Marine Biodiversity Monitoring: Insights from a 12-Year eDNA Time-Series

Applied Genomics fish biodiversity monitoring
  • March 22, 2024

Applied Genomics, a leader in eDNA-based biodiversity monitoring solutions, has revolutionised the field of marine ecology with its recent project, conducted in collaboration with Plymouth Marine Laboratory. This ground-breaking study, spanning 12 years, marks a significant advancement in long-term biodiversity monitoring using environmental DNA (eDNA). Analysis of 460 eDNA samples, collected weekly over this period, has provided unparalleled insights into the marine biodiversity of UK waters.







Despite generally low eDNA concentrations from small-volume samples, we obtained reliable results for all samples with no sample failures.

Large-volume inDepth eDNA samples contained significantly more DNA than small volume samples.

High-volume eDNA sample collection is more cost-effective than low-volume methods, yielding over twice the cost-benefit ratio despite higher consumable expenses.

One of the key innovations of this project was the use of the inDepth eDNA sampler, an automated system capable of filtering over 50 litres of seawater per sample across two tidal cycles. This approach not only enhanced the quantity of DNA collected but also significantly reduced the risk of sample contamination compared to traditional methods.

The ability of eDNA to detect a significantly higher number of species compared to conventional scientific trawling methods was one of the project’s key findings. This method detected a similar number and composition of fishes (Figure 1), including 133 unique fish species, and 152% more species overall, indicating its superior capability in capturing the true extent of marine biodiversity. The eDNA data, particularly when refined to spotlight indicator species, reveals a more pronounced decline in fish biodiversity than that suggested by traditional trawling methods. This divergence highlights the sensitivity of eDNA sampling in detecting subtle changes in ecosystem health. The congruence between the trawling and unfiltered eDNA data underscores the critical insights gained from eDNA analysis regarding the trajectory of biodiversity loss in coastal ecosystems.

The data presented in Figure 1 reveals a discernible decline in fish biodiversity when examining both conventional and eDNA-derived species counts. This trend is highlighted by the analysis of filtered eDNA data focusing on indicator species year-on-year, providing a targeted perspective on specific biodiversity shifts within the ecosystem.

Figure1: A comparative analysis of fish biodiversity as recorded by annual species count through scientific trawling (blue line) versus eDNA sampling (orange line), with a focused view on annual indicator species (grey line).

From a regulatory perspective, these findings are invaluable. The detailed data acquired through eDNA analysis provides a robust foundation for informed decision-making in line with sustainability disclosures required for Biodiversity Net Gain (BNG), Environmental, Social, and Governance (ESG) criteria, and the Corporate Sustainability Reporting Directive (CSRD). The depth and accuracy of the data are crucial for marine survey operations, offshore energy sectors, and government marine biodiversity regulators in making informed decisions that align with sustainability and conservation goals.

The data presented in Figure 2 reveals trends in marine food web integrity. Over the 12-year time-series, there were discernible and statistically significant declines in the diversity of fish that feed on benthic prey (benthivorous), fish that feed on other fishes (piscivorous), and generalist feeders.

This reduction in complexity of these marine food webs has serious and concerning implications for the long-term health of the marine ecosystem.

Figure 2: trends in marine food webs for benthivourous fishes (blue line), generalist feeders (orange line), piscivorous fishes (grey line), and planktivorous fishes (yellow line).

The capabilities of long-term eDNA-based monitoring demonstrated by Applied Genomics set a new standard in the industry. The insights gained from this project not only underline the company’s technical expertise but also its commitment to enhancing biosecurity and ecosystem understanding. By offering detailed insights into biodiversity trends and shifts in species distribution, Applied Genomics is aiding in the development of informed conservation strategies and providing valuable data for all stakeholders involved in marine ecosystem management.

The industry-leading work of Applied Genomics in eDNA-based marine biodiversity monitoring is a testament to the potential of this technology in transforming our understanding of marine ecosystems. Its implications for sustainability disclosures, regulatory decision-making, and the broader field of marine ecology are profound and far-reaching.

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