Abstract
Dark septate endophytes (DSE) are among the most abundant colonizers of plant roots. The form taxon DSE includes a broad range of fungal species that are only distantly related and the taxonomy of DSE has puzzled mycologists for years. In the following chapter we discuss the structure of diversity in dark septate endophytes. In the first part, we give an overview of the taxonomic placement of DSE and present a reference dataset of ITS sequences of well-characterized DSE taxa that can be used to classify DSE in future studies. The second part is dedicated to the diversity in the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC), which includes some of the most frequent and widespread DSE. Diversity of PAC is discussed on various levels ranging from single root segments to continents and from communities to genes.
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