K. A. Bjorndal, Foraging ecology and nutrition of sea turtles, The Biology of Sea Turtles, pp.199-231, 1997.

K. A. Bjorndal and J. B. Jackson, Roles of sea turtles in marine ecosystems: reconstructing the past, The Biology of Sea Turtles, pp.259-273, 2003.

S. S. Bouchard and K. A. Bjorndal, Sea turtles as biological transporters of nutrients and energy from marine to terrestrial ecosystems, Ecology, vol.81, pp.2305-2313, 2000.

L. B. Hannan, J. D. Roth, L. M. Ehrhart, and J. F. Weishampel, Dune vegetation fertilization by nesting sea turtles, Ecology, vol.88, pp.1053-1058, 2007.

J. Frazier, K. A. Eckert, K. A. Bjorndal, F. A. Abreu-grobois, and M. Donnelly, Research and management techniques for the conservation of sea turtles, 1999.

L. Bugoni, L. Krause, and M. V. Petry, Marine debris and human impacts on sea turtles in southern Brazil, Mar Pollut Bull, vol.42, pp.1330-1334, 2001.

J. Bourjea, S. Ciccione, and R. Ratsimbazafy, Marine turtles surveys in Nosy Iranja Kely, north-western Madagascar, West Indian Ocean J Mar Sci, vol.5, pp.209-212, 2006.

D. A. Pike, Climate influences the global distribution of sea turtle nesting, Glob Ecol Biogeogr, vol.22, pp.555-566, 2013.

T. Gerrodette and B. Taylor, Estimating Population Size. Research and Management Techniques for the Conservation of Sea Turtles, Publication, issue.4, 1999.

C. Jean, S. Ciccione, K. Ballorain, J. Georges, and J. Bourjea, Ultralight aircraft surveys reveal marine turtle population increases along the west coast of Reunion Island, Oryx, vol.44, pp.223-229, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00463990

S. P. Epperly, J. Braun, and A. J. Chester, Aerial surveys for sea turtles in North Carolina inshore waters, Oceanogr Lit Rev, vol.1, p.61, 1996.

T. A. Henwood, S. P. Epperly, K. L. Eckert, K. A. Bjorndal, F. A. Abreu-grobois et al., Research and Management Techniques for the Conservation of Sea Turtles, 1999.

B. Schroeder, S. Murphy, K. L. Eckert, K. A. Bjorndal, F. A. Abreu-grobois et al., Research and management techniques for the conservation of sea turtles, 1999.

D. Roos, D. Pelletier, S. Ciccione, M. Taquet, and G. Hughes, Aerial and snorkelling census techniques for estimating green turtle abundance on foraging areas: a pilot study in Mayotte Island (Indian Ocean), Aquat Living Resour, vol.18, pp.193-198, 2005.

K. Ballorain, S. Ciccione, J. Bourjea, H. Grizel, M. Enstipp et al., Habitat use of a multispecific seagrass meadow by green turtles Chelonia mydas at Mayotte Island, Mar Biol, vol.157, pp.2581-2590, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00516653

S. A. Eckert, K. L. Eckert, K. A. Bjorndal, F. A. Abreu-grobois, and M. Donnelly, Data acquisition systems for monitoring sea turtle behavior and physiology, Publication, issue.4, pp.88-93, 1999.

M. R. Enstipp, S. Ciccione, B. Gineste, M. Milbergue, K. Ballorain et al., Energy expenditure of freely swimming adult green turtles (Chelonia mydas) and its link with body acceleration, J Exp Biol, vol.214, pp.4010-4020, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00641697

K. Ballorain, J. Bourjea, S. Ciccione, A. Kato, N. Hanuise et al., Seasonal diving behaviour and feeding rhythms of green turtles at Mayotte Island, Mar Ecol Prog Ser, vol.483, pp.289-302, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00828460

T. Fukuoka, T. Narazaki, and K. Sato, Summer-restricted migration of green turtles Chelonia mydas to a temperate habitat of the northwest Pacific Ocean, Endanger Species Res, vol.28, pp.1-10, 2015.

D. P. Robinson, R. W. Jabado, C. A. Rohner, S. J. Pierce, K. P. Hyland et al., Satellite tagging of rehabilitated green sea turtles Chelonia mydas from the United Arab Emirates, including the longest tracked journey for the species, PloS One, vol.12, p.184286, 2017.

F. J. Schwartz, Behavioral and tolerance responses to cold water temperatures by three species of sea turtles (Reptilia, Cheloniidae) in North Carolina, Fla Mar Res Publ, vol.33, pp.16-18, 1978.

R. Hayashi, A checklist of turtle and whale barnacles (Cirripedia: Thoracica: Coronuloidea), J Mar Biol Assoc U K, vol.93, pp.143-182, 2013.

J. G. Frazier, I. Goodbody, and C. A. Ruckdeschel, Epizoan communities on marine turtles: II. Tunicates, Bull Mar Sci, vol.48, pp.763-765, 1991.

J. G. Frazier, J. E. Winston, and C. A. Ruckdeschel, Epizoan communities on marine turtles. III. Bryozoa, Bull Mar Sci, vol.51, pp.1-8, 1992.

J. Frazier, D. Margarttoulis, K. Muldoon, C. Potter, J. Rosewater et al., Epizoan communities on marine turtles, Mar Ecol, vol.6, pp.127-140, 1985.

R. Majewska, D. Stefano, M. Bolaños, F. Van-de-vijver, and B. , Hitchhinking on sea turtles: epizoic diatoms on olive ridleys (Lepidochelys olivacea) from the Pacific coast of Costa Rica, Diatomededelingen, vol.40, pp.35-42, 2016.

R. Majewska, B. Van-de-vijver, A. Nasrolahi, M. Ehsanpour, M. Afkhami et al., Shared epizoic taxa and differences in diatom community structure between green turtles (Chelonia mydas) from distant habitats, Microb Ecol, vol.74, p.28477173, 2017.

N. J. Robinson, R. Majewska, E. A. Lazo-wasem, R. Nel, F. V. Paladino et al., Epibiotic diatoms are universally present on all sea turtle species, PloS One, vol.11, issue.6, p.157011, 2016.

T. A. Frankovich, M. P. Ashworth, M. J. Sullivan, J. Vesela, and N. I. Stacy, Medlinella amphoroidea gen. et sp. nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta), Phytotaxa, vol.272, pp.101-114, 2016.

T. A. Frankovich, M. J. Sullivan, and N. Stacy, Three new species of Tursiocola (Bacillariophyta) from the skin of the West Indian manatee (Trichechus manatus), Phytotaxa, vol.204, pp.33-48, 2015.

T. A. Frankovich, M. J. Sullivan, and N. I. Stacy, Tursiocola denysii sp. nov.(Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta), Phytotaxa, vol.234, pp.227-236, 2015.

C. E. Wetzel, B. Van-de-vijver, and L. Ector, Luticola deniseae sp. nov. a new epizoic diatom from the Rio Negro (Amazon hydrographic basin), Vie MiLieu-Life Environ, vol.60, p.177, 2010.

C. E. Wetzel, B. Van-de-vijver, E. J. Cox, C. Bicudo-d-de, and L. Ector, Tursiocola podocnemicola sp. nov., a new epizoic freshwater diatom species from the Rio Negro in the Brazilian Amazon Basin, Diatom Res, vol.27, pp.1-8, 2012.

A. Pavlov, E. Jovanovska, C. E. Wetzel, L. Ector, and Z. Levkov, Freshwater Mastogloia (Bacillariophyceae) taxa from Macedonia, with a description of the epizoic M. sterijovskii sp. nov, Diatom Res, vol.31, pp.85-112, 2016.

B. J. Biggs and P. Gerbeaux, Periphyton development in relation to macro-scale (geology) and micro-scale (velocity) limiters in two gravel-bed rivers, New Zealand. N Z J Mar Freshw Res, vol.27, pp.39-53, 1993.

E. J. Cox, Observations on some benthic diatoms from North German lakes: The effect of substratum and light regime: With 3 figures in the text, Int Ver Für Theor Angew Limnol Verhandlungen, vol.22, pp.924-928, 1984.

F. Rimet, Recent views on river pollution and diatoms, Hydrobiologia, vol.683, pp.1-24, 2012.

E. Semary, Diatoms as bioindicators of littoral zone: a case study, Bangladesh J Bot, vol.45, pp.1113-1121, 2016.

S. C. Wu and E. A. Bergey, Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages, PloS One, vol.12, p.171910, 2017.

S. Fayolle, C. Moriconi, B. Oursel, C. Koenig, M. Suet et al., Epizoic algae distribution on the carapace and plastron of the European pond turtle (Emys orbicularis, Linnaeus, 1758): A study from the Camargue, Cryptogam Algol, vol.37, issue.4, pp.221-232, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01435259

M. Kahlert, R. Albert, E. Anttila, R. Bengtsson, C. Bigler et al., Harmonization is more important than experience-results of the first Nordic-Baltic diatom intercalibration exercise 2007 (stream monitoring), J Appl Phycol, vol.21, pp.471-482, 2009.

M. Kahlert, R. Albert, E. Anttila, R. Bengtsson, C. Bigler et al., Harmonization is more important than experience-results of the first Nordic-Baltic diatom intercalibration exercise 2007 (stream monitoring), J Appl Phycol, vol.21, pp.471-482, 2009.

P. Taberlet, E. Coissac, F. Pompanon, C. Brochmann, and E. Willerslev, Towards next-generation biodiversity assessment using DNA metabarcoding, Mol Ecol, vol.21, p.22486824, 2012.

P. D. Hebert, A. Cywinska, and S. L. Ball, Biological identifications through DNA barcodes, Proc R Soc Lond B Biol Sci, vol.270, pp.313-321, 2003.

L. Kermarrec, A. Franc, F. Rimet, P. Chaumeil, J. Frigerio et al., A next-generation sequencing approach to river biomonitoring using benthic diatoms, Freshw Sci, vol.33, pp.349-363, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02632667

J. A. Visco, L. Apothéloz-perret-gentil, A. Cordonier, P. Esling, L. Pillet et al., Environmental monitoring: inferring the diatom index from next-generation sequencing data, Environ Sci Technol, vol.49, pp.7597-7605, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01245156

J. Zimmermann, G. Glöckner, R. Jahn, N. Enke, and B. Gemeinholzer, Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies, Mol Ecol Resour, vol.15, pp.526-542, 2015.

, Water quality. Technical report for the routine sampling of benthic diatoms from rivers and lakes adapted for metabarcoding analyses, p.7, 2016.

. Cen and . En, Water quality-Guidance standard for the routine sampling and pretreatment of benthic diatoms from rivers, European Commitee for Standardisation, p.718, 2002.

. Cen and . En, Water quality-Guidance standard for the identification, enumeration and interpretation of benthic diatom samples from running waters, p.13, 2003.

A. Witkowski, H. Lange-bertalot, and D. Metzeltin, Diatom Flora Ofmarine Coasts I. Iconographia Diatomologica 7, Rugell. ARG Gantner Verlag KG, 2000.

M. K. Hein, B. M. Winsborough, and M. J. Sullivan, Bacillariophyta (diatoms) of the Bahamas, 2008.

M. Richard, Atlas du phytoplankton marine: Diatomophyceae. Natl Recherce Paris, vol.285, 1987.

Z. Levkov, Amphora sensu lato. Diatoms of Europe 5, p.916, 2009.

C. Riaux-gobin and A. Ay, New species in the marine diatom genus Olifantiella (Bacillariophyta, Biraphidineae) from Rodrigues Island (Western Indian Ocean), Fottea, vol.12, pp.199-217, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00722807

C. Riaux-gobin, A. Witkowski, P. Compère, and O. E. Romero, Cocconeis Ehrenberg taxa (Bacillariophyta) with a marginal row of simple processes: relationship with the valvocopula system and distinctive features of related taxa, Fottea Praha, vol.15, pp.139-154, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01212883

C. Riaux-gobin, A. Witkowski, D. Chevallier, and G. Daniszewska-kowalczyk, Two new Tursiocola species (Bacillariophyta) epizoic on green turtles (Chelo-nia mydas) in French Guiana and Eastern Caribbean, 2017.

V. Vasselon, I. Domaizon, F. Rimet, M. Kahlert, and A. Bouchez, Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?, Freshw Sci, vol.36, pp.162-177, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606868

V. Vasselon, F. Rimet, K. Tapolczai, and A. Bouchez, Assessing ecological status with diatoms DNA metabarcoding: scaling-up on a WFD monitoring network (Mayotte island, France), Ecol Indic, vol.82, pp.1-12, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02622658

F. Rimet, P. Chaumeil, F. Keck, L. Kermarrec, V. Vasselon et al., diatom: an openaccess and curated barcode database for diatoms and freshwater monitoring, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01426772

F. Rimet, N. Abarca, A. Bouchez, W. H. Kusber, R. Jahn et al., The potential of high throughput sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes, Fottea, vol.18, issue.1, pp.37-54, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02624468

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol Biol Evol, vol.27, pp.221-224, 2009.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

S. Kumar, G. Stecher, and K. Tamura, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

D. Silvestro and I. Michalak, raxmlGUI: a graphical front-end for RAxML, Org Divers Evol, vol.12, pp.335-337, 2012.

I. Letunic and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016.

S. F. Rivera, V. Vasselon, S. Jacquet, A. Bouchez, D. Ariztegui et al., Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment, Hydrobiologia, vol.807, pp.37-51, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02621047

L. Apothéloz-perret-gentil, A. Cordonier, F. Straub, J. Iseli, P. Esling et al., Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring, Mol Ecol Resour, vol.17, pp.1231-1242, 2017.

V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo et al., Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring, Methods Ecol Evol, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02623786

K. Tapolczai, A. Bouchez, C. Stenger-kovács, J. Padisák, and F. Rimet, Taxonomy-or trait-based ecological assessment for tropical rivers? Case study on benthic diatoms in Mayotte island, Sci Total Environ, vol.607, pp.1293-1303, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01604595

J. Tison, Y. Park, M. Coste, J. G. Wasson, L. Ector et al., Typology of diatom communities and the influence of hydro-ecoregions: a study on the French hydrosystem scale, Water Res, vol.39, pp.3177-3188, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02586449

R. Majewska, M. Santoro, F. Bolaños, G. Chaves, D. Stefano et al., Diatoms and other epibionts associated with olive ridley (Lepidochelys olivacea) sea turtles from the Pacific Coast of Costa Rica, PloS One, vol.10, p.130351, 2015.

D. G. Mann, S. M. Mcdonald, M. M. Bayer, S. J. Droop, V. A. Chepurnov et al., The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species, Phycologia, vol.43, pp.459-482, 2004.

K. M. Evans, A. H. Wortley, G. E. Simpson, V. A. Chepurnov, and D. G. Mann, A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta), J Phycol, vol.44, p.27041057, 2008.

C. Souffreau, P. Vanormelingen, B. Van-de-vijver, T. Isheva, E. Verleyen et al., Molecular evidence for distinct Antarctic lineages in the cosmopolitan terrestrial diatoms Pinnularia borealis and Hantzschia amphioxys, Protist, vol.164, pp.101-115, 2013.

B. Vanelslander, V. Creach, P. Vanormelingen, A. Ernst, V. A. Chepurnov et al., Ecological differentiation between sympatric pseudocryptic species in the estuarine benthic diatom Navicula phyllepta (Bacillariophyceae), J Phycol, vol.45, p.27032584, 2009.

L. Rovira, R. Trobajo, S. Sato, C. Ibáñez, and D. G. Mann, Genetic and physiological diversity in the diatom Nitzschia inconspicua, J Eukaryot Microbiol, vol.62, pp.815-832, 2015.

M. G. Kelly, R. Trobajo, L. Rovira, and D. G. Mann, Characterizing the niches of two very similar Nitzschia species and implications for ecological assessment, Diatom Res, vol.30, pp.27-33, 2015.

F. Rimet, V. Vasselon, A. Barbara, and A. Bouchez, Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes, Org Divers Evol, pp.1-12
URL : https://hal.archives-ouvertes.fr/hal-02625205

F. Keck, F. Rimet, A. Franc, and A. Bouchez, Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring, Ecol Appl, vol.26, pp.861-872, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01426854

F. Rimet and A. Bouchez, Biomonitoring river diatoms: implications of taxonomic resolution, Ecol Indic, vol.15, pp.92-99, 2012.

B. Chessman, I. Growns, J. Currey, and N. Plunkett-cole, Predicting diatom communities at the genus level for the rapid biological assessment of rivers, Freshw Biol, vol.41, pp.317-331, 1999.

R. Trobajo, L. Rovira, L. Ector, C. E. Wetzel, M. Kelly et al., Morphology and identity of some ecologically important small Nitzschia species, Diatom Res, vol.28, pp.37-59, 2013.

A. Guilcher, L. Berthois, L. Calvez, Y. Battistini, R. Crosnier et al., Les récifs coralliens et le lagon de l'île Mayotte (archipel des Comores, océan Indien): géomorphologie, sédimentologie, hydrologie, foraminifères, ORSTOM Paris, 1965.

L. K. Medlin, H. J. Elwood, S. Stickel, and M. L. Sogin, Morphological and genetic variation within the diatom Skeletonema costatum (Bacillariophyta): evidence for a new species, Skeletonema pseudocostatum, J Phycol, vol.27, pp.514-524, 1991.

L. K. Medlin, W. H. Kooistra, D. Potter, G. W. Saunders, and R. A. Andersen, Phylogenetic relationships of the 'golden algae'(haptophytes, heterokont chromophytes) and their plastids. Origins of algae and their plastids, pp.187-219, 1997.

F. Keck, V. Vasselon, K. Tapolczai, F. Rimet, and A. Bouchez, Freshwater biomonitoring in the information age, Front Ecol Environ, vol.15, pp.266-274, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01604509