Evaluating a multigene environmental DNA approach for biodiversity assessment.
Evaluating a multigene environmental DNA approach for biodiversity assessment.
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DOI：
10.1186/s13742-015-0086-1
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发表时间：
2015
期刊：
影响因子：
9.2
通讯作者：
Nelson N
中科院分区：
文献类型：
--
作者：
Drummond AJ;Newcomb RD;Buckley TR;Xie D;Dopheide A;Potter BC;Heled J;Ross HA;Tooman L;Grosser S;Park D;Demetras NJ;Stevens MI;Russell JC;Anderson SH;Carter A;Nelson N
对具有广泛分类覆盖范围的快速生物多样性评估工具的需求不断增加。在这里，我们评估了一套环境 DNA (eDNA) 标记与跨越生命树的下一代测序 (NGS)，并将其与沿 700 米海拔梯度的 10 个 20×20 米地块内的传统生物多样性监测工具进行比较。从六个 eDNA 数据集（16S、18S、ITS、trnL 各一个，COI 各一个）中，我们从 109 个 NCBI 分类学定义的门或同等门中识别出序列，对于给定的 eDNA 标记，序列范围从 31 到 60。 α 和 γ 多样性的估计对序列读数的数量敏感，而 β 多样性的估计则不太敏感。所有标记的平均图内 beta 多样性均低于图间。 COI和18S标记的土壤β多样性对eDNA标记的海拔变化的响应最强（COI：r=0.49，p<0.001；18S：r=0.48，p<0.001）。此外，这两个标记的成对β多样性与传统植被和无脊椎动物生物多样性测量计算出的多样性密切相关。使用基于土壤的 eDNA 方法，我们证明标准系统发育标记能够从 16S 的原核生物和广泛多样性的真核生物中恢复序列。 COI 和 18S eDNA 标记是地上生物多样性的最佳代表，因为这些标记的成对 beta 多样性与使用传统方法获得的标记之间存在高度相关性。本文的在线版本 (doi:10.1186/s13742-015-0086-1) 包含补充材料，可供授权用户使用。
There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient. From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures. Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods. The online version of this article (doi:10.1186/s13742-015-0086-1) contains supplementary material, which is available to authorized users.