Introduction

Rocks and minerals represent a vast reservoir of elements, many of them are essential to life. Bulk biological metals, such as Na, K, Mg and Ca, are among the eight most abundant elements in the Earth's crust and together make up 11.06% of crustal rock (Fraústo da Silva & Williams, 1993; Gadd, 2004). Rocks and minerals also include essential metals (e.g. Mn, Mo, Fe, Co, Ni, Cu, Zn) and, crucial for microbial and plant growth, phosphorus. Many elements have essential functional potential for the synthesis of biological macromolecules and energy capture (e.g. C, N, H, O, P, S), for the transmission of information (e.g. Na, K, Ca), for catalysis (e.g. Fe, Cu, Zn, Mo), for transfer of electrons (e.g. Fe), and for building solid structures (e.g. Ca, P, Si) (Fraústo da Silva & Williams, 1993). All these elements must be released into bioavailable forms that can be assimilated by the biota. Their release occurs via weathering of rock substrates and their mineral constituents through physical (mechanical), chemical and biological processes (Burford et al., 2003). Near-surface weathering of rocks and minerals (sub-aerial and sub-soil environments) often involves an interaction between all three types (White et al., 1992). In addition to mobilization of essential nutrients during lithospheric weathering, non-essential toxic metals (e.g. Cs, Al, Cd, Hg, Pb) may also be mobilized (Gadd, 1993, 2001a, b).

Introduction

In most environments, the spatial distribution of nutrient resources is not uniform. Such heterogeneity is particularly evident in mineral soils, where an additional level of spatial complexity prevails owing to the complex pore network in the solid phases of the soil. Mycelial fungi are well adapted to growth in such spatially complex environments, since the filamentous hyphae can grow with ease across surfaces and also bridge air gaps between such surfaces. This ability is significantly enhanced by the propensity of many species to translocate materials through hyphae between different regions of the mycelium. Thus, it has been suggested that hyphae growing through nutritionally impoverished zones of soil, or deleterious regions (e.g. localized deposits of organic pollutants, toxic metals, dry or waterlogged zones), can be supplemented by resources imported from distal regions of the mycelium (Morley et al., 1996). This has profound implications for the growth and functioning of mycelia and attendant effects upon the environment in which they live. Thus, the fungal mycelium represents an extremely efficient system for spatial exploration and exploitation.

The study of filamentous fungi through experimental means alone can be very difficult owing to the complexity of their natural growth habitat and the range of scales over which they grow and function. Mathematical modelling provides a complementary, powerful and efficient method of investigation and can provide new insight into the complex interaction between the developing mycelium and its environment.

Introduction

Soils contain a diverse range of fungi that are parasites on nematodes. They include more than 200 species representing all major taxonomic groups of fungi including deuteromycetes, basidiomycetes, chytridiomycetes and zygomycetes. Nematophagous fungi are found in all regions of the world, from the tropics to Antarctica. They are present in all sorts of soil environments, including agricultural and forest soils (Barron, 1977).

Based on the infection mechanisms, three broad groups can be recognized among the nematophagous fungi: the nematode-trapping and the endoparasitic fungi that attack free-living nematodes by using specialized structures, and the egg- and cyst-parasitic fungi that infect these stages with their hyphal tips (Barron, 1977). The nematode-trapping fungi are the best-known group, probably owing to their remarkable morphological adaptations and their dramatic infection of nematodes. With few exceptions, including the mushroom Hohenbuehelia (asexual state Nematoctonus) (Barron & Dierkes, 1977), the majority of the identified species of nematode-trapping fungi belong to a monophyletic clade among the apothecial ascomycetes (Liou & Tzean, 1997; Ahrén et al., 1998; Hagedorn & Scholler, 1999).

Nematode-trapping fungi can grow as saprophytes in soils. They enter the parasitic stage by developing specific morphological structures called traps. The traps develop from hyphal branches; they can either be formed spontaneously or be induced in response to signals from the environment, including peptides and other compounds secreted by the host nematode (Dijksterhuis et al., 1994). There is large variation in the morphology of trapping structures, even between closely related species (Fig. 12.1).

Introduction

The aim of this chapter is to summarize recent developments in the study of the natural abundance of stable isotopes, primarily 15N and 13C, in fungal sporocarps. The main focus will be on saprotrophic fungi but, owing to a scarcity of studies, considerable use is made of the more abundant literature on ectomycorrhizal fungi. A brief introduction to the terminology used in the determination and use of the stable isotopes 15N and 13C is provided. This is followed by a discussion of the most significant findings from investigations into ectomycorrhizal fungi and how these compare with the available data from saprotrophic fungi. Recent results from a study focusing on saprotrophic fungi are then presented. Finally, some suggestions are given as to where isotope data may be useful in investigating the ecology of saprotrophic fungi.

Microorganisms are integral components of most biogeochemical cycles in terrestrial ecosystems (Dighton, 1995). The role of fungi, in particular, in boreal and temperate forests is pivotal. Most of the trees in these forests form mutualistic associations with a wide range of ectomycorrhizal fungi (Smith & Read, 1997) while the breakdown of woody debris is almost exclusively carried out by saprotrophic fungi (Tanesaka et al., 1993). In addition to these essential ecological roles, fungi make up a large proportion of the total organism diversity in these systems. Despite their evident importance, relatively little is known about fungal activities in situ.

Dry rot in the twenty-first century

Santa Barbara in California is such a stunningly beautiful place that it seems reasonable that this apparent utopia is troubled by one or two things. In the context of fungi in the indoor environment, residents have encountered a pestilence that is transforming homes into rubble and sawdust. Its name is Meruliporia incrassata and it causes dry rot (Figs. 14.1, 14.2). I'll begin with the thoughts of journalist Matt Kettmann, who wrote a story for Santa Barbara's newspaper, The Independent, titled, ‘Invasion of the House-Eating Fungus’ (Kettmann, 2002). Matt interviewed the Kastner family, who had moved into a US $1.2 million ranch-style house. The nastiness began when, ‘a mysterious foam slowly started peeking out of the laundry room walls’. Dry rot was diagnosed and treated by an extermination company. Feeling confident that the fungus was gone, the family left for a vacation. When they returned, Matt explained, nearly a quarter of the house ‘was eaten in a mere week’. Christina Kastner remarked, ‘It came back with a vengeance – like it got mad.’ The problem was solved once the exterminators found a ‘taproot with the diameter of a grapefruit in the rear of the house’.

When it comes to fungal species and speciation, it is hard to find anything to say that has not already been said in several excellent recent reviews. The most comprehensive source of information is Burnett's recent book (Burnett, 2003), which expands upon the themes from his British Mycological Society Presidential Address (Burnett, 1983). In addition to reviewing mycological species concepts and speciation, he describes enough about basic mycology and the methodology of evolutionary studies to make chapters on defining fungal individuals and populations, or on the processes of evolution in fungi, useful for mycologists interested in evolution and for evolutionary biologists interested in fungi. Burnett's review of the early literature in fungal speciation is particularly helpful in the present age, when it seems as if literature that is not online is forgotten. A second source of information is Brasier (1997), who explored three of what he considered to be the four main elements contributing to fungal speciation: original interbreeding populations, natural selection on populations and reproductive isolation between populations. He left a discussion of mating systems to others. Brasier's discussion of natural selection is particularly good, and his figure comparing the narrow range of growth rates of dikaryotic hyphae taken from Schizophyllum commune fruiting bodies to the much broader range of growth rates for dikaryons synthesized from their haploid progeny is as clear a demonstration of the effects of selection as one could want.

Introduction

Basidiomycetes are the major agents of decomposition and nutrient cycling in forest ecosystems, occurring as both saprotrophs and mycorrhizal symbionts (Boddy & Watkinson, 1995; Smith & Read, 1997). The mycelium can scavenge and sequester nutrients from soil, concentrate nutrients from decomposing organic matter, relocate nutrients between different organic resources, and ultimately make nutrients available to plants to maintain primary productivity. Hyphae of both saprotrophic and ectomycorrhizal basidiomycetes that ramify through soil often aggregate to form rapidly extending, persistent, specialized high-conductivity channels termed cords (Rayner et al., 1994, 1999; Boddy, 1999; Watkinson, 1999; Cairney, 2005). These cords form complex networks that can extend for metres or hectares in the natural environment. The distribution of resources is extremely heterogeneous and unpredictable in space and time, and these fungi have developed species-specific strategies to search for new resources and to capitalize on resources landing on their mycelial systems (Chapter 6, this volume). Thus the architecture of the network is not static, but is continuously reconfigured in response to local nutritional or environmental cues, damage or predation, through a combination of growth, branching, fusion or regression (Boddy, 1999; Watkinson, 1999; Chapter 6, this volume). At this stage it is not clear whether specific global mechanisms exist to couple local sensory perception and responses over different length scales specifically to maximize the long-term success of the whole colony, or whether such collective behaviour is an emergent property arising solely from local interactions of individual hyphae.

Introduction

The majority of the vascular flowering plants have the ability to enter into symbiotic associations with a unique group of soil fungi, the arbuscular mycorrhizal (AM) fungi. The symbiosis develops in the roots of the plant, where the plant provides the fungus with a source of carbon and the fungus delivers mineral nutrients to the roots. In particular, the transfer of phosphorus from the AM fungus to the plant is widely documented, but there is evidence for zinc and nitrogen transport also (Hodge et al., 2001). For both symbionts, significant quantities of nutrients may be exchanged. It is estimated that the plant allocates up to 20% of its photosynthate to the roots to support the fungal symbiont, and some studies suggest that in an AM symbiosis the plant receives all of its phosphorus via the fungus (Bago et al., 2000; Smith et al., 2003). Phosphorus is a relatively immobile nutrient and is often present at concentrations in the soil that are limiting for plant growth. Consequently, improvements in phosphorus supply resulting from the AM fungus can have a significant impact on plant health and subsequently on plant biodiversity and ecosystem productivity (van der Heijden et al., 1998).

The AM symbiosis is an ancient association. Both molecular data and fossil evidence suggest that the AM fungi originated 460 MYA (Redeker et al., 2000) at a time when bryophytes were the predominant plant form.

What is multilocus typing?

Origins of the technique

The characterization of genetic variation has revolutionized our understanding of fungal populations and species. Traditionally, advances have been most rapid in the fields of medical mycology and phytopathology (Taylor et al., 1999b) owing to the need for effective molecular epidemiological tools. Epidemiological studies are typically concerned with disease outbreaks, the origin and spread of virulent strains, or the emergence of an interesting phenotype such as antibiotic resistance. Genetic variation in the genomes of pathogens provides a means by which isolates can be differentiated from one another (Taylor et al., 1999b). The characterization of this molecular variation has given rise to the field of molecular epidemiology, whereby genetic variation is used to address questions about the biology and transmission of infectious diseases. However, the techniques developed for molecular epidemiology are not limited to medical fields, and there is huge potential to apply these methodologies to non-disease-causing organisms.

The power of molecular epidemiology as an analytical tool has led to a period of rapid development, resulting in many methods for indexing genetic variation, such as VNTRs (variable number tandem repeats), MLEE (multilocus enzyme electrophoresis), RFLPs (restriction fragment length polymorphisms), RAPDs (randomly amplified polymorphic repeats) and PFGE (pulse field gel electrophoresis), to name but a few (Taylor et al., 1999b; McEwen et al., 2000). Typically, laboratories have tended to develop in-house techniques that are specifically focused on a particular problem, and are usually a variant on the above.

Introduction

Terrestrial fungi are commonly studied in the laboratory, growing on artificial media in which nutrients are typically homogeneously distributed and supplied in superabundance, the environment is sterile and microclimate (temperature, moisture, gaseous regime) usually relatively constant. This contrasts with the natural environment, in which: nutrients are often patchily and sparsely distributed or not readily available, because they are locked in recalcitrant material (e.g. lignin); many other organisms are encountered, including other fungi, bacteria and invertebrates; and microclimate is constantly changing, both temporally and spatially. This chapter explores the ways in which fungi cope with environmental heterogeneity. Similar situations are faced by macroorganisms and analogies are drawn. Emphasis is placed on basidiomycetes, not only because they have been studied in most detail, but because of their dominant role as decomposers and mutualistic symbionts (Boddy & Watkinson, 1995; Smith & Read, 1997) and because they are better adapted to respond to environmental heterogeneity over scales ranging from micrometres to many metres than are other fungi.

Both saprotrophic and ectomycorrhizal Basidiomycota form extensive mycelial systems in woodland soil and litter, but it is the former that are the focus of this review. Saprotrophic, cord-forming Basidiomycota that ramify at the soil–litter interface, interconnecting disparate litter components, provide most examples. The key feature of these fungi that fits them for growth in environments where resources are heterogeneously distributed is that they are non-resource-unit restricted, i.e. they can grow out of one resource in search of others.

An introduction to the phytopathogenic fungus Magnaporthe grisea

Magnaporthe grisea is a heterothallic, phytopathogenic ascomycete capable of infecting over 50 species of grass (Ou, 1985). The most economically important of the species infected by M. grisea is rice (Ou, 1985; Rossman et al., 1990), which is the staple diet of almost half the global human population. Rice blast disease, caused by M. grisea, is an extremely serious disease; despite modern advances, such as the development of fungicides and breeding of resistant rice cultivars, every year between 11% and 30% of the rice harvest is destroyed by this disease. A serious blast epidemic occurred in Bhutan in 1995 in which 1090 tonnes of rice was lost, with up to 100% crop losses for some farmers (Thinlay et al., 2000). The American Centre for Disease Control and Prevention has also classified rice blast disease as a significant biological weapon that could be deployed in acts of agricultural bioterrorism (Schaad et al., 2003).

Rice blast disease manifests itself as a number of different pathologies affecting stems, leaves and panicles of the rice plant (Talbot, 2003). Blast infections of stem nodes, for example, can cause the rice stem to rot before maturation of the seed and can result in complete loss of the rice crop (Ou, 1985). If leaves of rice seedlings are infected, a reduction in photosynthetic capacity can occur; growth is therefore impeded and seedlings often die.

Introduction

The saltmarshes of the Georgia, USA, Atlantic coast are expansive and highly productive. The marshes form the intertidal ecosystem 5–10 km wide extending from the barrier-island chain to the mainland. The predominant macrophyte of the marshes is smooth cordgrass (Spartina alterniflora Loisel.). Cross-marsh average annual production of smooth cordgrass shoots in Georgia has been measured at approximately 1.3 kg m− 2 of marsh (Newell, 2001a, from Dai & Wiegert, 1996). Like most grasses, smooth cordgrass does not abscise its leaf blades; they remain attached to the leaf sheath after senescence and death (Newell, 1993, and references therein). As new blades are produced at the apex of shoots, the bottom blades senesce and die, until the whole shoot dies after flowering. Therefore, a large crop of standing-dead litter is available to microbes for decomposition for much of the year (for leaf blades alone, up to 538 g dry mass m− 2) (Newell et al., 1998).

Because smooth cordgrass is produced in an intertidal marsh, one might suspect that tidal flooding would be a major wetting phenomenon for the standing-dead cordgrass leaves. However, the grass shoots extend above the flooding-tidal level most of the time: it is estimated that most of the dead-blade mass is wetted by tides only about 10% of the time on an annual-average basis (Newell et al., 1998).

Introduction

Over the past century the recognition of the presence of endosymbionts in a variety of arthropods has become well established (Buchner, 1965). Intense interest in the rickettsial endosymbionts, widespread among insects (van Meer et al., 1999), led to the discovery that they may induce sterility of the host, and increased rates of speciation have been attributed to their presence (Shoemaker et al., 1999). Bacteria also have long been known for their nutritional contributions to insects, but more recently indigenous gut bacteria have been recognized for their ability to prevent colonization of non-indigenous microbes. In fact the insect gut is considered a ‘hot spot’ of bacterial gene exchange and bacterial adaptation (Dillon & Dillon, 2004). Thus, important attributes that affect speciation, habitat utilization, and survival are provided by prokaryotic symbionts. By contrast, although there were a number of early reports of fungal endosymbionts of insects, fewer of them were substantiated after the original reports (Buchner, 1965). More recent work, however, indicates that insect–yeast interactions abound in nature, although the exact nature of many of the interactions is less well understood (Suh & Blackwell, 2005; Vega & Dowd, 2005).

Yeasts and yeast-like fungi from the guts of a small group of planthoppers (Homoptera) and beetles in three families (Coleoptera: Anobiidae, Cerambycidae and Scolytidae) have been studied most extensively. These fungi have a yeast growth form with single cells and asexual reproduction by budding, the hallmark of the ‘yeast habit’, although many yeasts actually have filamentous growth as well.