A. , Association French Normalization Organization Regulation (AFNOR), 1990.

O. Anneville and C. Leboulanger, Long-term changes in the vertical distribution of phytoplankton in the deep Alpine Lake Geneva : a response to the reoligotrophication, Atti Associazione italiana di oceanologia e limnologia, vol.14, pp.25-35, 2001.

G. B. Arhonditsis and M. T. Brett, Evaluation of the current state of mechanistic aquatic biogeochemical modeling, Marine Ecology Progress Series, vol.271, pp.13-26, 2004.

J. H. Bigelow, J. G. Bolten, D. Haven, and J. C. , Protecting an estuary from floods-A policy analysis of the Oosterschelde, 1977.

J. Blanquet, F. Botta, R. Champion, C. Ferret, N. Guigues et al., Impact des opérations de prélèvements sur la variabilité des résultats d'analyses, 2010.

S. A. Bocaniov, C. Ullmann, K. Rinke, K. G. Lamb, and B. Boehrer, Internal waves and mixing in a stratified reservoir : Insights from three-dimensional modeling, Limnologica-Ecology and Management of Inland Waters, vol.49, issue.0, pp.52-67, 2014.

B. Boehrer, P. Herzsprung, M. Schultze, and F. J. Millero, Calculating density of water in geochemical lake stratification models, Limnology and Oceanography : Methods, vol.8, pp.567-574, 2010.

B. Boehrer and M. Schultze, Stratification of lakes, Reviews of Geophysics, vol.46, issue.2, 2008.

E. Bradley, F. Coppin, P. A. , G. , and J. S. , Measurements of sensible and latent heat-flux in the western equatorial pacific-ocean, Journal of Geophysical Research-Oceans, vol.96, issue.S, pp.3375-3389, 1991.

M. Bresciani, D. Stroppiana, D. Odermatt, G. Morabito, G. et al., Assessing remotely sensed chlorophyll-a for the implementation of the Water Framework Directive in European perialpine lakes, Science of the Total Environment, vol.409, issue.17, pp.3083-3091, 2011.

H. Burchard and H. Baumert, On the performance of a mixed-layer model-based on the kappa-epsilon turbulence closure, Journal of Geophysical Research-Oceans, vol.100, issue.C5, pp.8523-8540, 1995.

J. Capblancq, Production primaire autotrophe, Limnologie générale, pp.228-252, 1995.

C. C. Carey, B. W. Ibelings, E. P. Hoffmann, D. P. Hamilton, and J. D. Brookes, Eco-physiological adaptations that favour freshwater cyanobacteria in a changing climate, Water Research, vol.46, issue.5, pp.1394-1407, 2012.

A. Catherine, M. Troussellier, B. , and C. , Design and application of a stratified sampling strategy to study the regional distribution of cyanobacteria, Water Research, vol.42, pp.4989-5000, 2008.

V. Chanudet, V. Fabre, and T. Van-der-kaaij, Application of a three-dimensional hydrodynamic model to the Nam Theun 2 Reservoir (Lao PDR), Journal of Great Lakes Research, vol.38, issue.2, pp.260-269, 2012.

P. Chassaing, Mécanique des fluides-éléments d'un premier parcours-2ème édition, 2000.

Y. W. Chen, C. X. Fan, K. Teubner, and M. Dokulil, Changes of nutrients and phytoplankton chlorophyll-alpha in a large shallow lake, Taihu, China : an 8-year investigation, Hydrobiologia, vol.506, issue.1-3, pp.273-279, 2003.

, Rapports sur les études et recherches entreprises dans le bassin lémanique, CIPEL, 2017.

, Report on the studies and research undertaken in the basin of lake geneva, CIPEL, 2017.

C. , The international thermodynamic equation of seawater-2010 : Calculation and use of thermodynamic properties, 2010.

J. R. Corman, P. B. Mcintyre, B. Kuboja, W. Mbemba, D. Fink et al., Upwelling couples chemical and biological dynamics across the littoral and pelagic zones of Lake Tanganyika, East Africa. Limnology and Oceanography, vol.55, issue.1, pp.214-224, 2010.

M. P. Curtarelli, E. Alcantara, C. D. Renno, A. T. Assireu, M. P. Bonnet et al., Modelling the surface circulation and thermal structure of a tropical reservoir using three-dimensional hydrodynamic lake model and remote-sensing data, Water and Environment Journal, vol.28, issue.4, pp.516-525, 2014.

Y. Cuypers, B. Vincon-leite, A. Groleau, B. Tassin, H. et al., Impact of internal waves on the spatial distribution of Planktothrix rubescens (cyanobacteria) in an alpine lake, ISME Journal, vol.5, issue.4, pp.580-589, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01208054

P. Danis and V. Roubeix, Physico-chimie soutenant la biologie des plans d'eau nationaux : principes et méthodes de définition des valeurs-seuils et amélioration des connaissances par la télédétection, Office, 2014.

J. De-bortoli and C. Argillier, Définition des conditions de référence et des limites des classes d'état sur la base d'une approche pressions/impacts-plans d'eau, paramètre chlorophylle-a, 2008.

. Deltares, D-Water Quality User Manual Version 4, vol.99, 2014.

. Deltares, Delft3D-FLOW User Manual Version, 2014.

. Deltares, Processes Library Description User Manual Version, 2014.

J. Downing, Y. Prairie, J. Cole, C. Duarte, L. Tranvik et al., The global abundance and size distribution of lakes, ponds, and impoundments, Limnology and Oceanography, vol.51, issue.5, pp.2388-2397, 2006.

S. W. Effler, B. A. Wagner, S. M. O'donnell, D. A. Matthews, D. M. O'donnell et al., An upwelling event at Onondaga Lake, NY : characterization, impact and recurrence, Hydrobiologia, vol.511, issue.1, pp.185-199, 2004.
DOI : 10.1023/b:hydr.0000014040.88372.82

H. C. Eilertsen, Spring blooms and stratification, Nature, vol.363, issue.6424, p.24, 1993.

, Directive 2000/60/EC of the European Parliament and of the Council establishing a framework for the Community action in the field of water policy, 2000.

J. Fabian and L. Budinski, Horizontal mixing in the shallow Palic Lake caused by steady and unsteady winds, Environmental Modeling and Assessment, vol.18, issue.4, pp.427-438, 2013.
DOI : 10.1007/s10666-013-9356-4

R. Feistel, TEOS-10 : A New International Oceanographic Standard for Seawater, Ice, Fluid Water, and Humid Air, International Journal of Thermophysics, vol.33, issue.8-9, pp.1335-1351, 2012.
DOI : 10.1007/s10765-010-0901-y

N. Filatov, A. Terzevik, R. Zdorovennov, V. Vlasenko, N. Stashchuk et al., Field studies of non-linear internal waves in lakes on the globe, Nonlinear Internal Waves in Lakes, pp.23-103, 2012.

J. Garnier, Typical and atypical features of phytoplankton in a changeing environment-8 years of reoligotrophication in a recently created sand-pit lake (Créteil lake, Archiv Fur Hydrobiologie, vol.125, issue.4, pp.463-478, 1992.

J. Garnier and D. Benest, Seasonal coupling between phytoplankton and bacterioplankton in a sand pit lake, Hydrobiologia, vol.207, pp.71-77, 1990.
DOI : 10.1007/bf00041442

J. Garnier, A. Chestérikoff, P. Testard, and B. Garban, Oligotrophication after a nutrient reduction in a shallow sand-pit lake (Créteil Lake, Paris suburbs, France) : a case of rapid restoration, Annales de Limnologie, vol.28, pp.253-262, 1992.

G. L. Geernaert, Measurements of the angle between the wing vector and the wind stress vector in the surface-layer over the north-sea, Journal of Geophysical Research-Oceans, vol.93, issue.C7, pp.8215-8220, 1988.

. Giec, Cinquième rapport d'évaluation des changements climatiques, 2014.

A. E. Gill, Atmosphere-Ocean Dynamics (International Geophysics Series, Volume 30), 1982.

A. Girbaciu, C. Girbaciu, E. Petcovici, and A. M. Dodocioiu, Water Quality Modelling Using Mike 11, Revista De Chimie, vol.66, issue.8, pp.1206-1211, 2015.

H. J. Gons, M. T. Auer, and S. W. Effler, MERIS satellite chlorophyll mapping of oligotrophic and eutrophic waters in the Laurentian Great Lakes. Remote Sensing of Environment, vol.112, pp.4098-4106, 2008.

E. Gorham and F. M. Boyce, Influence of lake surface-area and depth upon thermal stratification and the depth of the summer thermocline, Journal of Great Lakes Research, vol.15, issue.2, pp.233-245, 1989.

B. Guillermin, Utilisation de données satellites pour l'étude de l'hétérogénéité spatiale de la chlorophylle-a et de la température sur le Léman, 2015.

G. D. Haffner, M. L. Yallop, P. D. Hebert, and M. Griffiths, Ecological significance of upwelling events in Lake Ontario, Journal of Great Lakes Research, vol.10, issue.1, pp.28-37, 1984.

J. Halder, L. Decrouy, and T. W. Vennemann, Mixing of Rhone River water in Lake Geneva (Switzerland-France) inferred from stable hydrogen and oxygen isotope profiles, Journal of Hydrology, vol.477, pp.152-164, 2013.

C. E. Herdendorf, Large lakes of the world, Journal of Great Lakes Research, vol.8, issue.3, pp.379-412, 1982.

, BIBLIOGRAPHIE 151

D. Hering, A. Borja, J. Carstensen, L. Carvalho, M. Elliott et al., , 2010.

, The European Water Framework Directive at the age of 10 : A critical review of the achievements with recommendations for the future, Science of the Total Environment, vol.408, issue.19, pp.4007-4019

J. Huisman, P. Van-oostveen, and F. J. Weissing, Critical depth and critical turbulence : Two different mechanisms for the development of phytoplankton blooms, Limnology and Oceanography, vol.44, issue.7, pp.1781-1787, 1999.

B. W. Ibelings, L. C. Backer, W. E. Kardinaal, and I. Chorus, Current approaches to cyanotoxin risk assessment and risk management around the globe, Harmful Algae, vol.40, pp.63-74, 2014.

B. W. Ibelings, M. Vonk, H. F. Los, D. T. Van-der-molen, and W. M. Mooij, Fuzzy modeling of cyanobacterial surface waterblooms : Validation with NOAA-AVHRR satellite images, Ecological Applications, vol.13, issue.5, pp.1456-1472, 2003.

. Ipcc, Fifth assessment report, 2014.

S. Jacquet, I. Domaizon, A. , and O. , The need for ecological monitoring of freshwaters in a changing world : a case study of Lakes Annecy, Bourget, and Geneva. Environmental Monitoring and Assessment, vol.186, issue.6, pp.3455-3476, 2014.

S. Jacquet, O. Kerimoglu, F. Rimet, G. Paolini, A. et al., Cyanobacterial bloom termination : the disappearance of Planktothrix rubescens from Lake Bourget (France) after restoration, Freshwater Biology, vol.59, issue.12, pp.2472-2487, 2014.

E. Jeppesen, M. Sondergaard, J. Jensen, K. Havens, O. Anneville et al., Lake responses to reduced nutrient loadingan analysis of contemporary long-term data from 35 case studies, Freshwater Biology, vol.50, issue.10, pp.1747-1771, 2005.

K. R. Jin, J. H. Hamrick, and T. Tisdale, Application of three-dimensional hydrodynamic model for Lake Okeechobee, Journal of Hydraulic Engineering-ASCE, vol.126, issue.10, pp.758-771, 2000.

K. R. Jin, J. , and Z. G. , Application and validation of three-dimensional model in a shallow lake, Journal of Waterway Port Coastal and Ocean Engineering-ASCE, vol.131, issue.5, pp.213-225, 2005.

K. R. Jin, Z. G. Ji, and J. H. Hamrick, Modeling winter circulation in Lake Okeechobee, Florida. Journal of Waterway Port Coastal and Ocean Engineering-ASCE, vol.128, issue.3, pp.114-125, 2002.

S. E. Jorgensen, A review of recent developments in lake modelling, Eclogical Modelling, vol.221, issue.4, pp.689-692, 2010.

M. Kacikoc and M. Beyhan, Hydrodynamic and water quality modeling of Lake Egirdir, Clean-Soil Air Water, vol.42, issue.11, pp.1573-1582, 2014.

C. Kaiblinger, O. Anneville, R. Tadonleke, F. Rimet, J. C. Druart et al., Central European water quality indices applied to long-term data from peri-alpine lakes : test and possible improvements, Hydrobiologia, vol.633, issue.1, pp.67-74, 2009.

T. Kauer, T. Kutser, H. Arst, T. Danckaert, and T. Noges, Modelling primary production in shallow well mixed lakes based on MERIS satellite data, Remote Sensing of Environment, vol.163, pp.253-261, 2015.

B. L. Keeler, S. Polasky, K. A. Brauman, K. A. Johnson, J. C. Finlay et al., Linking water quality and well-being for improved assessment and valuation of ecosystem services, vol.109, pp.18619-18624, 2012.

M. G. Kelly, S. Birk, N. J. Willby, L. Denys, S. Drakare et al., Redundancy in the ecological assessment of lakes : Are phytoplankton, macrophytes and phytobenthos all necessary ?, Science of the Total Environment, vol.568, pp.594-602, 2016.

O. Kerimoglu, S. Jacquet, B. Vincon-leite, B. J. Lemaire, F. Rimet et al., Modelling the plankton groups of the deep, peri-alpine Lake Bourget, Ecological Modelling, vol.359, pp.415-433, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01636520

O. Kerimoglu and K. Rinke, Stratification dynamics in a shallow reservoir under different hydro-meteorological scenarios and operational strategies, Water Resources Research, vol.49, issue.11, pp.7518-7527, 2013.

I. Kiefer, D. Odermatt, O. Anneville, A. Wuest, and D. Bouffard, Application of remote sensing for the optimization of in-situ sampling for monitoring of phytoplankton abundance in a large lake, Science of the Total Environment, vol.527, pp.493-506, 2015.

A. Kolada, H. Ciecierska, J. Ruszczynska, and P. Dynowski, Sampling techniques and inter-surveyor variability as sources of uncertainty in Polish macrophyte metric for lake ecological status assessment, Hydrobiologia, vol.737, issue.1, pp.265-279, 2014.

R. Kopmann and M. Markofsky, Three-dimensional water quality modelling with TELEMAC-3D, Hydrological Processes, vol.14, pp.2279-2292, 2000.

G. Lacroix, P. Boet, J. Garnier, F. Lescher-moutoue, R. Pourriot et al., Factors controlling the phytoplankton community in the shallow lake of Créteil, France. Internationale Revue Der Gesamten Hydrobiologie, vol.74, pp.352-370, 1989.

A. Lane, The heat balance of the North Sea, 1989.

T. H. Leach, B. E. Beisner, C. C. Carey, P. Pernica, K. C. Rose et al., Patterns and drivers of deep chlorophyll maxima structure in 100 lakes : The relative importance of light and thermal stratification. Limnology and Oceanography, 2017.

U. Lemmin, Limnologie physique, Limnologie générale, pp.60-114, 1995.

J. Lenters, The Global Lake Temperature Collaboration (GLTC), pp.9-12, 2015.

L. F. Leon, R. E. Smith, M. R. Hipsey, S. A. Bocaniov, S. N. Higgins et al., Application of a 3D hydrodynamicbiological model for seasonal and spatial dynamics of water quality and phytoplankton in Lake Erie, Journal of Great Lakes Research, vol.37, pp.41-53, 2011.

M. Lesieur, La turbulence, 1994.
URL : https://hal.archives-ouvertes.fr/hal-00261428

Z. Li, Q. Chen, and Q. Xu, Modeling algae dynamics in Meiliang Bay of Taihu Lake and parameter sensitivity analysis, Journal of Hydro-Environment Research, vol.9, issue.2, pp.216-225, 2015.

H. Los, Eco-hydrodynamic modelling of primary production in coastal waters and lakes using BLOOM, 2009.

E. B. Mackay, I. D. Jones, S. J. Thackeray, and A. M. Folkard, Spatial heterogeneity in a small, temperate lake during archetypal weak forcing conditions, Fundamental and Applied Limnology, vol.179, issue.1, pp.27-40, 2011.

W. M. Marsh and M. M. Kaufman, Physical Geography : Great Systems and Global Environments, 2012.

M. P. Mccombs, R. P. Mulligan, and L. Boegman, Offshore wind farm impacts on surface waves and circulation in Eastern Lake Ontario, Coastal Engineering, vol.93, pp.32-39, 2014.

. Medde, Arrêté du 27 juillet 2015 modifiant l'arrêté du 25 janvier 2010 relatif aux méthodes et critères d'évaluation de l'état écologique, de l'état chimique et du potentiel écologique des eaux de surface pris en application des articles R. 212-10, R. 212-11 et R. 212-18 du code de l'environnement, 2015.

E. A. Medrano, R. E. Uittenbogaard, L. M. Pires, B. J. Van-de-wiel, and H. J. Clercx, Coupling hydrodynamics and buoyancy regulation in Microcystis aeruginosa for its vertical distribution in lakes, Ecological Modelling, vol.248, pp.41-56, 2013.

. Meem, Guide technique relatif à l'évaluation de l'état des eaux de surface continentales, 2016.

. Meem, Technical guide concerning the evaluation of the state of continental surface waters (rivers, canals and lakes), 2016.

M. Meybeck, Global distribution of lakes, Physics and Chemistry of Lakes, pp.1-35, 1995.

M. Meybeck, Les lacs et leur bassin, Limnologie générale, pp.6-59, 1995.

F. J. Millero, C. T. Chen, K. Schleicher, and A. Bradshaw, A new high-pressure equation of state for seawater, Deep-Sea Research Part A. Oceanographic Research Papers, vol.27, pp.255-264, 1980.

F. J. Millero and A. Poisson, International one-atmosphere equation of state of seawater, Deep-Sea Research Part A. Oceanographic Research Papers, vol.28, pp.625-629, 1981.

S. Missaghi and M. Hondzo, Evaluation and application of a three-dimensional water quality model in a shallow lake with complex morphometry, Ecological Modelling, vol.221, issue.11, pp.1512-1525, 2010.

S. J. Moe, A. L. Solheim, H. Soszka, M. Golub, A. Hutorowicz et al., Integrated assessment of ecological status and misclassification of lakes : The role of uncertainty and index combination rules, Ecological Indicators, vol.48, pp.605-615, 2015.

E. Moreno-ostos, S. L. Da-silva, I. De-vicente, C. , and L. , Interannual and between-site variability in the occurrence of clear water phases in two shallow Mediterranean lakes, Aquatic Ecology, vol.41, issue.2, pp.285-297, 2007.

C. H. Mortimer, Water movements in lakes during summer stratification ; evidence from the distribution of temperature in Windermere, Philosophical Transactions of the Royal Society B : Biological Sciences, vol.236, pp.353-404, 1952.

A. Nishri, A. Rimmer, and Y. Lechinsky, The mechanism of hypolimnion warming induced by internal waves, Limnology and Oceanography, vol.60, issue.4, pp.1462-1476, 2015.

K. A. Octavio, Vertical heat transport mechanisms in lakes and reservoirs. Master's thesis, 1977.

D. Odermatt, F. Pomati, J. Pitarch, J. Carpenter, M. Kawka et al., MERIS observations of phytoplankton blooms in a stratified eutrophic lake, Remote Sensing of Environment, vol.126, pp.232-239, 2012.

D. Oesch, J. M. Jaquet, R. Klaus, and P. Schenker, Multi-scale thermal pattern monitoring of a large lake (Lake Geneva) using a multi-sensor approach, International Journal of Remote Sensing, vol.29, issue.20, pp.5785-5808, 2008.

, Quatrième édition des directives pour la qualité de l'eau de boisson, Organisation mondiale de la santé, 2011.

C. M. O'reilly, Rapid and highly variable warming of lake surface waters around the globe, Geophysical Research Letters, p.42, 2015.

J. Padisak, G. Borics, I. Grigorszky, and E. Soroczki-pinter, Use of phytoplankton assemblages for monitoring ecological status of lakes within the Water Framework Directive : the assemblage index, Hydrobiologia, vol.553, pp.1-14, 2006.

H. W. Paerl and J. Huisman, Climate-Blooms like it hot, Science, vol.320, issue.5872, pp.57-58, 2008.
DOI : 10.1126/science.1155398

URL : http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/docs/cmnt081712/srcsd/paerlhot.pdf

S. C. Palmer, D. Odermatt, P. D. Hunter, C. Brockmann, M. Presing et al., Satellite remote sensing of phytoplankton phenology in Lake Balaton using 10 years of MERIS observations, Remote Sensing of Environment, vol.158, pp.441-452, 2015.

A. Pannard, E. , B. B. Bird, D. F. Braun, J. Planas et al., Recurrent internal waves in a small lake : Potential ecological consequences for metalimnetic phytoplankton populations, Limnology and Oceanography : Fluids and Environments, vol.1, pp.91-109, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00651044

A. Pasztaleniec, An advanced phytoplankton trophic index : Test and validation with a nationwide lake survey in Poland, International Review of Hydrobiology, vol.101, issue.12, pp.20-35, 2016.

R. E. Payne, Albedo of sea-surface, Journal of the Atmospheric Sciences, vol.29, issue.5, pp.959-970, 1972.

N. A. Phillips, A co-ordinate system having some special advantages for numerical forecasting, Journal of Meteorology, vol.14, pp.184-185, 1957.

S. Piccolroaz, Prediction of lake surface temperature using the air2water model : guidelines, challenges, and future perspectives, Advances in Oceanography and Limnology, vol.7, pp.36-50, 2016.

S. Plattner, D. M. Mason, G. A. Leshkevich, D. J. Schwab, R. et al., Classifying and forecasting coastal upwellings in Lake Michigan using satellite derived temperature images and buoy data, Journal of Great Lakes Research, vol.32, issue.1, pp.63-76, 2006.

F. W. Platzek, G. S. Stelling, J. A. Jankowski, and J. D. Pietrzak, Accurate vertical profiles of turbulent flow in z-layer models, Water Resources Research, vol.50, issue.3, pp.2191-2211, 2014.

. Bibliographie,

D. Pobel, J. Robin, H. , and J. , Influence of sampling strategies on the monitoring of cyanobacteria in shallow lakes : Lessons from a case study in France, Water Research, vol.45, issue.3, pp.1005-1014, 2011.
URL : https://hal.archives-ouvertes.fr/bioemco-00551032

F. Poeschke, J. Lewandowski, C. Engelhardt, K. Preuss, M. Oczipka et al., Upwelling of deep water during thermal stratification onset-A major mechanism of vertical transport in small temperate lakes in spring ? Water Ressources Research, vol.51, pp.9612-9627, 2015.

S. Poikane, N. Zampoukas, A. Borja, S. P. Davies, W. Van-de-bund et al., Intercalibration of aquatic ecological assessment methods in the European Union : Lessons learned and way forward, Environmental Science and Policy, vol.44, pp.237-246, 2014.

F. Pomati, J. Jokela, M. Simona, M. Veronesi, and B. W. Ibelings, An automated platform for phytoplankton ecology and aquatic ecosystem monitoring, Science and Technology, vol.45, issue.22, pp.9658-9665, 2011.

G. Porst, O. Miler, L. Donohue, T. Jurca, F. Pilotto et al., Efficient sampling methodologies for lake littoral invertebrates in compliance with the European Water Framework Directive, Hydrobiologia, vol.767, issue.1, pp.207-220, 2016.

F. Poschke, J. Lewandowski, C. Engelhardt, K. Preuss, M. Oczipka et al., Upwelling of deep water during thermal stratification onset-a major mechanism of vertical transport in small temperate lakes in spring ?, Water Resources Research, vol.51, issue.12, pp.9612-9627, 2015.

M. Preusse, F. Peeters, L. , and A. , Internal waves and the generation of turbulence in the thermocline of a large lake, Limnology and Oceanography, vol.55, issue.6, pp.2353-2365, 2010.

A. M. Razmi, D. A. Barry, R. Bakhtyar, N. Le-dantec, A. Dastgheib et al., Current variability in a wide and open lacustrine embayment in Lake Geneva (Switzerland), Journal of Great Lakes Research, vol.39, issue.3, pp.455-465, 2013.

A. M. Razmi, D. A. Barry, U. Lemmin, F. Bonvin, T. Kohn et al., Direct effects of dominant winds on residence and travel times in the wide and open lacustrine embayment, Aquatic Sciences, vol.76, pp.59-71, 2014.

J. S. Read, D. P. Hamilton, I. D. Jones, K. Muraoka, L. A. Winslow et al., Derivation of lake mixing and stratification indices from high-resolution lake buoy data, Environmental Modelling and Software, vol.26, issue.11, pp.1325-1336, 2011.

Y. Reyjol, C. Argillier, W. Bonne, A. Borja, A. D. Buijse et al., Assessing the ecological status in the context of the European Water Framework Directive : Where do we go now ?, Science of the Total Environment, vol.497, pp.332-344, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01775263

C. S. Reynolds, The Ecology of Phytoplankton, 1997.

F. Rimet, A. Bouchez, and K. Tapolczai, Spatial heterogeneity of littoral benthic diatoms in a large lake : monitoring implications, Hydrobiologia, vol.771, issue.1, pp.179-193, 2016.

A. Roguet, G. S. Laigle, C. Therial, A. Bressy, F. Soulignac et al., Neutral community model explains the bacterial community assembly in freshwater lakes, FEMS Microbiologiy Ecology, issue.11, p.91, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01494602

S. G. Schladow, S. O. Palmarsson, T. E. Steissberg, S. J. Hook, and F. E. Prata, An extraordinary upwelling event in a deep thermally stratified lake, Geophysical Research Letters, issue.15, p.31, 2004.

T. Schroeder, I. Behnert, M. Schaale, J. Fischer, and R. Doerffer, Atmospheric correction algorithm for MERIS above case-2 waters, International Journal of Remote Sensing, vol.28, issue.7-8, pp.1469-1486, 2007.

S. Sharma, A global database of lake surface temperatures collected by in situ and satellite methods from, 1985.

T. Shatwell, R. Adrian, and G. Kirillin, Planktonic events may cause polymicticdimictic regime shifts in temperate lakes, Scientific Reports, p.6, 2016.

M. N. Shimaraev, E. S. Troitskaya, V. V. Blinov, V. G. Ivanov, and R. Y. Gnatovskii, Upwellings in Lake Baikal, Doklady Earth Sciences, vol.442, issue.2, pp.272-276, 2012.

T. Shintani, A. De-la-fuente, Y. Nino, and J. Imberger, Generalizations of the Wedderburn number : Parameterizing upwelling in stratified lakes, Limnology and Oceanography, vol.55, issue.3, pp.1377-1389, 2010.

S. D. Smith, R. J. Anderson, W. A. Oost, C. Kraan, N. Maat et al., Sea-surface wind stress and drag coefficients : The hexos results, Boundary-Layer Meteorology, vol.60, issue.1-2, pp.109-142, 1992.

S. D. Smith and E. G. Banke, Variation of sea-surface drag coefficient with wind speed, Quarterly Journal of the Royal Meteorological Society, vol.101, issue.429, pp.665-673, 1975.

V. H. Smith and D. W. Schindler, Eutrophication science : Where do we go from here ?, Trends in Ecology and Evolution, vol.24, issue.4, pp.201-207, 2009.

U. Sommer, R. Adrian, L. D. Domis, J. J. Elser, U. Gaedke et al., Beyond the Plankton Ecology Group (PEG) Model : Mechanisms Driving Plankton Succession, vol.43, pp.429-448, 2012.

U. Sommer, Z. M. Gliwicz, W. Lampert, D. , and A. , The PEG-model of seasonal succession of planktonic events in fresh waters, Archiv Fur Hydrobiologie, vol.106, issue.4, pp.433-471, 1986.

M. Sondergaard, S. E. Larsen, L. S. Johansson, T. L. Lauridsen, J. et al., Ecological classification of lakes : Uncertainty and the influence of year-to-year variability, Ecological Indicators, vol.61, pp.248-257, 2016.

K. Song, M. A. Xenopoulos, J. M. Buttle, J. Marsalek, N. D. Wagner et al., Thermal stratification patterns in urban ponds and their relationships with vertical nutrient gradients, Journal of Environmental Managment, vol.127, pp.317-323, 2013.

F. Soulignac, O. Anneville, and P. Danis, Variabilité dans l'évaluation de l'état écologique des plans d'eau en France : mesure et modélisation, pp.Partenariat INRA-ONEMA, 2017.

F. Soulignac, B. Vinçon-leite, B. J. Lemaire, J. R. Martins, C. Bonhomme et al., Performance assessment of a 3d hydrodynamic model using high temporal resolution measurements in a shallow urban lake, Environmental Modeling and Assessment, vol.22, p.4, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01770079

T. E. Steissberg, S. J. Hook, and S. G. Schladow, Characterizing partial upwellings and surface circulation at Lake Tahoe, California-Nevada, USA with thermal infrared images, Remote Sensing of Environment, vol.99, issue.1-2, pp.2-15, 2005.

V. M. Stepanenko, A. Martynov, K. D. Johnk, Z. M. Subin, M. Perroud et al., A one-dimensional model intercomparison study of thermal regime of a shallow turbid midlatitude lake, Geoscientific Model Development, vol.5, pp.3993-4035, 2012.

M. Straskraba, Innovation and intellectual property rights, The Functioning of Freshwater Ecosystems, pp.13-83, 1980.

J. D. Strickland, H. Parsons, and T. R. , A Practical Handbook of Seawater Analysis, Second Edition (Fisheries Research Board of Canada, 1968.

H. U. Sverdrup, Journal du Conseil international pour l'exploration de la mer, vol.18, pp.287-295, 1953.

J. L. Wang, Y. J. Zhang, F. Yang, X. M. Cao, Z. Q. Bai et al., Spatial and temporal variations of chlorophyll-a concentration from 2009 to 2012 in Poyang Lake, China. Environmental Earth Sciences, vol.73, issue.8, pp.4063-4075, 2015.

S. B. Watson, C. Miller, G. Arhonditsis, G. L. Boyer, W. Carmichael et al., The re-eutrophication of Lake Erie : Harmful algal blooms and hypoxia, Harmful Algae, vol.56, pp.44-66, 2016.

R. G. Wetzel and G. Likens, Limnological Analyses, 2000.

A. Wuest and A. Lorke, Small-scale hydrodynamics in lakes, Annual Review of Fluid Mechanics, vol.35, pp.373-412, 2003.

L. Zhao, Y. Z. Li, R. Zou, B. He, X. Zhu et al., A three-dimensional water quality modeling approach for exploring the eutrophication responses to load reduction scenarios in Lake Yilong (China), Environmental Pollution, vol.177, pp.13-21, 2013.

Y. Zhu, J. Yang, J. Hao, and H. Shen, Numerical simulation of hydrodynamic characteristics and water quality in Yangchenghu lake, Advances in Water Resources and Hydraulic Engineering, pp.710-715, 2009.

M. J. Anderson, T. O. Crist, and J. M. Chase, Navigating the multiple meanings of ? diversity: a roadmap for the practicing ecologist, Ecol Lett, vol.14, pp.19-28, 2011.

J. M. Ayarza and L. Erijman, Balance of neutral and deterministic components in the dynamics of activated sludge floc assembly, Microb Ecol, vol.61, pp.486-95, 2011.

E. T. Azeria, J. Ibarzabal, and J. Boucher, Towards a better understanding of beta diversity: deconstructing composition patterns of saproxylic beetles breeding in recently burnt boreal forest, Research in Biodiversity-Models and Applications, 2011.

A. Barberánbarber´barberán and E. O. Casamayor, Global phylogenetic community structure and ?-diversity patterns in surface bacterioplankton metacommunities, Aquat Microb Ecol, vol.59, pp.1-10, 2010.

A. Baselga, D. Orme, and S. Villeger, Package 'betapart': Partitioning Beta Diversity into Turnover and Nestedness Components, 2013.

A. Baselga, Partitioning the turnover and nestedness components of beta diversity, Glob Ecol and Biogeogr, vol.19, pp.134-177, 2010.

B. E. Beisner, P. R. Peres-neto, and E. S. Lindströmlindstr¨lindström, The role of environmental and spatial processes in structuring lake communities from bacteria to fish, Ecology, vol.87, pp.2985-91, 2006.

S. J. Bent, J. D. Pierson, and L. J. Forney, Measuring species richness based on microbial community fingerprints: the emperor has no clothes, Appl Environ Microbiol, vol.73, pp.2399-401, 2007.

D. Borcard, F. Gillet, and P. Legendre, Numerical Ecology with R, 2011.

D. Borcard, P. Legendre, and P. Drapeau, Partialling out the spatial component of ecological variation, Ecology, vol.73, pp.1045-55, 1992.

D. Borcard and P. Legendre, All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices, Ecol Modell, vol.153, pp.51-68, 2002.

T. Castro-carrera, P. G. Toral, and N. R. Mcewan, Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae, J Dairy Sci, vol.97, pp.1661-1670, 2014.

A. Catherine, D. Mouillot, and N. Escoffier, Cost effective prediction of the eutrophication status of lakes and reservoirs, Freshw Biol, vol.55, pp.2425-2460, 2010.

A. Catherine, M. Troussellier, and C. Bernard, Design and application of a stratified sampling strategy to study the regional distribution of cyanobacteria, Water Res, vol.42, pp.4989-5001, 2008.

J. M. Chase, Stochastic community assembly causes higher biodiversity in more productive environments, Science, vol.328, pp.1388-91, 2010.

R. A. Chisholm and S. W. Pacala, Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities, Proc Natl Acad Sci U S A, vol.107, pp.15821-15826, 2010.

S. W. Culman, R. Bukowski, and H. G. Gauch, T-REX: software for the processing and analysis of T-RFLP data, BMC Bioinformatics, vol.10, p.171, 2009.

A. De-wever, K. Muylaert, and K. Van-der-gucht, Bacterial community composition in Lake Tanganyika: vertical and horizontal heterogeneity, Appl Environ Microbiol, vol.71, pp.5029-5066, 2005.

S. Drakare and A. Liess, Local factors control the community composition of cyanobacteria in lakes while heterotrophic bacteria follow a neutral model, Freshw Biol, vol.55, pp.2447-57, 2010.

O. F. Elsayed, E. Maillard, and S. Vuilleumier, Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor, Sci Total Environ, vol.499, pp.327-362, 2014.

B. Gilbert and J. R. Bennett, Partitioning variation in ecological communities: do the numbers add up?, J Appl Ecol, vol.47, pp.1071-82, 2010.

M. C. Horner-devine, M. A. Leibold, and V. H. Smith, Bacterial diversity patterns along a gradient of primary productivity, Ecol Lett, vol.6, pp.613-635, 2003.

S. P. Hubbell, The Unified Neutral Theory of Biodiversity and Biogeography, 2001.

L. Jardillier, M. Basset, and I. Domaizon, Institut National de la Statistique et desÉtudesÉconomiquesdes´desÉtudesdesÉtudes´desÉtudesÉconomiques, 2012. INSEE. La France en Bref-France in figures, Aquat Microb Ecol, vol.35, pp.259-73, 2004.

S. E. Jones, T. A. Cadkin, and R. J. Newton, Spatial and temporal scales of aquatic bacterial beta diversity, Front Microbiol, vol.318, pp.1-10, 2012.

S. E. Jones, R. J. Newton, and K. D. Mcmahon, Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes, Appl Environ Microbiol, vol.11, pp.2463-72, 2009.

A. D. Kent, A. C. Yannarell, and J. A. Rusak, Synchrony in aquatic microbial community dynamics, ISME J, vol.1, pp.38-47, 2007.

S. Langenheder and H. Ragnarsson, The role of environmental and spatial factors for the composition of aquatic bacterial communities, Ecology, vol.88, pp.2154-61, 2007.

S. Langenheder and A. J. Székelysz´székely, Species sorting and neutral processes are both important during the initial assembly of bacterial communities, ISME J, vol.5, pp.1086-94, 2011.

G. Lear and G. D. Lewis, Impact of catchment land use on bacterial communities within stream biofilms, Ecol Indic, vol.9, pp.848-55, 2009.

J. E. Lee, H. L. Buckley, and R. S. Etienne, Both species and neutral processes drive assembly of bacterial communities in aquatic microcosms, FEMS Microbiol Ecol, vol.86, pp.288-302, 2013.

P. Legendre, D. Borcard, M. Package, and &. Sti', Spacetime ANOVA Models Without Replications, version 1.0.2, 2012. Legendre P, de C ´ aceres M, Borcard D. Community surveys through space and time: testing the space-time interaction in the absence of replication, Ecology, vol.91, pp.262-72, 2010.

P. Legendre and O. Gauthier, Statistical methods for temporal and space?time analysis of community composition data, Proc R Soc B, vol.281, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00948693

M. A. Leibold, M. Holyoak, and N. Mouquet, The metacommunity concept: a framework for multi-scale community ecology

, Ecol Lett, vol.7, pp.601-614, 2004.

M. A. Leibold, Biodiversity and nutrient enrichment in pond plankton communities, Evol Ecol Res, vol.1, pp.73-95, 1999.

E. S. Lindströmlindstr¨lindström, M. Forslund, and G. Algesten, External control of bacterial community structure in lakes, Limnol Oceanogr, vol.51, pp.339-381, 2006.

E. S. Lindströmlindstr¨lindström, M. P. Kamst-van-agterveld, and G. Zwart, Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time, Appl Environ Microbiol, vol.71, pp.8201-8207, 2005.

E. S. Lindströmlindstr¨lindström and S. Langenheder, Local and regional factors influencing bacterial community assembly, Environ Microbiol Rep, vol.4, pp.1-9, 2012.

E. S. Lindströmlindstr¨lindström, Bacterioplankton community composition in five lakes differing in trophic status and humic content, Microb Ecol, vol.40, pp.104-117, 2000.

R. Logares, E. S. Lindströmlindstr¨lindström, and S. Langenheder, Biogeography of bacterial communities exposed to progressive long-term environmental change, ISME J, vol.7, pp.937-985, 2013.

J. B. Logue and E. S. Lindströmlindstr¨lindström, Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints, ISME J, vol.4, pp.729-767, 2010.

D. Marie, F. Partensky, and D. Jacquet, Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I

, Appl Environ Microbiol, vol.63, pp.186-93, 1997.

J. Martiny, B. Bohannan, and J. H. Brown, Microbial biogeography: putting microorganisms on the map, Nat Rev Microbiol, vol.4, pp.102-114, 2006.

S. L. Mclellan, E. J. Hollis, and M. M. Depas, Distribution and fate of Escherichia coli in lake Michigan following contamination with urban stormwater and combined sewer overflows, J Great Lakes Res, vol.33, pp.566-80, 2007.

K. Muylaert, K. Van-der-gucht, and N. Vloemans, Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes, Appl Environ Microbiol, vol.68, pp.4740-50, 2002.

C. E. Nelson, S. Sadro, and J. M. Melack, Contrasting the influences of stream inputs and landscape position on bacterioplankton community structure and dissolved organic matter composition in high-elevation lake chains, Limnol Oceanogr, vol.54, pp.1292-1305, 2009.

. Oecd, Eutrophication of Waters: Monitoring, Assessment and Control. Paris: Organization for Economic Cooperation and Development, 1982.

I. D. Ofit¸eruofit¸eru, M. Lunn, and T. P. Curtis, Combined niche and neutral effects in a microbial wastewater treatment community, Proc Natl Acad Sci U S A, vol.107, pp.15345-50, 2010.

J. Oksanen, F. G. Blanchet, and R. Kindt, Package 'vegan'. Community Ecology Package, version 2.2-1, 2015.

A. M. Osborn, E. R. Moore, and K. N. Timmis, An evaluation of terminalrestriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics, Environ Microbiol, vol.2, pp.39-50, 2000.

. Ostman¨oostman¨-ostman¨o, S. Drakare, and E. S. Kritzberg, Regional invariance among microbial communities, Ecol Lett, vol.13, pp.118-145, 2010.

C. Pedróspedr´pedrós-alí-o, Marine microbial diversity: can it be determined?, Trends Microbiol, vol.14, pp.257-63, 2006.

P. R. Peres-neto, P. Legendre, and S. Dray, Variation partitioning of species data matrices: estimation and comparison of fractions, Ecology, vol.87, pp.2614-2639, 2006.

L. Philippot, S. Andersson, and T. J. Battin, The ecological coherence of high bacterial taxonomic ranks, Nat Rev Microbiol, vol.8, pp.523-532, 2010.

M. K. Pholchan, J. Baptista, and R. J. Davenport, Microbial community assembly, theory and rare functions, Front Microbiol, vol.4, p.1013, 2013.

, R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, 2014.

M. Rogora, M. Minella, `. Orrùorr, and A. Orrù, A comparison between hightemperature catalytic oxidation and persulphate oxidation for the determination of total nitrogen in freshwater, Int J Environ Anal Chem, vol.86, pp.1065-78, 2006.

. Scheffer-m-ecology-of-shallow-lakes, C. O. Scopel, J. Harris, and S. L. Mclellan, Influence of nearshore water dynamics and pollution sources on beach monitoring outcomes at two adjacent Lake Michigan beaches, J Great Lakes Res, vol.32, pp.543-52, 2004.

B. Sercu, L. C. Werfhorst, and J. Van-der-murray, Storm drains are sources of human fecal pollution during dry weather in three urban southern California watersheds, Environ Sci Technol, vol.43, pp.293-301, 2009.

A. Shade, A. D. Kent, and S. E. Jones, Interannual dynamics and phenology of bacterial communities in a eutrophic lake, Limnol Oceanogr, vol.52, pp.487-94, 2007.

W. T. Sloan, M. Lunn, and S. Woodcock, Quantifying the roles of immigration and chance in shaping prokaryote community structure, Environ Microbiol, vol.8, pp.732-772, 2006.

J. Soininen, J. J. Korhonen, and J. Karhu, Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton, Limnol Oceanogr, vol.56, pp.508-528, 2011.

R. Stepanauskas, M. A. Moran, and B. A. Bergamaschi, Covariance of bacterioplankton composition and environmental variables in a temperate delta system, Aquat Microb Ecol, vol.31, pp.85-98, 2003.

A. J. Székelysz´székely and S. Langenheder, The importance of species sorting differs between habitat generalists and specialists in bacterial communities, FEMS Microbiol Ecol, vol.87, pp.102-114, 2014.

B. C. Thomson, E. Tisserant, and P. Plassart, Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites, Proc Natl Acad Sci U S A, vol.88, pp.20404-20413, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01269419

J. Van-dorst, A. Bissett, and A. S. Palmer, Community fingerprinting in a sequencing world, FEMS Microbiol Ecol, vol.89, pp.316-346, 2014.

M. Vellend, D. S. Srivastava, and K. M. Anderson, Assessing the relative importance of stochasticity in ecological communities, Oikos, vol.123, pp.1420-1450, 2014.

S. Woodcock, C. J. Van-der-gast, and T. Bell, Neutral assembly of bacterial communities, FEMS Microbiol Ecol, vol.62, pp.171-80, 2007.

A. C. Yannarell, A. D. Kent, and G. H. Lauster, Temporal patterns in bacterial communities in three temperate lakes of different trophic status, Microb Ecol, vol.46, pp.391-405, 2003.

A. C. Yannarell and E. W. Triplett, Geographic and environmental sources of variation in lake bacterial community composition geographic and environmental sources of variation in lake bacterial community composition, Appl Environ Microbiol, vol.71, pp.227-266, 2005.

A. C. Yannarell and E. W. Triplett, Within-and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales, Appl Environ Microbiol, vol.70, pp.214-237, 2004.

M. V. Zubkov and P. H. Burkill, Syringe pumped high speed flow cytometry of oceanic phytoplankton, Cytometry A, vol.69, pp.1010-1029, 2006.

T. Andersen and D. O. Hessen, Carbon, nitrogen, and phosphorus content of freshwater zooplankton, Limonol. Oceanogr, vol.36, pp.807-814, 1991.

T. R. Anderson, Plankton functional type modelling: running before we can walk?, J. Plank. Res, vol.27, pp.1073-1081, 2005.
DOI : 10.1093/plankt/fbi076

URL : https://academic.oup.com/plankt/article-pdf/27/11/1073/4481304/fbi076.pdf

O. Anneville, I. Domaizon, O. Kerimoglu, F. Rimet, and S. Jacquet, Blue-Green Algae in a "Greenhouse Century"? New insights from field data on climate change impacts on cyanobacteria abundance, Ecosystems, vol.18, pp.441-458, 2015.

O. Anneville, S. Souissi, S. Gammeter, and D. Straile, Seasonal and inter-annual scales of variability in phytoplankton assemblages: comparison of phytoplankton dynamics in three peri-alpine lakes over a period of 28 years, Freshw. Biol, vol.49, pp.98-115, 2004.

R. Armstrong, Grazing limitation and nutrient limitation in marine ecosystems: steady state solutions of an ecosystem model with multiple food chains, Limonol. Oceanogr, vol.39, pp.597-608, 1994.

M. Beniston, Mountain weather and climate: a general overview and a focus on climatic change in the Alps, Hydrobiologia, vol.562, pp.3-16, 2006.

T. Berge, S. Chakraborty, P. J. Hansen, and K. H. Andersen, Modeling succession of key resource-harvesting traits of mixotrophic plankton, ISME J, vol.11, pp.212-223, 2017.

F. Bignami, S. Marullo, R. Santoleri, and M. E. Schiano, Longwave radiation budget in the Mediterranean Sea, J. Geophys. Res, vol.100, p.2501, 1995.

J. F. Briand, S. Jacquet, C. Flinois, C. Avois-jacquet, C. Maisonnette et al., Variations in the microcystin production of Planktothrix rubescens (cyanobacteria) assessed from a four-year survey of Lac du Bourget (France) and from laboratory experiments, Microb. Ecol, vol.50, pp.418-428, 2005.

D. Bright and A. Walsby, The daily integral of growth by Planktothrix rubescens calculated from growth rate in culture and irradiance in Lake Zürich, New Phytolog, vol.146, pp.301-316, 2000.

J. Bruggeman and K. Bolding, A general framework for aquatic biogeochemical models, Environ. Model. Softw, vol.61, pp.249-265, 2014.

A. Bryhn, C. Girel, G. Paolini, and S. Jacquet, Predicting future effects from nutrient abatement and climate change on phosphorus concentrations in Lake Bourget, France. Ecol. Model, vol.221, pp.1440-1450, 2010.

H. Burchard, K. Bolding, W. Kühn, A. Meister, T. Neumann et al., Description of a flexible and extendable physical-biogeochemical model system for the water column, J. Mar. Syst, vol.61, pp.180-211, 2006.

C. Butterwick, S. I. Heaney, and J. F. Talling, Diversity in the influence of temperature on the growth rates of freshwater algae, and its ecological relevance, Freshw. Biol, vol.50, pp.291-300, 2005.

E. Carraro, N. Guyennon, D. Hamilton, L. Valsecchi, E. C. Manfredi et al., Coupling high-resolution measurements to a three-dimensional lake model to assess the spatial and temporal dynamics of the cyanobacterium Planktothrix rubescens in a medium-sized lake, Hydrobiologia, vol.698, pp.77-95, 2012.

B. Chen and H. Liu, Relationships between phytoplankton growth and cell size in surface oceans: Interactive effects of temperature, nutrients, and grazing, Limnol. Oceanogr, vol.55, pp.965-972, 2010.

D. Copetti, G. Tartari, G. Morabito, A. Oggioni, and E. Legnani, A biogeochemical model of Lake Pusiano (North Italy) and its use in the predictability of phytoplankton blooms: first preliminary results, J. Limnol, vol.65, pp.59-64, 2006.

K. Crane and J. Grover, Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities, J. Theor. Biol, vol.262, pp.517-527, 2010.

Y. Cuypers, B. Vinç-on-leite, A. Groleau, B. Tassin, and J. F. Humbert, Impact of internal waves on the spatial distribution of Planktothrix rubescens (cyanobacteria) in an alpine lake, ISME J, vol.5, pp.580-589, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01208054

M. T. Dokulil and K. Teubner, Deep living Planktothrix rubescens modulated by environmental constraints and climate forcing, Hydrobiologia, vol.698, pp.29-46, 2012.
DOI : 10.1007/978-94-007-5790-5_4

M. Droop, Vitamin B12 and marine ecology. IV. The kinetics of uptake, growth and inhibition in Monochrysis lutheri, J. Mar. Biol. Assoc. United Kingdom, vol.48, pp.689-733, 1968.
DOI : 10.1007/bf01609935

J. C. Druart and F. Rimet, Protocoles d'analyse du phytoplancton de l'INRA: prélèvement, dénombrement et biovolumes, 2008.

H. J. Dumont, I. De-velde, and S. Dumont, The dry weight estimate of biomass in a selection of Cladocera, Copepoda and Rotifera from the plankton, periphyton and benthos of continental waters, Oecologia, vol.19, pp.75-97, 1975.

K. F. Edwards, M. K. Thomas, C. A. Klausmeier, and E. Litchman, Allometric scaling and taxonomic variation in nutrient utilization traits and maximum growth rate of phytoplankton, Limnol. Oceanogr, vol.57, pp.554-566, 2012.

R. Eppley, Temperature and phytoplankton growth in the sea, Fish. Bull, vol.70, pp.1063-1085, 1972.

B. Ernst, S. J. Hoeger, E. O. Brien, and D. R. Dietrich, Abundance and toxicity of Planktothrix rubescens in the pre-alpine Lake Ammersee, Harmful Algae, vol.8, pp.329-342, 2009.

M. Fasham, H. Ducklow, and S. Mckelvie, A nitrogen-based model of plankton dynamics in the oceanic mixed layer, J. Mar. Res, vol.48, pp.591-639, 1990.

Z. Finkel, J. Beardall, K. Flynn, A. Quigg, T. Rees et al., Phytoplankton in a changing world: cell size and elemental stoichiometry, J. Plankt. Res, vol.32, pp.119-137, 2010.
DOI : 10.1093/plankt/fbp098

URL : https://academic.oup.com/plankt/article-pdf/32/1/119/4318366/fbp098.pdf

K. Flynn, D. Stoecker, A. Mitra, J. Raven, P. Glibert et al., Misuse of the phytoplankton-zooplankton dichotomy: the need to assign organisms as mixotrophs within plankton functional types, J. Plank. Res, vol.35, pp.3-11, 2012.

K. J. Flynn and A. Mitra, Building the "perfect beast": modelling mixotrophic plankton, J. Plank. Res, vol.31, pp.965-992, 2009.
DOI : 10.1093/plankt/fbp044

URL : https://academic.oup.com/plankt/article-pdf/31/9/965/4200414/fbp044.pdf

G. Gal, M. Hipsey, A. Parparov, U. Wagner, V. Makler et al., Implementation of ecological modeling as an effective management and investigation tool: Lake Kinneret as a case study, Ecol. Model, vol.220, pp.1697-1718, 2009.

N. Gallina, M. Beniston, and S. Jacquet, Estimating future cyanobacterial occurrence and importance in lakes: a case study with Planktothrix rubescens in Lake Geneva, Aquatic Sci, vol.79, pp.249-263, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608611

W. Gentleman, A. Leising, B. Frost, S. Strom, and J. Murray, Functional responses for zooplankton feeding on multiple resources: a review of assumptions and biological dynamics, Deep-Sea Res. II, vol.50, pp.2847-2875, 2003.

J. Grover, Resource competition in a variable environment: phytoplankton growing according to the variable-internal-stores model, Am. Natural, vol.138, pp.811-835, 1991.

J. Grover, Stoichiometry, herbivory and competition for nutrients: simple models based on planktonic ecosystems, J. Theoret. Biol, vol.214, pp.599-618, 2002.

C. Halstvedt, T. Rohrlack, T. Andersen, O. Skulberg, and B. Edvardsen, Seasonal dynamics and depth distribution of Planktothrix spp. in Lake Steinsfjorden (Norway) related to environmental factors, J. Plank. Res, vol.29, pp.471-482, 2007.

P. Hansen, P. Bjørnsen, and B. Hansen, Zooplankton grazing and growth: Scaling within the 2-2,000-m body size range, Limnol. Oceanogr, vol.42, pp.687-704, 1997.

D. O. Hessen, J. J. Elser, R. W. Sterner, and J. Urabe, Ecological stoichiometry: an elementary approach using basic principles, Limnol. Oceanogr, vol.58, pp.2219-2236, 2013.

S. Hodge, W. Arthur, and P. Mitchell, Effects of temporal priority on interspecific interactions and community development, Oikos, vol.76, pp.350-358, 1996.

R. R. Hood, E. A. Laws, R. A. Armstrong, N. R. Bates, C. W. Brown et al., Pelagic functional group modeling: progress, challenges and prospects, Deep Sea Res. II, vol.53, pp.459-512, 2006.

S. Jacquet, J. F. Briand, L. Christophe, C. Avois-jacquet, L. Oberhaus et al., The proliferation of the toxic cyanobacterium Planktothrix rubescens following restoration of the largest natural French lake, Harmful Algae, vol.4, pp.651-672, 2005.
URL : https://hal.archives-ouvertes.fr/halsde-00181790

S. Jacquet, I. Domaizon, and O. Anneville, The need for ecological monitoring of freshwaters in a changing world: a case study of Lakes Annecy, Bourget, and Geneva. Environ. Monit. Assess, vol.186, pp.3455-3476, 2014.

S. Jacquet, O. Kerimoglu, F. Rimet, G. Paolini, and O. Anneville, Cyanobacterial bloom termination: the disappearance of Planktothrix rubescens from Lake Bourget (France) after restoration, Freshw. Biol, vol.59, pp.2472-2487, 2014.

K. Jöhnk, J. Huisman, J. Sharples, B. Sommeijer, P. Visser et al., Summer heatwaves promote blooms of harmful cyanobacteria, Glob. Change Biol, vol.14, pp.495-512, 2008.

J. Jolliff, J. Kindle, I. Shulman, B. Penta, M. Friedrichs et al., Summary diagrams for coupled hydrodynamic-ecosystem model skill assessment, J. Mar. Syst, vol.76, pp.64-82, 2009.

N. Kamjunke, T. Henrichs, and U. Gaedke, Phosphorus gain by bacterivory promotes the mixotrophic flagellate Dinobryon spp. during re-oligotrophication, J. Plank. Res, vol.29, pp.39-46, 2007.

O. Kerimoglu, D. Straile, and F. Peeters, Role of phytoplankton cell size on the competition for nutrients and light in incompletely mixed systems, J. Theor. Biol, vol.300, pp.330-343, 2012.

O. Kerimoglu, D. Straile, and F. Peeters, Seasonal, inter-annual and long term variation in top-down versus bottom-up regulation of primary production, Oikos, vol.122, pp.223-234, 2013.

T. Kiørboe, How zooplankton feed: mechanisms, traits and trade-offs, Biol. Rev. Camb. Philos. Soc, vol.86, pp.311-339, 2011.

J. Kondo, Air-sea bulk transfer coefficients in diabatic conditions, Bound. Layer Meteorol, vol.9, pp.91-112, 1975.

A. Konopka, Buoyancy regulation and vertical migration by Oscillatoria Rubescens in Crooked Lake, Indiana. Br. Phycolog. J, pp.427-442, 1982.

J. Kromkamp and A. E. Walsby, A computer model of buoyancy and vertical migration in cyanobacteria, J. Plankt. Res, vol.12, pp.161-183, 1990.

R. Kurmayer and F. Jüttner, Strategies for the co-existence of zooplankton with the toxic cyanobacterium Planktothrix rubescens in Lake Zürich, J. Plank. Res, vol.21, pp.659-683, 1999.

L. Vu, B. Vinç-on-leite, B. Lemaire, B. Bensoussan, N. Calzas et al., High-frequency monitoring of phytoplankton dynamics within the European water framework directive: application to metalimnetic cyanobacteria, Biogeochemistry, vol.106, pp.229-242, 2011.
URL : https://hal.archives-ouvertes.fr/bioemco-00642853

E. Litchman, C. A. Klausmeier, O. M. Schofield, and P. G. Falkowski, The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level, Ecol. Lett, vol.10, pp.1170-1181, 2007.

E. Litchman, C. A. Klausmeier, and K. Yoshiyama, Contrasting size evolution in marine and freshwater diatoms, Proc. Natl. Acad. Sci, vol.106, pp.2665-2670, 2009.

E. Litchman, P. D. Pinto, C. A. Klausmeier, M. K. Thomas, and K. Yoshiyama, Linking traits to species diversity and community structure in phytoplankton, Hydrolobiologia, vol.653, pp.15-28, 2010.

S. Menden-deuer and E. Lessard, Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton, Limnol. Oceanogr, vol.45, pp.569-579, 2000.

J. Mieleitner and P. Reichert, Modelling functional groups of phytoplankton in three lakes of different trophic state, Ecol. Model, vol.211, pp.279-291, 2008.

A. Mitra, K. J. Flynn, J. M. Burkholder, T. Berge, A. Calbet et al., The role of mixotrophic protists in the biological carbon pump, Biogeosciences, vol.11, pp.995-1005, 2014.

F. Morel, Kinetics of nutrient uptake and growth in phytoplankton, J. Phycol, vol.23, pp.137-150, 1987.

L. Naselli-flores, R. Barone, I. Chorus, and R. Kurmayer, Toxic cyanobacterial blooms in reservoirs under a semiarid mediterranean climate: the magnification of a problem, Environ. Toxicol, vol.22, pp.399-404, 2007.

L. Oberhaus, M. Gelinas, B. Pinel-alloul, A. Ghadouani, and J. F. Humbert, Grazing of two toxic Planktothrix species by Daphnia pulicaria: potential for bloom control and transfer of microcystins, J. Plank. Res, vol.29, pp.827-838, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00711636

M. Omlin, P. Reichert, and R. Forster, Biogeochemical model of Lake Zürich: model equations and results, Ecol. Model, vol.141, pp.77-103, 2001.

K. Oubelkheir, A. Sciandra, and M. Babin, Bio-optical and biogeochemical properties of different trophic regimes in oceanic waters, Limnol. Oceanogr, vol.50, pp.1795-1809, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01893852

J. Padisák, É. Hajnal, L. Krienitz, J. Lakner, and V. Üveges, Rarity, ecological memory, rate of floral change in phytoplankton and the mystery of the Red Cock, Hydrobiologia, vol.653, pp.45-64, 2010.

M. Pahlow, H. Dietze, and A. Oschlies, Optimality-based model of phytoplankton growth and diazotrophy, Mar. Ecol. Prog. Ser, vol.489, pp.1-16, 2013.

C. Paulson and J. Simpson, Irradience measurements in the upper ocean, J. Phys. Oceanogr, vol.7, pp.952-956, 1977.

R. E. Payne, Albedo of the Sea Surface, J. Atmos. Sci, vol.29, pp.959-970, 1972.

T. Posch, M. M. Salcher, and J. Pernthaler, Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming, Nat. Clim. Change, vol.2, pp.809-813, 2012.

K. Rinke, P. Yeates, and K. O. Rothhaupt, A simulation study of the feedback of phytoplankton on thermal structure via light extinction, Freshw. Biol, vol.55, pp.1674-1693, 2010.

B. J. Robson, When do aquatic systems models provide useful predictions, what is changing, and what is next?, Environ. Model. Softw, vol.61, pp.287-296, 2014.

A. Rosati and K. Miyakoda, A general circulation model for upper ocean simulation, J. Phys. Oceanogr, vol.18, pp.1601-1626, 1988.

A. Ryabov, L. Rudolf, and B. Blasius, Vertical distribution and composition of phytoplankton under the influence of an upper mixed layer, J. Theor. Biol, vol.263, pp.120-133, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00564466

N. Salmaso, Long-term phytoplankton community changes in a deep subalpine lake: responses to nutrient availability and climatic fluctuations, Freshw. Biol, vol.55, pp.825-846, 2010.

N. Salmaso, F. Buzzi, L. Garibaldi, G. Morabito, and M. Simona, Effects of nutrient availability and temperature on phytoplankton development: a case study from large lakes south of the Alps, Aquatic Sci, vol.74, pp.555-570, 2012.

A. Schwaderer, K. Yoshiyama, P. De-tezanos-pinto, N. G. Swenson, C. Klausmeier et al., Eco-evolutionary differences in light utilization traits and distributions of freshwater phytoplankton, Limnol. Oceanogr, vol.56, pp.589-598, 2011.

Y. Shimoda and G. Arhonditsis, Phytoplankton functional type modelling: Running before we can walk? A critical evaluation of the current state of knowledge, Ecol. Model, vol.320, pp.29-43, 2016.

U. Sommer, R. Adrian, L. D. Domis, J. J. Elser, U. Gaedke et al., Beyond the Plankton Ecology Group (PEG) Model: mechanisms driving plankton succession, Annu. Rev. Ecol. Evol. Syst, vol.43, pp.429-448, 2012.

U. Sommer and A. Lewandowska, Climate change and the phytoplankton spring bloom: Warming and overwintering zooplankton have similar effects on phytoplankton, Glob. Change Biol, vol.17, pp.154-162, 2011.

J. Steele and E. Henderson, The role of predation in plankton models, J. Plank. Res, vol.14, pp.157-172, 1992.

D. Straile, Gross growth efficiencies of protozoan and metazoan zooplankton and their dependence on food concentration, predator-prey weight ratio, and taxonomic group, Limnol. Oceanogr, vol.42, pp.1375-1385, 1997.

K. Tapolczai, O. Anneville, J. Padisák, N. Salmaso, G. Morabito et al., Occurrence and mass development of Mougeotia spp. (Zygnemataceae) in large, deep lakes, Hydrobiologia, vol.745, pp.17-29, 2014.

N. Terseleer, J. Bruggeman, C. Lancelot, and N. Gypens, Trait-based representation of diatom functional diversity in a plankton functional type model of the eutrophied southern North Sea, Limnol. Oceanogr, vol.59, pp.1958-1972, 2014.

T. Thingstad, H. Havskum, K. Garde, and B. Riemann, On the strategy of 'eating your competitor': a mathematical analysis of algal mixotrophy, Ecology, vol.77, pp.2108-2118, 1997.

B. Vinç-on-leite, B. J. Lemaire, V. T. Khac, and B. Tassin, Long-term temperature evolution in a deep sub-alpine lake, Lake Bourget, France: how a one-dimensional model improves its trend assessment, Hydrobiologia, vol.731, pp.49-64, 2014.

B. Vinç-on-leite, B. Tassin, and J. C. Druart, Phytoplankton variability in Lake Bourget: phytoplankton dynamics and meteorology, Lakes Reserv, vol.7, pp.93-102, 2002.

B. Vinç-on-leite, B. Tassin, and J. M. Jaquet, Contribution of mathematical modeling to lake ecosystem understanding, Hydrobiologia, vol.300, pp.433-442, 1995.

A. Walsby, A. Avery, and F. Schanz, The critical pressures of gas vesicles in Planktothrix rubescens in relation to the depth of winter mixing in Lake Zurich, Switzerland. J. Plank. Res, vol.20, pp.1357-1375, 1998.

A. E. Walsby, G. Ng, C. Dunn, and P. A. Davis, Comparison of the depth where Planktothrix rubescens stratifies and the depth where the daily insolation supports its neutral buoyancy, New Phytolog, vol.162, pp.133-145, 2004.

A. E. Walsby and F. Schanz, Light-dependent growth rate determines changes in the population of Planktothrix rubescens over the annual cycle in Lake Zürich, Switzerland. New Phytolog, vol.154, pp.671-687, 2002.

B. Ward, S. Dutkiewicz, O. Jahn, and M. J. Follows, A size-structured food-web model for the global ocean, Limnol. Oceanogr, vol.57, pp.1877-1891, 2012.

B. A. Ward and M. J. Follows, Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux, Proc. Natl. Acad. Sci, vol.113, pp.2958-2963, 2016.
DOI : 10.1073/pnas.1517118113

URL : https://hal.archives-ouvertes.fr/hal-01483274

K. Wirtz and O. Kerimoglu, Optimality and variable co-limitation controls autotrophic stoichiometry, Front. Ecol. Evol, 2016.

K. W. Wirtz, Mechanistic origins of variability in phytoplankton dynamics: Part I: niche formation revealed by a size-based model, Mar. Biol, vol.160, pp.2319-2335, 2013.