Using eDNA for monitoring fish and invertebrate biodiversity in freshwater ecosystems

Global biodiversity is facing an extinction crisis leading to increasing pressure on industries to monitor their potential environmental impact. Relatedly, there is demand for more efficient biodiversity monitoring methods, resulting in growing interest in the use of environmental DNA (eDNA). Many questions, however, regarding the reliability of this relatively novel method remain, particularly for non-specialist end-users of the technology.

Here, the use of commercially available (in the UK) eDNA assays for monitoring freshwater fish and invertebrate biodiversity was compared to conventional surveillance techniques. Samples were collected from different habitats, on varying spatial scales and using multiple sampling regimes to assess how eDNA results were affected.

For aquatic macroinvertebrates and fish, more taxa were detected by eDNA than conventional surveys conducted in parallel, and for fish, all taxa detected by conventional monitoring were confirmed by eDNA.

For aquatic macroinvertebrates, several species were only detected through conventional methods, and the number of families detected by eDNA was lower than for conventional monitoring at all sites.

eDNA results varied significantly between sampling locations within lentic sites and, for lotic sites, with the number of subsamples collected.

In terms of  practical implications, this study demonstrates the need for bespoke sampling protocols when collecting eDNA samples. This study improves understanding of using eDNA for detecting aquatic taxa that could inform species surveillance protocols. These are essential if eDNA is to be used by practitioners as a regulatory monitoring tool.

全球生物多样性正面临灭绝危机，这给各行业带来了愈发严峻的监测其潜在环境影响的压力。与之相关的是，市场对更高效的生物多样性监测方法存在需求，这使得环境DNA（environmental DNA, eDNA）的应用愈发受到关注。然而，这种相对新颖的方法的可靠性仍存在诸多疑问，尤其是对于该技术的非专业终端用户而言。
本研究将英国市售的eDNA检测试剂盒用于淡水鱼类与无脊椎动物生物多样性监测的应用，与传统监测技术进行了对比。研究从不同生境、不同空间尺度采集样本，并采用多种采样方案，以评估eDNA检测结果的影响因素。
针对水生大型无脊椎动物与鱼类，eDNA检测到的类群数量多于同期开展的传统调查；对于鱼类而言，传统监测检出的所有类群均被eDNA确认。
而对于水生大型无脊椎动物，有部分物种仅能通过传统方法检出，且所有采样点中eDNA检测到的科类数量均低于传统监测。
eDNA检测结果在静水生境的采样点位间存在显著差异；对于流水生境，则与采集的子样本数量相关。
就实际应用而言，本研究表明采集eDNA样本时需制定定制化的采样方案。本研究加深了对利用eDNA检测水生类群的理解，可为物种监测方案提供参考，而若要将eDNA作为监管监测工具供从业者使用，这些结论至关重要。