Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

被引：866

作者：

Valentini, Alice ^{[1
]}

Taberlet, Pierre ^{[2
,3
]}

Miaud, Claude ^{[4
]}

Civade, Raphael ^{[5
]}

Herder, Jelger ^{[6
]}

Thomsen, Philip Francis ^{[7
]}

Bellemain, Eva ^{[1
]}

Besnard, Aurelien ^{[4
]}

Coissac, Eric ^{[2
,3
]}

Boyer, Frederic ^{[2
,3
]}

Gaboriaud, Coline ^{[1
]}

Jean, Pauline ^{[1
]}

Poulet, Nicolas ^{[8
]}

Roset, Nicolas ^{[9
]}

Copp, Gordon H. ^{[10
,11
]}

Geniez, Philippe ^{[4
]}

Pont, Didier ^{[5
]}

Argillier, Christine ^{[12
]}

Baudoin, Jean-Marc ^{[12
]}

Peroux, Tiphaine ^{[12
]}

Crivelli, Alain J. ^{[13
]}

Olivier, Anthony ^{[13
]}

Acqueberge, Manon ^{[14
]}

Le Brun, Matthieu ^{[15
]}

Moller, Peter R. ^{[16
]}

Willerslev, Eske ^{[7
]}

Dejean, Tony ^{[1
]}

机构：

[1] SPYGEN, Savoie Technolac, Bat Koala,17,Rue Lac St Andre BP 274, F-73375 Le Bourgei Du Lac, France

[2] CNRS, Lab Ecol Alpine LECA, F-38000 Grenoble, France

[3] Univ Grenoble Alpes, Lab Ecol Alpine LECA, F-38000 Grenoble, France

[4] CEFE UMR 5175, Lab Biogeog & Ecol Vertebres, F-34293 Montpellier, France

[5] IRSTEA, Hydrosyst & Bioproc Res Unit, F-92761 Antony, France

[6] RAVON, Postbus 1413, NL-6501 BK Nijmegen, Netherlands

[7] Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Copenhagen, Denmark

[8] ONEMA, Direct Act Sci & Tech, F-94300 Vincennes, France

[9] ONEMA, Rhone Alpes Reg Direct, F-69500 Bron, France

[10] Ctr Environm Fisheries & Aquaculture Sci, Pakefield Rd, Lowestoft NR33 0HT, Suffolk, England

[11] Trent Univ, Environm & Life Sci Grad Program, Peterborough, ON K9J 7B8, Canada

[12] IRSTEA UR HYAX, Ctr Aix En Provence, Pole ONEMA IRSTEA Hydroecol Plans Eau, F-13182 Aix En Provence, France

[13] Tour Valat, Sambuc, F-13200 Arles, France

[14] Agence Ctr Ouest, Ecosphere, F-45000 Orleans, France

[15] EDF R&D, LNHE Dept, F-78401 Chatou, France

[16] Univ Copenhagen, Nat Hist Museum Denmark, Univ Pk 15, DK-2100 Copenhagen, Denmark

来源：

MOLECULAR ECOLOGY | 2016年 / 25卷 / 04期

关键词：

amphibian; detection probability; environmental DNA; fish; monitoring; wildlife management; IN-SILICO APPROACH; SURVEILLANCE; CONSERVATION; LIMITATIONS; INFERENCE; BARCODE; RATES; EDNA;

D O I：

10.1111/mec.13428

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, invitro and insitu. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI=0.90-0.99) vs. 0.58 (CI=0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems. see also the Perspective by Hoffmann, Schubert and Calvignac-Spencer

引用

页码：929 / 942

页数：14