Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing—also called metabarcoding—of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.

中文翻译：

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使用环境 DNA 量化环境干预的影响

世界各地的环境法要求对建筑项目和人类发展的其他离散实例进行某种版本的环境影响评估。这些评估的信息要求因司法管辖区而异，但几乎都需要对生态系统的生物要素进行分析。环境 DNA (eDNA) 的扩增子测序（也称为元条形码）使得对这些环境中存在的许多物种的遗传物质进行采样和扩增成为可能，为环境影响分析提供了一种易于处理、强大且日益常见的方法。开发项目。在这里，我们分析了在含有鲑鱼的淡水流中进行两次涵洞清除之前、期间和之后采集的 18 个月时间序列的水样。我们还对多个控制流进行了采样，以制定强大的背景期望，以此来评估处理流中这种离散环境干预的影响。我们通过放大 12s MiFish mtDNA 位点和互补的物种特异性定量 PCR 数据来生成校准的定量元条形码数据，以产生跨时间、小溪和采样站的多物种绝对 eDNA 浓度估计值。然后，我们使用线性混合效应模型来揭示 eDNA 浓度随时间变化的模式，并估计涵洞移除对处理溪中鲑鱼的影响。我们重点分析四种常见的鲑科鱼类：切喉鳟鱼 ( Oncorhynchus clarkii )、银鲑鱼 ( Oncorhynchus kisutch )、虹鳟鱼 ( Oncorhynchus mykiss ) 和红鲑鱼 ( Oncorhynchus nerka )。我们发现处理河中的一个涵洞似乎没有影响，而第二个涵洞对鱼的通过有很大的影响。在两次施工期间，施工本身似乎只对鲑鱼物种产生短暂影响。在美国华盛顿州法院强制进行数十亿美元的道路涵洞更换的背景下，我们的结果表明，涵洞更换可以在施工对管理问题的关键物种影响极小的情况下进行。此外，eDNA 方法可以成为监测数百个涵洞的有效且高效的方法，以优先考虑需要更换的涵洞。更广泛地说，我们展示了一种使用 eDNA 进行环境影响报告的严格定量方法，该方法广泛适用于全球环境。