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  • 1
    Publication Date: 2024-05-24
    Description: Monitoring community composition of Foraminifera (single-celled marine protists) pro-vides valuable insights into environmental conditions in marine ecosystems. Despitethe efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) me-tabarcoding to assess the presence of multiple taxa, this has not been straightforwardfor Foraminifera partially due to the high genetic variability in widely used ribosomalmarkers. Here, we test the correctness in retrieving foraminiferal communities by me-tabarcoding of mock communities, bulk-DNA from coral reef sediment samples, andeDNA from their associated ethanol preservative using the recently sequenced cy-tochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we com-pared our results with large benthic foraminiferal communities previously reportedfrom the same sampling sites. Results from our mock communities demonstrate thatall species were detected in two mock communities and all but one in the remainingfour. Technical replicates were highly similar in number of reads for each assigned ASVin both the mock communities and bulk-DNA samples. Bulk-DNA showed a signifi-cantly higher species richness than their associated eDNA samples, and also detectedadditional species to what was already reported at the specific sites. Our study con-firms that metabarcoding using the foraminiferal COI marker adequately retrieves thediversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nu-clear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool toassess foraminiferal community composition under the condition that the referencedatabase is adequate to the target taxa.
    Keywords: bulk-sample ; DNA ; community composition ; coral reef ; environmental DNA ; foraminifera ; metabarcoding
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 2
    Publication Date: 2024-05-24
    Description: Highlights • Investigation into the potential of Porites microatolls for SST reconstruction. • Comparison between recent and more conventional coral paleoclimatology methods. • Application of Srsingle bondU and Li/Mg paleothermometer. • Accuracy and reproducibility of Sr/Ca proved to be the most suitable proxy for SST reconstruction. Abstract Massive dome-shaped coral Porites are the predominant choice for paleoclimate studies due to their consistent and reliable growth. When growing close to sea level, they become limited in their vertical growth and form so-called ‘microatolls’. Microatolls have not yet been extensively explored for paleoclimate reconstruction. Here, we investigate how reliable modern Porites microatolls are against empirical sea-surface temperature using Sr/Ca, δ18O, Li/Mg and Srsingle bondU paleothermometry methods on samples from the Society Islands, French Polynesia. Our results show Sr/Ca ratios have the lowest Standard Error of the Inverse Prediction (SEIP) at 0.415 °C (N = 41) with a calibration of Sr/Ca (mmol mol−1) = −0.082 ± 0.006 SST (°C) + 11.256 ± 0.170 and with high reproducibility across multiple corals. The reproducibility of δ18O was less good, with SEIP increasing to 0.829 °C (N = 41). Considering methods directly from the literature, Li/Mg ratio empirically corrected for Sr/Ca had the best balance between bias and precision where no local calibration could be available. This study independently evaluates and confirms the suitability of Porites microatolls from well-flushed environments for paleoclimate studies. Fossil dome-shaped Porites grow anywhere between near-surface and roughly 20 m depths which inherently incorporates uncertainty into any sea surface temperature reconstruction. This uncertainty is significantly reduced for microatolls due to their well-constrained bathymetry. The study represents a fundamental step in paleoclimate research targeting consistently near the water-air interface bringing reliability and, especially when combined with their ability to reconstruct past sea-level changes, microatolls have the potential to be central for future paleoenvironmental studies.
    Type: Article , PeerReviewed
    Format: text
    Format: archive
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  • 3
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    PANGAEA
    In:  Supplement to: Ko, W K Ginger; Chan, B S Vera; Dineshram, R; Choi, K S Dennis; Li, J Adela; Yu, Ziniu; Thiyagarajan, Vengatesen (2013): Larval and Post-Larval Stages of Pacific Oyster (Crassostrea gigas) Are Resistant to Elevated CO2. PLoS ONE, 8(5), e64147, https://doi.org/10.1371/journal.pone.0064147.t001
    Publication Date: 2024-05-24
    Description: Rising anthropogenic carbon dioxide (CO2) dissolving into coastal waters is decreasing the pH and carbonate ion concentration, thereby lowering the saturation state of calcium carbonate (CaCO3) minerals through a process named ocean acidification (OA). The unprecedented threats posed by such low pH on calcifying larvae of several edible oyster species have not yet been fully explored. Effects of low pH (7.9, 7.6, 7.4) on the early growth phase of Portuguese oyster (Crassostrea angulata) veliger larvae was examined at ambient salinity (34 ppt) and the low-salinity (27 ppt) treatment. Additionally, the combined effect of pH (8.1, 7.6), salinity (24 and 34 ppt) and temperature (24 °C and 30 °C) was examined using factorial experimental design. Surprisingly, the early growth phase from hatching to 5-day-old veliger stage showed high tolerance to pH 7.9 and pH 7.6 at both 34 ppt and 27 ppt. Larval shell area was significantly smaller at pH 7.4 only in low-salinity. In the 3-factor experiment, shell area was affected by salinity and the interaction between salinity and temperature but not by other combinations. Larvae produced the largest shell at the elevated temperature in low-salinity, regardless of pH. Thus the growth of the Portuguese oyster larvae appears to be robust to near-future pH level (〉 7.6) when combined with projected elevated temperature and low-salinity in the coastal aquaculture zones of South China Sea.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Bicarbonate ion; Biomass, ash free dry mass; Biomass, ash free dry mass, shell-free, standard deviation; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Crassostrea gigas; Development; EXP; Experiment; Figure; Filtering rate; Filtering rate, standard deviation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Growth rate, standard deviation; Incubation duration; Individuals; Laboratory experiment; Mollusca; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; Percentage; Percentage, standard deviation; pH; pH, standard deviation; Potentiometric; Potentiometric titration; Replicate; Respiration; Respiration rate, oxygen, per dry mass; Respiration rate, standard deviation; Salinity; Salinity, standard deviation; Single species; Size; Species; Stage; Temperate; Temperature; Temperature, standard deviation; Temperature, water; Treatment; Tsingdao; Zooplankton
    Type: Dataset
    Format: text/tab-separated-values, 9573 data points
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  • 4
    Publication Date: 2024-05-24
    Keywords: Acid-base regulation; Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Behaviour; Benthic animals; Benthos; Bicarbonate ion; Blood gas analyser, Eschweiler, MT 33; Calcite saturation state; Calculated after Heisler 1986; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Extrapallial fluid carbon dioxide; Extrapallial fluid partial pressure of carbon dioxide; Extrapallial fluid partial pressure of oxygen; Extrapallial fluid pH; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gas chromatography; Haemolymph, bicarbonate ion; Haemolymph, partial pressure of carbon dioxide; Haemolymph, partial pressure of oxygen; Haemolymph, pH; Haemolymph, total carbon dioxide; Heart rate; Helgoland, North Sea; Individual code; Laboratory experiment; Mollusca; Mytilus edulis; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; off_Helgoland_EPOCA; Oxygen optode, flow-through respirometry; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; Plethysmograph; Potentiometric; Potentiometric titration; Registration number of species; Respiration; Respiration rate, oxygen, per dry mass; Salinity; Single species; Species; Temperate; Temperature; Temperature, water; Treatment; Type; Uniform resource locator/link to reference
    Type: Dataset
    Format: text/tab-separated-values, 8241 data points
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  • 5
    Publication Date: 2024-05-24
    Keywords: Alice Springs; ASP; Baseline Surface Radiation Network; BSRN; GOB; Gobabeb; Israel; Macdonnell Ranges, Northern Territory, Australia; Monitoring station; MONS; Namib Desert, Namibia; Saudi Arabia; SBO; Sede Boqer; Solar Village; SOV
    Type: Dataset
    Format: 48 datasets
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  • 6
    Publication Date: 2024-05-24
    Description: Contaminants of emerging concern and ocean changes are key environmental stressors for marine species with possibly synergistic, but still unexplored, deleterious effects. In the present study the influence of a simulated ocean acidification scenario (pH = 7.6) was investigated on metabolism and sub-lethal effects of carbamazepine, CBZ (1 µg/L), chosen as one of the most widely diffused pharmaceuticals in marine organisms. A multidisciplinary approach was applied on mussels, M. galloprovincialis, integrating measurement of drug bioaccumulation with changes in the whole transcriptome, responsiveness of various biochemical and cellular biomarkers including immunological parameters, lipid and oxidative metabolism, onset of genotoxic effects. Chemical analyses revealed a limited influence of hypercapnia on accumulation and excretion of CBZ, while a complex network of biological responses was observed in gene expression profile and functional changes at cellular level. The modulation of gamma-aminobutyric acid (GABA) pathway suggested similarities with the Mechanism of Action known for vertebrates: immune responses, cellular homeostasis and oxidative system represented the processes targeted by combined stressors. The overall elaboration of results through a quantitative Weight of Evidence model, revealed clearly increased cellular hazard due to interactions of CBZ with acidification compared to single stressors.
    Keywords: Acetylcholinesterase activity, per protein mass; Acetylcholinesterase activity, per protein mass, standard error; Acyl-CoA oxidase activity, per protein mass; Acyl-CoA oxidase activity, per protein mass, standard deviation; Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthic animals; Benthos; Bicarbonate ion; Calcite saturation state; Calcite saturation state, standard deviation; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbamazepine, per dry mass; Carbamazepine, standard deviation; Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Catalase activity, per protein mass; Catalase activity, per protein mass, standard error; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); DNA fragmentation; DNA fragmentation, standard error; Experiment duration; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Glutathione, total, per unit wet mass; Glutathione, total, per unit wet mass, standard error; Glutathione reductase, per protein mass; Glutathione reductase, per protein mass, standard error; Glutathione S-transferase, activity per protein mass; Glutathione S-transferase, activity per protein mass, standard error; Granulocytes/Hyalinocytes ratio; Granulocytes/Hyalinocytes ratio, standard error; Hemocytes lysosomal membranes stability; Hemocytes lysosomal membranes stability, standard error; Hemocytes micronuclei frequency; Hemocytes micronuclei frequency, standard error; Immunology/Self-protection; Laboratory experiment; Lipofuscin; Lipofuscin, standard error; Malondialdehyde, per wet mass; Malondialdehyde, per wet mass, standard error; Mediterranean Sea; Mollusca; Mytilus galloprovincialis; Neutral lipids; Neutral lipids, standard error; OA-ICC; Ocean Acidification International Coordination Centre; Organic toxins; Other metabolic rates; Other studied parameter or process; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; pH, standard deviation; Phagocytosis; Phagocytosis, standard error; Potentiometric; Potentiometric titration; Registration number of species; Salinity; Salinity, standard deviation; Sample code/label; Selenium dependent glutathione peroxidases activity, per protein mass; Selenium dependent glutathione peroxidases activity, per protein mass, standard error; Single species; Species; Temperate; Temperature, water; Temperature, water, standard deviation; Total glutathione peroxidases activity, per protein mass; Total glutathione peroxidases activity, unit per protein mass, standard error; Total oxyradical scavenging capacity against hydroxyl radicals, unit per protein mass; Total oxyradical scavenging capacity against hydroxyl radicals, unit per protein mass, standard error; Total oxyradical scavenging capacity against peroxyl radicals, unit per protein mass; Total oxyradical scavenging capacity against peroxyl radicals, unit per protein mass, standard error; Total oxyradical scavenging capacity against peroxynitrite, unit per protein mass; Total oxyradical scavenging capacity against peroxynitrite, unit per protein mass, standard error; Treatment; Type; Uniform resource locator/link to reference
    Type: Dataset
    Format: text/tab-separated-values, 331 data points
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  • 7
    Publication Date: 2024-05-24
    Description: Between 2 and 6 littoral sediment samples were collected in 2018 and 2019 from nearshore (1-2 m depth) in each lake using a dredge (Wildco Petite Ponar Stainless Steel Grab) and dried at 60 °C overnight and homogenized using a porcelain mortar and pestle. Oven-dried sediment samples were digested using a microwave-assisted (CEM MARS 5) total digestion protocol (modified EPA method 3015a). Concentrations of total arsenic in digested sediment samples were determined by inductively-coupled plasma mass spectrometry (ICP-MS) on an Agilent 7900 at the University of Washington Tacoma.
    Keywords: (Trimethylarsaniumyl)acetate, per dry mass, tissue; 2-Hydroxyethyl-trimethylarsonium, per dry mass, tissue; Arsenate, per dry mass, tissue; arsenic; Arsenite, per dry mass, tissue; crayfish; DATE/TIME; Dimethylarsinic acid, per dry mass, tissue; Event label; fish; ICP-MS Agilent 7900; Inductively coupled plasma mass spectrometer (Agilent 7900); Lake_Killarney; LATITUDE; littoral sediment; LONGITUDE; Methylarsonic acid, per dry mass, tissue; MULT; Multiple investigations; Registration number of species; snail; Species; Steel_Lake; Sum; Tissue, sampling; Uniform resource locator/link to reference; United States; water column
    Type: Dataset
    Format: text/tab-separated-values, 176 data points
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  • 8
    Publication Date: 2024-05-24
    Description: Snail (Bellamya chinensis), crayfish (Pacifastacus leniusculus; Procambarus clarkii), and sunfish (Lepomis gibbosus; L. macrochirus) sampling occurred primarily over four dates in June 2019 in the entire nearshore (〈 2 m depth) area of each lake. Additional frozen crayfish samples from Killarney, Steel, and Pine Lakes collected in 2004, 2009, 2017, and 2018 were also analyzed. All crayfish were captured using minnow traps set overnight and baited with dog kibble. Snails were collected by hand via snorkeling or with a dip net from a boat. Sunfish were collected using beach seining. Snails, crayfish, and fish were euthanized and dissected for edible tissues (whole snail, excluding shell, crayfish tail meat, and fish muscle tissue (fillet)). Duplicate portions of each edible tissue of snail, crayfish, or fish specimen were dried at 60 °C overnight. Dried samples were homogenized using a porcelain mortar and pestle. Oven-dried animal tissues were digested using a microwave-assisted (CEM MARS 5) total digestion protocol (modified EPA method 3015a). Concentrations of total arsenic in digested animal tissue samples were determined by inductively-coupled plasma mass spectrometry (ICP-MS) on an Agilent 7900 at the University of Washington Tacoma.
    Keywords: Angle_Lake; arsenic; Arsenic, total, per dry mass, tissue; Bonney_Lake; crayfish; DATE/TIME; Event label; fish; ICP-MS Agilent 7900; Inductively coupled plasma mass spectrometer (Agilent 7900); Lake_Killarney; LATITUDE; littoral sediment; LONGITUDE; MULT; Multiple investigations; Pine_Lake; Registration number of species; snail; Species; Steel_Lake; Tissue, sampling; Uniform resource locator/link to reference; United States; water column
    Type: Dataset
    Format: text/tab-separated-values, 525 data points
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  • 9
    Publication Date: 2024-05-24
    Description: We report the results of an aquaria-based experiment testing the effects of low oxygen and suspended particles generated during a potential mining activities accident on the juveniles of the vent mussel Bathymodiolus azoricus. Mussels were collected from the Lucky Strike hydrothermal vent field (Azores, NE Atlantic) at 1700 m water depth in 2021. Mussels were maintained in 1 l aquaria and exposed to four experimental treatments for a period of two weeks at the DeepSeaLab aquaria facilities (Okeanos-University of the Azores): (1) control conditions (no added sediments and normal seawater oxygen ); (2) low oxygen (difference of 30 µmol from the normal oxygen concentration); (3) suspended polymetallic sulphide (PMS) particles; (4) Low oxygen + suspended polymetallic sulphide (PMS) particles. PMS particles were obtained by grinding PMS inactive chimney rocks collected at the hydrothermal vent field Lucky Strike. Particles types were in concentration of 420 mg/l on day 8 and day 11. The putative effects of low oxygen, PMS particles, and the cumulative effect(s) were evaluated through measurements of bulk mussel tissue samples by stable isotopes and elemental analyses, as follows: Continuous flow isotope mass spectrometry (CF-IRMS) was performed on a SerconHydra 20–22 (Sercon, UK) and Isoprime IRMS stable isotope ratio mass spectrometer, coupled to a EuroEA (EuroVector, Italy) elemental analyser for online sample preparation by Dumas-combustion. Delta Calculation was performed according to δ = [(Rsample – Rstandard)/Rstandard]*1000, where R is the ratio between the heavier isotope and the lighter one. δ15 NAir values are referred to air, δ13 CVPDB values are referred to PDB (Pee Dee Belemnite), and δ18O are referred to -VSMOW. The reference materials used were IAEA C3, IAEA CH7; IAEA 600; IAEA N1 and N2; IAEA 601 and IAEA 602. EuroEA (EuroVector, Italy) elemental analyser was used for online sample preparation by Dumas-combustion. For the elemental analyses the Certified Reference Materials were Sulfanilamide for C, N, H, S and Atropine for O.
    Keywords: Aquarium number; Azores_Sampling_Vent_mussel_Bathymodiolus_azoricus; Bathymodiolus; Carbon, per dry mass; carbon content; CF-IRMS, Sercon, SerconHydra 20–22; d13C; d15N; d18O; DATE/TIME; Deep-sea; Dry mass; elemental analysis; Elemental analyzer, EuroVector, EuroEA 3000; Event label; experiment; Experimental treatment; Experiment duration; Hydrogen, per dry mass; hydrogen content; iAtlantic; Incubation duration; Integrated Assessment of Atlantic Marine Ecosystems in Space and Time; Juveniles; Mussel; NE Atlantic; Nitrogen, per dry mass; nitrogen content; Oxygen; oxygen content; Sample ID; Sample material; Sediment plumes; Species, unique identification (Semantic URI); Species, unique identification (URI); Stable isotopes; Sulfur, total; sulfur content; δ13C; δ15N; δ18O
    Type: Dataset
    Format: text/tab-separated-values, 952 data points
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  • 10
    Publication Date: 2024-05-24
    Description: Although the oceanic widespread pelagic tunicate Soestia zonaria has been studied for more than a century, little ecological information exists. Soestia primarily occurs in tropical to warm-temperate regions. Soestia specimens were collected in 2008 and 2021 during two research expeditions (EXPORTS cruise to the Northeast Atlantic and TAN0806 over the Chatham Rise, New Zealand) using MOCNESS-1 net and large midwater trawl with maximum sampling depths of 1000 m. In total, 140 Soestia specimens (oral-atrial length: 7–54 mm) were analysed for biomass parameters (wet weight, dry weight, ash-free dry weight, water content, organic content) and stoichiometry (carbon and nitrogen content, carbon-to-nitrogen ratio).
    Keywords: Calculated; Calculated according to Larson (1986); Calculated according to Lüskow et al. (2021); Chatham Rise; Comment; Container, mass; Cruise/expedition; Date/Time of event; DEPTH, water; DVM; Elemental analyzer (EA), Elementar, vario MICRO cube; Event label; EXPORTS_P6; Gear; Intraspecific variability; LATITUDE; LONGITUDE; Mass; MIDOC; Midwater open and closing net system; Midwater trawl; MOC1; MOCNESS opening/closing plankton net 1 sqm; MWT; Net ID; North Atlantic; Number of specimens; Ocean and sea region; Pelagic tunicate; RULER; Ruler stick; Sample ID; see comment; Soestia zonaria, ash free dry mass; Soestia zonaria, ash mass; Soestia zonaria, carbon, per dry mass; Soestia zonaria, carbon/nitrogen ratio; Soestia zonaria, dry mass; Soestia zonaria, nitrogen, per dry mass; Soestia zonaria, oral-atrial length; Soestia zonaria, total length; Soestia zonaria, wet mass; Species, unique identification; Species, unique identification (Semantic URI); Species, unique identification (URI); Station label; stoichiometry; TAN0806; TAN0806_104; TAN0806_12; TAN0806_124; TAN0806_140; TAN0806_163; TAN0806_169; TAN0806_40; TAN0806_Test; Tangaroa; Tow ID
    Type: Dataset
    Format: text/tab-separated-values, 3003 data points
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