PyCO2SYS v1.8: marine carbonate system calculations in Python

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).

Pemodelan Sistem Karbonat di Laut Jawa

<p class="Papertext"><strong>Modeling Carbonate System in the Java Sea</strong>. Besides the global fossil fuel burning activities, forest fires in Kalimantan could potentially increase atmospheric CO₂ concentrations, impacting air-sea CO₂ gas exchange in the Java Sea and changing the balance of the marine carbonate system. This study uses a marine carbonate model to examine the processes that control CO₂ flux in the Java Sea and their relationship to CO₂ increase in the atmosphere. OCMIP-2 (<em>Ocean Carbon-Cycle Model Intercomparison Model Project, Phase-2</em>) is performed in this marine carbonate model coupled with the marine ecosystem model. The model results show that the quantity of carbon air flux differs during February and October 2000. More considerable flux is produced during February 2000, where the wind speeds are higher than in October 2000. However, the wind speeds have less impact when the CO₂ level in the atmosphere rises significantly. Due to the influence of a relatively high surface temperature in the tropical Java sea, the Java Sea functions as a carbon source to the atmosphere in general. In this case, the role of the <em>solubility pump</em> is more significant than that of biological processes in carbon absorption. Moreover, increased CO₂ in the atmosphere could alter the partial pressure equilibrium. In the case of 2002 forest fires (atmospheric CO₂ = 460 ppm), the carbon source of the Java Sea was less than before forest fires and even became carbon sink when atmospheric CO₂ rose to 1135.2 ppm based on the highest SSP scenario in 2100. This modeling also reveals marine acidification issues and could rapidly assess the future changes in marine ecosystems due to CO₂ levels rising in the atmosphere.</p>

Submarine Groundwater and River Discharges Affect Carbon Cycle in a Highly Urbanized and River-Dominated Coastal Area

Riverine carbon flux to the ocean has been considered in estimating coastal carbon budgets, but submarine groundwater discharge (SGD) has long been ignored. In this paper, the effects of both SGD and river discharges on the carbon cycle were investigated in the Guangdong-HongKong-Macao Greater Bay Area (GBA), a highly urbanized and river-dominated coastal area in China. SGD-derived nitrate (NO3–), dissolved organic carbon (DOC), and dissolved inorganic carbon (DIC) fluxes were estimated using a radium model to be (0.73–16.4) × 108 g/d, (0.60–9.94) × 109 g/d, and (0.77–3.29) × 1010 g/d, respectively. SGD-derived DOC and DIC fluxes are ∼2 times as great as riverine inputs, but SGD-derived NO3– flux is one-fourth of the riverine input. The additional nitrate and carbon inputs can stimulate new primary production, enhance biological pump efficiency, and affect the balance of the carbonate system in marine water. We found that SGD in the studied system is a potential net source of atmospheric CO2 with a flux of 1.46 × 109 g C/d, and river, however, is a potential net sink of atmospheric CO2 with a flux of 3.75 × 109 g C/d during the dry winter season. Two conceptual models were proposed illustrating the major potential processes of the carbon cycle induced by SGD and river discharges. These findings from this study suggested that SGD, as important as rivers, plays a significant role in the carbon cycle and should be considered in carbon budget estimations at regional and global scales future.

The Gulf of St. Lawrence Biogeochemical Model: A Modelling Tool for Fisheries and Ocean Management

The goal of this paper is to give a detailed description of the coupled physical-biogeochemical model of the Gulf of St. Lawrence that includes dissolved oxygen and carbonate system components, as well as a detailed analysis of the riverine contribution for different nitrogen and carbonate system components. A particular attention was paid to the representation of the microbial loop in order to maintain the appropriate level of the different biogeochemical components within the system over long term simulations. The skill of the model is demonstrated using in situ data, satellite data and estimated fluxes from different studies based on observational data. The model reproduces the main features of the system such as the phytoplankton bloom, hypoxic areas, pH and calcium carbonate saturation states. The model also reproduces well the estimated transport of nitrate from one region to the other. We revisited previous estimates of the riverine nutrient contribution to surface nitrate in the Lower St. Lawrence Estuary using the model. We also explain the mechanisms that lead to high ammonium concentrations, low dissolved oxygen, and undersaturated calcium carbonate conditions on the Magdalen Shallows.

Stratigraphy and petrophysical characteristics of Lower Paleocene cool-water carbonates, Faxe quarry, Denmark

The Faxe limestone quarry in eastern Denmark exposes Danian (Lower Paleocene) cool-water carbonate deposits. They constitute remnants of an apparent build-up that covers about 12 km2 today. The Danian deposits at Faxe are conspicuous due to their pronounced thickness of coral limestone relative to the regional carbonate system. In the Faxe quarry, scleractinian corals are uniquely exposed in up to 30 m high mounds. The rapid accumulation of scleractinians combined with induration of the mounds may locally have protected the limestone from Quaternary glacial erosion and created a Danian thickness anomaly at Faxe. The position of Faxe above a local fault-bounded basement high and the extent of coral limestone has been better defined by new mapping. A mapped lithostratigraphic surface in the quarry reveals the large-scale organisation of nested bryozoan mounds on three elongated ridges striking NW–SE. The main scleractinian coral mounds are located above this horizon. Data for reservoir characterisation, mainly of the bryozoan mounds, were collected as photographs of the outcrop, petrophysical and petrographical data from cored boreholes, and as ground-penetrating radar sections. Old boreholes and measured sections were used to reconstruct the build-up, and new nannofossil data allow a discussion of stratigraphy and accumulation rate. The petrophysical data show that common mound-building bryozoan packstone has higher permeability and lower capillary entry pressure than chalk, whereas less commonly occurring grain-dominated packstone and grainstone deposits from local higher-energy sites of the mound complex were found to have reduced amounts of coccolith mud, significantly higher permeability and a higher degree of lithification. Based on biostratigraphic age constraints, correlation of flint – limestone couplets and recog-nised hierarchical patterns, we develop a cyclostratigraphy for the middle Danian and suggest that cyclicity in lithology and petrophysical characteristics of bryozoan limestone are controlled by precession and eccentricity of the orbit of the Earth.