Skip to main content
SpringerLink
Log in

Protist DNA from Lake Sediments

  • Chapter
  • First Online:
Tracking Environmental Change Using Lake Sediments

Part of the book series: Developments in Paleoenvironmental Research ((DPER,volume 21))

  • 472 Accesses

Abstract

Protists are unicellular eukaryotes found in almost all biomes on Earth. Despite their critical importance in aquatic ecosystems, there is still a lack of information about how and if anthropogenic disturbances impact protists diversity and abundance. Improvements in molecular ecology techniques, and more specifically the study of protist communities through sedDNA approaches has greatly improved our understanding of the long-term changes in their diversity, distribution, and relative importance in lake ecosystems. In this chapter, we focus on the application of molecular biological techniques to sedimentary DNA (sedDNA) to investigate a broad temporal perspective on the biodiversity, community assemblages and populations dynamic of lake protists. We demonstrate how their paleo-reconstructions offer a panel of unique information related to their role in lake ecosystems (i.e., remobilization and recycling of carbon and nutrients, grazers and consumers in aquatic food webs), and provide the potential unlock new avenues for paleolimnological investigations.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
€32.70 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
EUR 29.95
Price includes VAT (France)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
EUR 139.09
Price includes VAT (France)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
EUR 179.34
Price includes VAT (France)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q (2019) Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol 66(1):4–119. https://doi.org/10.1111/jeu.12691

    Article  Google Scholar 

  • Anslan S, Kang W, Dulias K, Wünnemann B, Echeverría-Galindo P, Börner N, Schwarz A, Liu Y, Liu K, Künzel S, Kisand V, Rioual P, Peng P, Wang J, Zhu L, Vences M, Schwalb A (2022) Compatibility of diatom valve records with sedimentary ancient DNA amplicon data: a case study in a brackish, alkaline Tibetan lake. Front Earth Sci 10

    Google Scholar 

  • Armbrecht L, Herrando-Pérez S, Eisenhofer R, Hallegraeff GM, Bolch CJS, Cooper A (2020) An optimized method for the extraction of ancient eukaryote DNA from marine sediments. Mol Ecol Resour 20(4):906–919. https://doi.org/10.1111/1755-0998.13162

    Article  CAS  Google Scholar 

  • Armbrecht L, Hallegraeff G, Bolch CJS, Woodward C, Cooper A (2021a) Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes. Sci Rep 11:3220. https://doi.org/10.1038/s41598-021-82578-6

    Article  CAS  Google Scholar 

  • Armbrecht L, Eisenhofer R, Utge J, Sibert EC, Rocha F, Ward R, Pierella Karlusich JJ, Tirichine L, Norris R, Summers M, Bowler C (2021b) Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. ISME Commun 1(1):1–10. https://doi.org/10.1038/s43705-021-00070-8

    Article  Google Scholar 

  • Armbrecht L, Weber ME, Raymo ME, Peck VL, Williams T, Warnock J, Kato Y, Hernández-Almeida I, Hoem F, Reilly B, Hemming S, Bailey I, Martos YM, Gutjahr M, Percuoco V, Allen C, Brachfeld S, Cardillo FG, Du Z, Fauth G, Fogwill C, Garcia M, Glüder A, Guitard M, Hwang J-H, Iizuka M, Kenlee B, O’Connell S, Pérez LF, Ronge TA, Seki O, Tauxe L, Tripathi S, Zheng X (2022) Ancient marine sediment DNA reveals diatom transition in Antarctica. Nat Commun 13(1):5787. https://doi.org/10.1038/s41467-022-33494-4

    Article  CAS  Google Scholar 

  • Barouillet C, Vasselon V, Keck F, Millet L, Etienne D, Galop D, Rius D, Domaizon I (2022) Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes. Sci Rep 12(1):7899. https://doi.org/10.1038/s41598-022-12041-7

    Article  CAS  Google Scholar 

  • Barouillet C, Monchamp M-E, Bertilsson S, Brasell K, Domaizon I, Epp LS, Ibrahim A, Mejbel H, Nwosu EC, Pearman JK, Picard M, Thomson-Laing G, Tsugeki N, Von Eggers J, Gregory-Eaves I, Pick FR, Wood SA, Capo E (2023) Investigating the effects of anthropogenic stressors on lake biota using sedimentary DNA. Freshw Biol. https://doi.org/10.1111/fwb.14027

  • Beisser D, Graupner N, Bock C, Wodniok S, Grossmann L, Vos M, Sures B, Rahmann S, Boenigk J (2017) Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes. PeerJ 5:e2832. https://doi.org/10.7717/peerj.2832

    Article  CAS  Google Scholar 

  • Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27(4):233–243. https://doi.org/10.1016/j.tree.2011.11.010

    Article  Google Scholar 

  • Bjorbækmo MFM, Evenstad A, Røsæg LL, Krabberød AK, Logares R (2020) The planktonic protist interactome: where do we stand after a century of research? ISME J 14(2):544–559. https://doi.org/10.1038/s41396-019-0542-5

    Article  Google Scholar 

  • Boenigk J, Arndt H (2002) Bacterivory by heterotrophic flagellates: community structure and feeding strategies. Antonie Van Leeuwenhoek 81(1):465–480. https://doi.org/10.1023/A:1020509305868

    Article  Google Scholar 

  • Boere AC, Abbas B, Rijpstra WIC, Versteegh GJM, Volkman JK, Sinninghe Damsté JS, Coolen MJL (2009) Late-Holocene succession of dinoflagellates in an Antarctic fjord using a multi-proxy approach: paleoenvironmental genomics, lipid biomarkers and palynomorphs. Geobiology 7(3):265–281. https://doi.org/10.1111/j.1472-4669.2009.00202.x

    Article  CAS  Google Scholar 

  • Boere AC, Rijpstra WIC, De Lange GJ, Sinninghe Damsté JS, Coolen MJL (2011a) Preservation potential of ancient plankton DNA in Pleistocene marine sediments. Geobiology 9(5):377–393. https://doi.org/10.1111/j.1472-4669.2011.00290.x

    Article  CAS  Google Scholar 

  • Boere AC, Sinninghe Damsté JS, Rijpstra WIC, Volkman JK, Coolen MJL (2011b) Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records. Org Geochem 42(10):1216–1225. https://doi.org/10.1016/j.orggeochem.2011.08.005

    Article  CAS  Google Scholar 

  • Brasell KA, Pochon X, Howarth J, Pearman JK, Zaiko A, Thompson L, Vandergoes MJ, Simon KS, Wood SA (2022) Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies. Metabarcoding Metagenom 6:e78128. https://doi.org/10.3897/mbmg.6.78128

    Article  Google Scholar 

  • Bråte J, Logares R, Berney C, Ree DK, Klaveness D, Jakobsen KS, Shalchian-Tabrizi K (2010) Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME J 4(9):1144–1153. https://doi.org/10.1038/ismej.2010.39

    Article  CAS  Google Scholar 

  • Burki F (2014) The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb Perspect Biol 6(5):a016147. https://doi.org/10.1101/cshperspect.a016147

    Article  CAS  Google Scholar 

  • Burki F, Roger AJ, Brown MW, Simpson AGB (2020) The new tree of eukaryotes. Trends Ecol Evol 35(1):43–55. https://doi.org/10.1016/j.tree.2019.08.008

    Article  CAS  Google Scholar 

  • Burki F, Sandin MM, Jamy M (2021) Diversity and ecology of protists revealed by metabarcoding. Curr Biol 31(19):R1267–R1280. https://doi.org/10.1016/j.cub.2021.07.066

    Article  CAS  Google Scholar 

  • Capo E, Debroas D, Arnaud F, Domaizon I (2015) Is planktonic diversity well recorded in sedimentary DNA? Toward the reconstruction of past protistan diversity. Microb Ecol 70(4):865–875. https://doi.org/10.1007/s00248-015-0627-2

    Article  CAS  Google Scholar 

  • Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, Gauthier E, Massa C, Develle A-L, Pignol C, Lejzerowicz F, Domaizon I (2016) Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA. Mol Ecol 25(23):5925–5943. https://doi.org/10.1111/mec.13893

    Article  CAS  Google Scholar 

  • Capo E, Debroas D, Arnaud F, Perga M-E, Chardon C, Domaizon I (2017a) Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming. Environ Microbiol 19(7):2873–2892. https://doi.org/10.1111/1462-2920.13815

    Article  CAS  Google Scholar 

  • Capo E, Domaizon I, Maier D, Debroas D, Bigler C (2017b) 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(4):479–495. https://doi.org/10.1007/s10933-017-0005-9

    Article  Google Scholar 

  • Capo E, Rydberg J, Tolu J, Domaizon I, Debroas D, Bindler R, Bigler C (2019) How does environmental inter-annual variability shape aquatic microbial communities? A 40-year annual record of sedimentary DNA from a boreal Lake (Nylandssjön, Sweden). Front Ecol Evol 7

    Google Scholar 

  • Capo E, Giguet-Covex C, Rouillard A, Nota K, Heintzman PD, Vuillemin A, Ariztegui D, Arnaud F, Belle S, Bertilsson S, Bigler C, Bindler R, Brown AG, Clarke CL, Crump SE, Debroas D, Englund G, Ficetola GF, Garner RE, Gauthier J, Gregory-Eaves I, Heinecke L, Herzschuh U, Ibrahim A, Kisand V, Kjær KH, Lammers Y, Littlefair J, Messager E, Monchamp M-E, Olajos F, Orsi W, Pedersen MW, Rijal DP, Rydberg J, Spanbauer T, Stoof-Leichsenring KR, Taberlet P, Talas L, Thomas C, Walsh DA, Wang Y, Willerslev E, van Woerkom A, Zimmermann HH, Coolen MJL, Epp LS, Domaizon IG, Alsos I, Parducci L (2021a) Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: overview and recommendations. Quaternary 4(1):6. https://doi.org/10.3390/quat4010006

    Article  Google Scholar 

  • Capo E, Ninnes S, Domaizon I, Bertilsson S, Bigler C, Wang X-R, Bindler R, Rydberg J (2021b) Landscape setting drives the microbial eukaryotic community structure in four Swedish Mountain lakes over the Holocene. Microorganisms 9(2):355. https://doi.org/10.3390/microorganisms9020355

    Article  CAS  Google Scholar 

  • Capo E, Monchamp M-E, Coolen MJL, Domaizon I, Armbrecht L, Bertilsson S (2022) Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. Environ Microbiol 24(5):2201–2209. https://doi.org/10.1111/1462-2920.15913

    Article  CAS  Google Scholar 

  • Caron DA, Hu SK (2019) Are we overestimating protistan diversity in nature? Trends Microbiol 27(3):197–205. https://doi.org/10.1016/j.tim.2018.10.009

    Article  CAS  Google Scholar 

  • Caron DA, Hutchins DA (2013) The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps. J Plankton Res 35(2):235–252. https://doi.org/10.1093/plankt/fbs091

    Article  Google Scholar 

  • Chambouvet A, Berney C, Romac S, Audic S, Maguire F, De Vargas C, Richards TA (2014) Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments. BMC Microbiol 14(1):110. https://doi.org/10.1186/1471-2180-14-110

    Article  CAS  Google Scholar 

  • Ciobanu M-C, Burgaud G, Dufresne A, Breuker A, Rédou V, Ben Maamar S, Gaboyer F, Vandenabeele-Trambouze O, Lipp JS, Schippers A, Vandenkoornhuyse P, Barbier G, Jebbar M, Godfroy A, Alain K (2014) Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. ISME J 8(7):1370–1380. https://doi.org/10.1038/ismej.2013.250

    Article  Google Scholar 

  • Coolen MJL, Shtereva G (2009) Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea. FEMS Microbiol Ecol 70(3):525–539. https://doi.org/10.1111/j.1574-6941.2009.00756.x

    Article  CAS  Google Scholar 

  • Coolen MJL, Muyzer G, Rijpstra WIC, Schouten S, Volkman JK, Sinninghe Damsté JS (2004) Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake. Earth Planet Sci Lett 223:225–239. https://doi.org/10.1016/j.epsl.2004.04.014

    Article  CAS  Google Scholar 

  • Coolen MJL, Orsi WD, Balkema C, Quince C, Harris K, Sylva SP, Filipova-Marinova M, Giosan L (2013) Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene. Proc Natl Acad Sci 110(21):8609–8614. https://doi.org/10.1073/pnas.1219283110

    Article  Google Scholar 

  • Corinaldesi C, Danovaro R, Dell’Anno A (2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol 71(1):46–50. https://doi.org/10.1128/AEM.71.1.46-50.2005

    Article  CAS  Google Scholar 

  • Debroas D, Domaizon I, Humbert J-F, Jardillier L, Lepère C, Oudart A, Taïb N (2017) Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data. FEMS Microbiol Ecol 93(4):fix023. https://doi.org/10.1093/femsec/fix023

    Article  CAS  Google Scholar 

  • Delebecq G, Schmidt S, Ehrhold A, Latimier M, Siano R (2020) Revival of ancient marine dinoflagellates using molecular biostimulation. J Phycol 56(4):1077–1089. https://doi.org/10.1111/jpy.13010

    Article  CAS  Google Scholar 

  • Dell’Anno A, Danovaro R (2005) Extracellular DNA plays a key role in Deep-Sea ecosystem functioning. Science 309(5744):2179–2179. https://doi.org/10.1126/science.1117475

    Article  Google Scholar 

  • DeLong JP, Van Etten JL, Al-Ameeli Z, Agarkova IV, Dunigan DD (2023) The consumption of viruses returns energy to food chains. Proc Natl Acad Sci 120(1):e2215000120. https://doi.org/10.1073/pnas.2215000120

    Article  CAS  Google Scholar 

  • Domaizon I, Winegardner A, Capo E, Gauthier J, Gregory-Eaves I (2017) DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity. J Paleolimnol 58(1):1–21. https://doi.org/10.1007/s10933-017-9958-y

    Article  Google Scholar 

  • Dulias K, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U (2017) Sedimentary DNA versus morphology in the analysis of diatom-environment relationships. J Paleolimnol 57(1):51–66. https://doi.org/10.1007/s10933-016-9926-y

    Article  Google Scholar 

  • Edgcomb VP, Beaudoin D, Gast R, Biddle JF, Teske A (2011) Marine subsurface eukaryotes: the fungal majority. Environ Microbiol 13(1):172–183. https://doi.org/10.1111/j.1462-2920.2010.02318.x

    Article  CAS  Google Scholar 

  • Ellegaard M, Clokie MRJ, Czypionka T, Frisch D, Godhe A, Kremp A, Letarov A, McGenity TJ, Ribeiro S, John Anderson N (2020) Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun Biol 3(1):1–11. https://doi.org/10.1038/s42003-020-0899-z

    Article  CAS  Google Scholar 

  • Filker S, Sommaruga R, Vila I, Stoeck T (2016) Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns. Mol Ecol 25(10):2286–2301. https://doi.org/10.1111/mec.13633

    Article  CAS  Google Scholar 

  • Finlay BJ, Fenchel T (1999) Divergent perspectives on protist species richness. Protist 150(3):229–233. https://doi.org/10.1016/S1434-4610(99)70025-8

    Article  CAS  Google Scholar 

  • Finlay BJ, Fenchel T (2004) Cosmopolitan metapopulations of free-living microbial eukaryotes. Protist 155(2):237–244. https://doi.org/10.1078/143446104774199619

    Article  Google Scholar 

  • Foissner W (1999) Protist diversity: estimates of the near-imponderable. Protist 150(3):363–368. https://doi.org/10.1016/S1434-4610(99)70037-4

    Article  CAS  Google Scholar 

  • Fonseca BM, Câmara PEAS, Ogaki MB, Pinto OHB, Lirio JM, Coria SH, Vieira R, Carvalho-Silva M, Amorim ET, Convey P, Rosa LH (2022) Green algae (Viridiplantae) in sediments from three lakes on Vega Island, Antarctica, assessed using DNA metabarcoding. Mol Biol Rep 49(1):179–188. https://doi.org/10.1007/s11033-021-06857-1

    Article  CAS  Google Scholar 

  • Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie J-M, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra WHCF, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C, Stoeck T (2016) Benthic protists: the under-charted majority. FEMS Microbiol Ecol 92(8):fiw120. https://doi.org/10.1093/femsec/fiw120

    Article  CAS  Google Scholar 

  • Garner RE, Gregory-Eaves I, Walsh DA (2020) Sediment metagenomes as time capsules of lake microbiomes. mSphere 5(6):e00512-20. https://doi.org/10.1128/mSphere.00512-20

    Article  Google Scholar 

  • Garner RE, Kraemer SA, Onana VE, Huot Y, Gregory-Eaves I, Walsh DA (2022) Protist diversity and metabolic strategy in freshwater lakes are shaped by trophic state and watershed land use on a continental scale. mSystems 7(4):e00316-22. https://doi.org/10.1128/msystems.00316-22

    Article  CAS  Google Scholar 

  • Gauthier J, Walsh D, Selbie DT, Bourgeois A, Griffiths K, Domaizon I, Gregory-Eaves I (2021) Evaluating the congruence between DNA-based and morphological taxonomic approaches in water and sediment trap samples: analyses of a 36-month time series from a temperate monomictic lake. Limnol Oceanogr 66(8):3020–3039. https://doi.org/10.1002/lno.11856

    Article  CAS  Google Scholar 

  • Gauthier J, Walsh D, Selbie DT, Domaizon I, Gregory-Eaves I (2022) Sedimentary DNA of a human-impacted lake in Western Canada (Cultus Lake) reveals changes in micro-eukaryotic diversity over the past 200 years. Environmental DNA 4(5):1106–1119. https://doi.org/10.1002/edn3.310

    Article  CAS  Google Scholar 

  • Giner CR, Forn I, Romac S, Logares R, de Vargas C, Massana R (2016) Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes. Appl Environ Microbiol 82(15):4757–4766. https://doi.org/10.1128/AEM.00560-16

    Article  CAS  Google Scholar 

  • Grattepanche JD, Walker LM, Ott BM, Paim Pinto DL, Delwiche, CF, Lane CE, Katz LA (2018) Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data. Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/91

  • Grossmann L, Jensen M, Heider D, Jost S, Glücksman E, Hartikainen H, Mahamdallie SS, Gardner M, Hoffmann D, Bass D, Boenigk J (2016) Protistan community analysis: key findings of a large-scale molecular sampling. ISME J 10(9):2269–2279. https://doi.org/10.1038/ismej.2016.10

    Article  Google Scholar 

  • Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C (2014) Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One 9(2):e87624. https://doi.org/10.1371/journal.pone.0087624

    Article  CAS  Google Scholar 

  • Härnström K, Ellegaard M, Andersen TJ, Godhe A (2011) Hundred years of genetic structure in a sediment revived diatom population. Proc Natl Acad Sci 108(10):4252–4257. https://doi.org/10.1073/pnas.1013528108

    Article  Google Scholar 

  • Hou W, Dong H, Li G, Yang J, Coolen MJL, Liu X, Wang S, Jiang H, Wu X, Xiao H, Lian B, Wan Y (2014) Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan plateau. Sci Rep 4(1):6648. https://doi.org/10.1038/srep06648

    Article  CAS  Google Scholar 

  • Huang S, Herzschuh U, Pestryakova LA, Zimmermann HH, Davydova P, Biskaborn BK, Shevtsova I, Stoof-Leichsenring KR (2020) Genetic and morphologic determination of diatom community composition in surface sediments from glacial and thermokarst lakes in the Siberian Arctic. J Paleolimnol 64(3):225–242. https://doi.org/10.1007/s10933-020-00133-1

    Article  Google Scholar 

  • Huo S, Zhang H, Monchamp M-E, Wang R, Weng N, Zhang J, Zhang H, Wu F (2022a) Century-long homogenization of algal communities is accelerated by nutrient enrichment and climate warming in lakes and reservoirs of the north temperate zone. Environ Sci Technol 56(6):3780–3790. https://doi.org/10.1021/acs.est.1c06958

    Article  CAS  Google Scholar 

  • Huo S, Zhang H, Wang J, Chen J, Wu F (2022b) Temperature and precipitation dominates millennium changes of eukaryotic algal communities in Lake Yamzhog Yumco, southern Tibetan Plateau. Sci Total Environ 829:154636. https://doi.org/10.1016/j.scitotenv.2022.154636

    Article  CAS  Google Scholar 

  • Ibrahim A, Capo E, Wessels M, Martin I, Meyer A, Schleheck D, Epp LS (2021) Anthropogenic impact on the historical phytoplankton community of lake constance reconstructed by multimarker analysis of sediment-core environmental DNA. Mol Ecol 30(13):3040–3056. https://doi.org/10.1111/mec.15696

    Article  CAS  Google Scholar 

  • Jones RI (2000) Mixotrophy in planktonic protists: an overview. Freshw Biol 45(2):219–226. https://doi.org/10.1046/j.1365-2427.2000.00672.x

    Article  Google Scholar 

  • Kammerlander B, Breiner H-W, Filker S, Sommaruga R, Sonntag B, Stoeck T (2015) High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains. FEMS Microbiol Ecol 91(4):fiv010. https://doi.org/10.1093/femsec/fiv010

    Article  CAS  Google Scholar 

  • Kanbar HJ, Olajos F, Englund G, Holmboe M (2020) Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments. Appl Geochem 122:104728. https://doi.org/10.1016/j.apgeochem.2020.104728

    Article  CAS  Google Scholar 

  • Keck F, Millet L, Debroas D, Etienne D, Galop D, Rius D, Domaizon I (2020) Assessing the response of micro-eukaryotic diversity to the great acceleration using lake sedimentary DNA. Nat Commun 11(1):3831. https://doi.org/10.1038/s41467-020-17682-8

    Article  CAS  Google Scholar 

  • Kirkpatrick J, Walsh E, D’Hondt S (2016) Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales. Graduate School of Oceanography Faculty Publications https://doi.org/10.1130/G37933.1

  • Kisand V, Talas L, Kisand A, Stivrins N, Reitalu T, Alliksaar T, Vassiljev J, Liiv M, Heinsalu A, Seppä H, Veski S (2018) From microbial eukaryotes to metazoan vertebrates: wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years. Geobiology 16(6):628–639. https://doi.org/10.1111/gbi.12307

    Article  CAS  Google Scholar 

  • Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E (2022) A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612(7939):283–291. https://doi.org/10.1038/s41586-022-05453-y

    Article  CAS  Google Scholar 

  • Klouch KZ, Schmidt S, Andrieux-Loyer F, Le Gac M, Hervio-Heath D, Qui-Minet ZN, Quéré J, Bigeard E, Guillou L, Siano R (2016) Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France). FEMS Microbiol Ecol 92(7):fiw101. https://doi.org/10.1093/femsec/fiw101

    Article  CAS  Google Scholar 

  • Krantzberg G (1985) The influence of bioturbation on physical, chemical and biological parameters in aquatic environments: a review. Environ Pollut Ser A, Ecol Biol 39(2):99–122. https://doi.org/10.1016/0143-1471(85)90009-1

    Article  CAS  Google Scholar 

  • Lammers Y, Heintzman PD, Alsos IG (2021) Environmental palaeogenomic reconstruction of an ice age algal population. Commun Biol 4(1):1–11. https://doi.org/10.1038/s42003-021-01710-4

    Article  CAS  Google Scholar 

  • Lefranc M, Thénot A, Lepère C, Debroas D (2005) Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 71(10):5935–5942. https://doi.org/10.1128/AEM.71.10.5935-5942.2005

    Article  CAS  Google Scholar 

  • Lepère C, Domaizon I, Debroas D (2008) Unexpected importance of potential parasites in the composition of the freshwater small-eukaryote community. Appl Environ Microbiol 74(10):2940–2949. https://doi.org/10.1128/AEM.01156-07

    Article  CAS  Google Scholar 

  • Li G, Dong H, Hou W, Wang S, Jiang H, Yang J, Wu G (2016) Temporal succession of ancient phytoplankton community in Qinghai lake and implication for paleo-environmental change. Sci Rep 6(1):19769. https://doi.org/10.1038/srep19769

    Article  CAS  Google Scholar 

  • Li M, Bastos Gomes G, Zhao W, Hu G, Huang K, Yoshinaga T, Clark TG, Li W, Zou H, Wu S, Wang G (2023) Cultivation of fish ciliate parasites: progress and prospects. Rev Aquac 15(1):142–162. https://doi.org/10.1111/raq.12708

    Article  Google Scholar 

  • Likens GE (ed) (2010) Plankton of inland waters: a derivative of encyclopedia of inland waters. Academic Press/Elsevier, San Diego

    Google Scholar 

  • Lischke B, Weithoff G, Wickham SA, Attermeyer K, Grossart HP, Scharnweber K, HIlt S, Gaedke U (2016) Large biomass of small feeders: ciliates may dominate herbivory in eutrophic lakes. J Plankton Res 38(1):2–15. https://doi.org/10.1093/plankt/fbv102

    Article  Google Scholar 

  • Lynn DH, Doerder FP, Gillis PL, Prosser RS (2018) Tetrahymena glochidiophila n. sp., a new species of Tetrahymena (Ciliophora) that causes mortality to glochidia larvae of freshwater mussels (Bivalvia). Dis Aquat Org 127(2):125–136. https://doi.org/10.3354/dao03188

    Article  CAS  Google Scholar 

  • Mangot J-F, Domaizon I, Taib N, Marouni N, Duffaud E, Bronner G, Debroas D (2013) Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes. Environ Microbiol 15(6):1745–1758. https://doi.org/10.1111/1462-2920.12065

    Article  CAS  Google Scholar 

  • Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding Metagenom 6:e85794. https://doi.org/10.3897/mbmg.6.85794

    Article  Google Scholar 

  • Marzetz V, Spijkerman E, Striebel M, Wacker A (2020) Phytoplankton community responses to interactions between light intensity, light variations, and phosphorus supply. Front Environ Sci 8

    Google Scholar 

  • McCarthy FMG, Mertens KN, Ellegaard M, Sherman K, Pospelova V, Ribeiro S, Blasco S, Vercauteren D (2011) Resting cysts of freshwater dinoflagellates in southeastern Georgian Bay (Lake Huron) as proxies of cultural eutrophication. Rev Palaeobot Palynol 166(1):46–62. https://doi.org/10.1016/j.revpalbo.2011.04.008

    Article  Google Scholar 

  • Millette NC, Gast RJ, Luo JY, Moeller HV, Stamieszkin K, Andersen KH, Brownlee EF, Cohen NR, Duhamel S, Dutkiewicz S, Glibert PM, Johnson MD, Leles SG, Maloney AE, Mcmanus GB, Poulton N, Princiotta SD, Sanders RW, Wilken S (2023) Mixoplankton and mixotrophy: future research priorities. J Plankton Res:fbad020. https://doi.org/10.1093/plankt/fbad020

  • Mitra A, Flynn KJ, Burkholder JM, Berge T, Calbet A, Raven JA, Granéli E, Glibert PM, Hansen PJ, Stoecker DK, Thingstad F, Tillmann U, Våge S, Wilken S, Zubkov MV (2014) The role of mixotrophic protists in the biological carbon pump. Biogeosciences 11(4):995–1005. https://doi.org/10.5194/bg-11-995-2014

    Article  CAS  Google Scholar 

  • Mitra A, Flynn KJ, Tillmann U, Raven JA, Caron D, Stoecker DK, Not F, Hansen PJ, Hallegraeff G, Sanders R, Wilken S, McManus G, Johnson M, Pitta P, Våge S, Berge T, Calbet A, Thingstad F, Jeong HJ, Burkholder J, Glibert PM, Granéli E, Lundgren V (2016) Defining planktonic Protist functional groups on mechanisms for energy and nutrient acquisition: incorporation of diverse mixotrophic strategies. Protist 167(2):106–120. https://doi.org/10.1016/j.protis.2016.01.003

    Article  CAS  Google Scholar 

  • Miyazono A, Nagai S, Kudo I, Tanizawa K (2012) Viability of Alexandrium tamarense cysts in the sediment of Funka Bay, Hokkaido, Japan: over a hundred year survival times for cysts. Harmful Algae 16:81–88. https://doi.org/10.1016/j.hal.2012.02.001

    Article  Google Scholar 

  • Moguel B, Pérez L, Alcaraz LD, Blaz J, Caballero M, Muñoz-Velasco I, Becerra A, Laclette JP, Ortega-Guerrero B, Romero-Oliva CS, Herrera-Estrella L, Lozano-García S (2021) Holocene life and microbiome profiling in ancient tropical Lake Chalco. Mexico Sci Rep 11(1):13848. https://doi.org/10.1038/s41598-021-92981-8

    Article  CAS  Google Scholar 

  • More KD, Orsi WD, Galy V, Giosan L, He L, Grice K, Coolen MJL (2018) A 43 kyr record of protist communities and their response to oxygen minimum zone variability in the Northeastern Arabian Sea. Earth Planet Sci Lett 496:248–256. https://doi.org/10.1016/j.epsl.2018.05.045

    Article  CAS  Google Scholar 

  • Nanney DL, Park C, Preparata R, Simon EM (1998) Comparison of sequence differences in a variable 23S rRNA domain among sets of cryptic species of ciliated protozoa. J Eukaryot Microbiol 45(1):91–100. https://doi.org/10.1111/j.1550-7408.1998.tb05075.x

    Article  CAS  Google Scholar 

  • Nolte V, Pandey RV, Jost S, Medinger R, Ottenwälder B, Boenigk J, Schlötterer C (2010) Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol Ecol 19(14):2908–2915. https://doi.org/10.1111/j.1365-294X.2010.04669.x

    Article  CAS  Google Scholar 

  • Oikonomou A, Filker S, Breiner H-W, Stoeck T (2015) Protistan diversity in a permanently stratified meromictic Lake (lake Alatsee, SW Germany). Environ Microbiol 17(6):2144–2157. https://doi.org/10.1111/1462-2920.12666

    Article  Google Scholar 

  • Orlando L, Allaby R, Skoglund P, Der Sarkissian C, Stockhammer PW, Ávila-Arcos MC, Fu Q, Krause J, Willerslev E, Stone AC, Warinner C (2021) Ancient DNA analysis. Nat Rev Methods Primers 1(1):1–26. https://doi.org/10.1038/s43586-020-00011-0

    Article  CAS  Google Scholar 

  • Orsi W, Biddle JF, Edgcomb V (2013) Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PLoS One 8(2):e56335. https://doi.org/10.1371/journal.pone.0056335

    Article  CAS  Google Scholar 

  • Pachiadaki MG, Rédou V, Beaudoin DJ, Burgaud G, Edgcomb VP (2016) Fungal and prokaryotic activities in the marine subsurface biosphere at Peru margin and Canterbury Basin inferred from RNA-based analyses and microscopy. Front Microbiol 7

    Google Scholar 

  • Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EAD, Nitsche F, Romeralo M, Saunders GW, Simpson AGB, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D, Vargas C de (2012) CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms. PLOS Biology 10(11):e1001419. https://doi.org/10.1371/journal.pbio.1001419

  • Pawlowski J, Kelly-Quinn M, Altermatt F, Apothéloz-Perret-Gentil L, Beja P, Boggero A, Borja A, Bouchez A, Cordier T, Domaizon I, Feio MJ, Filipe AF, Fornaroli R, Graf W, Herder J, van der Hoorn B, Iwan Jones J, Sagova-Mareckova M, Moritz C, Barquín J, Piggott JJ, Pinna M, Rimet F, Rinkevich B, Sousa-Santos C, Specchia V, Trobajo R, Vasselon V, Vitecek S, Zimmerman J, Weigand A, Leese F, Kahlert M (2018) 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. https://doi.org/10.1016/j.scitotenv.2018.05.002

    Article  CAS  Google Scholar 

  • Pernthaler J, Posch T (2009) Microbial food webs. In: Likens GE (ed) Encyclopedia of inland waters. Academic, Oxford, pp 244–251

    Chapter  Google Scholar 

  • Pick FR, Caron DA (1987) Picoplankton and Nanoplankton biomass in Lake Ontario: relative contribution of phototrophic and heterotrophic communities. Can J Fish Aquat Sci 44:2164–2172. https://doi.org/10.1139/f87-265

    Article  Google Scholar 

  • Posch T, Köster O, Salcher MM, Pernthaler J (2012) Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming. Nature Clim Change 2(11):809–813. https://doi.org/10.1038/nclimate1581

    Article  CAS  Google Scholar 

  • Prosser RS, Lynn DH, Salerno J, Bennett J, Gillis PL (2018) The facultatively parasitic ciliated protozoan, Tetrahymena glochidiophila (Lynn, 2018), causes a reduction in viability of freshwater mussel glochidia. J Invertebr Pathol 157:25–31. https://doi.org/10.1016/j.jip.2018.07.012

    Article  CAS  Google Scholar 

  • Randlett M-È, Coolen MJL, Stockhecke M, Pickarski N, Litt T, Balkema C, Kwiecien O, Tomonaga Y, Wehrli B, Schubert CJ (2014) Alkenone distribution in Lake Van sediment over the last 270 ka: influence of temperature and haptophyte species composition. Quat Sci Rev 104:53–62. https://doi.org/10.1016/j.quascirev.2014.07.009

    Article  Google Scholar 

  • Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly A-M, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T (2021) Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. Water Res 191:116767. https://doi.org/10.1016/j.watres.2020.116767

    Article  CAS  Google Scholar 

  • Sanders RW (2009) Protists. In: Likens GE (ed) Encyclopedia of inland waters. Academic, Oxford, pp 252–260

    Chapter  Google Scholar 

  • Sandgren CD, Smol JP, Kristiansen J (eds) (1995) Chrysophyte algae: ecology, phylogeny and development. Cambridge University Press, Cambridge

    Google Scholar 

  • Sanyal A, Larsson J, van Wirdum F, Andrén T, Moros M, Lönn M, Andrén E (2022) Not dead yet: diatom resting spores can survive in nature for several millennia. Am J Bot 109(1):67–82. https://doi.org/10.1002/ajb2.1780

    Article  Google Scholar 

  • Seeber PA, von Hippel B, Kauserud H, Löber U, Stoof-Leichsenring KR, Herzschuh U, Epp LS (2022) Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems. Environmental DNA 4(5):1150–1163. https://doi.org/10.1002/edn3.315

    Article  CAS  Google Scholar 

  • Sherr EB, Sherr BF (2002) Significance of predation by protists in aquatic microbial food webs. Antonie Van Leeuwenhoek 81(1):293–308. https://doi.org/10.1023/A:1020591307260

    Article  CAS  Google Scholar 

  • Siano R, Lassudrie M, Cuzin P, Briant N, Loizeau V, Schmidt S, Ehrhold A, Mertens KN, Lambert C, Quintric L, Noël C, Latimier M, Quéré J, Durand P, Penaud A (2021) Sediment archives reveal irreversible shifts in plankton communities after world war II and agricultural pollution. Curr Biol 31(12):2682–2689.e7. https://doi.org/10.1016/j.cub.2021.03.079

    Article  CAS  Google Scholar 

  • Singer D, Seppey CVW, Lentendu G, Dunthorn M, Bass D, Belbahri L, Blandenier Q, Debroas D, de Groot GA, de Vargas C, Domaizon I, Duckert C, Izaguirre I, Koenig I, Mataloni G, Schiaffino MR, Mitchell EAD, Geisen S, Lara E (2021) Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environ Int 146:106262. https://doi.org/10.1016/j.envint.2020.106262

    Article  CAS  Google Scholar 

  • Smol JP (1985) The ratio of diatom frustules to chrysophycean statospores: a useful paleolimnological index. Hydrobiologia 123(3):199–208. https://doi.org/10.1007/BF00034378

    Article  Google Scholar 

  • Smol JP, Birks HJB, Last WM, Bradley RS, Alverson K (eds) (2001) Tracking environmental change using Lake sediments: terrestrial, algal, and siliceous indicators. Springer, Dordrecht

    Google Scholar 

  • Stoof-Leichsenring KR, Epp LS, Trauth MH, Tiedemann R (2012) Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation. Mol Ecol 21(8):1918–1930. https://doi.org/10.1111/j.1365-294X.2011.05412.x

    Article  CAS  Google Scholar 

  • Stoof-Leichsenring KR, Bernhardt N, Pestryakova LA, Epp LS, Herzschuh U, Tiedemann R (2014) A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect. J Paleolimnol 52(1):77–93. https://doi.org/10.1007/s10933-014-9779-1

    Article  Google Scholar 

  • Stoof-Leichsenring KR, Herzschuh U, Pestryakova LA, Klemm J, Epp LS, Tiedemann R (2015) Genetic data from algae sedimentary DNA reflect the influence of environment over geography. Sci Rep 5(1):12924. https://doi.org/10.1038/srep12924

    Article  CAS  Google Scholar 

  • Stoof-Leichsenring KR, Liu S, Jia W, Li K, Pestryakova LA, Mischke S, Cao X, Liu X, Ni J, Neuhaus S, Herzschuh U (2020a) Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China). Biodivers Data J 8:e57089. https://doi.org/10.3897/BDJ.8.e57089

    Article  Google Scholar 

  • Stoof-Leichsenring KR, Pestryakova LA, Epp LS, Herzschuh U (2020b) Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA. J Biogeogr 47(5):1166–1179. https://doi.org/10.1111/jbi.13786

    Article  Google Scholar 

  • Suthers I, Rissik D, Richardson A (eds) (2019) Plankton: a guide to their ecology and monitoring for water quality. CSIRO publishing

    Google Scholar 

  • Talas L, Stivrins N, Veski S, Tedersoo L, Kisand V (2021) Sedimentary ancient DNA (sedaDNA) reveals fungal diversity and environmental drivers of community changes throughout the Holocene in the present boreal Lake Lielais Svētiņu (eastern Latvia). Microorganisms 9(4):719. https://doi.org/10.3390/microorganisms9040719

    Article  CAS  Google Scholar 

  • Tõnno I, Talas L, Freiberg R, Kisand A, Belle S, Stivrins N, Alliksaar T, Heinsalu A, Veski S, Kisand V (2021) Environmental drivers and abrupt changes of phytoplankton community in temperate lake Lielais Svētiņu, eastern Latvia, over the last post-glacial period from 14.5 kyr. Quat Sci Rev 263:107006. https://doi.org/10.1016/j.quascirev.2021.107006

    Article  Google Scholar 

  • Triadó-Margarit X, Casamayor EO (2012) Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain). Environ Microbiol 14(9):2445–2456. https://doi.org/10.1111/j.1462-2920.2012.02797.x

    Article  Google Scholar 

  • Triadó-Margarit X, Casamayor EO (2015) High protists diversity in the plankton of sulfurous lakes and lagoons examined by 18s rRNA gene sequence analyses. Environ Microbiol Rep 7(6):908–917. https://doi.org/10.1111/1758-2229.12324

    Article  CAS  Google Scholar 

  • Vasselon V, Rimet F, Domaizon I, Monnier O, Reyjol Y, Bouchez A (2019) Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks. Metabarcoding Metagenom 3:e39646. https://doi.org/10.3897/mbmg.3.39646

    Article  Google Scholar 

  • Weisbrod B, Wood SA, Steiner K, Whyte-Wilding R, Puddick J, Laroche O, Dietrich DR (2020) Is a central sediment sample sufficient? Exploring spatial and temporal microbial diversity in a small lake. Toxins 12(9):580. https://doi.org/10.3390/toxins12090580

    Article  CAS  Google Scholar 

  • Weisse T, Montagnes DJS (2022) Ecology of planktonic ciliates in a changing world: concepts, methods, and challenges. J Eukaryot Microbiol 69(5):e12879. https://doi.org/10.1111/jeu.12879

    Article  Google Scholar 

  • Wetzel RG (2001) Limnology: Lake and river ecosystems. Elsevier

    Google Scholar 

  • Wurzbacher C, Fuchs A, Attermeyer K, Frindte K, Grossart H-P, Hupfer M, Casper P, Monaghan MT (2017) Shifts among Eukaryota, bacteria, and archaea define the vertical organization of a lake sediment. Microbiome 5(1):41. https://doi.org/10.1186/s40168-017-0255-9

    Article  Google Scholar 

  • Xiong W, Jousset A, Li R, Delgado-Baquerizo M, Bahram M, Logares R, Wilden B, de Groot GA, Amacker N, Kowalchuk GA, Shen Q, Geisen S (2021) A global overview of the trophic structure within microbiomes across ecosystems. Environ Int 151:106438. https://doi.org/10.1016/j.envint.2021.106438

    Article  Google Scholar 

  • Zhang H, Huo S, Cao X, Ma C, Zhang J, Wu F (2021) Homogenization of reservoir eukaryotic algal and cyanobacterial communities is accelerated by dam construction and eutrophication. J Hydrol 603:126842. https://doi.org/10.1016/j.jhydrol.2021.126842

    Article  CAS  Google Scholar 

  • Zimmermann HH, Stoof-Leichsenring KR, Dinkel V, Harms L, Schulte L, Hütt M-T, Nürnberg D, Tiedemann R, Herzschuh U (2023) Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing. Nat Commun 14(1):1650. https://doi.org/10.1038/s41467-023-36845-x

    Article  CAS  Google Scholar 

  • Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P (2019) DNA metabarcoding – need for robust experimental designs to draw sound ecological conclusions. Mol Ecol 28(8):1857–1862. https://doi.org/10.1111/mec.15060

    Article  Google Scholar 

Download references

Acknowledgements

We acknowledge financial support from the Pole Research & Development on Lacustrine Ecosystems (ECLA) of the French Biodiversity Agency (OFB) and the Severo Ochoa Excellence Program postdoctoral fellowship awarded in 2021 to Eric Capo (CEX2019-000928-S). We are very grateful to Kuldeep More, Thomas Weisse and Frances Pick for their critical reading of our chapter.

Author information

Authors and Affiliations

  1. INRAE, Université Savoie Mont Blanc, CARRTEL, Thonon le bains, France

    Cécilia Barouillet & Isabelle Domaizon

  2. Pôle R&D ECLA, INRAE, CARRTEL, Thonon-les-bains, France

    Cécilia Barouillet & Isabelle Domaizon

  3. Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden

    Eric Capo

Authors
  1. Cécilia Barouillet
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Isabelle Domaizon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eric Capo
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden

    Eric Capo

  2. INRAE, Université Savoie Mont Blanc CARRTEL, Thonon-les-Bains, France

    Cécilia Barouillet

  3. Paleoecological Environmental Assessment and Research Lab (PEARL) Department of Biology, Queen’s University, Kingston, ON, Canada

    John P. Smol

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Barouillet, C., Domaizon, I., Capo, E. (2023). Protist DNA from Lake Sediments. In: Capo, E., Barouillet, C., Smol, J.P. (eds) Tracking Environmental Change Using Lake Sediments. Developments in Paleoenvironmental Research, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-031-43799-1_6

Download citation

Publish with us

Policies and ethics

Search

Navigation