Posts Tagged 'individualmodeling'

Inorganic carbon and pH dependency of Trichodesmium’s photosynthetic rates

We established the relationship between photosynthetic carbon fixation rates and pH, CO2 and HCO3 concentrations in the diazotroph Trichodesmium erythraeum IMS101. Inorganic 14C-assimilation was measured in TRIS-buffered ASW medium where the absolute and relative concentrations of CO2, pH and HCO3 were manipulated. First, we varied the total dissolved inorganic carbon concentration (TIC) (< 0 to ~ 5 mM) at constant pH, so ratios of CO2 and HCO3 remained relatively constant. Second, we varied pH (~ 8.54 to 7.52) at constant TIC, so CO2 increased whilst HCO3 declined. We found that 14C-assimilation could be described by the same function of CO2 for both approaches but showed different dependencies on HCO3 when pH was varied at constant TIC than when TIC was varied at constant pH. A numerical model of Trichodesmium’s CCM showed carboxylation rates are modulated by HCO3 and pH. The decrease in Ci assimilation at low CO2, when TIC was varied, is due to HCO3 uptake limitation of the carboxylation rate. Conversely, when pH was varied, Ci assimilation declined due to a high-pH mediated increase in HCO3 and CO2 leakage rates, potentially coupled to other processes (uncharacterised within the CCM model) that restrict Ci assimilation rates under high-pH conditions.

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Probabilistic risk assessment of the effect of acidified seawater on development stages of sea urchin (Strongylocentrotus droebachiensis)

Growing evidence indicates that ocean acidification has a significant impact on calcifying marine organisms. However, there is a lack of exposure risk assessments for aquatic organisms under future environmentally relevant ocean acidification scenarios. The objective of this study was to investigate the probabilistic effects of acidified seawater on the life-stage response dynamics of fertilization, larvae growth, and larvae mortality of the green sea urchin (Strongylocentrotus droebachiensis). We incorporated the regulation of primary body cavity (PBC) pH in response to seawater pH into the assessment by constructing an explicit model to assess effective life-stage response dynamics to seawater or PBC pH levels. The likelihood of exposure to ocean acidification was also evaluated by addressing the uncertainties of the risk characterization. For unsuccessful fertilization, the estimated 50% effect level of seawater acidification (EC50 SW ) was 0.55 ± 0.014 (mean ± SE) pH units. This life stage was more sensitive than growth inhibition and mortality, for which the EC50 values were 1.13 and 1.03 pH units, respectively. The estimated 50% effect levels of PBC pH (EC50 PBC ) were 0.99 ± 0.05 and 0.88 ± 0.006 pH units for growth inhibition and mortality, respectively. We also predicted the probability distributions for seawater and PBC pH levels in 2100. The level of unsuccessful fertilization had 50 and 90% probability risks of 5.07–24.51 (95% CI) and 0–6.95%, respectively. We conclude that this probabilistic risk analysis model is parsimonious enough to quantify the multiple vulnerabilities of the green sea urchin while addressing the systemic effects of ocean acidification. This study found a high potential risk of acidification affecting the fertilization of the green sea urchin, whereas there was no evidence for adverse effects on growth and mortality resulting from exposure to the predicted acidified environment.

Continue reading ‘Probabilistic risk assessment of the effect of acidified seawater on development stages of sea urchin (Strongylocentrotus droebachiensis)’

Numerical modelling of physiological and ecological impacts of ocean acidification on coccolithophores


• Intracellular biochemical-kinetic processes of coccolithophore were modelled.
• The model showed that the calcification is promoted under an acidified environment.
• Calcite remains at saturation levels in a coccolith even when it is below saturation.
• A coccolith can dissolve even in water where calcite saturation exceeds 1.
• The behavior of coccolithophores in the ecosystem were also simulated numerically.
• High CO2 concentration could lead to an increase of coccolithophores to diatoms.


Ocean surface acidification due to increasing atmospheric CO2 concentration is currently attracting much attention. Coccolithophores distribute widely across the world’s oceans and represent a carbon sink containing about 100 million tonnes of carbon. For this reason, there is concern about dissolution of their shells, which are made of calcium carbonate, due to decreasing pH. In this study, intracellular calcification, photosynthesis, and mass transport through biomembranes of Emiliania huxleyi were modelled numerically for understanding biological response in calcifying organisms. Unknown parameters were optimised by a generic algorithm to match existing experimental results. The model showed that the production of calcium carbonate rather than its dissolution is promoted under an acidified environment. Calcite remains at saturation levels in a coccolith even when it is below saturation levels in the external seawater. Furthermore, a coccolith can dissolve even in water where calcite saturation exceeds 1, because the saturation may be below the threshold level locally around the cell membrane. The present model also showed that the different calcification rates of E. huxleyi with respect to rising CO2 concentrations reported in the literature are due to differences in experimental conditions; in particular, how the CO2 concentration is matched. Lastly, the model was able to reproduce differences in calcification rates among coccolithophore species. The above biochemical-kinetic model was then incorporated into an ecosystem model, and the behaviour of coccolithophores in the ecosystem and the influence of increases in CO2 concentration on water quality were simulated and validated by comparison with existing experimental results. The model also suggests that increased CO2 concentration could lead to an increase in the biomass ratio of coccolithophores to diatoms at high CO2 concentrations, particularly in oligotrophic environments, and to a consequent decrease in pH due to calcium dissolution.

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Ocean acidification affects coral growth by reducing skeletal density


Ocean acidification (OA) threatens coral reef futures by reducing the concentration of carbonate ions that corals need to construct their skeletons. However, quantitative predictions of reef futures under OA are confounded by mixed responses of corals to OA in experiments and field observations. We modeled the skeletal growth of a dominant reef-building coral, Porites, as a function of seawater chemistry and validated the model against observational data. We show that OA directly and negatively affects one component of the two-step growth process (density) but not the other (linear extension). Combining our growth model with Global Climate Model output, we show that skeletal density of Porites corals could decline by up to 20.3% over the 21st century solely due to OA.


Ocean acidification (OA) is considered an important threat to coral reef ecosystems, because it reduces the availability of carbonate ions that reef-building corals need to produce their skeletons. However, while theory predicts that coral calcification rates decline as carbonate ion concentrations decrease, this prediction is not consistently borne out in laboratory manipulation experiments or in studies of corals inhabiting naturally low-pH reefs today. The skeletal growth of corals consists of two distinct processes: extension (upward growth) and densification (lateral thickening). Here, we show that skeletal density is directly sensitive to changes in seawater carbonate ion concentration and thus, to OA, whereas extension is not. We present a numerical model of Porites skeletal growth that links skeletal density with the external seawater environment via its influence on the chemistry of coral calcifying fluid. We validate the model using existing coral skeletal datasets from six Porites species collected across five reef sites and use this framework to project the impact of 21st century OA on Porites skeletal density across the global tropics. Our model predicts that OA alone will drive up to 20.3 ± 5.4% decline in the skeletal density of reef-building Porites corals.

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Functional spatial contextualisation of the effects of multiple stressors in marine bivalves

Many recent studies have revealed that the majority of environmental stressors experienced by marine organisms (ocean acidification, global warming, hypoxia etc.) occur at the same time and place, and that their interaction may complexly affect a number of ecological processes. Here, we experimentally investigated the effects of pH and hypoxia on the functional and behavioural traits of the mussel Mytilus galloprovincialis, we then simulated the potential effects on growth and reproduction dynamics trough a Dynamic Energy Budget (DEB) model under a multiple stressor scenario. Our simulations showed that hypercapnia had a remarkable effect by reducing the maximal habitat size and reproductive output differentially as a function of the trophic conditions, where modelling was spatially contextualized. This study showed the major threat represented by the hypercapnia and hypoxia phenomena for the growth, reproduction and fitness of mussels under the current climate change context, and that a mechanistic approach based on DEB modelling can illustrate complex and site-specific effects of environmental change, producing that kind of information useful for management purposes, at larger temporal and spatial scales.

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Coccolithophore growth and calcification in a changing ocean

Coccolithophores are the most abundant calcifying phytoplankton in the ocean. These tiny primary producers have an important role in the global carbon cycle, substantially contributing to global ocean calcification, ballasting organic matter to the deep sea, forming part of the marine food web base, and influencing ocean-atmosphere CO2 exchange. Despite these important impacts, coccolithophores are not explicitly simulated in most marine ecosystem models and, therefore, their impacts on carbon cycling are not represented in most Earth system models. Here, we compile field and laboratory data to synthesize overarching, across-species relationships between environmental conditions and coccolithophore growth rates and relative calcification (reported as a ratio of particulate inorganic carbon to particulate organic carbon in coccolithophore biomass, PIC/POC). We apply our relationships in a generalized coccolithophore model, estimating current surface ocean coccolithophore growth rates and relative calcification, and projecting how these may change over the 21st century using output from the Community Earth System Model large ensemble. We find that average increases in sea surface temperature of ∼2-3 °C leads to faster coccolithophore growth rates globally ( >10% increase) and increased calcification at high latitudes. Roughly an ubiquitous doubling of surface ocean pCO2 by the end of the century has the potential to moderately stimulate coccolithophore growth rates, but leads to reduced calcification ( ∼25% decrease). Decreasing nutrient availability (from warming-induced increases in stratification) produces increases in relative calcification, but leads to ∼25% slower growth rates. With all drivers combined, we observe decreases in calcification and growth in most low and mid latitude regions, with possible increases in both of these responses in most high latitude regions. Major limitations of our coccolithophore model stem from a lack of conclusive physiological responses to changes in irradiance (we do not include light limitation in our model), and a lack of physiological data for major coccolithophore species. Species within the Umbellosphaera genus, for example, are dominant in mid to low latitude regions where we predict some of the largest decreases in coccolithophore growth rate and calcification.

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Numerical modeling of fish mortality at high CO2 concentrations representing acclimation

A mortality model was developed to predict the impact of high CO2 concentrations on marine fish. To allow for acclimation to a gradual increase of PCO2, the model includes acid–base regulation processes, such as respiration and ion-exchange at the gills. Because the physiological mechanism connecting a decrease in blood pH and mortality is not known, a statistical model was adopted. The mortality calculated for Japanese sillago experiencing a transient change of PCO2 compares moderately well with observations.

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Ocean acidification in the IPCC AR5 WG II

OUP book