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

金莲花是海洋中数量和生态上重要的浮游植物物种，以其世界性的分布和在沿海和开阔海域形成大型水华的能力而闻名。对E.huxleyi变种在培养上的研究发现，它们在生长、功能和活性潜力方面存在差异。E.huxleyi变异体携带的一些基因也不同。有人假设，这种基因组的可变性可能是这种浮游植物物种全球成功的基础，因为它允许变种适应不同的环境。然而，基因组含量和生态成功之间的直接联系仍不清楚。本项目旨在研究在不同的环境条件下，虎纹艾美耳球虫基因组的保守和可变部分如何与其成功及其动态有关。这项工作对于我们理解这种重要的浮游植物物种可能如何转变并对未来的变化做出反应至关重要。该项目还支持开展一系列实践活动，旨在向中学生传授海洋科学方面的高级计算数据分析。这些活动是与我们姐妹学校的编程女孩俱乐部合作的，这是一所位于马萨诸塞州新贝德福德的免费、非宗派的独立学校，面向低收入家庭的女孩。了解浮游植物多样性和表型是如何受环境变化驱动的，对于更好地预测未来海洋的碳循环动力学至关重要。虽然许多工作已经研究了浮游植物物种之间的竞争，但对于许多真核浮游植物来说，种内多样性和动态在很大程度上仍然未知。该项目的首要目标是通过一系列基因组分析、计算性实地调查和基于实验室的实验，确定泛基因组(一组可变基因)在赫氏棘豆生态和生物地理学中的作用。该项目正在对来自全球海洋的几个E.huxleyi分离株的基因组进行测序，并将它们与现有的基因组序列结合起来，以限制PAN基因组的核心和可变部分。利用这个新的PAN基因组参考数据库，并利用全球范围的元基因组学和元转录研究，该项目正在评估海洋地区虎纹伊蚊的生态型多样性，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一批测序菌株的生理和转录反应，以及它们对营养环境变化的反应。鉴于虎尾藻在海洋生态系统和全球碳循环中的重要作用，对其泛基因组及其对虎尾藻生物地理和生态的影响进行研究具有重要意义。这些动态很可能对预测这个物种，也许还有其他物种，如何应对未来海洋中不断变化的环境条件非常重要。这个奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.