cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.952135
title: Seawater carbonate chemistry and carapace material properties, cuticle atomic weight composition, elemental concentrations and thickness of juvenile California spiny lobsters (Panulirus interruptus)

description: Spiny lobsters rely on multiple biomineralized exoskeletal predator defenses that may be sensitive to ocean acidification (OA). Compromised mechanical integrity of these defensive structures may tilt predator-prey outcomes, leading to increased mortality in the lobsters' environment. Here, we tested the effects of OA-like conditions on the mechanical integrity of selected exoskeletal defenses of juvenile California spiny lobster, Panulirus interruptus. Young spiny lobsters reside in kelp forests with dynamic carbonate chemistry due to local metabolism and photosynthesis as well as seasonal upwelling, yielding daily and seasonal fluctuations in pH. Lobsters were exposed to a series of stable and diurnally fluctuating reduced pH conditions for three months (ambient pH/stable, 7.97; reduced pH/stable 7.67; reduced pH with low fluctuations, 7.67 ± 0.05; reduced pH with high fluctuations, 7.67 ± 0.10), after which we examined the intermolt composition (Ca and Mg content), ultrastructure (cuticle and layer thickness), and mechanical properties (hardness and stiffness) of selected exoskeletal predator defenses. Cuticle ultrastructure was consistently robust to pH conditions, while mineralization and mechanical properties were variable. Notably, the carapace was less mineralized under both reduced pH treatments with fluctuations, but with no effect on material properties, and the rostral horn had lower hardness in reduced/high fluctuating conditions without a corresponding difference in mineralization. Antennal flexural stiffness was lower in reduced, stable pH conditions compared to the reduced pH treatment with high fluctuations and not correlated with changes in cuticle structure or mineralization. These results demonstrate a complex relationship between mineralization and mechanical properties of the exoskeleton under changing ocean chemistry, and that fluctuating reduced pH conditions can induce responses not observed under the stable reduced pH conditions often used in OA research. Furthermore, this study shows that some juvenile California spiny lobster exoskeletal defenses are responsive to changes in ocean carbonate chemistry, even during the intermolt period, in ways that can potentially increase susceptibility to predation among this critical life stage.
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 2022-12-12.
DOI: 10.1594/pangaea.839102
title: Vertical profiles of environmental parameters measured on discrete water samples collected with Niskin bottles at station TARA_094 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.951473
title: Seawater carbonate chemistry and biomass, calcification and respiration rates of cold-water coral Desmophyllum dianthus in Comau Fjord

description: The stratified Chilean Comau Fjord sustains a dense population of the cold-water coral (CWC) Desmophyllum dianthus in aragonite supersaturated shallow and aragonite undersaturated deep water. This provides a rare opportunity to evaluate CWC fitness trade-offs in response to physico-chemical drivers and their variability. Here, we combined year-long reciprocal transplantation experiments along natural oceanographic gradients with an in situ assessment of CWC fitness. Following transplantation, corals acclimated fast to the novel environment with no discernible difference between native and novel (i.e. cross-transplanted) corals, demonstrating high phenotypic plasticity. Surprisingly, corals exposed to lowest aragonite saturation (Omega arag &lt; 1) and temperature (T &lt; 12.0 °C), but stable environmental conditions, at the deep station grew fastest and expressed the fittest phenotype. We found an inverse relationship between CWC fitness and environmental variability and propose to consider the high frequency fluctuations of abiotic and biotic factors to better predict the future of CWCs in a changing ocean.
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 2022-12-02.
DOI: 10.1594/pangaea.958552
title: Seawater carbonate chemistry and the intrinsic and extrinsic phenotypic characteristics and the survival of important calcifiers, the edib oysters Crassostrea angulata and C. hongkongensis

description: Ocean acidification (OA) has important effects on the intrinsic phenotypic characteristics of many marine organisms. Concomitantly, OA can alter the extended phenotypes of these organisms by perturbing the structure and function of their associated microbiomes. It is unclear, however, the extent to which interactions between these levels of phenotypic change can modulate the capacity for resilience to OA. Here, we explored this theoretical framework assessing the influence of OA on intrinsic (immunological responses and energy reserve) and extrinsic (gut microbiome) phenotypic characteristics and the survival of important calcifiers, the edible oysters Crassostrea angulata and C. hongkongensis. After one-month exposure to experimental OA (pH 7.4) and control (pH 8.0) conditions, we found species-specific responses characterised by elevated stress (hemocyte apoptosis) and decreased survival in the coastal species (C. angulata) compared with the estuarine species (C. hongkongensis). Phagocytosis of hemocytes was not affected by OA but in vitro bacterial clearance capability decreased in both species. Gut microbial diversity decreased in C. angulata but not in C. hongkongensis. Overall, C. hongkongensis was capable of maintaining the homeostasis of the immune system and energy supply under OA. In contrast, C. angulata's immune function was suppressed, and the energy reserve was imbalanced, which might be attributed to the declined microbial diversity and the functional loss of essential bacteria in the guts. This study highlights a species-specific response to OA determined by genetic background and local adaptation, shedding light on the understanding of host-microbiota-environment interactions in future coastal acidification.
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 2023-05-08.
DOI: 10.1594/pangaea.958503
title: Physiological response of E. huxleyi ecotype A, strain SO5.14 to changing carbonate chemistry under nutrient-replete conditions

description: Future oceanic conditions induced by anthropogenic greenhouse gas emissions include warming, acidification and reduced nutrient supply due to increased stratification. Some parts of the Southern Ocean are expected to show rapid changes, especially for carbonate mineral saturation. Here we compare the physiological response of the model coccolithophore Emiliania huxleyi (strain EHSO 5.14, originating from 50S, 149E) with pH/CO2 gradients (mimicking ocean acidification ranging from 1 to 4 × current pCO2 levels) under nutrient-limited (nitrogen and phosphorus) and -replete conditions. Both nutrient limitations decreased per cell photosynthesis (particulate organic carbon (POC) production) and calcification (particulate inorganic carbon (PIC) production) rates for all pCO2 levels, with more than 50% reductions under nitrogen limitation. These impacts, however, became indistinguishable from nutrient-replete conditions when normalized to cell volume. Calcification decreased three-fold and linearly with increasing pCO2 under all nutrient conditions, and was accompanied by a smaller ~30% nonlinear reduction in POC production, manifested mainly above 3 × current pCO2. Our results suggest that normalization to cell volume allows the major impacts of nutrient limitation (changed cell sizes and reduced PIC and POC production rates) to be treated independently of the major impacts of increasing pCO2 and, additionally, stresses the importance of including cell volume measurements to the toolbox of standard physiological analysis of coccolithophores in field and laboratory studies.
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 2023-05-05.
DOI: 10.15468/dl.xuxnhs
title: Occurrence Download

description: A dataset containing 3969 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ocypodidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3969 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015877-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.958560
title: Seawater carbonate chemistry and impact of climate change on direct and indirect species interactions

description: Recent marine climate change research has largely focused on the response of individual species to environmental changes including warming and acidification. The response of communities, driven by the direct effects of ocean change on individual species as well the cascade of indirect effects, has received far less study. We used several rocky intertidal species including crabs, whelks, juvenile abalone, and mussels to determine how feeding, growth, and interactions between species could be shifted by changing ocean conditions. Our 10 wk experiment revealed many complex outcomes which highlight the unpredictability of community-level responses. Contrary to our predictions, the largest impact of elevated CO2 was reduced crab feeding and survival, with a pH drop of 0.3 units. Surprisingly, whelks showed no response to higher temperatures or CO2 levels, while abalone shells grew 40% less under high CO2 conditions. Massive non-consumptive effects of crabs on whelks showed how important indirect effects can be in determining climate change responses. Predictions of species outcomes that account solely for physiological responses to climate change do not consider the potentially large role of indirect effects due to species interactions. For strongly linked species (e.g. predator-prey or competitor relationships), the indirect effects of climate change are much less known than direct effects, but may be far more powerful in reshaping future marine communities.
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 2023-05-08.
DOI: 10.1594/pangaea.957247
title: Surface water abiotic data from Costa dos Corais Marine Protected Area, from 2018 to 2019 - Reef zone from Maragogi to Japaratinga, Brazilian Northeast

description: Continental runoff is an important source of solutes and nutrients to coastal coral reefs. Nevertheless, they can also act as local stressors due to high coastal urbanization and the associated release of untreated effluents. Here we aimed to qualitatively investigate the effects of seasonality over reefs from the Costa dos Corais Marine Protected Area (Brazil) and to identify the influence of local rivers on the reefs' environmental status. Surface waters from the reef lagoon located at Maragogi (city from the state of Alagoas, northeast Brazil) and Japaratinga (city from the state of Alagoas, northeast Brazil) were sampled monthly from July 2018 to June 2019 and abiotic parameters were measured. Samples were taken with a 2 L Niskin bottle and stored for subsequent analyses of: total alkalinity (TA), pH, nitrate, nitrite, ammonium, dissolved inorganic phosphorus and silicate. For temperature, salinity and depth measurements it was used a RBR® C.T.D.
DOI: 10.1594/pangaea.958450
title: Seawater carbonate chemistry and micromechanical properties of the mineralized cuticle in juvenile red and blue king crabs

description: Ocean acidification (OA) adversely affects a broad range of marine calcifying organisms. Crustaceans, however, exhibit mixed responses to OA, with growth or survival negatively affected in some species, but unaffected or positively affected in others. In crustaceans, the mineralized cuticle resists mechanical loads, provides protection from the environment, and enables mobility, but little is known about how OA or interactions between OA and temperature affect its structure or function. Here, the effects of OA on the mechanics, structure, and composition of the cuticle in two Alaska king crab species was assessed. Juvenile blue king crabs (Paralithodes platypus) were exposed for a year to three pH levels, 8.1 (ambient), 7.8 and 7.5. Juvenile red king crabs (Paralithodes camtschaticus) were exposed for ~ 6 months to two pH levels, 8.0 and 7.8, at three temperatures: ambient, ambient + 2 °C, and ambient + 4 °C. Cuticle microhardness (a measure of resistance to permanent or plastic mechanical deformation), thickness, ultrastructure, and elemental composition were assessed in two body regions, the carapace and the crushing chela (claw). In both species tested, OA reduced endocuticle microhardness in the chela, but not in the carapace. There was no effect of pH or temperature on total procuticle thickness of the chela or carapace in either species. Reductions in microhardness were not driven by reduced calcium content of the shell. In fact, calcium content was significantly elevated in the carapace of blue king crabs and in the chela of red king crabs exposed to lower than ambient pH at ambient temperature, suggesting that calcium content alone is not a sufficient proxy for mechanical properties. Reduced chela microhardness, indicative of more compliant material, could compromise the utility of crushing chelae in feeding and defense.
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 2023-05-04.
DOI: 10.1594/pangaea.756651
title: Seawater carbonate chemistry and calcification during experiments with coral communities, 2000

description: Previous studies have demonstrated that coral and algal calcification is tightly regulated by the calcium carbonate saturation state of seawater. This parameter is likely to decrease in response to the increase of dissolved CO2 resulting from the global increase of the partial pressure of atmospheric CO2. We have investigated the response of a coral reef community dominated by scleractinian corals, but also including other calcifying organisms such as calcareous algae, crustaceans, gastropods and echinoderms, and kept in an open-top mesocosm. Seawater pCO2 was modified by manipulating the pCO2 of air used to bubble the mesocosm. The aragonite saturation state (omega arag) of the seawater in the mesocosm varied between 1.3 and 5.4. Community calcification decreased as a function of increasing pCO2 and decreasing omega arag. This result is in agreement with previous data collected on scleractinian corals, coralline algae and in a reef mesocosm, even though some of these studies did not manipulate CO2 directly. Our data suggest that the rate of calcification during the last glacial maximum might have been 114% of the preindustrial rate. Moreover, using the average emission scenario (IS92a) of the Intergovernmental Panel on Climate Change, we predict that the calcification rate of scleractinian-dominated communities may decrease by 21% between the pre-industrial period (year 1880) and the time at which pCO2 will double (year 2065).
description: Caution! Values are not truly measured! 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).Note that CO3 data was calculated from omega aragonite, solubility product of aragonite (Karag) and Ca concentration following: CO3=omega*Karag/Ca. Where the Karag=7.16*10**-7.Omega aragonite and calcification rate were digitized from scanned figure 1 using software GraphClick (http://www.arizona-software.ch).
description: Supplement to: Leclercq, Nicolas; Gattuso, Jean-Pierre; Jaubert, Jean (2000): CO2 partial pressure controls the calcification rate of a coral community. Global Change Biology, 6(3), 329-334
DOI: 10.1594/pangaea.842228
title: Compound-specific carbon isotopes of GDGT-derived biphytanes in six samples from Core 08 and Core 10
DOI: 10.1594/pangaea.958715
title: Seawater carbonate chemistry and community composition in mangrove ponds with pulsed hypoxic and acidified conditions

description: The potential resilience of biological communities to accelerating rates of global change has received considerable attention. We suggest that some shallow aquatic ecosystems, where temperature, dissolved oxygen (DO), and pH can exhibit extreme variation on short timescales of hours or days, provide an opportunity to develop a mechanistic understanding of species persistence and community assembly under harsh environmental conditions. Extreme diel swings in DO and pH have been observed in eutrophic temperate ecosystems, and here, we describe a similar phenomenon consistently occurring across tropical sites that included relatively remote atolls on the Meso-American barrier reefs in Belize and oligotrophic coastal lagoons in Panama. In particular, we documented large daily swings in temperature, DO, and pH within shallow ponds of Caribbean mangrove forests. Water in seven of 13 ponds went hypoxic (&lt;2 mg/L DO) during the multiday sampling period, and pH dipped nightly to low levels, falling below 7.0 in some ponds. Minimum pH and minimum DO were correlated, and showed a similar relationship in Belize and Panama, suggesting a common mechanism produced diel cycles. Remarkably, most ponds exhibited high abundance of macroalgae, macroinvertebrates, and fish, despite potentially stressful abiotic conditions. Although fish diversity was negatively correlated with pH range, our overall results from the ponds suggest that many species are sufficiently resistant such that a functionally complex community can persist in the midst of pulsed stressful conditions. We propose that the mangrove ponds could serve as a model ecosystem for investigating resistance and resilience of coastal marine communities to global change factors such as climate change, hypoxia, and ocean acidification.
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 2023-05-08.