Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river
Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river
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DOI：
10.1007/s10201-020-00645-9
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发表时间：
2020-11-15
期刊：
影响因子：
1.6
通讯作者：
Minamoto, Toshifumi
中科院分区：
文献类型：
--
作者：
Sakata, Masayuki K.;Watanabe, Takeshi;Minamoto, Toshifumi
近年来，生物多样性丧失已成为世界范围内最严重的环境问题之一，特别是在水生生态系统中。为了避免生物多样性的丧失，有必要对生物群落进行监测，环境DNA元条形码作为一种快速、无创、经济的水生生物多样性监测方法得到了发展。虽然这种方法已应用于各种环境和分类群，但仍然需要对有效的监测抽样方法进行详细评估。在这项研究中，我们探索了在单一地点对鱼类进行eDNA元条形码采样的方法，以最大限度地提高在自然小河中检测到的物种数量。我们考虑了以下三个参数：样品类型（水或沉积物）、样品在一个地点的位置（右岸、左岸和河中心）和水量（10-4000 mL）。结果表明，沉积eDNA检测到的物种数量与水溶液eDNA检测到的物种数量相当，但物种组成不同。无论在调查地点内的哪个位置取样，收集1000 mL水样即可使检测到的物种数量达到饱和。然而，在同一测点内，尽管距离较近（5 m），但沉积物eDNA在不同采样点之间的物种组成在空间上呈现异质性，在速度和沉积物颗粒分布等物理性质上没有明显差异。通过对整条河1000 mL水样的鱼类进行eDNA生物多样性监测，我们发现了比以往在同一地点进行的传统调查更多的鱼类。因此，水溶液eDNA元条形码方法与传统的调查方法一样有效，而沉积eDNA元条形码可以补充水溶液eDNA元条形码的结果。
In recent years, biodiversity loss has become one of the most serious environmental issues worldwide, especially in aquatic ecosystems. To avoid diversity loss, it is necessary to monitor biological communities, and environmental DNA (eDNA) metabarcoding has been developed as a rapid, noninvasive, and cost-effective method for aquatic biodiversity monitoring. Although this method has been applied to various environments and taxa, a detailed assessment of the efficient sampling methods for monitoring is still required. In this study, we explored eDNA metabarcoding sampling methods for fish at a single site to maximize the number of detected species using realistic effort in a natural, small river. We considered the following three parameters: sample type (water or sediment), sample position at a site (right and left shore and center of the river), and water volume (10-4000 mL). The results suggested that the number of detected species from sedimentary eDNA was equivalent to that from aqueous eDNA, although the species composition was different. The number of detected species could be saturated by collecting a 1000 mL water sample, regardless of sampling position within a survey site. However, sedimentary eDNA showed a spatially heterogeneous species composition between sampling positions within a survey site despite the short distance (5 m) between positions, without apparent differences in physical properties such as velocity and sediment particle distribution. By completing eDNA biodiversity monitoring of fish with 1000 mL water samples across the whole river, we detected more fish species than in previous traditional surveys conducted at the same sites. Thus, the aqueous eDNA metabarcoding method is as efficient as traditional surveys, while sedimentary eDNA metabarcoding could complement the results of aqueous eDNA metabarcoding.