Abstract

Studies on phytobiomes in cultivated plants has increased tremendously in the last few years. However, research to elucidate the role and evolution of these microbial endosymbionts in wild plants is still insufficient. One of the challenges in defining ecology and evolution of fungal endophytes relies in systematics. My research in the past 20 years has focused in part in first developing clear and meaningful taxonomy for various Ascomycota (e.g., Diaporthe, Tolypocladium, Trichoderma, and other Hypocreales). Second, I have studied intensively the evolution of ecological traits in Trichoderma, with emphasis on endophytic species. Results from my studies show that Trichoderma is not only ubiquitous in the soil, but also in living sapwood of various tropical trees. In addition, living woody plants contain exclusively endophytic Trichoderma spp. not found in any other niche. Evolution and radiation of endophytic species likely occurred from host/substrate shifts, from soil saprotroph to plant biotroph. Comparative genome analyses are also showing unique features in the endophytic species Trichoderma endophyticum. With solid taxonomy, species delimitation and phylogenetic analyses, it is then possible to infer the cryptic roles endophytes play in their hosts. This could be accomplished by evaluating their closest relatives and determining their most recent ancestors. Findings from these studies have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies. Intersecting ecological and evolutionary studies have therefore served me to use the information in applied agriculture. For example, culture-dependent and -independent metabarcoding analyses show that Trichoderma, in addition to other antagonistic fungi, dominate the endophytic fungal community in wild tropical trees, demonstrating a protective mutualism that may be altered in monoculture plantations. My studies also indicate that species composition in seedlings in the wild is significantly different from adult trees and that putative pathogens are more frequent in seedlings and absent in adults, whereas mycotrophs are absent in seedlings and abundant in adults. I also show that endophytic fungi in fruits of Ficus colubrinae with potential to be plant pathogenic do not survive the digestive tract of the bat Ectophylla alba. Dispersed seeds may benefit from frugivores by a reduction in the number of potentially pathogenic taxa. These results support well known hypotheses, such as the Janzen-Connell, Negative Density Dependence, and the Theory of Pest Pressure. With a better understanding of the evolution and ecology of endophytes, we have used many of these fungi in biological control tests against diseases of various tropical crops. For example, endophytic Trichoderma species are significantly more effective against several plant pathogens than non-endophytic isolates, including those from commercial preparations. In addition, some species can even promote growth. My research on phytobiomes in wild relatives of economically important tropical crops will continue to aim to understand their function in natural ecosystems and applications in agriculture.