Data Sheet 3_eDNA metabarcoding for qualitative and semi-quantitative assessment of phytoplankton towards eco-sustainable mariculture in the Mediterranean Sea.pdf

Phytoplankton communities play a crucial role in the sustainability of mariculture practices, particularly regarding the risks associated with potentially 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 labor-intensive and may fail to capture the full diversity of these organisms. Environmental DNA (eDNA) 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 analyze 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 center 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.

浮游植物群落（Phytoplankton communities）对海水养殖产业的可持续发展至关重要，尤其关乎那些可能引发藻华并产生毒素的潜在有害物种所带来的风险。这些有害物种不仅会通过污染海产品与供水系统威胁人类健康与安全，还会破坏海洋生态系统的微妙平衡。监测浮游植物的丰度与群落组成，是确保海水养殖兼具环境可持续性、经济可行性与消费者食用安全的必要举措，最终有助于保护海洋生物多样性及其长期健康。
传统的浮游植物鉴定方法往往劳动强度大，且无法全面覆盖这类生物的多样性。环境DNA（eDNA）宏条形码技术正逐渐成为一种创新工具，能够更全面地评估浮游植物生物多样性，尽管其暂无法实现严格的定量检测。在本研究中，我们采用eDNA宏条形码技术，对地中海某海水养殖设施周边的真核浮游植物群落组成进行了定性与半定量分析。
从定量角度而言，我们评估了每个操作分类单元（Operational Taxonomic Unit，OTU）获得的序列数能否作为不同采样位点间各分类群相对丰度的指示指标。我们在该海水养殖设施周边及中心共设置5个采样位点，每个位点设置3次生物学重复，并开展eDNA宏条形码分析。统计学分析结果显示，每个OTU的序列数在重复样本间具有显著一致性，这表明序列数可作为采样位点间分类群相对丰度的替代指标。据此，本研究证实了将eDNA宏条形码技术作为半定量工具的可行性。
从定性角度而言，我们成功表征了该海水养殖设施周边的真核浮游植物群落结构，检测到较高水平的生物多样性。同时，我们在低丰度样本中检出了潜在有害物种，凸显了eDNA宏条形码技术作为早期预警系统的潜力——这是保障海水养殖可持续性的核心要素之一。
本研究是首次将eDNA宏条形码技术应用于海水养殖环境中真核浮游植物的半定量与定性监测，可为生态可持续的养殖管理实践提供支撑。