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Fungi are well known as prolific sources of distinctive biologically active secondary metabolites. While some of these compounds are problematic (e.g., mycotoxins), a significant number of fungal natural products have found utility as important pharmaceuticals and agrochemicals, or as lead compounds in the development of such materials, and there is an ongoing need for new molecules of this type. Reasons for the production of these kinds of bioactive agents by fungi are seldom clear. It is widely accepted that natural products play important roles in the ecology of many different types of organisms, and chemical studies of ecological phenomena have led to the discovery of novel natural products that have bioactivities of potential practical importance. Although it is often hypothesized that some of the secondary metabolic capabilities of fungi may be similarly influenced by selection pressures exerted by other organisms, relatively little is known of the chemical ecology of fungal ecosystems. The literature provides considerable evidence suggesting specific types of fungi for which secondary metabolites may provide competitive advantages. The primary objective of this chapter is to provide examples of how observations in fungal ecology can be directly or indirectly linked to the search for new bioactive natural products, and to highlight new chemistry that has been discovered through our studies in this area over the past 10 years. [ABSTRACT FROM AUTHOR]

Fungi represent the most important and widespread group of organisms responsible for the recycling of primary plant biomass back into the ecosystem and are therefore essential for the maintenance of the global carbon cycle. The large group of saprobic fungi is specialized in the decomposition of dead plant cell wall material, including the biopolymers cellulose, hemicellulose, pectin and lignin. The ecological significance of these processes has promoted research within the last decades towards understanding the role of individual enzymatic and non-enzymatic components in the degradation of these complex polymers. Today, the fungi and their enzymes are used in numerous important biotechnological processes in the food, textile, and pulp and paper industries. Limited natural resources and the gradual introduction of environmentally friendly technologies open up new fields for their application, e.g. in the conversion of renewable plant biomass into industrially useful products such as sugars and bio-ethanol. This review summarises our current knowledge on the diversity of plant cell wall-degrading enzymes, their substrates and their producers. [ABSTRACT FROM AUTHOR]

Plants contain microorganisms that live inside their tissues without causing disease. These microorganisms, called endophytes, are generally overlooked because they are hidden from view. However, endophytes have diverse effects on plants, ecosystems, agriculture and human history. This chapter reviews the biology of endophytic fungi and their importance for plants, people, and biotechnology. Some common forage grasses contain endophytic fungi that produce toxic alkaloids. The alkaloids defend the grasses against herbivores, both insects and mammals, and affect plant growth. These endophytes have intimate associations with their hosts, and have coevolved with them over millions of years. In other cases, the endophytes may protect the plant host against pathogens, be latent pathogens themselves, or be accidental guests with no obvious effects on plant health. Fungal endophytes are very diverse, especially in the tropics, and include many new and unnamed species. On a practical level, endophytes are being exploited for pest control and drug discovery. Our knowledge of endophytes and their importance is still fragmentary, with many aspects waiting to be studied. [ABSTRACT FROM AUTHOR]

Mycorrhizal fungi are specialised root symbionts, engaging in intimate association with a great variety of plants. Although the association is generally assumed to be mutualistic, with bilateral nutrient exchange between the plant and fungal partners, it stretches over a wider range on the symbiotic continuum, including commensalism and antagonism. Traditionally perceived as being restricted to the root niche, mycorrhizal fungi actually thrive at the interface between two distinct habitats, host roots (a biotic habitat) and soil (an abiotic habitat). In the last decade, application of modern techniques and innovative combinations of methodological approaches has yielded valuable new insights on their functions in natural communities, and on the mechanisms underlying such processes. The fungal and plant genes, regulation of their expression, and biochemical pathways for nutrient exchange between symbiotic partners are now coming under intense study. At the same time, progress in molecular identification and characterization of fungal symbionts has provided a much more diverse and complex view of their multifunctional nature. A picture has emerged of greater than expected plasticity of these symbiotic organisms, which have therefore the potential of impacting their hosts from the molecular to the ecosystem level. [ABSTRACT FROM AUTHOR]

Fungivores of soil and litter are found in several animal groups, including mites, springtails, annelids and nematodes. Grazing of mycelium can modify the fungal community. Typically, grazing is selective. Feeding on a dominant fungus promotes greater fungal diversity by suppression of a mycelium which otherwise would be more abundant. By contrast, grazing on a fungus which is not dominant acts to reinforce established patterns of competition and further polarize the community, reducing diversity. Species richness can be reduced by the elimination of fungi by particularly intense grazing. Fungal responses to grazing vary. New growth can occur from previously inactive hyphae, but grazing can have strong negative impact on growth and metabolism of the hyphae which remain. Modifications to fungal growth are also seen in response to grazing of fungi on wood substrates. Overall, a picture emerges from studies under controlled conditions of a significant role for grazing to shape the fungal communities seen in the field. [ABSTRACT FROM AUTHOR]

Fungi are ubiquitous in aquatic ecosystems. They are important decomposers of plant litter in marshes and streams, and act as important intermediaries of carbon flow to higher trophic levels. Representatives of all major fungal phyla have been reported from aquatic habitats, although ascomycetes and their anamorphs (mostly hyphomycetes) dominate fungal communities in plant litter. Aquatic fungi possess the enzymatic capabilities to degrade the major plant constituents, with the possible exception of lignin. Fungi typically surpass bacteria in terms of both biomass and production associated with standing dead plant shoots in marshes and submerged leaf litter in streams. Peak fungal biomass in these systems usually constitutes 5-10% of the litter mass but can be as high as 15-23%. At the ecosystem scale, fungal production may exceed 100 g C m-2 year-1 in some habitats. The interplay of internal (e.g. litter carbon quality and nutrient concentration) and external factors (e.g. temperature, dissolved nutrients) regulates fungal activity which, in turn, controls rates of litter decomposition. To what extent fungi assume similar importance in aquatic habitats other than marshes and streams is poorly documented. [ABSTRACT FROM AUTHOR]

Fungi play a major role in the decomposition of plant and animal remains. Due to their taxonomic diversity, the functional diversity of saprotrophic fungi is large. Compared to other groups of organisms, they collectively produce a wide suite of enzymes capable of decomposing all organic compounds contained in plant and animal remains, effecting mineral nutrient release into soil pore water and thereby enhancing fertility in soil. In order to do this, sequential communities of fungi attack available resources. However, they do not perform these degradative functions alone, but establish close relationships with saprotrophic bacteria and soil fauna to access mineral nutrients from rock and organic remains. Fungi mediate nutrient cycling by retention of nutrients in their own biomass, and in assisting plant uptake via mycorrhizal associations. All of these processes are affected by pollutant chemicals, but fungi are also capable of decomposing some forms of chemical pollutants and mediating fluxes of heavy metals and radionuclides within the ecosystem. [ABSTRACT FROM AUTHOR]

Synthetic chemical pesticides have been the mainstay of insect pest control for over 50 years. However, insecticide resistance, pest resurgence and concern over the environmental impact of agricultural inputs give urgency to the search for alternative, biologically based forms of pest control. The impact on insect populations of natural epizootics caused in particular by fungal and viral pathogens demonstrates the potential of microbial pest control. Seminal attempts towards the end of the 19th Century to use the Deuteromycotina pathogen Metarhizium anisopliae for pest control inspired more recent extensive efforts to harness entomopathogenic fungi for biocontrol. This review outlines the current state of knowledge of insect fungal pathogens as it relates to their present use and future potential as mycoinsecticides. Topics include the commercial status of mycoinsecticides worldwide, constraints on efficiency, all aspects of the development of a fungus-based insecticide, potential targets, limitations on the commercial use of entomopathogenic fungi, and strain improvement. [ABSTRACT FROM AUTHOR]

Crop destruction by plant parasitic nematodes represents a major problem worldwide. Today the most common plant parasitic nematodes are controlled with chemical nematicides. During the second half of last century, the use of pesticides increased alarmingly with the aim of increasing agricultural production. The use of chemical pesticides has provided good solutions, but only in the short term. The introduction of natural enemies in the soil has resulted in an efficient method for the biological control of nematodes. Fungal antagonists of nematodes include nematode-trapping fungi, predacious fungi, endoparasitic fungi, egg parasitic fungi, and cyst parasitic fungi. The outermost layer of a nematode is considered to be of great importance in recognition by the fungus. The penetration mechanism by the fungus into the nematode is not well understood. However, it is known that lysing enzymes such as proteases and chitinases are involved in several steps of the host infection process. This chapter reviews and summarizes the knowledge accumulated on the mechanism of action and use of nemathophagous fungi for the control of plant parasitic nematodes in view of the most recent advances in the genomic era. [ABSTRACT FROM AUTHOR]

Canola (oilseed rape) has worldwide production led by China, Canada, Australia and Europe. Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, and blackleg, caused by Leptosphaeria maculans, are the two most economically important diseases of canola, e.g. in western Canada (yield loss 5-100%). Inefficient control resulting from cultural methods, resistant cultivars, and changes of pathogens into virulent strains, especially for blackleg, stress the need for an alternative, eco-friendly management, less dependent on chemical fungicides. Bacteria are excellent sources of biocontrol agents, owing to their multiple mechanisms of disease control. Compared to root pathogens, biological control of foliar pathogens has been less exploited for the phyllosphere, harsh conditions making it difficult for the biocontrol agent to establish, grow and survive. This chapter discusses these unfavourable chemical and physical conditions encountered by bacteria, and their mechanisms of adaptation, particularly how bacteria mediate phyllopshere biological control, with emphasis on sclerotinia stem rot and blackleg disease of canola. Understanding the pathogen life cycle, the growth stage at which the host is susceptible to infection, and the mechanism of host infection would help in the effective application of the bacterial antagonist. Time of application is highly critical, mediating disease control through, e.g. antibiosis, pre-emptive colonization, antifungal volatile production, and induction of systemic resistance in the host plant. If bacterial biocontrol agents are ever to become realistic alternatives to chemical pesticides, then it is essential that we unravel their control at the molecular level, including both biotic and abiotic factors regulating their expression. [ABSTRACT FROM AUTHOR]

Today, more than ever, the development of safer and environmentally feasible plant disease control alternatives has become a top priority due to the adverse effects of pesticides that create health hazards for human and other nontarget organisms. In this context, biological control is becoming an urgently needed component of modern agriculture. Biological control may be achieved by both direct and indirect strategies. The latter include the use of organic soil amendments, cross-protection, and induction of plant self-defense mechanisms. The direct approach involves the introduction of specific microbial antagonists into soil or plant material. Antagonistic interactions among microorganisms in nature include parasitism, antibiosis, and competition. In this chapter, we concentrate on mycoparasitism and plant-induced resistance, while emphasizing examples in which the research spans both basic and applied aspects of the phenomena. [ABSTRACT FROM AUTHOR]

Methods for mapping of fungi on various scales are concisely treated. General distribution patterns are described on global, continental, regional and local scales, including endemism, exemplified with different types of distribution maps. Expansions of distribution areas are treated, caused by both spontaneous spreading and by introductions of plants and fungi outside their original range. Decrease and possible extinctions of fungi are discussed. Attention is drawn to the growing concern regarding conservation of fungi and to the organizations dealing with this subject. Red Lists are considered an important tool to summarize the conservation status of fungi, using several categories of threat. Aims and methods of Red listing are described. Causes of decline of fungi are indicated, and the most important habitats of endangered fungi are mentioned. In addition, the negative impact of air pollution on fungi is noted. The usefulness of mycological reserves and the designation of important fungus areas are discussed. Research on harvests of wild edible fungi, and methods for legal protection of fungi are summarized. Examples of management to benefit fungi in nature reserves are given. [ABSTRACT FROM AUTHOR]

There has been significant interest in finding life in extreme environments and the impact which global climate change will have on ecosystem functioning. Microorganisms have received significant interest in the search for indicators of activity in extreme environments. This chapter examines available scientific information on the tolerance and functioning of fungal extremophiles in different ecosystems. It is important to consider the ecological context of work to examine fungal indicators of life in extreme environments. The ability of fungi to tolerate high or low temperatures suggests that there are species which can actively live and tolerate such extremes and use different mechanisms to survive such stress. Enzymes produced by both thermophiles and psychrophiles have received particular attention for biotechnological and pharmaceutical reasons. Life is primarily determined by the presence of water. The effects of types of water stress (ionic, non-ionic, matric) on the growth of fungi and the range of compatible solutes they are able to produce suggest that both yeasts and filamentous fungi have evolved to survive extreme environments by using active mechanisms for toleration stress, often involving compatible solutes. The discovery that slow-growing anaerobic fungi commonly exist in the gut of cattle has resulted in a wealth of information on the mechanisms of surviving in such environments. Acidophiles and alkalophile fungi have been found to be able to tolerate significant changes in pH, using different active and passive methods for overcoming such impose stress. The use of irradiation as a means of controlling spoilage moulds has received much attention. However, less is known about the tolerance mechanisms and the rapid repair systems which can be initiated under gamma irradiation. With changes in climate and greater exposure to UV-B light and interactions with other parameters, fungi are evolving to enable active survival and proliferation in extreme niche environments. [ABSTRACT FROM AUTHOR]

Fungi are of importance in the transformation of both organic and inorganic pollutants in the natural environment. While pollutants may exhibit toxicity, and cause changes in fungal community composition, fungi possess a range of mechanisms which confer resistance or tolerance. Many of these mechanisms can result in pollutant transformation to less-toxic forms, and are important components of natural biogeochemical cycles for major elements such as C, N, O, P and S as well as metals, metalloids and radionuclides. Some of the processes also have applications in bioremediation, e.g. in metal leaching, recovery and detoxification, and xenobiotic and organic pollutant degradation, and in the natural attenuation of polluted habitats. Pollutant interactions are complex and greatly influenced by environmental factors, while some effects are difficult to demonstrate and quantify because of the inadequacy of several common techniques used to study fungal populations. Some approaches using molecular biology and biomarkers are allowing a better understanding of community structure and responses to pollutants. However, it is clear that because of the complexity of the fungal growth form, their multiplicity of biological responses and interactions with pollutants and other organisms, and the complexity of the terrestrial (and other) environments, much research remains to be carried out. [ABSTRACT FROM AUTHOR]

In this chapter, we will elaborate on the impacts of the various land management practices associated with agriculture and forestry as they influence fungal structure and function. Because of the various management practices, fungi experience vastly different disturbance regimes. The impacts of these disturbances are expressed directly and by their effects on food-web structure and function. Hence, we will demonstrate that the disturbances associated with management practices affect, either directly or indirectly, ecosystem nutrient cycling, organic matter accumulation, and the formation and stabilization of soil structure. We will use examples from agroecosystems, grasslands, forest ecosystems, and soil restorations. [ABSTRACT FROM AUTHOR]

The unique structure and physiology of fungi make them sensitive and resilient in the face of natural disturbance. The degree to which density and diversity of fungi in soil are impacted by disturbance depends on the disturbance scale and frequency. As fungi play key roles in nutrient turnover and plant nutrition, disturbances that alter the fungal community feedback to impact ecosystem dynamics through changes to nutrient cycling, and alterations to plant diversity. In general, small-scale disturbances increase heterogeneity in pattern and process across landscapes, while catastrophic disturbances decrease diversity. As communities reestablish at these devastated sites, similarity to initial fungal communities depends on the availability of propagules and transport from adjacent sources. The type of fungal community that reestablishes at a given site can alter the reestablishing plant community structure and nutrient dynamics across the landscape. We suggest ultimately that understanding the roles of disturbance in structuring fungal communities, and the feedbacks from fungal communities to ecosystem functioning are crucial to understanding ecosystems, and the impacts of larger global-scale anthropogenic disturbances on natural systems. [ABSTRACT FROM AUTHOR]

For medicine, plant pathology, environmental studies and biological control, the identification of organisms in natural habitats can be indispensable. Before the development of molecular tools for species identification, microbiologists focused on that part of the fungal kingdom which is culturable, and groups of species were arranged according to morphology and biochemical tests. Throughout the last decades, novel techniques like immunological detection and, especially, PCR-based methods conquered the field of species identification. Additionally, probe hybridization techniques led to amendments in identification procedures, and oligonucleotide barcoding nowadays represents the most rapid and reliable way to detect organisms based on sequence information previously deposed in databases. [ABSTRACT FROM AUTHOR]

The Fungi apparently originated about one billion years ago from a common ancestral, aquatic eukaryotic protist that derived its nutrition as a chemotrophic osmotroph. Evolutionary morphological trends within the kingdom have involved losses of swimming spores, and acquisition of life cycle adaptations for terrestrial colonization. These include an extensive filamentous growth habit, together with spore production, dispersal, and survival mechanisms for aerial dissemination; and evolutionary physiological trends that have involved nutritional mode shifts, and losses and gains by lateral gene transfer (LGT) in metabolic trophic attributes. This chapter, first, recapitulates the phylogenetic and geological history of the fungi inferred from morphological and molecular systematics. Second, it addresses an issue not covered mechanistically by phylogenetics, namely, what drove the evolutionary origins of the fungi. This is accomplished by addition of the dimension of nutritional trophic property to the conventional phylogenetic tree, with emphasis on eukaryotes in general, the fungi, and the alphaproteobacteria (the hypothetical ancient mitochondrial endosymbiont). Bioenergetic electron flow diagrams, which provide a visual, conceptually powerful means to identify evolutionary energy connections between the mitochondrial endosymbiont and fungi, form the basis for understanding and predicting biogeochemical forces driving organism growth and ecology. The results indicate that the fungi are closely related metabolically to the ancestral mitochondrial eukaryote, although the trophic relationships are not always in complete accord with phylogenetic placement, presumably because of LGT, or retention of primordial properties by some advanced lines. [ABSTRACT FROM AUTHOR]