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  • 2020-2024  (33,012)
  • 2022  (33,012)
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  • 1
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    Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers (2022)
    PeerJ
    In:  PeerJ vol. 10 no. e13952
    Details
    Publication Date: 2024-07-03
    Description: Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 mm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.
    Keywords: Foraminifera ; Metabarcoding ; Beach ; Community composition ; Intertidal ; Molecular ; biodiversity
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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    PAPER (OA)
  • 2
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    Measurements of pCO2 and turbulence from an autonomous drifting buoy in 2019 during FALKOR cruise FK191120 (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Data from autonomous, drifting buoy with a floating chamber to measure insitu air-sea carbon dioxide (CO2) fluxes during RV Falkor cruise FK191120 in the southern Pacific during November-December 2019. The technique is described in detail in Ribas-Ribas et al. (2018) (https://doi.org/10.1525/elementa.275). The buoy is equipped with a sensor to measure aqueous and atmospheric partial pressure of CO2 (pCO2), and to monitor the increase or loss of CO2 inside the chamber. One complete cycle including two chamber measurements last 70 minutes. The buoy can be deployed for more than 15 hours, and at wind speeds of up to 10 m/s. Floating chambers are known to overestimate fluxes due to the creation of additional turbulence at the water surface. We check that by measuring turbulence with two Acoustic Doppler Velocimeter (ADV), one directly underneath the center of the floating chamber (equipped with an inertial motion unit) and the other one positioned sideways to measure turbulence outside the perimeter of the buoy.
    Keywords: Air-sea CO2 flux; CµC; Carbon microcycle: CO2 gradients in the ocean surface; gas exchange; gas transfer velocity; marine carbon cycle; ocean technology; Pacific Ocean; partial pressure of carbon dioxide
    Type: Dataset
    Format: application/zip, 9 datasets
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  • 3
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    Continuous wave and tide observations (2021) at DynaCom artificial islands in the back-barrier tidal flat, Spiekeroog, Germany, 2021-01 to 2021-10 (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Data presented here were collected between January 2021 to October 2021 within the research unit DynaCom (Spatial community ecology in highly dynamic landscapes: From island biogeography to metaecosystems, https://uol.de/dynacom/ ) of the Universities of Oldenburg, Göttingen, and Münster, the iDiv Leipzig and the Nationalpark Niedersächsisches Wattenmeer. Experimental islands and saltmarsh enclosed plots were created in the back barrier tidal flat and in the saltmarsh zone of the island of Spiekeroog. Local tide and wave conditions were recorded with a RBRduo TDǀwave sensor (RBR Ltd., Ontario/Canada). The sensor was bottom mounted in a shallow tidal creek (0.78 m NHN) through a steel girder (buried 0.3m deep in the sediment) and was positioned 10 cm above sediment surface, as was determined by using a portable differential GPS. This resulted in the sensor falling dry during low tide. For accurate depth calculations, raw pressure data were manually corrected for atmospheric pressure derived from a locally installed weather station. The sensor was pre-calibrated by the manufacturer and the sampling rate was 3 Hz with 1024 samples per burst at a sample interval of 10 min. Recorded data were internally logged until the readout with the Ruskin (V1.13.13) software. Date and time is given in UTC. Data handling was performed according to Zielinski et al. (2018): Post-processing of collected data was done using MATLAB (R2018a). Quality control was performed by (a) erasing data covering maintenance activities, (b) removing outliers, and (c) visually checks. Low-tide data is not removed, but were easily identified through the manually calculated water depth data, where all depths 〈 0.05m represented low tide data.
    Keywords: BEFmate; biodiversity - ecosystem functioning; DynaCom; experimental islands; FOR 2716: Spatial community ecology in highly dynamic landscapes: from island biogeography to metaecosystems; ICBM; Institut für Chemie und Biologie des Meeres; Metacommunity; salt marsh; Spiekeroog; water level; wave
    Type: Dataset
    Format: application/zip, 10 datasets
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  • 4
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    CT raw data and polyp-cavity segmentation (both DICOM format) of coral colony fragment SaM-ID43148 (GeoB11207) (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Sample SaM-ID43148 was retrieved during Meteor cruise M70-1 with the ROV MARUM-Quest from the Gondola Slide, southeast of the Gargano Promontory in the Adriatic Sea (Station M70/1-752, GeoB11207, 41°43.51'N, 17°02.78'E, 710 m water depth). The specimen was scanned with a Philips Brilliance iCT Elite 256 computer tomograph (x-ray source, voltage: 120 kV; current: 300 mA; physical resolution: 0.313 in xy-direction, respectively, 0.625 mm in z-direction; re-construction interval in z-direction: 0.3 mm; reconstruction: filtered Back Projection (fBP) mode and a bone kernel (YB (Enhanced)). Polyp-cavity (calice) segmentation was perfromed with the ZIB edition of the Amira software (Stalling et al., 2005; http://amira.zib.de) based on the new method describes in Schmitt et al. (submitted).
    Keywords: Binary Object; Binary Object (File Size); Binary Object (Media Type); calice segmentation; Center for Marine Environmental Sciences; Computed Tomography; Desmophyllum pertusum; GS: M70/1-752 (D 111); Lophelia pertusa; M70/1; M70/1_752; MARUM; Mediterranean Sea; Meteor (1986); polyp-cavity segmentation; Remote operated vehicle; ROV; SaM-ID43148
    Type: Dataset
    Format: text/tab-separated-values, 2 data points
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    DATA PANGAEA
  • 5
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    CT raw data and polyp-cavity segmentation (both DICOM format) of coral colony fragment GeoB12738-1 (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Lophelia pertusa colony fragment GeoB12738-1 was sampled from a living colony at 34°59.98'N, 07°04.51' in 738 m water depth with the MARUM ROV CHEROKEE during Pelagia cruise 64PE284 in the Meknes mud vulcano area, Gulf of Cádiz. The colony fragment was scanned using a Toshiba Aquilion 64™ computer tomograph (CT) at the hospital Klinikum Bremen-Mitte, with an x-ray source voltage of 120 kV and a current of 600 mA. The CT image stacks have a resolution of 0.35 mm in the x and y directions and 0.5 mm resolution in the z direction (0.3 mm reconstruction unit). Images were reconstructed using Toshiba's patented helical cone beam reconstruction technique. Polyp-cavity (calice) segmentation was perfromed with the ZIB edition of the Amira software (Stalling et al., 2005; http://amira.zib.de) based on the new method describes in Schmitt et al. (submitted).
    Keywords: 58735; 64PE284; Binary Object; Binary Object (File Size); Binary Object (Media Type); calice segmentation; Center for Marine Environmental Sciences; Computed Tomography; Desmophyllum pertusum; GeoB12738-1; Lophelia pertusa; MARUM; Meknes Carbonate Mound Provinces, small mounds N of Meknes mud volcano; Pelagia; polyp-cavity segmentation; Remote operated vehicle; ROV
    Type: Dataset
    Format: text/tab-separated-values, 2 data points
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  • 6
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    Pore-water salinity measurements in surface sediments (2021) within DynaCom experimental islands and saltmarsh enclosed plots at different elevation levels, Spiekeroog, Germany, 2021-01 to 2021-11 (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Data presented here were collected between January 2021 to November 2021 within the research unit DynaCom (Spatial community ecology in highly dynamic landscapes: From island biogeography to metaecosystems, https://uol.de/dynacom/) of the Universities of Oldenburg, Göttingen, and Münster, the iDiv Leipzig and the Nationalpark Niedersächsisches Wattenmeer. Experimental islands and saltmarsh enclosed plots were created in the back barrier tidal flat and in the saltmarsh zone of the island of Spiekeroog. Sediment samples for the determination of pore-water salinity in soil were taken bi-/monthly in surface sediments (0-3 cm depth). Samples were measured in the laboratory within two months after sampling according to DIN ISO 11265:1997-06.
    Keywords: BEFmate; BEFmate_C1low; BEFmate_C1pio; BEFmate_C1upp; BEFmate_C2low; BEFmate_C2pio; BEFmate_C2upp; BEFmate_C3low; BEFmate_C3pio; BEFmate_C3upp; BEFmate_C4low; BEFmate_C4pio; BEFmate_C4upp; BEFmate_C5low; BEFmate_C5pio; BEFmate_C5upp; BEFmate_C6low; BEFmate_C6pio; BEFmate_C6upp; BEFmate_I10low; BEFmate_I10pio; BEFmate_I10upp; BEFmate_I11low; BEFmate_I11pio; BEFmate_I11upp; BEFmate_I12low; BEFmate_I12pio; BEFmate_I12upp; BEFmate_I1low; BEFmate_I1pio; BEFmate_I1upp; BEFmate_I2low; BEFmate_I2pio; BEFmate_I2upp; BEFmate_I3low; BEFmate_I3pio; BEFmate_I3upp; BEFmate_I4low; BEFmate_I4pio; BEFmate_I4upp; BEFmate_I5low; BEFmate_I5pio; BEFmate_I5upp; BEFmate_I6low; BEFmate_I6pio; BEFmate_I6upp; BEFmate_I7low; BEFmate_I7pio; BEFmate_I7upp; BEFmate_I8low; BEFmate_I8pio; BEFmate_I8upp; BEFmate_I9low; BEFmate_I9pio; BEFmate_I9upp; BEFmate_S10low; BEFmate_S10pio; BEFmate_S10upp; BEFmate_S11low; BEFmate_S11pio; BEFmate_S11upp; BEFmate_S12low; BEFmate_S12pio; BEFmate_S12upp; BEFmate_S1low; BEFmate_S1pio; BEFmate_S1upp; BEFmate_S2low; BEFmate_S2pio; BEFmate_S2upp; BEFmate_S3low; BEFmate_S3pio; BEFmate_S3upp; BEFmate_S4low; BEFmate_S4pio; BEFmate_S4upp; BEFmate_S5low; BEFmate_S5pio; BEFmate_S5upp; BEFmate_S6low; BEFmate_S6pio; BEFmate_S6upp; BEFmate_S7low; BEFmate_S7pio; BEFmate_S7upp; BEFmate_S8low; BEFmate_S8pio; BEFmate_S8upp; BEFmate_S9low; BEFmate_S9pio; BEFmate_S9upp; BEFmate_Watt; biodiversity - ecosystem functioning; DATE/TIME; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; DIN ISO 11265:1997-06; DynaCom; Elevation of event; Event label; experimental islands; FOR 2716: Spatial community ecology in highly dynamic landscapes: from island biogeography to metaecosystems; Latitude of event; Longitude of event; Metacommunity; MULT; Multiple investigations; off Spiekeroog, German Bight, North Sea; Plot; pore-water salinity; Quality flag, salinity; Salinity, porewater; salt marsh; Sample ID; Sampling date; Spiekeroog
    Type: Dataset
    Format: text/tab-separated-values, 7236 data points
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  • 7
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    Physical Oceanography measured on bottle water samples during ODEN expedition SO21 for the Synoptic Arctic Survey (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Discrete bottle values of Temperature, Salinity, Dissolved Oxygen, Chlorophyll A fluorescence and Coloured Dissolved Organic Matter (CDOM) collected in the Arctic Ocean, over the western Eurasian Basin and Lomonosov Ridge, between 2 August and 11 September 2021, from I/B Oden. This is the Swedish contribution to the international Synoptic Arctic Survey. This dataset merges the bottle data from the full-depth physical CTD and the shallow biological CTD. Both systems had the standard SeaBird SBE911 plus system with dual sensors to measure in-situ temperature and conductivity and single sensors measuring pressure and oxygen. The physical CTD also had a CDOM sensor (Turner Cyclops fluorometer), while the Chl-A fluorometer (WET Labs, ECO-AFL/FL) was moved throughout the expedition between the two systems. Salinity, Oxygen, Chl-A fluorescence and CDOM were calibrated against sample data collected and analysed by the co-authors: - Salinity samples from the deep stations were analysed post-cruise using a salinometer (Guildline Autosal) and IAPSO standard seawater at the GEOMAR, Germany. - Dissolved oxygen was determined onboard using an automatic Winkler titration setup with UV detection (Scripps Institute of Oceanography Oxygen Titration System version 2.35m). - Chl-A concentration was determined post-cruise from flow cytometry (FCM) at Linnaeus University, Sweden. The samples consisted of 4 mL cryovials, of which 3.8 mL was sample water and 76 μL 25% EM grade glutaraldehyde solution (Glu stock). The samples incubated at room temperature for 5 minutes before flash freezing in liquid nitrogen and then placing in the -80 °C freezer in cryoboxes. - CDOM was determined post-cruise at the National Institute of Aquatic Resources - DTU Aqua, Denmark, following the method of Lawaetz and Stedmon (2009) This dataset contains the bottle data of the casts where bottles were fired. For more information about each sensor and their calibration, the reader is invited to check the cruise report (final version submitted on 20 September; shareable version with DOI coming soon)
    Keywords: Arctic; Arctic Ocean; Arctic Research Icebreaker Consortium: A strategy for meeting the needs for marine-based research in the Arctic; ARICE; Bottle data; Bottle number; CDOM; Chl-a; CTD, Sea-Bird, SBE 911plus; CTD/Rosette; DATE/TIME; Density, mass density; DEPTH, water; Der arktische Ozean 2020 – Ventilationszeitskalen, anthropogener Kohlenstoff und Variabilität in einer sich verändernden Umgebung; DFG_456675218; Event label; Fluorescence, chlorophyll; Fluorescence, colored dissolved organic matter; ITS-90, temperature scale; LATITUDE; LONGITUDE; New insights on ocean circulation and the fate of organic carbon in the Arctic Ocean; NOC; oceanography; Oden; Oxygen; Oxygen, dissolved; Practical Salinity Scale – 1978 (PSU78); Pressure, water; PSU78; Quality flag, absolute salinity; Quality flag, conservative water temperature; Quality flag, density; Quality flag, fluorescence, chlorophyll; Quality flag, fluorescence, colored dissolved organic matter; Quality flag, oxygen; Quality flag, potential water temperature; Quality flag, salinity; Quality flag, water temperature; Salinity; Salinity, absolute; Salinity; Temperature; SAS-Oden_2021; Seadatanet flag: Data quality control procedures according to SeaDataNet (2010); SO21; SO21_01-01; SO21_03-01; SO21_03-02; SO21_05-01; SO21_05-02; SO21_05-03; SO21_07-01; SO21_07-03; SO21_07-04; SO21_07-05; SO21_08-01; SO21_08-02; SO21_08-03; SO21_08-04; SO21_08-06; SO21_08-09; SO21_11-01; SO21_13-01; SO21_13-03; SO21_13-04; SO21_13-05; SO21_16-01; SO21_16-03; SO21_16-04; SO21_16-05; SO21_16-06; SO21_18-01; SO21_18-03; SO21_18-04; SO21_18-05; SO21_20-01; SO21_20-02; SO21_20-03; SO21_22-08; SO21_22-09; SO21_22-10; SO21_22-11; SO21_24-01; SO21_24-02; SO21_24-03; SO21_25-01; SO21_25-02; SO21_26-01; SO21_26-02; SO21_26-03; SO21_26-05; SO21_26-11; SO21_28-01; SO21_28-02; SO21_28-03; SO21_30-01; SO21_30-02; SO21_30-03; SO21_30-11; SO21_30-13; SO21_32-02; SO21_33-01; SO21_33-02; SO21_33-03; SO21_33-05; SO21_35-11; SO21_35-12; SO21_35-13; SO21_35-15; SO21_37-01; SO21_38-08; SO21_38-13; SO21_38-14; SO21_38-15; SO21_38-17; SO21_40-01; SO21_41-01; SO21_42-01; SO21_42-02; SO21_42-06; SO21_42-08; SO21_44-01; SO21_45-01; SO21_46-01; SO21_46-02; SO21_47-01; SO21_48-01; SO21_48-02; SO21_48-04; SO21_50-06; SO21_50-11; SO21_50-13; SO21_50-16; SO21_52-01; SO21_53-07; SO21_53-08; SO21_53-09; SO21_53-14; SO21_53-15; SO21_56-01; SO21_56-03; SO21_56-05; SO21_56-06; SO21_56-07; SO21_56-08; SO21_58-09; SO21_58-12; SO21_58-15; SO21_58-17; SO21_58-18; Synoptic Arctic Survey; Temperature, water; Temperature, water, conservative; Temperature, water, potential; TEOS-10; Thermodynamic Equation Of Seawater - 2010 (TEOS-10); WAOW; Why is the deep Arctic Ocean Warming?
    Type: Dataset
    Format: text/tab-separated-values, 49362 data points
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  • 8
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    Master tracks in different resolutions of METEOR cruise M179/1, Las Palmas - Punta Arenas, 2021-12-22 - 2022-01-12 (2022)
    PANGAEA
    In:  Carl von Ossietzky Universität Oldenburg, Germany
    Details
    Publication Date: 2024-07-02
    Description: Raw data acquired by position sensors on board RV METEOR during expedition M179_1 were processed to receive a validated master track which can be used as reference of further expedition data. During M179_1 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and two C and C Technologies GPS receivers C-NAV3050 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
    Keywords: Calculated; Course; CT; DAM_Underway; DAM Underway Research Data; DATE/TIME; FjordFlux-T; LATITUDE; LONGITUDE; M179/1; M179/1-track; Meteor (1986); Speed; Underway cruise track measurements
    Type: Dataset
    Format: text/tab-separated-values, 6066 data points
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  • 9
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    CT raw data and polyp-cavity segmentation (both DICOM format) of coral colony fragment C1W (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Sample C1W originates from Sula reef, off Norway, where it was taken with the submersible Jago during Poseidon cruise POS455 (position: 64.1110°N, 8.1187°E, 303 m water depth; white colourmorp. The coral colony fragment was scanned by a Toshiba Aquilion 64 computer tomograph (CT) at the hospital Klinikum Bremen-Mitte with an x-ray source voltage of 120 kV and a current of 600 mA. The CT image stack has a resolution of 0.35 mm in x-direction and y-direction and 0.5 mm resolution in z-direction (0.3 mm reconstruction unit). Images were reconstructed using Toshiba's patented helical cone beam reconstruction technique (TCOT) and are provided in DICOM-format. Polyp-cavity (calice) segmentation was perfromed with the ZIB edition of the Amira software (Stalling et al., 2005; http://amira.zib.de) based on the new method describes in Schmitt et al. (submitted).
    Keywords: Binary Object; Binary Object (File Size); Binary Object (Media Type); C1W; calice segmentation; Center for Marine Environmental Sciences; Computed Tomography; Desmophyllum dianthus; JAGO; Lophelia pertusa; MARUM; polyp-cavity segmentation; Submersible JAGO; Sula reef
    Type: Dataset
    Format: text/tab-separated-values, 2 data points
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  • 10
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    CT raw data and polyp-cavity segmentation (both DICOM format) of coral colony fragment TROND-CT10 (2022)
    PANGAEA
    Details
    Publication Date: 2024-07-02
    Description: Sample TROND-CT10 was dredged by Wolfgang Berger in September 1980 in Trondheim fjord, Norway (63°36'N, 10°32'E, 50-90\,m water depth) and we are grateful for getting access to the sample through MARUM administration. The specimen was scanned with a Philips Brilliance iCT Elite 256 computer tomograph (x-ray source, voltage: 120 kV; current: 300 mA; physical resolution: 0.212 in xy-direction, respectively, 0.625 mm in z-direction; re-construction interval in z-direction: 0.3 mm; reconstruction: filtered Back Projection (fBP) mode and a bone kernel (YB (Enhanced)). Polyp-cavity (calice) segmentation was perfromed with the ZIB edition of the Amira software (Stalling et al., 2005; http://amira.zib.de) based on the new method describes in Schmitt et al. (submitted).
    Keywords: Binary Object; Binary Object (File Size); Binary Object (Media Type); calice segmentation; Center for Marine Environmental Sciences; Computed Tomography; Desmophyllum pertusum; Dredge; DRG; Lophelia pertusa; MARUM; polyp-cavity segmentation; TROND-CT10; Trondheim fjord, Norway
    Type: Dataset
    Format: text/tab-separated-values, 2 data points
    Location Call Number Expected Availability
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