Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA.
Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA.
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DOI：
10.1111/mec.13481
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发表时间：
2016-01
影响因子：
4.9
通讯作者：
Kelly RP
中科院分区：
文献类型：
--
作者：
Port JA;O'Donnell JL;Romero-Maraccini OC;Leary PR;Litvin SY;Nickols KJ;Yamahara KM;Kelly RP
保护生物多样性是一项全球性挑战，需要关于大地理和时间尺度上物种分布和丰度的数据。然而，传统的调查海洋环境中移动的物种的分布和丰度的方法往往效率低下，对环境具有破坏性或资源密集型。环境DNA（eDNA）的元条码提供了一种新的手段，以评估生物多样性和更大的规模，但采用这种方法来调查整个动物群落在大型，动态的水生系统已放缓了显着的未知数周围的错误率的检测和相关的空间分辨率的eDNA调查。在这里，我们报告的结果，2.5公里的eDNA样带调查脊椎动物区系呈现沿着一个层次的不同的海洋栖息地与海带森林生态系统。使用针对海洋鱼类和哺乳动物线粒体12 S rRNA基因的PCR引物，我们生成了eDNA序列数据，并将其与同时进行的目视潜水调查进行比较。我们发现个体物种的eDNA和视觉调查趋势之间的空间一致性，eDNA是能够区分脊椎动物群落组合的栖息地分离小至60米。与调查相比，eDNA可靠地检测到脊椎动物，假阴性错误率较低（1/12分类群），并揭示了已知占据栖息地但被视觉方法忽视的神秘物种。本研究还提出了一个明确的会计假阴性和阳性的metabarcoding数据，这说明了基因标记的选择，复制，污染，偏见影响eDNA计数数据和生态的目标物种的eDNA检测率在一个开放的生态系统的影响。
Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.