Challenges and update on fungal endophytes: classification, definition, diversity, ecology, evolution and functions

Abstract Fungal endophytes have generally been considered as hidden microorganisms that reside asymptomatically within plant tissues and have been exploited for their potential in medicine and plant pathology. They are ubiquitous and associated with nearly all plant species sampled. Even though the exact roles of endophytic fungi within a plant is yet to be established, many speculate that they play important roles in obtaining nutrients and thus improve plant growth, confer plant immunity and promote resistance against biotic and abiotic stresses. It has been postulated that endophytes can exhibit different lifestyles and can even switch lifestyle (i.e., from endophytic to pathogenic or saprobic depending upon plant growth stages). However, there is limited evidence as to whether this switch really happens in vivo. Along the same line, with increasing knowledge of endophytic diversity, defining endophytes has not been easy given their multifaceted functions. The present study provides an updated account with comprehensive knowledge on several aspects including problems with existing definitions, isolation and identification techniques, theoretical and experimental evidence of the role of endophytes, contribution to fungal diversity as well as agenda for future research avenues. For years there has been a number of controversies and debates surrounding as to what exactly is an endophyte. Most of the previous definitions were ephemeral in nature and rather vague and could not realistically define an endophyte. Taking into account numerous biological aspects, we propose herein that endophytes can be defined as “asymptomatic microbial partners that are intimately associated and co-inhabit within healthy internal plant tissues with the ability to confer benefits, co-evolve and alter their lifestyle depending upon plant life stages and adverse conditions”. We also discuss the evolution of endophytes based on fossil data and their co-evolution with their host partners. Studies on fungal endophytes have relied mostly on culture-dependent methods to enable their characterization. However, it is generally well known that these methods suffer drawbacks and there is a need to address the challenges associated with lack of sporulation to enable morphological characterization, slow growth on artificial media, as well as contamination issues. These issues are discussed and addressed in detail here. The molecular mechanisms underlying endophytic colonization, avoidance of plant defense mechanisms, lifestyle changes, as well as their genomics and transcriptomics, are also reviewed. We analyze the possibility of endophytes being host-specific or associated with certain hosts and finally provide an account of their economic importance. This outline of fungal endophytes will provide a more comprehensive understanding of endophytes and can serve for boost research into the exploration and their potential applications in the future.