PyCO2SYS: marine carbonate system calculations in Python

Substantial natural variability can obscure the detection of anthropogenic long-term trends in the marine carbonate system (e.g., ocean acidification). Yet the magnitude of the trends and variability remains poorly constrained due to limited marine carbonate system observations. Here, we use a Bayesian machine-learning approach based on Gaussian Process Regression (GPR) to decompose total variability of ocean acidification-related variables into seasonal, interannual and long-term components. The method is first applied to three decades of observations from the Line P carbon program, the longest marine carbonate system timeseries in the Northeast Pacific (1990-2019), typically taking samples three times per year. We found that over the period from 1990 to 2019, the local oceanic uptake of anthropogenic carbon dioxide from the atmosphere was the main driver of long-term changes in the marine carbonate system, including acidification. The seasonal cycle of dissolved inorganic carbon and the aragonite saturation state (both indicators of ocean acidification) was the dominant contributor to total variability in the top 60-70 m of the water column, with a mean surface seasonal amplitude of 35 ± 3 µmol kg−1 and 0.31 ± 0.04, respectively. In this depth range, the magnitude of the interannual variability was at least half of the seasonal variability for most variables. We then apply GPR to output from a global ocean biogeochemical model subsampled as per availability of observations, to assess the observational effort required to detect future ocean carbon trends, with a particular focus on detecting signals related to potential marine carbon dioxide removal interventions.

The marine carbonate system is influenced by anthropogenic CO2 uptake, biogeochemical processes, and physical changes that involve freshwater input and removal. Two frequently used parameters to quantify seawater carbonate system are total alkalinity (TA) and total dissolved inorganic carbon (DIC). To account for the physical changes, both TA and DIC are usually normalized to a reference salinity (i.e., nTA and nDIC), and then the relationship between nTA and nDIC is used to identify major biogeochemical processes that regulate the carbonate system, based on process‐specific reaction stoichiometry. However, the theoretical basis of this interpretation has not been holistically examined. In this study, we validated this method under idealized conditions and discussed the associated assumptions and limitations. Furthermore, we applied this method to interpret field TA and DIC data from a lagoonal estuary in the northwestern Gulf of Mexico. Our results demonstrated that evaluating field data that encompass multiple stations and time periods could be problematic. In addition, various combinations of biogeochemical processes can lead to the same nTA–nDIC relationship, even though the relative importance of each individual process may vary significantly. Therefore, the stoichiometric relationship relying solely on TA and DIC data is not a definitive approach for uncovering dominant biogeochemical processes. Instead, measurements of process‐specific parameters are necessary.

Abstract. Autonomous sensors are required for a comprehensive documentation of the changes in the marine carbon system and thus to differentiate between its natural variability and anthropogenic impacts. Spectrophotometric determination of pH – a key variable of the seawater carbon system – is particularly suited to achieve precise and drift-free measurements. However, available spectrophotometric instruments are not suitable for integration into automated measurement systems (e.g. FerryBox) since they do not meet the major requirements of reliability, stability, robustness and moderate cost. Here we report on the development and testing of a~new indicator-based pH sensor that meets all of these requirements. This sensor can withstand the rough conditions during long-term deployments on ships of opportunity and is applicable to the open ocean as well as to coastal waters with a complex matrix and highly variable conditions. The sensor uses a high resolution CCD spectrometer as detector connected via optical fibers to a custom-made cuvette designed to reduce the impact of air bubbles. The sample temperature can be precisely adjusted (25 °C ± 0.006 °C) using computer-controlled power supplies and Peltier elements thus avoiding the widely used water bath. The overall setup achieves a measurement frequency of 1 min−1 with a precision of ±0.0007 pH units, an average offset of +0.0005 pH units to a reference system, and an offset of +0.0081 pH units to a certified standard buffer. Application of this sensor allows monitoring of seawater pH in autonomous underway systems, providing a key variable for characterization and understanding of the marine carbon system.

Using calculations based on the marine carbon system and on modelling, the sensitivity of Baltic Sea surface pH was examined. Transient long-term calculations demonstrated that the marine carbon system adjusts to lateral boundary conditions within some decades, as does salinity. Climate changes in temperature or salinity will only marginally affect the acid–base (pH) balance. Wetter or dryer climate will also play a minor role in the pH balance. The direct effect on seawater pH of acid precipitation over the Baltic Sea surface was demonstrated to be small. Acidification due to river transport of dissolved organic carbon (DOC) into the marine system seems marginal although mineralization of terrestrial DOC may cause extra marine acidification, but the effect has yet to be quantified. Increased nutrient load may increase the amplitude in the pH seasonal cycle and increase the acidification during winter time. Fossil fuel burning is likely to have both a direct and indirect effect through increased CO2 levels, altering seawater pH as well as changing the river chemistry. This may severely threaten some species in the Baltic Sea, particularly in the Northern Baltic.

Atmospheric carbon dioxide concentrations (pCO2) beyond ice core records have been reconstructed from δ11B derived from planktic foraminifera found in equatorial sediment cores. Here, I applied a carbon cycle model over the Plio‐Pleistocene to evaluate the assumptions leading to these numbers. During glacials times, simulated atmospheric pCO2 was unequilibrated with pCO2 in the equatorial surface ocean by up to 35 ppm while the δ11B‐based approaches assume unchanged (quasi)equilibrium between both. In the Pliocene, δ11B‐based estimates of surface ocean pH are lower in the Pacific than in the Atlantic resulting in higher calculated pCO2. This offset in pH between ocean basins is not supported by models. To calculate pCO2 in surface waters out of the δ11B‐based pH some assumptions on either total alkalinity or dissolved inorganic carbon are necessary. However, the assumed values of these under‐constrained variables were according to my results partly inconsistent with chemically possible combinations within the marine carbonate system. The model results show glacial/interglacial variability in total alkalinity of the order of 100 μmol/kg, which is rarely applied to proxy reconstructions. Simulated atmospheric pCO2 is tightly (r2 > 0.9) related to equatorial surface‐ocean pH, which can be used for consistency checks. Long‐term trends in volcanic CO2 outgassing and the strength of the continental weathering fluxes are still unconstrained, allowing for a wide range of possible atmospheric pCO2 across the Plio‐Pleistocene. Nevertheless, this carbon cycle analysis suggests that reported atmospheric pCO2 above 500 ppm in the Pliocene might, for various reasons, need to be revised to smaller numbers.

Vargas and collaborators (Vargas et al., 2018), therein V2018, reported measurements of pH, total alkalinity (AT), dissolved inorganic carbon (CT), dissolved oxygen (DO) and other hydrographic variables along a portion of the Strait of Magellan and associated fjords during the spring of 2010. Using the measured values of AT and pH to calculate the partial pressure of CO2 (pCO2), they showed that DO supersaturated waters in the upper 50 m depth were often associated with pCO2 higher than atmospheric CO2 levels. Here we show that this anomalous pattern arises because V2018′s carbonate system parameters were apparently incorrectly calculated, resulting in positively biased pCO2 values. AT measurements in this layer were often higher than the marine end‐member, which could indicate an additional source of bias. Biased carbonate system parameters used by V2018 imply a sub‐estimation of the capacity of CO2 uptake, with important consequences for local capacity to modulate the potential deleterious effects of freshening and ocean acidification on fjord biota. The critical analysis of the global sources of uncertainty in carbonate‐system parameters, and evaluation of internal and external consistency (i.e., with complementary hydrographic information or with previous reports), are necessary to detect bias, and generate data with sufficient quality to study the effect of ocean acidification on marine ecosystems (GOA‐ON, 2019).

The land-sea interface is characterized by rapid changes in thermodynamics constants and is influenced by local metabolic processes, watershed characteristics, tidal forcing and anthropogenic pressures. As a result, the aquatic carbonate system parameters are also rapidly changing along salinity gradients. In order to understand this variability and correctly represent it in biogeochemical models, detailed observations must be regularly obtained, and in the SEA-ReCap Project we do this in marginal seas such as the Black Sea or the North Sea. A research cruise was organised in autumn 2024 on the RV Heincke to sample the German exclusive economic zone of the North Sea and three major estuaries draining into the German Bight. Surface seawater pCO2 and pH were measured continuously using a FerryBox system installed on board. Total alkalinity was measured every 15 minutes with an automated sensor, while dissolved inorganic carbon was measured on board from discrete water samples. With all four carbonate system parameters directly observed, the land-ocean continuum can be well characterized. For example, all the dissolved inorganic carbon concentrations converged towards the open North Sea end-member of 2877 ± 4 µmol kg-1, but while the Elbe River estuary measurements decreased with decreasing salinity, to below 1800 µmol kg-1, the Ems and Weser measurements increased with decreasing salinity, exceeding 3100 µmol kg-1 at the most upstream locations sampled. The Elbe freshwater end-member, upstream of our last sampled location, is characterised by high primary production and low dissolved inorganic carbon, while the sampled area of Hamburg and further downstream is a site of remineralisation and dissolved inorganic carbon accumulation. The Ems and Weser Estuaries, on the other hand, are sources of dissolved inorganic carbon and alkalinity through denitrification and fluid mud anaerobic processes, leading to the high concentration freshwater end-members. Additionally, the seawater pCO2 in the open North Sea was 461 ± 4 µatm, while at the lowest salinities sampled in each estuary, the values exceeded 2000 µatm, indicating the dominance of heterotrophy. These results emphasise the large heterogeneity that can arise over small spatial scales and the sometimes contrasting patterns of the carbonate system in nearby estuaries. This has implications for the strength of the buffering capacity of the German Bight and the role of the coastal ocean as a carbon source or sink.

A novel design is demonstrated for a solid state, reagent-less sensor capable of rapid and simultaneous measurement of pH and Total Alkalinity (AT) using ion sensitive field effect transistor (ISFET) technology to provide a simplified means of characterization of the aqueous carbon dioxide system through measurement of two "master variables": pH and AT. ISFET-based pH sensors that achieve 0.001 precision are widely used in various oceanographic applications. A modified ISFET is demonstrated to perform a nanoliter-scale acid-base titration of AT in under 40 s. This method of measuring AT, a Coulometric Diffusion Titration, involves electrolytic generation of titrant, H+, through the electrolysis of water on the surface of the chip via a microfabricated electrode eliminating the requirement of external reagents. Characterization has been performed in seawater as well as titrating individual components (i.e., OH-, HCO3-, CO32-, B(OH)4-, PO43-) of seawater AT. The seawater measurements are consistent with the design in reaching the benchmark goal of 0.5% precision in AT over the range of seawater AT of ∼2200-2500 μmol kg-1 which demonstrates great potential for autonomous sensing.

This document describes the procedures and methods used to measure total carbon dioxide (TCO{sub 2}) and total alkalinity (TALK) at hydrographic stations taken during the R/V Knorr Indian Ocean cruises (Sections I8SI9S, I9N, I8NI5E, I3, I5WI4, I7N, I1, I10, and I2) in 1994-1996. The measurements were conducted as part of the World Ocean Circulation Experiment (WOCE). The expedition began in Fremantle, Australia, on December 1, 1994, and ended in Mombasa, Kenya, on January 22, 1996. During the nine cruises, 12 WOCE sections were occupied. Total carbon dioxide was extracted from water samples and measured using single-operator multiparameter metabolic analyzers (SOMMAs) coupled to coulometers. The overall precision and accuracy of the analyses was {+-} 1.20 {micro}mol/kg. The second carbonate system parameter, TALK, was determined by potentiometric titration. The precision of the measurements determined from 962 analyses of certified reference material was {+-} 4.2 {micro}mol/kg (REFERENCE). This work was supported by grants from the National Science Foundation, the U. S. Department of Energy, and the National Oceanographic and Atmospheric Administration. The R/V Knorr Indian Ocean data set is available as a numeric data package (NDP) from the Carbon Dioxide Information Analysis Center (CDIAC). The NDP consists of 18 oceanographic data files, two FORTRAN 77 data retrieval routine files, a readme file, and this printed documentation, which describes the contents and format of all files as well as the procedures and methods used to obtain the data. Instructions for accessing the data are provided.

The eastern Ross Sea is a key area to understand the role of the Amundsen Sea inflow of freshwater that can influence the Ross Sea water properties and salt budget. A survey was carried out in the eastern Ross Sea during the austral summer 2019–20 to evaluate the contribution of the Amundsen Sea Water (ASW) to the salinity variability. A total of 248 seawater samples were collected f\or the analysis of total alkalinity (AT) and pH. The data collected were used together with temperature and salinity to obtain a full description of the carbonate system properties including total inorganic carbon (CT), CO2 partial pressure (pCO2), calcium carbonate saturation state of aragonite and calcite (Ω), and Revelle factor. Moreover, we estimated the anthropogenic carbon (Cant) throughout the TrOCA method to better understand the carbon cycle, also considering the effect of atmospheric CO2 uptake on ocean acidification. We used principal component analysis (PCA) to investigate the major controls on the carbonate system parameters with the aim of defining their sensitivity as chemical tracers. The changes in carbonate chemistry in surface waters were mainly due to the physical properties. AT and pH traced the entry of the ASW showing limited mixing between water masses on the shelf area. Shelf waters were enriched in Cant, which resulted lower than the estimated value for shelf waters produced in western Ross Sea.

The effect of photon flux density on inorganic carbon accumulation and photosynthetic CO2 assimilation was determined by CO2 exchange studies at three, limiting CO2 concentrations with a ca-1 mutant of Chlamydomonas reinhardiii. This mutant accumulates a large internal inorganic carbon pool in the light which apparently is unavailable for photosynthetic assimilation. Although steady-state photosynthetic CO2 assimilation did not respond to the varying photon flux densities because of CO2 limitation, components of inorganic-carbon accumulation were not clearly light saturated even at 1100 μmol photons m(-2) s(-1), indicating a substantial energy requirement for inorganic carbon transport and accumulation. Steady-state photosynthetic CO2 assimilation responded to external CO2 concentrations but not to changing internal inorganic carbon concentrations, confirming that diffusion of CO2 into the cells supplies most of the CO2 for photosynthetic assimilation and that the internal inorganic carbon pool is essentially unavailable for photosynthetic assimilation. The estimated concentration of the internal inorganic carbon pool was found to be relatively insensitive to the external CO2 concentration over the small range tested, as would be expected if the concentration of this pool is limited by the internal to external inorganic carbon gradient. An attempt to use this CO2 exchange method to determine whether inorganic carbon accumulation and photosynthetic CO2 assimilation compete for energy at low photon flux densities proved inconclusive.

Reef coral calcification depends on regulation of pH in the internal calcifying fluid (CF) in which the coral skeleton forms. However, little is known about calcifying fluid pH (pHCF) regulation, despite its importance in determining the response of corals to ocean acidification. Here, we investigate pHCF in the coral Stylophora pistillata in seawater maintained at constant pH with manipulated carbonate chemistry to alter dissolved inorganic carbon (DIC) concentration, and therefore total alkalinity (AT). We also investigate the intracellular pH of calcifying cells, photosynthesis, respiration and calcification rates under the same conditions. Our results show that despite constant pH in the surrounding seawater, pHCF is sensitive to shifts in carbonate chemistry associated with changes in [DIC] and [AT], revealing that seawater pH is not the sole driver of pHCF Notably, when we synthesize our results with published data, we identify linear relationships of pHCF with the seawater [DIC]/[H+] ratio, [AT]/ [H+] ratio and [[Formula: see text]]. Our findings contribute new insights into the mechanisms determining the sensitivity of coral calcification to changes in seawater carbonate chemistry, which are needed for predicting effects of environmental change on coral reefs and for robust interpretations of isotopic palaeoenvironmental records in coral skeletons.

Low-molecular-weight organic acids as important factors impacting seawater acidification: A case study in the Jiaozhou Bay, China

In austral summer, from December 2008 to January 2009, we investigated the sea-ice carbon dioxide (CO(2)) system and CO(2) controls in the Amundsen and Ross Seas, Antarctica. We sampled seawater, brine and sea ice for the measurements of total alkalinity (A(T)), total inorganic carbon (DIC), pH, inorganic nutrients, particulate organic carbon (POC) and nitrogen (PON), chlorophyll a, pigments, salinity and temperature. Large variability in all measured parameters was observed in time and space due to the complex sea-ice dynamics. We discuss the controls of the sea-ice CO(2) system, such as brine rejection, biological processes, calcium carbonate (CaCO(3)) precipitation/dissolution and CO(2) exchange. Most (80 to 90%) of the DIC loss was due to brine rejection, which suggests that the sea ice acted as an efficient DIC sink from 0.8 and 2.6 mol m(-2) yr(-1) (9.6-31 g C m(-2) yr(-1)). The remaining change in DIC was to a large extent explained by net biological production. The A(T):DIC ratio in the sea ice was higher than in the under-ice water (UIW), with ratios reaching 1.7, which indicated CaCO(3) precipitation and concomitant DIC loss in the sea ice. Elevated A(T):DIC ratios and carbonate concentrations were also observed in the UIW, which reflect the solid CaCO(3) rejected from the ice during melt. The potential for uptake of atmospheric CO(2) in the mixed layer increased by approximately 56 mu atm due to the combined effect of CaCO(3) precipitation during ice formation, and ice melt in summer.

<p>The Western Tropical Atlantic is a crucial region when it comes to understanding the CO<sub>2</sub> dynamics in the tropics, as it is subject to large inputs of freshwater from the Amazon River and the ITCZ rainfall, as well as the input of CO<sub>2</sub>-rich waters from upwelling of subsurface water. This study aims to reconstruct the surface marine carbonate system from 1998 to 2018 using sea surface temperature (SST) and sea surface salinity (SSS) data from the PIRATA buoy at 8°N 38°W and describe its variability in time. Two empirical models were used to calculate total alkalinity (TA) and dissolved inorganic carbon (DIC) from SSS. From these two parameters and SST data, it was possible to calculate pH and CO<sub>2</sub> fugacity (<em>f</em>CO<sub>2</sub>) values. Only DIC, pH and <em>f</em>CO<sub>2</sub> showed a statistically significant trend in time, where DIC showed an increase of 0.717 µmol kg<sup>-1</sup> year<sup>-1</sup>, pH decreased 0.001394 pH units year<sup>-1</sup>, and <em>f</em>CO<sub>2</sub> had an increase of 1.539 µatm year<sup>-1</sup>. Two different seasons were observed when data were analyzed: a dry season from January to June, when SSTs were lower (around 27°C) and SSS was stable around 36, matching the period when the ITCZ is over the South American continent, Amazon river plume is restricted to western shelf areas and Equatorial upwelling is more active, and a rainy season from July to December, when SSTs were higher (around 28.5°C) and SSS had higher variability (from 31 to 36), matching the period when the ITCZ is at its northern range, the Amazon plume is spread eastwards through the North Brazil Current’s retroflection and the Equatorial upwelling is less intense. Along with that, TA, DIC and pH varied positively with SSS, with higher values (TA around 2350 µmol kg<sup>-1</sup>, DIC around 2025 µmol kg<sup>-1</sup> and pH around 8.060 pH units) during dry season and lower values (TA around 2300 µmol kg<sup>-1</sup>, DIC around 1990 µmol kg<sup>-1</sup> and pH around 8.050 pH units) during rainy season. On the other hand, <em>f</em>CO<sub>2</sub> varied positively with SST, with lower values (around 385 µatm) during dry, upwelling season and higher values (around 390 µatm) during rainy season, showing that both SSS and SST variability play an important role in the CO<sub>2</sub> solubility in the region.</p>