cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.945551
title: Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis)

description: The increase of CO2 by anthropogenic activities leads to a decrease of pH in the ocean surface due to ocean acidification (OA) process. Generally, OA not only reduces the rate of calcification in marine environments but also affects various physiological activities, especially in calcifiers, including edible oysters. Quantitative real-time PCR (qRT-PCR) is often used to detect gene expression in response to OA, which relies on the stability of internal control. However, the appropriate internal controls for OA experiments remain scarce especially in the marine calcifiers. Hence, this study developed internal controls for qRT-PCR assays using the Hong Kong oyster (Crassostrea hongkongensis) as a model to reveal gene expression profile during development under OA. In this study, 17 housekeeping genes were selected as the possible candidate of the internal controls. After a comprehensive interpretation from the multiple algorithms and software, GAPDH paired with RL23 is recommended for the normalization for planktonic larvae and benthic juveniles, but beyond that, TUBB and EF2 are recommended for post-metamorphic stage. Moreover, GAPDH and EF2 were suitable for various pH treatments, and TUBB, RL35 and RL23 could be the alternatives for OA experiments. These results are instrumental for the selection of internal control in Crassostrea hongkongensis during the development, and shed light on other molecular OA experiments in marine invertebrates for reference.
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 2022-06-20.The species name used in the paper is Crassostrea hongkongensis.
DOI: 10.1594/pangaea.957421
title: Seawater carbonate chemistry and scope for growth for juvenile Atlantic sea scallops (Placopecten magellanicus)

description: This study assessed the energy budget for juvenile Atlantic Sea Scallop, Placopecten magellanicus, during a natural drop in temperature (15.6°C to 5.8°C) over an 8-week time period during the fall at three different enrichment levels of carbon dioxide (CO2). Every 2 weeks, individuals were sampled for ecophysiological measurements of feeding activity, respiration rate (RR) and excretion rate (ER) to enable the calculation of scope for growth (SFG) and atomic oxygen:nitrogen ratios (O:N). In addition, 36 individuals per treatment were removed for shell height, dry tissue weight (DTW) and dry shell weight (DSW). We found a significant decrease in feeding rates as CO2 increased. Those rates also were significantly affected by temperature, with highest feeding at 9.4°C. No significant CO2 effect was observed for catabolic energy processes (RR and ER); however, these rates did increase significantly with temperature. The O:N ratio was not significantly affected by CO2, but was significantly affected by temperature. There was a significant interaction between CO2 and temperature for ER and the O:N ratio, with low CO2 levels resulting in a U-shaped response that was not sustained as CO2 levels increased. This suggests that the independent effects of CO2 and temperature observed at low levels are different once a CO2 threshold is reached. Additionally, there were significant differences in growth estimators (shell height and DSW), with the best growth occurring at the lowest CO2 level. In contrast to temperature variations that induced a trade-off response in energy acquisition and expenditure, results from this research support the hypothesis that sea scallops have a limited ability to alter physiological processes to compensate for increasing CO2.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-04-14.
DOI: 10.1594/pangaea.945725
title: Seawater carbonate chemistry and sperm count and fertilization rate of the mussel Mytilus galloprovincialis

description: The continued emissions of anthropogenic carbon dioxide are causing progressive ocean acidification (OA). While deleterious effects of OA on biological systems are well documented in the growth of calcifying organisms, lesser studied impacts of OA include potential effects on gamete interactions that determine fertilization, which are likely to influence the many marine species that spawn gametes externally. Here, we explore the effects of OA on the signalling mechanisms that enable sperm to track egg-derived chemicals (sperm chemotaxis). We focus on the mussel Mytilus galloprovincialis, where sperm chemotaxis enables eggs to bias fertilization in favour of genetically compatible males. Using an experimental design based on the North Carolina II factorial breeding design, we test whether the experimental manipulation of seawater pH (comparing ambient conditions to predicted end-of-century scenarios) alters patterns of differential sperm chemotaxis. While we find no evidence that male–female gametic compatibility is impacted by OA, we do find that individual males exhibit consistent variation in how their sperm perform in lowered pH levels. This finding of individual variability in the capacity of ejaculates to respond to chemoattractants under acidified conditions suggests that climate change will exert considerable pressure on male genotypes that can withstand an increasingly hostile fertilization environment.
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 2022-06-29.
DOI: 10.1594/pangaea.945654
title: Seawater carbonate chemistry and hatching success and hatching frequency of Ammodytes dubius

description: Rising oceanic pCO2 levels could affect many traits in fish early life stages, but only few species to date have shown direct CO2-induced survival reductions. This might partly be because species from less CO2-variable, offshore environments in higher latitudes are currently underrepresented in the literature. We conducted new experimental work on northern sand lance Ammodytes dubius, a keystone forage fish on offshore Northwest Atlantic sand banks, which was recently suggested to be highly CO2-sensitive. In two complementary trials, we produced embryos from wild, Gulf of Maine (GoM) spawners and reared them at several pCO2 levels (400–2000 µatm) in combination with static (6, 7, 10°C) and dynamic (10-&gt;5°C) temperature treatments. Again, we consistently observed large, CO2-induced reductions in hatching success (–23% at 1000 µatm, -61% at 2000 µatm), and the effects were temperature-independent. To distinguish pCO2 effects during development from potential impacts on hatching itself, some embryos were switched between high and control pCO2 treatments just prior to hatch. This indeed altered hatching patterns consistent with the CO2-impaired hatching hypothesis. High CO2 also delayed the day of first hatch in one trial and peak hatch in the other, where later-hatched larvae were of similar size but with progressively less endogenous energy reserves. For context, we extracted seasonal pCO2 projections for Stellwagen Bank (GoM) from regional ensemble simulations, which indicated a CO2-induced reduction in sand lance hatching success to 71% of contemporary levels by 2100. The species' unusual CO2 sensitivity has large ecological and scientific ramifications that warrant future in-depth research.
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 2022-06-20.
DOI: 10.1594/pangaea.945734
title: Seawater carbonate chemistry and growth, chain length, silica content, and toxin content of four species of diatoms and one toxic dinoflagellate

description: Phytoplankton induce defensive traits in response to chemical alarm signals from grazing zooplankton. However, these signals are potentially vulnerable to changes in pH and it is not yet known how predator recognition may be affected by ocean acidification. We exposed four species of diatoms and one toxic dinoflagellate to future pCO2 levels, projected by the turn of the century, in factorial combinations with predatory cues from copepods (copepodamides). We measured the change in growth, chain length, silica content, and toxin content. Effects of increased pCO2 were highly species specific. The induction of defensive traits was accompanied by a significant reduction in growth rate in three out of five species. The reduction averaged 39% and we interpret this as an allocation cost associated with defensive traits. Copepodamides induced significant chain length reduction in three of the four diatom species. Under elevated pCO2 Skeletonema marinoi reduced silica content by 30% and in Alexandrium minutum the toxin content was reduced by 30%. Using copepodamides to induce defensive traits in the absence of direct grazing provides a straightforward methodology to assess costs of defense in microplankton. We conclude that copepodamide signalling system is likely robust to ocean acidification. Moreover, the variable responses of different taxa to ocean acidification suggest that there will be winners and losers in a high pCO2 world, and that ocean acidification may have structuring effects on phytoplankton communities.
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 2022-06-29.
DOI: 10.1594/pangaea.931402
title: Seawater carbonate chemistry and environmental data, and nutrients of KOSMOS Bergen 2015 mesocosm study

description: The oceans' uptake of anthropogenic carbon dioxide (CO2) decreases seawater pH and alters the inorganic carbon speciation – summarized in the term ocean acidification (OA). Already today, coastal regions experience episodic pH events during which surface layer pH drops below values projected for the surface ocean at the end of the century. Future OA is expected to further enhance the intensity of these coastal extreme pH events. To evaluate the influence of such episodic OA events in coastal regions, we deployed eight pelagic mesocosms for 53 days in Raunefjord, Norway, and enclosed 56–61 m**3 of local seawater containing a natural plankton community under nutrient limited post-bloom conditions. Four mesocosms were enriched with CO2 to simulate extreme pCO2 levels of 1978-2069 μatm while the other four served as untreated controls. Here, we present results from multivariate analyses on OA-induced changes in the phyto-, micro-, and mesozooplankton community structure. Pronounced differences in the plankton community emerged early in the experiment, and were amplified by enhanced top-down control throughout the study period. The plankton groups responding most profoundly to high CO2 conditions were cyanobacteria (negative), chlorophyceae (negative), auto- and heterotrophic microzooplankton (negative), and a variety of mesozooplanktonic taxa, including copepoda (mixed), appendicularia (positive), hydrozoa (positive), fish larvae (positive), and gastropoda (negative). The restructuring of the community coincided with significant changes in the concentration and elemental stoichiometry of particulate organic matter. Results imply that extreme CO2 events can lead to a substantial reorganization of the planktonic food web, affecting multiple trophic levels from phytoplankton to primary and secondary consumers.
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 2021-05-11.
DOI: 10.1594/pangaea.945928
title: Seawater carbonate chemistry and survival and development of European eel embryos

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 2022-06-29.
DOI: 10.1594/pangaea.957364
title: Seawater carbonate chemistry and reproduction and offspring performance of Nematostella vectensis

description: Ocean acidification (OA) resulting from anthropogenic CO2 emissions is impairing the reproduction of marine organisms. While parental exposure to OA can protect offspring via carryover effects, this phenomenon is poorly understood in many marine invertebrate taxa. Here, we examined how parental exposure to acidified (pH 7.40) versus ambient (pH 7.72) seawater influenced reproduction and offspring performance across six gametogenic cycles (13 weeks) in the estuarine sea anemone Nematostella vectensis. Females exhibited reproductive plasticity under acidic conditions, releasing significantly fewer but larger eggs compared to ambient females after four weeks of exposure, and larger eggs in two of the four following spawning cycles despite recovering fecundity, indicating long-term acclimatization and greater investment in eggs. Males showed no changes in fecundity under acidic conditions, but produced a greater percentage of sperm with high mitochondrial membrane potential (MMP; a proxy for elevated motility), which corresponded with higher fertilization rates relative to ambient males. Finally, parental exposure to acidic conditions did not significantly influence offspring development rates, respiration rates, or heat tolerance. Overall, this study demonstrates that parental exposure to acidic conditions impacts gamete production and physiology but not offspring performance in N. vectensis, suggesting that increased investment in individual gametes may promote fitness.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-04-03.
DOI: 10.1594/pangaea.956752
title: Seawater carbonate chemistry and hemocyte physiology in the tanner crab (Chionoecetes bairdi)

description: We used flow cytometry to determine if there would be a difference in hematology, selected immune functions, and hemocyte pH (pHi), under two different, future ocean acidification scenarios (pH = 7.50, 7.80) compared to current conditions (pH = 8.09) for Chionoecetes bairdi, Tanner crab. Hemocytes were analyzed after adult Tanner crabs were held for two years under continuous exposure to acidified ocean water. Total counts of hemocytes did not vary among control and experimental treatments; however, there were significantly greater number of dead, circulating hemocytes in crabs held at the lowest pH treatment. Phagocytosis of fluorescent microbeads by hemocytes was greatest at the lowest pH treatment. These results suggest that hemocytes were dying, likely by apoptosis, at a rate faster than upregulated phagocytosis was able to remove moribund cells from circulation at the lowest pH. Crab hemolymph pH (pHe) averaged 8.09 and did not vary among pH treatments. There was no significant difference in internal pH (pHi) within hyalinocytes among pH treatments and the mean pHi (7.26) was lower than the mean pHe. In contrast, there were significant differences among treatments in pHi of the semi-granular+granular cells. Control crabs had the highest mean semi-granular+granular pHi compared to the lowest pH treatment. As physiological hemocyte functions changed from ambient conditions, interactions with the number of eggs in the second clutch, percentage of viable eggs, and calcium concentration in the adult crab shell was observed. This suggested that the energetic costs of responding to ocean acidification and maintaining defense mechanisms in Tanner crab may divert energy from other physiological processes, such as reproduction.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-03-20.
DOI: 10.1594/pangaea.957629
title: Seawater carbonate chemistry and larval viability, size, development, and shell mineralization of the eastern oyster (Crassostrea virginica)

description: Calcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO3). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-04-18.
DOI: 10.1594/pangaea.957625
title: Seawater carbonate chemistry and metabolic rate and nitrogenous waste handling in the early life stages of yellowfin tuna (Thunnus albacares)

description: Ocean acidification is predicted to have a wide range of impacts on fish, but there has been little focus on broad-ranging pelagic fish species. Early life stages of fish are thought to be particularly susceptible to CO2 exposure, since acid-base regulatory faculties may not be fully developed. We obtained yellowfin tuna (Thunnus albacares) from a captive spawning broodstock population and exposed them to control or 1900 μatm CO2 through the first three days of development as embryos transitioned into yolk sac larvae. Metabolic rate, yolk sac depletion, and oil globule depletion were measured to assess overall energy usage. To determine if CO2 altered protein catabolism, tissue nitrogen content and nitrogenous waste excretion were quantified. CO2 exposure did not significantly impact embryonic metabolic rate, yolk sac depletion, or oil globule depletion, however, there was a significant decrease in metabolic rate at the latest measured yolk sac larval stage (36 h post fertilization). CO2-exposure led to a significant increase in nitrogenous waste excretion in larvae, but there were no differences in nitrogen tissue accumulation. Nitrogenous waste accumulated in embryos as they developed but decreased after hatch, coinciding with a large increase in nitrogenous waste excretion and increased metabolic rate in newly hatched larvae. Our results provide insight into how yellowfin tuna are impacted by increases in CO2 in early development, but more research with higher levels of replication is needed to better understand long-term impacts and acid-base regulatory mechanisms in this important pelagic fish.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-04-18.