Previously, a species was defined as a group of individuals having common morphological characters. Based on the degree of discrimination adopted by the taxonomist—a scientist who identifies and classifies according to a nomenclature and classification system— approximately 70,000 species of fungi have been described based on morphological features such as the structure of conidiophores, the color and the method of formation of spores, the types of ascocarps, the features of basidium and many others. However, this number is considered to be grossly lower than the total number of fungal species. Hawksworth (1991) estimated the number of species of fungi based on the ratio between the species of vascular plants and the species of fungi in well-studied regions of the world. For the United States, this ratio is 1:1; for Finland 1:4; for Switzerland 1:4; and for India it is 1:0.5. The best-studied region is the British Isles, where the ratio is 1:6. These ratios show us the regions that require mycological studies. For example, the ratio for India is undoubtedly low because of the underexploration of the subcontinent's alpine, aquatic, arid and tropical environments. If the ratio of one fungus to six plants is applied to the global total of 250,000 species of vascular plants, the total number of fungal species comes close to 1.5 million. Only 5% of this estimated number of fungal species are actually documented. Where are the undiscovered fungi to be found? Unusual fungi lurk in unusual ecological niches and habitats (Subramanian, 1992).
Devising methods for their enumeration is difficult. Traditional isolation and enumeration techniques use the soil dilution plates, which in essence involve adding soil or a diluted suspension to petri dishes and covering with a suitable agar medium. It is estimated that there are up to a million fungal spores in a gram of dry soil. Some species can have unusual nutritional requirements and therefore uncultivable on media commonly employed and unidentifiable. There is no simple solution for estimating species diversity.
13.3 SPECIES RECOGNITION 13.3.1 MSR, BSR and PSR
The vast majority of the 70,000 described fungi were identified based on morphological characters. However, fungi are notorious for their phenotypic plasticity—a characteristic that led Buxton (1960) to comment that fungi are "a mutable and treacherous tribe." Individuals may show striking nongenetic variation depending on changes in the growth environment. Thus, forms that may in fact be closely related could be given the status of different species. On the other hand, a group of individuals could share certain morphological characters but, in fact, be genetically isolated. Therefore, for species recognition, morphological criteria (morphological species recognition, or MSR) alone are not sufficient. A species has been defined variously (Taylor et al., 2000) as "groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups" or "the smallest aggregation of populations with a common lineage that share unique, diagnosable phenotypic characters" or "a single lineage of ancestor-descendant populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate." An excellent example of species discriminated by mating tests (biological species recognition, or BSR) is provided by the fungus Neurospora. Shear and Dodge (1927) showed that by mating tests, the morphological species Monilia sitophila can be split into three species: N. crassa, N. sitophila and N. tetrasperma. However, the identification of a species mating test is not easy to apply as in approximately 20% of all fungi, grouped as Fungi Anamor-phici, the sexual stage either does not occur or the conditions under which it occurs are not known. The use of a mating test (reproductive success in crosses) in species identification is therefore of limited use.
With the recombinant DNA technology, long stretches of DNA can be cloned and sequenced and compared to determine whether two nucleic acid molecules are similar. Nucleic acid sequences are scanned and fitted by computer models into a branching tree pattern based on maximum parsimony. A software program is used to measure the summed average index of resemblance between fungi and arrange them into a branching tree diagram, i.e., a tree that unites the specimens having the most features in common to demonstrate the relative relationships in a group of individuals, with adjacent branches depicting the greatest or closest genetic similarity (Burnett, 2003). A phylogenetic system that classifies organisms according to their evolutionary sequence, that is, enables one to determine at a glance the ancestors and derivatives, is used in recognizing species. It is particularly useful in those organisms where the mating test cannot be applied. In this phylogenetic diagram, the branch points or nodes reflect divergence from a previously common sequence and the length of a branch or distance is a measure of the mean number of estimated character changes (substitutions) required to convert one sequence to another. A group of organisms is identified that is an out-group—an independent evolutionary lineage, qualifying as a reproductively isolated species (phylogenetic species recognition, or PSR). In Neurospora, correspondence existed between groups of individuals identified as species by BSR and PSR criteria; however, PSR provided the greater resolution (Dettman et al., 2003). Data from six loci (al-1, frq, gpd, mat a, mat A and ITS/5.8S rRNA) consistently suggested that among the five outbreeding species recognized on the bases of MSR or BSR, N. discreta diverged first. More species have been found by the criterion of PSR than by MSR or BSR.
Before the molecular techniques, the concept of variation was provided by E.C. Stakman and his associates who noted that a variety of crop plant bred for resistance to a particular species of a rust fungus failed to remain resistant to that particular fungus. They demonstrated that the species of the black (or stem) rust fungus, an obligate parasite on wheat and grasses (namely Puccinia graminis f.sp. tritici) could be subdivided into over 200 "physiological races." These varied in virulence characters; namely, the size and shape of lesions produced on leaves of different varieties of wheat called the "tester" varieties (Figure 13.1), although they were indistinguishable in morphological features such as the size of urediospores. The recognition of physiological races explained why no variety of wheat plant bred for resistance to a pathogen is permanent because a new physiological race can arise through sexual recombination. Puccinia graminis f.sp. tritici is heteroecious,
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