1

Heterokonts rC

Eukarya

Other Excavates Chlorachniophytes Plasmodiophoromycetes Cercomonads Foraminifera Brown Algae Xanthophyta

■ Chrysophyta Diatoms

Hyphochytriomycota,

■ Labyrinthulomycota, and Oomycota

■ Haptophytes

Cryptomonads Ciliates

■ Apicomplexa Dinoflagellates

Slime molds

Animals

Chytridiomycota Zygomycota Glomeromycota Ascomycota Basidiomycota

FIGURE 6.1 Possible phylogenetic relationships of major groups of organisms including those covered in this chapter (in bold). Groups with at least some photosynthetic members are indicated in green, and the vertical bars on lines leading to Oomycota and ciliates indicate the secondary loss of chloroplasts that must have occurred if a single endosymbiotic event and monophyly of the group encompassing brown algae through dinoflagellates are accepted. True fungi (Kingdom Fungi) are indicated in red and fungus-like organisms, often studied by mycologists, are indicated in pink. Branch lengths are arbitrary, and a number of polytomies and paraphyletic groups are omitted by simplification. Based on Palmer et al. (2004) and Lutzoni et al. (2004); for an alternate but largely congruent view of eukaryote relationships, see Baldauf (2003).

Alveolates ^

Amoebozoa

Opisthokonts

Fungi and cercozoan (chlorachniophytes) lineages (Palmer et al., 2004). Throughout the tree of life, a number of members of originally photoautotrophic lineages have lost their chloroplasts and become heterotrophic saprotrophs or parasites (notably the Plasmodiophoromycetes, Hyphochytriomycota, Labyrinthulomycota, Oomycota, and Apicomplexa such as Plasmodium, causing malaria). Various features of their ultrastructure and physiology, including sensitivity to selective antibiotics, reflect their true origins.

Fungi are enormously important in C and N cycling because of their ability to degrade complex substrates of plant origin which represent up to 90% of net primary productivity in most terrestrial ecosystems. In addition, the usually mutual-istic symbioses known as mycorrhizas between many fungi and plant roots, as well as the parasitic interactions leading to many plant diseases, have huge impacts in both ecological and economic terms (Chap. 10). The true fungi (Kingdom Fungi) are a monophyletic group; that is, the Phyla Chytridiomycota, Zygomycota, Glom-eromycota, Ascomycota, and Basidiomycota include all of the known descen-dents of a single common ancestor, which in turn is closely related to the common ancestor of metazoan animals (Kingdom Animalia; see Chap. 7). Yes, mushrooms and other fungi are among our closest relatives in the tree of life! A number of unrelated groups of eukaryotes that reproduce by spores and lack chlorophyll have traditionally been classified as fungi. These include the Plasmodio-phoromycetes (Cercozoa), Hyphochytriomycota, Labyrinthulomycota and Oomy-cota (Heterokonts), and slime molds (Amoebozoa). Representatives of all of these "aquatic" groups can be found in soil, where some cause major plant diseases and others are detritivores with importance in nutrient cycling. These groups will be treated briefly in this chapter along with the true fungi. Excellent reviews of the ecology of fungi in soil (and other habitats) are presented by Dix and Webster (1995) and Dighton et al. (2005). For good general references to fungi, see Alex-opoulos et al. (1996), Kirk et al. (2001), and Mueller et al. (2004); for soil fungi, see Domsch et al. (1993). Key references to the major groups are listed below where they are discussed.

Their life form and their strengths in biosynthesis and biocatalysis are among the characteristics that make fungi so special. The tubular cell called a hypha (plural hyphae) characterizes most fungi. Hyphae exhibit polar growth. The hyphal tips are expansible and flexible and are where most growth, secretion, and absorption take place. In contrast, the cylindrical side walls are much less metabolically active and become increasingly rigid with age. In theory, a fungal colony that is growing radially increases in biomass exponentially, but under less than ideal conditions (which can even be seen in cultures growing on nutrient-rich medium) the active cytoplasm can be seen to move forward with the expanding hyphal tips, leaving the older parts of the mycelium as empty tubes. This is a remarkable adaptation, which allows a mycelial fungus to explore its environment for food or other resources at a minimal cost. Nutrients in the walls of abandoned hyphae may even be recycled by autolysis and reused in the growing mycelial front. This latter feature is why direct microscopy or measures of N-acetylglucosamine digested from the chitinous walls of fungal hyphae (see Chap. 3) often overestimate fungal biovolume relative to measures of fungal DNA (see Chap. 4). Hyphae allow fungi to penetrate solids, whether soil, small particles of decomposing plant litter, a living plant cell, or the wood of a freshly fallen tree, and to traverse the dry spaces between moist or nutrient-rich microhabitats in soil. This ability leaves bacteria, the other main group of decomposers, behind on the surfaces and gives fungi a huge advantage in decomposition of plant litter and exploration of soil. Numbers of bacteria are primarily regulated by predation by bacterivorous nematodes (and perhaps even bac-terivorous fungi; Thorn, 2002), whereas fungi are regulated more by substrate quantity and quality (Wardle, 2002).

The other ability that allows many fungi to greatly outperform bacteria in decomposition of plant litter is their production of lignocellulose-degrading enzymes such as laccases, lignin, and manganese-dependent peroxidases and cellulases. Although cellulases are widespread (if not common) in bacteria, few bacteria (notably certain Streptomycetes) produce lignin peroxidases or have any ability to degrade lignocellulosic plant wastes. In defending their nutritional substrates from other fungi or bacteria, many fungi have developed potent antimicrobial compounds. The fungi are extremely rich sources of novel chemical compounds, often secreted into their environment (including appropriate culture media) as "extralites." Some of these we now exploit in medicine (e.g., penicillins from Penicillium, cyclosporin from Tolypocladium), whereas others are potent mycotoxins that we do our best to avoid in our food or animal feed (e.g., aflatoxins from Aspergillus, fumonisins from Fusarium). Mold fungi (anamorphic or asexual Ascomycota) have particularly been exploited for extralites of commercial or medical value, whereas the Zygomycota and Chytridiomycota appear to have little promise in this area, and the Basidiomycota are largely unexplored.

Hyphae of the Glomeromycota and Zygomycota are broad (frequently 10-20 ^m in diameter) and coenocytic (with multiple nuclei per cell). Hyphae of the Ascomycota and Basidiomycota are typically much narrower (2-5 ^m in diameter, although exceptionally less than 1 or greater than 10 ^m in diameter). In most Ascomycota and Basidiomycota, "primary mycelia," formed following germination of a haploid sexual spore, are uninucleate and haploid. "Secondary mycelia," formed following mating of compatible primary mycelia, are binucleate (dikaryotic or heterokaryotic, with two, usually different, haploid nuclei). Union of the two haploid nuclei occurs only in special cells of sexual fruiting bodies (asci in ascomata of Ascomycota or basidia of basidiomata of Basidiomycota) and is immediately followed by meiosis and the formation of haploid sexual spores (ascospores or basidiospores) that repeat the cycle. Several hundreds (or perhaps thousands) of species of Ascomycota and Basidiomycota have evolved a yeast-like growth habit of approximately elliptical cells that reproduce by budding or fission. The ability to grow as a yeast confers an advantage to these fungi when growing in aquatic systems (such as the nectar in flowers, insect hemolymph, or the fermentation of some of our favorite beverages), including some of high osmotic potential. However, the ability to convert back to a hyphal growth form enables certain yeasts (notably Candida albicans and its kin) to cause more invasive human infections. Thus, the genetics and biochemistry of yeast-hyphal dimorphism has attracted a great deal of research.

In fungi that form hyphae, the network of these cells that composes the individual is called a mycelium. The fungal mycelium is a powerful ecological force.

Through their mycelium, fungal individuals, species, and communities can dominate three-dimensional real estate (including the O horizon of many forest soils), transfer nutrients across macroscopic distances (meters, instead of the micrometer scale of the individual hypha), interconnect organisms at differing trophic levels, persist through time, and of course marshal the necessary resources to form sexual fruiting bodies. Different fungi have mycelia of considerably different scales. The complete individual of a Penicillium might be tens of micrometers in diameter (and produce on the order of 106 spores), whereas the mycelium of many mushrooms (Homobasidiomycetes) may be centimeters or meters in extent (but produce few to no propagules in soil), and the current record holder, a species of Armillaria, is known to occupy 40 hectares of forest soil. This has tremendous implications both for their biology and for analysis of their biodiversity, in which replicate "individuals" sampled may represent colonies grown from spores of a single parent mycelium of Penicillium or fruiting bodies all formed by a single mushroom mycelium.

It has been estimated that the fungal biomass in many soils exceeds the biomass of all other soil organisms combined, excepting plant roots. This situation is usually found wherever abiotic conditions (low nutrients, periodic or permanent drought, low temperatures, or short growing season) or low-quality litter (high C:N ratio, high lignin:N ratio, or high phenolic content) reduce the rate of litter turnover and nutrient cycling. In certain tropical or agronomic ecosystems, where there are fewer limitations on plant litter decomposition, soil fungi may be much less predominant in terms of their biomass, activities, or diversity. Even in these circumstances, it would be inaccurate to regard fungi as unimportant in the nutrient cycling or other ecological processes, since many parts of these processes take place even before plant litter hits the ground. Certain endophytic fungi, including members of the Xylariales (Ascomycota), switch from relatively quiescent symbionts to saprotrophs as leaves senesce. Dead leaves and other aerial fine litter in the tropics are also quickly colonized by decomposer basidiomycetes such as Marasmius, Mycena, and Coprinopsis—mushroom fungi with small, ephemeral fruiting bodies. Species of Marasmius even form a tangled net of tough, melanized rhizomorphs (differentiated hyphal cords) that trap falling leaves in the canopy or subcanopy.

Surveys of the diversity of soil fungi, which were popular during the 1960s and 1970s, have reappeared in the literature with the advent of DNA-based, culture-independent methods of analysis. Culture-based estimates of soil fungal diversity require considerable effort and taxonomic expertise (Chap. 3; see Bills and Polishook, 1994; Maggi et al., 2006). From a single soil sample, several hundred species may be obtained, and new species continue to be encountered after more than 10,000 isolates have been examined (Christensen, 1981)! These estimates, of course, preferentially detect fungi that produce numerous propagules in soil and grow readily on the isolation medium; Basidiomycota are largely overlooked (Warcup, 1950; Thorn et al., 1996). Knowing in advance that there is a high density of fungal species (number of different species per cubic centimeter, or gram dry weight, of soil) warns investigators using DNA-based methods that a large sample size

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