scholarly journals PyCO2SYS v1.8: marine carbonate system calculations in Python

2022 ◽  
Vol 15 (1) ◽  
pp. 15-43
Author(s):  
Matthew P. Humphreys ◽  
Ernie R. Lewis ◽  
Jonathan D. Sharp ◽  
Denis Pierrot

Abstract. Oceanic dissolved inorganic carbon (TC) is the largest pool of carbon that substantially interacts 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 the 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 written in Python, a popular scientific programming language, was previously available. 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 modelled 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 insights that guided the development of PyCO2SYS: for example, the fact that the marine carbonate system cannot be unambiguously solved from certain pairs of parameters. 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, last access: 23 December 2021) under the GNU General Public License v3, archived on Zenodo (Humphreys et al., 2021), and documented online (https://pyco2sys.readthedocs.io/en/latest/, last access: 23 December 2021).

2021 ◽  
Author(s):  
Matthew P. Humphreys ◽  
Ernie R. Lewis ◽  
Jonathan D. Sharp ◽  
Denis Pierrot

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).


2021 ◽  
Vol 3 ◽  
Author(s):  
Daniel J. Burt ◽  
Friederike Fröb ◽  
Tatiana Ilyina

Ocean Alkalinity Enhancement (OAE) simultaneously mitigates atmospheric concentrations of CO2 and ocean acidification; however, no previous studies have investigated the response of the non-linear marine carbonate system sensitivity to alkalinity enhancement on regional scales. We hypothesise that regional implementations of OAE can sequester more atmospheric CO2 than a global implementation. To address this, we investigate physical regimes and alkalinity sensitivity as drivers of the carbon-uptake potential response to global and different regional simulations of OAE. In this idealised ocean-only set-up, total alkalinity is enhanced at a rate of 0.25 Pmol a-1 in 75-year simulations using the Max Planck Institute Ocean Model coupled to the HAMburg Ocean Carbon Cycle model with pre-industrial atmospheric forcing. Alkalinity is enhanced globally and in eight regions: the Subpolar and Subtropical Atlantic and Pacific gyres, the Indian Ocean and the Southern Ocean. This study reveals that regional alkalinity enhancement has the capacity to exceed carbon uptake by global OAE. We find that 82–175 Pg more carbon is sequestered into the ocean when alkalinity is enhanced regionally and 156 PgC when enhanced globally, compared with the background-state. The Southern Ocean application is most efficient, sequestering 12% more carbon than the Global experiment despite OAE being applied across a surface area 40 times smaller. For the first time, we find that different carbon-uptake potentials are driven by the surface pattern of total alkalinity redistributed by physical regimes across areas of different carbon-uptake efficiencies. We also show that, while the marine carbonate system becomes less sensitive to alkalinity enhancement in all experiments globally, regional responses to enhanced alkalinity vary depending upon the background concentrations of dissolved inorganic carbon and total alkalinity. Furthermore, the Subpolar North Atlantic displays a previously unexpected alkalinity sensitivity increase in response to high total alkalinity concentrations.


2020 ◽  
Author(s):  
Maria Teresa Guerra ◽  
Carlos Rocha

<p>Organic and inorganic whole system metabolism for two Irish coastal areas were compared to evaluate carbonate system resilience to acidification. The two systems are characterized by contrasting watershed input types and composition. Kinvara Bay is fed by Submarine Groundwater Discharge (SGD) derived from a karstic catchment while Killary Harbour is fed by river discharge draining a siliciclastic catchment. Freshwater sources to sea have distinct Total Alkalinity (TA) and Dissolved Inorganic Carbon (DIC) concentrations, higher and lower than the open ocean, respectively, but both evidence seasonally variable low pH, ranging from 6.20 to 7.50. Retention of TA and DIC was calculated for the two areas using LOICZ methodology. In Kinvara bay, annually averaged retention of DIC was greater than for TA (5 × 10<sup>4</sup> and 1.5 × 10<sup>5</sup> mol d<sup>-1</sup>), suggesting the system is acidifying further. Conversely, Killary Harbour shows negative TA and DIC retention, with DIC:TA <1, suggesting an internal buffer against ocean acidification is operating.</p><p>Net Community Production (NCP) was calculated for both systems using Dissolved Oxygen data. Subsequently, we estimated Net Community Calcification (NCC) from the ratio between TA and DIC. NCP was always positive in Killary Harbour with an average of 318 mmol O<sub>2</sub> m<sup>-2 </sup>d<sup>-1</sup> (equivalent to 89 mol C m<sup>-2</sup> y<sup>-1</sup>). However, Kinvara Bay shows relatively lower positive NCP in spring and summer (average of 46 mmol O<sub>2</sub> m<sup>-2</sup> d<sup>-1</sup>), but negative NCP in autumn and winter. Therefore, Kinvara Bay’s Total Organic Carbon (TOC) production was low, at ~21 g m<sup>-2</sup> y<sup>-1</sup> and not enough to overcome acidification driven by the SGD source composition. These results emphasize the complexity of interactions between the drivers of coastal acidification rate, affecting our ability to accurately assess the resilience of the carbonate system in these areas to ocean acidification pressure in the future.</p>


2019 ◽  
Author(s):  
Kimberlee Baldry ◽  
Vincent Saderne ◽  
Daniel C. McCorkle ◽  
James H. Churchill ◽  
Susana Agusti ◽  
...  

Abstract. We use observations of dissolved inorganic carbon (DIC) and total alkalinity (TA) to assess the impact of ecosystem metabolic processes on coastal waters of the eastern Red Sea. A simple, single-end-member mixing model is used to account for the influence of mixing with offshore waters and evaporation/precipitation, and to model ecosystem-driven perturbations on the carbonate system chemistry of coral reefs, seagrass meadows and mangrove forests. We find that (1) along-shelf changes in TA and DIC exhibit strong linear trends that are consistent with basin-scale net calcium carbonate precipitation; (2) ecosystem-driven changes in TA and DIC are larger than offshore variations in > 85 % of sampled seagrass meadows and mangrove forests, changes which are influenced by a combination of longer water residence times and community metabolic rates; and (3) the sampled mangrove forests show strong and consistent contributions from both organic respiration and other sedimentary processes (carbonate dissolution and secondary redox processes), while seagrass meadows display more variability in the relative contributions of photosynthesis and other sedimentary processes (carbonate precipitation and oxidative processes).


2014 ◽  
Vol 11 (2) ◽  
pp. 2793-2822 ◽  
Author(s):  
M. Ribas-Ribas ◽  
V. M. C. Rérolle ◽  
D. C. E. Bakker ◽  
V. Kitidis ◽  
G. A. Lee ◽  
...  

Abstract. Four carbonate system variables were measured in surface waters during a cruise traversing northwestern European shelf seas in the summer of 2011. High resolution surface water data were collected for partial pressure of carbon dioxide (pCO2; using two independent instruments) and pHT, in addition to discrete measurements of total alkalinity and dissolved inorganic carbon. We thus overdetermined the carbonate system (four measured variables, two degrees of freedom) which allowed us to evaluate the level of agreement between the variables. Calculations of carbonate system variables from other measurements generally compared well (Pearson's correlation coefficient always ≥ 0.94; mean residuals similar to the respective uncertainties of the calculations) with direct observations of the same variables. We therefore conclude that the four independent datasets of carbonate chemistry variables were all of high quality, and as a result that this dataset is suitable to be used for the evaluation of ocean acidification impacts and for carbon cycle studies. A diurnal cycle with maximum amplitude of 41 μatm was observed in the difference between the pCO2; values obtained by the two independent analytical pCO2; systems, and this was partly attributed to irregular seawater flows to the equilibrator and partly to biological activity inside the seawater supply and one of the equilibrators. We discuss how these issues can be addressed to improve carbonate chemistry data quality on research cruises.


Ocean Science ◽  
2020 ◽  
Vol 16 (4) ◽  
pp. 847-862 ◽  
Author(s):  
Olivier Sulpis ◽  
Siv K. Lauvset ◽  
Mathilde Hagens

Abstract. Seawater absorption of anthropogenic atmospheric carbon dioxide (CO2) has led to a range of changes in carbonate chemistry, collectively referred to as ocean acidification. Stoichiometric dissociation constants used to convert measured carbonate system variables (pH, pCO2, dissolved inorganic carbon, total alkalinity) into globally comparable parameters are crucial for accurately quantifying these changes. The temperature and salinity coefficients of these constants have generally been experimentally derived under controlled laboratory conditions. Here, we use field measurements of carbonate system variables taken from the Global Ocean Data Analysis Project version 2 and the Surface Ocean CO2 Atlas data products to evaluate the temperature dependence of the carbonic acid stoichiometric dissociation constants. By applying a novel iterative procedure to a large dataset of 948 surface-water, quality-controlled samples where four carbonate system variables were independently measured, we show that the set of equations published by Lueker et al. (2000), currently preferred by the ocean acidification community, overestimates the stoichiometric dissociation constants at temperatures below about 8 ∘C. We apply these newly derived temperature coefficients to high-latitude Argo float and cruise data to quantify the effects on surface-water pCO2 and calcite saturation states. These findings highlight the critical implications of uncertainty in stoichiometric dissociation constants for future projections of ocean acidification in polar regions and the need to improve knowledge of what causes the CO2 system inconsistencies in cold waters.


2012 ◽  
Vol 9 (3) ◽  
pp. 2709-2753 ◽  
Author(s):  
F. Touratier ◽  
V. Guglielmi ◽  
C. Goyet ◽  
L. Prieur ◽  
M. Pujo-Pay ◽  
...  

Abstract. We relate here the distributions of two carbonate system key properties (total alkalinity, AT; and total dissolved inorganic carbon, CT) measured along a section in the Mediterranean Sea, going from Marseille (France) to the south of the Cyprus Island, during the 2008 BOUM cruise. The three main objectives of the present study are (1) to draw and comment on the distributions of AT and CT in the light of others properties like salinity, temperature, and dissolved oxygen, (2) to estimate the distribution of the anthropogenic CO2 (CANT) in the intermediate and the deep waters, and (3) to calculate the resulting variation of pH (acidification) since the beginning of the industrial era. Since the calculation of CANT is always an intense subject of debate, we apply two radically different approaches to estimate CANT: the very simple method TrOCA and the MIX approach, the latter being more precise but also more difficult to apply. A clear picture for the AT and the CT distributions is obtained: the mean concentration of AT is higher in the oriental basin while that of CT is higher in the occidental basin of the Mediterranean Sea, fully coherent with the previous published works. Despite of the two very different approaches we use here (TrOCA and MIX), the estimated distributions of CANT are very similar. These distributions show that the minimum of CANT encountered during the BOUM cruise is higher than 46.3 μmol kg−1 (TrOCA) or 48.8 μmol kg−1(MIX). All Mediterranean water masses (even the deepest) appear to be highly contaminated by CANT, as a result of the very intense advective processes that characterize the recent history of the Mediterranean circulation. As a consequence, unprecedented levels of acidification are reached with an estimated decrease of pH since the pre-industrial era of −0.148 to −0.061 pH unit, which places the Mediterranean Sea as one of the most acidified world marine ecosystem.


2018 ◽  
Vol 10 (4) ◽  
pp. 1901-1924 ◽  
Author(s):  
Gilles Reverdin ◽  
Nicolas Metzl ◽  
Solveig Olafsdottir ◽  
Virginie Racapé ◽  
Taro Takahashi ◽  
...  

Abstract. This paper presents the SURATLANT data set (SURveillance ATLANTique). It consists of individual data of temperature, salinity, parameters of the carbonate system, nutrients, and water stable isotopes (δ18O and δD) collected mostly from ships of opportunity since 1993 along transects between Iceland and Newfoundland (https://doi.org/10.17882/54517). We discuss how the data are validated and qualified, their accuracy, and the overall characteristics of the data set. The data are used to reconstruct seasonal cycles and interannual anomalies, in particular of sea surface salinity (SSS); inorganic nutrients; dissolved inorganic carbon (DIC); and its isotopic composition δ13CDIC, total alkalinity (At), and water isotope concentrations. Derived parameters such as fCO2 and pH are also estimated. The relation between salinity and At is estimated from these data to investigate the possibility to replace missing At when estimating other parameters of the carbonate system. When examining the average seasonal cycle in the deep ocean, in both these data with other climatologies, we find a period of small seasonal change between January and late April. On the Newfoundland shelf and continental slope, changes related with spring stratification and blooms occur earlier. The data were collected in a period of multi-decennial variability associated with the Atlantic multi-decadal variability with warming between 1994 and 2004–2007, and with the recent cooling having peaked in 2014–2016. We also observe strong salinification in 2004–2009 and fresher waters in 1994–1995 as well as since 2010 south of 54° N and in 2016–2017 north of 54° N. Indication of multi-decadal variability is also suggested by other variables, such as phosphate or DIC, but cannot be well resolved seasonally with the discrete sampling and in the presence of interannual variability. As a whole, over the 24 years, the ocean fCO2 trend (+1.9 µatm yr−1) is close to the atmospheric trend and associated with an increase in DIC (+0.77 µmol kg−1 yr−1). The data also revealed a canonical pH decrease of −0.0021 yr−1. There is also a decrease in δ13CDIC between 2005 and 2017 (in winter, −0.014 ‰ yr−1, but larger in summer, −0.042 ‰ yr−1), suggesting a significant anthropogenic carbon signal at play together with other processes (mixing, biological activity).


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mario Lebrato ◽  
Yiming V. Wang ◽  
Li-Chun Tseng ◽  
Eric P. Achterberg ◽  
Xue-Gang Chen ◽  
...  

AbstractShallow hydrothermal vents are of pivotal relevance for ocean biogeochemical cycles, including seawater dissolved heavy metals and trace elements as well as the carbonate system balance. The Kueishan Tao (KST) stratovolcano off Taiwan is associated with numerous hydrothermal vents emitting warm sulfur-rich fluids at so-called White Vents (WV) and Yellow Vent (YV) that impact the surrounding seawater masses and habitats. The morphological and biogeochemical consequences caused by a M5.8 earthquake and a C5 typhoon (“Nepartak”) hitting KST (12th May, and 2nd–10th July, 2016) were studied within a 10-year time series (2009–2018) combining aerial drone imagery, technical diving, and hydrographic surveys. The catastrophic disturbances triggered landslides that reshaped the shoreline, burying the seabed and, as a consequence, native sulfur accretions that were abundant on the seafloor disappeared. A significant reduction in venting activity and fluid flow was observed at the high-temperature YV. Dissolved Inorganic Carbon (DIC) maxima in surrounding seawater reached 3000–5000 µmol kg−1, and Total Alkalinity (TA) drawdowns were below 1500–1000 µmol kg−1 lasting for one year. A strong decrease and, in some cases, depletion of dissolved elements (Cd, Ba, Tl, Pb, Fe, Cu, As) including Mg and Cl in seawater from shallow depths to the open ocean followed the disturbance, with a recovery of Mg and Cl to pre-disturbance concentrations in 2018. The WV and YV benthic megafauna exhibited mixed responses in their skeleton Mg:Ca and Sr:Ca ratios, not always following directions of seawater chemical changes. Over 70% of the organisms increased skeleton Mg:Ca ratio during rising DIC (higher CO2) despite decreasing seawater Mg:Ca ratios showing a high level of resilience. KST benthic organisms have historically co-existed with such events providing them ecological advantages under extreme conditions. The sudden and catastrophic changes observed at the KST site profoundly reshaped biogeochemical processes in shallow and offshore waters for one year, but they remained transient in nature, with a possible recovery of the system within two years.


2009 ◽  
Vol 6 (10) ◽  
pp. 2145-2153 ◽  
Author(s):  
K. G. Schulz ◽  
J. Barcelos e Ramos ◽  
R. E. Zeebe ◽  
U. Riebesell

Abstract. Increasing atmospheric carbon dioxide (CO2) through human activities and invasion of anthropogenic CO2 into the surface ocean alters the seawater carbonate chemistry, increasing CO2 and bicarbonate (HCO3−) at the expense of carbonate ion (CO32−) concentrations. This redistribution in the dissolved inorganic carbon (DIC) pool decreases pH and carbonate saturation state (Ω). Several components of the carbonate system are considered potential key variables influencing for instance calcium carbonate precipitation in marine calcifiers such as coccolithophores, foraminifera, corals, mollusks and echinoderms. Unravelling the sensitivities of marine organisms and ecosystems to CO2 induced ocean acidification (OA) requires well-controlled experimental setups and accurate carbonate system manipulations. Here we describe and analyse the chemical changes involved in the two basic approaches for carbonate chemistry manipulation, i.e. changing DIC at constant total alkalinity (TA) and changing TA at constant DIC. Furthermore, we briefly introduce several methods to experimentally manipulate DIC and TA. Finally, we examine responses obtained with both approaches using published results for the coccolithophore Emiliania huxleyi. We conclude that under most experimental conditions in the context of ocean acidification DIC and TA manipulations yield similar changes in all parameters of the carbonate system, which implies direct comparability of data obtained with the two basic approaches for CO2 perturbation.


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