Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels. To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work. The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level. This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.
Environmental DNA (eDNA) metabarcoding is transforming biodiversity monitoring in aquatic environments where the method has repeatedly shown comparable or better performance than conventional approaches to fish monitoring. This method has been developed and deployed, primarily using shoreline sampling during the winter months, across 101 lakes in Great Britain alone, covering a wide spectrum of lake types and ecological quality. Previous analyses on a subset of these lakes indicated that 20 water samples per lake are sufficient to reliably estimate fish species richness, but it is unclear how reduced eDNA sampling effort affects richness, or other biodiversity estimates and metrics. As the number of samples strongly influences the cost of monitoring programmes, it is essential that sampling effort is optimised for a specific monitoring objective. The aim of this project was to explore the effect of reduced eDNA sampling effort on biodiversity metrics (namely species richness and community composition) using algorithmic and statistical resampling techniques. The results showed that reliable estimation of lake fish species richness could in fact usually be achieved with a much lower number of samples. For example, in almost 90% of lakes, 95% of complete fish richness could be detected with only 10 water samples, regardless of lake area. Similarly other measures of alpha and beta-diversity were not greatly affected by a reduction in sample size from 20 to 10 samples. We also found that there is no significant difference in detected species richness between shoreline and offshore sampling transects, allowing for simplified field logistics. This could potentially allow the effective sampling of a larger number of lakes within a given monitoring budget. However, rare species were more often missed with fewer samples, with potential implications for monitoring of invasive or endangered species. These results should inform the design of eDNA sampling strategies, so that these can be optimised to achieve specific monitoring goals.
DNA assessments are revolutionising biomonitoring opportunities across the globe, including the monitoring of rare and invasive species, creating biodiversity inventories, and developing pollution diagnostic and ecosystem resilience assessment methods. To date pollution and ecosystem resilience assessments have been based on assessing the diversity of familiar taxonomic groups but the introduction of DNA based methods will significantly increase the opportunities to exploit groups not previously used for this work. Environmental regulators and managers can derive many benefits from the adoption of these methods, such as improved understanding of environmental conditions, cost effective sample processing, overcoming taxonomic bottlenecks, either through shortages in trained taxonomists or utilising biota with challenging taxonomies. In addition to creating diversity based metrics DNA monitoring also allows for the assessment of functional attributes such as those that support important ecosystem services. The UK has been an early adopter of this technology and this paper will explore how the alignment of scientific advances have coincided with operational needs to create a fertile arena for the development of DNA based assessment methods that will be used in environmental regulation and management. Development projects advanced in the UK will be examined to identify the common and specific issues associated with them that have led to early engagement and adoption.
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