cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.944056
title: Seawater carbonate chemistry and kelp densities and coral coverages at three study locations and photosynthesis and calcification of corals measured in the laboratory

description: Ocean warming is altering the biogeographical distribution of marine organisms. In the tropics, rising sea surface temperatures are restructuring coral reef communities with sensitive species being lost. At the biogeographical divide between temperate and tropical communities, warming is causing macroalgal forest loss and the spread of tropical corals, fishes and other species, termed “tropicalization”. A lack of field research into the combined effects of warming and ocean acidification means there is a gap in our ability to understand and plan for changes in coastal ecosystems. Here, we focus on the tropicalization trajectory of temperate marine ecosystems becoming coral-dominated systems. We conducted field surveys and in situ transplants at natural analogues for present and future conditions under (i) ocean warming and (ii) both ocean warming and acidification at a transition zone between kelp and coral-dominated ecosystems. We show that increased herbivory by warm-water fishes exacerbates kelp forest loss and that ocean acidification negates any benefits of warming for range extending tropical corals growth and physiology at temperate latitudes. Our data show that, as the combined effects of ocean acidification and warming ratchet up, marine coastal ecosystems lose kelp forests but do not gain scleractinian corals. Ocean acidification plus warming leads to overall habitat loss and a shift to simple turf-dominated ecosystems, rather than the complex coral-dominated tropicalized systems often seen with warming alone. Simplification of marine habitats by increased CO2 levels cascades through the ecosystem and could have severe consequences for the provision of goods and services.
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 2022-05-11.
DOI: 10.1594/pangaea.939892
title: Seawater carbonate chemistry and respiration rate, ammonia excretion, O:N ratio and behaviour of sea urchins Paracentrotus lividus

description: CO2-driven ocean acidification affects many aspects of sea urchin biology. However, even in the same species, OA effects are often not univocal due to non-uniform exposure setups or different ecological history of the experimental specimens. In the present work, two groups of adult sea urchins Paracentrotus lividus from different environments (the Lagoon of Venice and a coastal area in the Northern Adriatic Sea) were exposed to OA in a long-term exposure. Animals were maintained for six months in both natural seawater (pHT 8.04) and end-of-the-century predicted condition (-0.4 units pH). Monthly, physiological (respiration rate, ammonia excretion, O:N ratio) and behavioural (righting, sheltering) endpoints were investigated. Both pH and time of exposure significantly influenced sea urchin responses, but differences between sites were highlighted, particularly in the first months. Under reduced pH, ammonia excretion increased and O:N decreased in coastal specimens. Righting and sheltering were impaired in coastal animals, whereas only righting decreased in lagoon ones. These findings suggested a higher adaptation ability in sea urchins from a more variable environment. Interestingly, as the exposure continued, animals from both sites were able to acclimate. Results revealed plasticity in the physiological and behavioural responses of sea urchins under future predicted OA conditions.
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 2022-1-6. In the experiment, two exposures have been carried out: one with sea urchin collected within the Lagoon of Venice, the other with animals from the Gulf of Trieste. Both exposures have been carried out in a facility placed within the Lagoon of Venice.
DOI: 10.1594/pangaea.836050
title: (Table 4) Vertical profile of seawater chemistry at station STJ17 in Hurricane Hole, U.S. Virgin Islands
DOI: 10.1594/pangaea.930756
title: Seawater carbonate chemistry and gene expression levels of the limpet Nacella concinna

description: Ocean acidification (OA) could become a serious threat for the Antarctic marine ecosystem over coming years, as the solubility of atmospheric CO2 and CaCO3 minerals increases at lower temperatures. We evaluated the effect of OA on the stress response of the limpet Nacella concinna by measuring gene expression levels. The experiment was performed with the two ecotypes (Littoral and Sublittoral) of the species during 54 days (IPCC, 2019 scenario RCP8.5; control, 375 ppm; low-pH treatment, 923 ppm). Exposure to low-pH treatment during 15 days triggered the down-regulation of two heat-shock protein genes (HSP70A, HSP70B) only in sublittoral individuals. Little variation in the relative expression values of all genes in both ecotypes was observed probably, due to a historical exposure to the substantial daily natural pH fluctuations recorded in the study area during the experiment. This study provides relevant baseline data for future OA experiments on coastal species in Antarctica.
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 2021-04-19.
DOI: 10.1594/pangaea.774584
title: Seawater carbonate chemistry and filtering rate of Strongylocentrotus purpuratus during experimetns, 2011

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.885870
title: DBL thickness in mm in fast and slow flow conditions, in pH 8.1 and pH 7.7, in the absence or presence of bryozoans

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 2018-02-02.
DOI: 10.15468/dl.azm7g5
title: Occurrence Download

description: A dataset containing 2225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Collinsia verna Nutt.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2225 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015864-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.887375
title: Boron isotopes measured on planktic foraminifera N. pachyderma from deglacial sediments of sediment core MD01-2416
DOI: 10.1594/pangaea.939436
title: Seawater carbonate chemistry and otop2l expression of sea urchins (Stongylocentrotus purpuratus)

description: Otopetrins comprise a family of proton-selective channels that are critically important for the mineralization of otoliths and statoconia in vertebrates but whose underlying cellular mechanisms remain largely unknown. Here, we demonstrate that otopetrins are critically involved in the calcification process by providing an exit route for protons liberated by the formation of CaCO3. Using the sea urchin larva, we examined the otopetrin ortholog otop2l, which is exclusively expressed in the calcifying primary mesenchymal cells (PMCs) that generate the calcitic larval skeleton. otop2l expression is stimulated during skeletogenesis, and knockdown of otop2l impairs spicule formation. Intracellular pH measurements demonstrated Zn2+-sensitive H+ fluxes in PMCs that regulate intracellular pH in a Na+/HCO3−-independent manner, while Otop2l knockdown reduced membrane proton permeability. Furthermore, Otop2l displays unique features, including strong activation by high extracellular pH (&gt;8.0) and check-valve–like outwardly rectifying H+ flux properties, making it into a cellular proton extrusion machine adapted to oceanic living conditions. Our results provide evidence that otopetrin family proton channels are a central component of the cellular pH regulatory machinery in biomineralizing cells. Their ubiquitous occurrence in calcifying systems across the animal kingdom suggest a conserved physiological function by mediating pH at the site of mineralization. This important role of otopetrin family proton channels has strong implications for our view on the cellular mechanisms of biomineralization and their response to changes in oceanic pH.
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 2021-12-16.
DOI: 10.1594/pangaea.949506
title: Molecular basis of ocean acidification sensitivity and adaptation in Mytilus galloprovincialis

description: Predicting the potential for species adaption to climate change is challenged by the need to identify the physiological mechanisms that underpin species vulnerability. Here we investigated the sensitivity to ocean acidification in marine mussels during early development, and specifically the trochophore stage. Using RNA and DNA sequencing and in situ RNA hybridization, we identified developmental processes associated with abnormal development and rapid adaptation to low pH. Trochophores exposed to low pH seawater exhibited 43 differentially expressed genes. Gene annotation and in situ hybridization of differentially expressed genes point to pH sensitivity of (1) shell field development and (2) cellular stress response. Five genes within these two processes exhibited shifts in allele frequencies indicative of a potential for rapid adaptation. This case study contributes direct evidence that protecting species' existing genetic diversity is a critical management action to facilitate species resilience to climate change.
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 2022-10-10.
DOI: 10.1594/pangaea.773850
title: Seawater carbonate chemistry, length and survival of Inland silverside, Menidia beryllina, during experiments, 2012

description: Absorption of anthropogenic carbon dioxide by the world's oceans is causing mankind's 'other CO2 problem', ocean acidification. Although this process will challenge marine organisms that synthesize calcareous exoskeletons or shells, it is unclear how it will affect internally calcifying organisms, such as marine fish. Adult fish tolerate short-term exposures to CO2 levels that exceed those predicted for the next 300 years (~2,000 ppm), but potential effects of increased CO2 on growth and survival during the early life stages of fish remain poorly understood. Here we show that the exposure of early life stages of a common estuarine fish (Menidia beryllina) to CO2 concentrations expected in the world's oceans later this century caused severely reduced survival and growth rates. When compared with present-day CO2 levels (~400 ppm), exposure of M. beryllina embryos to ~1,000 ppm until one week post-hatch reduced average survival and length by 74% and 18%, respectively. The egg stage was significantly more vulnerable to high CO2-induced mortality than the post-hatch larval stage. These findings challenge the belief that ocean acidification will not affect fish populations, because even small changes in early life survival can generate large fluctuations in adult-fish abundance.
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: Baumann, Hannes; Talmage, Stephanie C; Gobler, Christopher J (2012): Reduced early life growth and survival in a fish in direct response to increased carbon dioxide. Nature Climate Change, 2, 38-41
DOI: 10.1594/pangaea.939848
title: Seawater carbonate chemistry and survival of economically important blue crab (Callinectes sapidus) larvae

description: Many shallow coastal systems experience diel fluctuations in dissolved oxygen (DO) and pH that can intensify throughout the summer season and expose estuarine organisms to repeated episodes of coastal hypoxia and acidification. In temperate regions, larval release of the economically important blue crab Callinectes sapidus occurs in the summer, and while the earliest stage (zoea I) larvae are susceptible to persistent low DO and low pH conditions, their sensitivity to diel fluctuations is unknown. Here, a series of short-term (&lt;=96 h) experiments were conducted to investigate the survival of C. sapidus zoea I larvae exposed to a range of diel cycling hypoxic and acidified conditions and durations. Two experiments comparing a diel cycling DO/pH treatment (fluctuating from 30% air saturation to 103% averaging 66%/and from pH 7.26 to 7.80 averaging 7.53) to a static low DO/pH treatment (43%/7.35), a static moderate DO/pH treatment (68%/7.59), and a static control treatment (106%/7.94) indicated that survival in the diel cycling treatment was significantly lower than the moderate treatment (p &lt; 0.05) by 75 and 48% over 96 and 48 h, respectively, despite comparable mean experimental DO/pH values. Three other experiments aimed at identifying the effective minimum duration of low DO/low pH to significantly depress larval survival under diel cycling conditions revealed that 8 h of low DO/low pH (28%/7.43) over a 24-h diel cycle consistently decreased survival (p &lt; 0.05) relative to control conditions by at least 55% regardless of experimental duration (72-, 48-, and 24-h experiments). An increase in DO beyond saturation to supersaturation (160%) and pH beyond normocapnic to highly basified (8.34) conditions during the day phase of the diel cycle did not improve survival of larvae exposed to nocturnal hypoxia and acidification. Collectively, these experiments demonstrate that diel cycling does not provide newly hatched C. sapidus larvae a temporal refuge capable of ameliorating low DO/pH stress, but rather is more lethal than chronic exposure to comparable average DO/pH conditions. Given that larvae exposed to a single nocturnal episode of moderate hypoxia and acidification experience significantly reduced survival, such occurrences may depress larval recruitment.
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 2022-1-5.
DOI: 10.1594/pangaea.832536
title: Gene expression changes in the coccolithophore Emiliania huxleyi after 500 generations of selection to ocean acidification

description: Coccolithophores are unicellular marine algae that produce biogenic calcite scales and substantially contribute to marine primary production and carbon export to the deep ocean. Ongoing ocean acidification particularly impairs calcifying organisms, mostly resulting in decreased growth and calcification. Recent studies revealed that the immediate physiological response in the coccolithophore Emiliania huxleyi to ocean acidification may be partially compensated by evolutionary adaptation, yet the underlying molecular mechanisms are currently unknown. Here, we report on the expression levels of 10 candidate genes putatively relevant to pH regulation, carbon transport, calcification and photosynthesis in E. huxleyi populations short-term exposed to ocean acidification conditions after acclimation (physiological response) and after 500 generations of high CO2 adaptation (adaptive response). The physiological response revealed downregulation of candidate genes, well reflecting the concomitant decrease of growth and calcification. In the adaptive response, putative pH regulation and carbon transport genes were up-regulated, matching partial restoration of growth and calcification in high CO2-adapted populations. Adaptation to ocean acidification in E. huxleyi likely involved improved cellular pH regulation, presumably indirectly affecting calcification. Adaptive evolution may thus have the potential to partially restore cellular pH regulatory capacity and thereby mitigate adverse effects of ocean acidification.
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 2014-05-15.
description: Supplement to: Lohbeck, Kai T; Riebesell, Ulf; Reusch, Thorsten B H (2014): Gene expression changes in the coccolithophore Emiliania huxleyi after 500 generations of selection to ocean acidification. Proceedings of the Royal Society B-Biological Sciences, 281(1786), 20140003-20140003
DOI: 10.1594/pangaea.721194
title: Seawater carbonate chemistry, calcification and photosynthesis during experiments with corals, 2005

description: An investigation was conducted to determine the effects of elevated pCO2 on the net production and calcification of an assemblage of corals maintained under near-natural conditions of temperature, light, nutrient, and flow. Experiments were performed in summer and winter to explore possible interactions between seasonal change in temperature and irradiance and the effect of elevated pCO2. Particular attention was paid to interactions between net production and calcification because these two processes are thought to compete for the same internal supply of dissolved inorganic carbon (DIC). A nutrient enrichment experiment was performed because it has been shown to induce a competitive interaction between photosynthesis and calcification that may serve as an analog to the effect of elevated pCO2. Net carbon production, NPC, increased with increased pCO2 at the rate of 3 ± 2% (?mol CO2aq kg?1)?1. Seasonal change of the slope NPC-[CO2aq] relationship was not significant. Calcification (G) was strongly related to the aragonite saturation state ? a . Seasonal change of the G-? a relationship was not significant. The first-order saturation state model gave a good fit to the pooled summer and winter data: G = (8 ± 1 mmol CaCO3 m?2 h?1)(? a ? 1), r 2 = 0.87, P = 0.0001. Both nutrient and CO2 enrichment resulted in an increase in NPC and a decrease in G, giving support to the hypothesis that the cellular mechanism underlying the decrease in calcification in response to increased pCO2 could be competition between photosynthesis and calcification for a limited supply of DIC.
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: Langdon, Chris; Atkinson, M J (2005): Effect of elevated pCO2 on photosynthesis and calcification of corals and interactions with seasonal change in temperature/irradiance and nutrient enrichment. Journal of Geophysical Research: Oceans, 110, C09S07
DOI: 10.1594/pangaea.939835
title: Seawater carbonate chemistry and survival and growth of young‑of‑the‑year golden king crab (Lithodes aequispinus)

description: Ocean acidification, a reduction in the pH of the oceans caused by increasing CO2, can have negative physiological effects on marine species. In this study, we examined how CO2-driven acidification affected the growth and survival of juvenile golden king crab (Lithodes aequispinus), an important fishery species in Alaska. Juveniles were reared from larvae in surface ambient pH seawater at the Kodiak Laboratory. Newly molted early benthic instar crabs were randomly assigned to one of three pH treatments: (1) surface ambient pH  8.2, (2) likely in situ ambient pH 7.8, and (3) pH 7.5. Thirty crabs were held in individual cells in each treatment for 127 days and checked daily for molting or death. Molts and dead crabs were photographed under a microscope and measured using image analysis to assess growth and morphology. Mortality was primarily associated with molting in all treatments, differed among all treatments, and was highest at pH 7.5 and lowest at ambient pH. Crabs at pH 7.5 were smaller than crabs at ambient pH at the end of the experiment, both in terms of carapace length and wet mass; had a smaller growth increment after molting; had a longer intermolt period. Carapace morphology was not affected by pH treatment. Decreased growth and increased mortality in laboratory experiments suggest that lower pH could affect golden king crab stocks and fisheries. Future work should examine if larval rearing conditions affect the juvenile response to low pH.
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 2021-1-4.