HaploSEA · Including intraspecific diversity of eDNA analyses to develop a new holistic approach for Environmental Status Assessments of the benthic deep-sea

Including intraspecific diversity of eDNA analyses to develop a new holistic approach for Environmental Status Assessments of the benthic deep-sea

The deep sea remains one of the least explored and least understood ecosystems on Earth. Despite its remoteness, it is increasingly affected by human activities such as climate change, deep-sea fishing, oil and gas exploration, and pollution. While changes are clearly occurring, their meaning and consequences are difficult to assess within a vast, globally connected system. One of the main challenges is that deep-sea biodiversity is still largely unknown: many species have not yet been described, and species are currently going extinct faster than they can be formally identified. Modern genetic approaches, such as DNA metabarcoding of environmental DNA, provide new opportunities to study biodiversity by analysing entire communities from single water or sediment samples. However, these methods also have limitations. They can only identify species that are already described and reference-sequenced, leaving many detected organisms unnamed. Also, there is no objective quantitative measurement for the number of organisms. As a result, essential information needed to assess ecosystem health remains incomplete. Since the fundamental limitations of sampling and taxonomic knowledge cannot be resolved in the near future, the greatest potential lies in rethinking how existing data and methods are interpreted. The HaploSEA project was based on the hypothesis that even if the exact identity and number of species are unknown, changes in genetic diversity within species (intraspecific variation, such as haplotypes) can provide meaningful information about ecosystem dynamics and health. By integrating intragenetic analyses into already established genetic monitoring approaches, new insights can be gained without additional sampling effort or cost. The overall aim of the project was therefore to test whether observed genetic variability reflects real biological variability, even when species identities are unknown. This was addressed through three complementary studies investigating long-term trends, natural variability, and short-term impacts, with the goal of identifying indicator groups that could be used in future deep-sea ecosystem assessments.

Data: CORDIS, © European Union