Environmental DNA in groundwater ecosystems – the ultimate complementary biomonitoring tool?

Diversity assessments in subterranean aquatic ecosystems are notoriously complex due to the intrinsically cryptic nature of underground habitats. In combination with other factors, this aspect has triggered a substantial delay in recognising the array and value of subterranean biota when compared to surficial counterparts such as rivers and lakes. As a result, the crucial services provided by groundwater ecosystems are still mostly being overlooked and, when acknowledged, they are often solely related to hydrogeological aspects.

Given the importance of groundwaters as keystone ecosystems, this tendency is not only detrimental for the integrity of subterranean aquatic environments and their living biota, but it is affecting the resilience and sustainability of entire surficial ecosystems depending on underground water reservoirs. Nonetheless, similar to other scientific disciplines, technological advancements are shaping a rapid shift in perspectives and possibilities in assessing and monitoring aquatic diversity.

Particularly, recent developments in the field of molecular biology are opening new exciting opportunities in understanding phylogenetic, biogeographic and ecological patterns in aquatic (and terrestrial) environments. At the forefront of this biomonitoring revolution stands the environmental DNA (eDNA) analysis, a technique that makes use of next-generation sequencing to target fragments of DNA present in the environments as a result of biotic activities of resident communities in the habitat. Since its consolidation in 2012, eDNA has been applied, tested and validated as a complementary tool in a myriad of environments, including, even with a considerable delay, in groundwaters. In this talk we review the (recent) past, (buzzing) present and (promising) future of eDNA in aquatic subterranean environments with the goal of discussing the use, applicability and limitations of this powerful molecular test. We also provide an overview of case studies on novel collection methods (e.g., passive collection), technical aspects (e.g., in-field sequencing) and studies at a regional scale (e.g., participatory science initiatives). Moreover, we outline new field-specific opportunities derived from other eDNA-based investigations in oceans, wetlands and rivers – including combined eDNA-eRNA (environmental RNA) uses, global studies and predictive modelling.

Despite the limitations affecting its use in groundwater ecosystems, eDNA hosts great potential in unveiling neglected diversity patterns. This new era of subterranean biomonitoring will play a key role in increasing the spotlight on the importance of subterranean biota for the maintenance of ecological dynamics within the global water cycle and beyond.