Fungal Biology

J. W. Deacon

• Publisher: Wiley-Blackwell
• Year: 2013
• ISBN:
  9781118685075
• Edition: 4
• Topic: Scienze biologiche
• Subtopic: Biologia

Visit the accompanying website from the author at www.blackwellpublishing.com/deacon.

Fungal Biology is the fully updated new edition of this undergraduate text, covering all major areas of fungal biology and providing insights into many topical areas.

• Provides insights into many topical areas such as fungal ultrastructure and the mechanisms of fungal growth, important fungal metabolites and the molecular techniques used to study fungal populations.
• Focuses on the interactions of fungi that form the basis for developing biological control agents, with several commercial examples of the control of insect pests and plant diseases.
• Emphasises the functional biology of fungi, with examples from recent research.
• Includes a clear illustrative account of the features and significance of the main fungal groups.

Chapter 1

Introduction: the fungi and fungal activities

This chapter is divided into the following major sections:

• the place of fungi in the “Tree of Life” – setting the scene
• the characteristic features of fungi: defining the fungal kingdom
• the major activities of fungi as parasites, symbionts and saprotrophs
• fungi in biotechnology

Fungi are a unique group of organisms, different from all others in their behavior and cellular organization. Fungi also have an enormous range of activities – as pathogens of crop plants or humans, as decomposer organisms, as experimental “model organisms” for investigating genetics and cell biology, and as producers of many important metabolites. The uniqueness of fungi is a prominent feature of this book, which adopts a functional approach, focusing on topics of inherent interest and broad significance in fungal biology.

The uniqueness of fungi is reflected in the fact that they have the status of a kingdom, equivalent to the plant and animal kingdoms. So, fungi represent one of the three major evolutionary branches of multicellular organisms.

In terms of biodiversity, there are estimated to be at least 1.5 million different species of fungi, but only about 75,000 species (5% of the total) have been described to date. For comparison, there are estimated to be 4.9 million arthropod species and about 420,000 seed plants (Hawksworth 2001, 2002).

If the estimate of the number of fungal species is even remotely accurate then we still have much to learn, because even the fungi that we know about play many important roles. To set the scene, we can mention just a few examples:

• Fungi are the most important causes of crop diseases, responsible for billions of dollars worth of damage each year, and for periodic devastating disease epidemics.
• Fungi are the main decomposers and recyclers of organic matter, including the degradation of cellulose and wood by the specialized enzyme systems unique to fungi.
• Fungi produce some of the most toxic known metabolites, including the carcinogenic aflatoxins and other mycotoxins in human foods and animal feedstuffs.
• With the advance of the acquired immune deficiency syndrome (AIDS) and the increasing role of transplant surgery, fungi are becoming one of the most significant causes of death of immunocompromised and immunosuppressed patients. Fungal diseases that were once extremely rare are now commonplace in this sector of the population.
• Fungi have an enormous range of biochemical activities that are exploited commercially – notably the production of antibiotics (e.g. penicillins), steroids (for contraceptives), ciclosporins (used as immunosuppressants in transplant surgery), and enzymes for food processing and for the soft drinks industry.
• Fungi are major sources of food. They are used for bread-making, for mushroom production, in several traditional fermented foods, for the production of Quorn™ mycoprotein – now widely available in supermarkets and the only survivor of the many “single-cell protein” ventures of the late 1900s – and, of course, for the production of alcoholic drinks.
• Fungi can be used as “cellular factories” for producing heterologous (foreign) gene products. The first genetically engineered vaccine approved for human use was produced by engineering the gene for hepatitis B surface antigen into the yeast (Saccharomyces cerevisiae) genome. In this way the antigen can be produced and exported from the cells, then purified from the growth medium.
• The genome sequences of several fungi have now been determined, and in several cases the genes of fungi are found to be homologous (equivalent) to the genes of humans. So, fungi can be used to investigate many fundamental cell-biological processes, including the control of cell division and differentiation relevant to biomedical research.
• Fungi are increasingly being used as commercial biological control agents, providing alternatives to chemical pesticides for combating insect pests, nematodes, and plant-pathogenic fungi.

The first part of this book (Chapters 1–9) deals with the growth, physiology, behavior, genetics, and molecular genetics of fungi, including the roles of fungi in biotechnology. This part also includes an overview of the main fungal groups (Chapter 2). The second part (Chapters 10–16) covers the many ecological activities of fungi – as decomposers of organic matter, as spoilage agents, as plant pathogens, plant symbionts, and as pathogens of humans. A final chapter is devoted to the ways of preventing and controlling fungal growth, because this presents a major challenge in modern Fungal Biology.”

The place of fungi in the “tree of life” – setting the scene

The Tree of Life Web Project is a major collaborative internet-based endeavor (see Online resources at the end of this chapter). Its aim is ultimately to link all the main types of organism on Earth according to their natural phylogenetic relationships. The hope is that this will lead us closer to the very root of life on earth, which is currently estimated to be some 3.6–3.8 billion years ago (1 billion = 1000 million years; 109 years). However, fungi arrived much later on the scene. The oldest known fossil fungi date to the Ordovician era, between 460 and 455 million years ago – a time when the largest land plants are likely to have been bryophytes (liverworts and mosses). This accords remarkably well with recent phylogenetic analyses based on comparisons of gene sequences, discussed below.

Carl Woese of the University of Illinois at Urbana-Champaign, USA, has championed the use of molecular phylogenetics. The basis of this is to identify genes that are present in all living organisms and that have an essential role, so they are likely to be highly conserved, accumulating only small changes (mutations and back mutations) over large spans of evolutionary time. Comparisons of these sequences can then indicate the relationships between different organisms. There are limitations and uncertainties in this approach, because of the potential for lateral gene transfer between species and because there are known to be variable rates of gene evolution between different groups of organisms. However several highly conserved genes and gene families can be used to provide comparative data.

Most phylogenetic analyses are based primarily on the genes that code for the production of ribosomal RNA. Ribosomes are essential components of all living organisms because they are the sites of protein synthesis. They occur in large numbers in all cells, and they are composed of a mixture of RNA molecules (which have a structural role in the ribosome) and proteins. In prokaryotes (non-nucleate cells) the ribosomes contain three different size bands of ribosomal RNA (rRNA), defined by their sedimentation rates (S values, also known as Svedberg units) during centrifugation in a sucrose solution. These three rRNAs are termed 23S, 16S, and 5S. In eukaryotes (nucleate cells) there are also three rRNAs (28S, 18S, and 5.8S). The genes encoding all of these rRNAs are found in multiple copies in the genome, and the different rRNA genes can be used to resolve differences between organisms at different levels.

For most phylogenetic analyses the genes that code for 16S rRNA (of prokaryotes) and the equivalent 18S rRNA (of eukaryotes) are used. These small subunit rDNAs contain enough information to distinguish between organisms across the phylogenetic spectrum. Using this approach, several different phylogenetic trees have been generated, but many of them are essentially similar, and one example is shown in Fig. 1.1.

Several points arise from Fig. 1.1, both in general terms and specifically relating to fungi.

• Ribosomal DNA sequence analysis clearly demonstrates that there are three evolutionarily distinct groups of organisms, above the level of kingdom. These three groups – the Bacteria, Archaea, and Eucarya (eukaryotes) – are termed domains and the differences between them are matched by many differences in cellular structure and physiology.
• Beneath the level of domains, there is still uncertainty about the taxonomic ranks that should be assigned to organisms. Plants, animals, and fungi are almost universally regarded as separate kingdoms (Whittaker 1969). But, arguably, this status could also apply to the many “kingdoms” of bacteria, especially the enormous Proteobacteria kingdom which includes most Gram-negative bacteria. And, it could be argued that the many separate groups of unicellular eukaryotes (amoebae, slime moulds, flagellates, etc.) should also be regarded as kingdoms, based on their apparently long-term separation as judged by rDNA sequence divergence. However, many of these lower eukaryotes are still poorly studied, so they are often referred to collectively as “protists,” pending further resolution of their relationships.
• The major multicellular organisms – the animals, plants, and fungi – form a cluster at the very top of the Eucarya Domain, so they are often termed the “crown eukaryotes”. The interesting feature of these grou...