Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem
Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem
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DOI：
10.3389/fmars.2016.00283
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发表时间：
2017-01-01
影响因子：
3.7
通讯作者：
Samhouri, Jameal F.
中科院分区：
文献类型：
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作者：
Kelly, Ryan P.;Closek, Collin J.;Samhouri, Jameal F.
鉴于生态学和环境科学领域环境 DNA (eDNA) 调查的迅速兴起，将这些调查的结果与测量生物多样性的传统方法进行比较非常重要。在这里，我们将传统方法（手动拖网）的样本与在三个不同基因位点测序的配套 eDNA 样本进行比较。我们发现所得数据集之间仅存在部分分类重叠，每个数据集都反映了采样的近岸海洋环境中存在的较大类群的一部分。在 eDNA 测序调查的更大背景下，我们的结果表明，引物扩增偏差导致了 eDNA 检测中的大部分分类学偏差，并且使用广谱引物组检测任何给定分类单元的基线概率可能很低。无论是用不同的网捕鱼还是使用不同的 PCR 引物组，多种数据类型都可以提供共同生态系统的互补视图。然而，在现场交叉验证 eDNA 测序技术（无论是存在/不存在还是丰度）仍然很困难，特别是对于针对非常广泛的分类范围的引物组。最后，我们的结果强调了单一栖息地的多样性广度，尽管 eDNA 确实比传统采样方法捕获了更丰富的群落样本，但需要大量针对生物群不同子集的 eDNA 引物集才能以合理全面的方式调查任何生态群落。
Given the rapid rise of environmental DNA (eDNA) surveys in ecology and environmental science, it is important to be able to compare the results of these surveys to traditional methods of measuring biodiversity. Here we compare samples from a traditional method (a manual tow-net) to companion eDNA samples sequenced at three different genetic loci. We find only partial taxonomic overlap among the resulting datasets, with each reflecting a portion of the larger suite of taxa present in the sampled nearshore marine environment. In the larger context of eDNA sequencing surveys, our results suggest that primer amplification bias drives much of the taxonomic bias in eDNA detection, and that the baseline probability of detecting any given taxon with a broad-spectrum primer set is likely to be low. Whether catching fish with different nets or using different PCR primer sets, multiple data types can provide complementary views of a common ecosystem. However, it remains difficult to cross-validate eDNA sequencing techniques in the field, either for presence/absence or for abundance, particularly for primer sets that target very wide taxonomic ranges. Finally, our results highlight the breadth of diversity in a single habitat, and although eDNA does capture a richer sample of the community than traditional methods of sampling, a large number of eDNA primer sets focusing on different subsets of the biota would be necessary to survey any ecological community in a reasonably comprehensive way.