Fungi can be found in almost any environment, and play important roles in ecosystem processes such as nutrient cycling and degradation. Despite their importance, the vast majority of fungi have not yet been isolated and identified. Due to the difficulties inherent in culture-based methods, fungal ecologists have turned to community fingerprinting techniques, which utilise signal molecules to profile the fungal members of an environmental sample without culturing. Commonly used signal molecules include chitin, ergosterol, membrane lipids and nucleic acids. Several DNA-based fingerprinting methods have been successfully applied to fungal communities, including D/TGGE (denaturing/temperature gradient gel electrophoresis), SSCP (single-stranded conformational polymorphism), RISA (ribosomal intergenic spacer analysis), and T-RFLP (terminal restriction length fragment polymorphism). These techniques allow the fungal ecologist to rapidly profile fungal populations in an ecosystem, without the need for laborious culturing or cloning.

Filamentous fungi such as Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei are able to produce and secrete large concentrations of enzymes (e.g. amylases, proteases, cellulases) into the environment. Increasingly, these species and a few others are being used to produce recombinant proteins, particularly proteins of fungal origin (Table 1). For producing recombinant proteins (which may be a protein which the host organism already makes, i.e. an homologous protein, or a new, i.e. heterologous, protein), filamentous fungi offer the advantages of possessing an efficient secretion system, being able to glycosylate proteins and having higher specific growth rates than plant, insect or mammalian cells. Although the filamentous growth form causes more difficulties for mixing and aeration than does the unicellular growth form of yeast and bacteria, efficient fermentation technologies have been developed for antibiotic, organic acid and native enzyme production from filamentous fungi.

The long tubular branching hypha is the most important fungal growth form, although some fungi grow as discrete spherical or ellipsoidal yeast cells. Vacuoles are ubiquitous in yeast cells as well as in hyphae of filamentous fungi and can be readily stained by simple methods of dye uptake. They appear as spherical or tubular organelles of extremely variable size. Vacuoles are known or suspected to play several crucial roles in the physiology of vegetative growth. Only some of these roles are related to the activity of lytic intravacuolar enzymes. Thus, vacuoles can degrade redundant organelles, presumably recycling macromolecules, especially under conditions of nutrient starvation. They are also the destination of endocytotic vesicles originating by inward budding of the plasma membrane, thereby providing a mechanism of ‘face-lifting’ of the plasma membrane and a means of communication with the extracellular environment. Further, vacuoles store organic and inorganic nutrients, and they may detoxify the cytoplasm by sequestration of toxic substances.

The study of filamentous fungi can be difficult through experimental means alone due to the complexity of their natural growth habitat (e.g. soils) and the microscopic scale of growth (e.g. tip vesicle translocation and hyphal tip extension). Mathematical modelling provides a complimentary, powerful and efficient method of investigation. In this article, earlier mathematical models are briefly reviewed, before an overview of the construction and resultant predictions of a new model for fungal growth and function is given. Model predictions are compared to experimentally obtained data, giving new insight into the complex interaction between the developing mycelium and its environment.

Since the 1950s, antifungal drug discovery has identified three classes of natural products (griseofulvin, polyenes and echinocandins) and four classes of synthetic chemicals (allylamines, azoles, flucytosine and phenylmorpholines) with clinical value against fungal infections. For life threatening fungal disease, the polyene amphotericin B is still a common choice despite toxic side-effects. The azoles remain the most widely used group of anti fungals active against a wide range of mycoses, benefiting from creative chemistry to boost their effectiveness. More recently, the echinocandins show great promise, with caspofungin licensed for clinical use in 2002 and two other molecules close to registration. New advances in molecular genetics afford the promise of revealing new antifungal targets, together with new agents to inhibit those targets specifically.

Endothiella sp. was found associated with witches' broom symptoms of Tibouchina granulosa growing in a stretch of Atlantic rain forest in Rio de Janeiro, Brazil. The fungus was the anamorph of Cryphonectria cubensis the eucalypt canker fungus. Host-range studies were performed involving 40 plant species belonging to 19 families and showed that C. cubensis has a wide potential host-range, concentrated on the Myrtales but including Persea americana (avocado) and Pouteria caimito. These are members respectively of the subclasses Magnoliidae and Dilleniidae, distantly related to plants of the subclass to which both eucalypt and T. granulosa belong (Rosidae). The finding of C. cubensis in balance with a population of a native species at a site isolated and distant from both eucalypt and clove plantations might be regarded as reinforcing the hypothesis of a Neotropical origin for the fungus as opposed to the hypothesis of the fungus being from Oceania and having cloves as its original host. The new alternative hypothesis(of separate origins from endemic hosts in the Neotropics, Africa and Oceania) should nevertheless be also considered.

Many an undergraduate biologist will remember the excitement/fear of using radio-labelled substrates (usually 14C) during carefully supervised laboratory practicals. They will also remember the precautions taken to avoid contact with the radioactive source and to account for all the materials used. The use of radiolabelled compounds (mainly 3H, 14C, 32P or 35S) is commonplace though carefully controlled, and the utilisation of such compounds for field experiments is severely restricted. A further limitation in ecological research is that the radioactive isotope of nitrogen (13N) has a half life of only a few minutes.

Discovered in the late 19th century, Bordeaux Mixture was the world's first commercially successful fungicide. Among its achievements was the control of potato blight, the disease which had so famously devastated Irish crops earlier in the century. Although from the mid-1930s onward it was largely superseded in European and North Americn agriculture by progressively more sophisticated and expensive organic fungicides, Bordeaux Mixture, a simple mixture of copper sulphate and lime, remains a popular weapon for gardeners (Fig 1) and poorer Third World farmers fighting a range of foliar diseases. Modern formulation has improved its usefulness, there has been a lack of evolution of fungal resistance towards it and, above all, it has remained relatively cheap.

The natural phenomenon of bioluminescence is the emission of visible light by living organisms mediated by an enzyme-catalysed (‘luciferase’) reaction of molecular oxygen with a substrate (‘luciferin’). Bioluminescent organisms are diverse and widely distributed in nature, for example bacteria, dinoflagellates, fungi and insects. The luciferases show no homology to each other and the luciferins are also chemically unrelated. Molecular oxygen is the only common feature of bioluminescence reactions, indicating that the luminescent systems in most organisms may have evolved independently (Wilson & Hastings, 1998).

Ibotenic acid (α-amino-3-hydroxy-5-isoxazole acetic acid) was separated from spores and caps from Amanita muscaria by reversed phase high performance liquid chromatography and identified by flow injection analysis with mass spectrometric detection. The keto and enol tautomers of ibotenic acid were separated and their ratio of 96:4 in favour of the enol form was determined. On average the ibotenic acid content was 0.0054±0.0010% of the spores and 0.017±0.010% in fresh caps. Muscimol, the decarboxylated product from ibotenic acid, was neither detected in spores nor in caps. 50 nanomol of ibotenic acid, muscimol or extracts from spores or caps did not inhibit the growth of Bacillus subtilis.

Phytophthora ramorum is a recently described species responsible for sudden oak death syndrome and also causes symptoms such as twig wilt and dieback, stem lesions, necrosis of leaf midrib from the petiole and leaf tip necrosis on a range of ornamental plant species. In the USA, a reported epidemic of P. ramorum infections on trees belonging to several families including Fagaceae, Lauraceae and Ericaceae seems to be increasing and there are fears of similar epidemics occurring in woodlands in the UK and mainland Europe. This paper reviews the current state of knowledge and the research efforts being made to understand the biology, manage the disease and prevent widespread outbreaks of P. ramorum infections across Europe and the USA.

It cannot be denied that recent developments in sophistication, availability and cost of molecular biology techniques have had a profound effect on mycology. The ready availability of DNA sequence data has led to major developments in the study of the systematics, biochemistry and ecology of fungi. The introduction of molecular techniques has allowed significant steps to be made in genomics, and in many areas of applied mycology molecular based approaches have become routine for strain characterisation, pathogen detection and identification. Molecular methods are now starting to give major insights into how fungi function in the environment, where they are present, and how they interact with associated organisms.

This article reviews the current state of knowledge about the evolutionary history of lichenized ascomycetes within an integrated system of all ascomycetes. Substantial progress has been made since molecular techniques were applied to unravel evolutionary relationships. Molecular approaches detect how often the lichen symbiosis arose, test current classification concepts, and find the proper placement for species with uncertain relationships. Uncertainties in some evolutionary hypotheses still need to be resolved by studying further genes. The currently available phylogenetic trees show a number of convergent phenotypic developments in lichenized ascomycetes. The current classification of ascomycetes is reviewed in the light of recent molecular data.

Fungal pathogens are using several mechanisms to circumvent the inhibitory actions of antifungal drugs. The variety of these mechanisms was revealed in recent years by several laboratories with molecular approaches. Besides the identification of genes involved in antifungal drug resistance and the discovery of alternative pathways of resistance (i.e. biofilm formation), novel concepts in the understanding of the survival of fungal pathogen in the presence of antifungal drug (antifungal tolerance) have emerged.

The paper outlines the impact of molecular biology on the identification and detection of fungi and fungus-like micro-organisms. We have tried to use as little jargon as possible but avoiding it completely is very difficult. The article is centred around the ‘pseudofungus’ Phytophthora and its closest relatives, because that is the micro-organism with which we have had most experience. Nevertheless, most of the approaches and techniques mentioned are applicable to any fungus or fungus-like organism and, in that broader sense, the article should be of interest to those with no special interest in or knowledge of Phytophthora.

Eleven species of mushrooms are currently known to be utilized as a food source by the indigenous Patamona Amerindians of the rain forested Pakaraima Mountains of Guyana. The majority of these fungi are undescribed species; many belong to groups that are infrequently collected for the table by North Americans (e.g. Clavulinaceae, Sarcoscyphaceae, Amanitaceae) whereas groups which contain highly prized culinary mushrooms by north temperate standards (e.g. Cantharellaceae) are traditionally shunned by the Patamona. Here we discuss some of the more commonly collected mushroom species of the Patamona and their methods of preparation as well as some mushrooms that we have discovered to be choice edibles of the region.

The Glomeromycota is the newest fungal phylum. These are the arbuscular mycorrhizal (AM) fungi that form symbioses with the majority of land plant species. Fossil and molecular evidence suggest this is an ancient symbiosis, that may have been instrumental in enabling plants to colonise terrestrial habitats. The AM fungi gain carbon from their plant host, and the primary benefit to plants is thought to be the acquisition of phosphate, a highly immobile ion in soil. However, they are thought to have many other ecological benefits. Host specificity has been considered to be low in this group, as most fungi in culture will colonise most plants, but recent evidence suggests that some AM fungi show a degree of specificity. We review the evidence revealing the genetic structure of this ancient group of fungi. Although a consensus has not yet been reached, we suggest that understanding the evolution and genetic structure of this enigmatic group may be the key to understanding how they function in ecosystems.

We investigated post-fire morels (Morchella species), especially the “gray” morels of Idaho and Montana, by collecting ecological and genetic data and by interviewing commercial mushroom harvesters and buyers. Gray morels fruited exclusively in high-elevation Picea/Abies forests that had burned the preceding summer, predominantly in zones of moderate fire intensity as indicated by a layer of dead conifer needles on top of the fire ash. Genetic analysis revealed five varieties of morels among our specimens. Mushroom harvesters confirmed that gray morels are economically crucial to their business because they are typically large, heavy, and durable. Harvesters and buyers described the varieties of morels they encountered differently than mycologists did, but cooperative research could facilitate mutual understanding of morel diversity and benefit everyone involved.

In 1993, a new species of Phytophthora was first recognised as the cause of a disease killing both nursery and mature rhododendrons in Germany and The Netherlands. The same fungus was observed attacking Viburnum in 1998 in Germany. It was named as P. ramorum in 2001 (Werres et al., 2001).

Since 1995, a disease of native coastal oaks (Quercus and Lithocarpus spp.) has been observed in California and Oregon. A Phytophthora species was isolated from affected bark in 2000 and also confirmed as P. ramorum in 2001 (Rizzo et al., 2002). The disease caused by P. ramorum was named in the American popular press ‘sudden oak death’ following the extensive mortality caused by this fungus on the native Californian oaks (Rizzo et al., 2002). Since then the name of the disease has remained but with the increasing number of different hosts from which P. ramorum has been isolated and the range of symptoms, names such as ‘ramorum dieback’ and ‘ramorum leaf blight’ have been used to refer to the disease. The latin name ‘ramus’, meaning ‘branch’ refers to the pathogenicity of the fungus on branches (Werres et al., 2001).

The disease has been found in the following countries: Belgium, Canada, Denmark, France, Germany, Ireland, The Netherlands, Poland (interceptions), Norway, Slovenia, Spain, Sweden, UK, USA (California, Oregon and Washington). It is believed that the fungus has been introduced independently to northern Europe and western USA from an unidentified third country, i.e. it is not regarded as indigenous in either USA or Europe based on the recent discovery of the fungus, the differences in the population of the fungus between the two continents and the clonal structure of the sub-populations (Brasier, 2003; Rizzo & Garbelotto, 2003).

Carrots, irrespective of their origin and whether they have been grown conventionally or organically, almost always harbour spores of Thielaviopsis basicola and T. thielavioides on their surface. Infections become visible as dark green mould patches upon prolonged incubation in polythene bags. These moulds produce beautiful asexual reproductive organs which are described here. We also present the first report of the previously unknown ocurrence of repetitious conidial germination in both species.