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Natural processes such as upwelling of deeper-water masses change the physical-chemical conditions of the water column creating localized ocean acidification events that can have an impact on the natural communities. This study was performed in a coral reef system of an archetypical bay within the Tayrona National Natural Park (PNNT) (Colombia), and aimed to quantify net calcification rates of a foundational coral species within a temporal context (6 months) taking into account the dynamics of seasonal upwelling that influence the study area. Net calcification rates of coral fragments were obtained in situ by the alkalinity anomaly technique in short-term incubations (~2.5 h). We found a significant effect of the upwelling on net calcification rates (Gnet) (p < 0.05) with an 42% increase in CaCO3 accretion compared to non-upwelling season. We found an increase in total alkalinity (AT) and dissolved inorganic carbon (DIC) with decreased aragonite saturation (Ωara) for the upwelling months, indicating an influence of the Subtropical Under Water mass (SAW) in the PNNT coral community. Significant negative correlations between net calcification with temperature and Ωara, which indicates a positive response of M. auretenra with the upwelling conditions, thus, acting as “enhancer” of resilience for coral calcification.

The interplay between ocean circulation and coral metabolism creates highly variable biogeochemical conditions in space and time across tropical coral reefs. Yet, relatively little is known quantitatively about the spatiotemporal structure of these variations. To address this gap, we use the Coupled Ocean Atmosphere Wave and Sediment Transport (COAWST) model, to which we added the Biogeochemical Elemental Cycling (BEC) model computing the biogeochemical processes in the water column, and a coral polyp physiology module that interactively simulates coral photosynthesis, respiration and calcification. The coupled model, configured for the north-shore of Moorea Island, successfully simulates the observed (i) circulation across the wave regimes, (ii) magnitude of the metabolic rates, and (iii) large gradients in biogeochemical conditions across the reef. Owing to the interaction between coral net community production (NCP) and coral calcification, the model simulates distinct day versus night gradients, especially for pH and the saturation state of seawater with respect to aragonite (Ωα). The strength of the gradients depends non-linearly on the wave regime and the resulting residence time of water over the reef with the low wave regime creating conditions that are considered as “extremely marginal” for corals. With the average water parcel passing more than twice over the reef, recirculation contributes further to the accumulation of these metabolic signals. We find diverging temporal and spatial relationships between total alkalinity (TA) and dissolved inorganic carbon (DIC) (≈ 0.16 for the temporal vs. ≈ 1.8 for the spatial relationship), indicating the importance of scale of analysis for this metric. Distinct biogeochemical niches emerge from the simulated variability, i.e., regions where the mean and variance of the conditions are considerably different from each other. Such biogeochemical niches might cause large differences in the exposure of individual corals to the stresses associated with e.g., ocean acidification. At the same time, corals living in the different biogeochemical niches might have adapted to the differing conditions, making the reef, perhaps, more resilient to change. Thus, a better understanding of the mosaic of conditions in a coral reef might be useful to assess the health of a coral reef and to develop improved management strategies., Frontiers in Marine Science, 9, ISSN:2296-7745

The interplay between ocean circulation and coral metabolism creates highly variable biogeochemical conditions in space and time across tropical coral reefs. Yet, relatively little is known quantitatively about the spatiotemporal structure of these variations. To address this gap, we use the Coupled Ocean Atmosphere Wave and Sediment Transport (COAWST) model, to which we added the Biogeochemical Elemental Cycling (BEC) model computing the biogeochemical processes in the water column, and a coral polyp physiology module that interactively simulates coral photosynthesis, respiration and calcification. The coupled model, configured for the north-shore of Moorea Island, successfully simulates the observed (i) circulation across the wave regimes, (ii) magnitude of the metabolic rates, and (iii) large gradients in biogeochemical conditions across the reef. Owing to the interaction between coral net community production (NCP) and coral calcification, the model simulates distinct day versus night gradients, especially for pH and the saturation state of seawater with respect to aragonite (Ωα). The strength of the gradients depends non-linearly on the wave regime and the resulting residence time of water over the reef with the low wave regime creating conditions that are considered as “extremely marginal” for corals. With the average water parcel passing more than twice over the reef, recirculation contributes further to the accumulation of these metabolic signals. We find diverging temporal and spatial relationships between total alkalinity (TA) and dissolved inorganic carbon (DIC) (≈ 0.16 for the temporal vs. ≈ 1.8 for the spatial relationship), indicating the importance of scale of analysis for this metric. Distinct biogeochemical niches emerge from the simulated variability, i.e., regions where the mean and variance of the conditions are considerably different from each other. Such biogeochemical niches might cause large differences in the exposure of individual corals to the stresses associated with e.g., ocean acidification. At the same time, corals living in the different biogeochemical niches might have adapted to the differing conditions, making the reef, perhaps, more resilient to change. Thus, a better understanding of the mosaic of conditions in a coral reef might be useful to assess the health of a coral reef and to develop improved management strategies. ISSN:2296-7745

Marine sedimentary ikaite is the parent mineral to glendonite, stellate pseudomorphs found throughout the geological record which are most usually composed of calcite. Ikaite is known to be metastable at earth surface temperatures and pressures, readily breaking down to more stable carbonate polymorphs when exposed to warm (ambient) conditions. Yet the process of transformation of ikaite to calcite is not well understood, and there is an ongoing debate as to the palaeoclimatic significance of glendonites in the geological record. This study uses a combination of techniques to examine the breakdown of ikaite to calcite, outside of the ikaite growth medium, and to assess the palaeoclimatic and palaeoenvironmental significance of stable and clumped isotope compositions of ikaite-derived calcite. Powder X-ray diffraction shows that ikaite undergoes a quasi- solid-state transformation to calcite during heating of samples in air, yet when ikaite transforms under a high temperature differential, minor dissolution-recrystallisation may also occur with the ikaite structural waters. No significant isotopic equilibration to transformation temperature is observed in the resulting calcite. Therefore, in cases of transformation of ikaite in air, clumped and stable isotope thermometry can be used to reconstruct ikaite growth temperatures. In the case of ancient glendonites, where transformation of the ikaite occurred in contact with the interstitial waters of the host sediments over unknown timescales, it is uncertain whether the reconstructed clumped isotope temperatures reflect ikaite crystallisation or its transformation temperatures. Yet clumped and stable isotope thermometry may still be used conservatively to estimate an upper limit for bottom water temperatures. Furthermore, stable isotope along with element/Ca ratios shed light on the chemical environment of ikaite growth. Our data indicate that a range of (bio)geochemical processes may act to promote ikaite formation at different marine sedimentary sites, including bacterial sulphate reduction and anaerobic oxidation of methane. The colours of the ikaites, from light brown to dark brown, indicate a high organic matter content, favouring high rates of bacterial sulphate reduction as the main driver of ikaite precipitation. Highest Mg/Ca ratios are found in the most unstable ikaites, indicating that Mg acts to destabilise ikaite structure., Geochimica et Cosmochimica Acta, 334, ISSN:0016-7037, ISSN:1872-9533

International audience; The carbonate chemistry was investigated in the semiarid eutrophic Araruama Lagoon (Brazil), one of the largest hypersaline coastal lagoons in the world. Spatial surveys during winter and summer periods were performed, in addition to a diurnal sampling in summer. The hypersaline waters have higher concentrations of total alkalinity (TA) and dissolved inorganic carbon (DIC) than the seawater that feed the lagoon, due to evaporation. However, TA and DIC concentrations were lower than those expected from evaporation. Calcium carbonate (CaCO3) precipitation partially explained these deficits. The negative correlation between the partial pressure of CO2 (pCO2) and chlorophyll a (Chl a) indicated that DIC was also consumed by primary producers. The uptake by photosynthesis contributes to 57–63% of DIC deviation from evaporation, the remaining credited to CaCO3 precipitation. Marked pCO2 undersaturation was prevalent at the innermost region with shallow, confined, and phytoplankton-dominated waters, with a strong enrichment of heavier carbon isotope (δ13C-DIC up to 5.55‰), and highest pH (locally counter-acting the process of ocean acidification). Oversaturation was restricted to an urbanized region, and during night-time. The lagoon behaved as a marked CO2 sink during winter (− 15.32 to − 10.15 mmolC m−2 day−1), a moderate sink during summer (− 5.50 to − 4.67 mmolC m−2 day−1), with a net community production (NCP) of 93.7 mmolC m−2 day−1 and prevalence of net autotrophic metabolism. A decoupling between CO2 and O2 exchange rate at the air–water interface was attributed to differences in gas solubility, and high buffering capacity. The carbonate chemistry reveals simultaneous and antagonistic actions of CaCO3 precipitation and autotrophic metabolism on CO2 fluxes, and could reflect future conditions in populated and semiarid coastal ecosystems worldwide.

10 pages, 5 figures.-- Under a Creative Commons license., Understanding the ocean carbon sink and its future acidification-derived changes requires accurate and precise measurements with good spatiotemporal coverage. In addition, a deep knowledge of the thermodynamics of the seawater carbonate system is key to interconverting between measured and calculated variables. To gain insights into the remaining inconsistencies in the seawater carbonate system, we assess discrete water column measurements of carbon dioxide fugacity (fCO2), dissolved inorganic carbon (DIC), total alkalinity (TA), and pH measured with unpurified indicators, from hydrographic cruises in the Atlantic, Pacific, and Southern Oceans included in GLODAPv2.2020 (19,013 samples). An agreement of better than ± 3% between fCO2 measured and calculated from DIC and pH is obtained for 94% of the compiled dataset, while when considering fCO2 measured and calculated from DIC and TA, the agreement is better than ± 4% for 88% of the compiled dataset, with a poorer internal consistency for high-CO2 waters. Inspecting all likely sources of uncertainty from measured and calculated variables, we conclude that the seawater carbonate system community needs to (i) further refine the thermodynamic model of the seawater carbonate system, especially K2, including the impact of organic compounds and other acid-base systems on TA; (ii) update the standard operating procedures for the seawater carbonate system measurements following current technological and analytical advances, paying particular attention to the pH methodology that is the one that evolved the most; (iii) encourage measuring discrete water column fCO2 to further check the internal consistency of the seawater carbonate system, especially given the new era of sensor-based seawater measurements; and (iv) develop seawater Certified Reference Materials (CRMs) for fCO2 and pH together with seawater CRMs for TA and DIC over the range of values encountered in the global ocean. Our conclusions also suggest the need for a re-evaluation of the adjustments applied by GLODAPv2 to pH, which were based on DIC and TA consistency checks but not supported by fCO2 and DIC consistency, The research leading to these results was supported through NOAA's Ocean Acidification Program (OAP) via Award #NA17OAR0170332; through NERC via project NE/P021263/1; through the Spanish Research Agency via project PID2019-104279GB-C21/AEI/10.13039/501100011033; and through GAIN via grant IN607A2018/2, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Carbonate minerals are ubiquitous in most sediment-hosted mineral deposits. These deposits can contain a variety of carbonate types with complex paragenetic relationships. When normalized to chondritic values (CN), rare-earth elements and yttrium (REE+YCN) can be used to constrain fluid chemistry and fluid-rock interaction processes in both low- and high-temperature settings. Unlike other phases (e.g., pyrite), the application of in situ laser ablation-inductively coupled plasma-mass spectroscopy (LA-ICP-MS) data to the differentiation of pre-ore and hydrothermal carbonates remains relatively untested. To assess the potential applicability of carbonate in situ REE+Y data, we combined transmitted light and cathodoluminescence (CL) petrography with LA-ICP-MS analysis of carbonate mineral phases from (1) the Proterozoic George Fisher clastic dominated (CD-type) massive sulfide deposit and from (2) correlative, barren host rock lithologies (Urquhart Shale Formation). The REE+YCN composition of pre-ore calcite suggests it formed during diagenesis from diagenetic pore fluids derived from ferruginous, anoxic seawater. Hydrothermal and hydrothermally altered calcite and dolomite from George Fisher is generally more LREE depleted than the pre-ore calcite, whole-rock REE concentrations, and shale reference values. We suggest this is the result of hydrothermal alteration by saline Cl--rich mineralizing fluids. Furthermore, the presence of both positive and negative Eu/Eu* values in calcite and dolomite indicates that the mineralizing fluids were relatively hot (>250°C) and cooled below 200–250°C during ore formation. This study confirms the hypothesis that in situ REE+Y data can be used to differentiate between pre-ore and hydrothermal carbonate and provide important constraints on the conditions of ore formation., Helmholtz-Gemeinschaft http://dx.doi.org/10.13039/501100001656, https://doi.org/10.5880/GFZ.3.1.2020.005

Global‐scale ocean acidification has spurred interest in the capacity of seagrass ecosystems to increase seawater pH within crucial shoreline habitats through photosynthetic activity. However, the dynamic variability of the coastal carbonate system has impeded generalization into whether seagrass aerobic metabolism ameliorates low pH on physiologically and ecologically relevant timescales. Here we present results of the most extensive study to date of pH modulation by seagrasses, spanning seven meadows (Zostera marina) and 1000 km of U.S. west coast over 6 years. Amelioration by seagrass ecosystems compared to non‐vegetated areas occurred 65% of the time (mean increase 0.07 ± 0.008 SE). Events of continuous elevation in pH within seagrass ecosystems, indicating amelioration of low pH, were longer and of greater magnitude than opposing cases of reduced pH or exacerbation. Sustained elevations in pH of >0.1, comparable to a 30% decrease in [H+], were not restricted only to daylight hours but instead persisted for up to 21 days. Maximal pH elevations occurred in spring and summer during the seagrass growth season, with a tendency for stronger effects in higher latitude meadows. These results indicate that seagrass meadows can locally alleviate low pH conditions for extended periods of time with important implications for the conservation and management of coastal ecosystems., The most extensive study to date of pH modulation by seagrasses, spanning seven meadows (Zostera marina) and 1000 km of U.S. west coast over 6 years. Amelioration of low pH by seagrass ecosystems occurred most of the time, where events of continuous elevation in pH were longer and of greater magnitude than opposing cases of reduced pH or exacerbation. Sustained elevations in pH were not restricted only to daylight hours. Maximal pH elevations occurred in spring and summer during the seagrass growth season, with a tendency for stronger effects in higher latitude meadows.

Compared with the open ocean, knowledge of pH variability in coastal waters is rudimentary, especially in Africa. This is concerning as quantifying local pH conditions is critical when assessing the response of coastal species to future ocean acidification scenarios. The objective of this study was to capture some of the variability in pH at scales and sites relevant to coastal marine organisms in a South African temperate embayment (Algoa Bay, Indian Ocean). We used a sampling approach that captured spatial (at a resolution of ∼10 km), monthly and diel (24-hour) variability in pH and associated physical and biological parameters at offshore and shallow inshore sites in Algoa Bay. We found that pH and associated parameters (temperature, calculated pCO2, chlorophyll a) varied over space and time in Algoa Bay. The range in pH was 0.30 units at offshore sites and 0.46 at inshore sites, and the average pH was 8.10 (SD 0.06) and 8.10 (SD 0.13) at these sites, respectively, which is typical for coastal environments. Our results showed that both biological factors (at the offshore sites) and salinity (at the inshore sites) may influence temporal and spatial variability in pH. We also identified a shallow inshore site with high levels of macroalgal growth that had consistently higher average daytime pH levels (8.33 [SD 0.07]), which may serve as an ocean acidification refuge for coastal marine species. This is the first comprehensive pH-monitoring study to be implemented in a nearshore coastal area in Africa and provides recommendations for monitoring in other understudied regions.

Elemental contents change with shifts in macromolecular composition of marine phytoplankton. Recent studies focus on the responses of elemental contents of coccolithophores, a major calcifying phytoplankton group, to changing carbonate chemistry, caused by the dissolution of anthropogenically derived CO2 into the surface ocean. However, the effects of changing carbonate chemistry on biomacromolecules, such as protein and carbohydrate of coccolithophores, are less documented. Here, we disentangled the effects of elevated dissolved inorganic carbon (DIC) concentration (900 to 4,930μmolkg−1) and reduced pH value (8.04 to 7.70) on physiological rates, elemental contents, and macromolecules of the coccolithophore Emiliania huxleyi. Compared to present DIC concentration and pH value, combinations of high DIC concentration and low pH value (ocean acidification) significantly increased pigments content, particulate organic carbon (POC), and carbohydrate content and had less impact on growth rate, maximal relative electron transport rate (rETRmax), particulate organic nitrogen (PON), and protein content. In high pH treatments, elevated DIC concentration significantly increased growth rate, pigments content, rETRmax, POC, particulate inorganic carbon (PIC), protein, and carbohydrate contents. In low pH treatments, the extents of the increase in growth rate, pigments and carbohydrate content were reduced. Compared to high pH value, under low DIC concentration, low pH value significantly increased POC and PON contents and showed less impact on protein and carbohydrate contents; however, under high DIC concentration, low pH value significantly reduced POC, PON, protein, and carbohydrate contents. These results showed that reduced pH counteracted the positive effects of elevated DIC concentration on growth rate, rETRmax, POC, PON, carbohydrate, and protein contents. Elevated DIC concentration and reduced pH acted synergistically to increase the contribution of carbohydrate–carbon to POC, and antagonistically to affect the contribution of protein–nitrogen to PON, which further shifted the carbon/nitrogen ratio of E. huxleyi.

Ocean chemistry and carbonate sedimentation link Earth's climate, carbon cycle, and marine pH. The carbonate system in seawater is complex and there are large uncertainties in key parameters in deep time. Here, we link sedimentary textures formed in arid coastal environments and preserved in the rock record to past seawater carbonate chemistry. Prior to the mid-Mesozoic, tepee structures and pisoids – features associated with peritidal environments – co-vary with available shelf area during cycles of supercontinent formation and rifting. In contrast, tepees and pisoids are consistently scarce after the mid-Mesozoic, which coincides with a radiation in pelagic calcifiers as well as the breakup of Pangea. Numerical models suggest that the global and temporal abundances of tepee structures and pisoids are correlated with secular shifts in seawater chemistry, and that trends likely reflect the underlying influence of tectonics and biotic innovation on marine alkalinity and the saturation states of carbonate minerals. As independent sedimentary proxies, tepees and pisoids serve as benchmarks for global carbon cycle models and provide a new proxy record of seawater chemistry that can help discern links among tectonics, biotic innovation, and seawater chemistry.

To understand the effects of the glacial meltwater supply on carbonate chemistry and the air–sea CO2 flux within the fjord, water samples were collected in Bowdoin Fjord in northwestern Greenland for dissolved inorganic carbon (DIC) concentration, total alkalinity (TA), oxygen isotopic ratio (δ18O), and chlorophyll a concentration analyses in the summers of 2016 and 2017. The partial pressure of CO2 (pCO2) in surface water, calculated from DIC and TA, was less than 200 µatm, and was significantly lower than that in the atmosphere (399 ± 3 µatm). Therefore, surface water of the fjord acts as sink for CO2 in the atmosphere (–4.9 ± 0.7 mmol m–2 d–1). To evaluate the effects of freshwater and land-derived substances by glacial meltwater on pCO2 in the fjord, we calculated the changes of pCO2 in salinity and carbonate chemistry that would result from the inflow of glacial meltwater into the fjord. The calculated pCO2 was high near the calving front, where the contribution of glacier meltwater was significant. Examination of the relationship between salinity-normalized DIC and TA, which was considered DIC and TA input from the land, suggested that the land-derived high pCO2 freshwater affected mainly by the remineralization of the organic matter by bacterial activity was supplied to the Bowdoin Fjord.

Global-scale ocean acidification has spurred interest in the capacity of seagrass ecosystems to increase seawater pH within crucial shoreline habitats through photosynthetic activity. However, the dynamic variability of the coastal carbonate system has impeded generalization into whether seagrass aerobic metabolism ameliorates low pH on physiologically and ecologically relevant timescales. Here we present results of the most extensive study to date of pH modulation by seagrasses, spanning seven meadows (Zostera marina) and 1000km of U.S. west coast over 6years. Amelioration by seagrass ecosystems compared to non-vegetated areas occurred 65% of the time (mean increase 0.07±0.008SE). Events of continuous elevation in pH within seagrass ecosystems, indicating amelioration of low pH, were longer and of greater magnitude than opposing cases of reduced pH or exacerbation. Sustained elevations in pH of >0.1, comparable to a 30% decrease in [H+ ], were not restricted only to daylight hours but instead persisted for up to 21days. Maximal pH elevations occurred in spring and summer during the seagrass growth season, with a tendency for stronger effects in higher latitude meadows. These results indicate that seagrass meadows can locally alleviate low pH conditions for extended periods of time with important implications for the conservation and management of coastal ecosystems.

International audience; Increasing eutrophication of coastal waters generates disturbances in greenhouse gas (GHG) concentrations and emissions to the atmosphere that are still poorly documented, particularly in the tropics. Here, we investigated the concentrations and diffusive fluxes of carbon dioxide (CO2) and methane (CH4) in the urban-dominated Jacarepagua Lagoon Complex (JLC) in Southeastern Brazil. This lagoonal complex receives highly polluted freshwater and shows frequent occurrences of anoxia and hypoxia and dense phytoplankton blooms. Between 2017 and 2018, four spatial surveys were performed (dry and wet conditions), with sampling in the river waters that drain the urban watershed and in the lagoon waters with increasing salinities. Strong oxygen depletion was found in the rivers, associated with extremely high values of partial pressure of CO2 (pCO2; up to 20,417 ppmv) and CH4 concentrations (up to 288,572 nmol L−1). These high GHG concentrations are attributed to organic matter degradation from untreated domestic effluents mediated by aerobic and anaerobic processes, with concomitant production of total alkalinity (TA) and dissolved inorganic carbon (DIC). In the lagoon, GHG concentrations decreased mainly due to dilution with seawater and degassing. In addition, the phytoplankton growth and CH4 oxidation apparently consumed some CO2 and CH4, respectively. TA concentrations showed a marked minimum at salinity of ~20 compared to the two freshwater and marine end members, indicating processes of re-oxidation of inorganic reduced species from the low-salinity region, such as ammonia, iron, and/or sulfides. Diffusive emissions of gases from the entire lagoon ranged from 22 to 48 mmol C m−2 d−1 for CO2 and from 2.2 to 16.5 mmol C m−2 d−1 for CH4. This later value is among the highest documented in coastal waters. In terms of global warming potential (GWP) and CO2 equivalent emissions (CO2-eq), the diffusive emissions of CH4 were higher than those of CO2. These results highlight that highly polluted coastal ecosystems are hotspots of GHG emissions to the atmosphere, which may become increasingly significant in future global carbon budgets.

Spatial and temporal carbonate chemistry variability on coral reefs is influenced by a combination of seawater hydrodynamics, geomorphology, and biogeochemical processes, though their relative influence varies by site. It is often assumed that the water column above most reefs is well-mixed with small to no gradients outside of the benthic boundary layer. However, few studies to date have explored the processes and properties controlling these multi-dimensional gradients. Here, we investigated the lateral, vertical, and temporal variability of seawater carbonate chemistry on a Bermudan rim reef using a combination of spatial seawater chemistry surveys and autonomous in situ sensors. Instruments were deployed at Hog Reef measuring current flow, seawater temperature, salinity, pHT, pCO2, dissolved oxygen (DO), and total alkalinity (TA) on the benthos, and temperature, salinity, DO, and pCO2 at the surface. Water samples from spatial surveys were collected from surface and bottom depths at 13 stations covering ∼3 km2 across 4 days. High frequency temporal variability in carbonate chemistry was driven by a combination of diel light and mixed semi-diurnal tidal cycles on the reef. Daytime gradients in DO between the surface and the benthos suggested significant water column production contributing to distinct diel trends in pHT, pCO2, and DO, but not TA. We hypothesize these differences reflect the differential effect of biogeochemical processes important in both the water column and benthos (organic carbon production/respiration) vs. processes mainly occurring on the benthos (calcium carbonate production/dissolution). Locally at Hog Reef, the relative magnitude of the diel variability of organic carbon production/respiration was 1.4–4.6 times larger than that of calcium carbonate production/dissolution, though estimates of net organic carbon production and calcification based on inshore-offshore chemical gradients revealed net heterotrophy (−118 ± 51 mmol m–2 day–1) and net calcification (150 ± 37 mmol CaCO3 m–2 day–1). These results reflect the important roles of time and space in assessing reef biogeochemical processes. The spatial variability in carbonate chemistry parameters was larger laterally than vertically and was generally observed in conjunction with depth gradients, but varied between sampling events, depending on time of day and modifications due to current flow.

Netarts Bay is a shallow, temperate, tidal lagoon located on the northern coast of Oregon and the site of the Whiskey Creek Shellfish Hatchery (WCSH). Data collected with an autonomous continuous flow-through system installed at WCSH capable of high-resolution (1 Hz) partial pressure of aqueous CO2 (pCO2) and hourly total dissolved inorganic carbon (TCO2) measurements, with combined measurement uncertainties of < 2.0% and 0.5%, respectively, is analyzed over the 2014–2019 interval. Summer upwelling, wintertime downwelling, and in situ bay biogeochemistry represent significant modes of the observed variability in carbonate system dynamics. Summer upwelling is associated with large amplitude diel pCO2 variability, elevated TCO2 and alkalinity, but weak variability in salinity. Wintertime downwelling is associated with bay freshening by both local and remote sources, a strong tidal signature in salinity, TCO2, and alkalinity, with diel pCO2 variability much less amplified when compared to summer. Further, analysis of alkalinity-salinity relationships suggests multiple water masses inhabiting the bay during 1 year: mixing of end-members associated with direct precipitation, coastal rivers, southward displacement of the Columbia River plume, California Current surface and deep upwelled waters. The importance of in-bay processes such as net community metabolism during intervals of high productivity are apparent. These direct measurements of pCO2 and TCO2 have been useful to local hatchery owners who have monitored intake waters following historic seed-production failures related to high-CO2 conditions exacerbated by ocean acidification.

To quantitatively assess the inorganic carbon cycle in the eastern Indian sector of the Southern Ocean (80-150 degrees E, south of 60 degrees S), we measured ocean surface temperature, salinity, total alkalinity (TA), the partial pressure of carbon dioxide (pCO(2)), and concentrations of chlorophyll-a (chl a), dissolved inorganic carbon (DIC), and nutrients during the KY18 survey (December 2018-January 2019). The sea-air CO2 flux in this region was -8.3 +/- 12.7 mmol m(-2) day(-1) (-92.1 to +10.6 mmol m(-2) day(-1)). The ocean was therefore a weak CO2 sink. Based on the DIC and TA in the temperature minimum layer, we estimated the change of pCO(2) from winter to summer (delta pCO(2)) due to changes in water temperature, salinity, and biological activity (photosynthesis). The spatial distribution of pCO(2) in the western part (80-110 degrees E) of the study area was mainly driven by biological activity, which decreased pCO(2) from December to early January, and in the eastern part (110-150 degrees E) by temperature, which increased pCO(2) from January to February. We also examined the changes in the CO2 concentrations (xCO(2)) over time by comparing data from 1996 with our data (2018-2019). The oceanic and atmospheric xCO(2) increased by 23 and 45 ppm in 23 years, respectively. These changes of ocean xCO(2) were mainly driven by an increase in CO2 uptake from the atmosphere as a result of the rise in atmospheric xCO(2) and increase in biological activity associated with the change in the water-mass distribution.

Environmental change can have a significant impact on biogeochemical cycles at high latitudes and be particularly important in ecologically valuable fjord ecosystems. Seasonality in biogeochemical cycling in a sub-Arctic fjord of northern Norway (Kaldfjorden) was investigated from October 2016 to September 2018. Monthly changes in total inorganic carbon (CT), alkalinity (AT), major nutrients and calcium carbonate saturation (Ω) were driven by freshwater discharge, biological production and mixing with subsurface carbon-rich coastal water. Stable oxygen isotope ratios indicated that meteoric water (snow melt, river runoff, precipitation) had stratified and freshened surface waters, contributing to 81% of the monthly CT deficit in the surface layer. The timing and magnitude of freshwater inputs played an important role in Ω variability, reducing AT and CT by dilution. This dilution effect was strongly counteracted by the opposing effect of primary production that dominated surface water Ω seasonality. The spring phytoplankton bloom rapidly depleted nitrate and CT to drive highest Ω (~2.3) in surface waters. Calcification reduced AT and CT , which accounted for 21% of the monthly decrease in Ω during a coccolithophore bloom. Freshwater runoff contributed CT , AT and silicates of terrestrial origin to the fjord. Lowest surface water Ω (~1.6) resulted from organic matter remineralisation and mixing into subsurface water during winter and spring. Surface waters were undersaturated with respect to atmospheric CO2, resulting in modest uptake of −0.32 ± 0.03 mol C m−2 yr−1. Net community production estimated from carbon drawdown was 14 ± 2 g C m−2 yr−1 during the productive season. Kaldfjorden currently functions as an atmospheric CO2 sink of 3.9 ± 0.3 g C m−2 yr−1. Time-series data are vital to better understand the processes and natural variability affecting biogeochemical cycling in dynamic coastal regions and thus better predict the impact of future changes on important fjord ecosystems.

Estuaries are productive ecosystems that support extensive vertebrate and invertebrate communities, but some have suffered from an accelerated pace of acidification in their bottom waters. A major challenge in the study of estuarine acidification is strong temporal and spatial variability of carbonate chemistry resulting from a wide array of physical forces such as winds, tides and river flows. Most past studies of carbonate system dynamics were limited to the along channel direction, while lateral dynamics received less attention. Recent observations in Chesapeake Bay showed strong lateral asymmetry in the partial pressure of carbon dioxide (pCO2) and air-sea CO2 flux during a single wind event, but comparable responses to different wind events has yet to be investigated. In this work, a coupled hydrodynamic-carbonate chemistry model is used to understand wind-driven variability in the estuarine carbonate system. It is found that wind-driven lateral upwelling ventilates high DIC (Dissolved Inorganic Carbon) and CO2 deep water and raises surface pCO2, thereby modifying the air-sea CO2 flux. The upwelling also advects low pH water onto the adjacent shoals and reduces the aragonite saturation state Ω_arag in these shallow water environments, producing large temporal pH fluctuations and low pH events. Regime diagrams are constructed to summarize the effects of wind events on temporal pH and Ω_arag fluctuations and the lateral gradients in DIC, pH and pCO2 in the estuary. This modeling study provides a mechanistic explanation for the observed wind-driven lateral variability in DIC and pCO2 and reproduces large pH and Ω_arag fluctuations that could be driven by physical forcing. Given that current and historic mainstem Bay oyster beds are located in shallow shoals affected by this upwelling, a large fraction of the oyster beds (100-300 km2) could be exposed to carbonate mineral under-saturated 〖(Ω〗_arag

International audience; The interplay of coastal oceanographic processes usually results in partial pressures of CO 2 (pCO 2) higher than expected from the equilibrium with the atmosphere and even higher than those expected by the end of the century. Although this is a well-known situation, the natural variability of seawater chemistry at the locations from which tested organisms or communities originate is seldom considered in ocean acidification experiments. In this work, we aimed to evaluate the role of the carbonate chemistry dynamics in shaping the response of coastal phytoplankton communities to increased pCO 2 levels. The study was conducted at two coastal ecosystems off Chile, the Valdivia River estuary and the coastal upwelling ecosystem in the Arauco Gulf. We characterized the seasonal variability (winter/summer) of the hydrographic conditions, the carbonate system parameters, and the phytoplankton community structure at both sites. The results showed that carbonate chemistry dynamics in the estuary were mainly related to seasonal changes in freshwater discharges, with acidic and corrosive conditions dominating in winter. In the Arauco Gulf, these conditions were observed in summer, mainly associated with the upwelling of cold and high pCO 2 (>1,000 µatm) waters. Diatoms dominated the phytoplankton communities at both sites, yet the one in Valdivia was more diverse. Only certain phytoplankton groups in this latter ecosystem showed a significant correlations with the carbonate system parameters. When the impact of elevated pCO 2 levels was investigated by pCO 2 manipulation experiments, we did not observe any significant effect on the biomass of either of the two communities. Changes in the phytoplankton species composition and abundance during the incubations were related to other factors, such as competition and growth phases. Our findings highlight the importance of the natural variability of coastal ecosystems and the potential for local adaptation in determining responses of coastal phytoplankton communities to increased pCO 2 levels.

Tropical estuarine deltas generally present poorly buffered waters in their freshwaters. Carbonate chemistry predicts that mixture of such warm freshwater with seawater will create rapid consumption of the freshwater carbon dioxide (CO2) by the carbonate buffering capacity of the seawater. In this study, we used the Paraiba do Sul River as a laboratory to investigate how thermodynamics compare with biological processes, gas exchange, and tidal advection from mangrove. We conducted three spatial surveys covering the salinity gradient of the main channel and surrounding mangrove waters and one 24-h mooring in a mangrove creek. In the main channel, dissolved inorganic carbon (DIC) and total alkalinity (TA) showed closely conservative distribution along the salinity gradient, increasing seaward. The partial pressure of CO2 (pCO(2)) followed a bell-shaped curve predicted by carbonate chemistry for conservative mixing of river and ocean endmembers. During high river flow, pCO(2) sharply decreased between salinities 0 and 5 (1800 to 390 ppmv), a pCO(2) drawdown attributed to riverine outgassing and thermodynamics. Indeed, the mixing of TA-poor freshwater (363 +/- 16 mu mol kg(-1)) with TA-rich seawater creates a deficit of dissolved CO2 not related to biotic processes. During low river flow, the entire mixing zone was undersaturated in pCO(2) with an increasing trend seaward. However, observed pCO(2) values were slightly above those predicted by conservativity. Approximately half of this deviation was attributed to biological activity (net heterotrophy), and remaining deviation was assigned to the effects of gas exchange (18%) and water heating (36%). The effect of gas exchange was higher in fresh and low salinity waters, reflecting the higher outgassing/ingassing of CO2, and lower buffering capacity. Water heating was more important in mid- to high-salinities as a result of diel patterns of solar irradiance. Heterotrophy was slight and not able to outcompete thermodynamics and generate outgassing during estuarine mixing. Consistently, stable isotopic signatures of DIC (delta C-13-DIC) presented slight deviations below the conservative mixing, corroborating net heterotrophy in the main channel. Areas of CO2 uptake due to phytoplankton activity were identified but restricted to the freshwater endmember during low river flow, with lowest pCO(2) (up to 41 ppmv) and the highest chlorophyll a (up to 21.3 mu g L-1). The estuary was a CO2 sink during low river flow ( - 1.34 to -5.26 mmolC m(-2) d(-1)) and a source during high river flow (5.71 to 19.37 mmolC m(-2) d(-1)). In the mangrove creek, the pCO(2), DIC, delta C-13-DIC and TA presented deviations from the conservativity, with slopes between TA and DIC demonstrating organic carbon degradation mediated by aerobic respiration and sulphate reduction. Mangrove creek waters were a CO2 source (average of 134.81 mmolC m(-2) d(-1)), exhibiting high values of pCO(2) (up to 21,720 ppmv). The results reveal that the low buffering capacity in the main channel of tropical estuarine deltas can be the predominant driver of pCO(2), generating CO2 undersaturation along the mixing zone, a process overlooked in estuarine systems. Moreover, air-water CO2 exchange, thermal variability, and biological activities contribute to deviation of the carbonate system from conservative mixing in specific estuarine areas, also modulating pCO(2) variability.

Key Points In Kongsfjorden, an Arctic glacier fjord, freshwater from glacier runoff and ice meltwater decreases phosphate, alkalinity and DOM concentrations Estuarine mixing is the major driver of summer CO2 undersaturation in glacially modified waters and near‐corrosive conditions were observed Future changes will amplify ocean acidification in the inner‐fjord surface waters Abstract A detailed survey of a high Arctic glacier fjord (Kongsfjorden, Svalbard) was carried out in summer 2016, close to the peak of the meltwater season, in order to identify the effects of glacier runoff on nutrient distributions and the carbonate system. Short‐term weather patterns were found to exert a strong influence on freshwater content within the fjord. Freshwater inputs from glacier runoff and ice meltwater averaged (±SD) low nitrate (1.85±0.47 μM; 0.41±0.99 μM), orthophosphate (0.07±0.27 μM; 0.02 ±0.03 μM), dissolved organic carbon (27 ±14 μM in glacier runoff), total alkalinity (708±251 μmol kg‐1; 173±121 μmol kg‐1) and dissolved inorganic carbon (622±108 μmol kg‐1; 41±88 μmol kg‐1), as well as a modest silicate concentration (3.71±0.02 μM; 3.16±5.41 μM). pCO2 showed a non‐conservative behavior across the estuarine salinity gradient with a pronounced under‐saturation in the inner‐fjord, leading to strong CO2 uptake from the atmosphere. The combined effect of freshwater dilution and atmospheric CO2 absorption was the lowering of aragonite saturation state, to values that are known to negatively affect marine calcifiers (ΩAr, 1.07). Glacier discharge was therefore a strong local amplifier of ocean acidification. Future increases in discharge volume and the loss of marine productivity following the retreat of marine‐terminating glaciers inland are both anticipated to further lower ΩAr within inner‐fjord surface waters. This shift may be partially buffered by an increase in the mean freshwater total alkalinity as the fractional importance of iceberg melt to freshwater fjord inputs declines and runoff increases.

Publisher's version (útgefin grein), Lake Myvatn, Iceland, is one of the most biologically productive lakes in the northern hemisphere, despite seasonal ice cover. Hydrothermal and groundwater springs make up the dominant source to this lake, and we investigate their Mg isotope ratio to assess the effect of mid-ocean ridge hydrothermal springs, which are the primary modern sink of seawater magnesium. We also examine a time series in the only outflow from this lake, the Laxa River, to assess the effects of seasonal primary productivity on Mg isotopes. In the hydrothermal waters, there is a clear distinction between cold waters (largely unfractionated from primary basalt) and relatively hot waters, which exhibit over 1‰ fractionation, with consequences for the oceanic mass balance if the hydrothermal removal of Mg is not fully quantitative. The outflow Mg isotopes are similar to basalts (δ26Mg = −0.2 to −0.3) during winter but reach a peak of ∼0‰ in August. This fractionation corresponds to calcite precipitation during summer in Lake Myvatn, preferentially taking up light Mg isotopes and driving the residual waters isotopically heavy as observed, meaning that overall the lake is a CO2 sink., PP and the analyses were funded by NERC grant NE/I020571/2, and PP and MM are also supported by ERC Consolidator grant 682760 CONTROLPASTCO2.

An ecosystem model called the “EMAGIN-B.C. ver 1.0 (Ecosystem Model for Aquatic Geologic Integrated Network for Blue Carbon)”, describing the Carbon-Nitrogen-Phosphorus-Oxygen-Calcium cycle was developed to estimate/predict carbon capture and storage in estuaries. EMAGIN-B.C. analyzes (1) carbon burial, wherein carbon is captured biologically in the pelagic and benthic ecosystems and stored in deeper sediments, (2) CO 2 uptake at the ocean surface while considering the carbonate chemistry with total alkalinity and Dissolved Inorganic Carbon (DIC) production/consumption due to biochemical processes, (3) DIC capture associated with grazing at the trophic level among phytoplankton, zooplankton, and benthic fauna, (4) the effects of hypoxia on benthic fauna and bacteria by precise modeling of the biochemical oxygen production/consumption and the resultant hypoxia, and (5) the carbon transport by integration with the hydrodynamic model. EMAGIN-B.C. was applied to Tokyo Bay, a eutrophic, shallow coastal area, and reproduced the observations well. From the model outputs, it can be observed that Tokyo Bay shows functions of climate change mitigation. In the one-year carbon budget, Tokyo Bay captured 16.6% of the DIC from the atmosphere and river as organic matter by biological processes, and 3.9% of the total carbon flowing from the atmosphere and river was stored in the deeper sediment layer.

Although geographical patterns of species' sensitivity to environmental changes are defined by interacting multiple stressors, little is known about compensatory processes shaping regional differences in organismal vulnerability. Here, we examine large-scale spatial variations in biomineralization under heterogeneous environmental gradients of temperature, salinity and food availability across a 30° latitudinal range (3,334 km), to test whether plasticity in calcareous shell production and composition, from juveniles to large adults, mediates geographical patterns of resilience to climate change in critical foundation species, the mussels Mytilus edulis and M. trossulus. We find shell calcification decreased towards high latitude, with mussels producing thinner shells with a higher organic content in polar than temperate regions. Salinity was the best predictor of within-region differences in mussel shell deposition, mineral and organic composition. In polar, subpolar, and Baltic low-salinity environments, mussels produced thin shells with a thicker external organic layer (periostracum), and an increased proportion of calcite (prismatic layer, as opposed to aragonite) and organic matrix, providing potentially higher resistance against dissolution in more corrosive waters. Conversely, in temperate, higher salinity regimes, thicker, more calcified shells with a higher aragonite (nacreous layer) proportion were deposited, which suggests enhanced protection under increased predation pressure. Interacting effects of salinity and food availability on mussel shell composition predict the deposition of a thicker periostracum and organic-enriched prismatic layer under forecasted future environmental conditions, suggesting a capacity for increased protection of high-latitude populations from ocean acidification. These findings support biomineralization plasticity as a potentially advantageous compensatory mechanism conferring Mytilus species a protective capacity for quantitative and qualitative trade-offs in shell deposition as a response to regional alterations of abiotic and biotic conditions in future environments. Our work illustrates that compensatory mechanisms, driving plastic responses to the spatial structure of multiple stressors, can define geographical patterns of unanticipated species resilience to global environmental change.

Improving our ability to monitor ocean carbonate chemistry has become a priority as the ocean continues to absorb carbon dioxide from the atmosphere. This long-term uptake is reducing the ocean pH; a process commonly known as ocean acidification. The use of satellite Earth Observation has not yet been thoroughly explored as an option for routinely observing surface ocean carbonate chemistry, although its potential has been highlighted. We demonstrate the suitability of using empirical algorithms to calculate total alkalinity (AT) and total dissolved inorganic carbon (CT), assessing the relative performance of satellite, interpolated in situ, and climatology datasets in reproducing the wider spatial patterns of these two variables. Both AT and CT in situ data are reproducible, both regionally and globally, using salinity and temperature datasets, with satellite observed salinity from Aquarius and SMOS providing performance comparable to other datasets for the majority of case studies. Global root mean squared difference (RMSD) between in situ validation data and satellite estimates is 17 μmol kg−1 with bias

The Mg/Ca of planktic foraminifera Globigerinoides ruber (white) is a widely applied proxy for tropical and sub-tropical sea-surface temperature. The accuracy with which temperature can be reconstructed depends on how accurately relationships between Mg/Ca and temperature and the multiple secondary controls on Mg/Ca are known; however, these relationships remain poorly quantified under oceanic conditions. Here, we present new calibrations based on 440 sediment trap/plankton tow samples from the Atlantic, Pacific and Indian Oceans, including 130 new samples from the Bay of Bengal/Arabian Sea and the tropical Atlantic Ocean. Our results indicate temperature, salinity and the carbonate system all significantly influence Mg/Ca in G. ruber (white). We propose two calibration models: The first model assumes pH is the controlling carbonate system parameter. In this model, Mg/Ca has a temperature sensitivity of 6.0 ± 0.8 % /°C (2σ), a salinity sensitivity of 3.3 ± 2.2 % /PSU and a pH sensitivity of − 8.3 ± 7.7 % /0.1 pH units; The second model assumes carbonate ion concentration ([ CO 3 2 − ]) is the controlling carbonate system parameter. In this model, Mg/Ca has a temperature sensitivity of 6.7 ± 0.8 % /°C, a salinity sensitivity of 5.0 ± 3.0 % /PSU and a [ CO 3 2 − ] sensitivity of − 0.24 ± 0.11 % /μmol kg−1. In both models, the temperature sensitivity is significantly lower than the widely-applied sensitivity of 9.0 ± 0.6 % /°C. Application of our new calibrations to down-core data from the Last Glacial Maximum, considering whole ocean changes in salinity and carbonate chemistry, indicate a cooling of 2.4 ± 1.6 °C in the tropical oceans if pH is the controlling parameter and 1.5 ± 1.4 °C if [ CO 3 2 − ] is the controlling parameter.

Oceanic carbonate chemistry during the Cenozoic has affected the climatology, ecology, and marine geology of our planet; yet, we have limited means to know the evolution of that chemistry, due to a lack of preserved and unaltered seawater samples and a continuing paucity of proxies. Modeling is often used to address this problem; here, we offer a simple, data-driven, secular timescale, inverse model for the mean, Cenozoic, carbonate chemistry of the oceans. Inputs for the model include carbonate compensation depth (CCD), CaCO3 burial, seawater temperature, atmospheric CO2 and carbonate ion records, as well as a simple set of original, but justified, assumptions. The model retrodicts the total dissolved inorganic carbon (DIC), carbonate alkalinity (CAlk), and pH of the surface and deep waters of the ocean. The retrodicted DIC and CAlk records do not indicate any unusually elevated values in the early Cenozoic, as found in some past studies. If the CCD record from Lyle et al. (2008) is employed, the changes in DIC and CAlk appear entirely related to changes in the alkalinity input to the pelagic oceans and atmospheric CO2; however, with the CCD from Palike et al. (2012) , the increases in DIC and CAlk during the last 15 Ma reflect the effects of ocean cooling. Using either CCD-record, our model provides consistent retrodictions of the available pH record. Our results are not consistent with many past modeling assumptions, such as constancy of alkalinity in surface waters, or the ratio of shallow and deep carbonate ion concentrations. Finally, we use our results to provide new estimates of atmospheric CO2 based on Boron isotopes and find significantly lower CO2 values in the early Cenozoic than previous values.

© 2019 The Authors. Engineering in Life Sciences published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. Photosynthetic organisms developed various strategies to mitigate high light stress. For instance, aquatic organisms are able to spend excessive energy by exchanging dissolved CO2 (dCO2) and bicarbonate (HCO3-) with the environment. Simultaneous uptake and excretion of the two carbon species is referred to as inorganic carbon cycling. Often, inorganic carbon cycling is indicated by displacements of the extracellular dCO2 signal from the equilibrium value after changing the light conditions. In this work, we additionally use (i) the extracellular pH signal, which requires non- or weakly-buffered medium, and (ii) a dynamic model of carbonate chemistry in the aquatic environment to detect and quantitatively describe inorganic carbon cycling. Based on simulations and experiments in precisely controlled photobioreactors, we show that the magnitude of the observed dCO2 displacement crucially depends on extracellular pH level and buffer concentration. Moreover, we find that the dCO2 displacement can also be caused by simultaneous uptake of both dCO2 and HCO3- (no inorganic carbon cycling). In a next step, the dynamic model of carbonate chemistry allows for a quantitative assessment of cellular dCO2, HCO3-, and H+ exchange rates from the measured dCO2 and pH signals. Limitations of the method are discussed.

Decadal-scale pH trends for the open ocean are largely monotonic and controlled by anthropogenic CO2 invasion. In estuaries, though, such long-term pH trends are often obscured by a variety of other factors, including changes in net metabolism, temperature, estuarine mixing, and riverine hydrogeochemistry. In this study, we mine an extensive biogeochemical database in two North Carolina estuaries, the Neuse River estuary (NeuseRE) and New River estuary (NewRE), in an effort to deconvolute decadal-scale trends in pH and associated processes. By applying a Generalized Additive Mixed Model (GAMM), we show that temporal changes in NewRE pH were insignificant, while pH decreased significantly throughout much of the NeuseRE. In both estuaries, variations in pH were accompanied by increasing river discharge, and were independent of rising temperature. Decreases in bottom-water pH in the NeuseRE coincided with elevated primary production in surface waters, highlighting the importance of eutrophication on long-term acidification trends. Next, we used a simple mixing model to illustrate the impact of changing river discharge on estuarine carbonate chemistry. We found that increased riverine alkalinity loads to the NewRE likely buffered the impact of CO2-intrusion-induced acidification. In the NeuseRE, however, elevated dissolved inorganic carbon loads further decreased the buffering capacity, exacerbating the effects of CO2-intrusion-driven acidification. Taken together, the findings of this study show that future trajectories in estuarine pH will be shaped by complex interactions among global-scale changes in climate, regional-scale changes in precipitation patterns, and local-scale changes in estuarine biogeochemistry.

Corals exert a strong biological control over their calcification processes, but there is a lack of knowledge on their capability of long-term acclimatization to ocean acidification (OA). We used a dual geochemical proxy approach to estimate the calcifying fluid pH (pH(cf)) and carbonate chemistry of a Mediterranean coral (Balanophyllia europaea) naturally growing along a pH gradient (range: pH(TS) 8.07-7.74). The pH(cf) derived from skeletal boron isotopic composition (delta B-11) was 0.3-0.6 units above seawater values and homogeneous along the gradient (mean +/- SEM: Site 1 = 8.39 +/- 0.03, Site 2 = 8.34 +/- 0.03, Site 3 = 8.34 +/- 0.02). Also carbonate ion concentration derived from B/Ca was homogeneous [mean +/- SEM (mu mol kg(-1)): Site 1 = 579 +/- 34, Site 2 = 541 +/- 27, Site 3 = 568 +/- 30] regardless of seawater pH. Furthermore, gross calcification rate (GCR, mass of CaCO 3 deposited on the skeletal unit area per unit of time), estimated by a "bio-inorganic model" (IpHRAC), was homogeneous with decreasing pH. The homogeneous GCR, internal pH and carbonate chemistry confirm that the features of the "building blocks" - the fundamental structural components - produced by the biomineralization process were substantially unaffected by increased acidification. Furthermore, the pH up-regulation observed in this study could potentially explain the previous hypothesis that less "building blocks" are produced with increasing acidification ultimately leading to increased skeletal porosity and to reduced net calcification rate computed by including the total volume of the pore space. In fact, assuming that the available energy at the three sites is the same, this energy at the low pH sites could be partitioned among fewer calicoblastic cells that consume more energy given the larger difference between external and internal pH compared to the control, leading to the production of less building blocks (i.e., formation of pores skeleton structure, determining increased porosity). However, we cannot exclude that also dissolution may play a role in increasing porosity. Thus, the ability of scleractinian corals to maintain elevated pH(cf) relative to ambient seawater might not always be sufficient to counteract declines in net calcification under OA scenarios.

Carbon fluxes on coral reefs (net community production and net community calcification) aggregate the collective activity of all coral reef community members. This integrated approach provides powerful community-level insights, but is unable to resolve the finer-scale contributions of different reef functional groups to the community-scale rates. Tools are required to disaggregate the community-scale approaches and evaluate the performance of co-existing reef functional groups. Such assessments are necessary to improve forecasts of coral reef responses to global and local environmental change. We present results from a coral reef field study on One Tree Island reef in the Great Barrier Reef in September-October 2016 where we combined observations of total alkalinity, dissolved inorganic carbon (DIC), and the stable isotopic composition of dissolved inorganic carbon ($\delta^{13}C_{DIC}$) to estimate carbon isotopic fractionation during organic matter formation. Portions of the reef with greater abundance of non-calcifying algae fractionated DIC ~5 $\text{\textperthousand}$ more (stronger preference for $^{12}\text{C}$) during organic metabolism than did portions of the reef with a greater abundance of calcifiers. These results were consistent across a wide range of assumed isotopic fractionation factors for net calcification. We attribute the observed differences in carbon isotopic fractionation to the metabolic activities of the ecological community underlying each section of the reef, not to environmental factors such as light availability or water temperature. The patterns in carbon isotopic fractionation were generally consistent with inferred ratios of calcification to primary production in each reef zone, giving further confidence to our inference that differences in carbon isotopic fractionation can be related to differences in the ecological community on small spatial scales.

© 2018 The Authors. Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America Ocean acidification threatens many marine organisms, especially marine calcifiers. The only global-scale solution to ocean acidification remains rapid reduction in CO2emissions. Nevertheless, interest in localized mitigation strategies has grown rapidly because of the recognized threat ocean acidification imposes on natural communities, including ones important to humans. Protection of seagrass meadows has been considered as a possible approach for localized mitigation of ocean acidification due to their large standing stocks of organic carbon and high productivity. Yet much work remains to constrain the magnitudes and timescales of potential buffering effects from seagrasses. We developed a biogeochemical box model to better understand the potential for a temperate seagrass meadow to locally mitigate the effects of ocean acidification. Then we parameterized the model using data from Tomales Bay, an inlet on the coast of California, USA which supports a major oyster farming industry. We conducted a series of month-long model simulations to characterize processes that occur during summer and winter. We found that average pH in the seagrass meadows was typically within 0.04 units of the pH of the primary source waters into the meadow, although we did find occasional periods (hours) when seagrass metabolism may modify the pH by up to ±0.2 units. Tidal phasing relative to the diel cycle modulates localized pH buffering within the seagrass meadow such that maximum buffering occurs during periods of the year with midday low tides. Our model results suggest that seagrass metabolism in Tomales Bay would not provide long-term ocean acidification mitigation. However, we emphasize that our model results may not hold in meadows where assumptions about depth-averaged net production and seawater residence time within the seagrass meadow differ from our model assumptions. Our modeling approach provides a framework that is easily adaptable to other seagrass meadows in order to evaluate the extent of their individual buffering capacities. Regardless of their ability to buffer ocean acidification, seagrass meadows maintain many critically important ecosystem goods and services that will be increasingly important as humans increasingly affect coastal ecosystems.

Red coralline algae are projected to be sensitive to ocean acidification, particularly in polar oceans. As important ecosystem engineers, their potential sensitivity has broad implications, and understanding their carbon acquisition mechanisms is necessary for making reliable predictions. Therefore, we investigated the localized carbonate chemistry at the surface of Arctic coralline algae using microsensors. We report for the first time carbonate ion concentration and pH measurements ([CO3 2-]) at and above the algal surface in the microenvironment. We show that surface pH and [CO3 2-] are higher than the bulk seawater in the light, and even after hours of darkness. We further show that three species of Arctic coralline algae have efficient carbon concentrating mechanisms including direct bicarbonate uptake and indirect bicarbonate use via a carbonic anhydrase enzyme. Our results suggest that Arctic corallines have strong biological control over their surface chemistry, where active calcification occurs, and that net dissolution in the dark does not occur. We suggest that the elevated pH and [CO3 2-] in the dark could be explained by a high rate of light independent carbon fixation that reduces respiratory CO2 release. This mechanism could provide a potential adaptation to ocean acidification in Arctic coralline algae, which has important implications for future Arctic marine ecosystems.

Temperature, light and carbonate chemistry speciation all influence the growth, calcification and photosynthetic carbon fixation rates of coccolithophores to a similar degree. There have been multiple attempts to project the responses of coccolithophores to changes in carbonate chemistry, but the interaction with light and temperature remains elusive. Here we devise a simple conceptual model to derive a fit equation for coccolithophorid growth, photosynthetic carbon fixation and calcification rates in response to simultaneous changes in carbonate chemistry speciation, temperature and light conditions. The fit equation is able to account for up to 88% of the variability in measured metabolic rates. Equation projections indicate that temperature, light and carbonate chemistry speciation all have different modulating effects on both optimal growth conditions and the sensitivity of responses to extreme environmental conditions. Calculations suggest that a single extreme environmental condition (CO2, temperature, light) will reduce maximum rates regardless of how optimal the other environmental conditions may be. Thus, while the response of coccolithophores to ocean change depends on multiple variables, the one which is least optimal will have the most impact on overall rates. Finally, responses to ocean change are usually reported in terms of cellular rates. However, changes in cellular rates can be a poor predictor for assessing changes in production at the community level. We therefore introduce a new metric, the calcium carbonate production potential (CCPP), which combines the independent effects of changes in growth rate and cellular calcium carbonate content to assess how environmental changes will impact coccolith production. Direct comparison of CO2 impacts on cellular CaCO3 production rates and CCPP shows that while the former is still at 45% of its pre-industrial capacity at 1000 uatm, the latter is reduced to 10%.

The dynamics of the aragonite saturation state (Omega(arag)) were investigated in the eutrophic coastal waters of Guanabara Bay (RJ-Brazil). Large phytoplankton blooms stimulated by a high nutrient enrichment promoted the production of organic matter with strong uptake of dissolved inorganic carbon (DIC) in surface waters, lowering the concentrations of dissolved carbon dioxide (CO2aq), and increasing the pH, Omega(arag) and carbonate ion (CO32- especially during summer. The increase of Omega(arag) related to biological activity was also evident comparing the negative relationship between the Omega(arag) and the apparent utilization of oxygen (AOU), with a very close behavior between the slopes of the linear regression and the Redfield ratio. The lowest values of Omega(arag) were found at low-buffered waters in regions that receive direct discharges from domestic effluents and polluted rivers, with episodic evidences of corrosive waters (Omega(arag) < 1). This study showed that the eutrophication controlled the variations of Omega(arag) in Guanabara Bay.

Here we present a new model framework for an adjoint trajectory model of the carbon cycle, which can be used to constrain carbon dioxide emission rates over a specific time interval given only a path constraint on the fraction of carbon dioxide that remains airborne over that interval. Earth���s ocean and terrestrial biosphere act to quickly remove a large and variable portion of carbon dioxide emissions from the atmosphere, and thus measuring the atmospheric carbon dioxide concentra- tion at any given time provides limited insight into the global emission flux that is responsible for driving the time-dependent behavior of the atmospheric con- centration. Using the adjoint trajectory model presented here, we can, without having any information about the emission schedule, invoke the use of mathe- matical inverse methods to computationally search for an emission scenario that best reproduces a time series constraint of observed (or desired) atmospheric CO2 concentrations. This adjoint trajectory model utilizes a simple yet powerful 3-box transfer model to partition CO2 emissions between the atmosphere and ocean over time. The transfer functions that govern this 3-box model are also utilized to pro- vide a physical constraint on the acceptable set of emission scenario solutions. This thesis describes the governing mathematical framework of the adjoint trajectory model and provides a general algorithm for determining the unknown emission scenario that optimally reproduces the observed (or desired) atmospheric carbon dioxide trend. We show an example of the model performance in its current stage of development, and discuss its limitations and key areas for future development.

Increasing atmospheric CO2 levels have led to disastrous consequences that have impacted many people’s lives. In nature, photosynthesis is the primary sink of CO2 in the air and in the ocean. A better understanding of the light harvesting and utilization mechanisms can help us better design photosynthetic organisms or artificial photosynthetic systems to utilize and reduce CO2 levels in the natural environment. Thanks to advancements in computational biology and bioinformatics in the past decade, we are now capable of achieving this task from a new prospective, with data analysis accomplished more quantitatively and comprehensively than ever before. A marine diatom, Phaeodactylum tricornutum, was selected to be the model species in my study because of its wide range of light intensity tolerances and its capability of photoprotection to high light stress. The primary objective of this dissertation is to characterize the light utilization and photoprotection associated energy and metabolic mechanisms in this organism that allow it to have such extraordinary features. In the first chapter, the cross-compartment energy and metabolite rebalancing was investigated by flux simulation developed from physiological experimental data and genome scale metabolic modeling. In the second chapter, a novel instrument for simultaneous measurement of carbon uptake and oxygen evolution was developed to provide additional insight into the light utilization efficiencies during photoacclimation period. In the third chapter, a comprehensive study, using both classic physiology and novel machine learning approaches, was conducted to investigate the function of a high light stress related protein (LHCX1) in photoprotection during acclimation. Taken together, these chapters significantly improve our understanding of photoprotective and energy utilization mechanisms in P. tricornutum that enable their remarkable success in adaptations to varying light conditions.

Space-based observations offer unique capabilities for studying spatial and temporal dynamics of the upper ocean inorganic carbon cycle and, in turn, supporting research tied to ocean acidification (OA). Satellite sensors measuring sea surface temperature, color, salinity, wind, waves, currents, and sea level enable a fuller understanding of a range of physical, chemical, and biological phenomena that drive regional OA dynamics as well as the potentially varied impacts of carbon cycle change on a broad range of ecosystems. Here, we update and expand on previous work that addresses the benefits of space-based assets for OA and carbonate system studies. Carbonate chemistry and the key processes controlling surface ocean OA variability are reviewed. Synthesis of present satellite data streams and their utility in this arena are discussed, as are opportunities on the horizon for using new satellite sensors with increased spectral, temporal, and/or spatial resolution. We outline applications that include the ability to track the biochemically dynamic nature of water masses, to map coral reefs at higher resolution, to discern functional phytoplankton groups and their relationships to acid perturbations, and to track processes that contribute to acid variation near the land-ocean interface.

The impact of anthropogenic ocean acidification (OA) on marine ecosystems is a vital concern facing marine scientists and managers of ocean resources. Euthecosomatous pteropods (holoplanktonic gastropods) represent an excellent sentinel for indicating exposure to anthropogenic OA because of the sensitivity of their aragonite shells to the OA conditions less favorable for calcification. However, an integration of observations, experiments and modelling efforts is needed to make accurate predictions of how these organisms will respond to future changes to their environment. Our understanding of the underlying organismal biology and life history is far from complete and must be improved if we are to comprehend fully the responses of these organisms to the multitude of stressors in their environment beyond OA. This review considers the present state of research and understanding of euthecosomatous pteropod biology and ecology of these organisms and considers promising new laboratory methods, advances in instrumentation (such as molecular, trace elements, stable isotopes, palaeobiology alongside autonomous sampling platforms, CT scanning and high-quality video recording) and novel field-based approaches (i.e. studies of upwelling and CO2 vent regions) that may allow us to improve our predictive capacity of their vulnerability and/or resilience. In addition to playing a critical ecological and biogeochemical role, pteropods can offer a significant value as an early-indicator of anthropogenic OA. This role as a sentinel species should be developed further to consolidate their potential use within marine environmental management policy making.

The trace elemental composition of foraminiferal shell calcite is known to reflect the environment in which the shell was precipitated. Whereas conservative elements incorporated in foraminiferal shell carbonate reflect factors such as temperature (Mg), carbonate chemistry (B) and salinity (Na), the nutrient type elements (Ba, Cd, and possibly Zn) are useful tools to reconstruct biogeochemical cycling and past ocean circulation. Still also nutrient-type elements will be most likely influenced by factors other than their relative concentrations. Culturing benthic foraminifera under controlled carbonate chemistry conditions allows for disentanglement of impacts of different parameters of the carbon system on the elemental composition of foraminiferal calcite. Here we show that zinc incorporation in cultured specimens of the benthic foraminifer Ammonia tepida is correlated to changes in carbonate ion concentration ([CO32−]). By modeling activities of different chemical species of Zn in seawater over a range of [CO32−], we suggest that Zn2+ , rather than other relatively abundant Zn-species (e.g. ZnCO30 and ZnHCO3+) is taken up during biomineralization. Our results suggest that foraminiferal Zn/Ca might be especially useful when combined with other [CO32−] proxies, enabling reconstruction of past seawater element concentrations. Conversely, when the nutrient-type element concentrations are known, incorporation of Zn in foraminiferal shells can be used to reconstruct past sea water carbon speciation.

The present deliverable gathers and reports on the outcomes of the four parts of the first JERICO-NEXT workshop on sensors for nutrients, biology-related optical properties, variables of the marine carbonate system, and for coastal profiling. It provides descriptions of such systems and the way they are run, and critically assesses their current level of development from the specific perspective of the operations carried out routinely by the JERICO observing network, and by extension, in the general European context. Published Refereed Current

The trace elemental composition of foraminiferal shell calcite is known to reflect the environment in which the shell was precipitated. Whereas conservative elements incorporated in foraminiferal shell carbonate reflect factors such as temperature (Mg), carbonate chemistry (B) and salinity (Na), the nutrient type elements (Ba, Cd, and possibly Zn) are useful tools to reconstruct biogeochemical cycling and past ocean circulation. Still also nutrient-type elements will be most likely influenced by factors other than their relative concentrations. Culturing benthic foraminifera under controlled carbonate chemistry conditions allows for disentanglement of impacts of different parameters of the carbon system on the elemental composition of foraminiferal calcite. Here we show that zinc incorporation in cultured specimens of the benthic foraminifer Ammonia tepida is correlated to changes in carbonate ion concentration ([CO32−]). By modeling activities of different chemical species of Zn in seawater over a range of [CO32−], we suggest that Zn2+ , rather than other relatively abundant Zn-species (e.g. ZnCO30 and ZnHCO3+) is taken up during biomineralization. Our results suggest that foraminiferal Zn/Ca might be especially useful when combined with other [CO32−] proxies, enabling reconstruction of past seawater element concentrations. Conversely, when the nutrient-type element concentrations are known, incorporation of Zn in foraminiferal shells can be used to reconstruct past sea water carbon speciation.

The dynamics of the aragonite saturation state (Ωarag) were investigated in the eutrophic coastal waters of Guanabara Bay (RJ-Brazil). Large phytoplankton blooms stimulated by a high nutrient enrichment promoted the production of organic matter with strong uptake of dissolved inorganic carbon (DIC) in surface waters, lowering the concentrations of dissolved carbon dioxide (CO2aq), and increasing the pH, Ωarag and carbonate ion (CO32 −), especially during summer. The increase of Ωarag related to biological activity was also evident comparing the negative relationship between the Ωarag and the apparent utilization of oxygen (AOU), with a very close behavior between the slopes of the linear regression and the Redfield ratio. The lowest values of Ωarag were found at low-buffered waters in regions that receive direct discharges from domestic effluents and polluted rivers, with episodic evidences of corrosive waters (Ωarag < 1). This study showed that the eutrophication controlled the variations of Ωarag in Guanabara Bay.

The polar oceans are particularly vulnerable to ocean acidification; the lowering of seawater pH and carbonate mineral saturation states due to uptake of atmospheric carbon dioxide (CO2). High spatial variability in surface water pH and saturation states (Omega) for two biologically-important calcium carbonate minerals calcite and aragonite was observed in Ryder Bay, in the coastal sea-ice zone of the West Antarctic Peninsula. Glacial meltwater and melting sea ice stratified the water column and facilitated the development of large phytoplankton blooms and subsequent strong uptake of atmospheric CO2 of up to 55 mmol m(-2) day(-1) during austral summer. Concurrent high pH (8.48) and calcium carbonate mineral supersaturation (Omega aragonite similar to 3.1) occurred in the meltwater-influenced surface ocean. Biologically-induced increases in calcium carbonate mineral saturation states counteracted any effects of carbonate ion dilution. Accumulation of CO2 through remineralisation of additional organic matter from productive coastal waters lowered the pH (7.84) and caused deep-water corrosivity (Omega aragonite similar to 0.9) in regions impacted by Circumpolar Deep Water. Episodic mixing events enabled CO2-rich subsurface water to become entrained into the surface and eroded seasonal stratification to lower surface water pH (8.21) and saturation states (Omega aragonite similar to 1.8) relative to all surface waters across Ryder Bay. Uptake of atmospheric CO2 of 28 mmol m(-2) day(-1) in regions of vertical mixing may enhance the susceptibility of the surface layer to future ocean acidification in dynamic coastal environments. Spatially-resolved studies are essential to elucidate the natural variability in carbonate chemistry in order to better understand and predict carbon cycling and the response of marine organisms to future ocean acidification in the Antarctic coastal zone.

15 pages, 6 figures, supporting information https://dx.doi.org/10.1002/2017PA003155, It has been shown that the deep Eastern Equatorial Pacific (EEP) region was poorly ventilated during the Last Glacial Maximum (LGM) relative to Holocene values. This finding suggests a more efficient biological pump, which indirectly supports the idea of increased carbon storage in the deep ocean contributing to lower atmospheric CO2 during the last glacial. However, proxies related to respired carbon are needed in order to directly test this proposition. Here we present Cibicides wuellerstorfi B/Ca ratios from Ocean Drilling Program Site 1240 measured by laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) as a proxy for deep water carbonate saturation state (Δ[CO32−], and therefore [CO32−]), along with δ13C measurements. In addition, the U/Ca ratio in foraminiferal coatings has been analyzed as an indicator of oxygenation changes. Our results show lower [CO32−], δ13C, and [O2] values during the LGM, which would be consistent with higher respired carbon levels in the deep EEP driven, at least in part, by reduced deep water ventilation. However, the difference between LGM and Holocene [CO32−] observed at our site is relatively small, in accordance with other records from across the Pacific, suggesting that a “counteracting” mechanism, such as seafloor carbonate dissolution, also played a role. If so, this mechanism would have increased average ocean alkalinity, allowing even more atmospheric CO2 to be “sequestered” by the ocean. Therefore, the deep Pacific Ocean very likely stored a significant amount of atmospheric CO2 during the LGM, specifically due to a more efficient biological carbon pump and also an increase in average ocean alkalinity, We acknowledge funding by the Spanish Ministry of Economy, Industry and Competitiveness through grants CTM2009-08849 (ACDC Project) and CTM2012-32017 (MANIFEST Project), by Generalitat de Catalunya through grant 2014SGR1029 (Marine Biogeochemistry and Global Change research group), and by NERC grant NE/L006421/1. Isabel Cacho thanks the ICREA Academia program from the Generalitat de Catalunya

Climatological mean monthly distributions of pH in the total H+ scale, total CO2 concentration (TCO2), and the degree of CaCO3 saturation for the global surface ocean waters (excluding coastal areas) are calculated using a data set for pCO(2), alkalinity and nutrient concentrations in surface waters (depths