Soil fungi carry out three main functions in the ecosystem: (i) as sapro-trophs that digest and dissolve litter and detritus; (ii) as predators and parasites of soil organisms; and (iii) as symbionts of plants (as mycor-

rhizae or lichens) and insects. The organelles of fungal cells vary with phyla and classes as outlined below. In general, most groups have a cell wall that consists of chitin and other polysaccharides. The chitin polymer is synthesized from uridine-diphospho-N-acetylglucosamine precursors, which are added to the existing chain of chitin monomers. In the Archemycota taxa, the cell wall contains chitin, chitosan and poly glucuronic acid. In the Ascomycetes and Basidiomycetes, the cell wall contains chitin, glucans, gluco- or galacto-mannans and manno-proteins. These are all cross-linked together by hydrogen bonds into a protective matrix that forms a barrier about 0.2 ^m thick. The cell wall is composed of 80-90% carbohydrates. However, there are numerous important proteins that need to be exposed to the environment. These include recognition proteins for mating types, strains and species, as well as structural proteins and enzymes for substrate digestion. The cell membrane must include substrate receptors and carrier proteins. The role of the cell wall in supporting the cell is important during periods of water stress, as in plant cells, but it also serves as a defensive barrier to predation. The main reserve materials are glycogen and lipids. Mitochondria with plate-like cristae and peroxisomes are present in the Ascomycetes and Basidiomycetes, but they are absent in some Archemycota, such as the gut endosymbiont Enteromycetes species which contain hydrogenosomes instead. Mitosis is closed, with a persistent nucleolus which divides. Chromosome do not align along the spindle in a typical metaphase, as there are often too many chromosomes. The endomembrane network is prominent in saprotrophic species, especially in active hyphae where secretory enzymes are synthesized and accumulated. The Golgi-dictyosome are small with 2-5 cisternae. Some vacuoles also participate in osmoregulation and storage of amino acids, ions or other soluble nutrients. Many vesicles containing cell wall material are directed to the growing tip. In saprotrophic species, secretory vesicles containing digestive enzymes fuse with the cell membrane to release enzymes. Enzymes of up to 20 kDa may pass through the cell wall into the substrate. Common fungal exoenzymes are diverse and include proteases, amylases, cellulase (cellobiohydrolase), xylanases, pectin-degrading enzymes (lyase, esterase, pectate lyase and polygalac-turonase), ligninases (lignin peroxidases and manganese peroxidases) and other secreted enzymes. In all species, feeding is by osmotrophy from dissolved nutrients outside the cell wall. Haploid spores form as a result of sexual reproduction between two complementary karyotypes. The spore wall contains additional layers and it is thicker than in the vegetative cells. It holds an inactive cytoplasm with storage vesicles. The conidiospores are also resistant dispersal cells from successive mitotic divisions.

Three modes of growth are recognized in fungi (Fig. 1.20). One mode is called yeast growth and consists of cell division and separation

Fig. 1.20. Yeast form of growth in a fungus. Scale bar 10 ^m.

of cells into independent, but sometimes loosely attached cells. This mode of growth occurs in many Basidiomycetes and Ascomycetes, but also occurs in some Archemycota. A second form of growth occurs in Chytridiomycetes, Enteromycetes and Allomycetes, where one individual cell extends cytoplasmic branches into the substrate and forms a mononuclear thallus. The third mode of growth is called hyphal growth. This mode of growth produces a long extending filament without cytokinesis (cell separation) between successive nuclear divisions. Cell walls form completely, partially, rarely or not at all, depending on the taxonomic group. The repeated branching of growing hyphae forms a three-dimensional mass called the mycelium. In many orders, especially in the Ascomycetes and Basidiomycetes, hyphae of the same species, strain or individual are able to fuse. This is called anastomosis and requires a growing tip fusing with a complementary hypha. Some species of fungi may grow as hyphae under some conditions and as yeast under different conditions. The mechanism of growth is by tip elongation. In yeasts, a short hypha-like extension (the bud) forms which separates at cytokinesis into an independent cell with one nucleus and other organelles. Behind the growing tip of hyphae, the cell wall consolidates into a rigid structure. However, at branch initiation behind the growing tip, the cell wall must be loosened to allow for an extension of the cell membrane and a new elongating tip to form.

Yeast forms are primarily osmotrophic, with little or no secretion of digestive enzymes. Very few species can hydrolyse hemicelluloses, cellulose and pectins (unlike most filamentous saprotrophic fungal species). They are therefore very limited saprotrophs and depend on released nutrients in the soil or litter solution. Species have nutrient preferences, and there are soil/leaf specificity and niches. They are generally found in assemblage of species, not large colonies of one species.

In filamentous fungi, the hyphal cytoplasm is often separated by a cross-wall called a septum (Fig. 1.21). The details of septa can be a class characteristic. For example, in Ascomycetes, there are frequent septa that are perforated by one or more pores which allow passage of cytoplasm and organelles including nuclei. The septa separate the cytoplasm along the hyphae into compartments with one or more nuclei, but permit translocation of nutrients to other parts of the mycelium. In some species, a proteinaceous Woronin body will plug the septa if the adjacent cell is damaged. Basidiomycetes have septa that separate the hyphae after each nuclear division into compartments (cells) with one nucleus (homokaryon) or two nuclei from different mating types (heterokaryon). These septa are perforated by a single large pore. In some classes of Basidiomycetes, the pore is associated with modified endoplasmic reticu-lum closely appressed on both sides, and called dolipore septa. The dolipore ultrastructure is complex and regulates passage of material between the cells; notably, nuclei do not pass through. The role of septa is crucial in containing damage after a hypha is broken or invaded by a predator or parasite. Septal pores are blocked by cell wall deposition, and a new branch initiates a growing tip. The Archemycota generally have fewer septa. When they are present, the septa tend to be very perforated.

Fig. 1.21. Filamentous growth in fungi. (A) The H-junction between hyphae of complementary mating types in Zygomycetes (Archemycota), with a diploid spore at the junction. (B) Ascomycetes septate hyphae with terminal ascospores and a hook junction forming. (C) Basidiomycetes septate hyphae, with monokaryotic and dikaryotic cells. Scale bar 50 ^m.

Fig. 1.21. Filamentous growth in fungi. (A) The H-junction between hyphae of complementary mating types in Zygomycetes (Archemycota), with a diploid spore at the junction. (B) Ascomycetes septate hyphae with terminal ascospores and a hook junction forming. (C) Basidiomycetes septate hyphae, with monokaryotic and dikaryotic cells. Scale bar 50 ^m.

Species identification in fungi involves description of the morphology of spores and reproductive structures. Species producing only asexual reproductive structures traditionally have been placed in the deuteromycetes, an informal group of mitosporic fungi, until placed in their corresponding class. The taxonomy of fungi is complicated further, because many species with both yeast and hyphal growth forms were described as separate species and therefore have two species designations. From field samples, the morphology of asexual hyphae (or sterile hyphae) does not provide sufficient characters for identification. Most cannot be assigned to a taxonomic group without sequencing of DNA regions for molecular phylogenic analysis. When reproductive or dispersal structures form in culture, identification becomes possible, otherwise one is forced to rely on analysis of DNA sequences.

For further details on the biology and morphology of fungi, the student is directed to the literature cited in the text below, and to general texts such as Carlile et al. (2001), Kurtman and Fell (1998) and Moore (1998), or to web sites such as

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