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Protocole CIGESMED : Coralligenous Based Indicators to Evaluate and Monitor The"Good Ecological Status" of the Mediterranean Coastal Waters

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Protocole CIGESMED : Coralligenous Based Indicators to Evaluate and Monitor The Protocole CIGESMED : Coralligenous based Indicators to Evaluate and Monitor the"good ecological status" of the MEDiterranean coastal waters Contacts: [email protected] [email protected]. Marine station of Endoume – Chemin de la Batterie des Lions – 13007 Marseille Person in charge of the program: Jean-Pierre FERAL, research director Person in charge of the protocole’s redaction: Romain DAVID, engineer Authors: David R. (1), Arvanitidis C. (2), Çinar M.E. (3), Sartoretto S. (5) , Dubois S. (1), Erga Z. (1,3), Guillemain D. (1), Sakher S. (1), Thierry de Ville d’Avray L. (1), Zuberer F. (6), Chenuil A. (1), Féral J.-P. (1), (2014), with contributors* Protocole de suivi du coralligène en méditerranée, année 1 de CIGESMED (Coralligenous based Indicators to Evaluate and Monitor the "good ecological status" of the MEDiterranean coastal waters). Protocoles CIGESMED (1) AMU: Aix Marseille University - CNRS: National Center for Scientific Research (French) - IMBE Mediterranean Institute of marine and terrestrial Biodiversity and Ecology, Marine Research station of Endoume (CNRS, AMU, IRD, Avignon University) - MIO : Mediterranean Institut of Oceanography - SPE : Systèmes Pour l’Environnement, écosystemes côtiers. University of Corsica, Corte. (2) HCMR - Hellenic Centre for Marine Research - Institute of Marine Biology, Biotechnology and Aquaculture - Institute of Oceanography - Institute of Marine biological Resources, Thalassocosmos. (3) EGE University - Faculty of Fisheries - Dokuz Eylul University [Institute of Marine Sciences and Technology & Faculty of Science] - Cela Bayar University, Department of Biology - Ministry of Forestry and Water Affairs [General Directorate of Water Management], Izmir / Ankara. (4) LIGAMEN SME, Marseilles. (5) IFREMER (French Research Institute for Exploitation of the Sea), La Seyne sur Mer (6) NMPZ: Nationam Marine Park of Zakynthhos, Zakynthos. With the participation of: *: 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., Frémaux A., 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., Salomidi M., Sarropoulou E., Selva M., Sini M., Sourbes L., Simboura N., Taşkin E., Vacelet J., Valavanis V., Vasileiadou A., Verlaque M. Photo credits: © R. David, Z. Erga, D. Guillemain, F. Zuberer. 2 Protocoles CIGESMED Table of contents Table of contents ................................................................................................................... 3 I. Context ............................................................................................................................ 7 II. General Organization ...................................................................................................... 8 A. Four protocols “matrix”................................................................................................. 8 B. Choice of sites ............................................................................................................. 9 C. Additional sites specifications ...................................................................................... 9 D. Test of methods and pre-existent indexes (inter-calibration) ...................................... 11 E. Training sites and gear .............................................................................................. 11 F. Particular demands for the whole protocole ............................................................... 12 G. Safety ........................................................................................................................ 12 III. Protocols ......................................................................................................................14 A. Reminders on the concepts of coralligenous facies ................................................... 14 B. Module 1 : Protocol « Profiles and stands cartography » ........................................... 20 1. Principle .................................................................................................................20 2. Method ...................................................................................................................20 3. Sampling ................................................................................................................26 a. Operations ..........................................................................................................26 b. Data conditioning ................................................................................................30 c. Material list ..........................................................................................................30 d. Work time quantification ......................................................................................30 4. Deliverables ............................................................................................................31 a. Expected data .....................................................................................................31 b. Data processing perspectives .............................................................................32 5. In brief ....................................................................................................................33 C. Module 2 : Protocol of « Characterization by photo-quadrats ».................................. 38 1. Principle .................................................................................................................38 a. Inter-calibration on permanent transect ...............................................................39 b. Comparison of metrics variability between a permanent transect and random transects ....................................................................................................................39 c. Contextualisation of the metrics measured during the implementation of random transects ....................................................................................................................39 3 Protocoles CIGESMED d. Choice of the studied species .............................................................................40 2. Method ...................................................................................................................41 a. Inter-calibration on permanent transect ...............................................................43 b. Comparison of the variability of metrics values measured on a permanent transect and the ones obtained on a random transect .............................................................44 c. Contextualization of the metrics measured during the implementation of tandom transects ....................................................................................................................45 3. Sampling ................................................................................................................45 a. Operations ..........................................................................................................45 b. Data conditioning ................................................................................................48 c. Material list ..........................................................................................................49 d. Work time quantification ......................................................................................49 4. Delivrables ..............................................................................................................50 a. Expected results .................................................................................................50 b. Data analyses envisaged ....................................................................................51 5. In brief ....................................................................................................................53 D. Module 3 : Protocol « sample collection for metabarcoding x 4 » .............................. 58 1. Principle .................................................................................................................58 2. Method ...................................................................................................................58 3. Sampling ................................................................................................................59 a. Operations ..........................................................................................................59 b. Sample conditioning ............................................................................................59 c. Material list ..........................................................................................................60 d. Work time quantification ......................................................................................61 4. Delivrables ..............................................................................................................61 a. Expected results .................................................................................................61
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