, Année, 2004.

, Année, 2004.

S. K. Aalto and G. E. Newsome, Winds and the demic structure of a population of yellow perch (Perca flavescens), Can. J. Fish .Aquat. Sci, vol.50, pp.496-501, 1993.

. Afnor, NF EN 14757. Echantillonnage des poissons à l'aide de filets maillants, Rapport Afnor, vol.27, 2005.

. Afnor, NF EN 15204. Qualité de l'eau -Norme guide pour le dénombrement du phytoplancton par microscopie inversée (méthode Utermöhl), 2006.

. Afnor, NF EN 14407 -Qualité de l'eau -Guide pour l'identification et le dénombrement des échantillons de diatomées benthiques de rivières et de lacs, pp.1-13, 2014.

. Afnor, NF EN 13946 -Qualité de l'eau -Guide pour l'échantillonnage en routine et le prétraitement des diatomées benthiques de rivières et de plans d'eau, pp.1-18, 2016.

A. Afssa, Risques sanitaires liés à la présence de cyanobactéries dans l'eau. Évaluation des risques liés à la présence de cyanobactéries et de leurs toxines dans les eaux destinées à l'alimentation, à la baignade et autres activités récréatives, 2006.

A. De-l'eau and R. , Suivi des plans d'eau des bassins Rhône-Méditerranée et Corse en application de la Directive Cadre sur l'Eau, 2010.

A. Aglen, Empirical results on precision-effort relationships for acoustic surveys. ICES CM B/30: 28 p, 1989.

J. Alahuhta, J. Heino, and M. Et-luoto, Climate change and the future distributions of aquatic macrophytes across boreal catchments: Effects of climate change on aquatic macrophytes, Journal of Biogeography, vol.38, pp.383-393, 2011.

N. Angeli, L. Cretenoy, and D. Gerdeaux, Importance du peuplement piscicole dans la qualité des eaux: les biomanipulations, Gestion piscicole des grands plans d'eaux, pp.35-73, 2001.

O. Anneville and L. Lainé, Le zooplancton du lac d'Annecy, rapport SILA, 2004.

O. Anneville and K. Kaiblinger, Proposal for a phytoplankton lake index applicable to lakes of the Rhône-Alpes basin for the implementation of the European Water Framework Directive. Final report, vol.54, 2009.

O. Anneville, S. Souissi, J. C. Molinero, and D. Gerdeaux, Influences of human activity and climate on the stock-recruitment dynamics of whitefish, Coregonus lavaretus, in Lake Geneva, Fish. Manage. Ecol, vol.16, pp.492-500, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02666520

M. Appelberg, Swedish standard methods for sampling freshwater fish with multimesh, Report Inst. Freshwater Research, vol.26, p.p, 2000.

D. Auderset-joye, Contribution à l'écologie des Characées de Suisse, 1992.

G. Bailly and O. Et-schäfer, Guide illustré des Characées du nord-est de la France, 2010.

H. Balk and T. Lindem, Sonar 4, Sonar 5, Sonar 6 -Post-processing Systems. Operator Manual. Lindem Data Acquisition, 2006.

G. Balvay, Aperçu sur l'état des trois grands lacs savoyards, Rev. Inst. Pasteur Lyon, vol.1, pp.431-441, 1968.

R. D. Batt, S. R. Carpenter, and A. R. Ives, Extreme events in lake ecosystem time series, Limnology and Oceanography Letters, 2017.

T. Bell and J. Kalff, The contribution of picoplankton in marine and freshwater systems of different trophic status and depth, Limnol. Oceanogr, vol.46, pp.1243-1248, 2001.

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

L. Bigarré, J. Cabon, M. Baud, F. Pozet, and J. Castric, Ranaviruses associated with high mortalities in catfish in France, Bull. Eur. Ass. Fish Pathol, vol.28, issue.4, 2008.

I. Blindow, Decline of charophytes during eutrophication: comparison with angiosperms. ResearchGate, 28, pp.9-14, 2006.

I. Blindow, Long-and short-term dynamics of submerged macrophytes in two shallow eutrophiclakes, Freshwater Biology, vol.28, pp.15-27, 1992.

A. Boissezon, Distribution et dynamique des communautés de Characées: impact des facteurs environnementaux régionaux et locaux. University of Geneva, p.38416, 2014.

P. Bourrelly, Quelques pêches planctoniques dans le lac du Bourget et les lacs voisins, Verh. int. Verein. Theor. Angew. Limnol, vol.12, pp.253-255, 1955.

P. Bourrelly, Les Algues d'eau douce, Tome I: Les Algues vertes, pp.1-572, 1972.

P. Bourrelly, Les Algues d'eau douce, Les Algues jaunes et brunes, pp.1-517, 1981.

P. Bourrelly, Les Algues d'eau douce, Les Algues bleues et rouges, pp.1-606, 1985.

S. B. Brandt, Acoustic assessment of fish abundance and distribution, Fisheries Techniques, pp.385-432, 1996.

H. Brix, Do macrophytes play a role in constructed treatment wetlands? Water Science and Technology, vol.35, pp.11-17, 1997.

S. Brooks and H. Birks, The dynamics of Chironomidae (Insecta: Diptera) assemblages in response to environmental change during the past 700 years on Svalbardw, Journal of Paleolimnology, vol.31, pp.483-498, 2004.

S. J. Brooks, P. G. Langdon, and O. Heiri, The Identification and Use of Palaearctic Chironomidae Larvae in Palaeoecology, QRA Technical Guide, issue.10, p.276, 2007.

L. Brundin, Chironomiden und andere Bodentiere der Südschwedischen Urgebirgsseen, Rep. Inst. Freshwat. Res. Drottingholm, vol.30, pp.1-914, 1949.

C. W. Burns and L. M. Galbraith, The effects of land use on water quality and aquatic communities, J. Plankt. Res, vol.29, pp.127-139, 2007.

C. Callieri, Picophytoplankton in freshwater ecosystems: the importance of small-sized phototrophs, Freshw Rev, vol.1, pp.1-28, 2008.

R. Carignan and J. Et-kalff, Phosphorus Sources for Aquatic Weeds: Water or Sediments? Science, vol.207, pp.987-989, 1980.

P. Campton, Diagnostic de la gestion de la perche, vol.27, p.p, 2007.

A. Caudron, E. Lasne, C. Gillet, J. Guillard, and A. Chapigneulle, Thirty years of reoligotrophication do not contribute to restore self-sustaining fisheries of Arctic charr, Salvelinus alpinus, in Lake Geneva, Fisheries Research, vol.154, pp.165-171, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02634928

. Cbfc, Etude et cartographie de la flore et de la végétation de dix lacs du massif Jurassien, 2007.

, Etude des méthodes biologiques quantitative d'appréciation de la qualité des eaux, vol.218, 1982.

. Cen, Water quality -Guidance on the estimation of fish abundance with mobile hydroacoustic methods, 2009.

P. A. Chambers and J. Et-kaiff, Depth Distribution and Biomass of Submersed Aquatic Macrophyte Communities in Relation to Secchi Depth, Canadian Journal of Fisheries and Aquatic Sciences, vol.42, pp.701-709, 1985.

D. Circulaire, Typologie nationale relative aux eaux de surface, pp.2005-2016

S. Cirés and A. Ballo, A review of the phylogeny, ecology and toxin production of bloom-forming Aphanizomenon spp. and related species within the Nostocales (cyanobacteria), Harmful Alage, vol.54, pp.21-43, 2016.

. Cisalb, Gestion de la ressource piscicole du lac du Bourget, 2008.

. Cisalb, Suivi 2010 des populations piscicoles exploitées par la pêche amateur en bateau sur le lac du Bourget, 2011.

M. D. Clady, Influence of temperature and wind on the survival of early stages of yellow perch (Perca flavescens), C.J.F.A.S, vol.33, pp.1887-1893, 1976.

P. M. Cury, Y. J. Shin, B. Planque, J. M. Durant, J. M. Fromentin et al., Ecosystem oceanography for global change in fisheries, Trends Ecol. Evol, vol.23, pp.338-346, 2008.

Y. Cuypers, B. Vinçon-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, The ISME Journal, vol.5, pp.580-589, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01208054

D. Bernardi, R. Giussani, and G. , The effect of mass fish mortality on zooplankton structure and dynamics in a small Italian lake (Lago di Annone), Verh. Internat. Verein. Limnol, vol.21, pp.285-295, 1978.

C. Deceliéres-vergés, Caractérisation des métriques issue de l'échantillonnage de l'ichtyofaune lacustre et conséquences pour l'évaluation de la qualité du milieu, vol.165, 2008.

C. Deceliere-vergès and J. Guillard, Assessment of the pelagic fish communities: consequences for the lake fish monitoring, Knowl. Manage. Aquat. Ecosyst, vol.389, p.4, 2008.

F. Degiorgi, S. Cachera, J. Guillard, J. C. Raymond, and C. Vergés, Etat de santé du peuplement piscicole Facteur limitant ou ralentissant la restauration. Proposition de remédiation et de gestion halieutique. Cisalb, 73 p Diner N, Marchand P, vol.147, 1995.

M. Dittrich, P. Kurz, and B. Wehrli, The role of autotrophic picocyanobacteria in calcite precipitation in an oligotrophic lake, Geomicrobiol. J, vol.21, pp.45-53, 2004.

C. M. Duarte, Seagrass depth limits, Aquatic Botany, vol.40, pp.363-377, 1991.

C. M. Duarte, D. Planas, and J. Et-penuelas, Macrophytes, taking control of an ancestral home, 1994.

J. P. Dubois, C. Gillet, N. Hilgert, and G. Balvay, The impact of trophic changes over 45 years on the Eurasian perch, Perca fluviatilis, population of Lake Geneva, Aquat. Liv. Resour, vol.21, pp.1-10, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00857819

J. C. Druart and F. Rimet, Protocoles d'analyse du phytoplancton de l'INRA : prélèvement, dénombrement et biovolumes, pp.1-200, 2008.

M. Emmrich, I. J. Winfied, J. Guillard, A. Rustadbakken, C. Vergès et al., Strong correspondence between gillnet catch per unit effort and hydroacoustically derived fish biomass in stratified lakes, Freshw. Biol, vol.57, pp.2436-2448, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02597470

S. T. Forbes and O. Nakken, Manual of methods for fisheries resource survey and appraisal. Part. 2, The use of acoustic instruments for fish detection and abundance estimation, FAO Manuals in Fisheries Science, vol.5, 1972.

C. Forsberg, Nutritional studies of Chara in axenic cultures, Physiologia Plantarum, vol.18, pp.275-290, 1965.

V. Frossard, Etude de la biodiversioté benthique littorale du lac du Bourget. FEDER POIA 2014-2020 -Projet "Grands Lacs Alpins, 2017.

V. Frossard and D. Fontvieille, What is the invasiveness of Hemimysis anomala (Crustacea, Mysidae) in the large deep Lake Bourget, Hydrobiologia, vol.814, pp.219-232, 2018.

D. Gascuel, N. Bez, A. Forest, P. Guillotreau, F. Laloë et al., Future for marine fisheries in Europe (Manifesto of the Association Française d'Halieumétrie), Fish. Res, vol.109, pp.1-6, 2011.

D. Gerdeaux, O. Anneville, and D. Hefti, Fishery changes during re-oligotrophication in 11 peri-alpine Swiss and French lakes over the past 30 years, Acta Oecol, vol.30, pp.161-177, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02657799

D. Gerdeaux, Les fluctuations dans les populations de poissons d'eau douce, Conséquences sur les études écologiques. Revue Franc. Sciences de l'Eau, vol.4, pp.255-276, 1985.
URL : https://hal.archives-ouvertes.fr/hal-02716549

D. Giannetto, A. Carosi, E. Franchi, G. L. Porta, and M. Lorenzoni, Proposed standard weight (Ws) equation for European perch (Perca fluviatilis Linnaeus, 1758), J. Appl. Ichthyol, pp.1-6, 2011.

C. Giguet-covex, F. Arnaud, J. Poulenard, D. Enters, J. L. Reyss et al., Sedimentological and geochemical records of past trophic state and hypolimnetic anoxia in a large, hardwater Lake Bourget, French Alps, J. Palaeolimol, vol.43, pp.171-190, 2010.

C. Gillet, Le déroulement de la fraie des principaux poisons lacustres, Gerdeaux D (éditeur) gestion piscicole des grands plans d'eau, INRA, pp.241-282, 2001.

C. Gillet and P. Quetin, Effect of temperature changes on the reproductive cycle of roach in Lake Geneva from 1983 to, J. Fish Biol, vol.69, pp.518-534, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02657536

Z. M. Gliwicz, Studies on the feeding of pelagic zooplankton in lakes with varying trophy, Ekologia Polska, vol.17, pp.663-708, 1969.

C. J. Gobler, J. M. Burkholder, T. W. Davis, M. J. Harke, T. Johengen et al., The dual role of nitrogen supply in controlling the growth and toxicity of cyanobacterial blooms, Harmful Algae, vol.54, pp.87-97, 2016.

M. Godlewska, M. Colon, L. Doroszczyk, B. D?ugoszewski, C. Verges et al., Hydroacoustical measurements at two frequencies: 70 and 120 kHz -consequences on fish stock estimation, Fish. Res, vol.96, pp.11-16, 2009.

M. Godlewska, M. Colon, A. Jozwik, and J. Guillard, How pulse lengths impact fish stock estimations during hydroacoustic measurements at 70 kHz, Aquat. Liv. Res, vol.24, pp.71-78, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02651369

M. Godlewska, H. Balk, Z. Kaczkowski, T. Jurczak, K. Izydorczyk et al.,

&. Mankiewicz-boczek and J. , Night fish avoidance of Microcystis bloom revealed by simultaneous hydroacoustic measurements of both organisms, Fisheries research, vol.207, pp.74-84, 2018.

J. Guillard, E. Marchal, . Gerdeaux, and . Paris, L'hydroacoustique, méthode d'étude de la distribution spatiale et de l'abondance des peuplements pisciaires lacustres, La gestion piscicole des grands plans d'eaux, pp.215-239, 2001.

J. Guillard, M. E. Perga, M. Colon, and N. Angeli, Hydroacoustic assessment of young-of-year perch, Perca fluviatilis, population dynamics in an oligotrophic lake, Fish. Manag. Ecol, vol.13, pp.319-327, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02661132

J. Guillard and C. Vergés, The repeatability of fish biomass and size distribution estimates obtained by hydroacoustic surveys using various survey designs and statistical analyses, Int. Rev. Hydrobiol, vol.92, pp.605-617, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02657428

J. Guillard and A. Lebourges-dhaussy, Au coeur des bancs de poissons, Pour la Science, vol.436, pp.38-45, 2014.

I. G. Henderson and D. M. Harper, Bird distribution and habitat structure on Lake Naivasha, Kenya. African Journal of Ecology, vol.30, pp.223-232, 1992.

M. Henricsson, Nutritional studies of Chara globularis Thuill, Chara zeylanica Willd., and Chara haitensis Turpin, 1976.

R. Hilborn, Future directions in ecosystem based fisheries management: a personal perspective, Fish. Res, vol.108, pp.235-239, 2011.

R. A. Hough and D. A. Et-putt, Factors Influencing Photosynthetic Productivity of Chara vulgaris L. in a Moderately Productive Hardwater Lake, Journal of Freshwater Ecology, vol.4, pp.411-418, 1988.

É. Hubault, Études thermiques, chimiques et biologiques des eaux des lacs de l'Est de la France, Ann. Ec. Nat. Eaux Forêts, vol.10, pp.113-260, 1947.

B. Irmgra, Phosphorus toxicity in Chara, Aquatic Botany, vol.32, pp.393-395, 1988.

S. Jacquet, J. F. Briand, C. Leboulanger, A. , C. Paolini 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, F. Rimet, M. Perga, G. Paolini, F. Kerrien et al., , 2011.

S. Jacquet, O. Anneville, and I. Domaizon, Evolution de paramètres clés indicateurs de la qualité des eaux et du fonctionnement écologique des grands lacs péri-alpins (Léman, Annecy, Bourget): Etude comparative de trajectoires de restauration post-eutrophisation, Arch Sci, vol.65, pp.225-242, 2012.

S. Jacquet, , 2012.

S. Jacquet, S. Cachera, M. Colon, L. Espinat, C. Girel et al., , 2013.

S. Jacquet, O. Kerimoglu, F. Rimet, G. Paolini, and O. Anneville, Cyanobacterial bloom termination: the story of the disappearance of Planktothrix rubescens from a large restored deep peri-alpine lake, Freshw. Biol, vol.59, pp.2472-2487, 2014.

S. Jacquet, D. Barbet, C. Barbier, S. Cachera, M. Colon et al., , 2016.

, Suivi environnemental des eaux du lac du Bourget pour l'année 2015. Rapport INRA-CISALB-CALB, 205 pages

S. Jacquet, D. Barbet, S. Cachera, L. Crépin, L. Espinat et al., , 2019.

K. Kaiblinger, Water quality assessment in lakes with special focus on phytoplankton indices used within the EU Water Framework Directive (WFD), vol.45, 2008.

C. Kaiblinger, O. Anneville, R. Tadonléké, 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, Hydrobiol, vol.633, pp.67-74, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02660468

N. Kamjunke, D. Straile, and U. Gaedge, Response of heterotrophic bacteria, autotrophic picoplankton and heterotrophic nanoflagellates to re-oligotrophication, J. Plankt. Res, vol.31, pp.899-907, 2009.

P. H. Kansanen, P. L. Vayrynen, and T. , Ordination analysis and bioindices based on zoobenthos communities used to asses pollution of a lake in southern Finland, Hydrobiol, vol.202, pp.153-170, 1990.

J. R. Karr, Assessment of biotic integrity using fish communities. Fisheries, vol.6, pp.21-27, 1981.

M. G. Kelly, L. King, R. I. Jones, P. A. Barker, and B. J. Jamieson, Validation of diatoms as proxies for phytobenthos when assessing ecological status in lakes, Hydrobiologia, vol.610, pp.125-129, 2008.

L. King, G. Clarke, H. Bennion, M. Kelly, and M. Yallop, Recommendations for sampling littoral diatoms in lakes for ecological status assessments, Journal of Applied Phycology, vol.18, issue.1, pp.15-25, 2006.

W. Krzto?, J. Kosiba, A. Pociecha, and E. Wilk-wo?niak, The effect of cyanobacterial blooms on bioand functional diversity of zooplankton communities, Biodiversity and Conservation, vol.28, issue.7, pp.1815-1835, 2019.

L. Kufel and T. Et-ozimek, Can Chara control phosphorus cycling in Lake ?uknajno (Poland)? In E, 1994.

E. Mortensen, M. Jeppesen, &. L. Søndergaard, and . Nielsen, Nutrient Dynamics and Biological Structure in Shallow Freshwater and Brackish Lakes, pp.277-283

E. Laliberté and P. Legendre, A distance-based framework for measuring functional diversity from multiple traits, Ecology, vol.91, pp.299-305, 2010.

C. Laplace-treyture, J. Barbe, A. Dutartre, J. C. Druart, F. Rimet et al., Protocole standardisé d'échantillonnage, de conservation, d'observation et de dénombrement du phytoplancton en plan d'eau pour la mise en oeuvre de la DCE, pp.1-44, 2009.

C. Laplace-treyture, T. Feret, M. Menay, D. Bortoli, and J. , L'IPLAC : un indice phytoplancton, DCE compatible, pour les plans d'eau en France, Journées Internationales de Limnologie et d'Océanographie (JILO), 2012.
URL : https://hal.archives-ouvertes.fr/hal-02597490

A. Laurec and J. C. Le-guen, Dynamique des populations marines exploitées, Rapp. Scient. Techn. 45 CNEXO, vol.119, 1981.

T. L. Lauridsen, E. Jeppesen, S. A. Declerck, L. De-meester, J. M. Conde-porcuna et al., The importance of environmental variables for submerged macrophyte community assemblage and coverage in shallow lakes: differences between northern and southern Europe, 2015.

, Hydrobiologia, vol.744, pp.49-61

X. Lazzaro, Rôle structurant des poissons filtreurs omnivores sur la dynamique des communautés planctoniques et les efflorescences dans les lacs tropicaux peu profonds. HDR Univ. Pierre et Marie Curie -Paris, vol.6, 2009.

L. Roux and M. , Recherches biologiques dans les grands lacs de Savoie. Lacs du Bourget et d'Annecy. J. Abry & Cie (éds) Annecy, vol.164, p.pp, 1928.

R. Love, Dorsal-aspect target strength of an individual fish, J. Acoustical Soc. America, vol.49, pp.816-823, 1971.

D. Maclennan, P. G. Fernandes, and J. Dalen, A consistent approach to definitions and symbols in fisheries acoustics, ICES J. Mar. Sci, vol.59, pp.365-369, 2002.

M. Manca and P. Comoli, Seasonal changes in size of the feeding basket of Leptodora Kindtii (Focke) in Lago-Maggiore as related to variations in prey size selection, Limnol. Oceanogr, vol.40, pp.834-838, 1995.

A. Marchetto, C. Agostinelli, R. Alber, A. Behi, S. Balsamo et al., Indice per valutazione della qualità delle acque lacustri italiane a partire dalle diatomee epifitiche ed epilitiche, CNR, Italy. CNR-ISE, pp.75-92, 2013.

S. Mazard, M. Ostrowski, F. Partensky, and D. J. Scanlan, Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus, Environ. Microbiol, vol.14, pp.372-386, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01218506

T. Mehner, No empirical evidence for community-wide top-down control of prey fish density and size by fish predators in lakes, Limnol. Oceanogr, vol.55, pp.203-213, 2010.

T. Mehner, S. Busch, I. P. Helland, M. Emmrich, and J. Freyhof, Temperature related nocturnal vertical segregation of coexisting coregonids, Ecol. Freshw. Fish, vol.19, pp.408-419, 2010.

M. Menendez and A. Sanchez, Seasonal variations in P-I responses of Chara hispida L. and Potamogeton pectinatus L. from stream mediterranean ponds, Aquatic Botany, vol.61, pp.1-15, 1998.

A. L. Middelboe and S. Et-markager, Depth limits and minimum light requirements of freshwater macrophytes, Freshwater Biology, vol.37, pp.553-568, 1997.

G. Milbrink, T. Timm, and S. Lundberg, Indicative profundal oligochaete assemblages in selected small Swedish lakes, Hydrobiol, vol.468, pp.53-61, 2002.

, Millenium Assessment. 2005. Ecosystems and human well-being: Wetland and Water synthesis, 2005.

. Moldaenke, Algae Online Analyser User Manual, version 2, vol.88, 2002.

K. J. Murphy and J. W. Et-eaton, Effects of Pleasure-Boat Traffic on Macrophyte Growth in Canals, The Journal of Applied Ecology, vol.20, p.713, 1983.

S. L. Nielsen, K. Sand-jensen, J. Borum, and O. Et-geertz-hansen, Depth colonization of eelgrass (Zostera marina) and macroalgae as determined by water, pp.1025-1032

. Onema, Echantillonnage du peuplement piscicole du lac d'Annecy -Application du protocole EN 14757 -Rap. Onema, dél. rég, vol.27, 2007.

. Onema, Methode d'evaluation de la qualité écologique des plans d'eau basée sur les communautés de macrophytes, 2007.

. Onema, Eléments d'analyse. Rap. Onema, dél. rég, vol.27, 2010.

J. Padisak, L. O. Crossetti, and L. Naselli-flores, Use and misuse in the application of the phytoplankton functional classification: a critical review with updates, Hydrobiol, vol.621, pp.1-19, 2009.

S. L. Parker-stetter, L. G. Rudstam, P. J. Sullivan, and D. M. Warner, Standard operating procedures for fisheries acoustic surveys in the Great Lakes, Great Lakes Fish. Comm. Spec. Pub, pp.9-10, 2009.

W. H. Pearsall and P. Et-ullyott, Light Penetration into Fresh Water, Journal of Experimental Biology, vol.11, pp.89-93, 1934.

J. P. Pelletier and A. Orand, Appareil de prélèvement d'un échantillon dans un fluide, 1978.

E. Peltomaa and A. Ojala, Meteorological drivers of the dynamics of autotrophic picoplankton, Freshw. Biol, vol.57, pp.1005-1016, 2012.

M. E. Perga and L. Lainé, Evolution du zooplancton du Léman, Rapp. Comm. Int. prot. Eaux Léman contre Pollut. Campagne, 2008.

M. E. Perga, I. Domaizon, J. Guillard, V. Hamelet, and O. Anneville, Are cyanobacterial blooms trophic dead ends?, Oecologia, vol.172, issue.2, pp.551-562, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651948

S. Personnic, I. Domaizon, T. Sime-ngando, and S. Jacquet, Seasonal variations of microbial abundances and of virus-vs. flagellate-induced mortality of picoplankton in some peri-alpine lakes, J. Plank. Res, vol.31, pp.1161-1177, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00527095

V. I. Proctor, R: A language and environment for statistical computing. R Foundation for Statistical Computing, Journal of Phycology, vol.3, pp.90-92, 1967.

P. Quétin, J. Hustache, P. Perney, and G. Paolini, Analyse mathématique pour la comparaison des mesures de transparence de l'eau avec deux différents disques de Secchi. Le Cahier des Techniques de l'Inra, p.2020, 2020.

C. S. Reynolds, V. Huszar, C. Kruk, L. Naselli-flores, and S. Melo, Toward a functional classification of the freshwater phytoplankton, J. Plankt. Res, vol.24, pp.417-428, 2002.

F. Rimet, Recent views on river pollution and diatoms, Hydrobiologia, vol.683, pp.1-24, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02651508

F. Rimet, A. Bouchez, and B. Montuelle, Benthic diatoms and phytoplankton to assess nutrients in a large lake: Complementarity of their use in Lake Geneva, Ecological Indicators, vol.53, pp.231-239, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02636810

F. Rimet, A. Bouchez, and K. Tapolczai, Spatial heterogeneity of littoral benthic diatoms in a large lake: monitoring implications, Hydrobiologia, vol.771, pp.179-193, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02634391

W. J. Rip, M. R. Ouboter, and H. J. Et-los, Impact of climatic fluctuations on Characeae biomass in a shallow, restored lake in The Netherlands, Hydrobiologia, vol.584, pp.415-424

N. Rooney and J. Et-kalff, Inter-annual variation in submerged macrophyte community biomass and distribution: the influence of temperature and lake morphometry, Aquatic Botany, vol.68, pp.321-335, 2000.

L. Sandin, A. Schartau, J. Aroviita, F. Carse, D. Colvill et al., Water framework directive intercalibration technical report Northern Lake benthic invertebrate ecological assessment methods, 2014.

K. Sand-jensen, N. L. Pedersen, I. Thorsgaard, B. Moeslund, J. Borum et al., 100 years of vegetation decline and recovery in Lake Fure, Denmark. Journal of Ecology, vol.96, pp.260-271, 2008.

M. Scheffer, . Van-den, M. Berg, A. Breukelaar, C. Breukers et al., Vegetated areas with clear water in turbid shallow lakes, Aquatic Botany, vol.49, pp.193-196, 1994.

A. Schwarz and I. Hawes, Effects of changing water clarity on characean biomass and species composition in a large oligotrophic lake, Aquatic Botany, vol.56, pp.169-181, 1997.

G. V. Sgro, E. D. Reavie, J. C. Kingston, A. R. Kireta, M. J. Ferguson et al., A diatom quality index from a diatom-based total phosphorus inference model, Environmental Bioindicators, vol.2, issue.1, pp.15-34, 2007.

. Sila, Suivi scientifique du Lac d'Annecy, rapport, 2009.

E. J. Simmonds and D. N. Maclennan, Fisheries Acoustics: Theory and Practice, vol.437, 2005.

S. Smith, Use of statistical models for the estimation of abundance from groundfish survey data, Can. J. Fish. Aquatic Sci, vol.47, pp.894-903, 1990.

M. Sondergaard, L. Liboriussen, A. R. Pedersen, and E. Jeppesen, Lake restoration by fish removal: short-and long-term effects in 36 Danish Lakes, Ecosystems, vol.11, pp.1291-1305, 2008.

B. Sotton, O. Anneville, S. Cadel-six, I. Domaizon, S. Krys et al., Spatial match between P. rubescens and whitefish in a mesotrophic peri-alpine lake: evidence of toxins accumulation, Harmful Algae, vol.10, pp.749-758, 2011.

C. Stenger-kovacs, K. Buczko, E. Hajnal, and J. Padisak, Epiphytic, littoral diatoms as bioindicators of shallow lake trophic status: Trophic Diatom Index for Lakes (TDIL) developed in Hungary, Hydrobiologia, vol.589, pp.141-154, 2007.

H. Tachet, P. Richoux, M. Bournaud, and P. Ussegli-polatera, , p.588, 2010.

R. Tadonléké, Evidence of warming effects on phytoplankton productivity rates and their dependence on eutrophication status, Limnol. Oceanogr, vol.55, pp.973-982, 2010.

S. M. Thomaz, E. R. Cunha, and . Da, The role of macrophytes in habitat structuring in aquatic ecosystems: methods of measurement, causes and consequences on animal assemblages' composition and biodiversity, Acta Limnologica Brasiliensia, vol.22, pp.218-236, 2010.

K. Torn, G. Martin, J. Kotta, and M. Et-kupp, Effects of different types of mechanical disturbances on a charophyte dominated macrophyte community, Estuarine, Coastal and Shelf Science, vol.87, pp.27-32, 2010.

A. Tosheva and I. Et-traykov, Abundance and Macrophyte Composition in Reservoirs with Different Trophic Status, 2012.

D. Tupper-de-kerckhove, B. J. Shuter, and S. Milne, Acoustically derived fish size-spectra within a lake and the statistical power to detect environmental change, Can. J. Fish. Aquatic Sci, 2016.

E. Van-donk and W. J. Et-van-de-bund, Impact of submerged macrophytes including charophytes on phyto-and zooplankton communities: allelopathy versus other mechanisms, Aquatic Botany, vol.72, pp.261-274, 2002.

R. J. Van-wijk, Ecological studies on Potamogeton pectinatus LI General characteristics, biomass production and life cycles under field conditions, Aquatic Botany, vol.31, pp.211-258, 1988.

W. N. Vant, R. J. Davies-colley, J. S. Clayton, and B. T. Coffey, Macrophyte depth limits in North Island (New Zealand) lakes of differing clarity, Hydrobiologia, vol.137, pp.55-60, 1986.

V. Verneaux and J. Verneaux, Assessing lake functioning using the macrobenthic community with special reference to Chironomidae (Diptera). A subalpine lake (lake Annecy) as an example, Fundamental and Applied Limnology / Archiv für Hydrobiologie, vol.154, pp.68-78, 2002.

V. Verneaux, J. Verneaux, A. Schmitt, C. Lovy, and J. C. Lambert, The Lake Biotic Index (LBI): an applied method for assessing the biological quality of lakes using macrobenthos; the Lake Châlain (French Jura) as an example, Ann. Limnol. -Int. J. Lim, vol.40, pp.1-9, 2004.

S. Villéger, N. Mason, and M. D. , New multidimensional functional diversity indices for a multifaceted framework in functional ecology, Ecology, vol.89, pp.2290-2301, 2008.

B. Vincon-leite, P. E. Bournet, X. Gayte, D. Fontvieille, and B. Tassin, Impact of a flood event on the biogeochemical behaviour of a mesotrophic alpine lake: Lake Bourget (Savoy), Hydrobiol, vol.374, pp.361-377, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00779566

A. Wagner, S. Volkmann, and P. M. Dettinger-klemm, Benthic-pelagic coupling in lake ecosystems: the key role of chironomid pupae as prey of pelagic fish, Ecosphere, vol.3, pp.2-17, 2012.

W. Weaver and C. E. Shannon, The Mathematical Theory of Communication, 1949.

I. J. Winfield, J. M. Fletcher, J. B. James, and C. W. Bean, Assessment of fish populations in still waters using hydroacoustics and survey gill netting: Experiences with Arctic charr (Salvelinus alpinus) in the UK, 2009.

G. Wolfram and M. Dokulil, Leitfaden zur erhebung der biologischen qualitatselemente. Teil B2 -Phytoplankton, vol.50, 2007.

G. Wolfram, M. Dokulil, K. Pall, M. Reichmann, L. Schulz et al., Technical Report + Annexes, 2007.

H. Xu, H. W. Paerl, B. Qin, G. Zhu, and G. Et-gaoa, Nitrogen and phosphorus inputs control phytoplankton growth in eutrophic Lake Taihu, China. Limnology and Oceanography, vol.55, pp.420-432, 2010.

D. Yule, L. M. Evrard, S. Cachera, M. Colon, and J. Guillard, Comparing two fish sampling standards over time: largely congruent results but with caveats, Freshw. Biol, vol.58, pp.2074-2088, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651376

V. Annexe,

, Distributions des cibles en fonction de la profondeur, 2013.

V. Annexe,

, Rendements numériques dans les filets benthiques pour la grémille (GRE), le rotangle (ROT), le poisson chat (PCH), le brochet (BRO), le sandre (SAN) et la perche soleil

. Chambéry, Parmi les conférenciers, Florent Arthaud (enseignant chercheur au CARRTEL) a parlé des indicateurs de suivi de l'état et du fonctionnement écologique des milieux lacustres et périlacustres

, Le bilan global peut être résumé comme suit : -51,7% des tronçons présentent un bon état de fonctionnalité (excellent + bon)

, 3% des tronçons sont classés dans la catégorie moyen

, 0% des tronçons présentent un état dégradé (mauvais + très mauvais)

, Autrement dit, la moitié du lac est en bon état (voire excellent état) et 1/3 est en mauvais état (avec une grande majorité de très mauvais état)

, il est constaté ce qui suit : -La Chautagne (de Conjux à Champfleury) présente globalement des berges en bon état (65,2 %) -La Côte Est (de Champfleury à le Viviers-Plage) présente très peu de berges en bon état fonctionnel (68,5 % des berges Est sont en

, Île aux Cygnes à Bourdeau) et ses rives sont globalement en très mauvais état, vol.7

, -La Côte sauvage (Bourdeau-Conjux), qui représente 30% de berges

, Malgé les limites et quelques biais inhérents à toute méthode d'évaluation et de classification, les résultats obtenus sont intéressants et semblent très cohérents laissant à penser que cet indice est un bon outil d