Fungal pathogens are the chief agent of plant disease, effecting severe agricultural losses worldwide (Hyde et al. 2014; Punja and Raj 2003; Strange and Scott 2005; Horbach et al. 2011). Agrochemicals play a significant role in plant disease management and ensure sustainable and productive agriculture systems. However, the intensive use of chemicals (determined by frequent and high dose of pesticides) has adverse effects on human health, ecosystem functioning, and agricultural sustainability (Anderson et al. 2004; Vinale et al. 2008; Suryanarayanan et al. 2016). Biocontrol is a strategy used to control plant pathogens, resulting in minimal impact to the environment (De Waard et al. 1993; Vinale et al. 2008).

Endophytes reside asymptomatically within a plant for at least part of their life cycle (Carrol 1998; Huang et al. 2009; Sun et al. 2011; Clay et al. 2016). Fungal endophytes can be broadly classified into two groups, the clavicipitaceous (C) and the non-clavicipitaceous (NC). These endophytes are classified based on evolutionary relatedness, taxonomy, host plant range and ecological function (Hyde and Soytong 2008; Rodriguez et al. 2009; O’Hanlon et al. 2012; Santangelo et al. 2015). Clavicipitaceous endophytes, including Atkinsonella, Balansia, Balansiopsis, Echinodothis, EpichloSˇ, Myriogenospora and ParaepichloSˇspecies are commonly associated with grasses in the family Poaceae and rely on their host throughout their life cycle as mutualist species (Rodriguez et al. 2009; Purahong and Hyde 2011; O’Hanlon et al. 2012; De Silva et al. 2016). Non-clavicipitaceous endophytes, such as Fusarium sp., Colletotrichum sp., Phomopsis sp. and Xylaria sp. are found in most terrestrial plants, and might not inhabit the host plants for their entire life cycle (Rodriguez et al. 2009; Delaye et al. 2013; De Silva et al. 2016; Jayawardena et al. 2016).

Endophytes are neutral or beneficial to their plant hosts (Backman and Sikora 2008). They boost host plant growth, fitness, stress tolerance, and alter interactions with pests and pathogens (Oono et al. 2015; Clay et al. 2016). Endophytes also provide protection against herbivory (O’Hanlon et al. 2012; Santangelo et al. 2015). More importantly, endophytes have potential as an unexplored source of candidate strains for potential biocontrol applications (Ek-Ramos et al. 2013; Oono et al. 2015). For example, endophytic Ampelomyces species parasitize powdery mildews (Busby et al. 2016). Since powdery mildews are biotrophs, their antagonists act mainly through antibiosis and mycoparasitism (Busby et al. 2016). Biocontrol strategies utilize antagonistic mechanisms to disrupt the life cycle of pathogens, leading to the prevention of infection, reduction in colonization of host tissues, reductions in sporulation, and affecting the pathogen’s ability to survive (Punja and Raj 2003; Busby et al. 2016). The hyperparasitic antagonism may be mediated by factors such as include the as production of lytic enzymes and/or antibiotics, while other biocontrol agents may induce the host plant’s defense or just compete with the pathogen for nutrients and ecological niches (Yan et al. 2015; Busby et al. 2016; Lecomte et al. 2016; Schlegel et al. 2016).

Mejı´a et al. (2008) studied endophytes within the healthy leaves of Theobroma cacao, as well as their antagonism against the pathogenic Basidiomycota species Moniliophthora perniciosa (witches broom), Moniliophthora roreri (frosty pod rot) and the oomycete Phytophthora palmivora (black pod rot). The results showed that two endophytes, identfied as Colletotrichum gloeosporioides and Clonostachys rosea, respectively, decreased pod loss due to black pod rot, and reduced sporulating lesions in cacao pods caused by Moniliophthora roreri.

Endophytic fungi from various host plants have been shown to be effective biocontrol agents, including Alternaria sp. and Cladosporium sp., isolated from wheat (Huang et al. 2016), and Alternaria alternata, isolated from grapevine leaves (Zhang et al. 2017b). The use of antagonistic endophytes as biocontrol agents, such as Trichoderma and Chaetomium, present an attractive option for management of certain plant diseases. It is important to screen potential endophytes through in-vitro experiments following field experiments under different environment conditions. In future research using molecular technologies (e.g., metagenomics), ecological dynamics are essential to developing commercial biocontrol agents, as these contribute to sustainable agriculture. It is critical to note that the species isolated as endophytes from a certain host plant may be pathogenic to other plants. Moreover, a careful risk assessment that excludes the possibility for the overproduction of mycotoxins is a mandatory prerequisite for registrations of new biocontrol agents, regardless of whether the producer organisms are endophytes.