Posts Tagged 'modelling'

Continuous monitoring and future projection of ocean warming, acidification, and deoxygenation on the subarctic coast of Hokkaido, Japan

As the ocean absorbs excessive anthropogenic CO2 and ocean acidification proceeds, it is thought to be harder for marine calcifying organisms, such as shellfish, to form their skeletons and shells made of calcium carbonate. Recent studies have suggested that various marine organisms, both calcifiers and non-calcifiers, will be affected adversely by ocean warming and deoxygenation. However, regardless of their effects on calcifiers, the spatiotemporal variability of parameters affecting ocean acidification and deoxygenation has not been elucidated in the subarctic coasts of Japan. This study conducted the first continuous monitoring and future projection of physical and biogeochemical parameters of the subarctic coast of Hokkaido, Japan. Our results show that the seasonal change in biogeochemical parameters, with higher pH and dissolved oxygen (DO) concentration in winter than in summer, was primarily regulated by water temperature. The daily fluctuations, which were higher in the daytime than at night, were mainly affected by daytime photosynthesis by primary producers and respiration by marine organisms at night. Our projected results suggest that, without ambitious commitment to reducing CO2 and other greenhouse gas emissions, such as by following the Paris Agreement, the impact of ocean warming and acidification on calcifiers along subarctic coasts will become serious, exceeding the critical level of high temperature for 3 months in summer and being close to the critical level of low saturation state of calcium carbonate for 2 months in mid-winter, respectively, by the end of this century. The impact of deoxygenation might often be prominent assuming that the daily fluctuation in DO concentration in the future is similar to that at present. The results also suggest the importance of adaptation strategies by local coastal industries, especially fisheries, such as modifying aquaculture styles.

Continue reading ‘Continuous monitoring and future projection of ocean warming, acidification, and deoxygenation on the subarctic coast of Hokkaido, Japan’

The variable circulation and carbonate chemistry of ocean upwelling systems

Ocean upwelling is a process in which winds drive deep waters to the surface ocean. The biogeochemical state of these waters causes upwelling regions to have some of the strongest air-sea fluxes of carbon dioxide (CO2) and most productive fisheries in the global oceans. In this dissertation, I use Earth System models to investigate the variability and projected impacts of climate change on upwelling systems. I first use the Community Earth System Model Large Ensemble (CESM-LE) to project the impacts of climate change on upwelling in the California Current. The CESM-LE provides an ensemble of potential trajectories of the climate system that differ due to internal climate variability. I find that upwelling is expected to weaken over the next century in the summer and intensify poleward in the spring due to anthropogenic climate change. Next, I use the CESM-LE to highlight the role of internal climate variability in modulating air-sea CO2 fluxes in the major Eastern Boundary Upwelling Systems (EBUS). I identify the major mode of internal variability that influences air-sea CO2 flux in each EBUS. I then quantify how the given mode of variability modifies local conditions, which in turn leads to the anomalous air-sea CO2 fluxes. Following this, I use a version of the CESM-LE that is configured for climate prediction to examine predictability of ocean acidification in the California Current. I find that our system makes skillful forecasts of surface pH out to fourteen months relative to observations and has a potential ceiling of skillful prediction out to five years in some regions. Finally, I use the Model for Prediction Across Scales Ocean (MPAS-O) to investigate the pathways over which carbon upwells in the Southern Ocean. I seed a high-resolution version of MPAS-O with 1,000,000 Lagrangian floats and find that regions with complex ocean topography have a disproportionate influence on bringing carbon-rich waters from the deep Southern Ocean to the surface. The results of this dissertation highlight the value of using ensemble methods and the Lagrangian perspective in Earth System models to better understand the dynamic and variable biogeochemistry in ocean upwelling systems.

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A pronounced spike in ocean productivity triggered by the Chicxulub impact


There is increasing evidence linking the mass-extinction event at the Cretaceous-Paleogene boundary to an asteroid impact near Chicxulub, Mexico. Here we use model simulations to explore the combined effect of sulfate aerosols, carbon dioxide and dust from the impact on the oceans and the marine biosphere in the immediate aftermath of the impact. We find a strong temperature decrease, a brief algal bloom caused by nutrients from both the deep ocean and the projectile, and moderate surface ocean acidification. Comparing the modeled longer-term post-impact warming and changes in carbon isotopes with empirical evidence points to a substantial release of carbon from the terrestrial biosphere. Overall, our results shed light on the decades to centuries after the Chicxulub impact which are difficult to resolve with proxy data.

Plain Language Summary

The sudden disappearance of the dinosaurs and many other species during the end-Cretaceous mass extinction 66 million years ago marks one of the most profound events in the history of life on Earth. The impact of a large asteroid near Chicxulub, Mexico, is increasingly recognised as the trigger of this extinction, causing global darkness and a pronounced cooling. However, the links between the impact and the changes in the biosphere are not fully understood. Here, we investigate how life in the ocean reacts to the perturbations in the decades and centuries after the impact. We find a short-lived algal bloom caused by the upwelling of nutrients from the deep ocean and nutrient input from the impactor.

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Reversing ocean acidification along the Great Barrier Reef using alkalinity injection

The Great Barrier Reef (GBR) is a globally significant coral reef system supporting productive and diverse ecosystems. The GBR is under increasing threat from climate change and local anthropogenic stressors, with its general condition degrading over recent decades. In response to this, a number of techniques have been proposed to offset or ameliorate environmental changes. In this study, we use a coupled hydrodynamic-biogeochemical model of the GBR and surrounding ocean to simulate artificial ocean alkalinisation (AOA) as a means to reverse the impact of global ocean acidification on GBR reefs. Our results demonstrate that a continuous release of 90 000 t of alkalinity every 3 d over one year along the entire length of the GBR, following the Gladstone-Weipa bulk carrier route, increases the mean aragonite saturation state (Ωar) across the GBR’s 3860 reefs by 0.05. This change offsets just over 4 years (∼4.2) of ocean acidification under the present rate of anthropogenic carbon emissions. The injection raises Ωar in the 250 reefs closest to the route by ⩾0.15, reversing further projected Ocean Acidification. Following cessation of alkalinity injection Ωar returns to the value of the waters in the absence of AOA over a 6 month period, primarily due to transport of additional alkalinity into the Coral Sea. Significantly, our study provides for the first time a model of AOA applied along existing shipping infrastructure that has been used to investigate shelf scale impacts. Thus, amelioration of decades of OA on the GBR is feasible using existing infrastructure, but is likely to be extremely expensive, include as yet unquantified risks, and would need to be undertaken continuously until such time, probably centuries in the future, when atmospheric CO2 concentrations have returned to today’s values.

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Nonlinearity, irreversibility, and surprise – managing Atlantic cod under climate change

Climate change is at the forefront of today’s global challenges with its potential to turn into a runaway process. Fishing pressure acts in concert and exacerbates the impacts of climate change. The North Atlantic Ocean is no exemption of the increasing anthropogenic stress with Atlantic cod, Gadus Morhua, one of its most prominent fish species, displaying the ocean’s state. Most Atlantic cod stocks have experienced high rates of fishing and biomass declines, leading to renovation of fishing regulations and the implementation of rebuilding strategies. Today, the cod stocks differ considerably in trends and commercial status with 8 stocks considered collapsed and 57 % of today’s landings supplied by one single stock, the North East Arctic cod. What drives the collapse and what drives the recovery of a stock? Elucidating drivers of Atlantic cod productivity at low abundance is inevitable for sustainably managing the species in its changing habitat. This thesis attempts a comprehensive study on climate change impacts by addressing rising ocean temperature (paper I-III), temperature variability (paper II), acidification (paper III) and uncertainty (of the biology and as risk in management under the precautionary approach [paper IV]). Individual and synergistic impacts of climate change are discussed with a particular focus on nonlinear dynamics, including the potential for Allee effects (paper I-III). Allee effects describe the decrease in per capita growth rate at small population size, which can hinder population recovery by reinforcing degradation. Such a shift in the underlying biology can be irreversible and demands proactive and precautionary management measures. Application of precautionary measures to protect the environment and manage risks in situations of high uncertainty is a central tenet of the “precautionary approach”, a guiding principle in fisheries management. The poor state of various commercial fish stocks worldwide stands in contrast to the precautionary approach and suggests a subordinate role of science in fisheries management. In paper IV, Canada’s fisheries policy and advisory process is contrasted with the EU’s Common Fisheries Policy in regard to the precautionary approach and the role of science, in order to identify policy and institutional constraints that have hindered sustainable, precautionary management practices. Drawing from insights on climate change driven productivity changes (paper I-III) and the importance of a policy and institutional framework that acknowledges these (paper IV), this thesis ends with suggestions for scientifically informed, precautionary and sustainable fisheries management practices that can speed up recovery and allow for a vital fishery in the future.

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Effects of triclosan exposure on the energy budget of Ruditapes philippinarum and R. decussatus under climate change scenarios


  • Environmental triclosan levels alter the reproductive output of R. philippinarum.
  • Environmental triclosan levels reduce body mass in R. philippinarum.
  • R. decussatus growth was resilient to environmental changes.
  • Worst case scenario (TCS and climate change) will affect Manila clam production.


We built a simulation model based on Dynamic Energy Budget theory (DEB) to assess the growth and reproductive potential of the native European clam Ruditapes decussatus and the introduced Manila clam Ruditapes philippinarum under current temperature and pH conditions in a Portuguese estuary and under those forecasted for the end of the 21st c. The climate change scenario RCP8.5 predicts temperature increase of 3 °C and a pH decrease of 0.4 units. The model was run under additional conditions of exposure to the emerging contaminant triclosan (TCS) and in the absence of this compound. The parameters of the DEB model were calibrated with the results of laboratory experiments complemented with data from the literature available for these two important commercial shellfish resources. For each species and experimental condition (eight combinations), we used data from the experiments to produce estimates for the key parameters controlling food intake flux, assimilation flux, somatic maintenance flux and energy at the initial simulation time. The results showed that the growth and reproductive potential of both species would be compromised under future climate conditions, but the effect of TCS exposure had a higher impact on the energy budget than forecasted temperature and pH variations. The egg production of R. philippinarum was projected to suffer a more marked reduction with exposure to TCS, regardless of the climatic factor, while the native R. decussatus appeared more resilient to environmental causes of stress. The results suggest a likely decrease in the rates of expansion of the introduced R. philippinarum in European waters, and negative effects on fisheries and aquaculture production of exposure to emerging contaminants (e.g., TCS) and climate change.

Continue reading ‘Effects of triclosan exposure on the energy budget of Ruditapes philippinarum and R. decussatus under climate change scenarios’

Online-coupling of widely-ranged timescales to model coral reef development


  • A biophysical model framework for coral reef evolution is developed.
  • The model can be used to predict the coral response to the environment via process-based relations.
  • The model bridges the gap in timescales of processes from seconds to millennia.
  • Model predictions are within the accuracy of climate projections.
  • The model is an efficient tool for forecasting coral reef development to inform policy makers.


The increasing pressure on Earth’s ecosystems due to climate change is becoming more and more evident and the impacts of climate change are especially visible on coral reefs. Understanding how climate change interacts with the physical environment of reefs to impact coral growth and reef development is critically important to predicting the persistence of reefs into the future. In this study, a biophysical model was developed including four environmental factors in a feedback loop with the coral’s biology: (1) light; (2) hydrodynamics; (3) temperature; and (4) pH. The submodels are online coupled, i.e. regularly exchanging information and feedbacks while the model runs. This ensures computational efficiency despite the widely-ranged timescales. The composed biophysical model provides a significant step forward in understanding the processes that modulate the evolution of coral reefs, as it is the first construction of a model in which the hydrodynamics are included in the feedback loop.

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Projecting ocean acidification impacts for the Gulf of Maine to 2050: new tools and expectations

Ocean acidification (OA) is increasing predictably in the global ocean as rising levels of atmospheric carbon dioxide lead to higher oceanic concentrations of inorganic carbon. The Gulf of Maine (GOM) is a seasonally varying region of confluence for many processes that further affect the carbonate system including freshwater influences and high productivity, particularly near the coast where local processes impart a strong influence. Two main regions within the GOM currently experience carbonate conditions that are suboptimal for many organisms—the nearshore and subsurface deep shelf. OA trends over the past 15 years have been masked in the GOM by recent warming and changes to the regional circulation that locally supply more Gulf Stream waters. The region is home to many commercially important shellfish that are vulnerable to OA conditions, as well as to the human populations whose dependence on shellfish species in the fishery has continued to increase over the past decade. Through a review of the sensitivity of the regional marine ecosystem inhabitants, we identified a critical threshold of 1.5 for the aragonite saturation state (Ωa). A combination of regional high-resolution simulations that include coastal processes were used to project OA conditions for the GOM into 2050. By 2050, the Ωa declines everywhere in the GOM with most pronounced impacts near the coast, in subsurface waters, and associated with freshening. Under the RCP 8.5 projected climate scenario, the entire GOM will experience conditions below the critical Ωa threshold of 1.5 for most of the year by 2050. Despite these declines, the projected warming in the GOM imparts a partial compensatory effect to Ωa by elevating saturation states considerably above what would result from acidification alone and preserving some important fisheries locations, including much of Georges Bank, above the critical threshold.

Continue reading ‘Projecting ocean acidification impacts for the Gulf of Maine to 2050: new tools and expectations’

Patterns of element incorporation in calcium carbonate biominerals recapitulate phylogeny for a diverse range of marine calcifiers

Elemental ratios in biogenic marine calcium carbonates are widely used in geobiology, environmental science, and paleoenvironmental reconstructions. It is generally accepted that the elemental abundance of biogenic marine carbonates reflects a combination of the abundance of that ion in seawater, the physical properties of seawater, the mineralogy of the biomineral, and the pathways and mechanisms of biomineralization. Here we report measurements of a suite of nine elemental ratios (Li/Ca, B/Ca, Na/Ca, Mg/Ca, Zn/Ca, Sr/Ca, Cd/Ca, Ba/Ca, and U/Ca) in 18 species of benthic marine invertebrates spanning a range of biogenic carbonate polymorph mineralogies (low-Mg calcite, high-Mg calcite, aragonite, mixed mineralogy) and of phyla (including Mollusca, Echinodermata, Arthropoda, Annelida, Cnidaria, Chlorophyta, and Rhodophyta) cultured at a single temperature (25°C) and a range of pCO2 treatments (ca. 409, 606, 903, and 2856 ppm). This dataset was used to explore various controls over elemental partitioning in biogenic marine carbonates, including species-level and biomineralization-pathway-level controls, the influence of internal pH regulation compared to external pH changes, and biocalcification responses to changes in seawater carbonate chemistry. The dataset also enables exploration of broad scale phylogenetic patterns of elemental partitioning across calcifying species, exhibiting high phylogenetic signals estimated from both uni- and multivariate analyses of the elemental ratio data (univariate: λ = 0–0.889; multivariate: λ = 0.895–0.99). Comparing partial R2 values returned from non-phylogenetic and phylogenetic regression analyses echo the importance of and show that phylogeny explains the elemental ratio data 1.4–59 times better than mineralogy in five out of nine of the elements analyzed. Therefore, the strong associations between biomineral elemental chemistry and species relatedness suggests mechanistic controls over element incorporation rooted in the evolution of biomineralization mechanisms.

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Reviews and syntheses: spatial and temporal patterns in metabolic fluxes inform potential for seagrass to locally mitigate ocean acidification

As global change continues to progress, there is a growing interest in assessing any local levers that could be used to manage the social and ecological impacts of rising CO2 concentrations. While habitat conservation and restoration have been widely recognized for their role in carbon storage and sequestration at a global scale, the potential for managers to use vegetated habitats to mitigate CO2 concentrations at local scales in marine ecosystems facing the accelerating threat of ocean acidification (OA) has only recently garnered attention. Early studies have shown that submerged aquatic vegetation, such as seagrass beds, can locally draw down CO2 and raise seawater pH in the water column through photosynthesis, but empirical studies of local OA mitigation are still quite limited. Here, we leverage the extensive body of literature on seagrass community metabolism to highlight key considerations for local OA management through seagrass conservation or restoration. In particular, we synthesize the results from 62 studies reporting in situ rates of seagrass gross primary productivity, respiration, and/or net community productivity to highlight spatial and temporal variability in carbon fluxes. We illustrate that daytime net community production is positive overall, and similar across seasons and geographies. Full-day net community production rates, which illustrate the potential cumulative effect of seagrass beds on seawater biogeochemistry integrated over day and night, were also positive overall, but were higher in summer months in both tropical and temperate ecosystems. Although our analyses suggest seagrass meadows are generally autotrophic, the modeled effects on seawater pH are relatively small in magnitude. In addition, we illustrate that periods when full-day net community production is highest could be associated with lower nighttime pH and increased diurnal variability in seawater pCO2/pH. Finally, we highlight important areas for future research to inform the next steps for assessing the utility of this approach for management.

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Ocean acidification in the IPCC AR5 WG II

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