Posts Tagged 'biogeochemistry'

Effects of nearshore processes on carbonate chemistry dynamics and ocean acidification

Time series from open ocean fixed stations have robustly documented secular changes in carbonate chemistry and long-term ocean acidification (OA) trends as a direct response to increases in atmospheric carbon dioxide (CO2). However, few high-frequency coastal carbon time series are available in reef systems, where most affected tropical marine organisms reside. Seasonal variations in carbonate chemistry at Cheeca Rocks (CR), Florida, and La Parguera (LP), Puerto Rico, are presented based on 8 and 10 years of continuous, high-quality measurements, respectively. This dissertation synthesizes autonomous and bottle observations to model carbonate chemistry and to understand how physical and biological processes affect seasonal carbonate chemistry at both locations. The autonomous carbonate chemistry and oxygen observations are used to examine a mass balance approach using a 1-D model to determine net rates of ecosystem calcification and production (NEC and NEP) from communities close (<5km) to the buoys. The results provide evidence to suggest that seasonal response between benthic metabolism and seawater chemistry at LP is attenuated relative to that at CR because their differences in benthic cover and how benthic metabolism modifies the water chemistry. Simple linear trends cannot explain the feedback between metabolism and reef water chemistry using long-term observations over natural variations. The effects of community production on partial pressure of CO2 (pCO2sw) make these interactions complex at short- and long-term scales. Careful consideration should be taken when inferring local biogeochemical processes, given that pCO2sw (and presumably pH) respond on much shorter time and local scales than dissolved inorganic carbon (DIC) and total alkalinity (TA). The observations highlight the need for more comprehensive observing systems that can reliably measure both the fast-response (pCO2sw, pH) and slow-response (DIC) carbon pools.

Continue reading ‘Effects of nearshore processes on carbonate chemistry dynamics and ocean acidification’

The Northeast Atlantic is running out of excess carbonate in the horizon of cold-water corals communities

The oceanic uptake of atmospheric carbon dioxide (CO2) emitted by human activities alters the seawater carbonate system. Here, the chemical status of the Northeast Atlantic is examined by means of a high-quality database of carbon variables based on the GO-SHIP A25 section (1997–2018). The increase of atmospheric CO2 leads to an increase in ocean anthropogenic carbon (Cant) and a decrease in carbonate that is unequivocal in the upper and mid-layers (0–2,500 m depth). In the mid-layer, the carbonate content in the Northeast Atlantic is maintained by the interplay between the northward spreading of recently conveyed Mediterranean Water with excess of carbonate and the arrival of subpolar-origin waters close to carbonate undersaturation. In this study we show a progression to undersaturation with respect to aragonite that could compromise the conservation of the habitats and ecosystem services developed by benthic marine calcifiers inhabiting that depth-range, such as the cold-water corals (CWC) communities. For each additional ppm in atmospheric pCO2 the waters surrounding CWC communities lose carbonate at a rate of − 0.17 ± 0.02 μmol kg−1 ppm−1. The accomplishment of global climate policies to limit global warming below 1.5–2 ℃ will avoid the exhaustion of excess carbonate in the Northeast Atlantic.

Continue reading ‘The Northeast Atlantic is running out of excess carbonate in the horizon of cold-water corals communities’

A regional neural network approach to estimate water-column nutrient concentrations and carbonate system variables in the Mediterranean Sea: CANYON-MED

A regional neural network-based method, “CANYON-MED” is developed to estimate nutrients and carbonate system variables specifically in the Mediterranean Sea over the water column from pressure, temperature, salinity, and oxygen together with geolocation and date of sampling. Six neural network ensembles were developed, one for each variable (i.e., three macronutrients: nitrates (NO−33-), phosphates (PO3−443-) and silicates (SiOH4), and three carbonate system variables: pH on the total scale (pHT), total alkalinity (AT), and dissolved inorganic carbon or total carbon (CT), trained using a specific quality-controlled dataset of reference “bottle” data in the Mediterranean Sea. This dataset is representative of the peculiar conditions of this semi-enclosed sea, as opposed to the global ocean. For each variable, the neural networks were trained on 80% of the data chosen randomly and validated using the remaining 20%. CANYON-MED retrieved the variables with good accuracies (Root Mean Squared Error): 0.73 μ–1 for NO−33-, 0.045 μ–1 for PO3−443- and 0.70 μ–1 for Si(OH)4, 0.016 units for pHT, 11 μ–1 for AT and 10 μ–1 for CT. A second validation on the ANTARES independent time series confirmed the method’s applicability in the Mediterranean Sea. After comparison to other existing methods to estimate nutrients and carbonate system variables, CANYON-MED stood out as the most robust, using the aforementioned inputs. The application of CANYON-MED on the Mediterranean Sea data from autonomous observing systems (integrated network of Biogeochemical-Argo floats, Eulerian moorings and ocean gliders measuring hydrological properties together with oxygen concentration) could have a wide range of applications. These include data quality control or filling gaps in time series, as well as biogeochemical data assimilation and/or the initialization and validation of regional biogeochemical models still lacking crucial reference data. Matlab and R code are available at https://

Continue reading ‘A regional neural network approach to estimate water-column nutrient concentrations and carbonate system variables in the Mediterranean Sea: CANYON-MED’

Comparing subsurface seasonal deoxygenation and acidification in the Yellow Sea and Northern East China Sea along the North-to-South latitude gradient

To better understand the relationship between subsurface seasonal deoxygenation and acidification in the Yellow Sea and northern East China Sea (ECS), we examined carbonate system parameters and dissolved oxygen (DO) of seven field surveys conducted in 2017–2018, spanning all four seasons. Low pHT values of 7.71–7.80 and critically low aragonite saturation state (Ωarag) values of 1.07–1.40 along with undersaturated DO of mostly higher than 150 μmol O2 kg–1 occurred in the Yellow Sea Cold Water Mass area in summer and autumn, while hypoxic DO values of 49–63 μmol O2 kg–1 and extremely low pHT values of 7.68–7.74 as well as critically low Ωarag values of 1.21–1.39 were observed in the northern ECS in July 2018. At the beginning of warm-season stratification formation, the cold Yellow Sea waters had much higher DO but lower Ωarag values than those in relatively warmer ECS waters, while yearly initial pHT values rarely exhibited differences between the two coastal seas. During warm seasons, the central Yellow Sea accumulated respiration products beneath the thermocline in summer and autumn, while the northern ECS bottom waters preserved them only in summer. This study highlights fundamental roles of wintertime carbon dioxide (CO2) solubility along a north-to-south latitude gradient in the coastal acidification development. In comparison with the relatively low-latitude northern ECS subject to seasonal hypoxia, relatively high-latitude Yellow Sea exhibits higher CO2 solubility in winter and longer respiration-product accumulations in warm seasons, leading to lower Ωarag in the central Yellow Sea than those in the northern ECS. However, the present-day central Yellow Sea is free from hypoxia.

Continue reading ‘Comparing subsurface seasonal deoxygenation and acidification in the Yellow Sea and Northern East China Sea along the North-to-South latitude gradient’

Configuration and skill assessment of the coupled biogeochemical model for the carbonate system in the Bay of Bengal


  • A coupled physical-biogeochemical model (ROMS-PISCES) has been set up for the Bay of Bengal region to emulate the carbonate chemistry of this region.
  • The model has been run and rigorously evaluated using the available data sets and 8 statistical indices have been used to evaluate model skills.
  • The effect of wind stress and E-P has been evaluated through two numerical experiments, which uses two different bulk formulae to calculate the wind stresses.
  • The model is excellent in simulating the spatial heterogeneity and temporal variation of all the carbonate parameters thus giving a basis for further studies like the effect of physical dynamics, forecasting, etc.


The Bay of Bengal is a semi-enclosed ocean basin situated in the eastern part of the North Indian Ocean. Though the physical dynamical features of the Bay of Bengal have been studied and measured in detail, the carbonate chemistry of this basin has been less explored, and very few reliable data-sets exist. This paucity of data has emerged as a major challenge in modeling and understanding the carbonate system parameters for this region. In this study, a coupled physical-biogeochemical (ROMS-PISCES) model has been configured and run to emulate the surface carbonate system parameters (DIC, TALK, pCO2, and pH) for the Bay of Bengal region. Model skill assessment analysis has been performed using available observational data-sets. Two different numerical experiments have been performed (WB indicating the use of default bulk formulae of ROMS to calculate wind stress and WoB indicating the calculated wind stresses of QuikSCAT climatology product using different bulk formula), to understand which one reproduces the carbonate parameters better. Both the numerical experiments are rigorously compared for physical as well as carbonate system parameters. The numerical experiments have been passed through exhaustive statistical analysis by comparing it with the observed data-sets. The temperature, the primary driver affecting pH and pCO2 has been reproduced by both the experiments excellently, and the correlation value is more than 0.9 with RAMA buoy data (15o N, 90o E). The salinity, when compared with the NIOA climatology data, shows that the WoB experiment has better captured both the spatial and temporal variation of salinity. Both the numerical experiments have been compared individually with three sets of observed carbonate data. The WoB run has been found to emulate carbonate system parameters satisfactorily than the WB run. The pCO2 and pH show a good positive correlation with RAMA data and the values are 0.87, and 0.93, respectively.


Continue reading ‘Configuration and skill assessment of the coupled biogeochemical model for the carbonate system in the Bay of Bengal’

Effect of large-scale kelp and bivalve farming on seawater carbonate system variations in the semi-enclosed Sanggou Bay


• Large-scale kelp and bivalve farming are important biological drivers of carbonate chemistry variations within the Sanggou Bay.

• The fluctuation of carbonate systems in farming areas were much larger than those in non-farming area.

• Kelp farming may favour the calcification of farmed bivalves and provide essential refuge for these species during future ocean acidification.

• Farmed bivalves are capable of fixing larger amounts of inorganic carbon by calcification than that released into seawater by respiration.

Although cultured algae and shellfish can be the dominant species in some localized coastal waters, research on the effect of large-scale mariculture on the carbonate system variations in these local waters is still lacking. We conducted five cruises from May to September and studied spatiotemporal variations in the seawater carbonate system in the semi-closed Sanggou Bay, which is famous for its large-scale mariculture. Our results showed that both kelp and bivalve farming induced significant spatiotemporal variations in the carbonate system within the bay. When cultured kelp reached its highest biomass in May, the maximum ΔDIC, ΔpCO2 and ΔpHT between the seawater from the kelp farming area and the non-farming outer bay area was −156 μmol kg−1, −102 μatm and 0.15 pH units, respectively. However, no significant effect of kelp farming on seawater total alkalinity (TA) was observed. Kelp farming also caused the carbonate system variations of seawater from the bivalve farming area. Assuming no kelp was farmed in May, the average pH and pCO2 would reduce by 0.12 pH units and increase by 179 μatm, respectively, in the bivalve farming area. Bivalve farming significantly reduced seawater TA, indicating that fast deposition of calcium carbonate occurred in the bivalve farming area. Although bivalve respiration released CO2 into seawater and elevated seawater pCO2 level and reduced seawater pHT, surprisingly, seawater dissolved inorganic carbon (DIC) reduced significantly in the bivalve farming area. These results indicated that bivalves fixed a larger amount of inorganic carbon by calcification than that released into seawater by respiration. Overall, large-scale kelp and bivalve farming are important biological drivers of variations in the carbonate system within the semi-enclosed Sanggou Bay. Altered carbonate systems by kelp farming may favour calcification of farmed bivalves and provide an essential refuge for these species during the future ocean acidification.

Continue reading ‘Effect of large-scale kelp and bivalve farming on seawater carbonate system variations in the semi-enclosed Sanggou Bay’

Downscaling global ocean climate models improves estimates of exposure regimes in coastal environments

Climate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these predictions are then often used to parameterize laboratory experiments designed to assess biological and ecological responses to future change. However, nearshore ecosystems are affected by a range of physical processes such as tides, local winds, and surface and internal waves, causing local variability in conditions that often exceeds global climate models. Predictions of future climatic conditions at local scales, the most relevant to ecological responses, are largely lacking. To fill this critical gap, we developed a 2D implementation of the Regional Ocean Modeling System (ROMS) to downscale global climate predictions across all Representative Concentration Pathway (RCP) scenarios to smaller spatial scales, in this case the scale of a temperate reef in the northeastern Pacific. To assess the potential biological impacts of local climate variability, we then used the results from different climate scenarios to estimate how climate change may affect the survival, growth, and fertilization of a representative marine benthic invertebrate, the red abalone Haliotis rufescens, to a highly varying multi-stressor environment. We found that high frequency variability in temperature, dissolved oxygen (DO), and pH increases as pCO2 increases in the atmosphere. Extreme temperature and pH conditions are generally not expected until RCP 4.5 or greater, while frequent exposure to low DO is already occurring. In the nearshore environment simulation, strong RCP scenarios can affect red abalone growth as well as reduce fertilization during extreme conditions when compared to global scale simulations.

Continue reading ‘Downscaling global ocean climate models improves estimates of exposure regimes in coastal environments’

Impact of dust enrichment on Mediterranean plankton communities under present and future conditions of pH and temperature: an experimental overview

In Low Nutrient Low Chlorophyll areas, such as the Mediterranean Sea, atmospheric fluxes represent a considerable external source of nutrients likely supporting primary production especially during stratification periods. These areas are expected to expand in the future due to lower nutrient supply from sub-surface waters caused by enhanced stratification, likely further increasing the role of atmospheric deposition as a source of new nutrients to surface waters. Yet, whether plankton communities will react differently to dust deposition in a warmer and acidified environment remains an open question. The impact of dust deposition both in present and future climate conditions was assessed through three perturbation experiments in the open Mediterranean Sea. Climate reactors (300 L) were filled with surface water collected in the Tyrrhenian Sea, Ionian Sea and in the Algerian basin during a cruise conducted in May/June 2017 in the frame of the PEACETIME project. The experimental protocol comprised two unmodified control tanks, two tanks enriched with a Saharan dust analog and two tanks enriched with the dust analog and maintained under warmer (+3 °C) and acidified (−0.3 pH unit) conditions. Samples for the analysis of an extensive number of biogeochemical parameters and processes were taken over the duration of the experiments (3–4 d). Here, we present the general setup of the experiments and the impacts of dust seeding and/or future climate change scenario on nutrients and biological stocks. Dust addition led to a rapid and maximum input of nitrate whereas phosphate release from the dust analog was much smaller. Our results showed that the impacts of Saharan dust deposition in three different basins of the open Northwestern Mediterranean Sea are at least as strong as those observed previously in coastal waters. However, interestingly, the effects of dust deposition on biological stocks were highly different between the three investigated stations and could not be attributed to differences in their degree of oligotrophy but rather to the initial metabolic state of the community. Finally, ocean acidification and warming did not drastically modify the composition of the autotrophic assemblage with all groups positively impacted by warming and acidification, suggesting an exacerbation of effects from atmospheric dust deposition in the future.

Continue reading ‘Impact of dust enrichment on Mediterranean plankton communities under present and future conditions of pH and temperature: an experimental overview’

Impact of climate change on the primary production and related biogeochemical cycles in the coastal and sea ice zone of the Southern Ocean


• Changes in primary production in the Southern Ocean are analyzed in a comprehensive manner.

• General production increase is the sign of climate change in the Southern Ocean.

• Associated biogeochemical variables show regionally heterogenous signals of climate change.

• Sea ice affecting iron supply and stratification is a primary factor for CCSZ production change.

• Production change in SIZ is sensitive to change in iron supply arising from various mechanisms.


Climate change in the Southern Hemisphere has exerted impact on the primary production in the Southern Ocean (SO). Using a recently released reanalysis dataset on global biogeochemistry, a comprehensive analysis was conducted on the complex biogeochemical seasonal cycle and the impact of climate change with a focus in areas within the meridional excursion of the sea ice boundary—coastal and continental shelf zone (CCSZ) and seasonal sea ice zone (SIZ). The seasonal cycles of primary production and related nutrients are closely linked with the seasonal changes in sea ice and sea surface temperatures. As sea ice retreats and allows energy and gas exchange across the sea surface, phytoplankton growth is initiated, consuming accumulated nutrients within the shallow depth of ~40 m. The seasonal evolutions of physical, biological and chemical variables show both spatial and temporal consistency with each other. Climate change has altered the timing and amplitude of the seasonal cycle. While primary production has generally increased along with an intensified uptake of CO2, some areas show a reduction in production (e.g., Prydz Bay, eastern Indian Ocean). In the CCSZ, increased iron utilization and light availability allowed production to be increased. However, the mechanism by which these factors are altered varies from one location to another, including changes in sea ice cover, surface stratification, and downwelling/upwelling. In the SIZ, where iron is generally a limiting factor, iron supply is a key driver of changes in primary production regardless of other nutrients. There is a clear influence of climatic change on the biogeochemical cycle although the signal is still weak.

Continue reading ‘Impact of climate change on the primary production and related biogeochemical cycles in the coastal and sea ice zone of the Southern Ocean’

Inorganic carbon uptake strategies in coralline algae: plasticity across evolutionary lineages under ocean acidification and warming


• Ambient diffusive CO2 use of reef-building crustose coralline algae ranges from 35 to 65%.

• Algae largely maintain or increase bicarbonate use under ocean acidification and warming.

• Maintained or increased bicarbonate use is associated with sustained metabolic performance.

• Lineage predicts inorganic carbon uptake strategy.

• Proposed initial framework for inorganic carbon uptake strategies in crustose coralline algae.


Dissolved inorganic carbon (DIC) assimilation is essential to the reef-building capacity of crustose coralline algae (CCA). Little is known, however, about the DIC uptake strategies and their potential plasticity under ongoing ocean acidification (OA) and warming. The persistence of CCA lineages throughout historical oscillations of pCO2 and temperature suggests that evolutionary history may play a role in selecting for adaptive traits. We evaluated the effects of pCO2 and temperature on the plasticity of DIC uptake strategies and associated energetic consequences in reef-building CCA from different evolutionary lineages. We simulated past, present, moderate (IPCC RCP 6.0) and high pCO2 (RCP 8.5) and present and high (RCP 8.5) temperature conditions and quantified stable carbon isotope fractionation (13ε), organic carbon content, growth and photochemical efficiency. All investigated CCA species possess CO2-concentrating mechanisms (CCMs) and assimilate CO2 via diffusion to varying degrees. Under OA and warming, CCA either increased or maintained CCM capacity, which was associated with overall neutral effects on metabolic performance. More basal taxa, Sporolithales and Hapalidiales, had greater capacity for diffusive CO2 use than Corallinales. We suggest that CCMs are an adaptation that supports a robust carbon physiology and are likely responsible for the endurance of CCA in historically changing oceans.

Continue reading ‘Inorganic carbon uptake strategies in coralline algae: plasticity across evolutionary lineages under ocean acidification and warming’

Subscribe to the RSS feed

Powered by FeedBurner

Follow AnneMarin on Twitter

Blog Stats

  • 1,376,939 hits


Ocean acidification in the IPCC AR5 WG II

OUP book