Schindler, D. W. Lakes as sentinels and integrators for the effects of climate change on watersheds, airsheds, and landscapes. Limnol. Oceanogr. 54, 2349–2358 (2009).
Google Scholar
Steffen, W., Crutzen, P. J. & McNeill, J. R. The Anthropocene: are humans now overwhelming the great forces of nature. AMBIO J. Hum. Environ. 36, 614–621 (2007).
Steffen, W., Broadgate, W., Deutsch, L., Gaffney, O. & Ludwig, C. The trajectory of the anthropocene: The great acceleration. Anthropoc. Rev. 2, 81–98 (2015).
Google Scholar
Richardson, D. et al. Transparency, geomorphology and mixing regime explain variability in trends in lake temperature and stratification across Northeastern North America (1975–2014). Water 9, 442 (2017).
Google Scholar
Jane, S. F. et al. Widespread deoxygenation of temperate lakes. Nature 594, 66–70 (2021).
Google Scholar
Adrian, R. et al. Lakes as sentinels of climate change. Limnol. Oceanogr. 54, 2283–2297 (2009).
Google Scholar
Smol, J. P. Pollution of lakes and rivers: a paleoenvironmental perspective. (Blackwell Pub, 2008).
Bennion, H., Simpson, G. L. & Goldsmith, B. J. Assessing degradation and recovery pathways in lakes impacted by eutrophication using the sediment record. Front. Ecol. Evol. 3, (2015).
Arseneau, K. M. A., Driscoll, C. T., Cummings, C. M., Pope, G. & Cumming, B. F. Adirondack (NY, USA) reference lakes show a pronounced shift in chrysophyte species composition since ca. 1900. J. Paleolimnol. 56, 349–364 (2016).
Ellegaard, M. et al. Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun. Biol. 3, 169 (2020).
Google Scholar
Coolen, M. J. L. et al. Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene. Proc. Natl. Acad. Sci. 110, 8609–8614 (2013).
Google Scholar
Capo, E., Domaizon, I., Maier, D., Debroas, D. & Bigler, C. 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. 58, 479–495 (2017).
Google Scholar
Capo, E. et al. Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming: Long-term dynamics of microbial eukaryotes. Environ. Microbiol. 19, 2873–2892 (2017).
Google Scholar
Capo, E. et al. Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: Overview and recommendations. Quaternary 4, 6 (2021).
Google Scholar
Domaizon, I., Winegardner, A., Capo, E., Gauthier, J. & Gregory-Eaves, I. DNA-based methods in paleolimnology: New opportunities for investigating long-term dynamics of lacustrine biodiversity. J. Paleolimnol. 58, 1–21 (2017).
Google Scholar
Domaizon, I. et al. DNA from lake sediments reveals the long-term dynamics and diversity of Synechococcus assemblages. Biogeosciences 10, 3817–3838 (2013).
Google Scholar
Zhang, H. et al. Climate and nutrient-driven regime shifts of cyanobacterial communities in low-latitude plateau lakes. Environ. Sci. Technol. 55, 3408–3418 (2021).
Google Scholar
Keck, F. et al. Assessing the response of micro-eukaryotic diversity to the Great acceleration using lake sedimentary DNA. Nat. Commun. 11, 3831 (2020).
Google Scholar
Cockrell, C. The value of microorganisms. Environ. Ethics 27, 375–390 (2005).
Google Scholar
Sagova-Mareckova, M. et al. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Res. 191, 116767 (2021).
Google Scholar
Likens, G. Plankton of Inland Waters a derivative of Encyclopedia of Inland Waters. in (Elsevier Science & Technology Books, 2010).
Weisse, T. Functional diversity of aquatic ciliates. Eur. J. Protistol. 61, 331–358 (2017).
Google Scholar
Finlay, B. J. & Esteban, G. F. Freshwater protozoa: Biodiversity and ecological function. Biodivers. Conserv. 7, 1163–1186 (1998).
Google Scholar
Stoecker, D. K. & Lavrentyev, P. J. Mixotrophic plankton in the polar seas: A pan-arctic review. Front. Mar. Sci. 5, 292 (2018).
Google Scholar
Bick, H. Ciliated protozoa : an illustrated guide to the species used as biological indicators in freshwater biology. (World Health Organisation, 1972).
Curds, C. R. An illustrated key to the British Freshwater Ciliated Protozoa commonly found in activated sludge. (Her Majesty’s Stationary Office, 1969).
Pitsch, G. et al. Seasonality of planktonic freshwater ciliates: Are analyses based on V9 regions of the 18S rRNA gene correlated with morphospecies counts?. Front. Microbiol. 10, 248 (2019).
Google Scholar
Lynn, D. H. The Ciliated Protozoa. (Springer, 2010).
Adl, S. M. et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52, 399–451 (2005).
Google Scholar
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Google Scholar
Ibrahim, A. et al. Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA. Mol. Ecol. 30, 3040–3056 (2021).
Google Scholar
Mosher, J. J. & Findlay, R. H. Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams. Appl. Environ. Microbiol. 77, 7681–7688 (2011).
Google Scholar
Bennion, H., Monteith, D. & Appleby, P. Temporal and geographical variation in lake trophic status in the English Lake District: evidence from (sub)fossil diatoms and aquatic macrophytes. Freshw. Biol. 45, 394–412 (2000).
Google Scholar
Hornung, M. et al. The sensitivity of surface waters of Great Britain to acidification predicted from catchment characteristics. Environ. Pollut. 87, 207–214 (1995).
Google Scholar
Gámez-Virués, S. et al. Landscape simplification filters species traits and drives biotic homogenization. Nat. Commun. 6, 8568 (2015).
Google Scholar
Nielsen, T. F., Sand-Jensen, K., Dornelas, M. & Bruun, H. H. More is less: Net gain in species richness, but biotic homogenization over 140 years. Ecol. Lett. 22, 1650–1657 (2019).
Google Scholar
Magurran, A. E., Dornelas, M., Moyes, F., Gotelli, N. J. & McGill, B. Rapid biotic homogenization of marine fish assemblages. Nat. Commun. 6, 8405 (2015).
Google Scholar
Petsch, D. K. Causes and consequences of biotic homogenization in freshwater ecosystems: Biotic homogenization of freshwater systems. Internat. Rev. Hydrobiol. 101, 113–122 (2016).
Google Scholar
Perga, M.-E. et al. High-resolution paleolimnology opens new management perspectives for lakes adaptation to climate warming. Front. Ecol. Evol. 3, (2015).
Rioual, P. Limnological characteristics of 25 lakes of the French Massif Central. Ann. Limnol. Int. J. Lim. 38, 311–327 (2002).
Google Scholar
Belle, S. et al. Increase in benthic trophic reliance on methane in 14 French lakes during the Anthropocene. Freshw. Biol. 61, 1105–1118 (2016).
Google Scholar
Télesphore, S.-N. Population dynamics of autotrophic picoplankton in relation to environmental factors in a productive lake. Aquat. Sci. 57, 91–105 (1995).
Google Scholar
Esteban, G. F., Fenchel, T. & Finlay, B. J. Mixotrophy in Ciliates. Protist 161, 621–641 (2010).
Google Scholar
Woelfl, S. & Geller, W. Chlorella-bearing ciliates dominate in an oligotrophic North Patagonian lake (Lake Pirehueico, Chile). Freshw. Biol. 47, 231–242 (2002).
Google Scholar
Berninger, U.-G., Finlay, B. J. & Canter, H. M. The spatial distribution and ecology of Zoochlorellae-bearing ciliates in a productive pond. J. Protozool. 33, 557–563 (1986).
Google Scholar
Haraguchi, L., Jakobsen, H. H., Lundholm, N. & Carstensen, J. Phytoplankton community dynamic: A driver for ciliate trophic strategies. Front. Mar. Sci. 5, 272 (2018).
Google Scholar
Staehr, P. A., Testa, J. & Carstensen, J. Decadal changes in water quality and net productivity of a shallow danish estuary following significant nutrient reductions. Estuaries Coasts 40, 63–79 (2017).
Google Scholar
Jeppesen, E., Pierson, D. & Jennings, E. Effect of extreme climate events on lake ecosystems. Water 13, 282 (2021).
Google Scholar
Sonntag, B., Strüder-Kypke, M. C. & Summerer, M. Uroleptus willii nov. sp., a euplanktonic freshwater ciliate (Dorsomarginalia, Spirotrichea, Ciliophora) with algal symbionts: morphological description including phylogenetic data of the small subunit rRNA gene sequence and ecological notes. Denisia 23, 279–288 (2008).
Mitra, A. et al. The role of mixotrophic protists in the biological carbon pump. Biogeosciences 11, 995–1005 (2014).
Google Scholar
Munawar, M., Niblock, H., Fitzpatrick, M. & Lorimer, J. Ciliate ecology in the eutrophic Bay of Quinte, Lake Ontario: Community structure and feeding characteristics. Aquat. Ecosyst. Health Manage. 23, 35–44 (2020).
Google Scholar
Carrick, H. J. An under-appreciated component of biodiversity in plankton communities: The role of protozoa in Lake Michigan (a case study). Hydrobiologia 551, 17–32 (2005).
Google Scholar
Beaver, J. R. & Crisman, T. L. The role of ciliated protozoa in pelagic freshwater ecosystems. Microb. Ecol. 17, 111–136 (1989).
Google Scholar
Carrias, J.-F., Thouvenot, A., Amblard, C. & Sime-Ngando, T. Dynamics and growth estimates of planktonic protists during early spring in Lake Pavin France. Aquat. Microb. Ecol. 24, 163–174 (2001).
Google Scholar
Sherr, E. B. & Sherr, B. F. Significance of predation by protists in aquatic microbial food webs. Antonie Van Leeuwenhoek 81, 293–308 (2002).
Google Scholar
Van Wichelen, J. et al. Planktonic ciliate community structure in shallow lakes of lowland Western Europe. Eur. J. Protistol. 49, 538–551 (2013).
Google Scholar
Posch, T. et al. Network of interactions between ciliates and phytoplankton during spring. Front. Microbiol. 6, (2015).
DeNicola, D. M. & Kelly, M. Role of periphyton in ecological assessment of lakes. Freshw. Sci. 33, 619–638 (2014).
Google Scholar
Hao, B. et al. Warming effects on periphyton community and abundance in different seasons are influenced by nutrient state and plant type: A shallow lake mesocosm study. Front. Plant Sci. 11, 404 (2020).
Google Scholar
Schindler, D. E. Warmer climate squeezes aquatic predators out of their preferred habitat. Proc. Natl. Acad. Sci. USA 114, 9764–9765 (2017).
Google Scholar
Millet, L. et al. Diagnostic fonctionnel des systèmes lacustres de Gérardmer, Longemer et RetournemerUne approche combinée limnologie/paléolimnologie. 38 (2015).
Sabart, M. Projet DIVERSITOX (DIVERSIté des cyanoTOXines dans différents milieux aquatiques ligériens et relation avec la biodiversité microbienne). 28 (2018).
Jenny, J.-P. et al. A spatiotemporal investigation of varved sediments highlights the dynamics of hypolimnetic hypoxia in a large hard-water lake over the last 150 years. Limnol. Oceanogr. 58, 1395–1408 (2013).
Google Scholar
Nogués-Bravo, D., Araújo, M. B., Romdal, T. & Rahbek, C. Scale effects and human impact on the elevational species richness gradients. Nature 453, 216–219 (2008).
Google Scholar
Hayden, C. J. & Beman, J. M. Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA: Lake microbial ecology along an elevation gradient. Environ. Microbiol. 18, 1782–1791 (2016).
Google Scholar
Catalan, J. et al. Global change revealed by palaeolimnological records from remote lakes: A review. J. Paleolimnol. 49, 513–535 (2013).
Google Scholar
Novotny, A., Zamora-Terol, S. & Winder, M. DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species. Proc. R. Soc. B. 288, 20210908 (2021).
Google Scholar
Lei, Y., Stumm, K., Wickham, S. A. & Berninger, U. Distributions and biomass of benthic ciliates, foraminifera and amoeboid protists in marine, brackish, and freshwater sediments. J. Eukaryot. Microbiol. 61, 493–508 (2014).
Google Scholar
Foissner, W. & Berger, H. A user-friendly guide to the ciliates (Protozoa, Ciliophora) commonly used by hydrobiologists as bioindicators in rivers, lakes, and waste waters, with notes on their ecology. Freshw. Biol. 35, 375–482 (1996).
Google Scholar
Posch, T. et al. Size selective feeding in Cyclidium glaucoma (Ciliophora, Scuticociliatida) and its effects on bacterial community structure: A study from a continuous cultivation system. Microb. Ecol. 42, 217–227 (2001).
Google Scholar
Pawlowski, J. et al. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Sci. Total Environ. 637–638, 1295–1310 (2018).
Google Scholar
Ogram, Andrew., Sayler, G. S., Gustin, Denise. & Lewis, R. J. DNA adsorption to soils and sediments. Environ. Sci. Technol. 22, 982–984 (1988).
Parducci, L. et al. Shotgun environmental DNA, pollen, and macrofossil analysis of lateglacial lake sediments from southern Sweden. Front. Ecol. Evol. 7, 189 (2019).
Google Scholar
Pedersen, M. W. et al. Ancient and modern environmental DNA. Phil. Trans. R. Soc. B 370, 20130383 (2015).
Google Scholar
Epp, L. S. A global perspective for biodiversity history with ancient environmental DNA. Mol. Ecol. 28, 2456–2458 (2019).
Google Scholar
Puitika, T., Kasahara, Y., Miyoshi, N., Sato, Y. & Shimano, S. A taxon-specific oligonucleotide primer set for PCR-based detection of soil ciliate. Microb. Environ. 22, 78–81 (2007).
Google Scholar
Dopheide, A., Lear, G., Stott, R. & Lewis, G. Molecular characterization of ciliate diversity in stream biofilms. Appl. Environ. Microbiol. 74, 1740–1747 (2008).
Google Scholar
Mangot, J.-F. et al. Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes. Environ. Microbiol. 15, 1745–1758 (2013).
Google Scholar
Schloss, P. D. et al. Introducing mothur: open-source, platform independent, community-supported software for describing and comparing microbial communities. AEM 75, 7537–7541 (2009).
Google Scholar
Vaulot, D. pr2database/pr2database: PR2 version 4.12.0. (Zenodo, 2019). 10.5281/ZENODO.3362765.
Stoeck, T. et al. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology. Environ. Microbiol. 16, 430–444 (2014).
Google Scholar
Gao, F. et al. The all-data-based evolutionary hypothesis of ciliated protists with a revised classification of the Phylum Ciliophora (Eukaryota, Alveolata). Sci. Rep. 6, 24874 (2016).
Google Scholar
Foissner, W., Chao, A. & Katz, L. A. Diversity and geographic distribution of ciliates (Protista: Ciliophora). Biodivers Conserv 17, 345–363 (2008).
Google Scholar
R Core Team. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, 2020).
Oksanen, J. et al. vegan: Community Ecology PackageJari. (2020).
Therneau, T. & Atkinson, B. rpart: Recursive Partitioning and Regression Trees. (2019).
Shapiro, S. S. & Wilk, M. B. An analysis of variance test for normality (complete samples). Biometrika 52, 591–611 (1965).
Google Scholar
Conover, W. J., Johnson, M. E. & Johnson, M. M. A comparative study of tests for homogeneity of variances, with applications to the outer continental shelf bidding data. Technometrics 23, 351–361 (1981).
Google Scholar
Kruskal, W. H. & Wallis, W. A. Use of ranks in one-criterion variance analysis. J. Am. Stat. Assoc. 48, 907–911 (1952).
Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc.: Ser. B (Methodol.) 57, 289–300 (1995).
Google Scholar
Clarke, K. R. & Gorley, R. N. PRIMER v6: User manual/tutorial. (PRIMER-E, 2006).
QGIS Development Team. QGIS Geographic Information System. (QGIS Association, 2021).
Wickham, H. ggplot2: elegant graphics for dada analysis. (Springer-Verlag, 2016).
Pedersen, T. L. & Crameri, F. scico: colour palettes based on the scientific colour-maps. (2020).
Crameri, F., Shephard, G. E. & Heron, P. J. The misuse of colour in science communication. Nat. Commun. 11, 5444 (2020).
Google Scholar
Source: Ecology - nature.com