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.

尼日利亚渔业资源正快速衰减，凸显了开展有效生物多样性调查与全面物种编目工作的迫切需求，以指导保护与管理行动。然而，传统鱼类调查方法，如刺网（gillnets）与拖网（trawl surveys）调查，均具有侵入性强、耗时久且成本高昂的缺陷。环境DNA (eDNA) 元条形码技术已成为一种非侵入性的鱼类多样性调查手段，但该技术在尼日利亚水生生态系统中的应用仍十分有限。本研究针对12S核糖体RNA (12S rRNA) 靶向的eDNA元条形码技术，评估其在三大水体：杰巴水电站大坝（Jebba Hydroelectric Power Dam）、阿萨河（Asa River）及拉各斯潟湖（Lagos lagoon）中开展鱼类群落调查的潜力与局限性。同时，将本研究通过eDNA样本获取的鱼类群落组成，与此前基于传统采样技术发布的物种名录进行了对比分析。研究结果表明，利用eDNA元条形码技术开展尼日利亚鱼类生物多样性调查具备多项优势：可快速且非侵入性地识别鱼类类群，能够检测群落组成与生物多样性指标的差异，可发现传统方法遗漏的物种，还能同时检出受威胁物种与入侵物种。不过，本研究也明确了三大制约因素，若要在尼日利亚成功推广eDNA采样技术，必须解决这些问题：其一为采样实操的后勤难题，包括确定最优重复采样次数、选取合适的单站点水样体积、明确研究区域内所需的采样点数量，以及确定采样季内的最佳采样时段；其二是缺乏可用于精准物种鉴定的全面DNA参考数据库；其三则存在引物与分子标记的特异性问题。在构建完善的区域DNA参考库、优化适配的分子标记以及建立标准化的eDNA采样野外操作规范之前，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。