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退，凸显出开展有效生物多样性调查与全面物种编目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（trawl surveys），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（metabarcoding）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。本研究评估了基于12S核糖体RNA（12S rRNA）的eDNA元条形码技术，在三处水体（杰巴水电站大坝、阿萨河与拉各斯潟湖）中开展鱼类群落调查的潜力与局限。此外，本研究还将eDNA样本获取的鱼类群落组成，与此前基于传统采样技术发表的物种名录进行了对比。研究结果显示，在尼日利亚应用eDNA元条形码技术开展鱼类生物多样性调查具备多项优势：可快速、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数的差异，可识别传统方法遗漏的物种，还可同时检测受威胁物种与入侵物种。但研究同时明确了三项需加以解决的核心制约因素，方能成功将eDNA采样技术整合应用于尼日利亚的鱼类调查工作：其一为实地操作挑战，包括确定最优重复样本数量、选取各采样点的适宜水量、明确各研究区域所需的采样点总数，以及确定采样季内的最佳采样时段；其二是缺乏用于精准物种鉴定的全面DNA参考数据库；其三则是引物与标记的特异性问题。在建立完善的区域DNA参考库、优化适配的分子标记、确立标准化的eDNA采样野外规程之前，我们建议在尼日利亚将eDNA元条形码技术作为辅助调查工具，而非传统鱼类调查方法的替代方案。