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  • 1
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    Operational taxonomic units and taxonomy of a phytoplankton community during Maria S. Merian cruise MSM21/3 - Greenland (ARCHEMHAB) (2017)
    PANGAEA
    In:  Supplement to: Elferink, Stephanie; Neuhaus, Stefan; Wohlrab, Sylke; Toebe, Kerstin; Voß, Daniela; Gottschling, Marc; Lundholm, Nina; Krock, Bernd; Koch, Boris P; Zielinski, Oliver; Cembella, Allan; John, Uwe (2017): Molecular diversity patterns among various phytoplankton size-fractions in West Greenland in late summer. Deep Sea Research Part I: Oceanographic Research Papers, 121, 54-69, https://doi.org/10.1016/j.dsr.2016.11.002
    Details
    Publication Date: 2023-07-11
    Description: Arctic regions have experienced pronounced biological and biophysical transformations as a result of global change processes over the last several decades. Current hypotheses propose an elevated impact of those environmental changes on the biodiversity, community composition and metabolic processes of species. The effects on ecosystem function and services, particularly when invasive or toxigenic harmful species become dominant, can be expressed over a wide range of temporal and spatial scales in plankton communities. Our study focused on the comparison of molecular biodiversity of three size-fractions (micro-, nano-, picoplankton) in the coastal pelagic zone of West Greenland and their association with environmental parameters. Molecular diversity was assessed via parallel amplicon sequencing the 28S rRNA hypervariable D1/D2 region. We showed that biodiversity distribution within the area of Uummannaq Fjord, Vaigat Strait and Disko Bay differed markedly within and among size-fractions. In general, we observed a higher diversity within the picoplankton size fraction compared to the nano- and microplankton. In multidimensional scaling analysis, community composition of all three size fractions correlated with cell size, silicate and phosphate, chlorophyll a (chl a) and dinophysistoxin (DTX). Individually, each size fraction community composition also correlated with other different environmental parameters, i.e. temperature and nitrate. We observed a more homogeneous community of the picoplankton across all stations compared to the larger size classes, despite different prevailing environmental conditions of the sampling areas. This suggests that habitat niche occupation for larger-celled species may lead to higher functional trait plasticity expressed as an enhanced range of phenotypes, whereas smaller organisms may compensate for lower potential plasticity with higher diversity. The presence of recently identified toxigenic harmful algal bloom (HAB) species (such as Alexandrium fundyense and A. ostenfeldii) in the area points out the potential risk for this vulnerable ecosystem in a changing world.
    Type: Dataset
    Format: application/zip, 3 datasets
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  • 2
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    Comparative Metabarcoding and Metatranscriptomic Analysis of Microeukaryotes Within Coastal Surface Waters of West Greenland and Northwest Iceland (2019)
    PANGAEA
    Details
    Publication Date: 2023-07-11
    Description: Climate change alters environmental conditions that are expected to have a profound effect on the biodiversity, community composition, and metabolic processes of microeukaryotic plankton in Arctic and Subarctic coastal waters. The molecular biodiversity [large subunit (LSU) rRNA gene] of three plankton size-fractions (micro-, nano-, and picoplankton) from coastal waters of ice-influenced west Greenland was compared with fractions from ice-free northwest Iceland within their summer environmental context. Putative metabolic functions were determined by differentially expressed mRNA (metatranscriptomics) of the microplankton. Temperature and salinity variations were more closely correlated than inorganic macronutrients with metabolic functions and community composition. Temperature explained much of the community variance, approximately 20% among micro- and nanoplankton, whereas other environmental factors accounted for rather low fractional variance (〈7%). Species of smaller cell-size were more evenly distributed (Pielou's evenness index J) across regions, with a higher diversity and total abundance, and thereby indicating high plasticity. The metatranscriptomic profiles in these respective microeukaryotic communities revealed that diatoms were more plastic in their gene expression than dinoflagellates, but dinoflagellates had a more diverse, albeit homogeneously expressed, gene pool. This could be interpreted as expression of alternative lifestyle strategies, whereby the functionally more conservative diatoms fill their niches primarily through variable resource use, whereas dinoflagellates apparently differentiate their niches through more diverse lifestyles. Patterns of microeukaryotic diversity are thus primarily associated with differences in metabolic function and activity of diatom- versus dinoflagellate-dominated communities in Arctic and Subarctic waters during summer.
    Keywords: arctic microplankton; DNA-barcoding; marine pelagic; metabolic processes; microeukaryotic community; picoplankton
    Type: Dataset
    Format: application/zip, 3 datasets
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  • 3
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    Assessing dinophyte biodiversity in Bavarian lakes (Germany) by 18S v4 amplicon sequencing (2019)
    PANGAEA
    In:  Supplement to: Gottschling, Marc; Chacón, Juliana; Žerdoner Čalasan, Anže; Neuhaus, Stefan; Kretschmann, Juliane; Stibor, Herwig; John, Uwe (2020): Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany). Freshwater Biology, 65(2), 193-208, https://doi.org/10.1111/fwb.13413
    Details
    Publication Date: 2023-07-11
    Description: Seventeen surface plankton tow samples were collected from piers at thirteen localities in Upper Bavaria (Germany) in April 2017 using a plankton net (mesh size 20µm). The localities included eleven lakes (one lake was sampled at two sites) and one subsidiary river, to cover standing and flowing bodies of water as well. Four sites had been sampled twice. Environmental DNA was extracted using the Genomic DNA from Soil kit (Machery-Nagel; Düren, Germany) following the manufacturer's protocol. The small subunit (SSU or 18S) of the ribosomal RNA (rRNA) operon V4 region (~410 bp) was the amplification target. Due to PCR biases or PCR errors that may artificially increase diversity, each PCR reaction was performed in triplicates. Forward and reverse primers were those used by Xiao et al. (2017) (DOI: 10.1007/s12010-016-2358-3). DNA amplification (PCR) for subsequent Illumina amplicon sequencing (Illumina; San Diego, USA-CA) was carried out using 5ng/µl template DNA, 1 µM of each primer and 2x KAPA Hifi HotStart Ready Mix (Roche; Penzberg, Germany). Resulting PCR products were visualised in 1% agarose gels and were purified using AMPure XP Beads (Beckman Coulter; Brea, USA-CA). Dual indices and Illumina sequence adapters were attached by means of an Index PCR using the Nextera XT Index Kit (Illumina), and final PCR products were again purified using AMPure XP Beads. The library was validated using an Agilent 2100 Bioanalyzer Software and a DNA 1000 Chip (Agilent Technologies; Santa Clara, USA-CA) to verify the size of the resulting fragments. The final DNA libraries were equimolarly pooled and run in a MiSeq System (Illumina) after combining the denatured PhiX control library (15%) and the denatured amplicon library. Some 6.5 million 2 x 300 bp paired-end reads were produced and demultiplexed into seventeen samples from thirteen sites. Using Trimmomatic (v0.38), 3'-ends of the reads were trimmed based on read quality information. PEAR (v0.9.10) with default settings was used to merge the paired-end reads. Sequences, which could not be merged, were discarded. Primer-matching sequence segments were truncated from the amplicons by cutadapt (v1.9) and amplicons were only kept in the sequence pool, if both, the segment of the forward and of the reverse primer could be found. Remaining sequences were filtered for further quality features by vsearch (v2.3.0). Sequences were discarded, if they were outside a 50 bp radius above or below the median length of the primer-truncated amplicon (~387 bp), if they carry any ambiguity or if the expected number of miscalled bases of a sequence (sum of all base error probabilities of a sequence) was above 1. Chimera were predicted also by vsearch utilising the UCHIME algorithm with default settings in de-novo mode for each sample separately and removed from the sample files. About 4 million sequences passed all filtering steps and were used as input for the OTU-clustering, which was done by the tool Swarm (v2.1.8) with default settings. The most abundant amplicon of each OTU-cluster was used as an OTU representative. These sequences were annotated by the RDP classifier implemented in mothur (v1.38.1) using the Ref_NR99 version of release 128 of the SILVA SSU sequence set using a reference with a confidence cutoff of 90. The annotation of each representative sequence was used as annotation of the OTU cluster as well and added to the corresponding line of the OTU table.
    Type: Dataset
    Format: application/zip, 633 kBytes
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  • 4
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    OTU sample description of Maria S. Merian cruise MSM21/3 (ARCHEMHAB) (2019)
    PANGAEA
    In:  Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven
    Details
    Publication Date: 2024-02-02
    Description: Sampling was performed during the MSM-21/3 expedition (Cembella et al., 2016) aboard the RV Maria S. Merian at the western coast of Greenland and Iceland between July 27 to August 8, 2012 (Fig. 1). Water samples were collected in the epipelagic zone by Niskin bottles mounted on a rosette-sampler with conductivity, temperature and depth (CTD) sensors to measure temperature and salinity. In total, 15 stations were sampled at the surface layer (over the upper 30 m).
    Keywords: ARCHEMHAB; arctic microplankton; Area/locality; Baffin Bay; CTD/Rosette; CTD-RO; Date/Time of event; Davis Strait; Depth, bottom/max; Depth, top/min; DEPTH, water; DNA-barcoding; Elevation of event; Event label; Greenland Sea; Iceland Sea; Latitude of event; Longitude of event; Maria S. Merian; marine pelagic; metabolic processes; microeukaryotic community; MSM21/3; MSM21/3_504-1; MSM21/3_505-1; MSM21/3_506-1; MSM21/3_507-1; MSM21/3_508-1; MSM21/3_509-1; MSM21/3_510-1; MSM21/3_511-1; MSM21/3_512-1; MSM21/3_513-1; MSM21/3_514-1; MSM21/3_515-1; MSM21/3_516-1; MSM21/3_517-1; MSM21/3_527-1; MSM21/3_528-1; MSM21/3_529-1; MSM21/3_530-1; MSM21/3_531-1; MSM21/3_532-1; MSM21/3_533-1; MSM21/3_534-1; MSM21/3_539-1; MSM21/3_540-1; MSM21/3_541-1; picoplankton; Rubber boat, Zodiac; Sample ID; Size fraction; ZODIAC
    Type: Dataset
    Format: text/tab-separated-values, 315 data points
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  • 5
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    Inorganic nutrient measured during Maria S. Merian cruise MSM21/3 (ARCHEMHAB) (2019)
    PANGAEA
    In:  Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven
    Details
    Publication Date: 2024-02-02
    Keywords: Ammonium; ARCHEMHAB; arctic microplankton; Area/locality; Baffin Bay; Chlorophyll a; CTD/Rosette; CTD-RO; Date/Time of event; Davis Strait; DEPTH, sediment/rock; DNA-barcoding; Elevation of event; Event label; Greenland Sea; Iceland Sea; Latitude of event; Longitude of event; Maria S. Merian; marine pelagic; metabolic processes; microeukaryotic community; MSM21/3; MSM21/3_504-1; MSM21/3_505-1; MSM21/3_506-1; MSM21/3_507-1; MSM21/3_508-1; MSM21/3_509-1; MSM21/3_510-1; MSM21/3_511-1; MSM21/3_512-1; MSM21/3_513-1; MSM21/3_514-1; MSM21/3_515-1; MSM21/3_516-1; MSM21/3_517-1; MSM21/3_527-1; MSM21/3_528-1; MSM21/3_529-1; MSM21/3_530-1; MSM21/3_531-1; MSM21/3_532-1; MSM21/3_533-1; MSM21/3_534-1; MSM21/3_539-1; MSM21/3_540-1; MSM21/3_541-1; Nitrate; Nitrite; Phosphate; picoplankton; Rubber boat, Zodiac; Salinity; Sample ID; Silicate; Size fraction; Temperature, water; ZODIAC
    Type: Dataset
    Format: text/tab-separated-values, 943 data points
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  • 6
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    Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-altitude lakes (China) (2020)
    PANGAEA
    Details
    Publication Date: 2024-02-09
    Description: Compilation of environmental data for the 262 investigated localities, which include additional intra-lake localities taken within three large lakes namely: 16-KP-01-L02 (9 samples), 16-KP-03-L10 (5 samples), 16-KP-04-L19 (4 samples). The table includes information about the geographic coordinates, elevation, type of sample material, geographic region, water depth (at which samples were taken), pH, water conductivity, mean annual precipitation (MAP), mean annual temperature (MAP), July and January mean temperature. Annual mean temperature, mean temperature in July and January, and mean annual precipitation were downloaded from WorldClim 2 (www.worldclim.org), and are based on the average climate data for the years 1970–2000 at a spatial resolution of 30 seconds (ca. 1 km^2^). The site-specific climate data was interpolated to the location area by using the R packages raster Hijmans 2020. Hijmans RJ (2020) raster: Geographic Data Analysis and Modeling. R package version 3.1-5. URL: https://CRAN.R-project.org/package=raster. Plant diversity in the Arctic and at high altitudes strongly depends on and rebounds to climatic and environmental variability and is nowadays tremendously impacted by recent climate warming. Therefore, past changes in plant diversity in the high Arctic and high-altitude regions are used to infer climatic and environmental changes through time and allow future predictions. Sedimentary DNA is an established proxy for the detection of local plant diversity in lake sediments, but still relationships between environmental conditions and preservation of the plant sedDNA proxy are far from being fully understood. Studying modern relationships between environmental conditions and plant sedDNA will improve our understanding under which conditions sedDNA is well-preserved helping to a.) evaluate suitable localities for sedDNA approaches, b.) provide analogues for preservation conditions and c.) conduct reconstruction of plant diversity and climate change. This study investigates modern plant diversity applying a plant-specific metabarcoding approach on sedimentary DNA (sedDNA) of surface sediment samples from 262 lake localities covering a large geographical, climatic and ecological gradient. Latitude ranges between 25°N and 73°N and longitude between 81°E and 161°E, including lowland lakes and elevated lakes up to 5168 m a.s.l. Further, our sampling localities cover a climatic gradient ranging in mean annual temperature between -15°C to +18°C and in mean annual precipitation between 36–935 mm. The localities in Siberia span over a large vegetational gradient including tundra, open woodland and boreal forest. Lake localities in China include alpine meadow, shrub, forest and steppe and also cultivated areas. The assessment of plant diversity in the underlying data set was conducted by a specific plant metabarcoding approach.
    Keywords: 05-LC-02; 05-LC-03; 05-LC-04; 05-LC-05; 05-LC-06; 05-LC-07; 05-LC-08; 05-LC-10; 05-LC-11; 05-Yak-03; 05-Yak-05; 05-Yak-06; 05-Yak-08; 05-Yak-10; 05-Yak-11; 05-Yak-14; 05-Yak-16; 05-Yak-17; 05-Yak-18; 05-Yak-19; 05-Yak-21; 05-Yak-23; 05-Yak-24; 05-Yak-25; 05-Yak-26; 05-Yak-27; 05-Yak-28; 07-SA-07; 07-SA-21; 07-SA-23; 07-SA-26; 07-SA-31; 07-SA-33; 07-SA-34; 08-KO-01; 08-KO-03; 08-KO-04; 08-KO-06; 08-KO-07; 08-KO-09; 08-KO-11; 08-KO-12; 08-KO-13; 08-KO-14; 08-KO-15; 08-KO-16; 08-KO-17; 08-KO-18; 08-KO-19; 08-KO-20; 08-KO-21; 08-KO-22; 08-KO-23; 08-KO-24; 08-KO-26; 08-KO-28; 08-KO-29; 08-KO-30; 08-KO-31; 08-KO-32; 08-KO-33; 09-TIK-03; 09-TIK-04; 09-TIK-05; 09-TIK-08; 09-TIK-09; 09-TIK-13; 09-TIK-14; 11-CH-02; 11-CH-05; 11-CH-06; 11-CH-09; 11-CH-10; 11-CH-11; 11-CH-12; 11-CH-13; 11-CH-14; 11-CH-15; 11-CH-17; 11-CH-18; 11-CH-19; 11-CH-20; 13-TY-01; 13-TY-02; 13-TY-03; 13-TY-04; 13-TY-05; 13-TY-06; 13-TY-07; 13-TY-08; 13-TY-09; 13-TY-10; 13-TY-11; 13-TY-12; 13-TY-13; 13-TY-14; 13-TY-15; 13-TY-16; 13-TY-17; 13-TY-18; 13-TY-19; 13-TY-20; 13-TY-21; 13-TY-22; 13-TY-23; 13-TY-24; 13-TY-25; 13-TY-26; 13-TY-27; 13-TY-28; 13-TY-29; 13-TY-30; 13-TY-31; 13-TY-32; 14-OM-01; 14-OM-02; 14-OM-03; 14-OM-04; 14-OM-05; 14-OM-06; 14-OM-07; 16-KP-01-L01; 16-KP-01-L02; 16-KP-01-L02_2; 16-KP-01-L02_3; 16-KP-01-L02_4; 16-KP-01-L02_5; 16-KP-01-L02_6; 16-KP-01-L02_7; 16-KP-01-L02_8; 16-KP-01-L02_9; 16-KP-01-L03; 16-KP-01-L04; 16-KP-02-L05; 16-KP-02-L06; 16-KP-02-L07; 16-KP-02-L08; 16-KP-02-L09; 16-KP-03-L10; 16-KP-03-L10_2; 16-KP-03-L10_3; 16-KP-03-L10_4; 16-KP-03-L10_5; 16-KP-03-L11; 16-KP-03-L13; 16-KP-03-L14; 16-KP-03-L15; 16-KP-03-L16; 16-KP-03-L17; 16-KP-03-L18; 16-KP-04-L19; 16-KP-04-L19_1; 16-KP-04-L19_2; 16-KP-04-L19_4; 16-KP-04-L20; 16-KP-04-L21; 16-KP-04-L22; Ailike; Angrenjin_Co; Arctic; Argaa-Bere; AWI_Envi; AWI Arctic Land Expedition; B-6; Balybyrbym; Bamuco; based on WORLDCLIM data; Beringia/Kolyma_2008; Bosten; Byluyng Kjuel; Central and eastern Siberia; Chagan_nuur; Chatanga2011; Chloroplast DNA; Choktokhoi; Cona; Conductivity, electrical; Daihai; Dajiaco; Dali; Dazeco; DEPTH, water; Donggi-Cona; E_ling; EG; Ekman grab; Elevation of event; Elgene Kjuel; Event label; Gahai_DLH; Gahai_QHH; Hala; HAND; Jiang_Co; Jinzihai; Keluke; Keperveem_2016; Kh; Kocha; Kol_01; Kol_03; Kol_04; Kol_06; Kol_07; Kol_09; Kol_11; Kol_12; Kol_13; Kol_14; Kol_15; Kol_16; Kol_17; Kol_18; Kol_19; Kol_20; Kol_21; Kol_22; Kol_24; Kol_27; Kol_28; Kol_29; Kol_30; Kol_31; Kolyma River; Kubalakh; Kuhai; Kyunde; lakes; Lang_Co; Latitude of event; Location; Longitude of event; Metabarcoding; MULT; Multiple investigations; Northern China and Xingjiang; Ochugui-Kengerime; Oibon; Omoloy2014; Pengco; pH; Pipa; Plant diversity; Polar Terrestrial Environmental Systems @ AWI; Precipitation, annual mean; Qinghai-Lake; RU-Land_2005_Verkhoyansk; RU-Land_2007_Saskylakh; RU-Land_2008_Kolyma; RU-Land_2009_Lena-transect; RU-Land_2011_Khatanga; RU-Land_2013_Taymyr; RU-Land_2014_Omoloy; RU-Land_2016_Keperveem; S-02; S-03; S-06; S-07; S-08; S-09; S-10; S101; S105; S-12; S123; S133; S-14; S143; S-15; S16; S-16; S169; S-17; S200; S213; S-22; S229; S237; S244; S-25; S259; S-26; S263; S310; S344; S350; S358; S374; S379; S414; S417; S420; S434; S439; S440; S62; Sailimu; Sample ID; Sample material; Sampling by hand; Saskylakh2007; Saskylakh region (Sakha), Russia; Sedimentary DNA; Selinco; SET-01; SET-02; SET-03; SET-04; SET-05; SET-06; SET-07; SET-08; SET-09; SET-11; SET-12; SET-13; SET-14; SET-15; SET-16; SET-18; SET-19; SET-20; SET-21; SET-22; SET-23; SET-24; SET-25; SET-26; SET-27; SET-28; SET-29; SET-30; SET-31; SET-32; Shengco; Species dominance; Species present; Sugan; Taymyr2013; Temperature, air, January; Temperature, air, July; Temperature, annual mean; Tibet; Tibet Plateau; Tiksi2009; Toiogoi; Toson; trnL P6 loop; Tschukotka, Sibiria, Russia; Vegetation; Vegetation type; Water sampler, UWITEC; WSUWI; Wulungu; Xingxinghai; Yakutia2005; Zhaling; Zharinanmu_Co
    Type: Dataset
    Format: text/tab-separated-values, 4325 data points
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  • 7
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    Sample metadata during Maria S. Merian cruise MSM21/3 - Greenland (ARCHEMHAB) (2016)
    PANGAEA
    In:  Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven
    Details
    Publication Date: 2024-02-02
    Keywords: ARCHEMHAB; Baffin Bay; CTD/Rosette; CTD-RO; Date/Time of event; Davis Strait; Depth, bottom/max; Depth, top/min; Elevation of event; Event label; Latitude of event; Longitude of event; Maria S. Merian; MSM21/3; MSM21/3_504-1; MSM21/3_505-1; MSM21/3_506-1; MSM21/3_507-1; MSM21/3_508-1; MSM21/3_509-1; MSM21/3_510-1; MSM21/3_511-1; MSM21/3_512-2; MSM21/3_513-1; MSM21/3_514-1; MSM21/3_515-1; MSM21/3_516-1; MSM21/3_517-1; Sample ID; Size fraction
    Type: Dataset
    Format: text/tab-separated-values, 164 data points
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  • 8
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    Operational taxonomic units (OTU) of a phytoplankton community during Maria S. Merian cruise MSM21/3 - Greenland (ARCHEMHAB) (2016)
    PANGAEA
    In:  Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven
    Details
    Publication Date: 2024-02-02
    Keywords: ARCHEMHAB; Maria S. Merian; MSM21/3; MSM21/3_Greenland
    Type: Dataset
    Format: application/zip, 50 kBytes
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  • 9
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    Taxonomy of a phytoplankton community during Maria S. Merian cruise MSM21/3 - Greenland (ARCHEMHAB) (2016)
    PANGAEA
    In:  Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven
    Details
    Publication Date: 2024-02-02
    Keywords: ARCHEMHAB; Maria S. Merian; MSM21/3; MSM21/3_Greenland
    Type: Dataset
    Format: application/zip, 7.5 kBytes
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  • 10
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    Hydrogen isotopes and carbon isotope analyses of leaf wax fatty acids extracted from samples at IODP Site 353-U1445 (2020)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Keywords: Amplicon sequence variant; ARCHEMHAB; arctic microplankton; Baffin Bay; CTD/Rosette; CTD-RO; Davis Strait; Depth, bottom/max; Depth, top/min; DEPTH, water; DNA-barcoding; Event label; Greenland Sea; Iceland Sea; Identification; Maria S. Merian; marine pelagic; metabolic processes; microeukaryotic community; MSM21/3; MSM21/3_504-1; MSM21/3_505-1; MSM21/3_506-1; MSM21/3_507-1; MSM21/3_508-1; MSM21/3_509-1; MSM21/3_510-1; MSM21/3_511-1; MSM21/3_512-1; MSM21/3_513-1; MSM21/3_514-1; MSM21/3_515-1; MSM21/3_516-1; MSM21/3_517-1; MSM21/3_527-1; MSM21/3_528-1; MSM21/3_529-1; MSM21/3_530-1; MSM21/3_531-1; MSM21/3_532-1; MSM21/3_533-1; MSM21/3_534-1; MSM21/3_539-1; MSM21/3_540-1; MSM21/3_541-1; picoplankton; Rubber boat, Zodiac; Size fraction; ZODIAC
    Type: Dataset
    Format: text/tab-separated-values, 123280 data points
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