Study of fungi with endophytic and mycoparasitic lifestyles for their multiple effects on host traits

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With global warming, plants face increasing stress from drought and disease. Understanding how plant mycosymbionts (myks='fungus', sumbiosis='mutualism') improve plant resistance is critical for maintaining plant diversity, and sustainable crop production. Each evolutionary group of plants adapts by harboring mycosymbionts, a consortia of beneficial endophytes and mycoparasites residing within plant tissue. Forming the plant's 'second genome', they are among the main positive contributors to seed resilience and germination, a vital phase to a plant's lifecycle and adaptability. My program has established itself as a leader in this research area, as evidenced by leading the discovery of mycovitality (vitalitas='vital force'), which defines plant performance in a continuum with mycotrophy (trophe='nutrition'). Mycovitality (endophyte-seed association) induces coleorhiza-driven seed stratification and specific expression of phytohormone biosynthesis genes to achieve both improved germination/seedling emergence and stress tolerance in wheat (Triticaceae). The concept has peaked the interest of the global food security industry; however, a number of scientific questions still remain to be answered including, (a) over the course of the plant-fungus co-evolution, how have plants selected distinct, genome-specific profiles of seed endosymbionts? and (b) how does the endophytic inoculant manipulate the plant microbiome, so as to control plant behavioral adaptations and evolutionary pathways? Investigating the plant microbiome as a system demands meta-omics and comparative studies to unravel gray areas of plant-endophyte symbiosis. In this project, a combination of MiSeq next generation sequencing (NGS) technology will be applied to study the metagenomics of endosymbionts. The NGS will then be coupled with qPCR/microarray, confocal microscopy, FTIR spectroscopy and LC/MSMS analytical methods to elucidate plant's microbiome and metabolome responses to abiotic and biotic stresses. Quantifying metabolic shift in the seed tissues of Aegilops-Triticum host genotypes is essential for understanding endophytism's effect on seed germination. Mapping the expression of key functional genes across plant phenotypes will aid in elucidating the mechanisms by which endosymbionts improve host traits, with evolutionary effects on stress tolerance. Moreover, polyploidization events, which define the evolutionary divergence of cereals, will be key in explaining co-evolution. Comparing functional seed tissues of cereals' with those of Arabidopsis' using -omics techniques would identify specific phenotypical changes in the plant's ontogeny related to endosymbiosis. The overall goal is to generate fundamental knowledge on endosymbiosis so as to better understand plant evolutionary traits, thus creating a tool for improved crop stress resilience and productivity.