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eDNA

par Webmaster - 11 février 2015

Personnel involved :
-  Pierre Taberlet, Scientist
-  Eric Coissac, Scientist
-  Frédéric Boyer, Scientist
-  Christian Miquel, Research Engineer
-  Delphine Rioux, Technician

This technical platform has been set up to allow ecologists to perform large-scale analysis of environmental DNA via a metabarcoding approach. DNA metabarcoding refers to high throughput DNA-based identification of multiple species from environmental DNA. The main applications consist in diet analysis from feces, in biodiversity assessment using soil or water samples, and in palaeo-environment reconstruction using lake sediments and permafrost samples.

The eDNA platform is composed of three pre-PCR extraction rooms dedicated to feces, soil, and ancient DNA, and to several post-PCR rooms dedicated to the purification and the titration of PCR products. The next generation sequencing on Illumina platforms (HiSeq or MiSeq) is outsourced.

Beside the basic equipment (centrifuges, vortex, etc.), the eDNA platform is equipped with a 96 pipetting head (see pictures below) and two PCR machines with each two 384 heads. This allows the set up, the amplification, and the purification of more than 4500 PCR per day.

When carrying out large-scale sampling (soil or feces), the eDNA platform possesses all the equipment that can be transported and installed in the field to allow DNA extraction straight after the sampling, and to bring back the DNA on the extraction columns (see pictures below). Using this approach, large-scale extractions have been carried out in French Guiana, in China, and in South Africa.

The personnel involved in the eDNA platform has all the competences in designing new metabarcodes and testing them in silico, in designing the experiments (how many samples, how many sequence reads, how many positive and negative controls, how to produce a reference database, etc.), in carrying out the experiments at the bench, and in analyzing the output of the next generation sequencers (using a collection of program developed within the eDNA platform, and specifically dedicated to DNA metabarcoding ; http://metabarcoding.org/obitools).

  • Examples of paper published using data produced in the eDNA platform :

Bienert R, de Danieli S, Miquel C, Coissac E, Poillot C, Brun JJ, Taberlet P (2012) Tracking earthworm communities from soil DNA. Molecular Ecology, 21, 2017-2030.

De Barba M, Miquel C, Boyer F, Rioux D, Coissac E, Taberlet P (2014) DNA metabarcoding multiplexing for omnivorous diet analysis and validation of data accuracy. Molecular Ecology Resources, 14, 306-323.

Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS ONE, 6, e23398.

Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C (2012) Improved detection of an alien invasive species through environmental DNA barcoding : the example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology, 49, 953-959.

Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biology Letters, 4, 423-425.

Giguet-Covex C, Pansu J, Arnaud F, Rey P-J, Griggo C, Gielly L, Domaizon I, Coissac E, David F, Choler P, Poulenard J, Taberlet P (2014) Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nature Communications, 5:3221, doi:10.1038/ncomms4211.

Hibert F, Taberlet P, Chave J, Scotti-Saintagne C, Sabatier D, Richard-Hansen C (2013) Unveiling the diet of elusive rainforest herbivores in next generation sequencing era ? The tapir as a case study. PLoS ONE, 8, e60799.

Ibanez S, Manneville O, Miquel C, Taberlet P, Valentini A, Aubert S, Coissac E, Colace MP, Duparc Q, Lavorel S, Moretti M (2013) Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers. Oecologia, 173, 1459-1470.

Kowalczyk R, Taberlet P, Coissac E, Valentini A, Miquel C, Kamiński T, Wójcik JM (2011) Influence of management practices on large herbivore diet - case of European bison in Białowieża Primeval Forest (Poland). Forest Ecology and Management, 261, 821-828.

Pansu J, De Danieli S, Puissant J, Gonzalez J-M, Gielly L, Cordonnier T, Zinger L, Brun J-J, Choler P, Taberlet P, Cecillon L (2015) Landscape-scale distribution patterns of earthworms inferred from soil DNA. Soil Biology and Biochemistry, in press.

Pegard A, Miquel C, Valentini A, Coissac E, Bouvier F, François D, Taberlet P, Engel E, Pompanon F (2009) Universal DNA based methods for assessing the diet of grazing livestock and wildlife from faeces. Journal of Agricultural and Food Chemistry, 57, 5700-5706.

Quéméré E, Hibert F, Miquel C, Lhuillier E, Rasolondraibe E, Champeau J, Rabarivola C, Nusbaumer L, Chatelain C, Gautier L, Ranirison P, Crouau-Roy B, Taberlet P, Chikhi L (2013) A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range. PLoS ONE, 8, e58971.

Rayé G, Miquel C, Coissac E, Redjadj C, Loison A, Taberlet P (2011) New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing : chamois diet in autumn as a case study. Ecological Research, 26, 265-276.

Shehzad W, McCarthy TM, Pompanon F, Purevjav L, Coissac E, Riaz T, Taberlet P (2012) Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia. PLoS ONE, 7, e32104.

Shehzad W, Riaz T, Nawaz MA, Miquel C, Poillot C, Shah SA, Pompanon F, Coissac E, Taberlet P (2012) Carnivore diet analysis based on next generation sequencing : application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology, 21, 1951-1965.

Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, Sønstebø JH, Ims RA, Yoccoz NG, Taberlet P (2009) Analysing diet of small herbivores : the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology, 6, 16.

Sønstebø JH, Gielly L, Brysting A, Reidar E, Edwards M, Haile J, Willerslev E, Coissac E, Rioux D, Sannier J, Taberlet P, Brochmann C (2010) Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources, 10, 1009-1018.

Valentini A, Miquel C, Nawaz MA, Bellemain E, Coissac E, Pompanon F, Gielly L, Cruaud C, Nascetti G, Wincker P, Swenson JE, Taberlet P (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing : the trnL approach. Molecular Ecology Resources, 9, 51-60.

Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergaard M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp L, Pearman PB, Cheddadi R, Murray D, Bråthen KA, Yoccoz NG, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sønstebø JH, Murton J, Sher A, Rasmussen K, Rønn R, Mourier T, Cooper A, Austin J, Möller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjær K, Orlando L, Brochmann C, Taberlet P (2014) Fifty-five thousand years of arctic vegetation and megafaunal diet. Nature, 506, 47-51.

Yoccoz NG, Bråthen KA, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, de Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP, Orlando L, Brochmann C, Willerslev E, Taberlet P (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655.







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