True endophytic fungi (EF) are organisms inside plants never causing disease.

Fungal interactions in plants are a continuum from pathogenic to beneficial.

EF can manipulate their hosts to secure their own optimal habitat.

EF tools: effector proteins, miRNAs, phytohormones and specialised metabolites.

EF can confer abiotic stress tolerance and biological control of diseases.

The enigmatic endophytic fungi are beginning to reveal their secrets. Like pathogens, they can manipulate the host for their own benefit to create their own optimal habitat. Some endophytic manipulations induce resistance or otherwise outcompete pathogens and can thus be exploited for biological control. Like pathogens and other symbionts, endophytes produce effector proteins and other molecules, ranging from specialised metabolites, phytohormones and microRNAs, to manipulate their hosts and other microorganisms they meet. There is a continuum from endophyte to pathogen: some organisms can infest or cause disease in some hosts, but not in others. Molecular genetics approaches coupled with functional characterisation have demonstrated their worth for understanding the biological phenomena underlying endophytic fungal interactions.

© 2022 The Author(s). Published by Elsevier Ltd.