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

职业：黑暗中的多样性：整合环境遗传学、比较基因组学和公民科学，揭示地下水生物多样性

• 批准号: 2047939
• 负责人: Matthew Niemiller
• 金额: $ 102.99万
• 依托单位: University of Alabama in Huntsville
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2047939&HistoricalAwards=false
• 关键词: CAREER; Diversity; darkness; Integrating; environmental

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.

许多生物存在于地下水中，但这些生物的多样性和相互关系却知之甚少，部分原因是洞穴和其他地下栖息地的访问和研究特别具有挑战性。然而，新的采样和新兴的环境遗传学方法，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下的DNA。利用现代技术，可以分离和测序这种DNA，以识别，监测和研究生活在许多不同栖息地的生物体。该项目将利用传统的、eDNA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的生物多样性模式和驱动因素。此外，该项目将探讨水生洞穴生物如何应对与人类对地下水的空间和时间影响有关的栖息地变化。将制定在水生洞穴生态系统研究中采用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，重点是通过几个教育和外展计划在洞穴和科学中严重代表性不足的群体，包括以学生为中心的社区科学倡议水生洞穴生物多样性监测，3-5年级教育夏令营，本科生研究和培训计划，以及教师研讨会。最后，该项目将支持开发一个地下水和洞穴生物多样性数据和资源的在线数据门户网站，以供今后研究，并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eDNA取样与基因组方法相结合，如超保守元素和限制性位点相关DNA测序，在美国中部和东部的三个不同的喀斯特地貌区域内和之间，以不同的尺度比较物种和遗传多样性水平，以更好地了解空间格局和形成它们的基本过程。此外，还将利用人口基因组学方法研究人类对土地利用的影响对地下水人口和社区生物多样性的空间和时间模式的影响。最后，将研究eDNA与基因组方法的整合，以探索eDNA在利用洞穴沉积物岩心的时间序列分析深入了解地下水物种和群落的时空动态方面的应用。地下水生态系统对此类研究特别有吸引力，因为缺乏紫外线辐射，温度稳定，该项目由系统学和生物多样性科学计划和刺激竞争研究的既定计划（EPSCoR）联合资助。该奖项反映了NSF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。

项目成果

Fern Cave: A Hotspot of Subterranean Biodiversity in the Interior Low Plateau Karst Region of Alabama in the Southeastern United States

蕨洞：美国东南部阿拉巴马州内陆低高原喀斯特地区地下生物多样性的热点

• DOI: 10.3390/d15050633
• 发表时间: 2023
• 期刊: Diversity
• 作者: Niemiller, Matthew L.;Slay, Michael E.;Inebnit, Thomas;Miller, Benjamin;Tobin, Benjamin;Cramphorn, Brendan;Hinkle, Amata;Jones, Bradley D.;Mann, Nathaniel;Niemiller, K. Denise
• 通讯作者: Niemiller, K. Denise

The Crystal-Wonder Cave System: A New Hotspot of Subterranean Biodiversity in the Southern Cumberland Plateau of South-Central Tennessee, USA

水晶奇迹洞穴系统：美国田纳西州中南部坎伯兰高原地下生物多样性的新热点

• DOI: 10.3390/d15070801
• 发表时间: 2023
• 期刊: Diversity
• 作者: Niemiller, Matthew L.;Zigler, Kirk S.;Hinkle, Amata;Stephen, Charles D.;Cramphorn, Brendan;Higgs, Jared;Mann, Nathaniel;Miller, Brian T.;Niemiller, K. Denise;Smallwood, Kelly
• 通讯作者: Smallwood, Kelly