Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods
Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods
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DOI：
10.1371/journal.pone.0210357
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发表时间：
2019-01-31
期刊：
影响因子：
3.7
通讯作者：
Yamanaka, Hiroki
中科院分区：
文献类型：
--
作者：
Fujii, Kazuya;Doi, Hideyuki;Yamanaka, Hiroki
环境DNA（eDNA）方法用于群落分析是最近发展起来的。高通量平行DNA测序（HTS），又称eDNA元条形码，已越来越多地应用于eDNA研究中，以检测多个物种。然而，eDNA元条码编码方法需要在所有自然生态系统的传统方法的基础上进行验证，然后才能建立一个可靠的方法。迄今为止，相对较少的研究进行了eDNA元编码的鱼类在水生环境中，鱼类群落进行了密集调查，使用多种传统的方法。在这里，我们比较了鱼类群落的数据从eDNA元条形码与七个传统的多重捕获方法在31个回水湖泊在北海道，日本。我们发现，在31个湖泊中，鱼类的捕获和实地调查经常被水生植物和淤泥质沉积物打断。我们采集了1 L地表水，并使用HTS分析了eDNA。我们还使用七种不同的捕获方法调查了鱼类群落，包括各种类型的渔网和电捕鱼。在某些位点，我们无法检测到任何eDNA，可能是因为聚合酶链反应（PCR）抑制。我们还检测到海洋鱼类的污水来源的eDNA。比较eDNA元条形码和捕获方法，两种方法检测的鱼类群落相似，重叠率为70%。因此，我们的研究表明，在回水湖泊中检测鱼类群落，使用1 L地表水采样的eDNA metabarcoding的性能是类似的捕获方法。因此，eDNA元条形码可用于鱼类群落分析，但环境因素，可能会导致PCR抑制，应考虑在eDNA应用。
The use of environmental DNA (eDNA) methods for community analysis has recently been developed. High-throughput parallel DNA sequencing (HTS), called eDNA metabarcoding, has been increasingly used in eDNA studies to examine multiple species. However, eDNA metabarcoding methodology requires validation based on traditional methods in all natural ecosystems before a reliable method can be established. To date, relatively few studies have performed eDNA metabarcoding of fishes in aquatic environments where fish communities were intensively surveyed using multiple traditional methods. Here, we have compared fish communities' data from eDNA metabarcoding with seven conventional multiple capture methods in 31 backwater lakes in Hokkaido, Japan. We found that capture and field surveys of fishes were often interrupted by macrophytes and muddy sediments in the 31 lakes. We sampled 1 L of the surface water and analyzed eDNA using HTS. We also surveyed the fish communities using seven different capture methods, including various types of nets and electrofishing. At some sites, we could not detect any eDNA, presumably because of the polymerase chain reaction (PCR) inhibition. We also detected the marine fish species as sewage-derived eDNA. Comparisons of eDNA metabarcoding and capture methods showed that the detected fish communities were similar between the two methods, with an overlap of 70%. Thus, our study suggests that to detect fish communities in backwater lakes, the performance of eDNA metabarcoding with the use of 1 L surface water sampling is similar to that of capturing methods. Therefore, eDNA metabarcoding can be used for fish community analysis but environmental factors that can cause PCR inhibition, should be considered in eDNA applications.