cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.721856
title: Seawater carbonate chemistry, community calcification and photosynthesis during experiments with coral reefs at Shiraho reef, Ishigaki Island, southwest Japan, 2009

description: Seven coral reef communities were defined on Shiraho fringing reef, Ishigaki Island, Japan. Net photosynthesis and calcification rates were measured by in situ incubations at 10 sites that included six of the defined communities, and which occupied most of the area on the reef flat and slope. Net photosynthesis on the reef flat was positive overall, but the reef flat acts as a source for atmospheric CO2, because the measured calcification/photosynthesis ratio of 2.5 is greater than the critical ratio of 1.67. Net photosynthesis on the reef slope was negative. Almost all excess organic production from the reef flat is expected to be effused to the outer reef and consumed by the communities there. Therefore, the total net organic production of the whole reef system is probably almost zero and the whole reef system also acts as a source for atmospheric CO2. Net calcification rates of the reef slope corals were much lower than those of the branching corals. The accumulation rate of the former was approximately 0.5 m kyr?1 and of the latter was ~0.7-5 m kyr?1. Consequently, reef slope corals could not grow fast enough to keep up with or catch up to rising sea levels during the Holocene. On the other hand, the branching corals grow fast enough to keep up with this rising sea level. Therefore, a transition between early Holocene and present-day reef communities is expected. Branching coral communities would have dominated while reef growth kept pace with sea level rise, and the reef was constructed with a branching coral framework. Then, the outside of this framework was covered and built up by reef slope corals and present-day reefs were constructed.
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: Nakamura, T; Nakamori, T (2009): Estimation of photosynthesis and calcification rates at a fringing reef by accounting for diurnal variations and the zonation of coral reef communities on reef flat and slope: a case study for the Shiraho reef, Ishigaki Island, southwest Japan. Coral Reefs, 28(1), 229-250
DOI: 10.1594/pangaea.758189
title: Seawater carbonate chemistry and coverage and dry weight of Ecklonia radiata during experiments, 2010

description: Predictions about the ecological consequences of oceanic uptake of CO2 have been preoccupied with the effects of ocean acidification on calcifying organisms, particularly those critical to the formation of habitats (e.g. coral reefs) or their maintenance (e.g. grazing echinoderms). This focus overlooks the direct effects of CO2 on non-calcareous taxa, particularly those that play critical roles in ecosystem shifts. We used two experiments to investigate whether increased CO2 could exacerbate kelp loss by facilitating non-calcareous algae that, we hypothesized, (i) inhibit the recovery of kelp forests on an urbanized coast, and (ii) form more extensive covers and greater biomass under moderate future CO2 and associated temperature increases. Our experimental removal of turfs from a phase-shifted system (i.e. kelp- to turf-dominated) revealed that the number of kelp recruits increased, thereby indicating that turfs can inhibit kelp recruitment. Future CO2 and temperature interacted synergistically to have a positive effect on the abundance of algal turfs, whereby they had twice the biomass and occupied over four times more available space than under current conditions. We suggest that the current preoccupation with the negative effects of ocean acidification on marine calcifiers overlooks potentially profound effects of increasing CO2 and temperature on non-calcifying organisms.
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: Connell, Sean D; Russell, Bayden D (2010): The direct effects of increasing CO2 and temperature on non-calcifying organisms: increasing the potential for phase shifts in kelp forests. Proceedings of the Royal Society B-Biological Sciences, 277(1686), 1409-1415
DOI: 10.1594/pangaea.807748
title: Hydrochemistry measured on water bottle samples during Hakurei-Maru cruise NH94-2
DOI: 10.1594/pangaea.875706
title: Seawater carbonate chemistry and corrosion and results of the mechanical tests of cidaroid (Eucidaris tribuloides) and a euechinoid (Tripneustes ventricosus) in laboratory experiment

description: Echinoderms are considered as particularly sensitive to ocean acidification (OA) as their skeleton is made of high-magnesium calcite, one of the most soluble forms of calcium carbonate. Recent studies have investigated effects of OA on the skeleton of "classical" sea urchins (euechinoids) but the impact of etching on skeleton mechanical properties is almost unknown. Furthermore, the integrity of the skeleton of cidaroids has never been assessed although their extracellular fluid is undersaturated with respect to their skeleton and the skeleton of their primary spines is in direct contact with seawater. In this study, we compared the dissolution of test plates and spines as well as the spine mechanical properties (two-points bending tests) in a cidaroid (Eucidaris tribuloides) and a euechinoid (Tripneustes ventricosus) submitted to a 5-weeks acidification experiment (pHT 8.1, 7.7, 7.4). Test plates of both species were not affected by dissolution. Spines of E. tribuloides showed no mechanical effects at pHSW-T 7.4 despite traces of corrosion on secondary spines. On the contrary, spines of the T. ventricosus were significantly etched at both pHSW-T 7.7 and 7.4 and their fracture force reduced by 16 to 35%, respectively. This increased brittleness is probably of little significance with regards to predation protection but has consequences in terms of energy allocation.
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 2017-05-24.
description: Supplement to: Dery, Aurélie; Collard, Marie; Dubois, Philippe (2017): Ocean Acidification Reduces Spine Mechanical Strength in Euechinoid but Not in Cidaroid Sea Urchins. Environmental Science & Technology, 51(7), 3640-3648
DOI: 10.1594/pangaea.874743
title: Functional analysis of a tyrosinase gene involved in early larval shell biogenesis in Crassostrea angulata and its response to ocean acidification

description: The formation of the primary shell is a vital process in marine bivalves. Ocean acidification largely influences shell formation. It has been reported that enzymes involved in phenol oxidation, such as tyrosinase and phenoloxidases, participate in the formation of the periostracum. In the present study, we cloned a tyrosinase gene from Crassostrea angulata named Ca-tyrA1, and its potential function in early larval shell biogenesis was investigated. The Ca-tyrA1 gene has a full-length cDNA of 2430 bp in size, with an open reading frame of 1896 bp in size, which encodes a 631-amino acid protein that includes a 24-amino acid putative signal peptide. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that Ca-tyrA1 transcription mainly occurs at the trochophore stage, and the Ca-tyrA1 mRNA levels in the 3000 ppm treatment group were significantly upregulated in the early D-veliger larvae. WMISH and electron scanning microscopy analyses showed that the expression of Ca-tyrA1 occurs at the gastrula stage, thereby sustaining the early D-veliger larvae, and the shape of its signal is saddle-like, similar to that observed under an electron scanning microscope. Furthermore, the RNA interference has shown that the treatment group has a higher deformity rate than that of the control, thereby indicating that Ca-tyrA1 participates in the biogenesis of the primary shell. In conclusion, and our results indicate that Ca-tyrA1 plays a vital role in the formation of the larval shell and participates in the response to larval shell damages in Crassostrea angulata that were induced by ocean acidification.
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 2017-04-20.
description: Supplement to: Yang, Bingye; Pu, F; Li, lingling; You, W; Ke, C; Feng, Danqing (2017): Functional analysis of a tyrosinase gene involved in early larval shell biogenesis in Crassostrea angulata and its response to ocean acidification. Comparative Biochemistry and Physiology Part B: Biochemistry & Molecular Biology, 206, 8-15
DOI: 10.1594/pangaea.875262
title: Seawater carbonate chemistry and pH at the site of calcification within the calcifying fluid/medium of coralline algae in laboratory experiment

description: Coralline algae provide important ecosystem services but are susceptible to the impacts of ocean acidification. However, the mechanisms are uncertain, and the magnitude is species specific. Here, we assess whether species-specific responses to ocean acidification of coralline algae are related to differences in pH at the site of calcification within the calcifying fluid/medium (pHcf) using delta 11B as a proxy. Declines in delta 11B for all three species are consistent with shifts in delta 11B expected if B(OH)4- was incorporated during precipitation. In particular, the delta11B ratio in Amphiroa anceps was too low to allow for reasonable pHcf values if B(OH)3 rather than B(OH)4- was directly incorporated from the calcifying fluid. This points towards delta 11B being a reliable proxy for pHcf for coralline algal calcite and that if B(OH)3 is present in detectable proportions, it can be attributed to secondary postincorporation transformation of B(OH)4-. We thus show that pHcf is elevated during calcification and that the extent is species specific. The net calcification of two species of coralline algae (Sporolithon durum, and Amphiroa anceps) declined under elevated CO2, as did their pHcf. Neogoniolithon sp. had the highest pHcf, and most constant calcification rates, with the decrease in pHcf being 1/4 that of seawater pH in the treatments, demonstrating a control of coralline algae on carbonate chemistry at their site of calcification. The discovery that coralline algae upregulate pHcf under ocean acidification is physiologically important and should be included in future models involving calcification.
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 2017-05-17.
description: Supplement to: Cornwall, Christopher Edward; Comeau, Steeve; McCulloch, Malcolm T (2017): Coralline algae elevate pH at the site of calcification under ocean acidification. Global Change Biology
DOI: 10.1594/pangaea.907768
title: Seawater carbonate chemistry and aerobic performance of two tropical cephalopod species Idiosepius pygmaeus and Sepioteuthis lessoniana

description: Squid and many other cephalopods live continuously on the threshold of their environmental oxygen limitations. If the abilities of squid to effectively take up oxygen are negatively affected by projected future carbon dioxide (CO2) levels in ways similar to those demonstrated in some fish and invertebrates, it could affect the success of squid in future oceans. While there is evidence that acute exposure to elevated CO2 has adverse effects on cephalopod respiratory performance, no studies have investigated this in an adult cephalopod after relatively prolonged exposure to elevated CO2 or determined any effects on aerobic scope. Here, we tested the effects of prolonged exposure (&gt;=20% of lifespan) to elevated CO2 levels (~1000 μatm) on the routine and maximal oxygen uptake rates, aerobic scope and recovery time of two tropical cephalopod species, the two-toned pygmy squid, Idiosepius pygmaeus and the bigfin reef squid, Sepioteuthis lessoniana. Neither species exhibited evidence of altered aerobic performance after exposure to elevated CO2 when compared to individuals held at control conditions. The recovery time of I. pygmaeus under both control and elevated CO2 conditions was less than 1 hour, whereas S. lessoniana required approximately 8 hours to recover fully following maximal aerobic performance. This difference in recovery time may be due to the more sedentary behaviours of I. pygmaeus. The ability of these two cephalopod species to cope with prolonged exposure to elevated CO2 without detriment to their aerobic performance suggests some resilience to an increasingly high CO2 world.
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 2019-10-24.
description: Supplement to: Spady, Blake L; Nay, Tiffany J; Rummer, Jodie L; Munday, Philip L; Watson, Sue-Ann (2019): Aerobic performance of two tropical cephalopod species unaltered by prolonged exposure to projected future carbon dioxide levels. Conservation Physiology, 7(1)
DOI: 10.1594/pangaea.878281
title: Seawater carbon chemistry and net primary production and net calcification in coral reef communities

description: The threat represented by ocean acidification (OA) for coral reefs has received considerable attention because of the sensitivity of calcifiers to changing seawater carbonate chemistry. However, most studies have focused on the organismic response of calcification to OA, and only a few have addressed community-level effects, or investigated parameters other than calcification, such as photosynthesis. Light (photosynthetically active radiation, PAR) is a driver of biological processes on coral reefs, and the possibility that these processes might be perturbed by OA has important implications for community function. Here we investigate how CO2 enrichment affects the relationships between PAR and community net O2 production (Pnet), and between PAR and community net calcification (Gnet), using experiments on three coral communities constructed to match (i) the back reef of Mo'orea, French Polynesia, (ii) the fore reef of Mo'orea, and (iii) the back reef of O'ahu, Hawaii. The results were used to test the hypothesis that OA affects the relationship between Pnet and Gnet. For the three communities tested, pCO2 did not affect the Pnet-PAR relationship, but it affected the intercept of the hyperbolic tangent curve fitting the Gnet-PAR relationship for both reef communities in Mo'orea (but not in O'ahu). For the three communities, the slopes of the linear relationships between Pnet and Gnet were not affected by OA, although the intercepts were depressed by the inhibitory effect of high pCO2 on Gnet. Our result indicates that OA can modify the balance between net calcification and net photosynthesis of reef communities by depressing community calcification, but without affecting community photosynthesis.
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 2017-07-27.
description: Supplement to: Comeau, Steeve; Edmunds, Peter J; Lantz, Coulson A; Carpenter, Robert C (2017): Daily variation in net primary production and net calcification in coral reef communities exposed to elevated CO2. Biogeosciences, 14(14), 3549-3560
DOI: 10.1594/pangaea.890872
title: Seawater carbonate chemistry and gene abundance and community composition in two contrasting coastal marine sediments

description: Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2) and elevated temperature (ambient + 4 °C) on the abundance of taxonomic and functional microbial genes. Specific q-PCR primers were used to target archaeal, bacterial and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA) and bacterial nitrite reductase (nirS) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.
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 2018-05-23.
description: Supplement to: Currie, Ashleigh R; Tait, Karen; Parry, Helen E; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A M; Widdicombe, Steve; Stahl, Henrik (2017): Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments. Frontiers in Microbiology, 8
DOI: 10.1594/pangaea.908297
title: Seawater carbonate chemistry and phytoplankton primary production, and its trophic transfer to zooplankton in a subtropical eutrophic water (Wuyuan Bay, China)

description: Ocean acidification (OA) has potential to affect marine phytoplankton in ways that are partly understood, but there is less knowledge about how it may alter the coupling to secondary producers. We investigated the effects of OA on phytoplankton primary production, and its trophic transfer to zooplankton in a subtropical eutrophic water (Wuyuan Bay, China) under present day (400 μatm) and projected end-of-century (1000 μatm) pCO2 levels. Net primary production was unaffected, although OA did lead to small decreases in growth rates. OA had no measurable effect on micro-/mesozooplankton grazing rates. Elevated pCO2 had no effect on phytoplankton fatty acid (FA) concentrations during exponential phase, but saturated FAs increased relative to the control during declining phase. FA profiles of mesozooplankton were unaffected. Our findings show that short-term exposure of plankton communities in eutrophic subtropical waters to projected end-of-century OA conditions has little effect on primary productivity and trophic linkage to mesozooplankton.
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 2019-11-08.
description: Supplement to: Wang, Tifeng; Jin, Peng; Wells, Mark L; Trick, Charles G; Gao, Kunshan (2019): Insensitivities of a subtropical productive coastal plankton community and trophic transfer to ocean acidification: Results from a microcosm study. Marine Pollution Bulletin, 141, 462-471