Fungi have co-existed with animals and plants throughout the whole of the evolutionary time since these three groups of higher organisms originally separated from one another. Living together closely for this length of time has given rise to many cooperative ventures. We have already seen how many fungi have combined with plants as partners in mutually beneficial relationships such as mycorrhizas and lichens. In these symbiotic, or mutualistic, associations the partners each gain something from the partnership so that the association is more successful than either organism alone. The organisms concerned (often two but sometimes more) live in such close proximity to each other that their cells may intermingle and may even contribute to the formation of joint tissues, as they do in the lichen thallus, which is one of the most ancient mutualistic associations of all and found in some of the most inhospitable environments.

Wikipedia points out that ‘biodiversity’ is a new portmanteau word made up from ‘biology’ and ‘diversity’ that probably arrived in the English language in 1985. Wikipedia defines ‘biodiversity’ as ‘the variation of taxonomic life forms within a given ecosystem, biome or for the entire Earth.

Fungal biomass is a high-quality food source because it contains a good content of protein (typically 20–30% crude protein as a percentage of dry matter), which contains all the amino acids that are essential to human and animal nutrition. Add characteristically low-fat content to the protein, a chitinous wall as a source of dietary fibre, useful vitamin content, especially of B vitamins, and carbohydrate in the form of glycogen and a good food source can be considered an ideal food. Judging from archaeological and similar finds, mushrooms, toadstools and bracket fungi have been used by humans since before recorded history for both food and medicinal purposes.

This chapter considers the evolutionary origins and phylogenetics of fungi. We present these against the background of global evolution in the hope of improving appreciation of the timescales involved.

Fungi make crucial contributions to all ecosystems because of their abilities as decomposers. One of the most important kingdom-specific characteristics of fungi is that they obtain their nutrients by external digestion of substrates. In the real world though there is some digestion of inorganic substrates (see ), the bulk of the substrates that fungi recycle are the remains of animals and, most particularly, plants. In this chapter we give an account of the ways in which fungal hyphae obtain, absorb, metabolise, reprocess and redistribute nutrients.

Interactions with plants dominate the rest of the chapter. We describe all types of mycorrhiza: arbuscular (AM) endomycorrhizas, ericoid endomycorrhizas, arbutoid endomycorrhizas, monotropoid endomycorrhizas, orchidaceous endomycorrhizas, ectomycorrhizas and ectendomycorrhizas. The effects of mycorrhizas and their commercial applications, and the impact of environmental and climate changes are also discussed. Finally, we introduce lichens, endophytes and epiphytes.

In the last two chapters, we have shown how fungi can cause disease in plants and animals, and even other fungi, it is now our intention to discuss how fungal diseases might be controlled and, ideally, cured.

The key to control of any pest or cure of any disease, irrespective of the nature of the disease-causing organism, is a treatment that shows selective toxicity, which means that the treatment should inhibit or kill the disease-causing organism with little or no effect on the host. This concept of selective toxicity was established and demonstrated at the end of the nineteenth century by Paul Ehrlich, winner of the Nobel Prize in Physiology or Medicine in 1908.

In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in species in the wild, and they are jeopardising our food security. We have already mentioned some EIDs of plants, especially crop plants. We will discuss EIDs further in this chapter. Among animals, fungal EIDs have reduced population abundances in amphibians, bats and even corals, across many species and over large geographical areas, and the most recently recognised fungal disease of snakes may have caused declines in some snake populations in the eastern United States.

Most fungal mycelia contain haploid nuclei. This is a characteristic of Kingdom Fungi; unlike the other major eukaryotic groups, most true fungi are haploid. Even in fungus-like organisms in the Oomycota (Kingdom Straminipila), such as Phytophthora infestans, the cause of potato blight, the nuclei are diploid. This difference in ploidy is an important contrast between ‘true’ and ‘non-true’ fungi. Of course, there are exceptions to every rule and some true fungi are diploid, like Candida albicans, a yeast which causes disease in humans; and rhizomorphs and mushrooms of Armillaria mellea (a pathogen of trees that belongs to the Basidiomycota).

Although their mode of nutrition is important in defining members of Kingdom Fungi, the fundamental aspect of cell biology which sets most fungi off from most members of the other major kingdoms is the apical extension of their tubular hyphae. These possess controls which ensure that hyphae normally grow away from one another to form the typical ‘colony’ with an outwardly migrating growing front. Extension growth of the hypha is limited to the apex and this pattern of growth makes the vegetative fungal mycelium an exploratory, invasive organism; and exploration and invasion is the fundamental lifestyle of fungi. This lifestyle allows filamentous fungi to dominate their ecosystems because it gives them the tools they need to find and colonise new substrates rapidly.

We start this chapter with the basic genetics of fungi. Within a few decades of the rediscovery in 1900 of Mendel’s research with peas, his experiments had been repeated with yeast and had demonstrated that yeast genes operated to the same set of rules, as did the genes of plants and animals. During the next 50 years it was clearly established that the basic genetic architecture of fungi is typical of the eukaryotes. We limit our discussion of the basic (segregational) genetics of fungi because it is dealt with adequately elsewhere, so we concentrate here on highlighting some of the differences between most fungi and most other eukaryotes.

The mechanics depend on biochemistry, and so we have to examine metabolic regulation in relation to morphogenesis, as well as ideas about developmental commitment, and comparisons with other tissues and other organisms. We show how classic genetic approaches allowed some progress to be made in the study of fungal development and how this has been accelerated by genomics and other aspects of global analysis of macromolecules. Finally, we turn to the end-game in development: degeneration, senescence and death, and finish with a summary of the basic principles of fungal developmental biology.