NSF Postdoctoral Fellowship in Biology FY 2021: Using DNA-barcode lineage tracking to study ecological and evolutionary dynamics in the cucumber pathogen Erwinia tracheiphila

该行动资助2021财年NSF生物学博士后研究奖学金，研究基因组，环境和表型之间相互作用的生命规则的综合研究。该奖学金支持将以创新方式为《生活规则》领域作出贡献的研究员的研究和培训。这项研究的目的是利用新的遗传工具来了解一种经济上重要的黄瓜和南瓜病原体——嗜气管欧文菌的“进化自然史”。大肠杆菌通过叶子或花上的伤口感染植物，在植物的木质部分裂，并通过条纹黄瓜甲虫在植物之间传播。它是研究植物病原菌如何适应不同植物寄主和昆虫媒介环境的理想系统。通过一系列的感染实验，研究员将观察嗜气管杆菌的进化过程，并测量突变在南瓜、黄瓜和甲虫环境中的影响。这项研究将进一步加深我们对这种农业上重要病原体生物学的理解，并将作为建立一个新的模型系统的第一步，以更广泛地理解病原体的进化。在此期间，该研究员还将参加旧金山州立大学的促进计算包容性（PINC）计划，作为扩大参与计算生物学研究的努力的一部分。这种经验也将在教育和科学指导方面提供宝贵的培训。具体而言，本研究将利用现有的大肠杆菌菌株收集和dna条形码跟踪技术，以高分辨率研究大肠杆菌的进化过程。该研究员将进行遗传追踪进化实验和基于条形码的适应度分析，以测量在有或没有竞争对手（其他大肠杆菌菌株）和捕食者（噬菌体）的植物和昆虫体内环境中自然发生和工程（使用转座子诱变）突变的适应度效应。这项工作将提供一个全面的数据集，说明突变的适应度效应如何取决于环境、遗传背景和生态相互作用的交集。为了最大限度地扩大这个项目的影响，带条形码的大肠杆菌菌株库将提供给其他科学家，同时还有一个开源的交互式浏览器，研究人员可以使用它来探索数据并测试他们自己的假设。与加州大学伯克利分校和劳伦斯伯克利国家实验室的科学家一起工作，该研究员将获得功能性细菌遗传学、植物-微生物相互作用、实验设计和指导等方面的培训，这些将是成为一名成功的科学家或研究教授所必需的。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. This research aims to use new genetic tools to understand the “evolutionary natural history” of an economically important cucumber and squash pathogen, Erwinia tracheiphila. E. tracheiphila infects plants through wounds on leaves or flowers, divides in the xylem of the plant, and is transmitted between plants by striped cucumber beetles. It is an ideal system for studying how plant pathogens adapt to different plant host and insect vector environments. Through a series of infection experiments, the Fellow will observe the process of E. tracheiphila evolution and measure the effects of mutations in squash, cucumber, and beetle environments. This research will further our understanding of this agriculturally important pathogen’s biology and will serve as a first step towards building a new model system for understanding the evolution of pathogens more generally. The Fellow will also participate in the Promoting Inclusivity in Computing (PINC) program at San Francisco State University during this work as part of an effort to broaden participation in computational biology research. This experience will also provide valuable training in education and scientific mentorship.Specifically, this research will use existing E. tracheiphila strain collections and DNA-barcode tracking technologies to study how E. tracheiphila evolves in high resolution. The Fellow will conduct lineage-tracking evolution experiments and barcode-based fitness assays to measure the fitness effects of both naturally occurring and engineered (using transposon mutagenesis) mutations in in-vivo plant and insect environments with and without competitors (other E. tracheiphila strains) and predators (phage). This work will provide a comprehensive dataset on how the fitness effects of mutations depend on the intersection of the environment, the genetic background, and ecological interactions. To maximize the broader impacts of this project, the barcoded E. tracheiphila strain libraries will be made available to other scientists, along with an open-source interactive browser that researchers can use to explore the data and test their own hypotheses. Working with scientists at UC Berkeley and Lawrence Berkeley National Labs, the Fellow will gain training - in functional bacterial genetics, plant-microbial interactions, experimental design, and mentorship - that will be essential for a successful career as a scientist or research professor.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.