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

随着全球变暖，植物面临越来越大的干旱和疾病压力。了解植物真菌共生体（myks=“真菌”，sumbiosis=“共生”）如何提高植物抗性对于维持植物多样性和可持续作物生产至关重要。植物的每一个进化群体都通过庇护真菌共生体来适应，真菌共生体是一种有益的内生菌和真菌寄生在植物组织中的联合体。它们构成了植物的“第二基因组”，是种子恢复力和发芽的主要积极贡献者之一，这是植物生命周期和适应性的重要阶段。我的项目已经确立了自己在这一研究领域的领导地位，正如领导发现真菌活力（vitalitas=“生命力”）所证明的那样，它定义了真菌营养（trophe=“营养”）的连续体中的植物性能。真菌活力（内生菌-种子关联）诱导根瘤菌驱动的种子分层和植物激素生物合成基因的特异性表达，从而提高小麦（小麦科）的萌发/出苗能力和耐胁迫能力。这一概念引起了全球食品安全行业的极大兴趣；然而，许多科学问题仍然有待回答，包括(a)在植物-真菌共同进化的过程中，植物是如何选择独特的、基因组特异性的种子内共生体的？(b)内生接种剂如何操纵植物微生物群，从而控制植物的行为适应和进化途径？研究植物微生物组作为一个系统需要元组学和比较研究来解开植物-内生菌共生的灰色地带。本项目将结合MiSeq下一代测序（NGS）技术对内共生菌进行宏基因组学研究。然后，NGS将与qPCR/微阵列、共聚焦显微镜、FTIR光谱和LC/MSMS分析方法相结合，阐明植物的微生物组和代谢组对非生物和生物胁迫的响应。定量研究小麦-盾草寄主基因型种子组织代谢变化对了解内生作用对种子萌发的影响至关重要。绘制植物表型中关键功能基因的表达图谱将有助于阐明内共生体改善寄主性状的机制，并对胁迫耐受性产生进化影响。此外，确定谷物进化分化的多倍体化事件将是解释共同进化的关键。利用组学技术比较谷物和拟南芥的功能性种子组织，可以确定与内共生有关的植物个体发育的特定表型变化。总体目标是产生关于内共生的基础知识，以便更好地了解植物的进化特征，从而为提高作物的抗逆性和生产力创造工具。

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.