C. Amoros, , 1984.

, Bulletin Mensuel Société Linnéenne de Lyon, vol.53, pp.72-145

O. Anneville, G. Dur, F. Rimet, and S. Souissi, Plasticity in phytoplankton annual periodicity: an adaptation to longterm environmental changes, Hydrobiologia, vol.824, pp.121-141, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02621272

O. Anneville, S. Gammeter, and D. Straile, Phosphorus decrease and climate variability: mediators of synchrony in phytoplankton changes among European peri-alpine lakes, Freshwater Biol, vol.50, pp.1731-1746, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02678730

O. Anneville and C. Leboulanger, Long-term changes in the vertical distribution of phytoplankton biomass and primary production in Lake Geneva: a response to the olgotrophication, Atti Associazione Italiana Oceanologia Limnologia, vol.14, pp.25-35, 2001.

O. Anneville, J. C. Molinero, S. Souissi, G. Balvay, and D. Gerdeaux, Long-term changes in the copepod community of Lake Geneva, J. Plankton Res, vol.29, pp.49-59, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02660917

O. Anneville, J. C. Molinero, S. Souissi, and D. Gerdeaux, Seasonal and interannual variability of cladoceran communities in two peri-alpine lakes: uncoupled response to the 2003 heat wave, Journal of Plankton Research, vol.32, pp.913-925, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00761588

, Water quality -Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique), European Committee for Standardisation EN, vol.15204, pp.1-42, 2006.

R. Civade, T. Dejean, A. Valentini, N. Roset, J. Raymond et al., Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system, PLoS One, vol.11, p.157366, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01470192

P. Clastre, C. Pichot, and A. Chanzy, Vocabulary for analysis and experimentation on terrestrial and aquatic ecosystems. Portail Data INRAE V3, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01604193

J. Clobert, A. Chanzy, L. Galliard, J. Chabbi, A. Greiveldinger et al., How to integrate experimental research approaches in ecological and environmental studies: AnaEE France as an Example, Front. Ecol. Evol.-Agroecol, vol.6, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02350525

H. A. Dugan, S. L. Bartlett, S. M. Burke, J. P. Doubek, F. E. Krivak-tetley et al., Salting our freshwater lakes, Proceedings of the North American Society, vol.114, pp.4453-4458, 2017.

H. A. Dugan, J. C. Summers, N. K. Skaff, F. E. Krivak-tetley, J. P. Doubek et al., Long-term chloride concentrations in North American and European freshwater lakes, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608902

B. Dussart, Les Copépodes des eaux Continentales d'Europe Occidentale, Tome I : Calanoïdes et Harpacticoïdes, p.500, 1967.

B. Dussart, Les Copépodes des eaux Continentales d'Europe Occidentale, p.292, 1969.

V. Elbrecht, E. E. Vamos, K. Meissner, J. Aroviita, and L. F. , Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring, Methods Ecol. Evol, vol.8, pp.1265-1275, 2017.

L. Feret, A. Bouchez, and F. Rimet, Benthic diatom communities in high altitude lakes: a large scale study in the French Alps. Intern, J. Limnol, vol.53, pp.411-423, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02619291

B. Foley, I. D. Jones, S. C. Maberly, and B. Rippey, Long-term changes in oxygen depletion in a small temperate lake: effects of climate change and eutrophication, Freshwater Biol, vol.57, pp.278-289, 2012.

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

J. Guillard and C. Vergès, The repeatability of fish biomass and size distribution estimates obtained by hydroacoustic surveys using various sampling strategies and statistical analyses, Int. Rev. Hydrobiol, vol.92, pp.605-617, 2007.

D. Gumy and L. De-alencastro, , 2001.

L. Cipel,

P. Hebert, A. Cywinska, and S. L. Ball, Biological identifications through DNA barcodes, P. Roy. Soc. B, vol.270, pp.313-321, 2003.

S. Jacquet, D. Barbet, S. Cachera, L. Crepin, L. Espinat et al., , 2018.

. France,

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. Monitor. Assess, vol.186, pp.3455-3476, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02639966

S. Jacquet, O. Kerimoglu, F. Rimet, G. Paolini, and O. Anneville, Cyanobacterial bloom termination: the disappearance of Planktothrix rubescens from Lake Bourget after restoration, Freshwater Biol, vol.59, pp.2472-2487, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02634181

S. Jacquet, F. Rimet, and J. C. Druart, Composition and dynamics of the phytoplanktonic communities in 3 large and deep Western European Lakes: An outline of the evolution from, Phytoplankton: Biology, Classification and Environmental Impacts, pp.131-150, 2004.

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, pp.67-74, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02660468

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

L. Kermarrec, A. Franc, F. Rimet, P. Chaumeil, J. F. Humbert et al., Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms, Mol. Ecol. Res, vol.13, pp.607-619, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02644189

B. M. Kraemer, O. Anneville, S. Chandra, M. Dix, E. Kuusisto et al., Morphometry and average temperature affect lake stratification responses to climate change, Geophys. Res. Lett, vol.42, pp.4981-4988, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02640487

L. Moal, M. Gascuel-odoux, C. Ménesguen, A. Souchon, Y. Étrillard et al., Eutrophication: A new wine in an old bottle?, Sci. Total Environ, vol.651, pp.1-11, 2019.
URL : https://hal.archives-ouvertes.fr/hal-01880089

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, Limnol. Oceanogr, vol.63, pp.628-646, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02628735

E. Lefrançois, L. Apothéloz-perret-gentil, P. Blancher, S. Botreau, C. Chardon et al., Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program, Environ. Sci. Pollut. Res, pp.1-9, 2018.

C. Lepere, I. Domaizon, and D. Debroas, Unexpected importance of potential parasites in the composition of the freshwater small-eukaryote community, Appl. Environ. Microbiol, vol.74, pp.2940-2949, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00528208

J. Madin, S. Bowers, M. Schildhauer, S. Krivov, D. Pennington et al., An ontology for describing and synthesizing ecological observation data, Ecol. Inform, vol.2, pp.279-296, 2007.

J. F. Mangot, I. Domaizon, N. Taib, N. Marouni, E. Duffaud et al., Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes, Environ. Microbiol, vol.15, pp.1745-1758, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00821927

R. Marcé, G. George, P. Buscarinu, M. Deidda, J. Dunalska et al., Automatic High Frequency Monitoring for Improved Lake and Reservoir Management, Environ. Sci. Technol, vol.50, pp.10780-10794, 2016.

M. Mirtl, T. E. Borer, I. Djukic, M. Forsius, H. Haubold et al., Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions, Sci. Total Environ, vol.626, pp.1439-1462, 2018.

J. C. Molinero, O. Anneville, S. Souissi, G. Balvay, and D. Gerdeaux, Anthropogenic and climate forcing on the long-term changes of planktonic rotifers in Lake Geneva, Europe. J. Plankton Res, vol.28, pp.287-296, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02760724

J. C. Molinero, O. Anneville, S. Souissi, L. Lainé, and D. Gerdeaux, Decadal changes in water temperature and ecological time series in Lake Geneva, Europe-relationship to subtropical Atlantic climate variability, Climate Rese, vol.34, pp.15-23, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02653349

G. Monet, D. Barbet, A. Schellenberger, E. G. , and A. , OLA's Database Datatypes modeling diagrams. Portail Data INRAE, p.1, 2020.

G. Monet and D. Barbet, Terms of Use of OLA-IS (Observatory of LAkes -Information System, Portail Data INRAE, p.1, 2020.

B. Montuelle and A. Clemens, , 2015.

E. Graie, Domaine scientifique de la Doua, p.205

T. Nõges, O. Anneville, J. Guillard, J. Haberman, A. Järvalt et al., Fisheries impacts on lake ecosystem structure in the context of a changing climate and trophic state, J. Limnol, vol.77, pp.46-61, 2018.

C. M. O'reilly, S. R. Alin, P. Plisnier, A. S. Cohen, and B. A. Mckee, Climate change decreases aquatic ecosystem productivity of Lake Tanganyika, Africa. Nature, vol.424, pp.766-768, 2003.

C. M. O'reilly, S. Sharma, D. K. Gray, S. E. Hampton, J. S. Read et al., Rapid and highly variable warming of lake surface waters around the globe, Geophys. Res. Lett, vol.42, pp.10773-10781, 2015.

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, Hydrobiologia, vol.621, pp.1-19, 2009.

J. P. Pelletier, , 1983.

, Rev. Franc. Sci. Eau, vol.2, pp.339-366

J. P. Pelletier and A. Orand, , 1978.

M. Perga, V. Frossard, J. Alric, B. Arnaud, F. Berthon et al., High-resolution paleolimnology opens new management perspectives for lakes adaptation to climate warming, Front. Ecol. Evol, vol.3, pp.1-17, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01691615

D. Pont, M. Rocle, A. Valentini, R. Civade, P. Jean et al., Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation, Sci. Rep, vol.8, p.10361, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01834958

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

F. Rimet and J. Druart, A trait database for Phytoplankton of temperate lakes, Ann. Limnolog. -Internat. J. Limnol, vol.54, p.18, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02627684

F. Rimet, J. C. Druart, and O. Anneville, Exploring the dynamics of plankton diatom communities in Lake Geneva using emergent self-organizing maps, Ecol. Inform, vol.4, pp.99-110, 1974.
URL : https://hal.archives-ouvertes.fr/hal-02656963

F. Rimet, V. Vasselon, A. -keszte, B. Bouchez, and A. , Do we similarly assess diversity with microscopy and highthroughput sequencing? Case of microalgae in lakes, Org. Divers. Evol, vol.18, pp.51-62, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02625205

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

K. C. Rose, K. C. Weathers, A. L. Hetherington, and D. P. Hamilton, Insights from the Global Lake Ecological Observatory Network (GLEON), vol.6, pp.476-482, 2016.

A. Schellenberger, G. Monet, D. Barbet, M. D. Enrico, G. Fiocca et al., Software Architecture of the OLA Observatory Information System for Lake Environmental Research. Portail Data INRAE V2, 2019.

A. Schellenberger, P. Tcherniatinsky, V. J. Yayende-guedoka, R. Yahiaoui, M. D. Monet et al., Software architecture for environnemental research observatories information systems: central component. Portail Data INRAE V1, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02788490

S. Sharma, D. K. Gray, J. S. Read, O. Reilly, C. M. Schneider et al., A global database of lake surface temperatures collected by in situ and satellite methods from, Sci. Data, vol.2, p.150008, 1985.
URL : https://hal.archives-ouvertes.fr/hal-02638235

I. Shiklomanov, Water in crisis: A guide to the world's fresh water resources, 1993.

E. Steemann-nielsen, The use of radio-active carbon (C14) for measuring organic production in the sea, ICES J. Mar. Sci, vol.18, pp.117-140, 1952.

R. Stemberger, A guide to rotifers of the Laurentian Great Lakes. Scholar's Choice, p.186, 1979.

R. D. Tadonleke, J. Lazzarotto, O. Anneville, and J. C. Druart, Phytoplankton productivity increased in Lake Geneva despite phosphorus loading reduction, J. Plankton Res, vol.31, pp.1179-1194, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02668129

N. Taib, J. F. Mangot, I. Domaizon, G. Bronner, and D. Debroas, Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: New insights into the freshwater protist diversity, PLoS One, vol.8, pp.1-13, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00840867

K. Tapolczai, O. Anneville, J. Padisak, N. Salmaso, G. Morabito et al., Occurrence and mass development of Mougeotia spp. (Zygnemataceae) in large, deep lakes, Hydrobiologia, vol.745, pp.17-29, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02641434

Z. E. Taranu, G. Eaves, I. Leavitt, P. R. Bunting, L. Buchaca et al., Acceleration of cyanobacterial dominance in north temperate-subarctic lakes during the Anthropocene, Ecol. Lett, vol.18, pp.375-384, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02639692

H. Utermöhl, , 1958.

M. , Verein. Theor. Angew. Limnol, vol.9, pp.1-38

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

M. Voigt and W. Koste, Rotatoria, I: Textband, p.673, 1978.

M. Voigt, W. Koste, . Rotatoria, and . Ii:-tafelband, , p.237

G. A. Weyhenmeyer, J. Hartmann, D. O. Hessen, J. Kopá?ek, J. Hejzlar et al., Widespread diminishing anthropogenic effects on calcium in freshwaters, Sci. Rep, vol.9, pp.1-10, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02609508

C. Wohner, J. Peterseil, D. Poursanidis, T. Kliment, M. Wilson et al., DEIMS-SDR -A web portal to document research sites and their associated data, Ecol. Inform, vol.5, pp.15-24, 2019.

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