Eukaryotic organisms live in a prokaryote-dominated world. Increasing evidence has shown that almost every niche is occupied by prokaryotic microorganisms. These niches include marine, arid, and polar regions, as well as external and internal tissues of organisms’ bodies, including fungi. Recent investigations of human, insect, and plant internal tissues have revealed the presence of a diverse community of endosymbiotic bacteria, archaea, and viruses that interact with host organism and modulate its phenotypes (Moran et al. 2008; Soltani 2017). Indeed, the extended phenotype of endosymbiotic entities in eukaryotic world is prevalent. This is becoming a fact in fungal kingdom as well. Fungi live in diverse habitats and have adapted a vast variety of mechanisms to cope with such diverse niches. Among these mechanisms are endosymbiont exploitation, i.e., making use of endosymbiotic microbiome, such as endofungal bacteria and viruses (Araldi-Brondolo et al. 2017; Arora and Riyaz-Ul-Hassan 2019; Bao and Roossinck 2013; Soltani 2017). As we will see in the next sections, this phenomenon has great implications for fungal epigenetic engineering for potential uses in agroforestry, medicine, pharmacology, and bioindustry
