Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers

Fungal endophytes, a diverse group of primarily ascomycetous fungi defined functionally by their occurrence within asymptomatic photosynthetic tissues of plants, occur in all major lineages of land plants and in natural and anthropogenic communities ranging from the arctic to the tropics. Because of the tremendous diversity they encompass, ecological questions regarding the interactions of endophytes with the plants in which they live - and with other organisms that in turn interact with endophyte-plants symbiota – are difficalt to address. The goals of this review are to highlight progress, challenges, and frontiers in the study of foliar endophyte diversity, with the ultimate goal of encouraging research that both bridges the gap between, and advances, research in alpha taxonomy and ecology. I focus on four themes that are reflected in the recent and rapidly expanding literature regarding endophyte biology: (1) the taxonomic and ecological distinctiveness of endophytes relative to other nonpathogenic plant-associated fungi; (2) the insights that can be gained from studies that consider genotypes as the relevant unit of biological organization, especially in the context of traditional species-level taxonomy and robust phylogenetic methods that tie these genotypes and species together in an explicit evolutionary context; (3) the context-dependency of endophyte communities, highlighting the importance of both the identify of host plants and the geographic location in which plants occur; and (4) the complexity of the endophyte-pathogen-saprotroph continuum, and the challeges and exciting frontiers that lie in understanding the evolutionary relationships and ecological lability of fungi that exhibit these ecological modes. I argue that never before has the study of endophytic fungi been more exciting or more tractable, and that the potential for endophyte researchers to inform diverse areas of biology has never been greater.