Posts Tagged 'modeling'

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’

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’

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’

Ocean acidification has impacted coral growth on the Great Barrier Reef

Ocean acidification (OA) reduces the concentration of seawater carbonate ions that stony corals need to produce their calcium carbonate skeletons, and is considered a significant threat to the functional integrity of coral reef ecosystems. However, detection and attribution of OA impact on corals in nature are confounded by concurrent environmental changes, including ocean warming. Here we use a numerical model to isolate the effects of OA and temperature, and show that OA alone has caused 13±3% decline in the skeletal density of massive Porites corals on the Great Barrier Reef since 1950. This OA‐induced thinning of coral skeletons, also evident in Porites from the South China Sea but not in the central equatorial Pacific, reflects enhanced acidification of reef water relative to the surrounding open ocean. Our finding reinforces concerns that even corals that might survive multiple heatwaves are structurally weakened and increasingly vulnerable to the compounding effects of climate change.

Continue reading ‘Ocean acidification has impacted coral growth on the Great Barrier Reef’

The impact of intertidal areas on the carbonate system of the southern North Sea (update)

The coastal ocean is strongly affected by ocean acidification because of its shallow water depths, low volume, and the closeness to terrestrial dynamics. Earlier observations of dissolved inorganic carbon (DIC) and total alkalinity (TA) in the southern part of the North Sea, a northwest European shelf sea, revealed lower acidification effects than expected. It has been assumed that anaerobic degradation and subsequent TA release in the adjacent back-barrier tidal areas (Wadden Sea) in summertime is responsible for this phenomenon. In this study the exchange rates of TA and DIC between the Wadden Sea tidal basins and the North Sea and the consequences for the carbonate system in the German Bight are estimated using a 3D ecosystem model. The aim of this study is to differentiate the various sources contributing to observed high summer TA in the southern North Sea. Measured TA and DIC in the Wadden Sea are considered as model boundary conditions. This procedure acknowledges the dynamic behaviour of the Wadden Sea as an area of effective production and decomposition of organic material. According to the modelling results, 39 Gmol TA yr−1 were exported from the Wadden Sea into the North Sea, which is less than a previous estimate but within a comparable range. The interannual variabilities in TA and DIC, mainly driven by hydrodynamic conditions, were examined for the years 2001–2009. Dynamics in the carbonate system are found to be related to specific weather conditions. The results suggest that the Wadden Sea is an important driver for the carbonate system in the southern North Sea. On average 41 % of TA inventory changes in the German Bight were caused by riverine input, 37 % by net transport from adjacent North Sea sectors, 16 % by Wadden Sea export, and 6 % were caused by internal net production of TA. The dominant role of river input for the TA inventory disappears when focusing on TA concentration changes due to the corresponding freshwater fluxes diluting the marine TA concentrations. The ratio of exported TA versus DIC reflects the dominant underlying biogeochemical processes in the Wadden Sea. Whereas aerobic degradation of organic matter played a key role in the North Frisian Wadden Sea during all seasons of the year, anaerobic degradation of organic matter dominated in the East Frisian Wadden Sea. Despite the scarcity of high-resolution field data, it is shown that anaerobic degradation in the Wadden Sea is one of the main contributors of elevated summer TA values in the southern North Sea.

Continue reading ‘The impact of intertidal areas on the carbonate system of the southern North Sea (update)’

Effects of climate change on coastal ecosystem food webs: implications for aquaculture


• Food web models and scenarios were used to forecast effects of climate change.

• Modeled bays were vulnerable to the effects of climate change.

• In two of three study bays the ability to support bivalve aquaculture disappeared.


Coastal ecosystems provide important ecosystem services for millions of people. Climate change is modifying coastal ecosystem food web structure and function and threatens these essential ecosystem services. We used a combination of two new and one existing ecosystem food web models and altered scenarios that are possible with climate change to quantify the impacts of climate change on ecosystem stability in three coastal bays in Maine, United States. We also examined the impact of climate change on bivalve fisheries and aquaculture. Our modeled scenarios explicitly considered the predicted effects of future climatic change and human intervention and included: 1) the influence of increased terrestrial dissolved organic carbon loading on phytoplankton biomass; 2) benthic community change driven by synergisms between climate change, historical overfishing, and increased species invasion; and 3) altered trophic level energy transfer driven by ocean warming and acidification. The effects of climate change strongly negatively influenced ecosystem energy flow and ecosystem stability and negatively affected modeled bivalve carrying capacity in each of our models along the Maine coast of the eastern United States. Our results suggest that the interconnected nature of ecosystem food webs make them extremely vulnerable to synergistic effects of climate change. To better inform fisheries and aquaculture management, the effects of climate change must be explicitly incorporated.

Continue reading ‘Effects of climate change on coastal ecosystem food webs: implications for aquaculture’

A regional vulnerability assessment for the Dungeness crab (Metacarcinus magister) to changing ocean conditions: insights from model projections and empirical experiments

Among global coastal regions, the Northern California Current System (N-CCS) is already experiencing effects from ocean acidification and hypoxia during the summer, primarily due to the region’s seasonal upwelling, current systems, and high productivity. Oxygen, pH, and temperature conditions are expected to become more stressful with continued fossil fuel emissions under global climate change, posing a serious threat to the region’s fisheries. N-CCS fishing communities rely heavily on the economically and culturally important Dungeness crab (Metacarcinus magister). The fishery is currently sustainably managed, but potential negative impacts from changing ocean conditions on Dungeness crab life stages and populations could have adverse effects for the fishery and the communities that rely on it. To quantify the vulnerability of Dungeness crab life stages and populations to predicted future conditions, both model projections and empirical experiments need to be employed. A semi-quantitative, life stage-specific framework was adapted here to assess the vulnerability of Dungeness crab to low pH, low dissolved oxygen, and high temperature under present and future projected conditions in the seasonally dynamic N-CCS. This was achieved using a combination of regional ocean models, species distribution maps, larval transport models, a population matrix model, and a literature review. This multi-faceted approach revealed that crab vulnerability to the three climate stressors will increase in the future (year 2100) under the most intense emissions scenario, with vulnerability to low oxygen being the most severe to the N-CCS population overall. Increases in vulnerability were largely driven by the adult life stage, which contributes the most to population growth. Empirical experiments demonstrated that adult crab respiration rates increase exponentially with temperature, potentially making this life stage more susceptible to hypoxia in the future. Together, this work provides novel insights into the effects of changing ocean conditions on Dungeness crab populations, which may help inform fishery management strategies.

Continue reading ‘A regional vulnerability assessment for the Dungeness crab (Metacarcinus magister) to changing ocean conditions: insights from model projections and empirical experiments’

Temperature and salinity, not acidification, predict near-future larval growth and larval habitat suitability of Olympia oysters in the Salish Sea

Most invertebrates in the ocean begin their lives with planktonic larval phases that are critical for dispersal and distribution of these species. Larvae are particularly vulnerable to environmental change, so understanding interactive effects of environmental stressors on larval life is essential in predicting population persistence and vulnerability of species. Here, we use a novel experimental approach to rear larvae under interacting gradients of temperature, salinity, and ocean acidification, then model growth rate and duration of Olympia oyster larvae and predict the suitability of habitats for larval survival. We find that temperature and salinity are closely linked to larval growth and larval habitat suitability, but larvae are tolerant to acidification at this scale. We discover that present conditions in the Salish Sea are actually suboptimal for Olympia oyster larvae from populations in the region, and that larvae from these populations might actually benefit from some degree of global ocean change. Our models predict a vast decrease in mean pelagic larval duration by the year 2095, which has the potential to alter population dynamics for this species in future oceans. Additionally, we find that larval tolerance can explain large-scale biogeographic patterns for this species across its range.

Continue reading ‘Temperature and salinity, not acidification, predict near-future larval growth and larval habitat suitability of Olympia oysters in the Salish Sea’

Trophic pyramids reorganize when food web architecture fails to adjust to ocean change

As human activities intensify, the structures of ecosystems and their food webs often reorganize. Through the study of mesocosms harboring a diverse benthic coastal community, we reveal that food web architecture can be inflexible under ocean warming and acidification and unable to compensate for the decline or proliferation of taxa. Key stabilizing processes, including functional redundancy, trophic compensation, and species substitution, were largely absent under future climate conditions. A trophic pyramid emerged in which biomass expanded at the base and top but contracted in the center. This structure may characterize a transitionary state before collapse into shortened, bottom-heavy food webs that characterize ecosystems subject to persistent abiotic stress. We show that where food web architecture lacks adjustability, the adaptive capacity of ecosystems to global change is weak and ecosystem degradation likely.

Continue reading ‘Trophic pyramids reorganize when food web architecture fails to adjust to ocean change’

Coastal processes modify projections of some climate-driven stressors in the California Current System

Global projections for ocean conditions in 2100 predict that the North Pacific will experience some of the largest changes. Coastal processes that drive variability in the region can alter these projected changes, but are poorly resolved by global coarse resolution models. We quantify the degree to which local processes modify biogeochemical changes in the eastern boundary California Current System (CCS) using multi-model regionally downscaled climate projections of multiple climate-associated stressors (temperature, O2, pH, Ω, and CO2). The downscaled projections predict changes consistent with the directional change from the global projections for the same emissions scenario. However, the magnitude and spatial variability of projected changes are modified in the downscaled projections for carbon variables. Future changes in pCO2 and surface Ω are amplified while changes in pH and upper 200 meter Ω are dampened relative to the projected change in global models. Within the CCS, differences in global and downscaled climate stressors are spatially variable, and the northern CCS experiences the most intense modification. These projected changes are consistent with source waters lower in oxygen, higher in nutrients, and in combination with solubility-driven changes, altered future upwelled waters in the CCS. The results presented here suggest coastal process resolving projections are necessary for adequate representation of the magnitude of projected change in pH and carbon stressors in the CCS.

Continue reading ‘Coastal processes modify projections of some climate-driven stressors in the California Current System’

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Ocean acidification in the IPCC AR5 WG II

OUP book