DISSERTATION RESEARCH: Diversity and Functions of Interactions between the Liverwort Marchantia polymorpha and its Fungal Endophytes

植物是自然生态系统的重要组成部分，它们为其他生物提供栖息地，并影响土壤和大气的组成。真菌虽然不那么引人注目，但除了分解死亡物质外，它还显著影响着活植物的成功生长。生活在健康植物体内的真菌，被称为真菌内生菌（以下简称内生菌），可以在许多方面有益于植物，包括促进生长，增强抗病能力，增强对干旱等极端条件的适应能力。因此，了解内生菌如何与寄主植物相互作用对于管理野生生态系统以及提高林业和农业生产力至关重要，因为植物在气候变化中对极端天气做出了反应。迄今为止，在几乎所有的植物样本中都发现了内生菌，但对其功能背后的机制的直接研究很少。本项目研究了一种苔类植物内生菌的多样性及其功能。本项目将对一种模式地茅（Marchantia polymorpha）的内生菌多样性进行采样，并研究影响这种多样性的因素。多态霉在实验室中生长良好，因此本项目将直接测试单个内生菌的作用。利用遗传方法，研究人员将确定观察到的相互作用背后的可能机制。此外，本项目建立的研究体系将为植物与内生菌相互作用的研究提供许多机会。研究人员将从美国的10个种群中收集多形地药，并表征地药及其内生菌的多样性。将使用限制性位点相关DNA测序（RAD-seq）对整个基因组的样本位点进行评估。内部真菌多样性将通过对整个多形霉植株表面灭菌，提取总DNA，然后扩增和测序真菌条形码基因区域来取样。研究人员将测试真菌群落多样性与组成、宿主基因型和种群位置之间的相关性。这些数据将为以前的实验提供生态学背景，以测试培养的内生菌对多形芽孢杆菌在实验室生长分析中的影响。为了研究实验室观察到的苔类与内生菌相互作用背后的机制，研究人员将对植物和选定真菌在单独和一起生长时的转录组进行测序。将使用四种真菌：一种促进生长的真菌，一种有害的真菌，以及每种真菌的近亲，它们表现出中性的相互作用。比较治疗组和对照组之间的基因表达水平将使研究人员能够对哪些细胞系统可能在控制观察到的相互作用中起重要作用形成假设。

Plants are defining components of natural ecosystems where they provide habitats for other organisms and influence the composition of soils and the atmosphere. Fungi, though less conspicuous, significantly affect the success of living plants in addition to breaking down dead matter. Fungi that live inside healthy plants, called fungal endophytes (hereafter simply endophytes), can benefit plants in many ways, including promoting growth, enhancing disease resistance, and increasing resilience to extreme conditions such as drought. Therefore, understanding how endophytes interact with their host plants is critical for managing wild ecosystems as well as increasing productivity in forestry and agriculture as plants respond to extreme weather in a changing climate. Endophytes have been found in nearly all plants sampled to date but there are few direct studies of the mechanisms behind their functions. This project investigates the diversity and functions of endophytes in a liverwort. This project will sample the diversity of endophytes in a model liverwort, Marchantia polymorpha, and investigate what factors influence this diversity. M. polymorpha grows well in the laboratory, so this project will directly test the effects of individual endophytes. Using genetic methods, the researcher will identify possible mechanisms behind the observed interactions. In addition, the study system developed in this project will provide many future opportunities for plant-endophyte interaction research.The researchers will collect Marchantia polymorpha plants from ten populations across the USA and characterize the diversity of the liverworts and their endophytes. Liverwort genotypes will be assessed using Restriction-site Associated DNA sequencing (RAD-seq) to sample sites throughout the genome. Internal fungal diversity will be sampled by surface sterilizing whole M. polymorpha plants, extracting total DNA, then amplifying and sequencing a fungal barcoding gene region. The researchers will test for correlations between fungal community diversity and composition, host genotypes, and population locations. These data will provide an ecological context for previous experiments testing the effects of cultured endophytes on M. polymorpha in laboratory growth assays. To investigate the mechanisms behind the liverwort-endophyte interactions observed in the laboratory, the researchers will sequence the transcriptomes of the plant and selected fungi when grown alone and together. Four fungi will be used: a growth-enhancing fungus, a detrimental fungus, and close relatives of each which show a neutral interaction. Comparing the levels of gene expression between the treatments and controls will allow the researcher to form hypotheses about which cellular systems may be important in controlling the observed interactions.