A. Barnett, V. Méléder, L. Blommaert, B. Lepetit, P. Gaudin et al., Growth form defines physiological photoprotective capacity in intertidal benthic diatoms, ISME J, vol.9, pp.32-45, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01110925

R. R. Bidigare, M. Ondrusek, S. Fisheries, and D. A. Kiefer, In-vivo absorption properties of algal pigments, Proceedings of the 1990 Technical Symposium on Optics, Electro-Optics, and Sensors, pp.290-301, 1990.

L. Blommaert, J. Lavaud, W. Vyverman, and K. Sabbe, Behavioural versus physiological photoprotection in epipelic and epipsammic benthic diatoms, Eur. J. Phycol, vol.53, pp.146-155, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02326567

C. Brunet, R. Chandrasekaran, L. Barra, V. Giovagnetti, F. Corato et al., Spectral radiation dependent photoprotective mechanism in the diatom Pseudo-nitzschia multistriata, PLoS One, vol.9, p.87015, 2014.

P. Cartaxana, S. Cruz, C. Gameiro, and M. Kühl, Regulation of intertidal microphytobenthos photosynthesis over a diel emersion period is strongly affected by diatom migration patterns, Front. Microbiol, vol.7, p.872, 2016.

P. Cartaxana, M. Ruivo, C. Hubas, I. Davidson, J. Serôdio et al., Physiological versus behavioral photoprotection in intertidal epipelic and epipsammic benthic diatom communities, J. Exp. Mar. Biol. Ecol, vol.405, pp.120-127, 2011.

P. Cartaxana and J. Serôdio, Inhibiting diatom motility: A new tool for the study of the photophysiology of intertidal microphytobenthic biofilms, Limnol. Oceanogr. Methods, vol.6, pp.466-476, 2008.

E. Chevalier, F. Gévaert, and A. Créach, In situ photosynthetic activity and xanthophylls cycle development of undisturbed microphytobenthos in an intertidal mudflat, J. Exp. Mar. Biol. Ecol, vol.385, pp.44-49, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00482903

L. A. Clementson and B. Wojtasiewicz, Dataset on the absorption characteristics of extracted phytoplankton pigments, Data Brief, vol.24, p.103875, 2019.

H. Coelho, S. Vieira, and J. Serôdio, Endogenous versus environmental control of vertical migration by intertidal benthic microalgae, Eur. J. Phycol, vol.46, pp.271-281, 2011.

S. A. Cohn, Chapter 13 Photo-stimulated effects on diatom motility, Compr. Ser. Photosci, vol.1, pp.375-401, 2001.

S. A. Cohn, D. Halpin, N. Hawley, A. Ismail, Z. Kaplan et al., Comparative analysis of light-stimulated motility responses in three diatom species, Diatom Res, vol.30, pp.213-225, 2015.

S. A. Cohn, T. P. Spurck, and J. D. Pickett-heaps, High energy irradiation at the leading tip of moving diatoms causes a rapid change of cell direction, Diatom Res, vol.14, pp.193-206, 1999.

M. Consalvey, The Structure and Function of Microphytobenthic Biofilms, 2002.

M. Consalvey, B. Jesus, R. G. Perkins, V. Brotas, G. J. Underwood et al., Monitoring migration and measuring biomass in benthic biofilms: the effects of dark/far-red adaptation and vertical migration on fluorescence measurements, Photosyn. Res, vol.81, pp.91-101, 2004.

M. Consalvey, D. M. Paterson, and G. J. Underwood, The ups and down of life in a benthic biofilm: migration of benthic diatoms, Diatom Res, vol.19, pp.181-202, 2004.

S. Cruz and J. Serôdio, Relationship of rapid light curves of variable fluorescence to photoacclimation and non-photochemical quenching in a benthic diatom, Aquat. Bot, vol.88, pp.256-264, 2008.

D. Brouwer, J. F. Stal, and L. J. , Daily fluctuations of exopolymers in cultures of the benthic diatoms Cylindrotheca closterium and Nitzschia sp. (Bacillariophyceae), J. Phycol, vol.38, pp.464-472, 2002.

F. A. Depauw, A. Rogato, M. R. D'alcalá, and A. Falciatore, Exploring the molecular basis of responses to light in marine diatoms, J. Exp. Bot, vol.63, pp.1575-1591, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01528432

N. A. Dijkman and B. M. Kroon, Indications for chlororespiration in relation to light regime in the marine diatom Thalassiosira weissflogii, J. Photochem. Photobiol. B Biol, vol.66, pp.179-187, 2002.

G. Du, H. Yan, C. Liu, M. , and Y. , Behavioral and physiological photoresponses to light intensity by intertidal microphytobenthos, J. Oceanol. Limnol, vol.36, pp.293-304, 2018.

G. Y. Du, J. H. Oak, H. Li, C. , and I. K. , Effect of light and sediment grain size on the vertical migration of benthic diatoms, Algae, vol.25, pp.133-140, 2010.

M. Dubois, K. A. Gilles, J. K. Hamilton, P. A. Rebers, and F. Smith, Colorimetric method for determination of sugars and related substances, Anal. Chem, vol.28, pp.350-356, 1956.

J. W. Eaton and B. Moss, The estimation of numbers and pigment content in epipelic algal populations, Limnol. Oceanogr, vol.11, pp.584-595, 1966.

P. H. Eilers and J. C. Peeters, A model for the relationship between light intensity and the rate of photosynthesis in phytoplankton, Ecol. Model, vol.42, pp.199-215, 1988.

J. Ezequiel, M. Laviale, S. Frankenbach, P. Cartaxana, and J. Serôdio, Photoacclimation state determines the photobehaviour of motile microalgae: the case of a benthic diatom, J. Exp. Mar. Biol. Ecol, vol.468, pp.11-20, 2015.

S. Frankenbach, C. Pais, M. Martinez, M. Laviale, J. Ezequiel et al., Evidence for gravitactic behaviour in benthic diatoms, Eur. J. Phycol, vol.49, pp.429-435, 2014.

B. Frølund, R. Palmgren, K. Keiding, and P. H. Nielsen, Extraction of extracellular polymers from activated sludge using a cation exchange resin, Water Res, vol.30, pp.1749-1758, 1996.

T. Fujiki and S. Taguchi, Relationship between light absorption and the xanthophyll-cycle pigments in marine diatoms, Plankton Biol. Ecol, vol.48, pp.96-103, 2001.

T. Furukawa, M. Watanabe, and I. Shihira-ishikawa, Green-and bluelight-mediated chloroplast migration in the centric diatom Pleurosira laevis, Protoplasma, vol.203, pp.214-220, 1998.

M. Gilbert, A. Domin, A. Becker, W. , and C. , Estimation of primary productivity by chlorophyll a in vivo fluorescence in freshwater phytoplankton, Photosynthetica, vol.38, pp.111-126, 2000.

J. W. Goessling, S. Frankenbach, L. Ribeiro, J. Serôdio, and M. Kühl, Modulation of the light field related to valve optical properties of raphid diatoms: implications for niche differentiation in the microphytobenthos, Mar. Ecol. Prog. Ser, vol.588, pp.29-42, 2018.

D. Häder, Signal perception and amplification in photomovement of prokaryotes, Biochim. Biophys. Acta, vol.864, pp.107-122, 1986.

S. I. Hay, T. C. Maitland, and D. M. Paterson, The speed of diatom migration through natural and artificial substrata, Diatom Res, vol.8, pp.371-384, 1993.

K. Haynes, T. A. Hofmann, C. J. Smith, A. S. Ball, G. J. Underwood et al., Diatom-derived carbohydrates as factors affecting bacterial community composition in estuarine sediments, Appl. Environ. Microbiol, vol.73, pp.6112-6124, 2007.

T. Hernández-fariñas, L. Ribeiro, D. Soudant, C. Belin, C. Bacher et al., Contribution of benthic microalgae to the temporal variation in phytoplankton assemblages in a macrotidal system, J. Phycol, vol.53, pp.1020-1034, 2017.

L. V. Heukelem and C. S. Thomas, Computer-assisted high-performance liquid chromatography method development with applications to the isolation and analysis of phytoplankton pigments, J. Chromatogr. A, vol.910, pp.31-49, 2001.

H. Hillebrand, C. Dürselen, D. Kirschtel, U. Pollingher, and T. Zohary, Biovolume calculation for pelagic and benthic microalgae, J. Phycol, vol.35, pp.403-424, 1999.

T. Jakob, R. Goss, W. , and C. , Activation of diadinoxanthin deepoxidase due to a chlororespiratory proton gradient in the dark in the diatom Phaeodactylum tricornutum, Plant Biol, vol.1, pp.76-82, 1999.

T. Jauffrais, S. Drouet, V. Turpin, V. Méléder, B. Jesus et al., Growth and biochemical composition of a microphytobenthic diatom (Entomoneis paludosa) exposed to shorebird (Calidris alpina) droppings, J. Exp. Mar. Biol. Ecol, vol.469, pp.83-92, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02490709

B. Jesus, V. Brotas, L. Ribeiro, C. R. Mendes, P. Cartaxana et al., Adaptations of microphytobenthos assemblages to sediment type and tidal position, Cont. Shelf Res, vol.29, pp.1624-1634, 2009.

B. Jesus, R. G. Perkins, M. Consalvey, V. Brotas, and D. M. Paterson, Effects of vertical migrations by benthic microalgae on fluorescence measurements of photophysiology, Mar. Ecol. Prog. Ser, vol.315, pp.55-66, 2006.

A. Jungandreas, B. S. Costa, T. Jakob, M. Von-bergen, S. Baumann et al., The acclimation of Phaeodactylum tricornutum to blue and red light does not influence the photosynthetic light reaction but strongly disturbs the carbon allocation pattern, PLoS One, vol.9, p.99727, 2014.

M. Kühl, C. Lassen, and B. B. Jorgensen, Light penetration and light intensity in sandy marine sediments measured with irradiance and scalar irradiance fiber-optic microprobes, Mar. Ecol. Prog. Ser, vol.105, pp.139-148, 1994.

A. Kume, Importance of the green color, absorption gradient, and spectral absorption of chloroplasts for the radiative energy balance of leaves, J. Plant Res, vol.130, pp.501-514, 2018.

J. Lavaud and R. Goss, The peculiar features of non-photochemical fluorescence quenching in diatoms and brown algae, Non-Photochemical Quenching and Energy Dissipation in Plants, Algae and Cyanobacteria, pp.421-443, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01096599

J. Lavaud, B. Rousseau, E. , and A. L. , General features of photoprotection by energy dissipation in planktonic diatoms (Bacillariophyceae), J. Phycol, vol.40, pp.130-137, 2004.
URL : https://hal.archives-ouvertes.fr/hal-01094173

M. Laviale, A. Barnett, J. Ezequiel, B. Lepetit, S. Frankenbach et al., Response of intertidal benthic microalgal biofilms to a coupled lighttemperature stress: evidence for latitudinal adaptation along the Atlantic coast of Southern Europe, Environ. Microbiol, vol.17, pp.3662-3677, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01097838

M. Laviale, S. Frankenbach, and J. Serôdio, The importance of being fast: comparative kinetics of vertical migration and non-photochemical quenching of benthic diatoms under light stress, Mar. Biol, vol.163, p.10, 2016.

H. L. Macintyre, R. J. Geider, and D. C. Miller, Microphytobenthos: the ecological role of the "Secret Garden" of unvegetated, shallow-water marine habitats. I. Distribution, abundance and primary production, Estuaries, vol.19, pp.186-201, 1996.

D. H. Mclachlan, C. Brownlee, A. R. Taylor, R. J. Geider, and G. J. Underwood, Light-induced motile responses of the estuarine benthic diatoms Navicula perminuta and Cylindrotheca closterium (bacillariophyceae), J. Phycol, vol.45, pp.592-599, 2009.

V. Méléder, Y. Rincé, L. Barillé, P. Gaudin, R. et al., Spatiotemporal changes in microphytobenthos assemblages in a macrotidal flat, J. Phycol, vol.43, pp.1177-1190, 2007.

A. Mertens, A. Witkowski, H. Lange-bertalot, L. Ribeiro, and E. Rhiel, Navicula meulemansii sp. nov., (Bacillariophyaceae) from brackish waters in Europe and the U.S.A, Nova Hedwigia, vol.98, pp.201-212, 2014.

S. Mitbavkar and A. C. Anil, Vertical migratory rhythms of benthic diatoms in a tropical intertidal sand flat: Influence of irradiance and tides, Mar. Biol, vol.145, pp.9-20, 2004.

J. L. Mouget, P. Rosa, and G. Tremblin, Acclimation of Haslea ostrearia to light of different spectral qualities -Confirmation of 'chromatic adaptation' in diatoms, J. Photochem. Photobiol. B Biol, vol.75, pp.1-11, 2004.

J. Noyes, M. Sumper, and P. Vukusic, Light manipulation in a marine diatom, J. Mater. Res, vol.23, pp.3229-3235, 2008.

W. Nultsch, Phototactic and photokinetic action spectra of the diatom Nitschia communis, Photochem. Photobiol, vol.14, pp.705-712, 1971.

M. Olaizola and H. Y. Yamamoto, Short-term response of the diadinoxanthin cycle and fluorescence yield to high irradiance in Chaetoceros muelleri (Bacillariophyceae), J. Phycol, vol.30, pp.606-612, 1994.

I. Olenina, S. Hajdu, L. Edler, A. Andersson, N. Wasmund et al., Biovolumes and size-classes of phytoplankton in the Baltic Sea HELCOM Balt.Sea Environ, Proc. No. 106. Available online at, 2006.

F. Orvain, R. Galois, C. Barnard, A. Sylvestre, G. Blanchard et al., Carbohydrate production in relation to microphytobenthic biofilm development: an integrated approach in a tidal mesocosm, Microb. Ecol, vol.45, pp.237-251, 2003.

D. Paterson, Short-term changes in the erodibility of intertidal cohesive sediments related to the migratory behaviour of epipelic diatoms, Limnol. Oceanogr, vol.34, pp.223-234, 1989.

D. M. Paterson, The migratory behaviour of diatom assemblages in a laboratory tidal scanning electron microscopy micro-ecosystem examined by low temperature, Diatom Res, vol.1, pp.227-239, 1986.

D. M. Paterson, R. Perkins, M. Consalvey, and G. J. Underwood, Ecosystem function, cell micro-cycling and the structure of transient biofilms, Fossil and Recent Biofilms, pp.47-63, 2003.

G. Paulmier, Atlas des Diatomophycées des Côtes Françaises et des Aires Marines Adjacentes, 1997.

R. Perkins, G. Underwood, V. Brotas, G. Snow, B. Jesus et al., Responses of microphytobenthos to light: primary production and carbohydrate allocation over an emersion period, Mar. Ecol. Prog. Ser, vol.223, pp.101-112, 2001.

R. G. Perkins, J. Lavaud, J. Serôdio, J. L. Mouget, P. Cartaxana et al., Vertical cell movement is a primary response of intertidal benthic biofilms to increasing light dose, Mar. Ecol. Prog. Ser, vol.416, pp.93-103, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01095756

F. F. Pniewski, P. Biskup, I. Bubak, P. Richard, A. Lata?a et al., Photo-regulation in microphytobenthos from intertidal mudflats and non-tidal coastal shallows, Estuar. Coast. Shelf Sci, vol.152, pp.153-161, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01096631

. R-core-team, R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, 2017.

M. Ragni and M. R. Alcalà, Light as an information carrier underwater, J. Plankton Res, vol.26, pp.433-443, 2004.

L. L. Ribeiro, Intertidal Benthic Diatoms of the Tagus Estuary: Taxonomic Composition and Spatial-Temporal Variation, 2010.

F. E. Round, The epipsammon; a relatively unknown freshwater algal association, Br. Phycol. Bull, vol.2, pp.456-462, 1965.

F. E. Round and C. M. Happey, Persistent, vertical-migration rhythms in benthic microflora: Part IV a diurnal rhythm of the epipelic diatom association in non-tidal flowing water, Br. Phycol. Bull, vol.2, pp.463-471, 1965.

B. Schellenberger-costa, A. Jungandreas, T. Jakob, W. Weisheit, M. Mittag et al., Blue light is essential for high light acclimation and photoprotection in the diatom Phaeodactylum tricornutum, J. Exp. Bot, vol.64, pp.483-493, 2013.

B. Schellenberger-costa, M. Sachse, A. Jungandreas, C. R. Bartulos, A. Gruber et al., Aureochrome 1a is involved in the photoacclimation of the diatom Phaeodactylum tricornutum, PLoS One, vol.8, p.74451, 2013.

U. Schreiber, C. Klughammer, and J. Kolbowski, Assessment of wavelength-dependent parameters of photosynthetic electron transport with a new type of multi-color PAM chlorophyll fluorometer, Photosyn. Res, vol.113, pp.127-144, 2012.

J. Serôdio, S. Cruz, S. Vieira, and V. Brotas, Non-photochemical quenching of chlorophyll fluorescence and operation of the xanthophyll cycle in estuarine microphytobenthos, J. Exp. Mar. Biol. Ecol, vol.326, pp.157-169, 2005.

J. Serôdio, J. M. Da-silva, and F. Catarino, Nondestructive tracing of migratory rhythms of intertidal benthic microalgae using in vivo chlorophyll a fluorescence, J. Phycol, vol.33, pp.542-553, 1997.

J. Serôdio, J. Ezequiel, A. Barnett, J. L. Mouget, V. Meåéder et al., Efficiency of photoprotection in microphytobenthos: role of vertical migration and the xanthophyll cycle against photoinhibition, Aquat. Microb. Ecol, vol.67, pp.161-175, 2012.

J. Serôdio, S. Vieira, C. , and S. , Photosynthetic activity, photoprotection and photoinhibition in intertidal microphytobenthos as studied in situ using variable chlorophyll fluorescence, Cont. Shelf Res, vol.28, pp.1363-1375, 2008.

I. Shihira-ishikawa, T. Nakamura, S. I. Higashi, and M. Watanabe, Distinct responses of chloroplasts to blue and green laser microbeam irradiations in the centric diatom Pleurosira laevis, Photochem. Photobiol, vol.83, pp.1101-1109, 2007.

G. M. Silsbe and J. C. Kromkamp, Modeling the irradiance dependency of the quantum efficiency of photosynthesis, Limnol. Oceanogr. Methods, vol.10, pp.645-652, 2012.

D. J. Smith and G. J. Underwood, The production of extracellular carbohydrates by estuarine benthic diatoms: the effects of growth phase and light and dark treatment, J. Phycol, vol.36, pp.321-333, 2000.

D. J. Smith and G. J. Underwood, Exopolymer production by intertidal epipelic diatoms, Limnol. Oceanogr, vol.43, pp.1578-1591, 1998.

M. Spitschan, G. K. Aguirre, D. H. Brainard, and A. M. Sweeney, Variation of outdoor illumination as a function of solar elevation and light pollution, Sci. Rep, vol.6, p.26756, 2016.

N. Staats, L. J. Stal, and L. R. Mur, Exopolysaccharide production by the epipelic diatom Cylindrotheca closterium: effects of nutrient conditions, J. Exp. Mar. Biol. Ecol, vol.249, pp.13-27, 2000.

Y. Su, N. Lundholm, S. M. Friis, and M. Ellegaard, Implications for photonic applications of diatom growth and frustule nanostructure changes in response to different light wavelengths, Nano Res, vol.8, pp.2363-2372, 2015.

E. Takahashi, J. Ledauphin, D. Goux, and F. Orvain, Optimising extraction of extracellular polymeric substances (EPS) from benthic diatoms: comparison of the efficiency of six EPS extraction methods, Mar. Freshw. Res, vol.60, pp.1201-1210, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02472061

J. D. Taylor, B. A. Mckew, A. Kuhl, T. J. Mcgenity, and G. J. Underwood, Microphytobenthic extracellular polymeric substances (EPS) in intertidal sediments fuel both generalist specialist EPS-degrading bacteria, Limnol. Oceanogr, vol.58, pp.1463-1480, 2013.

C. S. Ting and T. G. Owens, Photochemical and nonphotochemical fluorescence quenching processes in the diatom Phaeodactylum tricornutum, Plant Physiol, vol.101, pp.1323-1330, 1993.

G. J. Underwood, M. Boulcott, C. A. Raines, and K. Waldron, Environmental effects on exopolymer production by marine benthic diatoms: dynamics, changes in composition, and pathways of production, J. Phycol, vol.40, pp.293-304, 2004.

G. J. Underwood and J. Kromkamp, Primary production by phytoplankton and microphytobenthos in estuaries, Adv. Ecol. Res, vol.29, pp.93-153, 1999.

G. J. Underwood, D. M. Paterson, and R. J. Parkes, The measurement of microbial carbohydrate exopolymers from intertidal sediments, Limnol. Oceanogr, vol.40, pp.1243-1253, 1995.

G. J. Underwood, R. G. Perkins, M. C. Consalvey, A. R. Hanlon, K. Oxborough et al., Patterns in microphytobenthic primary productivity : species-specific variation in migratory rhythms and photosynthetic efficiency in mixed-species biofilms, Limnol. Oceanogr, vol.50, pp.755-767, 2005.

E. Walpersdorf, M. Kühl, B. Elberling, T. Andersen, B. Hansen et al., situ oxygen dynamics and carbon turnover in an intertidal sediment, vol.566, pp.49-65, 2017.

K. Wenderoth and E. Rhiel, Influence of light quality and gassing on the vertical migration of diatoms inhabiting the Wadden Sea, Helgoland Mar. Res, vol.58, pp.211-215, 2004.

C. Wilhelm, A. Jungandreas, T. Jakob, and R. Goss, Light acclimation in diatoms: from phenomenology to mechanisms, Mar. Genomics, vol.16, pp.5-15, 2014.

M. L. Yallop, B. Winder, . De, D. M. Paterson, and L. J. Stal, Comparative structure, primary production and biogenic stabilization of cohesive and noncohesive marine sediments inhabited by microphytobenthos, Estuar. Coast. Shelf Sci, vol.39, pp.565-582, 1994.

S. Yamanaka, R. Yano, H. Usami, N. Hayashida, M. Ohguchi et al., Optical properties of diatom silica frustule with special reference to blue light, J. Appl. Phys, vol.103, p.74701, 2008.