CAREER: Characterizing the phylogenetic lineages and genomic factors enabling adaptation in free-living marine nematodes

职业：描述系统发育谱系和基因组因素，使自由生活的海洋线虫能够适应

• 批准号: 2144304
• 负责人: Holly Bik
• 金额: $ 126.48万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-01 至 2027-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2144304&HistoricalAwards=false
• 关键词: CAREER; Characterizing; phylogenetic; lineages; genomic

Free-living nematodes are one of the most abundant microbial phyla found in benthic habitats worldwide, representing 70-90% of metazoan life forms in marine sediments and performing key functions such as nutrient cycling and sediment stability. Yet, their unexplored diversity—and the extreme paucity of taxonomic and molecular data from benthic marine ecosystems— represents one of the major challenges in biology and currently limits our capacity to understand the accelerating consequences of environmental change. This project uses cutting-edge -Omics approaches in conjunction with classical morphological taxonomy to characterize patterns regarding the biodiversity, evolution, and ecology of free-living marine nematodes and their host-associated microbiomes. First, this work uses eDNA metabarcoding to determine how overall meiofaunal biodiversity changes across marine habitat transitions (depth, salinity) and gradients of environmental stress (pollution, oxygen availability). Second, the project identifies key nematode lineages which maintain “cosmopolitan” distributions across key marine gradients, and lineages which can tolerate the most extreme environmental stressors. Finally, this work characterizes the nematode genomic adaptations and host-associated microbiome patterns that may facilitate nematode dispersal and adaptation to extreme environmental stress. Educational activities are being strongly integrated with data generation and analysis of nematode -Omics datasets. The investigator leads an effort to build foundational computational skill sets in undergraduate and graduate students at the University of Georgia, establishing and growing a local bioinformatics community of practice. Weeklong summer hackathons aimed at intermediate bioinformatics learners merge data visualization and science communication tools and teach participants how to “tell stories through data”. Finally, this project engages undergraduate researchers in “sediments to species” workflows, providing interdisciplinary education in classical molecular systematics, bioinformatics, and science communication.The goal of this project is to carry out the first large-scale investigation of free-living marine nematodes that that collects molecular data across marine habitat transitions (salinity, depth) and gradients of environmental stress (pollution, oxygen availability), providing a comparative dataset for the existing body of historical (morphological) taxonomic studies. This research uses a novel approach that combines traditional light microcopy, environmental DNA sequencing, and single-worm genome sequencing in order to advance scientific knowledge of free-living nematodes and their ecological and evolutionary roles in marine habitats worldwide. The resulting datasets produce an important baseline of global nematode biodiversity in shallow-water and deep-sea marine habitats, and illuminate “dark areas” in the Nematode Tree of Life (lineages which are currently poorly sampled and lack molecular DNA barcodes). This project combines interdisciplinary research themes spanning marine nematode systematics, bioinformatics, and microbial ecology, with a strong integration of computational training and science communication for undergraduate and graduate students across all project aims. Research outputs are rapidly advancing our knowledge of the structure and function of seafloor habitats worldwide, and molecular datasets lay the groundwork for future genome-enabled studies of diverse free-living nematode groups.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.

自由生物线虫是全球底栖生物栖息地中发现的最丰富的微生物门之一，代表海洋沉积物中70-90％的后生生命形式，并执行关键功能，例如营养循环和沉积物稳定性。然而，它们的意外多样性以及底栖海洋生态系统中的分类学和分子数据的极度匮乏代表了生物学的主要挑战之一，目前限制了我们了解环境变化加速后果的能力。该项目使用尖端的 - 组方法与经典的形态分类学结合使用，以表征有关自由生活海洋线虫及其宿主相关的微生物组的生物多样性，进化和生态的模式。首先，这项工作使用Edna Metabarcoding来确定在海洋栖息地过渡（深度，盐度）和环境压力（污染，氧气可用性）之间的总体元素生物多样性如何变化。其次，该项目确定了关键的线虫谱系，这些谱系在关键的海洋梯度上保持“世界性”分布，以及可以耐受最极端环境压力的谱系。最后，这项工作表征了线虫基因组适应和与宿主相关的微生物组模式，这些模式可能支持线虫分散并适应对极端环境应激。教育活动与线虫 - 组数据集的数据生成和分析完全融合在一起。研究人员领导着在佐治亚大学的本科生和研究生中建立基础计算技能集，建立和发展当地的生物信息学实践社区。为期一周的夏季黑客马拉松旨在中级生物信息学学习者合并数据可视化和科学通信工具，并教会参与者如何“通过数据讲述故事”。 Finally, this project engages undergraduate Researchers in “sediments to species” workflows, providing interdisciplinary education in classical molecular systemics, bioinformatics, and science communication.The goal of this project is to carry out the first large-scale investment of free-living marine nematodes that collects molecular data across marine habitat transitions (salinity, depth) and gradients of environmental stress (pollution, oxygen可用性），为现有的历史（形态）分类学研究提供了比较数据集。这项研究使用了一种新型方法，该方法结合了传统的光学复制品，环境DNA测序和单Worm基因组测序，以促进自由生活线虫的科学知识及其在全球海洋栖息地中的生态和进化作用。所得的数据集在浅水和深海海洋栖息地中产生了重要的全球线虫生物多样性的重要基线，并照亮了线虫生命树中的“黑暗区域”（目前已经采样较差，缺乏分子DNA条形码）。该项目结合了跨学科研究主题，这些主题涵盖了海洋线虫系统，生物信息学和微生物生态学，以及针对所有项目目标的本科生和研究生的计算培训和科学沟通的牢固整合。研究成果正在迅速提高我们对全球海底栖息地的结构和功能的了解，分子数据集为对潜水员自由生活的线虫小组的未来基因组研究的研究奠定了基础。这项奖项反映了NSF的法定任务，并被认为是通过基金会的知识分子优点和广泛的影响来评估NSF的法定任务。