Collaborative Research: Defining the role of the pan genome in Emiliania huxleyi ecology and biogeography

赫胥黎藻（Emiliania huxleyi）是海洋中具有重要数量和生态意义的浮游植物，以其世界性分布和在沿海和开阔海域形成大规模水华的能力而闻名。在培养过程中对赫胥黎变异体进行了研究，发现它们在生长、功能和活动潜能方面存在差异。赫胥黎氏杆菌的变体在它们携带的一些基因上也有所不同。据推测，这种基因组变异性可能是这种浮游植物在全球成功的基础，因为它允许变异适应不同的环境。然而，基因组内容与生态成功之间的直接联系尚不清楚。该项目研究了赫胥黎氏杆菌基因组的保守和可变部分如何与其在不同环境条件下的成功和动态联系在一起。这项工作对我们了解这种重要的浮游植物物种如何转变并对未来的变化做出反应至关重要。该项目还支持一系列实践活动的发展，旨在教授中学生海洋科学中的高级计算数据分析。这些活动是与我们姐妹学校（Our Sisters School）的“编程女孩俱乐部”（Girls Who Code Club）合作开展的。这是一所位于马萨诸塞州新贝德福德（New Bedford）的面向低收入家庭女孩的免学费、非宗派独立学校。了解浮游植物的多样性和表型如何受到环境变化的驱动，对于更好地预测未来海洋的碳循环动态至关重要。虽然对浮游植物物种间的竞争进行了大量的研究，但对许多真核浮游植物的种内多样性和动态仍然知之甚少。该项目的总体目标是通过一系列的基因组分析、计算野外调查和实验室实验来确定泛基因组（可变基因集）在赫胥黎黎线虫生态学和生物地理学中的作用。该项目是对来自全球海洋的几株赫胥黎大肠杆菌的基因组进行测序，并将它们与现有的基因组序列相结合，以限制pan基因组的核心部分和可变部分。利用这一新的泛基因组参考数据库，并利用全球范围的宏基因组学和元转录组学调查，本项目估计了赫胥黎蛤在海洋区域的生态类型多样性，以确定环境选择的模式。该项目还侧重于在对照实验室研究中确定选定的测序菌株的生理和转录反应及其对营养环境变化的反应。由于赫胥黎沙蚕在海洋生态系统和全球碳循环中发挥着重要作用，因此考虑其全基因组及其对赫胥黎沙蚕生物地理和生态的影响非常重要。这些动态很可能对预测这个属，也许还有其他属，如何应对未来海洋中不断变化的环境条件非常重要。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。

Emiliania huxleyi is a numerically and ecologically important phytoplankton species in the ocean known for its cosmopolitan distribution and ability to form large blooms in coastal and open ocean regions. Studies of E. huxleyi variants in culture have found differences in growth, function and activity potential among them. The E. huxleyi variants also differ in some of the genes they carry. It has been hypothesized that this genomic variability may underlie the global success of this phytoplankton species by allowing adaptation of variants to diverse environments. Yet, the direct connection between genomic content and ecological success remains unclear. This project investigates how the conserved and variable portions of E. huxleyi genome may be connected to its success and its dynamics under varied environmental conditions. This work is critical to our understanding of how this important phytoplankton species may shift and respond to future changes. This project also supports the development of a series of hands-on activities designed to teach middle school students advance computational data analysis in ocean science. These activities are in collaboration with the Girls Who Code Club at the Our Sisters School, ‘a tuition-free, non-sectarian, independent school for girls from low-income families’ located in New Bedford, MA. Understanding how phytoplankton diversity and phenotype are driven by changes in the environment is crucial for better predicting carbon cycle dynamics in the future ocean. While much work has investigated competition among phytoplankton species, intraspecific diversity and dynamics remain largely unknown for many eukaryotic phytoplankton. The overarching goal of this project is to define the role of the pan genome (set of variable genes) in E. huxleyi ecology and biogeography through a series of genomic analyses, computational field surveys, and laboratory-based experiments. This project is sequencing the genomes of several E. huxleyi isolates from across the global ocean and combining them with existing genome sequences to constrain the core and variable portions of the pan genome. Using this new pan genome reference database and leveraging global scale metagenomics and metatranscriptomic surveys, this project is estimating ecotype diversity of E. huxleyi across ocean regions to identify patterns of environmental selection. This project additionally focuses on identifying the physiological and transcriptional responses of a selection of sequenced strains and their responses to shifts in their nutrient environments in controlled laboratory studies. As E. huxleyi plays such a significant role in marine ecosystems and the global carbon cycle it is important that its pan genome and its impact on the biogeography and ecology of E. huxleyi is taken into consideration. It is likely that these dynamics are acutely important to predicting how this genus, and perhaps others, respond to changing environmental conditions in the future ocean.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.