Description: Here we provide optimised vertical eddy diffusivity estimates for the PeECE III and KOSMOS 2013 mesocosm experiment, obtained from a model-based reanalysis. These diffusivities are derived from the observed temperature and salinity profiles that have been published in Schulz et al., 2008. Furthermore, we make our model code available, providing an adjustable tool to simulate vertical mixing in any other pelagic mesocosm. We also provide the interpolated and regridded temperature and salinity profiles of the PeECE III experiment as well as the density profiles which we calculated from the temperature and salinity profiles using the R package seacarb (Lavigne et al., 2011). These data files are required as input to run simulations of the PeECE III experiment with the 1D mesocosm mixing model. The columns of the environmental files (required input files for the model) from left to right are: Experiment year, month, day, Julian day, photosynthetically active radiation (PAR) [W/m^2], temperature [C], salinity [PSU], CO2 concentration [ppm], wind speed [m/s]. The rows list the respective value of each hour of the experiment. Temperature and salinity in this table are hourly interpolated values of the daily measurements published by the PeECE III team (2005). PAR has been calculated from global radiation data of Bergen provided by Olseth et al., 2005. In the temperature, salinity and density files, the rows indicate the depth (0.5 m resolution, the first row is the surface, the last row is the bottom), whereas the columns indicate the experiment time at an hourly resolution.

Description: Estuary-type circulation is a residual circulation in coastal systems with horizontal density gradients. It drives the accumulation of suspended particulate matter in coastal embayments where density gradients are sustained by some freshwater inflow from rivers. Ebenhöh et al. (Ecol Model 174(3):241–252, 2004) found that shallow water depth can explain nutrient gradients becoming established towards the coast even in the absence of river inflow. The present study follows their concept and investigates the characteristic transport of organic matter towards the coast based on idealised scenarios whereby an estuary-type circulation is maintained by surface freshwater fluxes and pronounced shoaling towards the coast. A coupled hydrodynamical and biogeochemical model is used to simulate the dynamics of nutrient gradients and to derive budgets of organic matter flux for a coastal transect. Horizontal nutrient gradients are considered only in terms of tidal asymmetries of suspended matter transport. The results show that the accumulation of organic matter near the coast is not only highly sensitive to variations in the sinking velocity of suspended matter but is also noticeably enhanced by an increase in precipitation. This scenario is comparable with North Sea conditions. By contrast, horizontal nutrient gradients would be reversed in the case of evaporation-dominated inverse estuaries (cf. reverse gradients of nutrient and organic matter concentrations). Credible coastal nutrient budget calculations are required for resolving trends in eutrophication. For tidal systems, the present results suggest that these calculations require an explicit consideration of freshwater flux and asymmetries in tidal mixing. In the present case, the nutrient budget for the vertically mixed zone also indicates carbon pumping from the shelf sea towards the coast from as far offshore as 25 km.

Description: Highlights: • Elemental C:N:P variations of organic matter are simulated at monitoring site BY15. • No N2 fixation needed to explain observed PO4PO4 and pCO2pCO2 levels after spring bloom. • Model features relevance of DOP production and remineralization for N2 fixation. • Model estimates of annual N2 fixation are View the MathML source297±24mmolNm-2a-1. • Model estimates of annual total production are View the MathML source14.16±0.71molCm-2a-1. Abstract: For most marine ecosystems the growth of diazotrophic cyanobacteria and the associated amount of nitrogen fixation are regulated by the availability of phosphorus. The intensity of summer blooms of nitrogen (N2) fixing algae in the Baltic Sea is assumed to be determinable from a surplus of dissolved inorganic phosphorus (DIP) that remains after the spring bloom has ended. But this surplus DIP concentration is observed to continuously decrease at times when no appreciable nitrogen fixation is measured. This peculiarity is currently discussed and has afforded different model interpretations for the Baltic Sea. In our study we propose a dynamical model solution that explains these observations with variations of the elemental carbon-to-nitrogen-to-phosphorus (C:N:P) ratio during distinct periods of organic matter production and remineralization. The biogeochemical model resolves seasonal C, N and P fluxes with depth at the Baltic Sea monitoring site BY15, based on three assumptions: (1) DIP is utilized by algae though not needed for immediate growth, (2) the uptake of dissolved inorganic nitrogen (DIN) is hampered when the algae׳s phosphorus (P) quota is low, and (3) carbon assimilation continues at times of nutrient depletion. Model results describe observed temporal variations of DIN, DIP and chlorophyll-a concentrations along with partial pressure of carbon dioxide (pCO2)(pCO2). In contrast to other model studies, our solution does not require N2 fixation to occur shortly after the spring bloom to explain DIP drawdown and pCO2pCO2 levels. Model estimates of annual N2 fixation are View the MathML source297±24mmolNm-2a-1. Estimates of total production are View the MathML source14200±700mmolCm-2a-1, View the MathML source1400±70mmolNm-2a-1, and View the MathML source114±5mmolPm-2a-1 for the upper 50 m. The models C, N and P fluxes disclose preferential remineralization of P and of organic N that was introduced via N2 fixation. Our results are in support of the idea that P uptake by phytoplankton during the spring bloom contributes to the consecutive availability of labile dissolved organic phosphorus (LDOP). The LDOP is retained within upper layers and its remineralization affects algal growth in summer, during periods of noticeable N2 fixation.

Description: Global biogeochemical ocean models are used to predict the future evolution of so-called oxygen minimum zones (OMZ), and the associated environmental and possible socio-economic impacts. Different models give different results and vary largely in their biogeochemical, physical and numerical setup. In order to assess the ability of the models to describe the present state as a necessary condition for skillful predictions into the future, they are usually compared against observed distributions of oxygen and other variables, such as thickness of oxygen minimum zones, nutrients, tracers for circulation and/or water mass age. We here examine different metrics for skill evaluation particularly of model representations of oxygen (and OMZs), for a wide range of global biogeochemical models. Among the metrics considered are Taylor plots, volume distributions of oxygen, volume of OMZ, preformed oxygen, and metrics that combine various diagnostic biogeochemical tracers. We finally investigate the impact these metrics may have for the “choice” of any best model, and discuss their applicability for different research or societal questions.

Description: Highlights: • Sensitivities of annual carbon (C), nitrogen (N) and phosphorus (P) flux estimates to parameter variations are determined. • Model parameters that specify annual inventories are compared with those that determine timing and magnitude of bloom events. • Seven model parameters are of primary importance, affecting C, N and P budgets simultaneously. • Nine parameters have negligible effects on annual budget estimates and on seasonal trajectories. • Parameter categorization provides important prior information for parameter optimization in the central Baltic Sea. Abstract: This study describes a sensitivity analysis that allows the parameters of a one-dimensional ecosystem model to be ranked according to their specificity in determining biochemical key fluxes. Key fluxes of interest are annual (a) total production (TP), (b) remineralization above the halocline (RM), and (c) export at 50 m (EX) at the Baltic Sea monitoring site BY15 located in the Gotland Deep basin. The model resolves mass flux of carbon (C), nitrogen (N), and phosphorous (P), while considering nitrogen fixation explicitly. Our first null hypothesis is that the variation of the value of every single model parameter affects each annual C, N, and P budget simultaneously. Our second null hypothesis states that the variation of every parameter value induces changes at least in either of the annual C, N or P budgets. Our analyses falsify both null hypotheses and reveal that 8 out of 36 parameters must be regarded redundant, as their variation neither alter annual key fluxes nor produce considerable time-shifts in model trajectories at the respective site. Seven parameters were found to induce substantial changes in annual C, N, and P flux estimates simultaneously. The assimilation efficiency of zooplankton turned out to be of vital importance. This parameter discriminates between the assimilation and destruction of algal prey during grazing. The fraction of unassimilated dead algal cells is critical for the amount of organic matter exported out of the euphotic zone. The maximum cellular N:C quota of diazotrophs and the degradation/hydrolysis rate of detrital carbon are two parameters that will likely remain unconstrained by time series data, but both affect the annual C budget considerably. Overall, our detailed specification of model sensitivities to parameter variations will facilitate the formulation of a well-posed inverse problem for the estimation of C, N and P fluxes from stock observations at the Gotland Deep.

Description: To describe the underlying processes involved in oceanic plankton dynamics is crucial for the determination of energy and mass flux through an ecosystem and for the estimation of biogeochemical element cycling. Many planktonic ecosystem models were developed to resolve major processes so that flux estimates can be derived from numerical simulations. These results depend on the type and number of parameterizations incorporated as model equations. Furthermore, the values assigned to respective parameters specify a model's solution. Representative model results are those that can explain data; therefore, data assimilation methods are utilized to yield optimal estimates of parameter values while fitting model results to match data. Central difficulties are (1) planktonic ecosystem models are imperfect and (2) data are often too sparse to constrain all model parameters. In this review we explore how problems in parameter identification are approached in marine planktonic ecosystem modelling. We provide background information about model uncertainties and estimation methods, and how these are considered for assessing misfits between observations and model results. We explain differences in evaluating uncertainties in parameter estimation, thereby also discussing issues of parameter identifiability. Aspects of model complexity are addressed and we describe how results from cross-validation studies provide much insight in this respect. Moreover, approaches are discussed that consider time- and space-dependent parameter values. We further discuss the use of dynamical/statistical emulator approaches, and we elucidate issues of parameter identification in global biogeochemical models. Our review discloses many facets of parameter identification, as we found many commonalities between the objectives of different approaches, but scientific insight differed between studies. To learn more from results of planktonic ecosystem models we recommend finding a good balance in the level of sophistication between mechanistic modelling and statistical data assimilation treatment for parameter estimation

Description: The effect of ocean acidification on growth and calcification of the marine algae Emiliania huxleyi was investigated in a series of mesocosm experiments where enclosed water volumes that comprised a natural plankton community were exposed to different carbon dioxide (CO2) concentrations. Calcification rates observed during those experiments were found to be highly variable, even among replicate mesocosms that were subject to similar CO2 perturbations. Here, data from an ocean acidification mesocosm experiment are reanalysed with an optimality-based dynamical plankton model. According to our model approach, cellular calcite formation is sensitive to variations in CO2 at the organism level. We investigate the temporal changes and variability in observations, with a focus on resolving observed differences in total alkalinity and particulate inorganic carbon (PIC). We explore how much of the variability in the data can be explained by variations of the initial conditions and by the level of CO2 perturbation. Nine mesocosms of one experiment were sorted into three groups of high, medium, and low calcification rates and analysed separately. The spread of the three optimised ensemble model solutions captures most of the observed variability. Our results show that small variations in initial abundance of coccolithophores and the prevailing physiological acclimation states generate differences in calcification that are larger than those induced by ocean acidification. Accordingly, large deviations between optimal mass flux estimates of carbon and of nitrogen are identified even between mesocosms that were subject to similar ocean acidification conditions. With our model-based data analysis we document how an ocean acidification response signal in calcification can be disentangled from the observed variability in PIC.

Description: Despite the huge extent of the ocean's surface, until now relatively little attention has been paid to the sea surface microlayer (SML) as the ultimate interface where heat, momentum and mass exchange between the ocean and the atmosphere takes place. Via the SML, large-scale environmental changes in the ocean such as warming, acidification, deoxygenation, and eutrophication potentially influence cloud formation, precipitation, and the global radiation balance. Due to the deep connectivity between biological, chemical, and physical processes, studies of the SML may reveal multiple sensitivities to global and regional changes. Understanding the processes at the ocean's surface, in particular involving the SML as an important and determinant interface, could therefore provide an essential contribution to the reduction of uncertainties regarding ocean-climate feedbacks. This review identifies gaps in our current knowledge of the SML and highlights a need to develop a holistic and mechanistic understanding of the diverse biological, chemical, and physical processes occurring at the ocean-atmosphere interface. We advocate the development of strong interdisciplinary expertise and collaboration in order to bridge between ocean and atmospheric sciences. Although this will pose significant methodological challenges, such an initiative would represent a new role model for interdisciplinary research in Earth System sciences.

Description: Chlorophyll (chl a) concentration in coastal seas exhibits variability on various spatial and temporal scales. Resuspension of particulate matter can somewhat limit algal growth, but can also enhance productivity because of the intrusion of nutrient-rich pore water from sediments or bottom water layers into the whole water column. This study investigates whether characteristic changes in net phytoplankton growth can be directly linked to resuspension events within the German Bight. Satellite-derived chl a were used to derive spatial patterns of net rates of chl a increase/decrease (NR) in 2003 and 2004. Spatial correlations between NR and mean water column irradiance were analysed. High correlations in space and time were found in most areas of the German Bight (R2 〉 0.4), suggesting a tight coupling between light availability and algal growth during spring. These correlations were reduced within a distinct zone in the transition between shallow coastal areas and deeper offshore waters. In summer and autumn, a mismatch was found between phytoplankton blooms (chl a 〉 6 mg m−3) and spring-tidal induced resuspension events as indicated by bottom velocity, suggesting that there is no phytoplankton resuspension during spring tides. It is instead proposed here that frequent and recurrent spring-tidal resuspension events enhance algal growth by supplying remineralized nutrients. This hypothesis is corroborated by a lag correlation analysis between resuspension events and in-situ measured nutrient concentrations. This study outlines seasonally different patterns in phytoplankton productivity in response to variations in resuspension, which can serve as a reference for modelling coastal ecosystem dynamics.