and aid in uptake of water and nutrients, particularly phosphate (Smith and Read, 1997). Large, multinucleate asexual spores (sometimes referred to as chlamydospores or azygospores) are formed in soil or roots, and the morphology of these spores forms almost the sole basis for their taxonomy. Glomalin, a glyco-protein excreted by glomalean fungi, is associated with aggregate stability in soils (Wright and Upadhyaya, 1998; Rillig, 2004). Approximately 150 species in six genera are known (Kirk et al., 2001), and these form symbioses with approximately 70% of all land plants, particularly herbaceous plants and woody plants of the tropics (Brundrett, 2002). Taxonomic and ecological references to the group include Gerdemann and Trappe (1974) and Morton and Benny (1990).
Within the Zygomycota are two very different classes of fungi: the Trichomycetes and Zygomycetes. Trichomycetes (about 200 species) are obligate endosymbionts of arthropods (Benny, 2001; Kirk et al., 2001). Approximately 800 species in eight orders of Zygomycetes are known (Benny et al., 2001; Kirk et al., 2001). Many are saprobes (Mucorales and relatives), and others are parasites of arthropods and other invertebrates or of other fungi (Zoopagales, Entomophthorales, and Kickxellales). Rhizopus and Mucor (both Mucorales) are weedy molds readily isolated from soil. In the earlier literature, the saprobic Mucorales were often referred to as "sugar fungi." The accompanying view held that these organisms are rapid colonists making use of the soluble sugars before secondary colonists become established during the succession of different fungi on rich and freshly deposited substrates such as dung and fallen fruits (Garrett, 1963). In reality, the early appearance of Mucorales on such substrates reflects their rapid rates of growth and sporulation; in many cases the "secondary colonists" are already there and digesting the more recalcitrant substrates, but are slower to sporulate and come to our notice (Pugh, 1974; Cooke and Rayner, 1984). Still, the term "sugar fungi" accurately portrays the typical growth substrate of these fungi. They are not noted for their extracellular degradative enzymes and may frequently depend on soluble breakdown products provided by lignocellulose-degrading ascomycetes or basid-iomycetes (Cooke and Rayner, 1984). From here, it may have been a short step to direct, biotrophic parasitism of the decomposer fungi, a nutritional mode found among some Mucorales and related groups (O'Donnell, 1979; Benny et al., 2001). The references listed previously provide an entry point for the literature on taxonomy and ecology of soil Zygomycetes.
The Ascomycota are the largest group in number of species (approximately 33,000, plus another 16,000 known only as asexual forms) and span a range of nutritional modes from parasites and pathogens of plants, animals, and other fungi through mutualists (forming both lichens and some ectomycorrhizas) and sapro-trophs (Kirk et al., 2001). Meiosis and production of sexual spores (ascospores) occurs within a sac-shaped cell, the ascus. It has often puzzled other biologists that mycologists may refer to the same fungus by two (or more) different names depending on whether it reproduces sexually (referred to as the teleomorph) or asexually (anamorph). A separate, artificial phylum (Deuteromycota, or "Fungi Imperfecti") and a number of artificial class names (Agonomycetes, Coelomycetes, Deuteromycetes, Hyphomycetes) have been used for fungi that lack known sexual structures, but the majority of these are asexual relatives of Ascomycota (Seifert and Gams, 2001). Most fungal systematists have abandoned the Deuteromycota, and many are now trying to unify the classification of these fungi as they are linked by phylogenetic analyses of their DNA sequences. Among the filamentous Ascomycota are many of the most important soil-borne pathogens of crop plants, including wilts caused by Fusarium and Verticillium and root and stem rots caused by Cochliobolus, Giberella, Gaeumannomyces, Phymatotrichopsis, and Sclerotinia (Farr et al., 1989; Holliday, 1989; Agrios, 1997). The most familiar and economically important molds, including Aspergillus and Penicillium, are asexual forms of Ascomycota that are also abundant in soils: Aspergillus more commonly in tropical soils and Penicillium more commonly in cool temperate and boreal soils (Christensen, 1981). Key literature to the identification of anamorphic and teleo-morphic Ascomycota includes Ellis (1971, 1976), Pitt (1979), von Arx (1981), Domsch et al. (1993), and Klich (2002), with additional references provided by Kirk et al. (2001) and Mueller et al. (2004).
Yeasts are fungi adapted to life in aqueous environments often of high osmotic potential, through growth of separate, usually elliptical cells that divide by budding or fission (Barnett et al., 1990; Kurtzman and Fell, 1998). Most yeasts, including the most economically important ones such as Saccharomyces cerevisiae, belong in the Ascomycota (Kurtzman and Sugiyama, 2001). Many yeasts are found in association with fruits, flowers, and other rich sources of readily assimilated sugars and other carbohydrates, but others (particularly basidiomycetous yeasts in Cryptococcus, Rhodosporidium, Rhodotorula, and Sporobolomyces) are found in soil, where they may be closely associated with plant roots or may be important members of the decomposer consortium breaking down plant and animal wastes (Lachance and Starmer, 1998; Fell et al., 2001).
Lichens are symbiotic associations between fungi and green algae or cyanobac-teria, in which the fungal partner (mycobiont) forms a characteristic structure called a thallus (what we see as a lichen) that encloses and protects the alga or cyanobacterium (photobiont) (Hale, 1983; Nash, 1996). Just as with mycorrhizal symbioses, lichens evolved independently in the Zygomycota, Ascomycota, and Basidiomycota (Gargas et al., 1995; Lutzoni et al., 2004), but by far the majority of lichen species (over 20,000 described species) are in the Ascomycota (Kirk et al., 2001). Lichens form the dominant ground cover over large areas of arctic and alpine environments. The cryptobiotic soil crusts that protect soils in arid environments may include lichens, together with consortia of fungi (States and Christensen, 2001), algae, and cyanobacteria (West, 1990; Belnap and Lange, 2001). Brodo et al. (2001) provide a beautiful and highly useful introduction to lichen identification and biology.
The Basidiomycota differ from Ascomycota primarily by production of sexual spores (basidiospores) outside the basidium, the cell in which meiosis takes place. Approximately 30,000 species are known. The Basidiomycota may be divided into the subphyla Ustilaginomycotina (smuts), Urediniomycotina (rusts), and Hymeno-mycotina, the latter divided into the Classes Heterobasidiomycetes ( jelly fungi) and Homobasidiomycetes (mushrooms and relatives) (modified from Kirk et al., 2001, and McLaughlin and McLaughlin, 2001). Only the last group is important in soil, although various stages of the life cycles of smuts and jelly fungi may occur in soil and be important to their survival. The Homobasidiomycetes, with approximately 13,000 described species, include gilled mushrooms, boletes, polypores, coral fungi, stinkhorns, and crust fungi, many with their mycelial phase occurring in soil (Hibbett and Thorn, 2001). This great diversity has mostly been overlooked in surveys of soil fungi. Within the Homobasidiomycetes are some very important soil-borne pathogens of crop plants, including Rhizoctonia (sexual states in Thanatephorus and several other genera; Roberts, 1999), and of forest trees, including Armillaria, Phellinus, and Ganoderma (Tainter, 1996). The majority of Homobasidiomycetes (perhaps 8500 described species) are saprotrophic leaf- and wood-decomposing fungi; their activities may extend well into the mineral horizons of soil wherever organic materials are present (Rayner and Boddy, 1988; Hibbett and Thorn, 2001).
Approximately 4500 described species of Homobasidiomycetes form ectomy-corrhizal relations with woody vascular plants in 30 families. Forests of ectomyc-orrhizal trees are dominant over much of the temperate, boreal, and alpine regions of the world, whereas tropical forests are mostly dominated by species with arbuscular mycorrhizas, with ectomycorrhizal trees widely dispersed or locally dominant (Smith and Read, 1997; Brundrett, 2002). Boreal forests with very few species of trees (perhaps 2 or 3 dominants) form ectomycorrhizas with hundreds or even thousands of species of fungi. By contrast, highly diverse tropical forests (with 80-100 species per hectare) form arbuscular mycorrhizas with a handful of morphos-pecies of Glomales. Each of these represents an evolutionary conundrum.
Homobasidiomycetes also include nematode-destroying fungi, fungi cultivated by leaf-cutting ants and their relatives, and "corpse-finder fungi" that fruit near animal corpses or accumulations of dung or urine (Thorn, 2002). Their tremendous range of nutritional modes and their persistent, extensive mycelia make Homobasidiomycetes of great importance in spanning space, time, and trophic levels within terrestrial ecosystems. There is a tremendous literature for identification of mushrooms and other Homobasidiomycetes, among which Moser (1983), Gilbertson and Ryvarden (1986-1987), Jülich and Stalpers (1980), and Stalpers (1993, 1996) are good starting points for temperate taxa, with additional references provided in Kirk et al. (2001) and Mueller et al. (2004). Unfortunately, there are few morphological characters and no useful references for identifying cultures of these fungi isolated from soil; the best hope lies in the growing database of ribosomal DNA sequences.
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