CAREER: Diversity in the darkness: Integrating environmental genetics, comparative genomics, and citizen science to shed light on groundwater biodiversity

在地下水中发现了许多生物，但人们对这些生物的多样性和相互关系知之甚少，部分原因是洞穴和其他地下栖息地特别难以进入和研究。然而，新的采样和新兴的环境遗传方法，如环境DNA (eDNA)，为研究具有挑战性的生态系统中的生物多样性提供了巨大的希望。环境DNA是生活在环境中的生物体留在环境中的DNA。有了现代技术，就有可能分离出这种DNA并对其进行测序，从而鉴定、监测和研究生活在许多不同栖息地的生物体。该项目将利用传统、dna和基因组方法来确定美国中部和东部洞穴地下水栖息地内部和之间生物多样性的模式和驱动因素。此外，该项目将探索水生洞穴生物如何对其栖息地的变化做出反应，这些变化与人类对地下水的空间和时间影响有关。将开发在水生洞穴生态系统研究中使用eDNA及其与基因组方法相结合的最佳做法。研究将直接涉及K-12学生和教育工作者、本科生和研究生、博士后研究人员和社区科学家，重点关注在洞穴和科学领域代表性严重不足的群体，通过几个教育和推广项目，包括以学生为中心的水生洞穴生物多样性监测社区科学倡议、3-5年级的教育夏令营、本科生研究和培训项目以及教师讲习班。最后，该项目将支持开发地下水和洞穴生物多样性数据和资源的在线数据门户，以供未来研究和支持保护和管理工作。该项目将利用现有的大量标本和组织收集，并将传统和DNA采样与基因组方法（如超保守元件和限制性位点相关DNA测序）相结合，比较美国中部和东部三个不同喀斯特生物地理区域内和之间不同尺度的物种和遗传多样性水平，以更好地了解空间格局及其形成过程。此外，人类对土地利用的影响对地下水种群和社区生物多样性时空格局的影响将采用种群基因组方法进行研究。最后，将研究eDNA与基因组方法的结合，通过对洞穴沉积物岩心的时间序列分析，探索eDNA在地下水物种和群落时空动态方面的应用。地下水生态系统对这类研究特别有吸引力，因为地下水栖息地缺乏紫外线辐射，温度稳定，微生物活动普遍较低，可能会促进eDNA的长期持久性。该项目由系统学和生物多样性科学计划和促进竞争性研究的既定计划（EPSCoR）共同资助。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。

Many organisms are found in subterranean water (groundwater), yet the diversity and relationships of these organisms are poorly known, in part because caves and other subterranean habitats are particularly challenging to access and study. However, new sampling and emerging environmental genetic approaches, such as environmental DNA (eDNA), offer great promise for studying biodiversity in challenging ecosystems. Environmental DNA is DNA that is left in the environment by the organisms that live there. With modern techniques it is possible to isolate and sequence this DNA to identify, monitor, and study the organisms living in many different habitats. This project will harness traditional, eDNA, and genomic approaches to identify patterns and drivers of biodiversity within and among cave groundwater habitats in the central and eastern United States. In addition, this project will explore how aquatic cave organisms have responded to changes to their habitats that are associated with human impacts on groundwater both spatially and over time. Best practices for employing eDNA and its integration with genomic approaches in the study of aquatic cave ecosystems will be developed. Research will directly involve K-12 students and educators, undergraduate and graduate students, postdoctoral researchers, and community scientists, with an emphasis on groups that are grossly underrepresented in caving and science through several educational and outreach programs, including a student-focused community-science initiative for aquatic cave biodiversity monitoring, grades 3–5 educational summer camps, an undergraduate student research and training program, and teacher workshops. Finally, this project will support the development of an online data portal for groundwater and cave biodiversity data and resources for future research and support conservation and management efforts.This project will harness a large, existing specimen and tissue collection and integrate traditional and eDNA sampling with genomic approaches, such as ultraconserved elements and restriction site-associated DNA sequencing, to compare levels of species and genetic diversity at different scales within and among three diverse karst biogeographic regions in the central and eastern United States to better understand spatial patterns and the underlying processes that shape them. In addition, the effects of human impacts in land use on spatial and temporal patterns of biodiversity in groundwater populations and communities will be examined using population genomic approaches. Finally, the integration of eDNA with genomic approaches will be studied to explore the application of eDNA in providing insights into the spatial and temporal dynamics of groundwater species and communities using time-series analysis of sediment cores in caves. Groundwater ecosystems are particularly attractive for such studies, as the lack of UV radiation, stable temperatures, and generally low microbial activity in groundwater habitats may promote long-term eDNA persistence.This project is jointly funded by the Systematics and Biodiversity Science program and the Established Program to Stimulate Competitive Research (EPSCoR).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.