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.
seqAll_mixEUK
Demultiplexing 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.fas
Sample;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;