Description: Highlights: • We examine the role of marine particle for regulating trace element distribution. • We review the state of the art for modelling the oceanic distribution of specific tracers: Thorium, Protactinium, Iron, and Aluminium. • We review the state of the art for modelling particle distribution in large scale ocean biogeochemical model. The distribution of trace elements in the ocean is governed by the combined effects of various processes, and by exchanges with external sources. Modelling these represents an opportunity to better understand and quantify the mechanisms that regulate the oceanic tracer cycles. Observations collected during the GEOTRACES program provide an opportunity to improve our knowledge regarding processes that should be considered in biogeochemical models to adequately represent the distributions of trace elements in the ocean. Here we present a synthesis about the state of the art for simulating selected trace elements in biogeochemical models: Protactinium, Thorium, Iron and Aluminium. In this contribution we pay particular attention on the role of particles in the cycling of these tracers and how they may provide additional constraints on the transfer of matter in the ocean.

Description: We present a suite of experiments with a hierarchy of biogeochemical models of increasing complexity coupled to an offline global ocean circulation model based on the “transport matrix method”. Biogeochemical model structures range from simple nutrient models to more complex nutrient-phytoplankton–zooplankton-detritus-DOP models. The models’ skill is assessed by various misfit functions with respect to observed phosphate and oxygen distributions. While there is generally good agreement between the different metrics employed, an exception is a cost function based on the relative model-data misfit. We show that alterations in parameters and/or structure of the models – especially those that change particle export or remineralization profile – affect subsurface and mesopelagic phosphate and oxygen, particularly in the upwelling regions. Visual inspection of simulated biogeochemical tracer distributions as well as the evaluation of different cost functions suggest that increasing complexity of untuned, unoptimized models, simulated with parameters commonly used in large-scale model studies does not necessarily improve performance. Instead, variations in individual model parameters may be of equal, if not greater, importance.

Description: Amodel is presented that simulates the formation of marine aggregates from particles of different origin inside amodel of pelagic biological processes. Experiments are carried out with parameterizations appropriate for different types of aggregates, using different kinds of physical forcing, and compared to observations of dissolved inorganic nitrogen (DIN), particulate organic nitrogen (PON), marinesnow concentration, and sedimentation. The occurrence of large, macroscopically visible aggregates (marinesnow) can best be simulated with parameterizations that have been derived from in situ observations of marinesnow, but not with aparameterization sufficient for dense particles. The parameterization strongly determines the amount and timing of deep export, as well as the post-bloom development of the food web in the upper layers. Detritus in aggregates plays a role mainly during times when zooplankton are abundant, as e.g. in the western Arabian Sea during Southwest Monsoon. Then the large aggregates as fast sinking vehicles may remove detritus quickly from shallow and mid-water depth, preventing the accumulation of nutrients that are produced via detritus decomposition. In this region, detritus contributes strongly to deep sedimentation. The nitrogenbudget at this location with regard to the observations cannot be closed: depending on model type, either the model simulates too high sedimentation, or too high DIN. Possible causes for this mismatch include undercollection by sediment traps, inaccurate representation of physical processes in the model and the neglect of biological processes, such as production of dissolved organic matter or denitrification.

Description: We investigate the effects of different vertical grid resolutions and algorithms for the calculation of particle sinking on the sedimentation and remineralization of particulate organic matter. Simulations carried out with an idealized 1D model of detritus sinking show that a coarse vertical resolution, such as used in many global biogeochemical models, tends to enhance the particle flux through numerical mixing within the vertical boxes, and thereby simulates deeper remineralization, compared to a model with a fine vertical resolution. This effect can be ameliorated by assuming a distribution of detritus within the individual grid boxes that corresponds to the prescribed sinking and remineralization parameters. Experiments of the different flux algorithms, carried out with 3D global biogeochemical models of different vertical grid resolution reveal impacts on simulated biogeochemical tracer distributions that are similar to those obtained by substantial variations in biogeochemical model parameters. Our results indicate that numerical schemes have to be considered when comparing biogeochemical parameter values of different models and also when porting biogeochemical models among different circulation models.

Description: The effect of phytoplankton cell size on the variation of nutrient uptake and exudation rates is examined: we first present an overview of the relationship between the variation of the growth and loss parameters and cell size. We then investigate the effect of cell-size-dependent parameters on the development of an entire phytoplankton community by means of a numerical, vertically resolved nutrient phytoplankton model. The model represents phytoplankton size distributions in three different ways, namely one configuration with explicit representation of 14 size classes, one configuration with constant-slope power-law spectral representation, and one configuration with variable-slope power-law spectral representation. The size-dependent configurations are further compared to a size-independent configuration. Consistent with theory, the explicit and variable-slope spectral model simulations predict increased importance of larger cells, or "flat" size distribution under conditions of low light and high nutrients, while smaller cells ("steep" size distributions) may dominate in oligotrophic, well-lit regimes. In some situations the variable-slope spectral model seems to be sufficient to reflect the phytoplankton size distribution; however, especially in the deep phytoplankton maximum a unimodal rather than power-law spectral description might be more appropriate to reproduce results of the explicit 14-size-class model. The assumption of a fixed spectral slope, according to which larger size classes gain importance especially during bloom periods, is not consistent with the underlying theory, and does not agree with the results of the size-discrete model. The comparison of model predictions with variations of phytoplankton size distribution observed in the field is hampered by the sparsity of data, especially for the winter season. A half-saturation constant that represents the nutrient uptake of the entire phytoplankton community (K*) compares well to published values. (C) 2007 Elsevier Ltd. All rights reserved.

Description: Zooplankton organisms are a central part of pelagic ecosystems. They feed on all kinds of particulate matter and their egested fecal pellets contribute substantially to the passive sinking flux to depth. Some zooplankton species also conduct diel vertical migrations (DVMs) between the surface layer (where they feed at nighttime) and midwater depth (where they hide at daytime from predation). These DVMs cause the active export of organic and inorganic matter from the surface layer as zooplankton organisms excrete, defecate, respire, die, and are preyed upon at depth. In the Eastern Tropical North Atlantic (ETNA), the daytime distribution depth of many migrators (300–600 m) coincides with an expanding and intensifying oxygen minimum zone (OMZ). We here assess the day and night-time biomass distribution of mesozooplankton with an equivalent spherical diameter of 0.39–20 mm in three regions of the ETNA, calculate the DVM-mediated fluxes and compare these to particulate matter fluxes and other biogeochemical processes. Integrated mesozooplankton biomass in the ETNA region is about twice as high at a central OMZ location (cOMZ; 11° N, 21° W) compared to the Cape Verde Ocean Observatory (CVOO; 17.6° N, 24.3° W) and an oligotrophic location at 5° N, 23° W (5N). An Intermediate Particle Maximum (IPM) is particularly strong at cOMZ compared to the other regions. This IPM seems to be related to DVM activity. Zooplankton DVM was found to be responsible for about 31–41% of nitrogen loss from the upper 200m of the water column. Gut flux and mortality make up about 31% of particulate matter supply to the 300–600 m depth layer at cOMZ, whereas it makes up about 32% and 41% at CVOO and 5N, respectively. Resident and migrant zooplankton are responsible for about 7–27% of the total oxygen demand at 300–600 m depth. Changes in zooplankton abundance and migration behavior due to decreasing oxygen levels at midwater depth could therefore alter the elemental cycling of oxygen and carbon in the ETNA OMZ and impact the removal of nitrogen from the surface layer.

Description: We show how to represent changes in the distribution of size and sinking speed of marine particles by a two-parameter model. In contrast to fully size-resolved models, this representation holds promise for constructing ocean biogeochemical models with detailed spatial resolution and seasonally varying sinking speed. We treat the mass and number of particles as separate state variables, each obeying its own conservation law. Average size and sinking speed of particles change as particles aggregate or the largest particles sink out. The distribution of particle sizes is assumed to follow a power law, whose exponent changes as a function of average particle size. Compared to biogeochemical models with constant particle sinking speed, our approach imposes a modest increase in computational cost and produces important effects like more rapid sinking immediately following a phytoplankton bloom. Compared to models that use hundreds of size classes to represent the detailed evolution of particle size distribution, our approach offers a major reduction in computational cost, while maintaining realistic behaviour like the sudden onset of significant aggregation when particles are sufficiently abundant.

Description: A growing population on a planet with limited resources demands finding new sources of protein. Hence, fisheries are turning their perspectives towards mesopelagic fish, which have, so far, remained relatively unexploited and poorly studied. Large uncertainties are associated with regards to their biomass, turn-over rates, susceptibility to environmental forcing and ecological and biogeochemical role. Models are useful to disentangle sources of uncertainties and to understand the impact of different processes on the biomass. In this study, we employed two food-web models – OSMOSE and the model by Anderson et al. (2019, or A2019) – coupled to a regional physical–biogeochemical model to simulate mesopelagic fish in the Eastern Tropical South Pacific ocean. The model by A2019 produced the largest biomass estimate, 26 to 130% higher than OSMOSE depending on the mortality parameters used. However, OSMOSE was calibrated to match observations in the coastal region off Peru and its temporal variability is affected by an explicit life cycle and food web. In contrast, the model by A2019 is more convenient to perform uncertainty analysis and it can be easily coupled to a biogeochemical model to estimate mesopelagic fish biomass. However, it is based on a flow analysis that had been previously applied to estimate global biomass of mesopelagic fish but has never been calibrated for the Eastern Tropical South Pacific. Furthermore, it assumes a steady-state in the energy transfer between primary production and mesopelagic fish, which may be an oversimplification for this highly dynamic system. OSMOSE is convenient to understand the interactions of the ecosystem and how including different life stages affects the model response. The combined strengths of both models allow us to study mesopelagic fish from a holistic perspective, taking into account energy fluxes and biomass uncertainties based on primary production, as well as complex ecological interactions.

Description: Highlights: • Modelled fish biomass was affected by interannual variability in the plankton food. • The effects were small compared with the high variability in observations. • Fish were highly affected by changes in the larval mortality of anchovy. Abstract: The Northern Humboldt Current System is the most productive eastern boundary upwelling system, generating about 10 % of the global fish production, mainly coming from small pelagic fish. It is bottom-up and top-down affected by environmental and anthropogenic variability, such as El-Niño Southern Oscillation and fishing pressure, respectively. The high variability of small pelagic fish in this system, as well as their economic importance, call for a careful management aided by the use of end-to-end models. This type of models represent the ecosystem as a whole, from the physics, through plankton up to fish dynamics. In this study, we utilised an end-to-end model consisting of a physical–biogeochemical model (CROCO-BioEBUS) coupled one-way with an individual-based fish model (OSMOSE). We investigated how time-variability in plankton food production affects fish populations in OSMOSE and contrasted it against the sensitivity of the model to two parameters with high uncertainty: the plankton accessibility to fish and fish larval mortality. Relative interannual variability in the modelled fish is similar to plankton variability. It is, however, small compared with the high variability seen in fish observations in this productive ecosystem. In contrast, changes in larval mortality have a strong effect on anchovies. In OSMOSE, it is a common practice to scale plankton food for fish, accounting for processes that may make part of the total plankton in the water column unavailable. We suggest that this scaling should be done constant across all plankton groups when previous knowledge on the different availabilities is lacking. In addition, end-to-end modelling systems should consider environmental impacts on other biological processes such as larval mortality in order to better capture the interactions between environmental processes, plankton and fish.