Method for "Sample collection for metabarcoding"

jeudi 4 juin 2015
par  Aurélien DE JODE, Dorian GUILLEMAIN, Romain DAVID
popularité : 10%

NOT YET OPEN TO VALIDATION
Index of "Sample collection for metabarcoding"
1. Principle
2. Method
3. Sampling
4. Deliverables
5. To summarize
Back to protocols Index
How to cite this content :

David R., Arvanitidis C., Çinar M.E., Dubar J., Dubois S., Erga Z., Guillemain D., Sartoretto S., Thierry de Ville d’Avray L., Zuberer F., Chenuil A., Féral J.-P., (2014), with contributors : Açik Çinar S., Andral B., Aurelle D., Aysel V., Bakir K., Bellan G., Bellan-Santini D., Bouchoucha M., Celik C., Chatzigeorgiou G., Chatzinikolaou E., Chenesseau S., Dağli E., Dailianis T., Dimitriadis C., D’Iribarne C., Doğan A., Dounas C., Egea E., Elguerrabi W., Emery E., Evcen A., Faulwetter S., Gatti G., Gerovasileiou V., Güçver S.M., Issaris Y., Katağan T., Keklikoglou K., Kirkim F., Koçak F., Koutsoubas D., Marschal C., Önen M., Önen S., Öztürk B., Panayiotidis P., Pavloudi C., Pergent G., Pergent-Martini C., Poursanidis D., Ravel C., Reizopoulou S., Rocher C., Ruiton S., Sakher S., Salomidi M., Sarropoulou E., Selva M., Sini M., Sourbes L., Simboura N., Taşkin E., Vacelet J., Valavanis V., Vasileiadou A., Verlaque M. Protocols for monitoring of coralligenous habitats of mediterannean (Coralligenous based Indicators to Evaluate and Monitor the "good ecological status" of the MEDiterranean coastal waters) Protocoles de suivi du coralligène en méditerranée (Coralligenous
based Indicators to Evaluate and Monitor the "good ecological status" of the MEDiterranean coastal waters).

[§ 1] Samples will be collected by scraping the surface with an ice axe (Figure 1). Four scraping areas will be determined on specific profiles, at 30 or 45 m depth, as explained below (Figure 2) :
(1) Randomly choose a point in the center of a profile?, sufficiently homogeneous and place one dive weight (1 kg).
(2) Place the extremity of a 1 m long rope knotted at the dive weight (Figure 1) corresponding to the selected point, scrape a 10 cm x 10 cm area (materialised by a PVC quadrat) at the opposite extremity of the rope. If there is a large organisms (e.g. an erect gorgonian), a piece of a few centimeters is sufficient and it is not requested to remove it entirely (this should be reported somewhere). However, it is necessary to collect all epibionts.
(3) Rotate the rope of 90°, without moving the selected central point with the weight, and scrape again a 10 cm x 10 cm area. Repeat this step until four replicates are collected. 
 (4) In the case the extremity of the rope falls in an area which is not suitable for scraping, shift following the rope’s direction (translation), and take the sample in the first suitable area.

PNG - 110.1 ko

Figure 1 : Device used to place the areas of the four replicates (1) and ice axe used for scraping (2)

[§ 2] Sampling activities have to be carried out in specific seasons : in France, February and the end of the summer (august-september) were a priori chosen, to avoid the high variability of assemblages during recruitment seasons. However, our first great sampling was performed in 2015 between april and june !

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Figure 2 : methodology of localization of the samples scraped

[§ 3] The number of replicates is a compromise between statistic robustness and environment preservation. A maximum of caution will be used to avoid habitat? perturbation.

Attention : do not degrade a future sampling zone by performing the first scrapings.

WE EXPECT YOUR SUGGESTIONS OF CORRECTIONS !

- Deadline : 14th December 2015
- Please add comments for each paragraph (§) by means of a corrected new version (one form per §)
- It is recommended to add scientific references if necessary

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