cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.955745
title: Seawater carbonate chemistry and calcification of coral Acropora hyacinthus

description: To investigate the effect of diel variation in pCO2 on coral calcification, branches of Acropora hyacinthus were collected in 2 habitats (upstream and downstream in a unidirectional flow) in a shallow back reef in Moorea, French Polynesia, where different diel amplitudes of pCO2 oscillation were expected. Corals were maintained for 6 wk under different pCO2 regimes (constant versus oscillatory), each delivered in 3 configurations: constant conditions of 400 µatm, 700 µatm, and 1000 µatm pCO2, or oscillatory conditions varying daily from 280 to 550 µatm, 550 to 1000 µatm, or 400 to 2000 µatm, with minima and maxima during the day and night, respectively. Calcification rates in all treatments tended to increase over time, and the interaction between Time and pCO2 regime (i.e. constant versus oscillating) was significant (or close to significant) for upstream corals due to higher calcification in oscillatory pCO2. A significant pCO2 regime effect was detected in the highest pCO2 for downstream corals, with higher calcification in the 400 to 2000 µatm oscillatory pCO2 treatment compared to the 1000 µatm constant pCO2 treatment. After 6 wk, calcification of A. hyacinthus was affected significantly by habitat, the pCO2 level, and the pCO2 regime. Calcification generally was reduced by high pCO2 and was ≥21% greater in 400 to 2000 µatm oscillatory pCO2 versus 1000 µatm constant pCO2 treatment. Increased calcification in the 400 to 2000 µatm oscillatory pCO2 treatment suggests that natural diel oscillations in pCO2 could play a role by reducing the locally negative effects of rising pCO2 associated with ocean acidification on coral calcification.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2023-02-16.
DOI: 10.1594/pangaea.833325
title: EPOCA Svalbard 2010 mesocosm experiment: bacterial community structure

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).
DOI: 10.1594/pangaea.955746
title: Seawater carbonate chemistry in the experiment of transcriptomic responses of coralline algae to global change stressors

description: Crustose coralline algae (CCA) are calcifying red macroalgae that play important ecological roles including stabilisation of reef frameworks and provision of settlement cues for a range of marine invertebrates. Previous research into the responses of CCA to ocean warming (OW) and ocean acidification (OA) have found magnitude of effect to be species-specific. Response to OW and OA could be linked to divergent underlying molecular processes across species. Here we show Sporolithon durum, a species that exhibits low sensitivity to climate stressors, had little change in metabolic performance and did not significantly alter the expression of any genes when exposed to temperature and pH perturbations. In contrast, Porolithon onkodes, a major coral reef builder, reduced photosynthetic rates and had a labile transcriptomic response with over 400 significantly differentially expressed genes, with differential regulation of genes relating to physiological processes such as carbon acquisition and metabolism. The differential gene expression detected in P. onkodes implicates possible key metabolic pathways, including the pentose phosphate pathway, in the stress response of this species. We suggest S. durum is more resistant to OW and OA than P. onkodes, which demonstrated a high sensitivity to climate stressors and may have limited ability for acclimatisation. Understanding changes in gene expression in relation to physiological processes of CCA could help us understand and predict how different species will respond to, and persist in, future ocean conditions predicted for 2100.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2023-02-16.
DOI: 10.1594/pangaea.932922
title: Seawater carbonate chemistry and acid–base balance in the hæmolymph of European abalone (Haliotis tuberculata)

description: Ocean acidification (OA) and the associated changes in seawater carbonate chemistry pose a threat to calcifying organisms. This is particularly serious for shelled molluscs, in which shell growth and microstructure has been shown to be highly sensitive to OA. To improve our understanding of the responses of abalone to OA, this study investigated the effects of CO2-induced ocean acidification on extra-cellular acid–base parameters in the European abalone Haliotis tuberculata. Three-year-old adult abalone were exposed for 15 days to three different pH levels (7.9, 7.7, 7.4) representing current and predicted near-future conditions. Hæmolymph pH and total alkalinity were measured at different time points during exposure and used to calculate the carbonate parameters of the extracellular fluid. Total protein content was also measured to determine whether seawater acidification influences the composition and buffer capacity of hæmolymph. Extracellular pH was maintained at seawater pH 7.7 indicating that abalones are able to buffer moderate acidification (−0.2 pH units). This was not due to an accumulation of HCO3− ions but rather to a high hæmolymph protein concentration. By contrast, hæmolymph pH was significantly decreased after 5 days of exposure to pH 7.4, indicating that abalone do not compensate for higher decreases in seawater pH. Total alkalinity and dissolved inorganic carbon were also significantly decreased after 15 days of low pH exposure. It is concluded that changes in the acid–base balance of the hæmolymph might be involved in deleterious effects recorded in adult H. tuberculata facing severe OA stress. This would impact both the ecology and aquaculture of this commercially important species.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2021-06-22.
DOI: 10.1594/pangaea.933051
title: Seawater carbonate chemistry and elemental ratios in biogenic marine calcium carbonates

description: Elemental ratios in biogenic marine calcium carbonates are widely used in geobiology, environmental science, and paleoenvironmental reconstructions. It is generally accepted that the elemental abundance of biogenic marine carbonates reflects a combination of the abundance of that ion in seawater, the physical properties of seawater, the mineralogy of the biomineral, and the pathways and mechanisms of biomineralization. Here we report measurements of a suite of nine elemental ratios (Li/Ca, B/Ca, Na/Ca, Mg/Ca, Zn/Ca, Sr/Ca, Cd/Ca, Ba/Ca, and U/Ca) in 18 species of benthic marine invertebrates spanning a range of biogenic carbonate polymorph mineralogies (low-Mg calcite, high-Mg calcite, aragonite, mixed mineralogy) and of phyla (including Mollusca, Echinodermata, Arthropoda, Annelida, Cnidaria, Chlorophyta, and Rhodophyta) cultured at a single temperature (25°C) and a range of pCO2 treatments (ca. 409, 606, 903, and 2856 ppm). This dataset was used to explore various controls over elemental partitioning in biogenic marine carbonates, including species-level and biomineralization-pathway-level controls, the influence of internal pH regulation compared to external pH changes, and biocalcification responses to changes in seawater carbonate chemistry. The dataset also enables exploration of broad scale phylogenetic patterns of elemental partitioning across calcifying species, exhibiting high phylogenetic signals estimated from both uni- and multivariate analyses of the elemental ratio data (univariate: lambda = 0–0.889; multivariate: lambda = 0.895–0.99). Comparing partial R2 values returned from non-phylogenetic and phylogenetic regression analyses echo the importance of and show that phylogeny explains the elemental ratio data 1.4–59 times better than mineralogy in five out of nine of the elements analyzed. Therefore, the strong associations between biomineral elemental chemistry and species relatedness suggests mechanistic controls over element incorporation rooted in the evolution of biomineralization mechanisms.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2021-06-24.
DOI: 10.1594/pangaea.955456
title: Seawater carbonate chemistry and net calcification of Porites, Zoanthus growth and maximum PSII efficiency of Porites and Zoanthus

description: Ocean acidification (OA) threatens the persistence of reef-building corals and the habitat they provide. While species-specific effects of OA on marine organisms could have cascading effects on ecological interactions like competition, few studies have identified how benthic reef competitors respond to OA. We explored how two common Caribbean competitors, branching Porites and a colonial zoanthid (Zoanthus), respond to the factorial combination of OA and competition. In the laboratory, we exposed corals, zoanthids and interacting corals and zoanthids to ambient (8.01 ± 0.03) and OA (7.68 ± 0.07) conditions for 60 days. The OA treatment had no measured effect on zoanthids or coral calcification but decreased Porites maximum PSII efficiency. Conversely, the competitive interaction significantly decreased Porites calcification but had minimal-to-no countereffects on the zoanthid. Although this interaction was not exacerbated by the 60-day OA exposure, environmental changes that enhance zoanthid performance could add to the dominance of zoanthids over corals. The lack of effects of OA on coral calcification indicates that near-term competitive interactions may have more immediate consequences for some corals than future global change scenarios. Disparate consequences of competition have implications for community structure and should be accounted for when evaluating local coral reef trajectories.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2023-02-10.
DOI: 10.1594/pangaea.955830
title: Seawater carbonate chemistry and Synechococcus growth from pCO2 experiments

description: Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene transcription in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the 'helper' bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different transcription of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene transcription patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing transcription patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. If similar broad alterations in microbial ecophysiology occur in the ocean as atmospheric pCO2 increases, they could lead to substantially altered ecosystem functioning and community composition.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2023-02-20.
DOI: 10.1594/pangaea.933100
title: Seawater carbonate chemistry and ion-transporting capacity and aerobic respiration of larval white seabass (Atractoscion nobilis)

description: Ocean acidification (OA) has been proposed to increase the energetic demand for acid-base regulation at the expense of larval fish growth. Here, white seabass (Atractoscion nobilis) eggs and larvae were reared at control (542 +/- 28 μatm) and elevated pCO2 (1,831 +/- 105 μatm) until five days post-fertilization (dpf). Skin ionocytes were identified by immunodetection of the Na+/K+-ATPase (NKA) enzyme. Larvae exposed to elevated pCO2 possessed significantly higher skin ionocyte number and density compared to control larvae. However, when ionocyte size was accounted for, the relative ionocyte area (a proxy for total ionoregulatory capacity) was unchanged. Similarly, there were no differences in relative NKA abundance, resting O2 consumption rate, and total length between control and treatment larvae at 5 dpf, nor in the rate at which relative ionocyte area and total length changed between 2–5 dpf. Altogether, our results suggest that OA conditions projected for the next century do not significantly affect the ionoregulatory capacity or energy consumption of larval white seabass. Finally, a retroactive analysis of the water in the recirculating aquarium system that housed the broodstock revealed the parents had been exposed to average pCO2 of 1,200 μatm for at least 3.5 years prior to this experiment. Future studies should investigate whether larval white seabass are naturally resilient to OA, or if this resilience is the result of parental chronic acclimation to OA, and/or from natural selection during spawning and fertilization in elevated pCO2.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2021-06-24.
DOI: 10.15468/dl.y6jr3v
title: Occurrence Download

description: A dataset containing 1844 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-124.61417 -58.3117,-30.43715 -58.3117,-30.43715 30.92629,-124.61417 30.92629,-124.61417 -58.3117))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)",
 "Year 2020-2024"
 ]
}

 The dataset includes 1844 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015870-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.915941
title: Seawater carbonate chemistry and growth and survival of native and commercial oysters

description: The effects of climate change, including ocean acidification and ocean heatwaves, on biological communities in estuaries are often uncertain. Part of the uncertainty is due to the complex suite of environmental factors in addition to acidification and warming that influence the growth of shells and skeletons of many estuarine organisms. The goal of this study was to document spatial and temporal variation in water column properties and to measure the in situ effects on larval and recently settled stages of ecologically important Olympia oysters (Ostrea lurida) and commercially important Pacific oysters (Crassostrea gigas) in a low‐inflow estuary with a Mediterranean climate in Northern California. Our results reveal that seasonal inputs of upwelled or riverine water create important and predictable gradients of carbonate system parameters, temperature, salinity, dissolved oxygen (DO), and other variables that influence oyster performance, and that the influence of these gradients is contingent upon the location in the estuary as well as seasonal timing. During upwelling events (dry season), temperature, carbonate chemistry, and DO had the greatest impact on oyster performance. During runoff events (wet season), gradients in salinity, nutrient concentrations, and total alkalinity driven by river discharge were comparatively more important. These results suggest that the spatial importance of carbonate chemistry and temperature are seasonally variable and are two of several other factors that determine oyster performance. We use these results to discuss future impacts on oysters given projected regional changes in the frequency and magnitude of upwelling and precipitation‐driven runoff events.
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 2020-04-30.
DOI: 10.1594/pangaea.854719
title: Phytoplankton calcification as an effective mechanism to alleviate cellular calcium poisoning

description: Marine phytoplankton has developed the remarkable ability to tightly regulate the concentration of free calcium ions in the intracellular cytosol at a level of ~ 0.1 µmol /l in the presence of seawater Ca2+ concentrations of 10 mmol/1. The low cytosolic calcium ion concentration is of utmost importance for proper cell signalling function. While the regulatory mechanisms responsible for the tight control of intracellular Ca2+ concentration are not completely understood, phytoplankton taxonomic groups appear to have evolved different strategies, which may affect their ability to cope with changes in seawater Ca2+ concentrations in their environment on geological time scales. For example, the Cretaceous (145 to 66 Ma ago), an era known for the high abundance of coccolithophores and the production of enormous calcium carbonate deposits, exhibited seawater calcium concentrations up to four times present-day levels. We show that calcifying coccolithophore species (Emiliania huxleyi, Gephyrocapsa oceanica and Coccolithus braarudii) are able to maintain their relative fitness (in terms of growth rate and photosynthesis) at simulated Cretaceous seawater calcium concentrations, whereas these rates are severely reduced under these conditions in some non-calcareous phytoplankton species (Chaetoceros sp., Ceratoneis closterium and Heterosigma akashiwo). Most notably, this also applies to a non-calcifying strain of E. huxleyi which displays a calcium-sensitivity similar to the non-calcareous species. We hypothesize that the process of calcification in coccolithophores provides an efficient mechanism to alleviate cellular calcium poisoning and thereby offered a potential key evolutionary advantage, responsible for the proliferation of coccolithophores during times of high seawater calcium concentrations. The exact function of calcification and the reason behind the highly-ornate physical structures of coccoliths remain elusive.
description: This study was funded by the Australian Research Council (DP 1093801) and Conselho Nacional de Desenvolvimento Científico e Tecnológico Brasil (CNPq, Processo: 405585/2013-6)
description: Supplement to: Müller, Marius N; Barcelos e Ramos, Joana; Schulz, Kai Georg; Riebesell, Ulf; Kaźmierczak, J; Gallo, F; Mackinder, Luke C M; Li, Y; Nesterenko, P N; Trull, Tom W; Hallegraeff, Gustaaf M (2015): Phytoplankton calcification as an effective mechanism to alleviate cellular calcium poisoning. Biogeosciences, 12(21), 6493-6501