Biodiversity of Fungi

Inventory and Monitoring Methods

Mercedes S. Foster, Gerald F. Bills, Mercedes S. Foster, Gerald F. Bills

• Publisher: Academic Press
• Year: 2011
• ISBN:
  9780080470269
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

Biodiversity of Fungi is essential for anyone collecting and/or monitoring any fungi. Fascinating and beautiful, fungi are vital components of nearly all ecosystems and impact human health and our economy in a myriad of ways. Standardized methods for documenting diversity and distribution have been lacking. A wealth of information, especially regrading sampling protocols, compiled by an international team of fungal biologists, make Biodiversity of Fungi an incredible and fundamental resource for the study of organismal biodiversity.

Chapters cover everything from what is a fungus, to maintaining and organizing a permanent study collection with associated databases; from protocols for sampling slime molds to insect associated fungi; from fungi growing on and in animals and plants to mushrooms and truffles. The chapters are arranged both ecologically and by sampling method rather than by taxonomic group for ease of use. The information presented here is intended for everyone interested in fungi, anyone who needs tools to study them in nature including naturalists, land managers, ecologists, mycologists, and even citizen scientists and sophiscated amateurs.

• Covers all groups of fungi - from molds to mushrooms, even slime molds
• Describes sampling protocols for many groups of fungi
• Arranged by sampling method and ecology to coincide with users needs
• Beautifully illustrated to document the range of fungi treated and techniques discussed
• Natural history data are provided for each group of fungi to enable users to modify suggested protocols to meet their needs

PART I

GENERAL ISSUES

1 FUNGI AND THEIR ALLIES

MEREDITH. BLACKWELL, JOSEPH W. SPATAFORA

A BROAD VIEW OF EUKARYOTES

KINGDOM FUNGI

PHYLUM CHYTRIDIOMYCOTA (ZOOSPORIC FUNGI)

PHYLUM ZYGOMYCOTA

CLADE GLOMALES

PHYLUM ASCOMYCOTA

Class Archiascomycetes

Class Saccharomycetes

Class Euascomycetes

PHYLUM BASIDIOMYCOTA

Class Ustilaginiomycetes

Class Urediniomycetes

Class Hymenomycetes

KINGDOM STRAMINIPILA (HETEROKONT ZOOSPORIC ORGANISMS)

Oomycota

Hyphochytriomycetes

Labyrinthulales and Thraustochytriales (and Aplanochytrium)

SLIME MOLDS

Plasmodiophorales (Parasitic Slime Molds)

Myxomycetes, Protostelids, and Dictyostelids (Plasmodial and Cellular Slime Molds)

Acrasid Slime Molds

CONCLUSIONS

Fungi are heterotrophic organisms that permeate our environment. With few exceptions fungi have filamentous bodies enclosed by cell walls, are nonmotile, and reproduce both sexually and asexually by spores. During the last decade, mycologists have made unprecedented progress toward producing a phylogenetic classification of fungi; a skeleton phylogeny based on analyses of DNA characters was developed relatively early on (Bruns et al. 1991; Alexopoulos et al. 1996; McLaughlin et al. 2001). Such a phylogeny serves as a basis on which hypotheses of fungal evolution can be developed. One important finding has been that “fungi” are polyphyletic (Table 1.1); their morphologies are convergent, having been derived independently from among several independent eukaryotic lineages (Fig. 1.1). A monophyletic group, exclusive of slime molds and oomycetes, is well defined and supported as “true fungi,” a kingdom-level taxon (Barr 1992; Bruns et al. 1993; Baldauf et al. 2000; Keeling et al. 2000).

TABLE 1.1 Fungi and Fungus-like Organisms Previously Classified as Fungi^*

Fungi

Chytridiomycota

Zygomycota

Ascomycota

Basidiomycota

Straminipila

Oomycota

Hyphochytriomycota

Labyrinthulales

Thraustochytriales

Slime molds

Plasmodiophorales

Myxomycota

Dictyosteliomycota

Acrasiomycota

* Taxonomic ranks of the clades are not indicated (see text).

FIGURE 1.1 Phylogenetic positions of organisms studied by mycologists (bold text). The tree is unrooted, and all organisms are eukaryotic (i.e., they possess nuclei and other membrane-bounded organelles). The tree is based on phylogenetic analyses of sequences of up to four protein-coding (α-tubulin, β-tubulin, actin, and elongation factor 1-alpha [EF-1α]) regions in addition to rDNA.

(Based on Baldauf et al. 2000.)

Historically fungi have been compared with plants and included in the study of botany. Contemporary studies, however, indicate that members of Kingdom Fungi are most closely related to animals, not plants, possibly through a choanoflagellate-like ancestor (Barr 1992; Baldauf and Palmer 1993; Wainright et al. 1993; Ragan et al. 1996; Baldauf et al. 2000; Cavalier-Smith 2001). The phylogenetic positions of other groups once considered as fungi are not always well defined among eukaryotes (see “Kingdom Straminipila” and “Slime Molds,” later in this chapter).

Thus far, fewer than 800 fungi or fungus-like taxa have been included together in any single phylogenetic reconstruction (Tehler et al. 2000), a number representing less than 1% of the 80,000 currently listed species (see Hawksworth et al. 1995). Estimates of up to 1.5 million species of fungi (six times more than the number of recognized species of land plants) are daunting; the missing fungi must be discovered, identified, and incorporated into the taxonomic framework. In addition to the relatively low numbers of taxa included in the trees, taxonomic coverage across higher taxa is limited. Until now only molecular characters from ribosomal RNA genes (rDNA) have been used widely in phylogenetic studies of fungi. The recent increase in use of other DNA regions and incorporation of phenotypic characters to resolve conflicting trees based on single genes and analytical approaches is encouraging.

Fungal classification, as opposed to phylogeny, is in a state of flux. Ideally, classifications should reflect phylogenetic relationships, but the relationships of all the groups covered in this volume have not been resolved nor have all of the groups been represented in analyses. Thus, the formal and complex classification systems that have been devised (e.g., Cavalier-Smith 2001) may vary in their inclusiveness. Systematists who study many types of organisms face this situation. Nevertheless, one reactionary suggestion called for a moratorium on publication of higher-level taxonomic systems until 2050 (Karatygin 1999). Hibbett and Donoghue (1998) suggested a more practical solution—the use of clade names rather than formal taxon designations. We use this approach, especially for higher taxa, in the following discussion.

Nowhere are examples of convergent evolution more evident than among organisms occupying the same habitat, which are grouped together for treatment in this volume. In this chapter we review the current state of knowledge of the phylogeny of true fungi (Kingdom Fungi) and fungus-like organisms placed in several additional distinct clades (Table 1.1). The two-volume work edited by McLaughlin et al. (2001) provides detailed information on fungi and fungus-like organisms; only a few of the chapters are cited here.

A BROAD VIEW OF EUKARYOTES

Previous studies based on small subunit rRNA genes (SSU rDNA) suggest that it may not be possible to reconstruct patterns of an ancient rapid radiation of the so-called “crown eukaryotes” (see “Kingdom Fungi,” later in this chapter), especially when based solely on characters from rDNA. Baldauf and colleagues (Baldauf et al. 2000), in contrast, used multiple genes and partitioning of data to develop a hypothesis of the relationships of the large diverse group of eukaryotes, which includes fungi and fungus-like organisms (Fig. 1.1). Their study differed from others in its approach because Baldauf and colleagues (2000) analyzed deduced amino acid sequences from four protein-coding regions (α-tubulin, β-tubulin, actin, and elongation factor 1-alpha [EF-1α]) in addition to rDNA. Consequently, they obtained better resolution of the deep branches in the tree (that is, those that represent the earliest divergences over a great period).

Many of the relationships proposed in Baldauf and colleagues’ (2000) study were not entirely new; however, the large data set they used supported several controversial or conflicting tree branches, depending on their use of either rDNA or protein-coding genes. Relationships identified or strengthened in their phylogenetic analyses included the Fungi-Microsporidia link, the grouping of dictyostelid and plasmodial slime molds, and the remote basal position of the acrasid slime molds. In some instances, correspondence of non-molecular traits (e.g., flagellum type) and arrangement of mitochondrial cristae provided additional support. Taking a broad view of fungi and fungus-like organisms and using a wide variety of characters, Baldauf and colleagues (2000) derived the following relationships (Fig. 1.1):

• Kingdom Fungi, (traditionally the phyla Ascomycota, Basidiomycota, Zygomycota, and Chytridiomycota; see “Kingdom Fungi,” later in this chapter) comprises a monophyletic group of “true” Fungi.

• Microsporidia are a sister group to Fungi, and these two taxa form a monophyletic grouping with the Metazoa (animals) linked by a choanoflagellate-like common ancestor.

• Although still scantily sampled, dictyostelid...