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ORIGINAL RESEARCH article

Front. Mar. Sci.

Sec. Marine Conservation and Sustainability

Volume 12 - 2025 | doi: 10.3389/fmars.2025.1688716

This article is part of the Research TopicEcosystem Monitoring and Effect Assessment of Multiple Human Activities Using Environmental DNA (eDNA) TechnologyView all articles

eDNA Metabarcoding for Qualitative and Semi-Quantitative Assessment of Phytoplankton Towards Eco-Sustainable Mariculture in the Mediterranean Sea

Provisionally accepted
  • 1Universita del Salento Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Lecce, Italy
  • 2agenzia regionale per la protezione ambientale-campania, Caserta, Italy
  • 3Universiteti Ismail Qemali Vlore, Vlorë, Albania
  • 4University of Salento, Lecce, Italy

The final, formatted version of the article will be published soon.

Phytoplankton communities play a crucial role in the sustainability of mariculture practices, regarding the risks associated with harmful species that can cause algal blooms and toxin production. These harmful species can have devastating effects, not only threatening human health and safety through the contamination of seafood and water supplies but also disrupting the delicate balance of marine ecosystems. Monitoring phytoplankton levels and composition is essential to ensure that mariculture remains environmentally sustainable, economically viable, and safe for consumers. Ultimately, this contributes to the preservation of marine biodiversity and its long-term health. Traditional methods for phytoplankton identification are often labour-intensive and may fail to capture the full diversity of these organisms. Environmental DNA metabarcoding is emerging as an innovative tool that offers a more comprehensive assessment of phytoplankton biodiversity, although it does not yet provide a strictly quantitative measure. In our research, we employed eDNA metabarcoding to analyse eukaryotic phytoplankton community composition, both qualitatively and semi-quantitatively, along a mariculture facility located in the Mediterranean Sea. From a quantitative perspective, we evaluated whether the number of sequences obtained for each OTU could serve as an indicator of the relative abundance of each taxonomic group across different sites. We considered five sampling sites around and at the centre of the mariculture facility and conducted eDNA metabarcoding analyses with three replicates per site. Statistical analysis revealed that the number of sequences per OTU were significantly consistent among replicates. This suggests that the number of sequences can be used as a proxy concerning the relative abundance of taxonomic groups across sampling sites. Consequently, this research opens the possibility of using eDNA metabarcoding as a semi-quantitative tool. From a qualitative perspective, we were able to characterize the structure of eukaryotic phytoplankton communities around the mariculture plant, detecting a high level of biodiversity. We also identified potentially dangerous species at low abundance, highlighting the potential of eDNA metabarcoding as an early warning system, an essential aspect for ensuring sustainability in mariculture. This study represents a pioneering effort in utilizing eDNA metabarcoding for both the semi-quantitative and qualitative monitoring of eukaryotic phytoplankton in mariculture supporting eco-sustainable management practices.

Keywords: environmental DNA, eDNA metabarcoding, Phytoplankton monitoring, mariculturefacilities, quantitative analysis, harmful algal blooms

Received: 19 Aug 2025; Accepted: 06 Oct 2025.

Copyright: © 2025 Zangaro, Vadrucci, Ismailaj, Specchia and Pinna. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Valeria Specchia, valeria.specchia@unisalento.it
Maurizio Pinna, maurizio.pinna@unisalento.it

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