Evaluating eDNA metabarcoding for fish biodiversity assessment in Nigerian aquatic ecosystems: potential, limitations, and comparisons with traditional methods

Fishery resources in Nigeria are experiencing a rapid decline, underscoring the urgent need for effective biodiversity surveys and comprehensive species documentation to guide conservation and management efforts. However, traditional methods for fish surveys, such as gillnets and trawl surveys, are intrusive, time-intensive, and costly. Environmental DNA (eDNA) metabarcoding has emerged as a non-invasive method for surveying fish diversity, yet its application in Nigerian aquatic ecosystems remains limited. This study evaluated the potential and limitations of 12S rRNA-based eDNA metabarcoding to survey fish communities across three water bodies (Jebba Hydroelectric Power Dam, Asa River, and Lagos lagoon). We also compared fish community composition obtained from our eDNA samples with previously published inventories based on traditional sampling techniques. Our study revealed several advantages of using eDNA metabarcoding for fish biodiversity surveys in Nigeria, including the rapid and non-invasive identification of fish taxa, the detection of differences in community composition and biodiversity metrics, the identification of species overlooked by traditional methods, and the ability to detect both threatened and invasive species. However, we identified three major constraints that must be addressed for the successful integration of eDNA sampling techniques in Nigeria. First are the logistical challenges, including determining the optimal number of replicates, selecting the appropriate water volume per site, determining the required number of sampling sites per study area, and identifying the most suitable time within the season for sampling. Second is the lack of a comprehensive DNA reference database for accurate species identification. Third are the issues with primer and marker specificity. Until a comprehensive regional DNA reference library is developed, suitable molecular markers are optimized, and standardized field protocols for eDNA sampling are established, we recommend using eDNA metabarcoding as a complementary survey tool rather than a replacement for conventional fish survey methods in Nigeria.

尼日利亚的渔业资源正经历快速衰退，凸显出开展有效生物多样性调查与全面物种记录以指导保护与管理工作的迫切需求。然而，传统鱼类调查方法，如刺网（gillnets）与拖网调查，具有侵入性强、耗时久且成本高昂的缺陷。环境DNA（environmental DNA, eDNA）元条形码技术（metabarcoding）已成为一种非侵入性的鱼类多样性调查手段，但它在尼日利亚水生生态系统中的应用仍十分有限。本研究评估了基于12S核糖体RNA（12S rRNA）的eDNA元条形码技术在三个水体——杰巴水电站大坝、阿萨河与拉各斯潟湖——中调查鱼类群落的潜力与局限性。我们还将eDNA样本获得的鱼类群落组成，与此前基于传统采样技术发表的物种名录进行了对比。本研究揭示了在尼日利亚开展鱼类生物多样性调查时使用eDNA元条形码技术的多项优势：包括快速且非侵入性地识别鱼类类群、检测群落组成与生物多样性指标的差异、发现传统方法遗漏的物种，以及同时检测受威胁物种与入侵物种的能力。不过，我们也识别出了三大亟待解决的限制因素，方能成功在尼日利亚整合eDNA采样技术的应用。首先是后勤保障层面的挑战，包括确定最优重复样本数量、选取每个采样点的适宜水体体积、确定研究区域内所需的采样点数量，以及明确采样季内的最佳采样时间。其次是缺乏用于精准物种识别的全面DNA参考数据库。第三则是引物与分子标记的特异性问题。在构建完善的区域性DNA参考文库、优化适配的分子标记，并建立标准化的eDNA采样野外操作流程之前，我们建议在尼日利亚将eDNA元条形码技术作为传统鱼类调查方法的补充工具，而非替代方案。