cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.835310
title: Acclimatization of the crustose coralline alga Porolithon onkodes to variable pCO2

description: Ocean acidification (OA) has important implications for the persistence of coral reef ecosystems, due to potentially negative effects on biomineralization. Many coral reefs are dynamic with respect to carbonate chemistry, and experience fluctuations in pCO2 that exceed OA projections for the near future. To understand the influence of dynamic pCO2 on an important reef calcifier, we tested the response of the crustose coralline alga Porolithon onkodes to oscillating pCO2. Individuals were exposed to ambient (400 µatm), high (660 µatm), or variable pCO2 (oscillating between 400/660 µatm) treatments for 14 days. To explore the potential for coralline acclimatization, we collected individuals from low and high pCO2 variability sites (upstream and downstream respectively) on a back reef characterized by unidirectional water flow in Moorea, French Polynesia. We quantified the effects of treatment on algal calcification by measuring the change in buoyant weight, and on algal metabolism by conducting sealed incubations to measure rates of photosynthesis and respiration. Net photosynthesis was higher in the ambient treatment than the variable treatment, regardless of habitat origin, and there was no effect on respiration or gross photosynthesis. Exposure to high pCO2 decreased P. onkodes calcification by &gt;70%, regardless of the original habitat. In the variable treatment, corallines from the high variability habitat calcified 42% more than corallines from the low variability habitat. The significance of the original habitat for the coralline calcification response to variable, high pCO2 indicates that individuals existing in dynamic pCO2 habitats may be acclimatized to OA within the scope of in situ variability. These results highlight the importance of accounting for natural pCO2 variability in OA manipulations, and provide insight into the potential for plasticity in habitat and species-specific responses to changing ocean chemistry.
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 2014-08-27.
description: Supplement to: Johnson, Maggie Dorothy; Moriarty, Vincent; Carpenter, Robert C (2014): Acclimatization of the Crustose Coralline Alga Porolithon onkodes to Variable pCO2. PLoS ONE, 9(2), e87678
DOI: 10.1594/pangaea.909062
title: Seawater carbonate chemistry and fitness of the edible mussel Mytilus chilensis

description: High latitudes are considered particularly vulnerable to ocean acidification, since they are naturally low in carbonate ions. The edible mussel Mytilus chilensis is a common calcifier inhabiting marine ecosystems of the southern Chile, where culturing of this species is concentrated and where algal blooms produced by the toxic dinoflagellate A. catenella are becoming more frequent. Juvenile Mytilus chilensis were exposed to experimental conditions simulating two environmental phenomena: pCO2 increase and the presence of paralytic shellfish toxins (PST) produced by the toxic dinoflagellate Alexandrium catenella. Individuals were exposed to two levels of pCO2: 380 μatm (control condition) and 1000 μatm (future conditions) over a period of 39 days (acclimation), followed by another period of 40 days exposure to a combination of pCO2 and PST. Both factors significantly affected most of the physiological variables measured (feeding, metabolism and scope for growth). However, these effects greatly varied over time, which can be explained by the high individual variability described for mussels exposed to different environmental conditions. Absorption efficiency was not affected by the independent effect of the toxic diet; however, the diet and pCO2 interaction affected it significantly. The inhibition of the physiological processes related with energy acquisition by diets containing PST, may negatively impact mussel fitness, which could have important consequences for both wild and cultured mussel populations, and thus, for socioeconomic development in southern Chile.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) 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 2019-11-20.
description: Supplement to: Mellado, Carla; Chaparro, Oscar R; Duarte, Cristian; Villanueva, Paola A; Ortiz, Alejandro; Valdivia, Nelson; Torres, Rodrigo; Navarro, Jorge M (2019): Ocean acidification exacerbates the effects of paralytic shellfish toxins on the fitness of the edible mussel Mytilus chilensis. Science of the Total Environment, 653, 455-464
DOI: 10.1594/pangaea.910336
title: Seawater carbonate chemistry and embryo survival, larval survival, size at hatch and post-larval growth rates of coastal forage fish, Menidia menidia

description: Coastal ecosystems experience substantial natural fluctuations in pCO2 and dissolved oxygen (DO) conditions on diel, tidal, seasonal and interannual timescales. Rising carbon dioxide emissions and anthropogenic nutrient input are expected to increase these pCO2 and DO cycles in severity and duration of acidification and hypoxia. How coastal marine organisms respond to natural pCO2 * DO variability and future climate change remains largely unknown. Here, we assess the impact of static and cycling pCO2 * DO conditions of various magnitudes and frequencies on early life survival and growth of an important coastal forage fish, Menidia menidia. Static low DO conditions severely decreased embryo survival, larval survival, time to 50% hatch, size at hatch and post-larval growth rates. Static elevated pCO2 did not affect most response traits, however, a synergistic negative effect did occur on embryo survival under hypoxic conditions (3.0 mg/L). Cycling pCO2 * DO, however, reduced these negative effects of static conditions on all response traits with the magnitude of fluctuations influencing the extent of this reduction. This indicates that fluctuations in pCO2 and DO may benefit coastal organisms by providing periodic physiological refuge from stressful conditions, which could promote species adaptability to climate change.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) 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 2019-12-20.
DOI: 10.1594/pangaea.873802
title: Measurements of microbial processes, dissolution, water and porewater chemistry during experiments on two coral reef sediments: Davies Reef MPB growth and chamber fluxes

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 is 2017-03-22.
DOI: 10.1594/pangaea.872400
title: Sea hare Aplysia punctata (mollusca: Gastropoda) can maintain shell calcification under extreme ocean acidification

description: Ocean acidification is expected to cause energetic constraints upon marine calcifying organisms such as molluscs and echinoderms, because of the increased costs of building or maintaining shell material in lower pH. We examined metabolic rate, shell morphometry, and calcification in the sea hare Aplysia punctata under short-term exposure (19 days) to an extreme ocean acidification scenario (pH 7.3, 2800 µatm pCO2), along with a group held in control conditions (pH 8.1, 344 µatm pCO2). This gastropod and its congeners are broadly distributed and locally abundant grazers, and have an internal shell that protects the internal organs. Specimens were examined for metabolic rate via closed-chamber respirometry, followed by removal and examination of the shell under confocal microscopy. Staining using calcein determined the amount of new calcification that occurred over 6 days at the end of the acclimation period. The width of new, pre-calcified shell on the distal shell margin was also quantified as a proxy for overall shell growth. Aplysia punctata showed a 30% reduction in metabolic rate under low pH, but calcification was not affected. This species is apparently able to maintain calcification rate even under extreme low pH, and even when under the energetic constraints of lower metabolism. This finding adds to the evidence that calcification is a largely autonomous process of crystallization that occurs as long as suitable haeomocoel conditions are preserved. There was, however, evidence that the accretion of new, noncalcified shell material may have been reduced, which would lead to overall reduced shell growth under longer-term exposures to low pH independent of calcification. Our findings highlight that the chief impact of ocean acidification upon the ability of marine invertebrates to maintain their shell under low pH may be energetic constraints that hinder growth of supporting structure, rather than maintenance of calcification.
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 is 2017-02-20.
description: Supplement to: Carey, Nicholas; Dupont, Sam; Sigwart, Julia D (2016): Sea hare Aplysia punctata (mollusca: Gastropoda) can maintain shell calcification under extreme ocean acidification. Biological Bulletin, 231(2), 142-151
DOI: 10.1594/pangaea.873825
title: Measurements of microbial processes, dissolution, water and porewater chemistry during experiments on two coral reef sediments: Percolation

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 is 2017-03-22.
DOI: 10.1594/pangaea.910338
title: Seawater carbonate chemistry and hatching, survival and development rate of Calanus pacificus

description: We characterized the vertical distribution of Calanus pacificus eggs and larvae and the carbonate chemistry that they are exposed to in Puget Sound, WA. We found that, under stratified conditions, more than 90% of eggs and nauplii stages 1–4 were distributed above the pycnocline, in seawater with pH higher than 7.7. In addition, eggs and larvae from 101 females were reared for 5 days under a range of pH conditions (7.2–8.0) to investigate how pH sensitivity varies among individuals. We observed a slight increase in naupliar survival at pH 7.3 in Individual Brood experiments, while in Mixed Brood experiments, exposure to pH 7.3 led to a small decline in hatching success. In a Split Brood experiment, inter-individual variability among different females' broods masked pH effects. These results indicate that C. pacificus early life stages are generally tolerant to short-term direct effects of ocean acidification.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) 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 2019-12-20.
description: Supplement to: McLaskey, Anna K; McElhany, Paul; Busch, Shallin D; Maher, Michael; Winans, Amanda K; Keister, Julie E (2019): Early life stages of Calanus pacificus are neither exposed nor sensitive to low pH waters. Journal of Plankton Research, fbz059
DOI: 10.1594/pangaea.913398
title: Seawater carbonate chemistry and crystallographic vital effect of the coral skeleton

description: Distinguishing between environmental and species-specific physiological signals, recorded in coral skeletons, is one of the fundamental challenges in their reliable use as (paleo)climate proxies. To date, characteristic biological bias in skeleton-recorded environmental signatures (vital effect) was shown in shifts in geochemical signatures. Herein, for the first time, we have assessed crystallographic parameters of bio-aragonite to study the response of the reef-building coral Stylophora pistillata to experimental seawater acidification (pH 8.2, 7.6 and 7.3). Skeletons formed under high pCO2 conditions show systematic crystallographic changes such as better constrained crystal orientation and anisotropic distortions of bio-aragonite lattice parameters due to increased amount of intracrystalline organic matrix and water content. These variations in crystallographic features that seem to reflect physiological adjustments of biomineralizing organisms to environmental change, are herein called crystallographic vital effect (CVE). CVE may register those changes in the biomineralization process that may not yet be perceived at the macromorphological skeletal level.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) 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 2020-03-06.
DOI: 10.1594/pangaea.839098
title: Vertical profiles of environmental parameters measured on discrete water samples collected with Niskin bottles at station TARA_091 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.892842
title: Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis

description: Cnidarians harbor a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here, we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons. Deep sequencing of small RNA libraries constructed from A. viridis adults sampled at a natural CO2 gradient off Vulcano Island, Italy, identified 70 distinct miRNAs. Eight were homologous to previously reported miRNAs in cnidarians, whereas 62 appeared novel. Nine miRNAs were recognized as differentially expressed along the natural seawater pH gradient. We found a highly abundant and diverse population of piRNAs, with a substantial fraction showing ping–pong signatures. We identified nearly 22% putative piRNAs potentially targeting transposable elements within the A. viridis genome. The A. viridis genome appeared similar in size to that of other hexacorals with a very high divergence of transposable elements resembling that of the sea anemone genus Exaiptasia. The genome encodes and expresses a high number of small regulatory RNAs, which include novel miRNAs and piRNAs. Differentially expressed small RNAs along the seawater pH gradient indicated regulatory gene responses to environmental stressors.
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: Urbarova, Ilona; Patel, Hardip; Forêt, S; Karlsen, Bard Ove; Jørgensen, Tor Erik; Hall-Spencer, Jason M; Johansen, Steinar D (2018): Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing. Genome Biology and Evolution, 10(2), 410-426
DOI: 10.1594/pangaea.888447
title: Seawater carbonate chemistry and biomarker pigments and phytoplankton community composition in different biogeochemical regions of the Southern Ocean

description: The ongoing rise in atmospheric CO2 concentration is causing rapid increases in seawater pCO2levels. However, little is known about the potential impacts of elevated CO2 availability on the phytoplankton assemblages in the Southern Ocean's oceanic regions. Therefore, we conducted four incubation experiments using surface seawater collected from the subantarctic zone (SAZ) and the subpolar zone (SPZ) in the Australian sector of the Southern Ocean during the austral summer of 2011-2012. For incubations, FeCl3 solutions were added to reduce iron (Fe) limitation for phytoplankton growth. Ambient and high (~750 µatm) CO2 treatments were then prepared with and without addition of CO2-saturated seawater, respectively. Non-Fe-added (control) treatments were also prepared to assess the effects of Fe enrichment (overall, control, Fe-added, and Fe-and-CO2-added treatments). In the initial samples, the dominant phytoplankton taxa shifted with latitude from haptophytes to diatoms, likely reflecting silicate availability in the water. Under Fe-enriched conditions, increased CO2 level significantly reduced the accumulation of biomarker pigments in haptophytes in the SAZ and AZ, whereas a significant decrease in diatom markers was only detected in the SAZ. The CO2-related changes in phytoplankton community composition were greater in the SAZ, most likely due to the decrease in coccolithophore biomass. Our results suggest that an increase in CO2, if it coincides with Fe enrichment, could differentially affect the phytoplankton community composition in different geographical regions of the Southern Ocean, depending on the locally dominant taxa and environmental conditions.
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 2018-04-11.
description: Supplement to: Endo, H; Hattori, Hiroshi; Mishima, Tsubasa; Hashida, Gen; Sasaki, H; Nishioka, Jun; Suzuki, Koji (2017): Phytoplankton community responses to iron and CO2 enrichment in different biogeochemical regions of the Southern Ocean. Polar Biology, 40(11), 2143-2159
DOI: 10.1594/pangaea.834210
title: Sea urchin response to rising pCO2 shows ocean acidification may fundamentally alter the chemistry of marine skeletons

description: Ocean acidification caused by an increase in pCO2 is expected to drastically affect marine ecosystem composition, yet there is much uncertainty about the mechanisms through which ecosystems may be affected. Here we studied sea urchins that are common and important grazers in the Mediterranean (Paracentrotus lividus and Arbacia lixula). Our study included a natural CO2 seep plus reference sites in the Aegean Sea off Greece. The distribution of A. lixula was unaffected by the low pH environment, whereas densities of P. lividus were much reduced. There was skeletal degradation in both species living in acidified waters compared to reference sites and remarkable increases in skeletal manganese levels (P. lividus had a 541% increase, A. lixula a 243% increase), presumably due to changes in mineral crystalline structure. Levels of strontium and zinc were also altered. It is not yet known whether such dramatic changes in skeletal chemistry will affect coastal systems but our study reveals a mechanism that may alter inter-species interactions.
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 2014-07-22.
description: Supplement to: Bray, Laura; Pancucci-Papadopulou, M A; Hall-Spencer, Jason M (2014): Sea urchin response to rising pCO2 shows ocean acidification may fundamentally alter the chemistry of marine skeletons. Mediterranean Marine Science, 15(3), 510-519