cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.924121
title: Raw data for chemical and physical parameters across all days and station locations

description: Coral reefs feed millions of people worldwide, provide coastal protection and generate billions of dollars annually in tourism revenue. The underlying architecture of a reef is a biogenic carbonate structure that accretes over many years of active biomineralization by calcifying organisms, including corals and algae. Ocean acidification poses a chronic threat to coral reefs by reducing the saturation state of the aragonite mineral of which coral skeletons are primarily composed, and lowering the concentration of carbonate ions required to maintain the carbonate reef. Reduced calcification, coupled with increased bioerosion and dissolution, may drive reefs into a state of net loss this century. Our ability to predict changes in ecosystem function and associated services ultimately hinges on our understanding of community- and ecosystem-scale responses. Past research has primarily focused on the responses of individual species rather than evaluating more complex, community-level responses. Here we use an in situ carbon dioxide enrichment experiment to quantify the net calcification response of a coral reef flat to acidification. We present an estimate of community-scale calcification sensitivity to ocean acidification that is, to our knowledge, the first to be based on a controlled experiment in the natural environment. This estimate provides evidence that near-future reductions in the aragonite saturation state will compromise the ecosystem function of coral reefs.
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 2020-10-27.
DOI: 10.15468/dl.j6egj6
title: Occurrence Download

description: A dataset containing 3016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is IDN.29.1_1",
 "IucnRedListCategory is NT",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 3016 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015868-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.924122
title: Seawater carbonate chemistry and male and female behavioural lateralization in a temperate goby

description: Rising atmospheric CO2 and ocean acidification are fundamentally altering conditions for life of all marine organisms, including phytoplankton. Differences in CO2 related physiology between major phytoplankton taxa lead to differences in their ability to take up and utilize CO2. These differences may cause predictable shifts in the composition of marine phytoplankton communities in response to rising atmospheric CO2. We report an experiment in which seven species of marine phytoplankton, belonging to four major taxonomic groups (cyanobacteria, chlorophytes, diatoms, and coccolithophores), were grown at both ambient (500 μatm) and future (1,000 μatm) CO2 levels. These phytoplankton were grown as individual species, as cultures of pairs of species and as a community assemblage of all seven species in two culture regimes (high‐nitrogen batch cultures and lower‐nitrogen semicontinuous cultures, although not under nitrogen limitation). All phytoplankton species tested in this study increased their growth rates under elevated CO2 independent of the culture regime. We also find that, despite species‐specific variation in growth response to high CO2, the identity of major taxonomic groups provides a good prediction of changes in population growth and competitive ability under high CO2. The CO2‐induced growth response is a good predictor of CO2‐induced changes in competition (R2 &gt; .93) and community composition (R2 &gt; .73). This study suggests that it may be possible to infer how marine phytoplankton communities respond to rising CO2 levels from the knowledge of the physiology of major taxonomic groups, but that these predictions may require further characterization of these traits across a diversity of growth conditions. These findings must be validated in the context of limitation by other nutrients. Also, in natural communities of phytoplankton, numerous other factors that may all respond to changes in CO2, including nitrogen fixation, grazing, and variation in the limiting resource will likely complicate this prediction.
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 2020-10-27.
DOI: 10.1594/pangaea.968501
title: Seawater carbonate chemistry and stable carbon isotope composition of DIC over a 27 + h period from Tetiaroa Atoll, French Polynesia

description: In this pilot study, we use co-located semi-hourly measurements of total dissolved inorganic carbon (DIC), total alkalinity, and the stable carbon isotope composition of DIC (δ13CDIC) over a 27 + h period from Tetiaroa Atoll, French Polynesia, to investigate the potential for reef carbonate chemistry to record information related to benthic photosynthetic community composition and response to natural gradients in ambient acidity and dissolved carbon dioxide.This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were downloaded from Mendeley Data (see Source) by the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) 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 2024-05-17.
DOI: 10.1594/pangaea.881077
title: Seawater carbonate chemistry and variation in community development

description: Ocean acidification represents a pervasive environmental change that is predicted to affect a wide range of species, yet our understanding of the emergent ecosystem impacts is very limited. Many studies report detrimental effects of acidification on single species in lab studies, especially those with calcareous shells or skeletons. Observational studies using naturally acidified ecosystems have shown profound shifts away from such calcareous species, and there has been an assumption that direct impacts of acidification on sensitive species drive most ecosystem responses. We tested an alternative hypothesis that species interactions attenuate or amplify the direct effects of acidification on individual species. Here, we show that altered competitive dynamics between calcareous species and fleshy seaweeds drive significant ecosystem shifts in acidified conditions. Although calcareous species recruited and grew at similar rates in ambient and low pH conditions during early successional stages, they were rapidly overgrown by fleshy seaweeds later in succession in low pH conditions. The altered competitive dynamics between calcareous species and fleshy seaweeds is probably the combined result of decreased growth rates of calcareous species, increased growth rates of fleshy seaweeds, and/or altered grazing rates. Phase shifts towards ecosystems dominated by fleshy seaweed are common in many marine ecosystems, and our results suggest that changes in the competitive balance between these groups represent a key leverage point through which the physiological responses of individual species to acidification could indirectly lead to profound ecosystem changes in an acidified ocean.
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 2017-09-28.
description: Supplement to: Kroeker, Kristy J; Micheli, Fiorenza; Gambi, Maria Cristina (2012): Ocean acidification causes ecosystem shifts via altered competitive interactions. Nature Climate Change, 3(2), 156-159
DOI: 10.1594/pangaea.929942
title: Seawater carbonate chemistry and behaviour, physiological metrics in blacktip reef shark (Carcharhinus melanopterus)

description: Ocean warming and acidification act concurrently on marine ectotherms with the potential for detrimental, synergistic effects; yet, effects of these stressors remain understudied in large predatory fishes, including sharks. We tested for behavioural and physiological responses of blacktip reef shark (Carcharhinus melanopterus) neonates to climate change relevant changes in temperature (28 and 31 °C) and carbon dioxide partial pressures (pCO2; 650 and 1050 µatm) using a fully factorial design. Behavioural assays (lateralisation, activity level) were conducted upon 7–13 days of acclimation, and physiological assays (hypoxia tolerance, oxygen uptake rates, acid–base and haematological status) were conducted upon 14–17 days of acclimation. Haematocrit was higher in sharks acclimated to 31 °C than to 28 °C. Significant treatment effects were also detected for blood lactate and minimum oxygen uptake rate; although, these observations were not supported by adequate statistical power. Inter-individual variability was considerable for all measured traits, except for haematocrit. Moving forward, studies on similarly 'hard-to-study' species may account for large inter-individual variability by increasing replication, testing larger, yet ecologically relevant, differences in temperature and pCO2, and reducing measurement error. Robust experimental studies on elasmobranchs are critical to meaningfully assess the threat of global change stressors in these data-deficient 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 2021-03-30.
DOI: 10.1594/pangaea.823320
title: Seawater carbonate chemistry and physiological response of the Mediterranean crustose coralline alga Lithophyllum cabiochae to elevated pCO2 and temperature

description: The response of respiration, photosynthesis, and calcification to elevated pCO2 and temperature was investigated in isolation and in combination in the Mediterranean crustose coralline alga Lithophyllum cabiochae. Algae were maintained in aquaria during 1 year at near-ambient conditions of irradiance, at ambient or elevated temperature (+3 °C), and at ambient (ca. 400 µatm) or elevated pCO2 (ca. 700 µatm). Respiration, photosynthesis, and net calcification showed a strong seasonal pattern following the seasonal variations of temperature and irradiance, with higher rates in summer than in winter. Respiration was unaffected by pCO2 but showed a general trend of increase at elevated temperature at all seasons, except in summer under elevated pCO2. Conversely, photosynthesis was strongly affected by pCO2 with a decline under elevated pCO2 in summer, autumn, and winter. In particular, photosynthetic efficiency was reduced under elevated pCO2. Net calcification showed different responses depending on the season. In summer, net calcification increased with rising temperature under ambient pCO2 but decreased with rising temperature under elevated pCO2. Surprisingly, the highest rates in summer were found under elevated pCO2 and ambient temperature. In autumn, winter, and spring, net calcification exhibited a positive or no response at elevated temperature but was unaffected by pCO2. The rate of calcification of L. cabiochae was thus maintained or even enhanced under increased pCO2. However, there is likely a trade-off with other physiological processes. For example, photosynthesis declines in response to increased pCO2 under ambient irradiance. The present study reports only on the physiological response of healthy specimens to ocean warming and acidification, however, these environmental changes may affect the vulnerability of coralline algae to other stresses such as pathogens and necroses that can cause major dissolution, which would have critical consequence for the sustainability of coralligenous habitats and the budgets of carbon and calcium carbonate in coastal Mediterranean ecosystems.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2013-11-27.
description: Supplement to: Martin, Sophie; Cohu, Stéphanie; Vignot, Céline; Zimmerman, Guillaume; Gattuso, Jean-Pierre (2013): One-year experiment on the physiological response of the Mediterranean crustose coralline alga, Lithophyllum cabiochae, to elevated pCO2 and temperature. Ecology and Evolution, 3(3), 676-693
DOI: 10.1594/pangaea.929951
title: Seawater carbonate chemistry and growth response of calcifying marine epibionts

description: In coastal marine environments, physical and biological forces can cause dynamic pH fluctuations from microscale (diffusive boundary layer [DBL]) up to ecosystem‐scale (benthic boundary layer [BBL]). In the face of ocean acidification (OA), such natural pH variations may modulate an organism's response to OA by providing temporal refugia. We investigated the effect of pH fluctuations, generated by the brown alga Fucus serratus' biological activity, on the calcifying epibionts Balanus improvisus and Electra pilosa under OA. For this, both epibionts were grown on inactive and biologically active surfaces and exposed to (1) constant pH scenarios under ambient (pH 8.1) or OA conditions (pH 7.7), or (2) oscillating pH scenarios mimicking BBL conditions at ambient (pH 7.7–8.6) or OA scenarios (pH 7.4–8.2). Furthermore, all treatment combinations were tested at 10°C and 15°C. Against our expectations, OA treatments did not affect epibiont growth under constant or fluctuating (BBL) pH conditions, indicating rather high robustness against predicted OA scenarios. Furthermore, epibiont growth was hampered and not fostered on active surfaces (fluctuating DBL conditions), indicating that fluctuating pH conditions of the DBL with elevated daytime pH do not necessarily provide temporal refugia from OA. In contrast, results indicate that factors other than pH may play larger roles for epibiont growth on macrophytes (e.g., surface characteristics, macrophyte antifouling defense, or dynamics of oxygen and nutrient concentrations). Warming enhanced epibiont growth rates significantly, independently of OA, indicating no synergistic effects of pH treatments and temperature within their natural temperature range.
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 2021-03-30.
DOI: 10.1594/pangaea.854960
title: (Table S2) Water temperature, salinity, carbonate system parameters and dissolved inorganic nutrient concentrations at 5, 20 and 40 m at all stations (V1-3 and C1-3), Columbretes Islands
DOI: 10.1594/pangaea.917470
title: Seawater carbonate chemistry and phytoplankton biomass and species composition of a unique temperate rocky coastal hydrothermal vent system

description: In situ effects of ocean acidification are increasingly studied at submarine CO2 vents. Here we present a preliminary investigation into the water chemistry and biology of cool temperate CO2 vents near Whakaari–White Island, New Zealand. Water samples were collected inside three vent shafts, within vents at a distance of 2 m from the shaft and at control sites. Vent samples contained both seawater pH on the total scale (pHT) and carbonate saturation states that were severely reduced, creating conditions as predicted for beyond the year 2100. Vent samples showed lower salinities, higher temperatures and greater nutrient concentrations. Sulfide levels were elevated and mercury levels were at concentrations considered toxic at all vent and control sites, but stable organic and inorganic ligands were present, as deduced from Cu speciation data, potentially mediating harmful effects on local organisms. The biological investigations focused on phytoplankton, zooplankton and macroalgae. Interestingly, we found lower abundances but higher diversity of phytoplankton and zooplankton at sites in the direct vicinity of Whakaari. Follow-up studies will need a combination of methods and approaches to attribute observations to specific drivers. The Whakaari vents represent a unique ecosystem with considerable biogeochemical complexity, which, like many other vent systems globally, require care in their use as a model of 'future oceans'.
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 2020-05-6.
DOI: 10.1594/pangaea.914328
title: Seawater carbonate chemistry and calcification rate, calcifying fluid pH, calcifying fluid DIC, photosynthetic rates, metabolic alteration of pH in the DBL of corals and coralline algae

description: Natural variability in pH in the diffusive boundary layer (DBL), the discrete layer of seawater between bulk seawater and the outer surface of organisms, could be an important factor determining the response of corals and coralline algae to ocean acidification (OA). Here, two corals with different morphologies and one coralline alga were maintained under two different regimes of flow velocities, pH, and light intensities in a 12 flumes experimental system for a period of 27 weeks. We used a combination of geochemical proxies, physiological and micro-probe measurements to assess how these treatments affected the conditions in the DBL and the response of organisms to OA. Overall, low flow velocity did not ameliorate the negative effect of low pH and therefore did not provide a refugia from OA. Flow velocity had species-specific effects with positive effects on calcification for two species. pH in the calcifying fluid (pHcf) was reduced by low flow in both corals at low light only. pHcf was significantly impacted by pH in the DBL for the two species capable of significantly modifying pH in the DBL. The dissolved inorganic carbon in the calcifying fluid (DICcf) was highest under low pH for the corals and low flow for the coralline, while the saturation state in the calcifying fluid and its proxy (FWHM) were generally not affected by the treatments. This study therefore demonstrates that the effects of OA will manifest most severely in a combination of lower light and lower flow habitats for sub-tropical coralline algae. These effects will also be greatest in lower flow habitats for some corals. Together with existing literature, these findings reinforce that the effects of OA are highly context dependent, and will differ greatly between habitats, and depending on species composition.
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 2020-03-18.
DOI: 10.1594/pangaea.547937
title: Hydrochemistry measured on water bottle samples during BELGICA cruise BG06/09

description: Units for oxygen and total alkalinity were converted based on density.
DOI: 10.1594/pangaea.778449
title: Seawater carbonate chemistry and eggs, larvae and hatching success of Gadus morhua during experiments (Experiment 2), 2012

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).