Posts Tagged 'methods'

The ocean carbon and acidification data system

The Ocean Carbon and Acidification Data System (OCADS) is a data management system at the National Oceanic and Atmospheric Administration (NOAA) National Centers for Environmental Information (NCEI). It manages a wide range of ocean carbon and acidification data, including chemical, physical, and biological observations collected from research vessels, ships of opportunity, and uncrewed platforms, as well as laboratory experiment results, and model outputs. Additionally, OCADS serves as a repository for related Global Ocean Observing System (GOOS) biogeochemistry Essential Ocean Variables (EOVs), e.g., oxygen, nutrients, transient tracers, and stable isotopes. OCADS endeavors to be one of the world’s leading providers of ocean carbon and acidification data, information, products, and services. To provide the best data management services to the ocean carbon and acidification research community, OCADS prioritizes adopting a customer-centric approach and gathering knowledge and expertise from the research community to improve its data management practices. OCADS aims to make all ocean carbon and acidification data accessible via a single portal, and welcomes submissions from around the world:

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Stability of alkalinity in ocean alkalinity enhancement (OAE) approaches – consequences for durability of CO2 storage (update)

According to modelling studies, ocean alkalinity enhancement (OAE) is one of the proposed carbon dioxide removal (CDR) approaches with large potential, with the beneficial side effect of counteracting ocean acidification. The real-world application of OAE, however, remains unclear as most basic assumptions are untested. Before large-scale deployment can be considered, safe and sustainable procedures for the addition of alkalinity to seawater must be identified and governance established. One of the concerns is the stability of alkalinity when added to seawater. The surface ocean is already supersaturated with respect to calcite and aragonite, and an increase in total alkalinity (TA) together with a corresponding shift in carbonate chemistry towards higher carbonate ion concentrations would result in a further increase in supersaturation, and potentially to solid carbonate precipitation. Precipitation of carbonate minerals consumes alkalinity and increases dissolved CO2 in seawater, thereby reducing the efficiency of OAE for CO2 removal. In order to address the application of alkaline solution as well as fine particulate alkaline solids, a set of six experiments was performed using natural seawater with alkalinity of around 2400 µmol kgsw−1. The application of CO2-equilibrated alkaline solution bears the lowest risk of losing alkalinity due to carbonate phase formation if added total alkalinity (ΔTA) is less than 2400 µmol kgsw−1. The addition of reactive alkaline solids can cause a net loss of alkalinity if added ΔTA > 600 µmol kgsw−1 (e.g. for Mg(OH)2). Commercially available (ultrafine) Ca(OH)2 causes, in general, a net loss in TA for the tested amounts of TA addition, which has consequences for suggested use of slurries with alkaline solids supplied from ships. The rapid application of excessive amounts of Ca(OH)2, exceeding a threshold for alkalinity loss, resulted in a massive increase in TA (> 20 000 µmol kgsw−1) at the cost of lower efficiency and resultant high pH values > 9.5. Analysis of precipitates indicates formation of aragonite. However, unstable carbonate phases formed can partially redissolve, indicating that net loss of a fraction of alkalinity may not be permanent, which has important implications for real-world OAE application.

Our results indicate that using an alkaline solution instead of reactive alkaline particles can avoid carbonate formation, unless alkalinity addition via solutions shifts the system beyond critical supersaturation levels. To avoid the loss of alkalinity and dissolved inorganic carbon (DIC) from seawater, the application of reactor techniques can be considered. These techniques produce an equilibrated solution from alkaline solids and CO2 prior to application. Differing behaviours of tested materials suggest that standardized engineered materials for OAE need to be developed to achieve safe and sustainable OAE with solids, if reactors technologies should be avoided.

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Assessing the impact of different carbonate system parameters on benthic foraminifera from controlled growth experiments

Insights into past marine carbon cycling and water mass properties can be obtained by means of geochemical proxies calibrated through controlled laboratory experiments with accurate seawater carbonate system (C-system) manipulations. Here, we explored the use of strontium/calcium ratio (Sr/Ca) of the calcite shells of benthic foraminifera as a potential seawater C-system proxy through a controlled growth experiment with two deep-sea species (Bulimina marginata and Cassidulina laevigata) and one intertidal species (Ammonia T6). To this aim, we used two experimental set-ups to decouple as much as possible the individual components of the carbonate system, i.e., changing pH at constant dissolved inorganic carbon (DIC) and changing DIC at constant pH. Four climatic chambers were used with different controlled concentrations of atmospheric pCO2 (180 ppm, 410 ppm, 1000 ppm, 1500 ppm). Our results demonstrated that pH did not influence the survival and growth of the three species. However, low DIC conditions (879 μmol kg−1) negatively affected B. marginata and C. laevigata through reduced growth, whereas no effect was observed for Ammonia T6. Our results also showed that Sr/Ca was positively correlated with total Alkalinity (TA), DIC and bicarbonate ion concentration ([HCO3]) for Ammonia T6 and B. marginata; i.e., DIC and/or [HCO3] were the main controlling factors. For these two species, the regression models were coherent with published data (existing so far only for Ammonia T6) and showed overall similar slopes but different intercepts, implying species-specific effects. Furthermore, the Sr/Ca – C-system relationship was not impacted by ontogenetic trends between chamber stages, which is a considerable advantage for paleo-applications. This applied particularly to Ammonia T6 that calcified many chambers compared to the two other species. However, no correlation with any of the C-system parameters was observed for Sr/Ca in C. laevigata. This might imply either a strong species-specific effect and/or a low tolerance to laboratory conditions leading to a physiological stress, thereby impacting the Sr incorporation into the calcite lattice of C. laevigata.

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Understanding the dynamic response of Durafet-based sensors: a case study from the Murderkill Estuary-Delaware Bay system (Delaware, USA)


  • A SeapHOx sensor package was deployed in a dynamic estuarine environment.
  • The responses of the Durafet’s internal and external reference electrodes were assessed.
  • Previously unreported dynamic errors in their temperature and salinity responses were characterized.
  • A dynamic sensor response correction for the external reference electrode was developed.


The use of Durafet-based sensors has proliferated in recent years, but their performance in estuarine waters (salinity < 20) where rapid changes in temperature and salinity are frequently observed requires further scrutiny. Here, the responses of the Honeywell Durafet and its internal (pHINT) and external (pHEXT) reference electrodes integrated into a SeapHOx sensor at the confluence of the Murderkill Estuary and Delaware Bay (Delaware, USA) were assessed over extensive ranges of temperature (1.34–32.27°C), salinity (1.17–29.82), and rates of temperature (dT/dt; −1.46 to +1.53°C (0.5 h)−1) and salinity (dSalt/dt; −3.55 to +11.09 (0.5 h)−1) change. Empirical analyses indicated dynamic errors in the temperature and salinity responses of the internal and external reference electrodes, respectively, driven by tidal mixing were introduced into our pH time-series. These dynamic errors drove large anomalies between pHINT and pHEXT (denoted ΔpHINT−EXT) that reached >±0.8 pH in winter when the lowest temperatures and maximum tidal salinity variability occurred and >±0.15 pH in summer when the highest temperatures and minimum tidal salinity variability occurred. The ΔpHINT−EXT anomalies demonstrated a clear linear relationship with dSalt/dt thereby making dSalt/dt the strongest limiting factor of reference electrode response in our application. A dynamic sensor response correction for the external reference electrode (solid-state chloiride ion-selective electrode, Cl-ISE) was also developed and applied in the voltage domain. This correction reduced winter and summer ΔpHINT−EXT anomaly ranges by >40% and 68.7%, respectively. Summer anomalies were notably reduced to <±0.04 pH across all measurements. Further, this correction also removed the first-order salinity dependence of these anomalies. Consequently, dynamic errors in reference electrode response cannot be ignored and must be considered in future experimental designs. Further work to better understand the dynamic temperature and salinity responses of both reference electrodes is underway. Ultimately, we hope this work will stimulate further discussion around the role and treatment of large ΔpHINT−EXT anomalies as a part of future data quality control and data reporting as well as the dynamic errors in reference electrode response that drive them in the context of Sensor Best Practices.

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Alkalinity biases in CMIP6 Earth System Models and implications for simulated CO2 drawdown via artificial alkalinity enhancement

The partitioning of CO2 between atmosphere and ocean depends to a large degree not only on the amount of dissolved inorganic carbon (DIC) but also of alkalinity in the surface ocean. That is also why, in the context of negative emission approaches ocean alkalinity enhancement is discussed as one potential approach. Although alkalinity is thus an important variable of the marine carbonate system little knowledge exists how its representation in models compares with measurements. We evaluated the large-scale alkalinity distribution in 14 CMIP6 models against the observational data set GLODAPv2 and showed that most models as well as the multi-model-mean underestimate alkalinity at the surface and in the upper ocean, while overestimating alkalinity in the deeper ocean. The decomposition of the global mean alkalinity biases into contributions from physical processes (preformed alkalinity), remineralization, and carbonate formation and dissolution showed that the bias stemming from the physical redistribution of alkalinity is dominant. However, below the upper few hundred meters the bias from carbonate dissolution can become similarly important as physical biases, while the contribution from remineralization processes is negligible. This highlights the critical need for better understanding and quantification of processes driving calcium carbonate dissolution in microenvironments above the saturation horizons, and implementation of these processes into biogeochemical models.

For the application of the models to assess the potential of ocean alkalinity enhancement to increase ocean carbon uptake and counteract ocean acidification, a back-of-the-envelope calculation was conducted with each model’s global mean surface alkalinity and DIC as input parameters. We find that the degree of compensation of DIC and alkalinity biases at the surface is more important for the marine CO2 uptake capacity than the alkalinity biases themselves. The global mean surface alkalinity bias relative to GLODAPv2 in the different models ranges from -85 mmol kg-1 (-3.6 %) to +50 mmol kg-1 (+2.1 %) (mean: -25 mmol kg-1 or -1.1 %), while for DIC the relative bias ranges from -55 mmol kg-1 (-2.6 %) to 53 mmol kg-1 (+2.5 %) (mean: -13 mmol kg-1 or -0.6 %). Because of this partial compensation, all but two of the CMIP6 models evaluated here overestimate the Revelle factor at the surface and thus overestimate the CO2-draw-down after alkalinity addition by up to 13 % and pH increase by up to 7.2 %. This overestimate has to be taken into account when reporting on efficiencies of ocean alkalinity enhancement experiments using CMIP6 models.

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The effect of pH on the larvae of two sea urchin species using different pH manipulation methods

Climate change alters ocean pH, temperature, and salinity, which presents challenges for oceanic organisms, especially those with calcium carbonate skeletons. Our research examines how decreasing pH impacts larval survivorship and calcium carbonate skeletal development of two sea urchin species, Lytechinus variegatus and Arbacia punctulata. Based on previous work in various sea urchin species, it is expected that as pH decreases, survivorship decreases and skeletal malformations increase. Both L. variegatus and A. punctulata have been used in prior studies to explore pH change on survivorship and development, but these studies incorporated various outcomes and pH manipulation methods, limiting how comparable they are. Therefore, we wanted to measure the same outcomes between species and compare the effect of different pH manipulation within species. We altered pH by either HCL addition or CO2 bubbling through seawater. Larvae, at a concentration of 3 larvae/ml, were exposed to seawater of pH 8.4, 8.0, or 7.6. For each treatment, survivorship of 30-40 larvae was measured daily for 10-14 days depending on the trial. Larval malformations were quantified for about 10 larvae from daily fixed samples. Larval arm length, body length, and body width were measured using Image J. For both methods of pH manipulation and both species, there was a statistically significant (p<0.001) decrease in survivorship as pH decreases consistent with the prediction. Preliminary analysis of skeletal deformities suggests malformations increase as pH decreases, but data are still being collected. Similar abnormalities observed between species regardless of pH manipulations include uneven or missing arms and misshapen aboral sides. The effect of pH on larval survivorship and development in L. variegatus and A. punctulata are comparable to observations in other species suggesting effects are consistent across manipulation methods and species. With this research, we can continue to fine-tune methodology and build on our understanding of how climate change-driven ocean acidification can impact species.

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Observations of seawater carbonate chemistry in the Southern California Current

The ocean has taken up roughly a quarter of the total anthropogenic carbon emissions (Gruber et al., 2019). This addition causes changes in carbonate system equilibrium, decreasing ocean pH, which impacts marine organisms, ecosystems, and humans reliant on marine resources (Doney et al., 2020). The study of the changing carbonate chemistry and its impact on the ocean requires the refinement of measurement techniques, observational programs, models and the sharing of data. Chapter 1 focuses on measurement techniques by assessing the stability of tris pH buffer in artificial seawater stored in bags. These bagged reference materials can be used by both benchtop and autonomous instruments to aid in quality control of measurements of carbonate chemistry. Chapter 2 focuses on continued observation, with the oldest inorganic carbon time series in the Pacific. This time series in the Southern California Current helps confirm the rate of anthropogenic ocean acidification observed in other regions of the ocean. Chapter 3 focuses on models by using seasonal cycles determined in Chapter 2 to build a mixed layer carbon budget at the location of the time series. Chapter 4 focuses on the sharing of data by summarizing and publishing previously unavailable observations of carbonate chemistry in the Southern California Current going back as far as 1983.

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Unifying biological field observations to detect and compare ocean acidification impacts across marine species and ecosystems: what to monitor and why (update)

Approximately one-quarter of the CO2 emitted to the atmosphere annually from human activities is absorbed by the ocean, resulting in a reduction of seawater pH and shifts in seawater carbonate chemistry. This multi-decadal process, termed “anthropogenic ocean acidification” (OA), has been shown to have detrimental impacts on marine ecosystems. Recent years have seen a globally coordinated effort to measure the changes in seawater chemistry caused by OA, with best practices now available for these measurements. In contrast to these substantial advances in observing physicochemical changes due to OA, quantifying their biological consequences remains challenging, especially from in situ observations under real-world conditions. Results from 2 decades of controlled laboratory experiments on OA have given insight into the likely processes and mechanisms by which elevated CO2 levels affect biological process, but the manifestation of these process across a plethora of natural situations has yet to be fully explored. This challenge requires us to identify a set of fundamental biological and ecological indicators that are (i) relevant across all marine ecosystems, (ii) have a strongly demonstrated link to OA, and (iii) have implications for ocean health and the provision of ecosystem services with impacts on local marine management strategies and economies. This paper draws on the understanding of biological impacts provided by the wealth of previous experiments, as well as the findings of recent meta-analyses, to propose five broad classes of biological indicators that, when coupled with environmental observations including carbonate chemistry, would allow the rate and severity of biological change in response to OA to be observed and compared. These broad indicators are applicable to different ecological systems, and the methods for data analysis suggested here would allow researchers to combine biological response data across regional and global scales by correlating rates of biological change with the rate of change in carbonate chemistry parameters. Moreover, a method using laboratory observation to design an optimal observing strategy (frequency and duration) and observe meaningful biological rates of change highlights the factors that need to be considered when applying our proposed observation strategy. This innovative observing methodology allows inclusion of a wide diversity of marine ecosystems in regional and global assessments and has the potential to increase the contribution of OA observations from countries with developing OA science capacity.

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Can marine hydrothermal vents be used as natural laboratories to study global change effects on zooplankton in a future ocean?

It is claimed that oceanic hydrothermal vents (HVs), particularly the shallow water ones, offer particular advantages to better understand the effects of future climate and other global change on oceanic biota. Marine hydrothermal vents (HVs) are extreme oceanic environments that are similar to projected climate changes of the earth system ocean (e.g., changes of circulation patterns, elevated temperature, low pH, increased turbidity, increased bioavailability of toxic compounds. Studies on hydrothermal vent organisms may fill knowledge gaps of environmental and evolutionary adaptations to this extreme oceanic environment. In the present contribution we evaluate whether hydrothermal vents can be used as natural laboratories for a better understanding of zooplankton ecology under a global change scenario.

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An automated microfluidic analyzer for in situ monitoring of total alkalinity

We have designed, built, tested, and deployed an autonomous in situ analyzer for seawater total alkalinity. Such analyzers are required to understand the ocean carbon cycle, including anthropogenic carbon dioxide (CO2) uptake and for mitigation efforts via monitoring, reporting, and verification of carbon dioxide removal through ocean alkalinity enhancement. The microfluidic nature of our instrument makes it relatively lightweight, reagent efficient, and amenable for use on platforms that would carry it on long-term deployments. Our analyzer performs a series of onboard closed-cell titrations with three independent stepper-motor driven syringe pumps, providing highly accurate mixing ratios that can be systematically swept through a range of pH values. Temperature effects are characterized over the range 5–25 °C allowing for field use in most ocean environments. Each titration point requires approximately 170 μL of titrant, 830 μL of sample, 460 J of energy, and a total of 105 s for pumping and optical measurement. The analyzer performance is demonstrated through field data acquired at two sites, representing a cumulative 25 days of operation, and is evaluated against laboratory measurements of discrete water samples. Once calibrated against onboard certified reference material, the analyzer showed an accuracy of −0.17 ± 24 μmol kg–1. We further report a precision of 16 μmol kg–1, evaluated on repeated in situ measurements of the aforementioned certified reference material. The total alkalinity analyzer presented here will allow measurements to take place in remote areas over extended periods of time, facilitating affordable observations of a key parameter of the ocean carbon system with high spatial and temporal resolution.

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Advancing best practices for assessing trends of ocean acidification time series

Assessing the status of ocean acidification across ocean and coastal waters requires standardized procedures at all levels of data collection, dissemination, and analysis. Standardized procedures for assuring quality and accessibility of ocean carbonate chemistry data are largely established, but a common set of best practices for ocean acidification trend analysis is needed to enable global time series comparisons, establish accurate records of change, and communicate the current status of ocean acidification within and outside the scientific community. Here we expand upon several published trend analysis techniques and package them into a set of best practices for assessing trends of ocean acidification time series. These best practices are best suited for time series capable of characterizing seasonal variability, typically those with sub-seasonal (ideally monthly or more frequent) data collection. Given ocean carbonate chemistry time series tend to be sparse and discontinuous, additional research is necessary to further advance these best practices to better address uncharacterized variability that can result from data discontinuities. This package of best practices and the associated open-source software for computing and reporting trends is aimed at helping expand the community of practice in ocean acidification trend analysis. A broad community of practice testing these and new techniques across different data sets will result in improvements and expansion of these best practices in the future.

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The DIC carbon isotope evolutions during CO2 bubbling: implications for ocean acidification laboratory culture

Ocean acidification increases pCO2 and decreases pH of seawater and its impact on marine organisms has emerged as a key research focus. In addition to directly measured variables such as growth or calcification rate, stable isotopic tracers such as carbon isotopes have also been used to more completely understand the physiological processes contributing to the response of organisms to ocean acidification. To simulate ocean acidification in laboratory cultures, direct bubbling of seawater with CO2 has been a preferred method because it adjusts pCO2 and pH without altering total alkalinity. Unfortunately, the carbon isotope equilibrium between seawater and CO2 gas has been largely ignored so far. Frequently, the dissolved inorganic carbon (DIC) in the initial seawater culture has a distinct 13C/12C ratio which is far from the equilibrium expected with the isotopic composition of the bubbled CO2. To evaluate the consequences of this type of experiment for isotopic work, we measured the carbon isotope evolutions in two chemostats during CO2 bubbling and composed a numerical model to simulate this process. The isotopic model can predict well the carbon isotope ratio of dissolved inorganic carbon evolutions during bubbling. With help of this model, the carbon isotope evolution during a batch and continuous culture can be traced dynamically improving the accuracy of fractionation results from laboratory culture. Our simulations show that, if not properly accounted for in experimental or sampling design, many typical culture configurations involving CO2 bubbling can lead to large errors in estimated carbon isotope fractionation between seawater and biomass or biominerals, consequently affecting interpretations and hampering comparisons among different experiments. Therefore, we describe the best practices on future studies working with isotope fingerprinting in the ocean acidification background.

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Understanding the current use and future needs of CO2 in seawater certified reference materials

Certified reference materials (CRMs) are fundamental for accurate and precise measurements of seawater CO2 system parameters and research related to ocean acidification and oceanic carbon cycles. Currently, there is a single global source of reference materials for total alkalinity, dissolved inorganic carbon, and pH in seawater and a calibrated HCl titrant for seawater alkalinity analysis (Andrew Dickson Laboratory, Scripps Institution of Oceanography, University of California San Diego). When production of these materials was halted during lab closures due to the Covid-19 pandemic, a shortage of CRMs ensued and highlighted the risks associated with having a single producer of CRMs. Distribution of CRMs was halted from for a year starting in March 2020. The U.S. Interagency Working Group on Ocean Acidification, which is responsible for coordinating U.S. federal activities related to ocean acidification, is engaging in efforts to increase resilience in the production and distribution of reference materials for the quality control of measurements of seawater CO2 system parameters. Increasing resilience of CRM production includes exploring multiple nodes of production inside the U.S. and whether a country outside of the United States could develop a production site. In parallel with U.S. efforts, the Global Ocean Acidification Observing Network (GOA-ON) is also working to advance efforts to improve international CRM resilience through its program for the UN Decade of Ocean Science for Sustainable Development: OARS, Ocean Acidification Research for Sustainability.

A new model for CRM production and certification, both within the US and internationally, must be informed by an understanding of the current and future use of CRMs. Specifically, it is vital to understand who uses CRMs, how and where CRMs are used, how many CRMs are currently used, and how many CRMs are expected to be used in the future. To better understand these aspects of CRM use, the GOA-ON executive secretariat created a questionnaire on CRM usage in collaboration with the Interagency Working Group on Ocean Acidification. The questionnaire was shared with the carbonate chemistry research community in April 2021. It was released approximately one month after Dr. Andrew Dickson presented a webinar in which he discussed his current reference material production system at Scripps Institution of Oceanography and options for the future of CRM production. The questionnaire was made available on social media platforms, including the Ocean Acidification Information Exchange, and was shared with webinar attendees. Additionally, the Dickson laboratory, GOA-ON, and the Ocean Carbon and Biogeochemistry Program (OCB) shared the questionnaire with their contacts. The questionnaire was made available along with a link to a recording of Dr. Dickson’s webinar and a link to an Ocean Acidification Information Exchange post about the webinar which contains questions, discussions, and a pdf copy of the presentation slides. Members of the OA and carbonate chemistry research communities voluntarily elected to participate in the questionnaire. It was encouraged that only one representative from each laboratory or research group provide answers.

A total of 247 individuals voluntarily responded to the questionnaire, although not every participant responded to every question. This document describes the responses that were received. All responses are presented in aggregate form as all individual responses are confidential and will not be released publicly.

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Feedbacks of CaCO3 dissolution effect on ocean carbon sink and seawater acidification: a model study

The oceanic absorption of atmospheric CO2 acidifies seawater, which accelerates CaCO3 dissolution of calcifying organisms, a process termed dissolution effect. Promoted CaCO3 dissolution increases seawater ALK (alkalinity), enhancing ocean carbon sink and mitigating ocean acidification. We incorporate different parameterizations of the link between CaCO3 dissolution and ocean acidification into an Earth System Model, to quantify the feedback of the dissolution effect on the global carbon cycle. Under SRES A2 CO2 emission scenario and its extension with emissions of 5,000 PgC in ~400 years, in the absence of the dissolution effect, accumulated ocean CO2 uptake between year 1800 and 3500 is 2,041 PgC. The consideration of the dissolution effect increases ocean carbon sink by 195–858 PgC (10–42%), and mitigates the decrease in surface pH by 0.04–0.17 (a decrease of 10–48% in [H+] (hydrogen ion concentration)), depending on the prescribed parameterization scheme. In the epipelagic zone, relative to the Arc-Atlantic Ocean, the Pacific-Indian Ocean experiences greater acidification, leading to greater dissolution effects and the resultant stronger feedbacks on ocean carbon sink and acidification in the Pacific-Indian Ocean. Noteworthy, the feedback of dissolution effect on ocean carbon sink can be comparable with or stronger than the feedback from CO2-induced radiative warming. Our study highlights the potentially critical role played by CaCO3 dissolution effect in the ocean carbon sink, global carbon cycle and climate system.

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Pathfinder v1.0.1: a Bayesian-inferred simple carbon–climate model to explore climate change scenarios

The Pathfinder model was developed to fill a perceived gap within the range of existing simple climate models. Pathfinder is a compilation of existing formulations describing the climate and carbon cycle systems, chosen for their balance between mathematical simplicity and physical accuracy. The resulting model is simple enough to be used with Bayesian inference algorithms for calibration, which enables assimilation of the latest data from complex Earth system models and the IPCC sixth assessment report, as well as a yearly update based on observations of global temperature and atmospheric CO2. The model’s simplicity also enables coupling with integrated assessment models and their optimization algorithms or running the model in a backward temperature-driven fashion. In spite of this simplicity, the model accurately reproduces behaviours and results from complex models – including several uncertainty ranges – when run following standardized diagnostic experiments. Pathfinder is an open-source model, and this is its first comprehensive description.

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CalcPlotAnomaly: a set of functions in MATLAB for the computation and plotting of anomalies of oceanographic and meteorological parameters


  • An Octave-compatible MATLAB code for computing anomalies over whole time periods, months and seasons.
  • CalcPlotAnomaly functions include time series and grids in the anomaly computation.
  • The computation results can be plotted with CalcPlotAnomaly.
  • CalcPlotAnomaly is a system that can be used in decision-making to minimize the impact of natural disasters.


CalcPlotAnomaly is a set of source code functions implemented in MATLAB and compatible with Octave, these functions are used for the computation of oceanographic (physical and biogeochemical), and meteorological parameter anomalies that are used by geoscientists and decision-makers. They use as input time-ordered data from observed data (in situ, satellite, or radar) and interannual model outputs (raw data, analysis, or reanalysis). These anomalies can be computed over the whole period, by months or seasons. Also included are functions for plotting anomalies in the form of time series.

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Long-term variability of satellite derived total alkalinity in the southwest Bay of Bengal


  • Computed TA data validated in BoB region.
  • Spatial and temporal variability in TA are mostly due to variability in SSS and SST.
  • TA in BoB region, seasonal and inter-annual pattern over past 17 years.


The seasonal and inter-annual variability of Total Alkalinity (TA) concentration was studied in the Bay of Bengal from 2003 to 2019 by using MODIS-Aqua derived sea surface temperature (SST) and sea surface salinity (SSS) products. The satellite derived TA showed a positive relationship with in-situ TA with (R2 = 0.67, RMSE = ±27.53 μMol/kg, SEE = ±32.16 and uncertainty error = 2287μMol/kg). The seasonal SST, SSS and TA portray the clear seasonal pattern between the seasons without any rapid change increase or decrease in trend observed over the years. In contrast to other seasons, the spring inter-monsoon was observed to have a warm surface water temperature with high salinity and TA. Strong wind and excessive cloud cover during the summer monsoon result in the reduction of ocean surface heat, which favours sea surface cooling and shallow mixed layer depth, resulting in low SST, SSS, and TA compared to the spring inter-monsoon. During fall inter-monsoon, the reversal of East India coastal current directs warm water from north to south and the weak wind that prevails in this region enhances stratification. During winter, low-saline water compensates the static stability loss by thermal inversion from the sea surface resulting in surface cooling with coldest SST, low SSS and TA during this period.

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Coral reef carbonate accretion rates track stable gradients in seawater carbonate chemistry across the U.S. Pacific Islands

The U.S. Pacific Islands span a dramatic natural gradient in climate and oceanographic conditions, and benthic community states vary significantly across the region’s coral reefs. Here we leverage a decade of integrated ecosystem monitoring data from American Samoa, the Mariana Archipelago, the main and Northwestern Hawaiian Islands, and the U.S. Pacific Remote Island Areas to evaluate coral reef community structure and reef processes across a strong natural gradient in pH and aragonite saturation state (Ωar). We assess spatial patterns and temporal trends in carbonate chemistry measured in situ at 37 islands and atolls between 2010 and 2019, and evaluate the relationship between long-term mean Ωar and benthic community cover and composition (benthic cover, coral genera, coral morphology) and reef process (net calcium carbonate accretion rates). We find that net carbonate accretion rates demonstrate significant sensitivity to declining Ωar, while most benthic ecological metrics show fewer direct responses to lower-Ωar conditions. These results indicate that metrics of coral reef net carbonate accretion provide a critical tool for monitoring the long-term impacts of ocean acidification that may not be visible by assessing benthic cover and composition alone. The perspectives gained from our long-term, in situ, and co-located coral reef environmental and ecological data sets provide unique insights into effective monitoring practices to identify potential for reef resilience to future ocean acidification and inform effective ecosystem-based management strategies under 21st century global change.

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Advancing real-time pH sensing capabilities to monitor coastal acidification as measured in a productive and dynamic estuary (Ría de Arousa, NW Spain)

Ocean acidification has critical impacts on marine ecosystems, but presents knowledge gaps on the ecological impacts requiring large-scale monitoring of physicochemical conditions to predict biological responses to ocean pH projections. The threat is especially significant in coastal regions like upwelling areas which are more sensitive and appear to respond more rapidly to anthropogenic perturbations. These ecosystems, such as the northwest coast of the Iberian Peninsula are characterized by complex physical and biogeochemical interactions, supporting enormous biological productivity and productive fisheries. The distribution of pH in upwelling systems has high variability on short temporal and spatial scales preventing a complete picture of acidification, which exhibit long-term pH rates markedly different from the measured in open waters. This motivation to significantly expand the coverage of pH monitoring in coastal areas has driven us to develop an autonomous pH monitoring instrument (from now on SURCOM) based on the Honeywell Durafet® pH electrode. A relevant feature is that SURCOM transmits near real-time pH and temperature measurements every 10.5 min through SIGFOX®, a low-power, low-bandwidth network for data transmission. This very careful design allows us to achieve a very low power consumption for the complete system resulting in 3 years of full autonomy with no other need than external cleaning and calibration. In this paper we describe the setup and the data set obtained by a SURCOM instrument over 240 days in a highly productive and dynamic coastal ecosystem, the Ría de Arousa embayment, providing valuable information on the performance of these low-cost and highly stable sensors, with potential for improving the pH variability description in nearshore systems and for reinforcing the monitoring-modeling of coastal acidification.

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Neural networks and the seawater CO2 system. From the global ocean to the Ría de Vigo

This doctoral dissertation is structured in six chapters and two appendices. From this point the reader is warned about the independent numbering in each chapter, both for sections and subsections as well as for figures and tables, that is, the numbering restarts at the beginning of each chapter. Chapter I is divided into two parts. On the one hand, the topic of the doctoral dissertation is introduced in a general way to put in context the different research studies that are part of it. This introduction presents the key concepts on climate change and ocean acidification necessary to approach the reading of the following chapters. On the other hand, the main and secondary objectives that are addressed in the next chapters are detailed. Chapter II develops the construction of a global and seasonal climatology of total alkalinity. The chapter details for the first time in the thesis the use of neural networks. This methodology is used throughout the manuscript, highlighting the peculiarities associated with each study in each of the chapters where it is applied. This chapter has been published in Earth System Science Data: Chapter III describes the development of a total dissolved inorganic carbon climatology. In general terms, a methodology similar to that of chapter II is used, although with certain relevant nuances such as the inclusion of a new database. In this chapter, a pCO2 climatology is also generated in a secondary way to evaluate the consistency between the two climatologies previously generated in this thesis. This chapter has been published in Earth System Science Data:

Chapter IV completely changes the scale of the previous two chapters and focuses on the study of sweater CO2 chemistry system on a regional scale. Specifically, neural networks are used to generate time series of total alkalinity and pH at various locations in the Ría de Vigo. From the time series, the magnitude of seasonal variability and interannual trends for these variables are analyzed. This chapter has been published in Biogeosciences Discussions:, 2021 Chapter V contains an analysis of the variability of the hydrogen ion concentration and the aragonite saturation state in the Ría de Vigo. This analysis is carried out from the time series of these variables that are constructed thanks to the study developed in chapter IV. Chapters II to V are structured in the same way as a typical scientific article, thus containing an introduction, methodology, results, discussion and conclusions about each study. Finally, chapter VI summarizes the main conclusions derived from the complete work shown through this doctoral thesis. It is worth noting the inclusion of two appendices in the final part of the thesis. Appendix I details the meaning of each of the acronyms, abbreviations and symbols used throughout the manuscript. Appendix II contains a summary of the doctoral dissertation in Spanish

Continue reading ‘Neural networks and the seawater CO2 system. From the global ocean to the Ría de Vigo’

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