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

合作研究：定义泛基因组在赫胥黎艾米利亚生态学和生物地理学中的作用

• 批准号: 1948025
• 负责人: Harriet Alexander
• 金额: $ 44.22万
• 依托单位: Woods Hole Oceanographic Institution
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-03-15 至 2025-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1948025&HistoricalAwards=false
• 关键词: Collaborative; Research; Defining; role; pan

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.

赫氏艾米利亚藻是海洋中数量和生态上重要的浮游植物物种，以其世界性分布以及在沿海和公海地区形成大规模水华的能力而闻名。研究E.在培养物中的赫胥黎变体已经发现它们之间在生长、功能和活性潜力方面的差异。急诊huxleyi变异体携带的一些基因也不同。 据推测，这种基因组变异可能是这种浮游植物物种在全球取得成功的基础，因为它允许变异体适应不同的环境。然而，基因组内容和生态成功之间的直接联系仍然不清楚。本项目研究了E. huxleyi基因组可能与其成功及其在不同环境条件下的动态有关。这项工作对于我们了解这种重要的浮游植物物种如何转变和应对未来的变化至关重要。该项目还支持开发一系列旨在教授中学生海洋科学高级计算数据分析的实践活动。这些活动是与我们姐妹篇学校的女孩编码俱乐部合作开展的，这是一所位于马萨诸塞州新贝德福德的“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。虽然许多工作已经调查了浮游植物物种之间的竞争，种内多样性和动态仍然在很大程度上未知的许多真核浮游植物。该项目的首要目标是确定泛基因组（可变基因组）在大肠杆菌中的作用。huxleyi生态学和植物地理学通过一系列的基因组分析，计算现场调查，和实验室为基础的实验。这个项目是对几个E. huxleyi从全球海洋中分离并将它们与现有的基因组序列结合以限制泛基因组的核心和可变部分。利用这个新的泛基因组参考数据库，并利用全球规模的宏基因组学和元转录组学调查，该项目正在估计E。huxleyi跨越海洋区域，以确定环境选择的模式。该项目还侧重于确定选定的测序菌株的生理和转录反应，以及它们对受控实验室研究中营养环境变化的反应。例如E. huxleyi在海洋生态系统和全球碳循环中起着重要作用，因此研究其泛基因组及其对E. huxleyi被考虑在内。这些动态很可能对于预测该属以及其他属如何应对未来海洋不断变化的环境条件至关重要。该奖项反映了NSF的法定使命，并且通过使用基金会的知识产权进行评估，被认为值得支持优点和更广泛的影响审查标准。