DOI: 10.5061/dryad.6vd87
title: Data from: Long-term dynamics in microbial eukaryotes communities: a paleolimnological view based on sedimentary DNA

description: Assessing the extent to which changes in lacustrine biodiversity are
 affected by anthropogenic or climatic forces requires extensive
 palaeolimnological data. We used high-throughput sequencing to generate
 time-series data encompassing over 2200 years of microbial eukaryotes
 (protists and Fungi) diversity changes from the sedimentary DNA record of
 two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland).
 From 176 samples, we sequenced a large diversity of microbial eukaryotes,
 with a total 16 386 operational taxonomic units distributed within 50
 phylogenetic groups. Thus, microbial groups, such as Chlorophyta,
 Dinophyceae, Haptophyceae and Ciliophora, that were not previously
 considered in lacustrine sediment record analyses appeared to be potential
 biological markers of trophic status changes. Our data suggest that shifts
 in relative abundance of extant species, including shifts between rare and
 abundant taxa, drive ecosystem responses to local and global environmental
 changes. Community structure shift events were concomitant with major
 climate variations (more particularly in Lake Igaliku). However, this
 study shows that the impacts of climatic fluctuations may be overpassed by
 the high-magnitude eutrophication impacts, as observed in the
 eutrophicated Lake Bourget. Overall, our data show that DNA preserved in
 sediment constitutes a precious archive of information on past
 biodiversity changes.
description: seqAll_mixEUKDemultiplexing file from MiSEQ sequencing (2 x 250 bp) of a Mock community (16 species) amplifiying with the following primers: 960F: GGCTTAATTTGACTCAACRCG 1419R: GGGCATCACAGACCTGTTAT For obtaining this file, the paired-end reads were merged together using UPARSE tools (option -fastq_mergepairs with a minimal overlap equal to 150 and no mismatch allowed) (Edgar, 2013). and the merged sequences were then submitted to the following cleaning procedures: (i) no undefined bases (Ns), (ii) a minimum sequence length of 200 bp, and (iii) no sequencing error in the forward and reverse primers. Composition of the mock community: A50 Eukaryota;Rhizaria;Cercozoa; A31 Eukaryota;Alveolata;Perkinsea; A54 Eukaryota;Cryptophyceae A34 Eukaryota;Stramenopiles;Chrysophyceae; A44 Eukaryota;Fungi; PG5-14 Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Chlorophyceae PG5-26 Eukaryota;Alveolata;Ciliophora; PG5-28 Eukaryota;Fungi;Cryptomycota; BI109 Eukaryota;Fungi;Cryptomycota; (LKM11 clade) B24 Eukaryota;Stramenopiles;Bicosoecida; B64 Eukaryota;Fungi;Chytridiomycota; B79 Eukaryota;Fungi;Dikarya; B26 Eukaryota;Alveolata;Perkinsozoa BA97 Eukaryota;Cryptophyta; B36 Eukaryota;Stramenopiles;Ochrophyta;Chrysophyceae; BA231 Eukaryota;Alveolata;Ciliophora;Alveolate_1;samples_strandplus.fasSample;Composite_depth (cm);Dating / Time (AD); BourgetAC0135C;1-2;2010-2012; BourgetAC0135E;1-2;2010-2012; BourgetAC0139D;9-10;1993-1995; BourgetAC0139E;9-10;1993-1995; BourgetAC0141D;13-14;1987-1989; BourgetAC0141E;13-14;1987-1989; BourgetAC0143D;17-18;1979-1981; BourgetAC0143E;17-18;1979-1981; BourgetAC0146C;24-25;1968-1970; BourgetAC0146E;24-25;1968-1970; BourgetAC0148C;28-29;1959-1961; BourgetAC0148E;28-29;1959-1961; BourgetAC0151D;33-34;1949-1951; BourgetAC0151E;33-34;1949-1951; BourgetAC011C;39-40;1938-1940; BourgetAC011D;39-40;1938-1940; BourgetAC013C;45-46;1927-1929; BourgetAC013D;45-46;1927-1929; BourgetAC015B;51-52;1914-1916; BourgetAC015D;51-52;1914-1916; BourgetAC017C;57-58;1901-1903; BourgetAC017D;57-58;1901-1903; BourgetAC021C;69-70;1871-1873; BourgetAC021D;69-70;1871-1873; BourgetAC023C;75-76;1854-1857; BourgetAC023D;75-76;1854-1857; BourgetAC025C;81-82;1837-1840; BourgetAC025D;81-82;1837-1840; BourgetAC027B;87-88;1819-1822; BourgetAC027D;87-88;1819-1822; BourgetAC029C;92-93;1805-1810; BourgetAC029D;92-93;1805-1810; BourgetAC033B;104-105;1760-1765; BourgetAC033D;104-105;1760-1765; BourgetAC037C;117-118;1700-1705; BourgetAC037D;117-118;1700-1705; BourgetAC040B;132-133;1595-1605; BourgetAC040C;132-133;1595-1605; BourgetAC042C;138-139;1545-1555; BourgetAC042D;138-139;1545-1555; BourgetAC048B;156-157;1385-1395; BourgetAC048D;156-157;1385-1395; BourgetAC052B;168-169;1290-1295; BourgetAC052D;168-169;1290-1295; BourgetAC056B;180-181;1205-1210; BourgetAC056D;180-181;1205-1210; BourgetAC060C;192-193;1135-1140; BourgetAC060D;192-193;1135-1140; BourgetAC064C;205-206;1070-1075; BourgetAC064D;205-206;1070-1075; BourgetAC068C;217-218;1020-1025; BourgetAC068D;217-218;1020-1025; BourgetAC072C;226-227;980-985; BourgetAC072D;226-227;980-985; BourgetAC080B;250-251;880-885; BourgetAC080D;250-251;880-885; BourgetAC082B;256-257;850-855; BourgetAC082C;256-257;850-855; BourgetAC084B;262-263;820-825; BourgetAC084D;262-263;820-825; BourgetAC086B;268-269;790-795; BourgetAC086D;268-269;790-795; BourgetAC088C;274-275;755-760; BourgetAC088D;274-275;755-760; BourgetAC090B;280-281;715-720; BourgetAC090C;280-281;715-720; BourgetAC092B;286-287;670-680; BourgetAC092D;286-287;670-680; BourgetAC096C;298-299;570-580; BourgetAC096D;298-299;570-580; BourgetAC098C;304-305;515-525; BourgetAC098D;304-305;515-525; BourgetAC0100C;310-311;455-465; BourgetAC0100E;310-311;455-465; BourgetAC0102C;316-317;390-400; BourgetAC0102D;316-317;390-400; BourgetAC0104C;322-323;325-335; BourgetAC0104D;322-323;325-335; BourgetAC0106B;328-329;255-265; BourgetAC0106C;328-329;255-265; BourgetAC0109B;338-339;135-145; BourgetAC0109C;338-339;135-145; BourgetAC0111B;343-344;80-90; BourgetAC0111D;343-344;80-90; BourgetAC0113B;349-350;15-25; BourgetAC0113C;349-350;15-25; BourgetAC0115C;355-356;-45/-35; BourgetAC0115D;355-356;-45/-35; BourgetAC0117B;361-362;-95/-85; BourgetAC0117C;361-362;-95/-85; IgalikuAC0I2A;0.5-1;2009-2010; IgalikuAC0I2B;0.5-1;2009-2010; IgalikuAC0I4A;1.5-2;2003-2005; IgalikuAC0I4B;1.5-2;2003-2005; IgalikuAC0I6A;2.5-3;1988-1997; IgalikuAC0I6B;2.5-3;1988-1997; IgalikuAC0I8A;3.5-4;1966-1974; IgalikuAC0I8B;3.5-4;1966-1974; IgalikuAC0I10A;4.5-5;1961-1963; IgalikuAC0I10B;4.5-5;1961-1963; IgalikuAC0I12A;5.5-6;1939-1954; IgalikuAC0I12B;5.5-6;1939-1954; IgalikuAC0I14A;6.5-7;1900-1920; IgalikuAC0I14B;6.5-7;1900-1920; IgalikuAC0I16A;7.5-8;1865-1880; IgalikuAC0I16B;7.5-8;1865-1880; IgalikuAC0I18A;8.5-9;1835-1850; IgalikuAC0I18B;8.5-9;1835-1850; IgalikuAC0I20A;9.5-10.5;1790-1820; IgalikuAC0I20B;9.5-10.5;1790-1820; IgalikuAC0I24A;13.5-14.5;1680-1725; IgalikuAC0I24B;13.5-14.5;1680-1725; IgalikuAC0I28A;17.5-18.5;1595-1605; IgalikuAC0I28B;17.5-18.5;1595-1605; IgalikuAC0I32A;21.5-22.5;1450-1490; IgalikuAC0I32B;21.5-22.5;1450-1490; IgalikuAC0I36A;25.5-26.5;1320-1345; IgalikuAC0I36B;25.5-26.5;1320-1345; IgalikuAC0I38A;27-27.5;1305-1315; IgalikuAC0I38B;27-27.5;1305-1315; IgalikuAC0I40A;28-28.5;1260-1290; IgalikuAC0I40B;28-28.5;1260-1290; IgalikuAC0I42A;29-29.5;1230-1240; IgalikuAC0I42B;29-29.5;1230-1240; IgalikuAC0I44A;30-30.5;1210-1220; IgalikuAC0I44B;30-30.5;1210-1220; IgalikuAC0I46A;31-31.5;1200-1205; IgalikuAC0I46B;31-31.5;1200-1205; IgalikuAC0I48A;32-32.5;1190-1195; IgalikuAC0I48B;32-32.5;1190-1195; IgalikuAC0I50A;33-33.5;1185-1190; IgalikuAC0I50B;33-33.5;1185-1190; IgalikuAC0I52A;34-34.5;1170-1180; IgalikuAC0I52B;34-34.5;1170-1180; IgalikuAC0I54A;35-35.5;1155-1165; IgalikuAC0I54B;35-35.5;1155-1165; IgalikuAC0I56A;36-36.5;1140-1150; IgalikuAC0I56B;36-36.5;1140-1150; IgalikuAC0I58A;37-37.5;1130-1135; IgalikuAC0I58B;37-37.5;1130-1135; IgalikuAC0I60A;38-38.5;1110-1120; IgalikuAC0I60B;38-38.5;1110-1120; IgalikuAC0I62A;39-39.5;1080-1095; IgalikuAC0I62B;39-39.5;1080-1095; IgalikuAC0I64A;40-40.5;1045-1055; IgalikuAC0I64B;40-40.5;1045-1055; IgalikuAC0I66A;41-41.5;1030-1035; IgalikuAC0I66B;41-41.5;1030-1035; IgalikuAC0I68A;42-42.5;1023-1026; IgalikuAC0I68B;42-42.5;1023-1026; IgalikuAC0I70A;43-43.5;1018-1021; IgalikuAC0I70B;43-43.5;1018-1021; IgalikuAC0I72A;44-44.5;1010-1015; IgalikuAC0I72B;44-44.5;1010-1015; IgalikuAC0I74A;45-45.5;990-1000; IgalikuAC0I74B;45-45.5;990-1000; IgalikuAC0I76A;46-46.6;960-975; IgalikuAC0I76B;46-46.6;960-975; IgalikuAC0I78A;47-47.5;925-940; IgalikuAC0I78B;47-47.5;925-940; IgalikuAC0I80A;48-48.5;900-910; IgalikuAC0I80B;48-48.5;900-910; IgalikuAC0I82A;49-49.5;890-895; IgalikuAC0I82B;49-49.5;890-895; IgalikuAC0I84A;50-50.5;875-880; IgalikuAC0I84B;50-50.5;875-880; IgalikuAC0I92A;57.5-58.5;685-700; IgalikuAC0I92B;57.5-58.5;685-700; IgalikuAC0I100A;65.5-66.5;360-370; IgalikuAC0I100B;65.5-66.5;360-370; IgalikuAC0I108A;73.5-74.5;80-95; IgalikuAC0I108B;73.5-74.5;80-95; IgalikuAC0I116A;81.5-82.5;-50/-40; IgalikuAC0I116B;81.5-82.5;-50/-40; IgalikuAC0I124A;89.5-90.5;-195/-180; IgalikuAC0I124B;89.5-90.5;-195/-180;