Posts Tagged 'communitymodeling'

Building tools to model the effects of ocean acidification and how it scales from physiology to fisheries

Ocean acidification is a direct consequence of elevated atmospheric carbon dioxide caused by anthropogenic fossil fuel burning and is one of multiple climate-related stressors in marine environments. Understanding of how these stressors will interact to affect marine life and fisheries is limited. In this thesis, I used integrated modelling approaches to scale the effects of biophysical drivers from physiology to population dynamics and fisheries. I focused on ocean acidification and how it interacts with other main drivers such as temperature and oxygen. I used a dynamic bioclimatic envelope model (DBEM) to project the effects of global environmental change on fisheries under two contrasting scenarios of climate change—the low optimistic climate change scenario in line with the 2015 Paris Agreement to limit global warming to 1.5˚ C, and the high climate change scenario on par with our current ‘business-as-usual’ trajectory. First, I developed an ex-vessel fish price database and explored methods using various ocean acidification assumptions. Ex-vessel fish prices are essential for fisheries economic analyses, while model development of ocean acidification effects are important to better understand the uncertainties surrounding acidification and the sensitivity of the model to these uncertainties. These tools and methods were then used to project the impacts of ocean acidification, in the context of climate change, on global invertebrate fisheries—the species group most sensitive to acidification. My results showed that areas with greater acidification have greater negative responses to climate change, e.g. polar regions. However, ocean warming will likely be a greater driver in species distributions and may overshadow direct effects of acidification. While greater climate change will generally have negative consequences on fisheries, Arctic regions may see increased fisheries catch potential as species shift poleward. Canada’s Arctic remains one of the most pristine marine regions left in the world and climate-driven increases in fisheries potential will have major implications for biodiversity and local indigenous reliance on marine resources. In the face of global environmental change, my thesis provides databases, modelling approaches, scenario development, and assessments of global change necessary for adaptation and mitigation of climate-related effects on marine fisheries.

Continue reading ‘Building tools to model the effects of ocean acidification and how it scales from physiology to fisheries’

Comparison of two carbon-nitrogen regulatory models calibrated with mesocosm data


• OBM is more skilful than CN-REcoM when calibrated and validated with mesocosm data.

• OBM suggests that ocean acidification (OA) may stimulate carbon fixation rates in algae.

• Also, OA may elevate metabolic stress in phytoplankton, according to OBM.

• CN-REcoM imposes weak constraints on parameter values, hence solutions are flexible.

• As OBM is constrained by the physiological trade-offs, solutions are rigid and robust.


Marine phytoplankton can regulate their stoichiometric composition in response to variations in the availability of nutrients, light and the pH of seawater. Varying elemental composition of photoautotrophs affects several important ecological and biogeochemical processes, e.g., primary and export production, nutrient cycling, calcification, and grazing. Here we compare two plankton ecosystem models that consider regulatory mechanisms of cellular carbon and nitrogen, driving the physiological acclimation of photoautotrophs. The Carbon:Nitrogen Regulated Ecosystem Model (CN-REcoM) and the optimality-based model (OBM) differ in their representation of phytoplankton dynamics, i.e. nutrient acquisition, synthesis of chlorophyll a, and growth. All other model compartments (zooplankton, detritus, dissolved inorganic and organic matter) and processes (grazing, aggregation, remineralisation) remain identical in both models.

We assess the skills of the two models against data from an ocean acidification mesocosm experiment with three CO2 treatments. Neither model accounts for any carbon dioxide (CO2) effects explicitly. Instead, we assimilate data of the different CO2 treatments separately into the models. Thereby we aim at identifying optimal model parameter values that might correlate with differences in CO2 conditions. For the OBM, optimal parameter estimates of Qmin (subsistence N:C ratio) and V (maximum potential photosynthesis rate of photoautotrophs) turned out to be higher for mesocosms exposed to high CO2 compared to those with low CO2 concentrations. By contrast, a similar correlation is not observed for the CN-REcoM. A possible physiological interpretation of higher estimates of Qmin and V according to the OBM is that phytoplankton may experience environmental stress under more acidic conditions, and hence must invest more energy/resources for maintaining basic cellular functions. Our data assimilation reveals that the parameters of the OBM are better constrained by the data than those of the CN-REcoM. Furthermore, the OBM is better able than CN-REcoM to reproduce data that were not used for parameter optimization.

Continue reading ‘Comparison of two carbon-nitrogen regulatory models calibrated with mesocosm data’

Modelling the environmental niche space and distributions of cold-water corals and sponges in the Canadian northeast Pacific Ocean


• We present the first comparison of realized niche space among six major, habitat-forming cold-water coral and sponge (CWCS) groups (sponge classes: Hexactinellida, Demospongiae; coral orders: Alcyonacea, Scleractinia, Antipatharia, Pennatulacea) occurring in the Northeast Pacific region of Canada (NEPC).
• The environmental gradients influencing CWCS niche space and breadth is driven by dissolved inorganic carbon, total alkalinity, and dissolved oxygen.
• Significant niche separation occurs among CWCS groups; high tolerance and marginality generally identify CWCS as specialists occurring in uncommon habitat conditions within the NEPC.
• Species distribution models developed for each CWCS group all share severely low dissolved oxygen ([O2] < 0.5 ml L−1) as a major predictor of habitat.
• Areas that are predicted to be suitable habitat for multiple CWCW groups primarily occurs primarily within 500–1400 m bottom depths on the continental slope and at offshore seamounts that have summits that reach into this depth range.


Cold water coral and sponge communities (CWCS) are important indicators of vulnerable marine ecosystems (VMEs) and are used to delineate areas for marine conservation and fisheries management. Although the Northeast Pacific region of Canada (NEPC) is notable for having unique CWCS assemblages and is the location of >80% of Canadian seamounts, the extent of potential CWCS-defined VMEs in this region is unknown. Here, we used a diverse set of environmental data layers (n=30) representing a range of bathymetric derivatives, physicochemical variables, and water column properties to assess the primary factors influencing the niche separation and potential distributions of six habitat-forming groups of CWCS in the NEPC (sponge classes: Hexactinellida, Demospongiae; coral orders: Alcyonacea, Scleractinia, Antipatharia, Pennatulacea). The primary environmental gradients that influence niche separation among CWCS are driven by total alkalinity, dissolved inorganic carbon, and dissolved oxygen. Significant niche separation among groups indicates CWCS to be primarily specialists occurring in rare habitat conditions in the NEPC. Species distribution models (SDMs) developed for each CWCS group shared severely low dissolved oxygen levels ([O2] < 0.5 ml L−1) as a top predictor for habitat suitability in the NEPC. Niche separation is further emphasized by differences in the model-predicted areas of suitable habitat among CWCS groups. Although niches varied among taxa, the general areas of high habitat suitability for multiple CWCS groups in the NEPC occurred within the 500–1400 m bottom depth range which is strongly associated with the extensive oxygen minimum zone (OMZ) characterizing this region. As a result, the largest continuous area of potential CWCS habitat occurred along the continental slope with smaller, isolated patches also occurring at several offshore seamounts that have summits that extend into OMZ depths. Our results provide insight into the factors that influence the distributions of some of the most important habitat-forming taxa in the deep ocean and create an empirical foundation for supporting cold-water coral and sponge conservation in the NEPC.

Continue reading ‘Modelling the environmental niche space and distributions of cold-water corals and sponges in the Canadian northeast Pacific Ocean’

Impacts of the changing ocean-sea ice system on the key forage fish Arctic cod (Boreogadus saida) and subsistence fisheries in the Western Canadian Arctic—evaluating linked Climate, Ecosystem and Economic (CEE) models

This study synthesizes results from observations, laboratory experiments and models to showcase how the integration of scientific methods and indigenous knowledge can improve our understanding of (a) past and projected changes in environmental conditions and marine species; (b) their effects on social and ecological systems in the respective communities; and (c) support management and planning tools for climate change adaptation and mitigation. The study links climate-ecosystem-economic (CEE) models and discusses uncertainties within those tools. The example focuses on the key forage species in the Inuvialuit Settlement Region (Western Canadian Arctic), i.e., Arctic cod (Boreogadus saida). Arctic cod can be trophically linked to sea-ice algae and pelagic primary producers and are key vectors for energy transfers from plankton to higher trophic levels (e.g., ringed seals, beluga), which are harvested by Inuit peoples. Fundamental changes in ice and ocean conditions in the region affect the marine ecosystem and fish habitat. Model simulations suggest increasing trends in oceanic phytoplankton and sea-ice algae with high interannual variability. The latter might be linked to interannual variations in Arctic cod abundance and mask trends in observations. CEE simulations incorporating physiological temperature limits data for the distribution of Arctic cod, result in an estimated 17% decrease in Arctic cod populations by the end of the century (high emission scenario), but suggest increases in abundance for other Arctic and sub-Arctic species. The Arctic cod decrease is largely caused by increased temperatures and constraints in northward migration, and could directly impact key subsistence species. Responses to acidification are still highly uncertain, but sensitivity simulations suggests an additional 1% decrease in Arctic cod populations due to pH impacts on growth and survival. Uncertainties remain with respect to detailed future changes, but general results are likely correct and in line with results from other approaches. To reduce uncertainties, higher resolution models with improved parameterizations and better understanding of the species’ physiological limits are required. Arctic communities should be directly involved, receive tools and training to conduct local, unified research and food chain monitoring while decisions regarding commercial fisheries will need to be precautionary and adaptive in light of the existing uncertainties.

Continue reading ‘Impacts of the changing ocean-sea ice system on the key forage fish Arctic cod (Boreogadus saida) and subsistence fisheries in the Western Canadian Arctic—evaluating linked Climate, Ecosystem and Economic (CEE) models’

Toxic algae silence physiological responses to multiple climate drivers in a tropical marine food chain

Research on the effects of climate change in the marine environment continues to accelerate, yet we know little about the effects of multiple climate drivers in more complex, ecologically relevant settings – especially in sub-tropical and tropical systems. In marine ecosystems, climate change (warming and freshening from land run-off) will increase water column stratification which is favorable for toxin producing dinoflagellates. This can increase the prevalence of toxic microalgal species, leading to bioaccumulation of toxins by filter feeders, such as bivalves, with resultant negative impacts on physiological performance. In this study we manipulated multiple climate drivers (warming, freshening, and acidification), and the availability of toxic microalgae, to determine their impact on the physiological health, and toxin load of the tropical filter-feeding clam, Meretrix meretrix. Using a structural equation modeling (SEM) approach, we found that exposure to projected marine climates resulted in direct negative effects on metabolic and immunological function and, that these effects were often more pronounced in clams exposed to multiple, rather than single climate drivers. Furthermore, our study showed that these physiological responses were modified by indirect effects mediated through the food chain. Specifically, we found that when bivalves were fed with a toxin-producing dinoflagellate (Alexandrium minutum) the physiological responses, and toxin load changed differently and in a non-predictable way compared to clams exposed to projected marine climates only. Specifically, oxygen consumption data revealed that these clams did not respond physiologically to climate warming or the combined effects of warming, freshening and acidification. Our results highlight the importance of quantifying both direct and, indirect food chain effects of climate drivers on a key tropical food species, and have important implications for shellfish production and food safety in tropical regions.

Continue reading ‘Toxic algae silence physiological responses to multiple climate drivers in a tropical marine food chain’

Direct and indirect impacts of marine acidification on the ecosystem services provided by coralligenous reefs and seagrass systems

Increasing emissions of CO2 and the resultant ocean acidification (OA) will have large implications for the marine ecosystems sustained by habitat-forming species and their related ecosystem services (ES), with potentially significant impacts on human well-being. Here, we provide an assessment of the direct and indirect impacts of OA on ES. The changes in the functioning of coralligenous reefs and Posidonia oceanica meadows promoted by OA were investigated by i) synthesizing current knowledge into conceptual models. The models were then used to, ii) assessing the impacts of exposure of the selected taxa at the acidification level associated with two CO2 emission scenarios and iii) using the conceptual model outputs to project the cascading impacts from individuals to functions to ES.

The results highlight that the combination of the direct and indirect effects of acidification will alter many functions of both coralligenous and P.oceanica systems, triggering habitat modifications and the loss of highly valuable ES.

While the exact timing of the expected changes will depend on the severity of the emission scenarios, significant and hardly reversible changes can be expected as quickly as a few decades under the business-as-usual scenario, and many ecosystem services are at risk even under much more conservative scenarios.

Continue reading ‘Direct and indirect impacts of marine acidification on the ecosystem services provided by coralligenous reefs and seagrass systems’

Highest plasticity of carbon‐concentrating mechanisms in earliest evolved phytoplankton

Phytoplankton photosynthesis strongly relies on the operation of carbon‐concentrating mechanisms (CCMs) to accumulate CO2 around their carboxylating enzyme ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO). Earlier evolved phytoplankton groups were shown to exhibit higher CCM activities to compensate for their RuBisCO with low CO2 specificities. Here, we tested whether earlier evolved phytoplankton groups also exhibit a higher CCM plasticity. To this end, we collected data from literature and applied a Bayesian linear meta‐analytic model. Our results show that with elevated pCO2, photosynthetic CO2 affinities decreased strongest and most consistent for the earlier evolved groups, i.e., cyanobacteria and dinoflagellates, while CO2‐dependent changes in affinities for haptophytes and diatoms were smaller and less consistent. In addition, responses of maximum photosynthetic rates toward elevated pCO2 were generally small and inconsistent across species. Our results demonstrate that phytoplankton groups with an earlier origin possess a high CCM plasticity, whereas more recently evolved groups do not, which likely results from evolved differences in the CO2 specificity of RuBisCO.

Continue reading ‘Highest plasticity of carbon‐concentrating mechanisms in earliest evolved phytoplankton’

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Ocean acidification in the IPCC AR5 WG II

OUP book