Jorn Bruggeman

Bolding & Bruggeman ApS

A wealth of information on metabolic parameters of a species can be inferred from observations on species that are phylogenetically related. Phylogeny-based information can complement direct empirical evidence, and is particularly valuable if experiments on the species of interest are not feasible. The PhyloPars web server provides a statistically...

The quantitative characterization of the ecology of individual phytoplankton taxa is essential for model resolution of many aspects of aquatic ecosystems. Existing literature cannot directly parameterize all phytoplankton taxa of interest, as many traits and taxa have not been sampled. However, valuable clues on the value of traits are found in the...

Current aquatic ecosystem models accommodate increasing amounts of physiological detail, but marginalize the role of biodiversity by aggregating multitudes of different species. We propose that at present, understanding of aquatic ecosystems is likely to benefit more from improved descriptions of biodiversity and succession than from incorporation...

Squid species show pronounced interannual variability in population size. While this may partially reflect changes in fisheries pressure, it is thought to be primarily the result of environmental variability. Most squid have an annual life cycle with only a short period dedicated to reproduction. With little overlap between generations, the environ...

Data assimilation (DA) in marine and freshwater systems combines numerical models and observations to deliver the best possible characterization of a waterbody's physical and biogeochemical state. DA underpins the widely used 3D ocean state reanalyses and forecasts produced operationally by, e.g., the Copernicus Marine Service. The use of DA in nat...

Data assimilation (DA) in marine and freshwater systems combines numerical models and observations to deliver the best possible characterisation of a water body’s physical and biogeochemical state. This underpins the widely used 3D ocean state reanalyses and forecasts produced operationally by e.g. the Copernicus Marine Service. The use of DA in na...

Chromophoric dissolved organic matter (CDOM) significantly contributes to the non-water absorption budget in the Mediterranean Sea. The absorption coefficient of CDOM, aCDOM(λ), is measurable in situ and can be retrieved remotely, although ocean-colour algorithms do not distinguish it from the absorption of detritus. These observations can be used...

Plain Language Summary Oxygen is one of the most relevant ecosystem parameters in marine systems and in lakes. In shallow systems, the overall oxygen budget is often controlled by the sedimentary oxygen demand, and it is therefore crucial to account for the exchange of oxygen and other solutes between the sediment and the water column. In this, con...

The decrease of the Lake Urmia water level from its peak around 1995 to present has had dramatic consequences for the lake ecosystem. To restore the lake, the salinity must be brought back to salinity values well below saturation levels. In this chapter, we adapt a 3D hydrodynamical ocean model to the physical and chemical setting in Lake Urmia. Th...

Chromophoric dissolved organic matter (CDOM) significantly contributes to the non-water absorption budget in the Mediterranean Sea. The absorption coefficient of CDOM, αCDOM(λ), is measurable in situ and remotely from different platforms and can be used as an indicator of the concentration of other relevant biogeochemical variables, e.g., dissolved...

The Agulhas Bank, an area of broad continental shelf extending 250 km offshore of South Africa, sustains rich and productive fisheries. However, its primary production is driven by a complex mosaic of biophysical mechanisms, highly variable in time and space. The key drivers include a system of multiple costal upwellings, complex shelf currents and...

We use modelling and assimilation tools to explore the impact of biogeochemistry on physics in the shelf sea environment, using North-West European Shelf (NWES) as a case study. We demonstrate that such impact is significant: the attenuation of light by biogeochemical substances heats up the upper 20 m of the ocean by up to 1 °C and by a similar ma...

The increasing rate of marine invasions to Western Europe in recent decades highlights the importance of addressing the central questions of invasion biology: what allows an invader to be successful, and which species are likely to become invasive? Consensus is currently lacking regarding the key traits that determine invasiveness in marine species...

Carbon Capture and Storage (CCS) provides a mechanism by which CO2 can be removed from the atmosphere and stored in reservoirs. Regulations and stakeholder assurance require monitoring to show storage is robust. The marine environment is heterogeneous and dynamic, and baselines are extremely variable. Hence, distinguishing anomalous CO2 from natura...

The General Ocean Turbulence Model (GOTM) is a one-dimensional water column model, including a set of state-of-the-art turbulence closure models, and has widely been used in various applications in the ocean modeling community. Here, we extend GOTM to include a set of newly developed ocean surface vertical mixing parameterizations of Langmuir turbu...

Oceanography has entered an era of new observing platforms, such as biogeochemical‐Argo floats and gliders, some of which will provide three‐dimensional maps of essential ecosystem variables on the North‐West European (NWE) Shelf. In a foreseeable future operational centers will use multi‐platform assimilation to integrate those valuable data into...

The General Ocean Turbulence Model (GOTM) is a one-dimensional water column model including a set of state-of-the-art turbulence closure models, and has widely been used in various applications in the ocean modeling community. Here we extend GOTM to include a set of newly developed ocean surface vertical mixing parameterizations of Langmuir turbule...

A global sensitivity analysis of a lake ecosystem model (GOTM-FABM-PCLake) was undertaken to test the impacts of lake morphology on parameter sensitivity in three different lakes. The analysis was facilitated by the Parallel Sensitivity and Auto-Calibration tool (parsac) and included a screening step with the density-based Borgonovo’s method follow...

Different hypotheses have been proposed explaining plankton community assembly and how changes in biodiversity can impact ecosystem function. Mixoplankton (photo-phago-trophs) are important members of the plankton, but science lacks a clear understanding of their role in plankton succession. Here, we used a modelling approach to evaluate the season...

Planktonic ecosystems are usually modeled in terms of autotrophic and heterotrophic compartments. However, the trophic strategy of unicellular organisms can take a range of mixotrophic strategies with both autotrophic and heterotrophic contributions. The dominant emerging strategy found in nature depends on the environment (both biotic and abiotic...

Understanding ecosystem state on the North‐West European (NWE) Shelf is of major importance for both economy and climate research. The purpose of this work is to advance our modeling of in‐water optics on the NWE Shelf, with important implications for how we model primary productivity, as well as for assimilation of water‐leaving radiances. We impl...

Phytoplankton phenology and the length of the growing season have implications that cascade through trophic levels and ultimately impact the global carbon flux to the seafloor. Coupled hydrodynamic‐ecosystem models must accurately predict timing and duration of phytoplankton blooms in order to predict the impact of environmental change on ecosystem...

The goal of this work was to develop and configure a model to simulate Lake Urmia’s biogeochemical and physicochemical regime changes. A specially designed vertical box model was constructed to describe the lake’s processes of evaporation, salt formation, and transport of matter inside the water column and the sediments. The modified biogeochemical...

Understanding and explaining the structure of communities in response to environmental gradients is a central goal in ecology. Trait‐based approaches are promising but yet rarely applied to understand community dynamics in response to changing environmental conditions. Here, we investigate seasonal succession patterns of functional traits in phytop...

High-turbidity water is a common feature in the estuary and inner shelf. Sediment suspension functions as a modulator that directly influences the interactions among nutrients, phytoplankton and other related ecosystem variables. A physical-biological coupling model system was applied to examine the impact of sediment front on interactions among on...

We present a model that estimates the spectral phytoplankton absorption coefficient ( a p h ( λ ) ) of four phytoplankton groups (picophytoplankton, nanophytoplankton, dinoflagellates, and diatoms) as a function of the total chlorophyll-a concentration (C) and sea surface temperature (SST). Concurrent data on a p h ( λ ) (at 12 visible wavelengths)...

Benthic communities, critical to the health and function of marine ecosystems, are under increasing pressure from anthropogenic impacts such as pollution, eutrophication and climate change. In order to refine predictions of likely future changes in benthic communities resulting from these impacts, we must first better constrain their responses to n...

Benthic macrofauna, as an element of rich and diverse benthic communities of the shelf seas, play a key role in marine biogeochemical cycles and support a wide range of ecosystem services. To better understand how macrofauna affects mass and energy fluxes within the seabed and between the bed and the pelagic, it is fundamental to characterise their...

Dynamic energy budget (DEB) theory offers a comprehensive framework for understanding the overall physiological performance (growth, development, respiration, reproduction, etc.) of an organism over the course of its life cycle. We present here a simplified DEB model for the swimming crab Liocarcinus depurator. To the best of our knowledge, this is...

This Special Report on the Ocean and Cryosphere1 in a Changing Climate (SROCC) was prepared following an IPCC Panel decision in 2016 to prepare three Special Reports during the Sixth Assessment Cycle2 . By assessing new scientific literature3 , the SROCC4 responds to government and observer organization proposals. The SROCC follows the other two Sp...

Mixotrophy is widespread among protist plankton displaying diverse functional forms within a wide range of sizes. However, little is known about the niches of different mixotrophs and how they affect nutrient cycling and trophodynamics in marine ecosystems. Here we built a plankton food web model incorporating mixotrophic functional diversity. A di...

KEY MESSAGES • Total maximum catch potential in the world’s exclusive economic zones (EEZs)1 (excluding those bordering semi-enclosed seas) was projected by applying two distinct approaches to likely decrease under climate change by 2.8 percent to 5.3 percent and 7.0 percent to 12.1 percent by 2050 relative to 2000 under the “strong mitigation” (RC...

How can the essential properties of community structure and ecosystem functioning be captured from a limited number of traits in organisms? In August 2017, 120 researchers from 31 nations met over four days at Solstrand to answer this question.

Calcite microfossils are widely used to study climate and oceanography in Earth’s geological past. Coccoliths, readily preserved calcite plates produced by a group of single-celled surface-ocean dwelling algae called coccolithophores, have formed a significant fraction of marine sediments since the Late Triassic. However, unlike the shells of foram...

Results from culture experiments used to calibrate the model. DIC and CO2 are given in mM and μM respectively. PIC:POC is the molar ratio of particulate organic carbon per cell to particulate inorganic carbon per cell. Division rate is given as the average number of cell divisions per day. Cell radius is given in μm. Carbon isotopic compositions of...

Supplementary Note, Supplementary Figures and Supplementary References

Interactions between seawater and benthic systems play an important role in global biogeochemical cycling. Benthic fluxes of some chemical elements (e.g., C, N, P, O, Si, Fe, Mn, S) alter the redox state and marine carbonate system (i.e., pH and carbonate saturation state), which in turn modulate the functioning of benthic and pelagic ecosystems. T...

This study presents FABM-PCLake, a redesigned structure of the PCLake aquatic ecosystem model, which we implemented in the Framework for Aquatic Biogeochemical Models (FABM). In contrast to the original model, which was designed for temperate, fully mixed freshwater lakes, the new FABM-PCLake represents an integrated aquatic ecosystem model that ca...

Over the past several years, phylogenetic comparative studies have increasingly approached trait evolution in a multivariate context, with a number of taxa that continues to rise dramatically. Recent methods for phylogenetic comparative studies have provided ways to incorporate measurement error and to address computational challenges. However, mis...

The input of acid substances (like SO2) into the sea has been recognized as an environmental issue that needs to be considered in terms of ocean acidification; acid inputs and techniques to deal with them have implications for member states' obligations under the Water Framework Directive and Marine Strategy Framework Directive. This study provides...

The European Regional Seas Ecosystem Model (ERSEM) is one of the most established ecosystem models for the lower trophic levels of the marine food web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North Sea to a generic tool for ecosystem simula...

End-to-end modelling is a rapidly developing strategy for modelling in marine systems science and management. However, problems remain in the area of data matching and sub-model compatibility. A mechanism and novel interfacing system (Couplerlib) is presented whereby a physical-biogeochemical model (General Ocean Turbulence Model-European Regional...

This study presents FABM-PCLake, a complete redesign of the PCLake aquatic ecosystem model, which we implemented into the Framework for Aquatic Biogeochemical Models (FABM). In contrast to the original model, which was designed for temperate, fully mixed freshwater lakes, the new FABM-PCLake represents an integrated aquatic ecosystem model that ena...

Interaction between seawater and benthic sediments plays an important role in global biogeochemical cycling. Benthic fluxes of chemical elements (C, N, P, O, Si, Fe, Mn, S) directly affect redox state and acidification (i.e. pH and carbonate saturation), which in turn determine the functioning of the benthic and pelagic ecosystems. The redox state...

Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been...

The ERSEM model is one of the most established ecosystem models for the lower trophic levels of the marine food-web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North-Sea to a generic tool for ecosystem simulations from shelf seas to the 5 glob...

End to end modelling is an attractive and rapidly developing approach to solve developing strategies in marine systems science and management. However problems remain in the area of data matching and sub-model compatibility. A mechanism and novel interfacing system (Couplerlib) is presented whereby a physical/biogeochemical model (GOTM-ERSEM) that...

The factors regulating phytoplankton community composition play a crucial role in structuring aquatic food webs. However, consensus is still lacking about the mechanisms underlying the observed biogeographical differences in cell size composition of phytoplankton communities. Here we use a trait-based model to disentangle these mechanisms in two co...

Supplementary Material

Internet: www.niva.no Title Bottom RedOx Model (BROM) general description and application for seasonal anoxia simulations Topic group Oceanography, biogeochemistry Geographical area North Sea Distribution Open Printed NIVA Client(s) NIVA Client ref. Abstract The details of biogeochemical transfer of matter at the sediment-water boundary were modell...

We introduce a trait-based description of diatom functional diversity to an existing plankton functional type (PFT) model, implemented for the eutrophied coastal ecosystem in the Southern Bight of the North Sea. The trait-based description represents a continuum of diatom species, each characterized by a distinct cell volume, and includes size depe...

Rising CO2 is expected to drive a myriad of environmental changes in the surface ocean. Deciphering the phytoplankton response to this complex change is difficult. Here we determine whether a trend in the biological fractionation of stable carbon isotopes (εp) has occurred over the past 50 years. εp is primarily controlled by the acquisition and in...

Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing import...