Microfungal endophytes in roots

A wide range of ascomycetous microfungi inhabits roots without forming the anatomical features typical of mycorrhizas or causing overt signs of pathogenesis. The most-studied taxa have darkly pigmented hyphal walls and are referred to as dark septate endophytes (DSE). We provide a dichotomous key and annotated descriptions for a cross-section of the most common dark septate endophytes. The term DSE is sometimes used to imply taxonomic and physiological similarity even though a diverse range of root endophytic taxa form pigmented hyphae. Among these, Phialocephala fortinii Wang & Wilcox is a well-known representative; it is widespread, easily observed in roots, and readily grown in culture and with plants. Nevertheless, the basis of its symbiotic relationship with plants remains ambiguous. It may be a weak pathogen, a saprotroph on senescent root tissues, or a mutualist. More detailed studies of interactions between identified taxa of microfungal endophytes and host plants are necessary to elucidate the functional basis of these symbioses; it may be necessary to look beyond the paradigms of traditional mycorrhizal and pathogenic associations to understand the ecological roles of these fungi. Reports of cryptic speciation in Phialocephala fortinii emphasize the need for accurate identification of isolates of microfungal endophytes used in experiments.