Department Aquatic Ecology

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

In times of rapid environmental changes, baseline biodiversity data are crucial for management. In freshwaters, fish inventories are commonly based on the capture and morphological identification of specimens. The sampling of environmental DNA (eDNA) provides an alternative to assess diversity across large catchments. Here, we used extensive historic data of fish communities collected across 89 river sites in all major catchments of Switzerland and compared their diversity and community composition to a single campaign of eDNA and electrofishing, respectively. Locally, we found that eDNA provided diversity estimates similar to the integrated historic richness, while the electrofishing campaign captured a significantly lower local richness. Fish species locally recorded by electrofishing were nested (Jaccard's dissimilarity index) within the respective eDNA community for most sites. Finally, eDNA sequence reads positively correlated with the overall electrofishing biomass. Despite the congruences, the eDNA data did not correlate well with the electrofishing water quality index. Overall, eDNA was more accurately assessing overall diversity than a simultaneous electrofishing campaign, but yet cannot be directly used to calculate fish-based water quality indices.

The impacts of global change—from shifts in climate to overfishing to land use change—can depend heavily on local abiotic context. Building an understanding of how to downscale global change scenarios to local impacts is often difficult, however, and requires historical data across large gradients of variability. Such data are often not available—particularly in peer reviewed or gray literature. However, these data can sometimes be gleaned from casual records of natural history—field notebooks, data sheet marginalia, course notes, and more. Here, we provide an example of one such approach for the Gulf of Maine, as we seek to understand how environmental context can influence local outcomes of region-wide shifts in subtidal community structure. We explore a decade of hand-drawn algal cover maps around Appledore Island made by Dr. Art Borror while teaching at the Shoals Marine Lab. Appledore's steep wave exposure gradient—from exposed to the open ocean to fully protected—provides a living laboratory to test interactions between global change and local conditions. We then recreate Borror's methods two and a half decades later. We show that overfishing-driven urchin outbreaks in the 1980s were slowed or stopped by wave exposure and benthic topography. Similarly, local variation appears to have curtailed current invasions by filamentous red algae. Last, some formerly dominant kelps have disappeared over the past 40 years—an observation verified by subtidal surveys. Global change is altering life in the seas around us. While underutilized, solid natural history observations stand as a key resource for us to begin to understand how global change will translate to the heterogeneous mosaic of life in a future Gulf of Maine and other ecosystems around the world.