Free DNA in environment and its use in systematics of macrofungi

Abstract

On the basis of the review of numerous scientific publications, in our article there is compared the effectiveness of various study methods of macrofungi groups, the species diversity of which remains largely unknown. Macrofungi form the visible fruit body. They are found in most environmental conditions, but are most common in forest ecosystems, where they are reducers. Macrofungi belong to the Ascomycota and Basidiomycota types within the Dikarya subkingdom and are divided into saprotroph, parasitic and mycorrhizal fungi. Saprotroph species play a main part in the decomposition of organic matter of soil, fallen leaves and dead wood. Parasitic macrofungi cause a number of diseases of other mushrooms, plants and animals (mostly invertebrates). Mycorrhizal fungi form a symbiotic system with plant roots, which is useful for both partners. There are known over 90000 species of macrofungi that is about 60 % of the number of all described fungal species in the present (Deacon, 2006; Orgiazzi et al., 2016). Macrofungi are considered to be studied in the best way, but their species diversity remains largely unknown. For example, in the course of over last 60 years more 56000 species of macrofungi have been identified in Australasia, China, and Japan, of which 35000 species, or 62 %, are unknown (Mueller et al., 2007). At the same time, in China and Japan the part of new macrofungal species was 37 %, and in Australasia – 72 %. To determine the diversity of macrofungi three methods can be used: a collections of fruit bodies, mycelium cultivation on the agar substrate and free fungal DNA in the environment. The study of collections are used most commonly. However, in the case when mushrooms have large fruit bodies, but they are short-lived, this method is not always able to detect them and attach them to the collection. For other two methods, the presence of fruit bodies is not obligatory. But the mycelium cultivation method also has a drawback, since not all mycorrhizal and parasitic mushrooms can be cultivated in the laboratory because they can’t exist outside the symbiosis with the roots of living plants or outside the host's body, respectively. Altogether together both collection studying and mycelium cultivation methods can find a significant majority of the environmental fungal taxons, which form fruit bodies. However, they can not reflect the relative prevalence of species. The method of molecular genetic analysis of the environmental DNA (eDNA) has the greatest advantages of other two, since it is also suitable for the discovery of such taxonomic units. This method has allowed to identify new branches, including ancient branched fungal lines, such as Cryptomycota or Archaeorhizomycetes. True, sometimes the method of eDNA analysis does not find taxonomic units, which are detected by the collection of fruit bodies or by mycelium cultivating. But this may have been due to sample incompleteness or to errors in the complex process of eDNA analysis. Since in these analysis there are used fragments of DNA or RNA only a few hundred bases long, this method is not able to detect a number of biological indices that can be obtained by examining of a fungal collection or culture. Thus to obtain most complete information about macrofungal community structure as well as their genomic, physiological and ecological properties it is necessary to use all three methods.