Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys.
Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys.
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DOI：
10.1371/journal.pone.0122763
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Minamoto T
中科院分区：
文献类型：
--
作者：
Doi H;Uchii K;Takahara T;Matsuhashi S;Yamanaka H;Minamoto T
最近开发了一种环境 DNA (eDNA) 分析方法，通过使用定量实时 PCR (qPCR) 量化目标 DNA 拷贝数来估计水生动物的分布。一种新的定量 PCR 技术，液滴数字 PCR (ddPCR)，将 PCR 反应分成数千个液滴，并检测每个液滴中的扩增，从而可以直接定量目标 DNA。我们在涉及不同数量鲤鱼的中生态实验中使用 eDNA 评估了 qPCR 和 ddPCR 的定量准确性，以估计物种丰度和生物量。我们发现，ddPCR 比 qPCR 更准确地量化鲤鱼 eDNA 浓度以及鲤鱼丰度和生物量，特别是在低 eDNA 浓度下。此外，ddPCR 的分析误差比 qPCR 更小。因此，ddPCR 更适合测量水中的 eDNA 浓度，并且比 qPCR 提供更准确的目标物种丰度和生物量结果。我们还通过ddPCR和qPCR发现鲤鱼丰度与eDNA浓度之间的关系强于生物量与eDNA之间的关系；这表明，通过对体重变化较小的物种进行 eDNA 分析，可以更好地估计丰度。
An environmental DNA (eDNA) analysis method has been recently developed to estimate the distribution of aquatic animals by quantifying the number of target DNA copies with quantitative real-time PCR (qPCR). A new quantitative PCR technology, droplet digital PCR (ddPCR), partitions PCR reactions into thousands of droplets and detects the amplification in each droplet, thereby allowing direct quantification of target DNA. We evaluated the quantification accuracy of qPCR and ddPCR to estimate species abundance and biomass by using eDNA in mesocosm experiments involving different numbers of common carp. We found that ddPCR quantified the concentration of carp eDNA along with carp abundance and biomass more accurately than qPCR, especially at low eDNA concentrations. In addition, errors in the analysis were smaller in ddPCR than in qPCR. Thus, ddPCR is better suited to measure eDNA concentration in water, and it provides more accurate results for the abundance and biomass of the target species than qPCR. We also found that the relationship between carp abundance and eDNA concentration was stronger than that between biomass and eDNA by using both ddPCR and qPCR; this suggests that abundance can be better estimated by the analysis of eDNA for species with fewer variations in body mass.
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影响因子：
5.7
作者：
Dejean, Tony;Valentini, Alice;Miaud, Claude
通讯作者：
Miaud, Claude
影响因子：
5
作者：
Kim, Tae Gwan;Jeong, So-Yeon;Cho, Kyung-Suk
通讯作者：
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影响因子：
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作者：
Strain MC;Lada SM;Luong T;Rought SE;Gianella S;Terry VH;Spina CA;Woelk CH;Richman DD
通讯作者：
Richman DD
影响因子：
3.7
作者：
Thomsen PF;Kielgast J;Iversen LL;Møller PR;Rasmussen M;Willerslev E
通讯作者：
Willerslev E
影响因子：
7.4
作者：
Hindson, Benjamin J.;Ness, Kevin D.;Masquelier, Donald A.;Belgrader, Phillip;Heredia, Nicholas J.;Makarewicz, Anthony J.;Bright, Isaac J.;Lucero, Michael Y.;Hiddessen, Amy L.;Legler, Tina C.;Kitano, Tyler K.;Hodel, Michael R.;Petersen, Jonathan F.;Wyatt, Paul W.;Steenblock, Erin R.;Shah, Pallavi H.;Bousse, Luc J.;Troup, Camille B.;Mellen, Jeffrey C.;Wittmann, Dean K.;Erndt, Nicholas G.;Cauley, Thomas H.;Koehler, Ryan T.;So, Austin P.;Dube, Simant;Rose, Klint A.;Montesclaros, Luz;Wang, Shenglong;Stumbo, David P.;Hodges, Shawn P.;Romine, Steven;Milanovich, Fred P.;White, Helen E.;Regan, John F.;Karlin-Neumann, George A.;Hindson, Christopher M.;Saxonov, Serge;Colston, Bill W.
通讯作者：
Colston, Bill W.