Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System.
Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System.
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DOI：
10.1371/journal.pone.0157366
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Pont D
中科院分区：
文献类型：
--
作者：
Civade R;Dejean T;Valentini A;Roset N;Raymond JC;Bonin A;Taberlet P;Pont D
在过去的几年里，环境DNA（eDNA）的研究引起了人们的关注，原因有很多，包括其在监测和保护目的方面的优势。到目前为止，在水生环境中，大多数eDNA研究都集中在使用物种特异性标记检测单个物种。最近，物种清单的基础上分析的一个单一的通用标记，针对一个更大的分类组（eDNA元条形码）已被证明是有用的硬骨鱼和两栖动物的生物多样性调查。这种方法包括原位过滤大量的水，然后对来自12S rDNA线粒体基因的一个短的鉴别片段进行扩增和测序。在这项研究中，我们更进一步，调查的空间代表性（即生态可靠性和信号在空间上的变化）的eDNA metabarcoding大型鱼类生物多样性评估在淡水系统，包括lentic和lotic环境。我们测试了这种方法的能力，以表征大规模组织的鱼类群落沿着纵向梯度，从一个湖泊流出的河流。首先，我们的研究结果证实，eDNA metabarcoding是更有效的比一个单一的传统的采样活动，以检测物种的存在，特别是在河流。其次，使用这种方法获得的物种列表是一个累积所有传统的采样会议时，自1995年和1988年以来的湖泊和河流，分别获得。总之，eDNA metabarcoding给出了一个忠实的描述当地的鱼类生物多样性的研究系统，更具体地说，在几公里的范围内沿着河在我们的研究条件下，即比传统的鱼类采样点。
In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.