Using Gaussian Process Regression to disentangle marine carbonate system trends and variability

Abstract. Oceanic dissolved inorganic carbon (TC) is the largest pool of carbon that interacts considerably with the atmosphere on human timescales. Oceanic TC is increasing through uptake of anthropogenic carbon dioxide (CO2), and seawater pH is decreasing as a consequence. Both the exchange of CO2 between ocean and atmosphere and the pH response are governed by a set of parameters that interact through chemical equilibria, collectively known as the marine carbonate system. To investigate these processes, at least two of the marine carbonate system's parameters are typically measured – most commonly, two from TC, total alkalinity (AT), pH, and seawater CO2 fugacity (fCO2; or its partial pressure, pCO2, or its dry-air mole fraction, xCO2) – from which the remaining parameters can be calculated and the equilibrium state of seawater solved. Several software tools exist to carry out these calculations, but no fully functional and rigorously validated tool was previously available for Python, a popular scientific programming language. Here, we present PyCO2SYS, a Python package intended to fill this capability gap. We describe the elements of PyCO2SYS that have been inherited from the existing CO2SYS family of software and explain subsequent adjustments and improvements. For example, PyCO2SYS uses automatic differentiation to solve the marine carbonate system and calculate chemical buffer factors, ensuring that the effect of every solute and reaction is accurately included in all its results. We validate PyCO2SYS with internal consistency tests and comparisons against other software, showing that PyCO2SYS produces results that are either virtually identical or different for known reasons, with the differences negligible for all practical purposes. We discuss new insights that arose during the development process, for example that the marine carbonate system cannot be unambiguously solved from the total alkalinity and carbonate ion parameter pair. Finally, we consider potential future developments to PyCO2SYS and discuss the outlook for this and other software for solving the marine carbonate system. The code for PyCO2SYS is distributed via GitHub ( https://github.com/mvdh7/PyCO2SYS ) under the GNU General Public License v3, archived on Zenodo (Humphreys et al., 2021), and documented online ( https://PyCO2SYS.readthedocs.io ).

Emissions of anthropogenic carbon dioxide (CO2) to the atmosphere and the consequent effects of climate change and ocean acidification on coral reef ecosystems have motivated significant interest in describing and understanding the CO2–carbonic acid system of diverse coral reef environments. Although numerous studies have been successful in monitoring reef metabolism both in the field and in the laboratory, physical and biological forcings produce distinct conditions among environments. Due to the geographic isolation and associated difficulties with measuring marine carbon chemistry in waters of the Papahānaumokuākea Marine National Monument (PMNM), relatively few studies have described the CO2–carbonic acid system and carbonate saturation state gradients of these waters. Yet, PMNM remains one of the largest conservation areas in the world with extensive and diverse coral reef ecosystems that could offer valuable insight into our current and future understanding about regional and global impacts of ocean acidification. In order to provide a broad overview of latitudinal trends and features of the marine carbon system in PMNM waters, continuous measurements for surface seawater fugacity of CO2 (fCO2) and pH were collected during August 2011 and July 2012 cruises of the NOAA Ship Hi’ialakai. These measurements indicate that pH and fCO2 are three times more variable in nearshore monument waters relative to open ocean transect measurements. This variability can be observed up to 50 km away from the nearest reef and is likely the result of the direct and significant impact of coral reef metabolism on marine carbon chemistry around the islands and atolls. The relationship between total alkalinity and dissolved inorganic carbon is consistent with net calcification which creates an alkalinity sink throughout PMNM waters. Additionally, our measurements show clear latitudinal trends in fCO2, pH, and aragonite saturation state that are influenced by environmental forcings, including temperature, wind speed, and residence time of the water. Collectively, our results suggest that coral reefs located at the northernmost atolls of PMNM may be the most susceptible to the adverse impacts of climate change and ocean acidification.

Temporal variations in the surface aragonite saturation state of the Yellow Sea: Observations at the Socheongcho Ocean Research Station during 2017–2022

Based on measurements from the WOCE/JGOFS global CO2 survey, the CLIVAR/CO2 Repeat Hydrography Program and the Canadian Line P survey, we have observed an average decrease of 0.34% yr−1 in the saturation state of surface seawater in the Pacific Ocean with respect to aragonite and calcite. The upward migrations of the aragonite and calcite saturation horizons, averaging about 1 to 2 m yr−1, are the direct result of the uptake of anthropogenic CO2 by the oceans and regional changes in circulation and biogeochemical processes. The shoaling of the saturation horizon is regionally variable, with more rapid shoaling in the South Pacific where there is a larger uptake of anthropogenic CO2. In some locations, particularly in the North Pacific Subtropical Gyre and in the California Current, the decadal changes in circulation can be the dominant factor in controlling the migration of the saturation horizon. If CO2 emissions continue as projected over the rest of this century, the resulting changes in the marine carbonate system would mean that many coral reef systems in the Pacific would no longer be able to sustain a sufficiently high rate of calcification to maintain the viability of these ecosystems as a whole, and these changes perhaps could seriously impact the thousands of marine species that depend on them for survival.

Abstract. The largest pH decline and widespread undersaturation with respect to aragonite in this century due to uptake of anthropogenic carbon dioxide in the Arctic Ocean have been projected. The reductions in pH and aragonite saturation state in the Arctic Ocean have been caused by the melting of sea ice as well as by an increase in the concentration of atmospheric carbon dioxide. Therefore, future projections of pH and aragonite saturation in the Arctic Ocean will be affected by how rapidly the reduction in sea ice occurs. The observed recent Arctic sea-ice loss has been more rapid than projected by many of the climate models that contributed to the Intergovernmental Panel on Climate Change Fourth Assessment Report. In this study, the impact of sea-ice reduction rate on projected pH and aragonite saturation state in the Arctic surface waters was investigated. Reductions in pH and aragonite saturation were calculated from the outputs of two versions of an Earth system model with different sea-ice reduction rates under similar CO2 emission scenarios. The newer model version projects that Arctic summer ice-free condition will be achieved by the year 2040, and the older version predicts ice-free condition by 2090. The Arctic surface water was projected to be undersaturated with respect to aragonite in the annual mean when atmospheric CO2 concentration reaches 513 (606) ppm in year 2046 (2056) in new (old) version. At an atmospheric CO2 concentration of 520 ppm, the maximum differences in pH and aragonite saturation state between the two versions were 0.1 and 0.21 respectively. The analysis showed that the decreases in pH and aragonite saturation state due to rapid sea-ice reduction were caused by increases in both CO2 uptake and freshwater input. Thus, the reductions in pH and aragonite saturation state in the Arctic surface waters are significantly affected by the difference in future projections for sea-ice reduction rate. Our results suggest that the future reductions in pH and aragonite saturation state could be significantly faster than previously projected if the sea-ice reduction in the Arctic Ocean keeps its present pace.

Cadmium is one of the major heavy metal pollutions in coastal waters, and it is well known that cadmium at trace concentration is toxic to macroalgae. Change in marine carbonate system and ocean acidification caused by elevated atmospheric CO2 also alter physiological characteristics of macroalgae. However, less research is focused on the combined impacts of elevated CO2 and cadmium pollution on the growth and physiology in macroalgae. In this study, the maricultivated macroalga Pyropia haitanensis (Rhodophyta) was cultured at three levels of Cd2+ (control, 4 and 12mgL-1) and two concentrations of CO2, the ambient CO2 (AC, 410ppm) and elevated CO2 (HC, 1100ppm). The results showed that 12mgL-1 Cd2+ significantly suppressed the relative growth rate and superoxide dismutase activity in AC-grown P. haitanensis, while such inhibition extents by Cd2+ were alleviated in HC-grown algae. Cd2+ had no effects on efficiency of electron transport (α) and maximum electron transport rate (ETRmax), but α was increased by elevated CO2. Cd2+ dramatically suppressed the maximum net photosynthesis oxygen evolution rate (NPRm) and the minimum saturation irradiance (Ik) when the algal thalli were grown at AC, while such suppression of NPRm by Cd2+ was much decreased when the thalli were grown at HC. Collectively, our results suggested that elevated CO2 would alleviate Cd2+ toxicity on P. haitanensis.

Abstract. The coastal ecosystem of the Gulf of Alaska (GOA) is especially vulnerable to the effects of ocean acidification and climate change. Detection of these long-term trends requires a good understanding of the system’s natural state. The GOA is a highly dynamic system that exhibits large inorganic carbon variability on subseasonal to interannual timescales. This variability is poorly understood due to the lack of observations in this expansive and remote region. We developed a new model setup for the GOA that couples the three-dimensional Regional Oceanic Model System (ROMS) and the Carbon, Ocean Biogeochemistry and Lower Trophic (COBALT) ecosystem model. To improve our conceptual understanding of the system, we conducted a hindcast simulation from 1980 to 2013. The model was explicitly forced with temporally and spatially varying coastal freshwater discharges from a high-resolution terrestrial hydrological model, thereby affecting salinity, alkalinity, dissolved inorganic carbon, and nutrient concentrations. This represents a substantial improvement over previous GOA modeling attempts. Here, we evaluate the model on seasonal to interannual timescales using the best available inorganic carbon observations. The model was particularly successful in reproducing observed aragonite oversaturation and undersaturation of near-bottom water in May and September, respectively. The largest deficiency in the model is its inability to adequately simulate springtime surface inorganic carbon chemistry, as it overestimates surface dissolved inorganic carbon, which translates into an underestimation of the surface aragonite saturation state at this time. We also use the model to describe the seasonal cycle and drivers of inorganic carbon parameters along the Seward Line transect in under-sampled months. Model output suggests that the majority of the near-bottom water along the Seward Line is seasonally undersaturated with respect to aragonite between June and January, as a result of upwelling and remineralization. Such an extensive period of reoccurring aragonite undersaturation may be harmful to ocean acidification-sensitive organisms. Furthermore, the influence of freshwater not only decreases the aragonite saturation state in coastal surface waters in summer and fall, but it simultaneously decreases the surface partial pressure of carbon dioxide (pCO2), thereby decoupling the aragonite saturation state from pCO2. The full seasonal cycle and geographic extent of the GOA region is under-sampled, and our model results give new and important insights for months of the year and areas that lack in situ inorganic carbon observations.

Rising temperatures and ocean acidification due to anthropogenic climate change pose ominous threats to coral reef ecosystems in the Gulf of Mexico (GoM) and the western Caribbean Sea. Unfortunately, the once structurally complex coral reefs in the GoM and Caribbean have dramatically declined since the 1970s; relatively few coral reefs still exhibit a mean live coral cover of >10%. Additional work is needed to characterize future climate stressors on coral reefs in the GoM and the Caribbean Sea. Here, we use climate model simulations spanning the period of 2015–2100 to partition and assess the individual impacts of climate stressors on corals in the GoM and the western Caribbean Sea. We use a top‐down modeling framework to diagnose future projected changes in thermal stress and ocean acidification and discuss its implications for coral reef ecosystems. We find that ocean temperatures increase by 2°C–3°C over the 21st century, and surpass reported regional bleaching thresholds by mid‐century. Whereas ocean acidification occurs, the rate and magnitude of temperature changes outpace and outweigh the impacts of changes in aragonite saturation state. A framework for quantifying and communicating future risks in the GoM and Caribbean using reef risk projection maps is discussed. Without substantial mitigation efforts, the combined impact of increasing ocean temperatures and acidification are likely to stress most existing corals in the GoM and the Caribbean, with widespread economic and ecological consequences.

As a consequence of anthropogenic CO2-driven ocean acidification (OA), coastal waters are becoming increasingly challenging for calcifiers due to reductions in saturation states of calcium carbonate (CaCO3) minerals. The response of calcification rate is one of the most frequently investigated symptoms of OA. However, OA may also result in poor quality calcareous products through impaired calcification processes despite there being no observed change in calcification rate. The mineralogy and ultrastructure of the calcareous products under OA conditions may be altered, resulting in changes to the mechanical properties of calcified structures. Here, the warm water biofouling tubeworm, Hydroides elegans, was reared from larva to early juvenile stage at the aragonite saturation state (ΩA) for the current pCO2 level (ambient) and those predicted for the years 2050, 2100 and 2300. Composition, ultrastructure and mechanical strength of the calcareous tubes produced by those early juvenile tubeworms were examined using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) and nanoindentation. Juvenile tubes were composed primarily of the highly soluble CaCO3 mineral form, aragonite. Tubes produced in seawater with aragonite saturation states near or below one had significantly higher proportions of the crystalline precursor, amorphous calcium carbonate (ACC) and the calcite/aragonite ratio dramatically increased. These alterations in tube mineralogy resulted in a holistic deterioration of the tube hardness and elasticity. Thus, in conditions where ΩA is near or below one, the aragonite-producing juvenile tubeworms may no longer be able to maintain the integrity of their calcification products, and may result in reduced survivorship due to the weakened tube protection.

Biotic processes in the ocean play a crucial role in driving and mediating natural long-term ocean carbon storage. IPCC assessment exercises find high uncertainty, and therefore low confidence, around the magnitude and sign of change in future ocean carbon storage. This uncertainty is due to a lack of mechanistic understanding of relevant biological processes and/ or a paucity of observational data which limits robust parameterisations in global ocean biogeochemical models. Our study aims to identify and prioritise the processes that have a strong impact on future ocean carbon storage, with tractability from both a modelling and observational perspective. These processes could be the focus of future studies that aim to improve parameterisations in global biogeochemical models used in Earth System Models. We undertook a gap analysis to identify key processes and highlight future research priorities around three areas: net primary production (NPP), interior remineralisation and alkalinity. Here we evaluate CMIP6 model projections to 2100 under the high emissions SSP5-8.5 scenario to determine both the spread and uncertainty in NPP, particulate organic carbon transfer efficiency through the ocean interior and surface salinity-normalised alkalinity. We undertook a model interrogation of which processes are represented, their level of parameterised complexity and the variability in the parameterisation approach. Our analysis shows that CMIP6 models generally agree on the sign of change for transfer efficiency, but display a wide spread for NPP and salinity-normalised alkalinity by the end of the 21st century. Combining our analysis of CMIP6 models and gaps in knowledge allows the potential key processes and uncertainties driving future changes in key biological components of the ocean carbon cycle to be identified. By highlighting the potential gaps that require attention, the representation of biological processes in global ocean biogeochemical models can be improved in future modelling efforts. 

We demonstrate that the global cooling resulting from a range of nuclear conflict scenarios would temporarily increase the pH in the surface ocean by up to 0.06 units over a 5‐year period, briefly alleviating the decline in pH associated with ocean acidification. Conversely, the global cooling dissolves atmospheric carbon into the upper ocean, driving a 0.1 to 0.3 unit decrease in the aragonite saturation state ( ) that persists for 10 years. The peak anomaly in pH occurs 2 years post conflict, while the anomaly peaks 4‐ to 5‐years post conflict. The decrease in would exacerbate a primary threat of ocean acidification: the inability of marine calcifying organisms to maintain their shells/skeletons in a corrosive environment. Our results are based on sensitivity simulations conducted with a state‐of‐the‐art Earth system model integrated under various black carbon (soot) external forcings. Our findings suggest that regional nuclear conflict may have ramifications for global ocean acidification.

The spatiotemporal variabilities and drivers of ocean acidification (OA) metrics, [H+], pH, and aragonite saturation state (Ωarag) across environmental gradients remain poorly constrained. We use a novel high‐precision measurement of underway pH to investigate the hemispheric‐scale distributions of OA metrics from East Asia to the Arctic Ocean. While temperature and its induced air‐sea gas exchange fundamentally control the OA metrics distributions, we show that biological activity exerts the most prominent but different modifications on pH and Ωarag patterns. Strong photosynthesis counteracts the temperature‐driven pH pattern but reinforces that of Ωarag. Ice melt‐induced dilution in the Arctic Ocean additionally strengthens the Ωarag‐temperature relationship but insignificantly affects [H+] and pH. This study provides the first coherent assessment of comprehensive processes on OA metrics across large spatial regions, and highlights the potential of sea‐ice melt in changing Ωarag distribution, which should be included by Earth system models projecting future climate change.

Regulation of air-sea CO2 flux and aragonite saturation state in coral reef ecosystems along the eastern coast of Hainan Island, China.

The global decrease in seawater pH known as ocean acidification has important ecological consequences and is an imminent threat for numerous marine organisms. Even though the deep sea is generally considered to be a stable environment, it can be dynamic and vulnerable to anthropogenic disturbances including increasing temperature, deoxygenation, ocean acidification and pollution. Lophelia pertusa is among the better-studied cold-water corals but was only recently documented along the US West Coast, growing in acidified conditions. In the present study, coral fragments were collected at ∼300 m depth along the southern California margin and kept in recirculating tanks simulating conditions normally found in the natural environment for this species. At the collection site, waters exhibited persistently low pH and aragonite saturation states (Ωarag) with average values for pH of 7.66 ± 0.01 and Ωarag of 0.81 ± 0.07. In the laboratory, fragments were grown for three weeks in “favorable” pH/Ωarag of 7.9/1.47 (aragonite saturated) and “unfavorable” pH/Ωarag of 7.6/0.84 (aragonite undersaturated) conditions. There was a highly significant treatment effect (P < 0.001) with an average% net calcification for favorable conditions of 0.023 ± 0.009% d−1 and net dissolution of −0.010 ± 0.014% d-1 for unfavorable conditions. We did not find any treatment effect on feeding rates, which suggests that corals did not depress feeding in low pH/ Ωarag in an attempt to conserve energy. However, these results suggest that the suboptimal conditions for L. pertusa from the California margin could potentially threaten the persistence of this cold-water coral with negative consequences for the future stability of this already fragile ecosystem.

An approach was developed to help evaluate and predict the combined effects of ocean acidification and deoxygenation on calcifying organisms along the coast of Japan. The Coastal and Regional Ocean COmmunity (CROCO) modeling system was set up to couple the Regional Ocean Modeling System (ROMS) to the Pelagic Interaction Scheme for Carbon and Ecosystem Studies (PISCES) biogeochemical model and used to reproduce physical and biochemical processes in the area around Miyako Bay, Iwate Prefecture, Japan. Future scenario cases were also set up, which used initial and boundary conditions based on Future Ocean Regional Projection (FORP) simulations. Present day simulations were able to reproduce the general features of observed physical and biochemical parameters, except for some rapid decreases in salinity, pH and aragonite saturation state (Ωarag). This suggests that more local factors which have not been introduced into the model, such as submarine groundwater discharge, may be involved, or that river inputs may be underestimated. Results of the future projections suggest a significant impact of global warming and ocean acidification on calcifying organisms for the worst case of climate change under the Representative Concentration Pathway (RCP) 8.5 scenario. In particular, it is feared that values of Ωaragwould approach the critical level for calcifying organisms (Ωarag&amp;lt; 1.1) throughout the year, under which decreased larval shell lengths and malformation have been observed experimentally for the locally grownHaliotis discus hannai(Ezo Abalone) species. However, these findings may not be true for a different coastal locality, and this study highlights and continues to stress the importance of developing model setups capable of incorporating both regional and local factors affecting ocean acidification and deoxygenation.