Département Ecologie aquatique

Marine heatwaves (MHWs) are episodes of anomalous warming in the ocean that can last from a few days to years. MHWs have different characteristics in terms of intensity, duration and frequency and generate thermal stress in marine ecosystems. In reef ecosystems, they are one of the main causes of the decreased presence and abundance of corals, invertebrates and fish. The deleterious capacity of thermal stress often depends on biotic factors, such as the trophic control of predators on prey. Despite the evidence of thermal stress and biotic factors affecting individual species, the combined effects of both stressors on entire reef ecosystems are much less studied. Here, using a food web modelling approach, we estimated the rate of change in species' biomass due to different MHW characteristics. Specifically, we modelled the mechanistic link between species' consumption rate and seawater temperature (thermal stressor), simulating species' biomass dynamics for different MHW characteristics under different trophic control assumptions (top-down, mixed trophic control and bottom-up). We find that total reef ecosystem biomass declined by 10% ± 5% under MHWs with severe intensity and a top-down control assumption. The bottom-up control assumption moderates the total ecosystem biomass reduction by 5% ± 5%. Irrespective of the MHW characteristics and the trophic control assumption, the most substantial biomass changes occur among top, mesopredators and corals (5% to 20% ± 10%). We show that reef ecosystems where predators exert top-down control on prey are prone to suffer species abundance declines under strong MHW events. We identify food web trophic control as a crucial driver that modulates the impacts of MHWs. Overall, our results provide a unified understanding of the interplay between abiotic stressors and biotic factors in reef ecosystems under extreme thermal events, offering insights into present baselines and future ecological states for reef ecosystems.

The collection of environmental DNA (eDNA) and subsequent metabarcoding are useful tools for assessing marine fish biodiversity noninvasively. It is of particular importance to evaluate biodiversity in regions that are hard to access and thus less well studied. Sampling and preservation methods tailored to the specific circumstances are required. Aquatic eDNA is often captured on filters made of different materials and pore sizes, and subsequently stored under divergent conditions for varying periods of time. Previous studies on multispecies detection in marine systems have primarily focused on capture and extraction effects. Our study, in contrast, examined the effects of filter type, storage method, and storage time on DNA yield, alpha (i.e., ZOTU richness) and beta diversity (i.e., ZOTU composition) recovered from a marine ecosystem in Shark Bay, Western Australia. We compared two different filter types (cellulose-nitrate filters with pore sizes of 0.45 μm; glass-fiber filters with pore sizes of 0.1 μm), two storage methods (preservation in Longmire's solution and drying, respectively), various storage times (30–68 days) on two metabarcoding assays using different fish-specific primers. Our results showed that storage time decreased DNA yield and affected alpha and beta diversity estimates. Cellulose-nitrate filters stored in Longmire's solution proved to be the best combination with the smallest decrease in DNA yield, no effect on alpha diversity and consistent community compositions. Storing glass-fiber filters in Longmire's solution led to a decrease in eDNA yield and alpha diversity estimates with increasing storage time. Furthermore, the largest change in beta diversity for each metabarcode was found for glass-fiber filters regardless of storage method. Our results highlight the importance of considering storage time and interactions between storage method and filter when analyzing eDNA results, especially when storing samples for an extended time period or comparison of samples stored for different durations.

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'.