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

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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.