B. Beisner, D. Haydon, C. , and K. , Alternative stable states in ecology, Front. Ecol. Environ, vol.1, p.1, 2003.

E. Capo, D. Debroas, F. Arnaud, and I. Domaizon, Is planktonic diversity well recorded in sedimentary DNA? Toward the reconstruction of past protistan diversity, Microb. Ecol, vol.70, pp.865-875, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01254671

E. Capo, D. Debroas, F. Arnaud, T. Guillemot, V. Bichet et al., Long-term dynamics in microbial eukaryotes communities : a palaeolimnological view based on sedimentary DNA, Mol. Ecol, vol.25, pp.5925-5943, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01568922

E. Capo, D. Debroas, F. Arnaud, M. Perga, C. Chardon et al., Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming, Environ. Microbiol, vol.19, pp.2873-2892, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01598575

E. Capo, I. Domaizon, D. Maier, D. Debroas, and C. Bigler, To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments, J. Paleolimnol, vol.58, pp.479-495, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01734500

D. A. Caron, A. Z. Worden, P. D. Countway, E. Demir, and K. B. Heidelberg, Protists are microbes too: a perspective, ISME J, vol.3, pp.4-12, 2009.

S. R. Carpenter, D. Ludwig, and W. A. Brock, Management of eutrophication for lakes subject to potentially irreversible change, Ecol. Appl, vol.9, pp.751-771, 1999.

J. A. Cram, C. T. Chow, R. Sachdeva, D. M. Needham, A. E. Parada et al., Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years, ISME J, vol.9, pp.563-580, 2015.

D. R. Dawdy and N. C. Matalas, Statistical and probability analysis of hydrologic data, part III: analysis of variance, covariance and time series, Handbook of Applied Hydrology, a Compendium of Water-Resources Technology, pp.8-68, 1964.

D. Debroas, I. Domaizon, J. Humbert, L. Jardillier, C. Lepère et al., Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data, FEMS Microbiol. Ecol, vol.93, pp.1-14, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01599376

D. Debroas, M. Hugoni, and I. Domaizon, Evidence for an active rare biosphere within freshwater protists community, Mol. Ecol, vol.24, pp.1236-1247, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01245679

I. Domaizon, A. Winegardner, E. Capo, J. Gauthier, and I. Gregory-eaves, DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity, J. Paleolimnol, vol.58, pp.1-21, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01607544

N. Dubois, É. Saulnier-talbot, K. Mills, P. Gell, R. Battarbee et al., First human impacts and responses of aquatic systems: a review of palaeolimnological records from around the world, Anthr. Rev, vol.5, pp.28-68, 2018.

R. C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, vol.10, pp.996-998, 2013.

R. C. Edgar, B. J. Haas, J. C. Clemente, C. Quince, and R. Knight, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, pp.2194-2200, 2011.

D. Fabbri, A. Adamiano, G. Falini, R. De-marco, and I. Mancini, Analytical pyrolysis of dipeptides containing proline and amino acids with polar side chains. Novel 2,5-diketopiperazine markers in the pyrolysates of proteins, J. Anal. Appl. Pyrolysis, vol.95, pp.145-155, 2012.

S. Filker, R. Sommaruga, I. Vila, and T. Stoeck, Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns, Mol. Ecol, vol.25, pp.2286-2301, 2016.

J. A. Fuhrman, J. A. Cram, and D. M. Needham, Marine microbial community dynamics and their ecological interpretation, Nat. Rev. Microbiol, vol.13, pp.133-146, 2015.

V. Gälman, G. Petterson, and I. Renberg, A comparison of sediment varves (1950-2003 AD) in two adjacent lakes in northern sweden, J. Paleolimnol, vol.35, pp.837-853, 2006.

V. Gälman, J. Rydberg, and C. Bigler, Decadal diagenetic effects on d13C and d15N studied in varved lake sediment, Limnol. Oceanogr, vol.54, pp.917-924, 2009.

R. J. Gast, M. R. Dennett, C. , and D. A. , Characterization of protistan assemblages in the ross sea, antarctica, by denaturing gradient gel electrophoresis, Appl. Environ. Microbiol, vol.70, pp.2028-2037, 2004.

C. R. Giner, É. Balagu, V. Krabberød, A. K. Ferrera, I. Re et al., Quantifying long-term recurrence in planktonic microbial eukaryotes, Mol. Ecol, vol.28, pp.923-935, 2018.

G. Grosbois, H. Mariash, T. Schneider, and M. Rautio, Under-ice availability of phytoplankton lipids is key to freshwater zooplankton winter survival, Sci. Rep, vol.7, p.11543, 2017.

S. E. Hampton, A. W. Galloway, S. M. Powers, T. Ozersky, K. H. Woo et al., Ecology under lake ice, Ecol. Lett, vol.20, pp.98-111, 2017.

T. Hastie and R. Tibshirani, Generalized additive models, Stat. Sci, vol.1, pp.297-310, 1986.

T. C. Hsieh, K. H. Ma, and A. Chao, iNEXT: an R package for interpolation and extrapolation of species diversity (Hill numbers), Methods Ecol. Evol, vol.7, pp.1451-1456, 2016.

Y. Huot, M. Babin, F. Bruyant, C. Grob, M. S. Twardowski et al., Does chlorophyll a provide the best index of phytoplankton biomass for primary productivity studies?, Biogeosci. Discuss, vol.4, pp.707-745, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00330232

B. W. Ibelings, R. Portielje, E. H. Lammens, R. Noordhuis, . Van-den et al., Resilience of alternative stable states during the recovery of shallow lakes from eutrophication: Lake Veluwe as a case study, Ecosystems, vol.10, pp.4-16, 2007.

M. Ishiwatari, R. Ishiwatari, H. Sakashita, T. Tatsumi, and H. Tominaga, Pyrolysis of chlorophyll a after preliminary heating at a moderate temperature: Implications for the origin of prist-1-ene on kerogen pyrolysis, J. Anal. Appl. Pyrolysis, vol.18, pp.207-218, 1991.

N. A. James and D. S. Matteson, ecp: An R Package for Nonparametric Multiple Change Point Analysis of Multivariate Data, vol.8, 2013.

E. Jeppesen, J. P. Jensen, M. Sondergaard, T. Lauridsen, and F. Landkildehus, Trophic structure, species richness and biodiversity in Danish lakes: changes along a phosphorus gradient, Freshw. Biol, vol.45, pp.201-218, 2000.

S. Kosten, V. L. Huszar, E. Bécares, L. S. Costa, E. Donk et al., Warmer climates boost cyanobacterial dominance in shallow lakes, Glob. Chang. Biol, vol.18, pp.118-126, 2012.

M. Lizotte, Phytoplankton and primary production, Polar Lakes and Rivers: Limnology of Arctic and Antarctic Aquatic Ecosystems, pp.157-178, 2008.

D. Maier, Combining Limnology and Paleolimnology: A Refined Understanding of Environmental Sediment Signal Formation in a Varved Lake, vol.2, p.1097345, 2017.

D. Maier, S. Diehl, and C. Bigler, Inter-annual variation in seasonal diatom sedimentation reveals the importance of late winter processes and their timing for sediment signal formation, Limnol. Ocean, vol.64, pp.1186-1199, 2019.

P. A. Meyers, R. ;. Ishiwatari, P. Spaak, I. Domaizon, N. Dubois et al., Lacustrine organic geochemistryan overview of indicators of organic matter sources and diagenesis in lake sediments, Nat. Ecol. Evol, vol.20, pp.317-324, 1993.

B. Moss, Cogs in the endless machine: Lakes, climate change and nutrient cycles: a review, Sci. Total Environ, vol.434, pp.130-142, 2012.

I. Mukherjee, Y. Hodoki, and S. Nakano, Seasonal dynamics of heterotrophic and plastidic protists in the water column of Lake Biwa, Japan. Aquat. Microb. Ecol, vol.80, pp.123-137, 2017.

L. Naselli-flores and R. Barone, Phytoplankton dynamics and structure : a comparative analysis in natural and man-made water bodies of different trophic state, Hydrobiologia, vol.438, pp.65-74, 2000.

R. J. Newton, S. E. Jones, A. Eiler, K. D. Mcmahon, and S. Bertilsson, A guide to the natural history of freshwater lake bacteria. Microbiol, Mol. Biol. Rev, vol.75, pp.14-49, 2011.

R. T. Nguyen, H. R. Harvey, X. Zang, J. D. Van-heemst, M. Hetényi et al., Preservation of algaenan and proteinaceous material during the oxic decay of Botryococcus braunii as revealed by pyrolysis-gas chromatography/mass spectrometry and 13C NMR spectroscopy, Org. Geochem, vol.34, pp.261-270, 2003.

S. Ninnes, J. Tolu, C. Meyer-jacob, T. M. Mighall, and R. Bindler, Investigating molecular changes in organic matter composition in two Holocene lake-sediment records from central Sweden using pyrolysis-GC/MS, J. Geophys. Res. Biogeosciences, vol.122, pp.1423-1438, 2017.

A. J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, P. R. Minchin et al., The vegan Package. Community Ecology Package. Available online at, 2015.

H. W. Paerl, Assessing and managing nutrient-enhanced eutrophication in estuarine and coastal waters: interactive effects of human and climatic perturbations, Ecol. Eng, vol.26, pp.40-54, 2006.

H. W. Paerl and J. Huisman, Climate. Blooms like it hot, Science, vol.320, pp.57-58, 2008.

E. Peinerud, J. Ingri, and C. Pontér, Non-detrital Si concentrations as an estimate of diatom concentrations in lake sediments and suspended material, Chem. Geol, vol.177, pp.229-239, 2001.

G. Petterson, I. Renberg, S. S. De-luna, P. Arnqvist, J. Anderson et al., Climatic influence on the inter-annual variability of late-Holocene minerogenic sediment supply in a boreal forest catchment, Earth Surf. Process. Landforms, vol.35, pp.390-398, 2010.

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

S. D. Princiotta and R. W. Sanders, Heterotrophic and mixotrophic nanoflagellates in a mesotrophic lake: abundance and grazing impacts across season and depth, Limnol. Oceanogr, vol.62, pp.632-644, 2017.

E. Pruesse, C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig et al., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, vol.35, pp.7188-7196, 2007.

I. Renberg, Improved methods for sampling, photographing and varve-counting of varved lake sediments, Boreas, vol.10, pp.255-258, 1981.

I. Renberg, Photographic demonstration of the annual nature of a varve type common in N. Swedish lake sediments, Hydrobiologia, vol.140, pp.93-95, 1986.

L. Romero-viana, À. Juli, R. Camacho, A. Vicente, E. Miracle et al., Climate signal in varve thickness: Lake La Cruz (Spain), a case study, J. Paleolimnol, vol.40, pp.703-714, 2008.

K. M. Rühland, A. M. Paterson, and J. P. Smol, Lake diatom responses to warming: reviewing the evidence, J. Paleolimnol, vol.54, pp.1-35, 2015.

J. Rydberg, Wavelength dispersive X-ray fluorescence spectroscopy as a fast, non-destructive and cost-effective analytical method for determining the geochemical composition of small loose-powder sediment samples, J. Paleolimnol, vol.52, pp.265-276, 2014.

J. Rydberg and A. Martínez-cortizas, Geochemical assessment of an annually laminated lake sediment record from northern Sweden: a multi-core, multi-element approach, J. Paleolimnol, vol.51, pp.499-514, 2014.

P. Salmi and K. Salonen, Regular build-up of the spring phytoplankton maximum before ice-break in a boreal lake, Limnol. Oceanogr, vol.61, pp.240-253, 2016.

A. Shade, H. Peter, S. D. Allison, D. L. Baho, M. Berga et al., Fundamentals of microbial community resistance and resilience, Front. Microbiol, vol.3, p.417, 2012.

E. Sherr and B. Sherr, Role of microbes in pelagic food webs: a revised concept, Limnol. Oceanogr, vol.33, pp.1225-1227, 1988.

M. Simon, P. López-garcía, P. Deschamps, D. Moreira, G. Restoux et al., Marked seasonality and high spatial variability of protist communities in shallow freshwater systems, ISME J, vol.9, pp.1941-1953, 2015.

G. Simpson, A. , and N. , Deciphering the effect of climate change and separating the influence of confounding factors in sediment core records using additive models, Limnol. Ocean, vol.54, pp.2529-2541, 2009.

G. L. Simpson, Modelling palaeoecological time series using generalised additive models, Front. Ecol. Evol, vol.6, p.149, 2018.

E. M. Soares, C. C. Figueredo, B. Gücker, and I. G. Boëchat, Effects of growth condition on succession patterns in tropical phytoplankton assemblages subjected to experimental eutrophication, J. Plankton Res, vol.35, pp.1141-1153, 2013.

J. Tolu, L. Gerber, J. Boily, and R. Bindler, High-throughput characterization of sediment organic matter by pyrolysis-gas chromatography/mass spectrometry and multivariate curve resolution: a promising analytical tool in (paleo)limnology, Anal. Chim. Acta, vol.880, pp.93-102, 2015.

J. Tolu, J. Rydberg, C. Meyer-jacob, L. Gerber, and R. Bindler, Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lake, Biogeosciences, vol.14, pp.1773-1792, 2017.

T. J. Tse, L. E. Doig, S. Tang, X. Zhang, W. Sun et al., Combining high-throughput sequencing of sedaDNA and traditional paleolimnological techniques to infer historical trends in cyanobacterial communities, Environ. Sci. Technol, vol.52, pp.6842-6853, 2018.

Y. Van-de-peer, P. Rijk, J. Wuyts, T. Winkelmans, D. Wachter et al., The european small subunit ribosomal RNA database, Nucleic Acids Res, vol.28, pp.175-176, 2000.

A. Vuillemin, D. Ariztegui, F. Horn, J. Kallmeyer, and W. D. Orsi, Microbial community composition along a 50 000-year lacustrine sediment sequence, FEMS Microbiol. Ecol, vol.94, pp.1-14, 2018.

K. A. Warner, R. Fowler, R. Northington, M. , and H. , Comparison using two years with ice-out that differed by more than three how does changing ice-out affect arctic versus ice-out that differed by more than three weeks, vol.10, pp.1-20, 2018.

G. A. Weyhenmeyer, M. Meili, and D. M. Livingstone, Nonlinear temperature response of lake ice breakup, Geophys. Res. Lett, vol.31, pp.6-9, 2004.

C. M. Whipps, J. W. Fournie, D. A. Morrison, C. Azevedo, and E. Matos, Phylogeny of fish-infecting Calyptospora species (Apicomplexa: Eimeriorina), Parasitol. Res, vol.111, pp.1331-1342, 2012.

H. Wickham, ggplot2: Elegant Graphics for Data Analysis, pp.9-26, 2016.

C. E. Williamson, J. E. Saros, W. F. Vincent, and J. P. Smol, Lakes and reservoirs as sentinels, integrators, and regulators of climate change, Limnol. Oceanogr, vol.54, pp.2273-2282, 2009.

S. Wood, Package 'mgcv, 2015.