In the realm of environmental research, understanding the intricacies of marine biodiversity has long been a challenging, yet crucial endeavour. Christina Pavloudi, a data scientist and postdoctoral researcher at EMBRC ERIC, delves into the world of microbial ecology and marine biology, shedding light on the significance of environmental DNA (eDNA) reference libraries. In a recent conversation, Christina provided insights into the pivotal role of eDNA in identifying organisms within marine environments and the challenges and advancements in this field while highlighting the importance of Open Access
What is environmental DNA (eDNA)?
At the heart of Christina’s work lies eDNA, which involves extracting DNA traces of organisms from the environment and analysing it to identify the species present. This process relies on reference libraries, databases containing marker gene sequences unique for each species. By comparing eDNA sequences with those in reference libraries, researchers can identify the organisms in a given environment.
However, Christina highlights a significant challenge: the incompleteness of existing reference libraries. Despite ongoing efforts to fill these gaps, the task remains monumental due to the vastness of marine biodiversity and the intricacies in accomplishing a reference library with all the possible organisms that is out there, alongside the coordination of single efforts from scientists in building such a complex database.
The importance of reference libraries
Reference libraries serve as the cornerstone of species identification using DNA-based tools in environmental research. Without them, DNA sequences lack context, impeding accurate identification of organisms. Christina emphasizes the necessity of adhering to standards and guidelines to ensure the quality and completeness of reference libraries.
It is also a significant challenge to curate, maintain and complete such databases while solving errors that might occur in their building. Nonetheless, there are substantial efforts around the world to gather information for and manage eDNA reference libraries.
Emerging technologies and policy implications
Due to the importance of these reference resources, emerging technologies, such as data mining and machine learning, are being deployed to enhance metadata within reference libraries. Christina underscores the importance of policymakers’ support in funding research projects aimed at developing and maintaining these libraries, for example, through the scope of marine protected areas (MPAs) and creating or completing databases for specific ecosystems and/or regions. eDNA is now a beacon on biodiversity monitoring and is deployed in policy contexts which helps monitor MPAs and assess policy impact.
eDNA sampling and the availability of robust reference libraries can contribute to the early detection and control of invasive species, notably being a major part of European Union policies. As Christina mentions “the more complete a library is, the more species it can identify, the earliest it can identify invasive species”.
Open Science: key to develop biodiversity knowledge
At the heart of Christina’s discussion lies the importance of open access in eDNA research. Open Science ensures that scientific knowledge and data are freely available to the global community, fostering collaboration and accelerating scientific progress. Christina emphasizes that without open access to eDNA reference libraries, researchers would face significant barriers in conducting taxonomic assignments and advancing our understanding of marine ecosystems -without it, scientists’ hands are tied.
As mentioned before, one of the major challenges of reference libraries are the completeness of them, and Christina underscores the necessity of open access and FAIR data in addressing this issue, as it enables researchers worldwide to contribute to and utilize these libraries. By sharing data and collaborating across institutions and disciplines, the scientific community can work faster together to fill gaps in reference libraries and enhance their completeness and accuracy.
Christina also highlights the potential of open access to engage citizen scientists in eDNA research. By making data and research findings accessible to the public, citizen scientists can contribute to data collection efforts, help expand reference libraries, whilst being educated on marine biodiversity issues. Open access facilitates transparency and inclusivity, allowing individuals from diverse backgrounds to participate in scientific research and conservation efforts.
Furthermore, Christina emphasizes the role of policymakers in supporting open access initiatives in eDNA research. By funding research projects and advocating for open access policies, policymakers can ensure that scientific knowledge remains accessible to all. Open access not only benefits researchers but also informs evidence-based decision-making and environmental policy development.
As eDNA based research continues to evolve, open access will play a crucial role in shaping the future of marine biodiversity conservation and management. Christina envisions a future where open access to eDNA data drives scientific discovery, informs conservation strategies, and empowers communities to actively participate in marine ecosystem monitoring and protection.