11 Understanding the Biodiversity and Functions of Root Fungal Endophytes: The Ascomycete Harpophora oryzae as a Model Case

Abstract

The ecological significance of root–fungal symbiosis has been extensively documented. Apart from mycorrhizal associations, roots are also dominated by diverse fungal endophytes, as revealed by both culturing and sequencing-based approaches. Dark septate endophytes (DSEs), habitat-adapted endophytes, and some opportunistic fungi from soil (e.g., nematophagous and entomopathogenic fungi, Trichoderma) represent the main root associates and have consequently received more attentions by virtue of their ubiquity and their key role in benefiting plant fitness. In this chapter, we review the current knowledge about fungal endophytism and particularly illustrate a novel DSE, Harpophora oryzae, that originates from roots of wild rice (Oryza granulata). H. oryzae has been proven to be effective for promoting plant growth and conferring tolerance to rice blast disease. There is clear evidence that H. oryzae adopts a biotrophic lifestyle and induces a local and systemic resistance against the disease. Importantly, H. oryzae is a close relative of Magnaporthe oryzae, the most devastating pathogen of rice. This allows a holistic view of evolution of root fungal endophytes from pathogenic ancestors deciphered by a comparative genomic approach. A robust combination of metabolomic and transcriptomic analysis in the two binary fungal–root systems (H. oryzae and M. oryzae) uncovered further details about the key elements leading to either mutualistic or pathogenic interactions.