The Impact of Molecular Data in Fungal Systematics

P.D. Bridge*; B.M. Spooner†; P.J. Roberts†    * British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, United Kingdom
† Mycology Section, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom

I INTRODUCTION TO FUNGAL SYSTEMATICS

A THE KINGDOM FUNGI

The kingdom Fungi is a large, diverse group of organisms that range in size from simple yeast cells of less than 5 μm in diameter, up to complex fruiting bodies that may reach 1 m in size, and to diffuse colonial organisations that are reported to exist over areas of more than 800 Ha (Anon, 1992; Barnard, 2000).

The concept of a “fungus” has developed over many years, and the historic definition of fungi as nonphotosynthetic plants has been shown to be both too simplistic and phylogenetically inaccurate. The definition of the fungal kingdom has been refined as more functional, structural, chemical, and molecular information has become available and the kingdom is now loosely defined as nonphotosynthetic eukaryotes with cell walls containing chitin and β-glucans, and a wholly absorptive nutrition. Fungi do not have amoeboid pseudopodial stages and may occur as both single-celled and multicelled organisms. Fungal cells contain mitochondria with flattened cristae, and Golgi bodies or individual cisternae are present (Carlile et al., 2001; Hawksworth et al., 1995). As this definition of the fungi has been developed, various organisms have become included or excluded from the kingdom. One example of this is the zoosporic Oomycetes, where the cell wall is largely composed of cellulose and glucans. This group includes well-known plant pathogens such as species of Pythium and Phytophthora and the aquatic pathogen Saprolegnia, and this group is now accommodated in the Straminipila (also spelled Stramenopila; see Leipe et al. (1994) and Dick (2001)) or Chromista (Kirk et al., 2001). Conversely, obligate mammalian parasites in the genus Pneumocystis, previously considered to be protozoan, have been placed as a basal group in the fungi (Pneumocystidiomycetes), largely on the basis of cell wall composition and analysis of DNA sequences (Pixley et al., 1991; Sjamsuridzal et al., 1997).

Phyla within the fungi are defined primarily on the basis of life cycles, mode of reproduction, and cell wall and septum structure. Currently the kingdom consists of the Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota, and Glomeromycota. Historically the Chytridiomycota has been placed in groups now included in the Straminipila, but it has been retained in the fungi on the basis of members having chitin in the cell walls and lacking mastigonemes, and DNA sequence analysis (Hawksworth et al., 1995). One important feature of the fungi is that many have life cycles that consist of two or more stages. These are primarily differentiated by the mode of reproduction and may be asexual, where growth and reproduction is by mitosis, or sexual, where reproduction involves meiosis. A fungus either producing asexual diaspores or no spores at all is termed anamorphic or imperfect, and the sexual state when present is termed the teleomorph or the perfect state. The mode of sexual reproduction is a major characteristic for assigning individual fungi to phyla, and a fungus that is known only from its vegetative state cannot be easily placed in a phylum using traditional morphological analysis. Historically such fungi were placed in an additional phylum, the “Deuteromycota.” This placement, however, suggests a phylogenetic relationship between vegetative fungi that has been demonstrated to be incorrect. Vegetative fungi are now considered as mitosporic forms of the major phyla, and the term “Deuteromycota” should not be used (Reynolds and Taylor, 1993).

When anamorph and teleomorph forms both exist and occur separately, there are generally dual names, with one name being used for the anamorph and a different name being used for the teleomorph. In some cases, the morphology of the anamorph can be very basic, and so apparently similar anamorphic forms may produce different and sometimes unrelated teleomorphs. This occurs commonly in the Ascomycetes, and examples of common anamorphic genera with more than one genus of teleomorph include Phoma, Aspergillus, and Paecilomyces. The term holomorph is used for any specimen where the teleomorph and one or more anamorphic state is present, and in nearly all cases, the holomorph name is the same as that of the teleomorph.

Although biochemical and molecular criteria are now used to define the fungi as a kingdom, the systematics of fungi has developed historically from observational characteristics, particularly those involved in growth and reproduction. Among the most important characteristics are those associated with the type of spore, the way in which it is produced, and the way in which it is released. As a result, it can be extremely difficult to identify a fungus by classic methods if spores or spore-bearing structures are not produced, a major limitation to systematics, particularly with environmental or culture-based studies. Fungal nomenclature is governed by the International Code of Botanical Nomenclature (Greuter et al., 2000), and reference collections of type, and authenticated, material are maintained as dried specimens in herbaria. Although this is generally satisfactory for the larger fungi, smaller specimens and microfungi do not always retain key features or do not preserve as scientifically useful specimens when dried, and most microfungi are routinely maintained in culture. However, this is only practical when the fungi can be grown in pure culture, and for the many species that presently cannot be cultured, the reference material may be limited to dried material, often associated with material from a host organism. Dried material can be used to obtain both chemical and molecular data (Bruns et al., 1990; Paterson and Hawksworth, 1985), although the recovery of these will be dependent on the age of the material and its storage history.

B TRADITIONAL SYSTEMATIC TOOLS

Below the level of phylum, fungal systematics is largely based on life cycle and developmental characteristics, the gross morphology of the fruiting body, features of spore production and discharge, ultrastructure of walls, septa, and other structures, together with features of the host, habitat, and niche. An important feature of fungal systematics is that characteristics used to group or separate one group of fungi may be used differently in another group. An example of this is host specificity, where this characteristic is of major importance in defining species in many rust (Uredinales) and smut (Ustilaginales) fungi. In Fusarium, however, many different host-specific populations may occur within a single species, and the host-specific groups are often further subdivided into cultivar-specific races (Armstrong and Armstrong, 1958).

Two major limitations to the use of the traditional micromorphological and life cycle–based characteristics are the lack of specificity shown by some fungi, and a high level of phenotypic plasticity. Although highly host-specific pathogenic forms exist in Fusarium oxysporum, the species is a common soil organism and can occur on a very wide range of materials as a spoilage organism. Similarly, other genera such as Penicillium and Trichoderma can occur on a wide range of substrates, and individual species, such as Trichoderma viride, have been reported from both the polar regions and the tropics (McRae and Seppelt, 1999; Wijesekera et al., 1996). Many fungi can show considerable variation...