Description: The global marine iron cycle has been modeled using REcoM2 (Regulated Ecosystem Model 2) coupled with the ocean circulation model MITgcm (MIT General Circulation Model). A general description of the model can be found in the supporting material for Hauck et al. 2013. In the simulations producing this data set, the organic complexation of iron was made dependent on seawater pH and concentration of dissolved organic matter. With this parameterization, the effect of pH change on the iron cycle and the biological feedback to the iron cycle have been examined through the pathway of ligand binding. In this data set, model output of dissolved iron (DFe), dissolved organic carbon (DOC), stability constants of ligands, free Fe concentration and net primary production (NPP) are included. Four different simulations are considered: R_std (standard), R_constL (with constant 1 nM ligand concentration), R_progL (with one prognostic ligand) and R_ph (with future pH field).

Description: Acidification (OA), a global threat to the world's oceans, is projected to significantly grow if CO2 continues to be emitted into the atmosphere at high levels. This will result in a slight decrease in pH. Since the latter is a logarithmic scale of acidity, the higher acidic seawater is expected to have a tremendous impact on marine living resources in the long-term. An 8-week laboratory experiment was designed to assess the impact of the projected pH in 2100 and beyond on fish survival, health, growth, and fish meat quality. Two projected scenarios were simulated with the control treatment, in triplicates. The control treatment had a pH of 8.10, corresponding to a pCO2 of 321.37 ± 11.48 µatm. The two projected scenarios, named Predict_A and Predict_B, had pH values of 7.80-pCO2 = 749.12 ± 27.03 and 7.40-pCO2 = 321.37 ± 11.48 µatm, respectively. The experiment was preceded by 2 weeks of acclimation. After the acclimation, 20 juvenile black sea breams (Acanthopagrus schlegelii) of 2.72 ± 0.01 g were used per tank. This species has been selected mainly due to its very high resistance to diseases and environmental changes, assuming that a weaker fish resistance will also be susceptibly affected. In all tanks, the fish were fed with the same commercial diet. The seawater's physicochemical parameters were measured daily. Fish samples were subjected to physiological, histological, and biochemical analyses. Fish growth, feeding efficiency, protein efficiency ratio, and crude protein content were significantly decreased with a lower pH. Scanning electron microscopy revealed multiple atrophies of microvilli throughout the small intestine's brush border in samples from Predict_A and Predict_B. This significantly reduced nutrient absorption, resulting in significantly lower feed efficiency, lower fish growth, and lower meat quality. As a result of an elevated pCO2 in seawater, the fish eat more than normal but grow less than normal. Liver observation showed blood congestion, hemorrhage, necrosis, vacuolation of hepatocytes, and an increased number of Kupffer cells, which characterize liver damage. Transmission electron microscopy revealed an elongated and angular shape of the mitochondrion in the liver cell, with an abundance of peroxisomes, symptomatic of metabolic acidosis.

Description: In this study, we used MITgcm-REcoM2 to simulate the stepwise glacial-interglacial atmospheric pCO2 change. A general description of the model can be found in the supporting material for Hauck et al. 2013. There are seven simulations included in this dataset: two control runs for interglacial and glacial conditions (IG_ctl, G_ctl); three region-specific sensitivity runs(IG_Gso, IG_Gna, IG_Gns); and two simulations regarding the glacial iron fertilization in the Southern Ocean. Dissolved Inorganic Carbon (DIC) and Export Production in all runs are included in this study, and the potential temperature (THETA), salinity (SALT), meridional velocity (VVEL), sea ice concentration(SIarea), air-sea surface pCO2 (dpCO2surface) difference are available in IG_ctl, IG_Gso, IG_Gna, IG_Gns, and G_ctl.

Description: We propose an alternative scheme for the use of 224Ra/228Th disequilibria to investigate carbon and nutrient export from a permeable sandy seabed. Sediment profiles of dissolved 224Ra, total 224Ra and 228Th were determined at two different intertidal sand systems - an intertidal sandy beach near Weitou Bay in Fujian (China), and a tidal sand flat in the Wadden Sea near Cuxhaven (Germany). Dramatic deficit of total 224Ra relative to 228Th was identified in the upper 20 or 30 cm sand layer over the sand systems. We construct a simple two-dimensional advective cycling model to simulate interfacial fluid transport in a sand system that is subject to periodic tidal inundation and swash actions. Based on the 224Ra/228Th disequilibria in the sediment, the model gives estimates of 20.3, 9.1, and 1.9 L m−2 h−1 for water exchange flux at the high tide, mid-tide, and low tide position over the sandy beach at Weitou Bay, respectively. In comparison, the model provides an estimate of 7.2 L m−2 h−1 for water exchange flux at the tidal sand flat in the Wadden Sea. The production of dissolved inorganic carbon (DIC) in porewater is the rate-limiting step for DIC export from the sandy beach into the sea, and can be reasonably simulated as a first-order kinetic reaction. The pattern of interfacial fluid transport over the beach facilitates a horizontal zonation of redox condition in the sediment, which evolves progressively from a fully oxic state at the high tide position to a suboxic state at the low tide position. There is clear evidence of nitrogen loss via denitrification in the suboxic status, and we estimate a nitrogen removal rate of 3.3 mmolN m−2 d−1 at this site. For the two intertidal sand systems, DIC export fluxes range from 20.1 to 89.4 mmolC m−2 d−1, comparable in magnitude to fluxes determined in organic rich estuarine sediments. In the meantime, export fluxes of dissolved inorganic nitrogen (DIN) change from 0.8 to 18.6 mmolN m−2 d−1. Overall, this study suggests that the role of sandy sediments in the biogeochemical cycling of carbon and nutrients needs to be revisited.

Description: The cycling of carbon in the oceans is affected by feedbacks driven by changes in climate and atmospheric CO2. Understanding these feedbacks is therefore an important prerequisite for projecting future climate. Marine biogeochemistry models are a useful tool but, as with any model, are a simplification and need to be continually improved. In this study, we coupled the Finite-volumE Sea ice–Ocean Model (FESOM2.1) to the Regulated Ecosystem Model version 3 (REcoM3). FESOM2.1 is an update of the Finite-Element Sea ice–Ocean Model (FESOM1.4) and operates on unstructured meshes. Unlike standard structured-mesh ocean models, the mesh flexibility allows for a realistic representation of small-scale dynamics in key regions at an affordable computational cost. Compared to the previous coupled model version of FESOM1.4–REcoM2, the model FESOM2.1–REcoM3 utilizes a new dynamical core, based on a finite-volume discretization instead of finite elements, and retains central parts of the biogeochemistry model. As a new feature, carbonate chemistry, including water vapour correction, is computed by mocsy 2.0. Moreover, REcoM3 has an extended food web that includes macrozooplankton and fast-sinking detritus. Dissolved oxygen is also added as a new tracer. In this study, we assess the ocean and biogeochemical state simulated with FESOM2.1–REcoM3 in a global set-up at relatively low spatial resolution forced with JRA55-do (Tsujino et al., 2018) atmospheric reanalysis. The focus is on the recent period (1958–2021) to assess how well the model can be used for present-day and future climate change scenarios on decadal to centennial timescales. A bias in the global ocean–atmosphere preindustrial CO2 flux present in the previous model version (FESOM1.4–REcoM2) could be significantly reduced. In addition, the computational efficiency is 2–3 times higher than that of FESOM1.4–REcoM2. Overall, it is found that FESOM2.1–REcoM3 is a skilful tool for ocean biogeochemical modelling applications.

Description: 〈jats:p〉Abstract. In this paper we describe the implementation of the carbon isotopes 13C and 14C (radiocarbon) into the marine biogeochemistry model REcoM3. The implementation is tested in long-term equilibrium simulations where REcoM3 is coupled with the ocean general circulation model FESOM2.1, applying a low-resolution configuration and idealized climate forcing. Focusing on the carbon-isotopic composition of dissolved inorganic carbon (δ13CDIC and Δ14CDIC), our model results are largely consistent with reconstructions for the pre-anthropogenic period. Our simulations also exhibit discrepancies, e.g. in upwelling regions and the interior of the North Pacific. Some of these differences are due to the limitations of our ocean circulation model setup, which results in a rather shallow meridional overturning circulation. We additionally study the accuracy of two simplified modelling approaches for dissolved inorganic 14C, which are faster (15 % and about a factor of five, respectively) than the complete consideration of the marine radiocarbon cycle. The accuracy of both simplified approaches is better than 5 %, which should be sufficient for most studies of Δ14CDIC. 〈/jats:p〉