Posts Tagged 'modeling'

Assessing coral reef condition indicators for local and global stressors using Bayesian networks

Coral reefs are highly valued ecosystems currently threatened by both local and global stressors. Given the importance of coral reef ecosystems, a Bayesian network approach can benefit an evaluation of threats to reef condition. To this end, we used data to evaluate the overlap between local stressors (overfishing and destructive fishing, watershed‐based pollution, marine‐based pollution, and coastal development threats), global stressors (acidification and thermal stress) and management effectiveness with indicators of coral reef health (live coral index, live coral cover, population bleaching, colony bleaching and recently killed corals). Each of the coral health indicators had Bayesian networks constructed globally and for Pacific, Atlantic, Australia, Middle East, Indian Ocean, and Southeast Asia coral reef locations. Sensitivity analysis helped evaluate the strength of the relationships between different stressors and reef condition indicators. The relationships between indicators and stressors were also evaluated with conditional analyses of linear and nonlinear interactions. In this process, a standardized direct effects analysis was emphasized with a target mean analysis to predict changes in the mean value of the reef indicator from individual changes to the distribution of the predictor variables. The standardized direct effects analysis identified higher risks in the Middle East for watershed‐based pollution with population bleaching and Australia for overfishing and destructive fishing with living coral. For thermal stress, colony bleaching and recently killed coral in the Indian Ocean were found to have the strongest direct associations. For acidification threat, Australia had a relatively strong association with colony bleaching and the Middle East had the strongest overall association with recently killed coral although extrapolated spatial data were used for the acidification estimates. The Bayesian network approach helped to explore the relationships among existing databases used for policy development in coral reef management by examining the sensitivity of multiple indicators of reef condition to spatially‐distributed stress.

Continue reading ‘Assessing coral reef condition indicators for local and global stressors using Bayesian networks’

Retrieving monthly and interannual total-scale pH (pHT) on theEast China Sea shelf using an artificial neural network:ANN-pHT-v1 (update)

While our understanding of pH dynamics has strongly progressed for open-ocean regions, for marginal seas such as the East China Sea (ECS) shelf progress has been constrained by limited observations and complex interactions between biological, physical and chemical processes. Seawater pH is a very valuable oceanographic variable but not always measured using high-quality instrumentation and according to standard practices. In order to predict total-scale pH (pH(T)) and enhance our understanding of the seasonal variability of pHT on the ECS shelf, an artificial neural network (ANN) model was developed using 11 cruise datasets from 2013 to 2017 with coincident observations of pHT, temperature (T), salinity (S), dissolved oxygen (DO), nitrate (N), phosphate (P) and silicate (Si) together with sampling position and time. The reliability of the ANN model was evaluated using independent observations from three cruises in 2018, and it showed a root mean square error accuracy of 0.04. The ANN model responded to T and DO errors in a positive way and S errors in a negative way, and the ANN model was most sensitive to S errors, followed by DO and T errors. Monthly water column pHT for the period 2000-2016 was retrieved using T, S, DO, N, P and Si from the Changjiang biology Finite-Volume Coastal Ocean Model (FVCOM). The agreement is good here in winter, while the reduced performance in summer can be attributed in large part to limitations of the Changjiang biology FVCOM in simulating summertime input variables.

Continue reading ‘Retrieving monthly and interannual total-scale pH (pHT) on theEast China Sea shelf using an artificial neural network:ANN-pHT-v1 (update)’

Global trends of ocean CO2 sink and ocean acidification: an observation-based reconstruction of surface ocean inorganic carbon variables

Ocean acidification is likely to impact marine ecosystems and human societies adversely and is a carbon cycle issue of great concern. Projecting the degree of ocean acidification and the carbon-climate feedback will require understanding the current status, variability, and trends of ocean inorganic carbon system variables and the ocean carbon sink. With this goal in mind, we reconstructed total alkalinity (TA), dissolved inorganic carbon (DIC), CO2 partial pressure (pCO2sea), sea–air CO2 flux, pH, and aragonite saturation state (Ωarg) for the global ocean based on measurements of pCO2sea and TA. We used a multiple linear regression approach to derive relationships to explain TA and DIC and obtained monthly 1° × 1° gridded values of TA and DIC for the period 1993–2018. These data were converted to pCO2sea, pH, and Ωarg, and monthly sea-air CO2 fluxes were obtained in combination with atmospheric CO2. Mean annual sea–air CO2 flux and its rate of change were estimated to be − 2.0 ± 0.5 PgC year−1 and − 0.3 (PgC year−1) decade−1, respectively. Our analysis revealed that oceanic CO2 uptake decreased during the 1990s and has been increasing since 2000. Our estimate of the globally averaged rate of pH change, − 0.0181 ± 0.0001 decade−1, was consistent with that expected from the trend of atmospheric CO2 growth. However, rates of decline of pH were relatively slow in the Southern Ocean (− 0.0165 ± 0.0001·decade−1) and in the western equatorial Pacific (− 0.0148 ± 0.0002·decade−1). Our estimate of the globally averaged rate of pH change can be used to verify Indicator 14.3.1 of Sustainable Development Goals.

Continue reading ‘Global trends of ocean CO2 sink and ocean acidification: an observation-based reconstruction of surface ocean inorganic carbon variables’

Impact of temperature increase and acidification on growth and the reproductive potential of the clam Ruditapes philippinarum using DEB


  • A simulation model based on DEB theory was parameterized for the Manila clam.
  • The pH forecast in 2100 will limit the growth of Manila clam.
  • The temperature forecast in 2100 enhances the reproductive potential of Manila clam.


We built a simulation model based on Dynamic Energy Budget theory (DEB) to assess the growth and reproductive potential of the Manila clam Ruditapes philippinarum under different temperature and pH conditions, based on environmental values forecasted for the end of the 21st c. under climate change scenarios. The parameters of the DEB model were calibrated with the results of seasonal growth experiments under two levels of temperature (ambient and plus 2–3 °C) and three levels of pH (8.1 used as control and 7.7 and 7.3 representing acidification). The results showed that R. philippinarum is expected to have moderate growth in length or individual body mass (ultimate length and body weight would be larger than current values by 2–3%) when taking into account only the effect of temperature increase. However, acidification is likely to have a deleterious effect on growth, with a decrease of 2–5% length or body weight under the pH value of 7.7 forecasted for the end of the 21st c, or 10–15% under a more extreme scenario (pH = 7.3). However, the aggregated reproductive potential, integrated along a lifetime of 10 years, is likely to increase by 30% with temperature increase. Decreasing pH would impact negatively on reproductive potential, but in all simulations under warmer conditions, reproductive potential values were higher than current, suggesting that temperature increase would compensate losses due to acidification. The results are discussed in relation to their possible impact on aquaculture and fisheries of this important commercial bivalve.

Continue reading ‘Impact of temperature increase and acidification on growth and the reproductive potential of the clam Ruditapes philippinarum using DEB’

OceanSODA-ETHZ: A global gridded data set of the surface ocean carbonate system for seasonal to decadal studies of ocean acidification

Ocean acidification has altered the ocean’s carbonate chemistry profoundly since preindustrial times, with potentially serious consequences for marine life. Yet, no long-term global observation-based data set exists that permits to study changes in ocean acidification for all carbonate system parameters over the last few decades. Here, we fill this gap and present a methodologically consistent global data set of all relevant surface ocean parameters, i.e., dissolved inorganic carbon (DIC), total alkalinity (TA), partial pressure of CO2 (pCO2), pH, and the saturation state with respect to mineral CaCO3 (Ω) at monthly resolution over the period 1985 through 2018 at a spatial resolution of 1 × 1°. This data set, named OceanSODA-ETHZ, was created by extrapolating in time and space the surface ocean observations of pCO2 (from the Surface Ocean CO2 ATlas (SOCAT)) and total alkalinity (TA, from the Global Ocean Data Analysis Project (GLODAP)) using the newly developed Geospatial Random Cluster Ensemble Regression (GRaCER) method. This method is based on a two-step (cluster-regression) approach, but extends it by considering an ensemble of such cluster-regressions, leading to higher robustness. Surface ocean DIC, pH, and Ω were then computed from the globally mapped pCO2 and TA using the thermodynamic equations of the carbonate system. For the open ocean, the cluster regression method estimates pCO2 and TA with global near-zero biases and root mean squared errors of 12 µatm and 13 µmol kg−1, respectively. Taking into account also the measurement and representation errors, the total error increases to 14 µatm and 21 µmol kg−1, respectively. We assess the fidelity of the computed parameters by comparing them to direct observations from GLODAP, finding surface ocean pH and DIC global biases of near zero, and root mean squared errors of 0.023 and 16 µmol kg−1, respectively. These errors are very comparable to those expected by propagating the total errors from pCO2 and TA through the thermodynamic computations, indicating a robust and conservative assessment of the errors. We illustrate the potential of this new dataset by analyzing the climatological mean seasonal cycles of the different parameters of the surface ocean carbonate system, highlighting their commonalities and differences. The OceanSODA-ETHZ data can be downloaded from (Gregor and Gruber, 2020).

Continue reading ‘OceanSODA-ETHZ: A global gridded data set of the surface ocean carbonate system for seasonal to decadal studies of ocean acidification’

Physical and biogeochemical drivers of alongshore pH and oxygen variability in the California Current System

In the California Current System (CCS), the nearshore environment experiences natural exposure to low pH and reduced oxygen in response to coastal upwelling. Anthropogenic impacts further decrease pH and oxygen below biological thresholds, making the CCS particularly vulnerable to ocean acidification and hypoxia. Results from a coupled physical‐biogeochemical model reveal a strongly heterogeneous alongshore pattern of nearshore pH and oxygen in the central CCS, both in their long‐term means and trends. This spatial structuring is explained by an interplay between alongshore variability in local upwelling intensity and subsequent primary production, modulated by nearshore advection and regional geostrophic currents. The model solution suggests that the progression of ocean acidification and hypoxia will not be spatially homogeneous, thereby highlighting the need to consider subregional processes when assessing natural and anthropogenic impacts on coastal ecosystems in eastern boundary current upwelling regions.

Continue reading ‘Physical and biogeochemical drivers of alongshore pH and oxygen variability in the California Current System’

Permian–Triassic mass extinction pulses driven by major marine carbon cycle perturbations

The Permian/Triassic boundary approximately 251.9 million years ago marked the most severe environmental crisis identified in the geological record, which dictated the onwards course for the evolution of life. Magmatism from Siberian Traps is thought to have played an important role, but the causational trigger and its feedbacks are yet to be fully understood. Here we present a new boron-isotope-derived seawater pH record from fossil brachiopod shells deposited on the Tethys shelf that demonstrates a substantial decline in seawater pH coeval with the onset of the mass extinction in the latest Permian. Combined with carbon isotope data, our results are integrated in a geochemical model that resolves the carbon cycle dynamics as well as the ocean redox conditions and nitrogen isotope turnover. We find that the initial ocean acidification was intimately linked to a large pulse of carbon degassing from the Siberian sill intrusions. We unravel the consequences of the greenhouse effect on the marine environment, and show how elevated sea surface temperatures, export production and nutrient input driven by increased rates of chemical weathering gave rise to widespread deoxygenation and sporadic sulfide poisoning of the oceans in the earliest Triassic. Our findings enable us to assemble a consistent biogeochemical reconstruction of the mechanisms that resulted in the largest Phanerozoic mass extinction.

Continue reading ‘Permian–Triassic mass extinction pulses driven by major marine carbon cycle perturbations’

Projected expansion of Trichodesmium’s geographical distribution and increase in growth potential in response to climate change

Estimates of marine N2 fixation range from 52 to 73 Tg N/year, of which we calculate up to 84% is from Trichodesmium based on previous measurements of nifH gene abundance and our new model of Trichodesmium growth. Here, we assess the likely effects of four major climate change‐related abiotic factors on the spatiotemporal distribution and growth potential of Trichodesmium for the last glacial maximum (LGM), the present (2006–2015) and the end of this century (2100) by mapping our model of Trichodesmium growth onto inferred global surface ocean fields of pCO2, temperature, light and Fe. We conclude that growth rate was severely limited by low pCO2 at the LGM, that current pCO2 levels do not significantly limit Trichodesmium growth and thus, the potential for enhanced growth from future increases in CO2 is small. We also found that the area of the ocean where sea surface temperatures (SST) are within Trichodesmium‘s thermal niche increased by 32% from the LGM to present, but further increases in SST due to continued global warming will reduce this area by 9%. However, the range reduction at the equator is likely to be offset by enhanced growth associated with expansion of regions with optimal or near optimal Fe and light availability. Between now and 2100, the ocean area of optimal SST and irradiance is projected to increase by 7%, and the ocean area of optimal SST, irradiance and iron is projected to increase by 173%. Given the major contribution of this keystone species to annual N2 fixation and thus pelagic ecology, biogeochemistry and CO2 sequestration, the projected increase in the geographical range for optimal growth could provide a negative feedback to increasing atmospheric CO2 concentrations.

Continue reading ‘Projected expansion of Trichodesmium’s geographical distribution and increase in growth potential in response to climate change’

Remnant kelp bed refugia and future phase-shifts under ocean acidification

Ocean warming, ocean acidification and overfishing are major threats to the structure and function of marine ecosystems. Driven by increasing anthropogenic emissions of CO2, ocean warming is leading to global redistribution of marine biota and altered ecosystem dynamics, while ocean acidification threatens the ability of calcifying marine organisms to form skeletons due to decline in saturation state of carbonate Ω and pH. In Tasmania, the interaction between overfishing of sea urchin predators and rapid ocean warming has caused a phase-shift from productive kelp beds to overgrazed sea urchin barren grounds, however potential impacts of ocean acidification on this system have not been considered despite this threat for marine ecosystems globally. Here we use automated loggers and point measures of pH, spanning kelp beds and barren grounds, to reveal that kelp beds have the capacity to locally ameliorate effects of ocean acidification, via photosynthetic drawdown of CO2, compared to unvegetated barren grounds. Based on meta-analysis of anticipated declines in physiological performance of grazing urchins to decreasing pH and assumptions of nil adaptation, future projection of OA across kelp-barrens transition zones reveals that kelp beds could act as important pH refugia, with urchins potentially becoming increasingly challenged at distances >40 m from kelp beds. Using spatially explicit simulation of physicochemical feedbacks between grazing urchins and their kelp prey, we show a stable mosaicked expression of kelp patches to emerge on barren grounds. Depending on the adaptative capacity of sea urchins, future declines in pH appear poised to further alter phase-shift dynamics for reef communities; thus, assessing change in spatial-patterning of reef-scapes may indicate cascading ecological impacts of ocean acidification.

Continue reading ‘Remnant kelp bed refugia and future phase-shifts under ocean acidification’

Combining mesocosms with models to unravel the effects of global warming and ocean acidification on temperate marine ecosystems

Ocean warming and species exploitation have already caused large-scale reorganization of biological communities across the world. Accurate projections of future biodiversity change require a comprehensive understanding of how entire communities respond to global change. We combined a time-dynamic integrated food web modelling approach (Ecosim) with a community-level mesocosm experiment to determine the independent and combined effects of ocean warming and acidification, and fisheries exploitation, on a temperate coastal ecosystem. The mesocosm enabled important physiological and behavioural responses to climate stressors to be projected for trophic levels ranging from primary producers to top predators, including sharks. We show that under current-day rates of exploitation, warming and ocean acidification will benefit most species in higher trophic levels (e.g. mammals, birds, demersal finfish) in their current climate ranges, with the exception of small pelagic fish, but these benefits will be reduced or lost when these physical stressors co-occur. We show that increases in exploitation will, in most instances, suppress any positive effects of human-driven climate change, causing individual species biomass to decrease at high-trophic levels. Species diversity at the trailing edges of species distributions is likely to decline in the face of ocean warming, acidification and exploitation. We showcase how multi-level mesocosm food web experiments can be used to directly inform dynamic food web models, enabling the ecological processes that drive the responses of marine ecosystems to scenarios of global change to be captured in model projections and their individual and combined effects to be teased apart. Our approach for blending theoretical and empirical results from mesocosm experiments with computational models will provide resource managers and conservation biologists with improved tools for forecasting biodiversity change and altered ecosystem processes due to climate change.

Continue reading ‘Combining mesocosms with models to unravel the effects of global warming and ocean acidification on temperate marine ecosystems’

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Ocean acidification in the IPCC AR5 WG II

OUP book