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

自由生活的线虫是世界范围内底栖生物栖息地中最丰富的微生物门之一，占海洋沉积物后生动物生命形式的70-90%，并发挥着营养循环和沉积物稳定性等关键功能。然而，它们未被探索的多样性——以及来自底栖海洋生态系统的分类和分子数据的极度缺乏——代表了生物学的主要挑战之一，目前限制了我们理解环境变化加速后果的能力。本项目采用尖端的组学方法结合经典形态分类学来表征自由生活的海洋线虫及其宿主相关微生物群的生物多样性、进化和生态模式。首先，这项工作使用eDNA元条形码来确定海洋栖息地转变（深度、盐度）和环境压力梯度（污染、氧气可用性）中整体小动物生物多样性的变化。其次，该项目确定了在关键海洋梯度上保持“世界性”分布的关键线虫谱系，以及能够承受最极端环境压力的谱系。最后，本工作描述了线虫的基因组适应和宿主相关的微生物组模式，这些模式可能促进线虫的扩散和对极端环境胁迫的适应。教育活动正在与数据生成和线虫组学数据集的分析紧密结合。他带领佐治亚大学的本科生和研究生建立基础计算技能，建立和发展当地的生物信息学实践社区。针对中级生物信息学学习者的为期一周的夏季黑客马拉松，将数据可视化和科学传播工具结合起来，教参与者如何“通过数据讲故事”。最后，本项目邀请本科生参与“从沉积物到物种”的工作流程，提供经典分子系统学、生物信息学和科学传播的跨学科教育。该项目的目标是对自由生活的海洋线虫进行首次大规模调查，收集海洋栖息地转变（盐度，深度）和环境压力梯度（污染，氧气可用性）的分子数据，为现有的历史（形态）分类研究提供比较数据集。本研究采用传统的光显微复制、环境DNA测序和单虫基因组测序相结合的新方法，以提高对自由生活线虫及其在全球海洋栖息地的生态和进化作用的科学认识。由此产生的数据集为浅水和深海海洋栖息地的全球线虫生物多样性提供了一个重要的基线，并照亮了线虫生命树中的“黑暗区域”（目前采样不足且缺乏分子DNA条形码的谱系）。该项目结合了跨学科的研究主题，包括海洋线虫系统学、生物信息学和微生物生态学，并将计算训练和科学交流结合起来，为本科生和研究生提供所有项目目标。研究成果正在迅速推进我们对全球海底栖息地结构和功能的认识，而分子数据集为未来对各种自由生活的线虫群体进行基因组研究奠定了基础。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。

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.