Data from: Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206-L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina-sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.

淡水水生动物群落对环境变化与干扰尤为敏感。管理机构常将鱼类与两栖类的生物多样性作为生态系统健康的指示指标，并以此制定管理优先级、评估管理策略。传统水生生物评估依赖网具、诱捕装置及电捕鱼设备捕获生物，这类方法对珍稀物种的检出率普遍偏低，且可能对受保护物种的个体造成损伤。本研究旨在探究环境DNA（eDNA, environmental DNA）采样与元条形码（metabarcoding）分析能否精准测定不同结构水生群落的物种多样性。研究人员在重复设置的206升中型实验生态系统（mesocosms）中，调控了8种鱼类与1种两栖类的种群密度及相对丰度。从水样中滤取环境DNA后，对6个线粒体基因片段开展Illumina测序，以此测定每个中型实验生态系统内的物种多样性。元条形码分析在所有处理组的重复样本中均检出了全部9个物种。此外，本研究发现物种丰度与测序读数丰度之间存在微弱但显著的正相关关系。本研究结果证实，环境DNA采样与元条形码分析方法可有效提升自然环境中水生物种多样性的量化精度，同时为将环境DNA元条形码分析作为大型水生动物物种丰度的评估指标指明了可行方向。