Harnessing Environmental DNA Metabarcoding for the Detection and Mapping of Vulnerable Marine Ecosystems in the Mediterranean Sea

The overexploitation of marine resources by commercial fisheries poses significant threats to marine biodiversity and ecosystem stability. Vulnerable Marine Ecosystems (VMEs) require urgent protection to mitigate the adverse impacts of fishing activities, especially deep-sea bottom trawling. Given our incomplete knowledge of the marine environment, rapid and precise localization of VMEs is a priority to protect them effectively. Traditional methods for identifying VMEs are often limited by logistical challenges, high costs, and potential sampling biases. In this study, we assess the effectiveness of environmental DNA (eDNA) metabarcoding as an innovative tool for detecting and mapping VMEs in the Mediterranean Sea. eDNA samples were gathered at 19 sampling sites during a scientific fishing campaign in the Eastern Ionian Sea. Through the amplification of the COI mitochondrial gene, we identified a total of 285 unique taxa. A total of seven VME Indicator (VMEI) taxa were detected. A Joint Species Distribution Model (JSDM), using Hierarchical Modelling of Species Communities (HMSC), was used to investigate possible relationships between VMEI taxa and environmental covariates. Predicted distribution patterns of VMEI taxa were used to calculate a richness-weighted VME index. Taxon richness was highest at sites with high VME Index values. These findings demonstrate the potential of eDNA metabarcoding to effectively map the distribution of VMEI taxa, identify key environmental drivers influencing their occurrence and assess overall ecosystem vulnerability. We argue that an integration of eDNA-based approaches with traditional fisheries surveys could significantly enhance biodiversity assessments and improve conservation strategies in data-limited marine environments.

商业渔业对海洋资源的过度开发，正对海洋生物多样性与生态系统稳定性构成严峻威胁。脆弱海洋生态系统(Vulnerable Marine Ecosystems, VMEs)亟需开展保护工作，以缓解捕捞活动——尤其是深海海底拖网捕捞——带来的负面影响。鉴于当前人类对海洋环境的认知仍存在不足，快速且精准地定位VMEs，已成为有效开展保护工作的优先事项。传统的VME识别方法往往受限于后勤保障难题、高额成本以及潜在的采样偏差。本研究评估了环境DNA(eDNA)宏条形码技术作为创新工具，在地中海海域检测并绘制VMEs分布图谱的有效性。研究团队在爱奥尼亚海东部的一次科学捕捞航次中，于19个采样点位采集了eDNA样本。通过对线粒体细胞色素c氧化酶亚基I(COI)基因的扩增，共鉴定出285个独特类群，其中检测到7个VME指示物(VME Indicator, VMEI)类群。本研究采用联合物种分布模型(Joint Species Distribution Model, JSDM)，结合物种种群层次建模(Hierarchical Modelling of Species Communities, HMSC)方法，探究VMEI类群与环境协变量之间的潜在关联。基于VMEI类群的预测分布格局，研究人员计算得到了丰富度加权VME指数。在VME指数较高的采样点位，类群丰富度也相对最高。上述研究结果证实，环境DNA宏条形码技术可有效绘制VMEI类群的分布格局、识别影响其分布的关键环境驱动因子，并评估整体生态系统的脆弱性。研究团队认为，将基于eDNA的研究方法与传统渔业调查相结合，可显著提升数据受限海洋环境中的生物多样性评估水平，并优化保护策略。