cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.892892
title: Seawater carbonate chemistry and cytoskeleton, lysozymes, and nitric oxide in hemocytes of blood clams, Tegillarca granosa.

description: An enormous amount of anthropogenic carbon dioxide (CO2) has been dissolved into the ocean, leading to a lower pH and changes in the chemical properties of seawater, which has been termed ocean acidification (OA). The impacts of pCO2-driven acidification on immunity have been revealed recently in various marine organisms. However, the mechanism causing the reduction in phagocytosis still remains unclear. Therefore, the impacts of pCO2-driven OA at present and near-future levels (pH values of 8.1, 7.8, and 7.4) on the rate of phagocytosis, the abundance of cytoskeleton components, the levels of nitric oxide (NO), and the concentration and activity of lysozymes (LZM) of hemocytes were investigated in a commercial bivalve species, the blood clam (Tegillarca granosa). In addition, the effects of OA on the expression of genes regulating actin skeleton and nitric oxide synthesis 2 (NOS2) were also analyzed. The results obtained showed that the phagocytic rate, cytoskeleton component abundance, concentration and activity of LZM of hemocytes were all significantly reduced after a 2-week exposure to the future OA scenario of a pH of 7.4. On the contrary, a remarkable increase in the concentration of NO compared to that of the control was detected in clams exposed to OA. Furthermore, the expression of genes regulating the actin cytoskeleton and NOS were significantly up-regulated after OA exposure. Though the mechanism causing phagocytosis seemed to be complicated based on the results obtained in the present study and those reported previously, our results suggested that OA may reduce the phagocytosis of hemocytes by (1) decreasing the abundance of cytoskeleton components and therefore hampering the cytoskeleton-mediated process of engulfment, (2) reducing the concentration and activity of LZM and therefore constraining the degradation of the engulfed pathogen through an oxygen-independent pathway, and (3) inducing the production of NO, which may negatively regulate immune responses.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2016) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2018-08-06.
description: Supplement to: Su, Wenhao; Rong, Jiahuan; Zha, Shanjie; Yan, Maocang; Fang, Jun; Liu, Guangxu (2018): Ocean Acidification Affects the Cytoskeleton, Lysozymes, and Nitric Oxide of Hemocytes: A Possible Explanation for the Hampered Phagocytosis in Blood Clams, Tegillarca granosa. Frontiers in Physiology, 9
DOI: 10.1594/pangaea.786445
title: (Table 1) Ratio of hydroxy-GDGT vs. the total core GDGT was calculated based on the detection of hydroxy-GDGT

description: Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) 1H–13C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sediment, allowed us to identify one major compound as a monohydroxy-GDGT with acyclic biphytanyl moieties (OH-GDGT-0). NMR spectroscopic and mass spectrometric data indicate the presence of a tertiary hydroxyl group suggesting the compounds are the tetraether analogues of the widespread hydroxylated archaeol derivatives that have received great attention in geochemical studies of the last two decades. Three other related compounds were assigned as acyclic dihydroxy-GDGT (2OH-GDGT-0) and monohydroxy-GDGT with one (OH-GDGT-1) and two cyclopentane rings (OH-GDGT-2). Based on the identification of hydroxy-GDGT core lipids, a group of previously reported unknown intact polar lipids (IPLs), including the ubiquitously distributed H341-GDGT (Lipp J. S. and Hinrichs K. -U. (2009) Structural diversity and fate of intact polar lipids in marine sediments. Geochim. Cosmochim. Acta 73, 6816–6833), and its analogues were tentatively identified as glycosidic hydroxy-GDGTs. In addition to marine sediments, we also detected hydroxy-GDGTs in a culture of Methanothermococcus thermolithotrophicus. Given the previous finding of the putative polar precursor H341-GDGT in the planktonic marine crenarchaeon Nitrosopumilus maritimus, these compounds are synthesized by representatives of both cren- and euryarchaeota. The ubiquitous distribution and apparent substantial abundance of hydroxy-GDGT core lipids in marine sediments (up to 8% of total isoprenoid core GDGTs) point to their potential as proxies.
description: Supplement to: Liu, Xiao-Lei; Lipp, Julius S; Simpson, Jeffrey H; Lin, Yu-Shih; Summons, Roger E; Hinrichs, Kai-Uwe (2012): Mono- and dihydroxyl glycerol dibiphytanyl glycerol tetraethers in marine sediments: Identification of both core and intact polar lipid forms. Geochimica et Cosmochimica Acta, 89, 102-115
DOI: 10.1594/pangaea.868353
title: Coral pH regulation of the calcifying fluid is modulated by seawater dissolved inorganic carbon concentration

description: Reef coral calcification depends on regulation of pH in the internal calcifying fluid in which the coral skeleton forms. However, little is known about calcifying fluid pH (pHCF) regulation, despite its importance in determining the response of corals to ocean acidification. Here, we investigate the impact of seawater dissolved inorganic carbon (DIC) concentration on calcifying fluid pH in the coral Stylophora pistillata in seawater with manipulated [DIC] and constant pH. Our results reveal that regulation of pHCF and calcification rates are sensitive to changes in seawater [DIC] in the light and dark. While part of this relationship can be explained by changes in rates of photosynthesis and respiration, our data point to the importance of seawater DIC in pH regulation of the coral's calcifying cells. Our findings contribute towards a mechanistic understanding of how and why coral calcification is sensitive to changes in seawater carbonate chemistry, which is needed for predicting effects of environmental change on coral reefs and for robust interpretations of isotopic paleoenvironmental records in coral skeletons.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2015) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation is 2016-11-14.
description: Supplement to: Comeau, Steeve; Tambutté, Eric; Carpenter, Robert C; Edmunds, Peter J; Evensen, Nicolas R; Allemand, Denis; Ferrier-Pagès, Christine; Tambutté, Sylvie; Venn, Alexander A (2017): Coral calcifying fluid pH is modulated by seawater carbonate chemistry not solely seawater pH. Proceedings of the Royal Society B-Biological Sciences, 284(1847), 20161669
DOI: 10.1594/pangaea.824707
title: Seawater carbonate chemistry and calcification in the tropical urchin Echinometra viridis in a laboratory experiment

description: Atmospheric carbon dioxide (pCO2) has risen from approximately 280 to 400 ppm since the Industrial Revolution, due mainly to the combustion of fossil fuels, deforestation, and cement production. It is predicted to reach as high as 900 ppm by the end of this century. Ocean acidification resulting from the release of anthropogenic CO2 has been shown to impair the ability of some marine calcifiers to build their shells and skeletons. Here, we present the results of ocean acidification experiments designed to assess the effects of an increase in atmospheric pCO2 from ca. 448 to 827 ppm on calcification rates of the tropical urchin Echinometra viridis. Experiments were conducted under the urchin's winter (20 °C) and summer (30 °C) water temperatures in order to identify seasonal differences in the urchin's response to ocean acidification. The experiments reveal that calcification rates decreased for urchins reared under elevated pCO2, with the decline being more pronounced under wintertime temperatures than under summertime temperatures. These results indicate that the urchin E. viridis will be negatively impacted by CO2-induced ocean acidification that is predicted to occur by the end of this century. These results also suggest that impact of CO2-induced ocean acidification on urchin calcification will be more severe in the winter and in cooler waters.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2013-12-18.
description: Supplement to: Courtney, T; Westfield, Isaac T; Ries, Justin B (2013): CO2-induced ocean acidification impairs calcification in the tropical urchin Echinometra viridis. Journal of Experimental Marine Biology and Ecology, 440, 169-175
DOI: 10.1594/pangaea.834082
title: Impacts of groundwater discharge at Myora Springs (North Stradbroke Island, Australia) on the phenolic metabolism of eelgrass, Zostera muelleri, and grazing by the juvenile rabbitfish, Siganus fuscescens

description: Myora Springs is one of many groundwater discharge sites on North Stradbroke Island (Queensland, Australia). Here spring waters emerge from wetland forests to join Moreton Bay, mixing with seawater over seagrass meadows dominated by eelgrass, Zostera muelleri. We sought to determine how low pH / high CO2 conditions near the spring affect these plants and their interactions with the black rabbitfish (Siganus fuscescens), a co-occurring grazer. In paired-choice feeding trials S. fuscescens preferentially consumed Z. muelleri shoots collected nearest to Myora Springs. Proximity to the spring did not significantly alter the carbon and nitrogen contents of seagrass tissues but did result in the extraordinary loss of soluble phenolics, including Folin-reactive phenolics, condensed tannins, and phenolic acids by ?87%. Conversely, seagrass lignin contents were, in this and related experiments, unaffected or increased, suggesting a shift in secondary metabolism away from the production of soluble, but not insoluble, (poly)phenolics. We suggest that groundwater discharge sites such as Myora Springs, and other sites characterized by low pH, are likely to be popular feeding grounds for seagrass grazers seeking to reduce their exposure to soluble phenolics.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne et al, 2014) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation is 2014-07-15.
description: Supplement to: Arnold, Thomas; Freundlich, Grace; Weilnau, Taylor; Verdi, Arielle; Tibbetts, Ian R (2014): Impacts of groundwater discharge at Myora Springs (North Stradbroke Island, Australia) on the phenolic metabolism of eelgrass, Zostera muelleri, and grazing by the juvenile rabbitfish, Siganus fuscescens. PLoS ONE, 9(8), e104738
DOI: 10.1594/pangaea.717486
title: Seawater carbonate chemistry and calcification during tropical reef studies at Moorea (French Polynesia), 1996

description: Community metabolism was investigated using a Lagrangian flow respirometry technique on 2 reef flats at Moorea (French Polynesia) during austral winter and Yonge Reef (Great Barrier Reef) during austral summer. The data were used to estimate related air-sea CO2 disequilibrium. A sine function did not satisfactorily model the diel light curves and overestimated the metabolic parameters. The ranges of community gross primary production and respiration (Pg and R; 9 to 15 g C m-2 d-1) were within the range previously reported for reef flats, and community net calcification (G; 19 to 25 g CaCO3 m-2 d-1) was higher than the 'standard' range. The molar ratio of organic to inorganic carbon uptake was 6:1 for both sites. The reef flat at Moorea displayed a higher rate of organic production and a lower rate of calcification compared to previous measurements carried out during austral summer. The approximate uncertainty of the daily metabolic parameters was estimated using a procedure based on a Monte Carlo simulation. The standard errors of Pg,R and Pg/R expressed as a percentage of the mean are lower than 3% but are comparatively larger for E, the excess production (6 to 78%). The daily air-sea CO2 flux (FCO2) was positive throughout the field experiments, indicating that the reef flats at Moorea and Yonge Reef released CO2 to the atmosphere at the time of measurement. FCO2 decreased as a function of increasing daily irradiance.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI).
description: Supplement to: Gattuso, Jean-Pierre; Pichon, Michel; Delesalle, Bruno; Canon, C; Frankignoulle, Michel (1996): Carbon fluxes in coral reefs. I. Lagrangian measurement of community metabolism and resulting air-sea CO2 disequilibrium. Marine Ecology Progress Series, 145, 109-121
DOI: 10.1594/pangaea.892891
title: Seawater carbonate chemistry and chemical composition and functional properties of Ulva rigida

description: Ulva is increasingly viewed as a food source in the world. Here, Ulva rigida was cultured at two levels of temperature (14, 18°C), pH (7.95, 7.55, corresponding to low and high pCO2), and nitrate conditions (6 μmol L-1, 150 μmol L-1), to investigate the effects of ocean warming, acidification, and eutrophication on food quality of Ulva species. High temperature increased the content of each amino acid. High nitrate increased the content of all amino acid except aspartic acid and cysteine. High temperature, pCO2, and nitrate also increased content of most fatty acids. The combination of high temperature, pCO2, and nitrate increased the swelling capacity, water holding capacity, and oil holding capacity by 15.60%, 7.88%, and 16.32% respectively, compared to the control. It seems that future ocean environment would enhance the production of amino acid and fatty acid as well as the functional properties in Ulva species.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2016) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2018-08-06.
description: Supplement to: Gao, Guang; Clare, Anthony S; Chatzidimitriou, Eleni; Rose, Craig; Caldwell, Gary S (2018): Effects of ocean warming and acidification, combined with nutrient enrichment, on chemical composition and functional properties of Ulva rigida. Food Chemistry, 258, 71-78
DOI: 10.1594/pangaea.728725
title: Seawater carbonate chemistry and processes during experiments with phytoplankton Emiliania huxleyi (CS369), 2009
DOI: 10.1594/pangaea.868590
title: Snapping shrimp experiments

description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2015) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation is 2016-11-15.
DOI: 10.1594/pangaea.807745
title: Hydrochemistry measured on water bottle samples during Hakurei-Maru cruise NH93-1
DOI: 10.1594/pangaea.892373
title: Parameters of the carbonate system for each sample in the OA experiments
DOI: 10.1594/pangaea.892816
title: Seawater carbonate chemistry parameters

description: Ocean acidification causes an accumulation of CO2 in marine organisms and leads to shifts in acid-base parameters. Acid-base regulation in gill breathers involves a net increase of internal bicarbonate levels through transmembrane ion exchange with the surrounding water. Successful maintenance of body fluid pH depends on the functional capacity of ion-exchange mechanisms and associated energy budget. For a detailed understanding of the dependence of acid-base regulation on water parameters, we investigated the physiological responses of the shore crab Carcinus maenas to 4 weeks of ocean acidification [OA, P(CO2)w = 1800 µatm], at variable water bicarbonate levels, paralleled by changes in water pH. Cardiovascular performance was determined together with extra-(pHe) and intracellular pH (pHi), oxygen consumption, haemolymph CO2 parameters, and ion composition. High water P(CO2) caused haemolymph P(CO2) to rise, but pHe and pHi remained constant due to increased haemolymph and cellular [HCO3-]. This process was effective even under reduced seawater pH and bicarbonate concentrations. While extracellular cation concentrations increased throughout, anion levels remained constant or decreased. Despite similar levels of haemolymph pH and ion concentrations under OA, metabolic rates, and haemolymph flow were significantly depressed by 40 and 30%, respectively, when OA was combined with reduced seawater [HCO3-] and pH. Our findings suggest an influence of water bicarbonate levels on metabolic rates as well as on correlations between blood flow and pHe. This previously unknown phenomenon should direct attention to pathways of acid-base regulation and their potential feedback on whole-animal energy demand, in relation with changing seawater carbonate parameters.
DOI: 10.1594/pangaea.839129
title: Vertical profiles of environmental parameters measured on discrete water samples collected with Niskin bottles at station TARA_112 during the Tara Oceans expedition 2009-2013

description: The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of evironmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set includes properties of seawater, particulate matter and dissolved matter that were measured from discrete water samples collected with Niskin bottles during the 2009-2013 Tara Oceans expedition. Properties include pigment concentrations from HPLC analysis (10 depths per vertical profile, 25 pigments per depth), the carbonate system (Surface and 400m; pH (total scale), CO2, pCO2, fCO2, HCO3, CO3, Total alkalinity, Total carbon, OmegaAragonite, OmegaCalcite, and dosage Flags), nutrients (10 depths per vertical profile; NO2, PO4, N02/NO3, SI, quality Flags), DOC, CDOM, and dissolved oxygen isotopes. The Service National d'Analyse des Paramètres Océaniques du CO2, at the Université Pierre et Marie Curie, determined CT and AT potentiometrically. More than 200 vertical profiles of these properties were made across the world ocean. DOC, CDOM and dissolved oxygen isotopes are available only for the Arctic Ocean and Arctic Seas (2013).
description: marc.picheral@obs-vlfr.fr&gt;2014-10-03T13:23:32&gt;D:\process_ctd_data\Tara_validated_CTD_data_20121011\Tara_Oceans_Data_RVSS-NISKIN_2009-2013_20141003&gt;
DOI: 10.1594/pangaea.840590
title: Temperature and acidification variability reduce physiological performance in the intertidal zone porcelain crab Petrolisthes cinctipes

description: We show here that increased variability of temperature and pH synergistically negatively affects the energetics of intertidal zone crabs. Under future climate scenarios, coastal ecosystems are projected to have increased extremes of low tide-associated thermal stress and ocean acidification-associated low pH, the individual or interactive effects of which have yet to be determined. To characterize energetic consequences of exposure to increased variability of pH and temperature, we exposed porcelain crabs, Petrolisthes cinctipes, to conditions that simulated current and future intertidal zone thermal and pH environments. During the daily low tide, specimens were exposed to no, moderate or extreme heating, and during the daily high tide experienced no, moderate or extreme acidification. Respiration rate and cardiac thermal limits were assessed following 2.5 weeks of acclimation. Thermal variation had a larger overall effect than pH variation, though there was an interactive effect between the two environmental drivers. Under the most extreme temperature and pH combination, respiration rate decreased while heat tolerance increased, indicating a smaller overall aerobic energy budget (i.e. a reduced O2 consumption rate) of which a larger portion is devoted to basal maintenance (i.e. greater thermal tolerance indicating induction of the cellular stress response). These results suggest the potential for negative long-term ecological consequences for intertidal ectotherms exposed to increased extremes in pH and temperature due to reduced energy for behavior and reproduction.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne et al, 2014) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation is 2014-12-09.
description: Supplement to: Paganini, Adam W; Miller, Nathan A; Stillman, Jonathon H (2014): Temperature and acidification variability reduce physiological performance in the intertidal zone porcelain crab Petrolisthes cinctipes. Journal of Experimental Biology, 217(22), 3974-3980
DOI: 10.1594/pangaea.831668
title: Experiment: Study on the effects of near-future ocean acidification on marine yeasts: a microcosm approach

description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2014-02-11.