A. A. Aleem, THE DIATOM COMMUNITY INHABITING THE MUD-FLATS AT WHITSTABLE, New Phytologist, vol.24, issue.2, pp.174-188, 1950.
DOI : 10.1080/00378941.1877.10830022

W. Admiraal and H. Peletier, Distribution of diatom species on an estuarine mud flat and experimental analysis of the selective effect of stress, Journal of Experimental Marine Biology and Ecology, vol.46, issue.2, pp.157-175, 1980.
DOI : 10.1016/0022-0981(80)90029-5

M. Agatz, R. M. Asmus, and B. Deventer, Structural changes in the benthic diatom community along a eutrophication gradient on a tidal flat, Helgoland Marine Research, vol.53, issue.2, pp.92-101, 1999.
DOI : 10.1007/PL00012144

A. Aminot and R. Kérouel, Dosage automatique des nutriments dans les eaux marines: méthodes en flux continu, 2007.

C. Barranguet, &. J. Kromkamp, and J. Peene, Factors controlling primary production and photosynthetic characteristics of intertidal microphytobenthos, Marine Ecology Progress Series, vol.173, pp.117-126, 1998.
DOI : 10.3354/meps173117
URL : http://www.int-res.com/articles/meps/173/m173p117.pdf

G. F. Blanchard, J. Guarini, M. Orvain, F. Sauriau, and P. G. , Dynamic behaviour of benthic microalgal biomass in intertidal mudflats, Journal of Experimental Marine Biology and Ecology, vol.264, issue.1, pp.85-100, 2001.
DOI : 10.1016/S0022-0981(01)00312-4

V. Brotas, T. Cabrita, A. Portugal, J. Serôdio, and F. Catarino, Spatio-temporal distribution of microphytobenthic biomass in intertidal flats of Tagus estuary, Hydrobiologia, vol.301, pp.300-93, 1995.

J. F. De-brouwer, S. Bjelic, E. M. De-deckere, and L. J. Stal, Interplay between biology and sedimentology in a mudflat (Biezelingse Ham, Westerschelde, The Netherlands), Continental Shelf Research, vol.20, issue.10-11, pp.1159-1177, 2000.
DOI : 10.1016/S0278-4343(00)00017-0

L. B. Cahoon, J. E. Nearhoof, and C. L. Tilton, Sediment Grain Size Effect on Benthic Microalgal Biomass in Shallow Aquatic Ecosystems, Estuaries, vol.22, issue.3, pp.735-741, 1999.
DOI : 10.2307/1353106

X. Chen, W. Zhou, S. T. Pickett, W. Li, L. Han et al., Diatoms are better indicators of urban stream conditions: A case study in Beijing, China, Ecological Indicators, vol.60, pp.265-274, 2016.
DOI : 10.1016/j.ecolind.2015.06.039

M. Christie, K. Dyer, G. Blanchard, A. Cramp, H. Mitchener et al., Temporal and spatial distributions of moisture and organic contents across a macro-tidal mudflat, Continental Shelf Research, vol.20, issue.10-11, pp.1219-1241, 2000.
DOI : 10.1016/S0278-4343(00)00020-0

T. Cibic, O. Blasutto, C. Falconi, and S. F. Umani, Microphytobenthic biomass, species composition and nutrient availability in sublittoral sediments of the Gulf of Trieste (northern Adriatic Sea), Estuarine, Coastal and Shelf Science, vol.75, issue.1-2, pp.50-62, 2007.
DOI : 10.1016/j.ecss.2007.01.020

K. R. Clarke and M. Ainsworth, A method of linking multivariate community structure to environmental variables, Marine Ecology Progress Series, vol.92, pp.205-219, 1993.
DOI : 10.3354/meps092205

J. Cochero, M. Licursi, and N. Gómez, Changes in the epipelic diatom assemblage in nutrient rich streams due to the variations of simultaneous stressors, Limnologica - Ecology and Management of Inland Waters, vol.51, issue.63, pp.15-231793, 2015.
DOI : 10.1016/j.limno.2014.10.004

L. L. Guo, Z. H. Sui, and Y. Liu, Quantitative analysis of dinoflagellates and diatoms community via Miseq sequencing of actin gene and v9 region of 18S rDNA, Scientific Reports, vol.8, issue.1, p.34709, 2016.
DOI : 10.1038/ismej.2013.253

C. J. Lorenzen, DETERMINATION OF CHLOROPHYLL AND PHEO-PIGMENTS: SPECTROPHOTOMETRIC EQUATIONS1, Limnology and Oceanography, vol.12, issue.2, pp.343-346, 1967.
DOI : 10.4319/lo.1967.12.2.0343

M. Lundkvist, M. Grue, P. L. Firend, and M. R. Flindt, The relative contributions of physical and microbiological factors to cohesive sediment stability, Continental Shelf Research, vol.27, issue.8, pp.1143-1152, 2007.
DOI : 10.1016/j.csr.2006.01.021

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, issue.2, pp.186-201, 1996.
DOI : 10.2307/1352224

S. Masmoudi, N. Nguyen-deroche, A. Caruso, H. Ayadi, A. Morant-manceau et al., Cadmium, Copper, Sodium and Zinc Effects on Diatoms: from Heaven to Hell ??? a Review, Cryptogamie, Algologie, vol.34, issue.2, 2013.
DOI : 10.7872/crya.v34.iss2.2013.185

D. C. Miller, R. J. Geider, and H. L. Macintyre, Microphytobenthos: The Ecological Role of the "Secret Garden" of Unvegetated, Shallow-Water Marine Habitats. II. Role in Sediment Stability and Shallow-Water Food Webs, Estuaries, vol.19, issue.2, pp.202-212, 1996.
DOI : 10.2307/1352225

S. Mitbavkar and A. C. Anil, Diatoms of the microphytobenthic community: population structure in a tropical intertidal sand flat, Marine Biology, vol.140, pp.41-57, 2002.

S. Mitbavkar and A. C. Anil, Diatoms of the microphytobenthic community in a tropical intertidal sand flat influenced by monsoons: spatial and temporal variations, Marine Biology, vol.36, issue.4, pp.693-709, 2006.
DOI : 10.1080/0269249X.1994.9705319

M. B. Moniz and I. Kaczmarska, Barcoding of Diatoms: Nuclear Encoded ITS Revisited, Protist, vol.161, issue.1, pp.7-34, 2010.
DOI : 10.1016/j.protis.2009.07.001

E. R. Nodine and E. E. Gaiser, Distribution of Diatoms Along Environmental Gradients in the Charlotte Harbor, Florida (USA), Estuary and Its Watershed: Implications for Bioassessment of Salinity and Nutrient Concentrations, Estuaries and Coasts, vol.84, issue.4, pp.864-879, 2014.
DOI : 10.1016/j.ecss.2009.06.026

S. H. Oh and C. H. Koh, Distribution of diatoms in the surficial sediments of the Mangyung-Dongjin tidal flat, west coast of Korea (Eastern Yellow Sea), Marine Biology, vol.21, issue.3, pp.487-496, 1995.
DOI : 10.1007/BF00350883

D. R. Oppenheim, The Distribution of Epipelic Diatoms along an Intertidal Shore in Relation to Principal Physical Gradients, Botanica Marina, vol.23, issue.1, pp.65-72, 1988.
DOI : 10.1111/j.1529-8817.1982.tb03166.x

D. M. Paterson, Short-term changes in the erodibility of intertidal cohesive sediments related to the migratory behavior of epipelic diatoms, Limnology and Oceanography, vol.34, issue.1, pp.223-234, 1989.
DOI : 10.4319/lo.1989.34.1.0223

M. Potapova and D. F. Charles, Diatom metrics for monitoring eutrophication in rivers of the United States, Ecological Indicators, vol.7, issue.1, pp.48-70, 2007.
DOI : 10.1016/j.ecolind.2005.10.001

M. V. Propp, V. G. Tarasoff, I. I. Cherbadgi, and N. V. Lootzik, Benthic-pelagic oxygen and nutrient exchange in a coastal region of the Sea of Japan, pp.265-284, 1980.

L. Ribeiro, Intertidal benthic diatoms of the Tagus estuary: taxonomic composition and spatial-temperal variation (Thesis), 2010.

F. E. Round, A diatom assemblage living below the surface of intertidal sand flats, Marine Biology, vol.1, issue.3, pp.219-223, 1979.
DOI : 10.1007/BF00395784

F. E. Round, R. M. Crawford, and D. G. Mann, The Diatoms, 1990.

S. Rysgaard, P. B. Christensen, and L. P. Nielsen, Seasonal variation in nitrification and denitrification in estuarine sediment colonized by benthic microalgae and bioturbating infauna, Marine Ecology Progress Series, vol.126, pp.111-121, 1995.
DOI : 10.3354/meps126111
URL : http://www.int-res.com/articles/meps/126/m126p111.pdf

K. Sabbe, Short-term fluctuations in benthic diatom numbers on an intertidal sandflat in the Westeschelde estuary (Zeeland, the Netherlands), Hydrobiologia, pp.269-270, 1993.

J. Seeberg-elverfeldt, M. Schlüter, T. Feseker, and M. Kölling, Rhizon sampling of porewaters near the sediment-water interface of aquatic systems, Limnology and Oceanography: Methods, vol.3, issue.8, pp.361-371, 2005.
DOI : 10.4319/lom.2005.3.361

J. Serôdio and F. Catarino, Fortnightly light and temperature variability in estuarine intertidal sediments and implications for microphytobenthos primary productivity, Aquatic Ecology, vol.33, issue.3, pp.235-241, 1999.
DOI : 10.1023/A:1009989229098

J. Serôdio and F. Catarino, Modelling the primary productivity of intertidal microphytobenthos:time scales of variability and effects of migratory rhythms, Marine Ecology Progress Series, vol.192, pp.13-30, 2000.
DOI : 10.3354/meps192013

T. Skinner, J. B. Adams, and P. T. Gama, The effect of mouth opening on the biomass and community structure of microphytobenthos in a small oligotrophic estuary, Estuarine, Coastal and Shelf Science, vol.70, issue.1-2, pp.161-168, 2006.
DOI : 10.1016/j.ecss.2006.04.007

J. P. Smol and E. F. Stoermer, The Diatoms: Applications for the environmental and earth sciences, 2010.
DOI : 10.1017/CBO9780511763175

A. G. Solimini, A. Cardoso, and A. S. Heiskanen, Indicators and methods for the ecological status assessment under the Water Framework Directive, 2006.

N. Spilmont, D. Davoult, and A. Migné, Benthic primary production during emersion: In situ measurements and potential primary production in the Seine Estuary (English Channel, France), Marine Pollution Bulletin, vol.53, issue.1-4, pp.49-55, 2003.
DOI : 10.1016/j.marpolbul.2005.09.016
URL : https://hal.archives-ouvertes.fr/hal-00104531

R. J. Stevenson, Y. Pan, K. M. Manoylov, C. A. Parker, D. P. Larsen et al., Development of diatom indicators of ecological conditions for streams of the western US, Journal of the North American Benthological Society, vol.27, issue.4, pp.1000-1016, 2008.
DOI : 10.1899/08-040.1.s1

R. J. Stevenson, Y. Pan, and H. Van-dam, Assessing environmental conditions in rivers and streams with diatoms, The Diatoms: Applications for the Environmental and Earth Sciences, pp.57-85, 2010.
DOI : 10.1017/cbo9780511613005.003

J. C. Taylor, P. A. De-la-rey, and L. Van-rensburg, Recommendations for the collection, preparation and enumeration of diatoms from riverine habitats for water quality monitoring in South Africa, African Journal of Aquatic Science, vol.30, issue.1, pp.65-75, 2005.
DOI : 10.2989/16085910509503836

T. Braak, C. J. &?milauer, and P. , CANOCO Reference Manual and CanoDraw for WindowsUser's Guide: Software for Canonical Community Ordination (version 4.5), 2002.

D. C. Thornton, L. F. Dong, G. J. Underwood, and D. B. Nedwell, Factors affecting microphytobenthic biomass, species composition and production in the Colne Estuary (UK), Aquatic Microbial Ecology, vol.27, pp.285-300, 2002.
DOI : 10.3354/ame027285

C. R. Tomas, Identifying Marine Diatoms and Dinoflagellates, 1996.

R. Trobajo, D. G. Mann, E. Clavero, K. M. Evans, P. Vanormelingen et al., species complex (Bacillariophyceae), European Journal of Phycology, vol.360, issue.4, pp.413-425, 2010.
DOI : 10.1080/09670260600942635

B. E. Rott, E. Pipp, and P. Pfister, Diatom methods developed for river quality assessment in Austria and a cross-check against numerical trophic indication methods used in Europe, Algological Studies, vol.110, issue.1, pp.91-115, 2003.
DOI : 10.1127/1864-1318/2003/0110-0091

G. J. Underwood, SEASONAL AND SPATIAL VARIATION IN EPIPELIC DIATOM ASSEMBLAGES IN THE SEVERN ESTUARY, Diatom Research, vol.45, issue.2, pp.451-472, 1994.
DOI : 10.2307/1934940

G. J. Underwood, Microphytobenthos and phytoplankton in the Severn estuary, UK: Present situation and possible consequences of a tidal energy barrage, Marine Pollution Bulletin, vol.61, issue.1-3, pp.83-91, 2010.
DOI : 10.1016/j.marpolbul.2009.12.015

G. J. Underwood and J. Kromkamp, Primary Production by Phytoplankton and Microphytobenthos in Estuaries, Advances in Ecological Research, vol.29, pp.93-153, 1999.
DOI : 10.1016/S0065-2504(08)60192-0

G. J. Underwood, J. Philips, and K. Saunders, Distribution of estuarine benthic diatom species along salinity and nutrient gradients, European Journal of Phycology, vol.33, issue.2, pp.173-183, 1998.
DOI : 10.1080/09670269810001736673
URL : http://www.tandfonline.com/doi/pdf/10.1080/09670269810001736673?needAccess=true

A. Vilmi, S. M. Karjalainenc, S. Hellstenc, and J. Heinoa, Bioassessment in a metacommunity context: Are diatom communities structured solely by species sorting? Ecological Indicators, pp.86-94, 2016.

C. Welker, E. Sdrigotti, S. Covelli, and J. Faganeli, Microphytobenthos in the Gulf of Trieste (Northern Adriatic Sea): Relationship with Labile Sedimentary Organic Matter and Nutrients, Estuarine, Coastal and Shelf Science, vol.55, issue.2, 2002.
DOI : 10.1006/ecss.2001.0901