Organic matter deposition/resuspension in a one-dimensional physical-biogeochemical model. A modelling study

The shallow water configuration of the gulf of Trieste allows the propagation of the stress due to wind and waves along the whole water column down to the bottom. When the stress overcomes a particular threshold it produces resuspension processes of the benthic detritus. The benthic sediments in the North Adriatic are rich of organic matter, transported here by many rivers. This biological active particulate, when remaining in the water, can be transported in all the Adriatic basin by the basin-wide circulation. In this work is presented a first implementation of a resuspension/deposition submodel in the oceanographic coupled physical-biogeochemical 1-dimensional numerical model POM-BFM. At first has been considered the only climatological wind stress forcing, next has been introduced, on the surface, an annual cycle of wave motion and finally have been imposed some exceptional wave event in different periods of the year. The results show a strong relationship between the efficiency of the resuspension process and the stratification of the water column. During summer the strong stratification can contained a great quantity of suspended matter near to the bottom, while during winter even a low concentration of particulate can reach the surface and remains into the water for several months without settling and influencing the biogeochemical system. Looking at the biologic effects, the organic particulate, injected in the water column, allow a sudden growth of the pelagic bacteria which competes with the phytoplankton for nutrients strongly inhibiting its growth. This happen especially during summer when the suspended benthic detritus concentration is greater.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Two different 3D biogeochemical models for the NW mediterranean sea: validation with Meris data and intercomparison

Report for the scientific sojourn carried out at the University of New South Wales from February to June the 2007. Two different biogeochemical models are coupled to a three dimensional configuration of the Princeton Ocean Model (POM) for the Northwestern Mediterranean Sea (Ahumada and Cruzado, 2007). The first biogeochemical model (BLANES) is the three-dimensional version of the model described by Bahamon and Cruzado (2003) and computes the nitrogen fluxes through six compartments using semi-empirical descriptions of biological processes. The second biogeochemical model (BIOMEC) is the biomechanical NPZD model described in Baird et al. (2004), which uses a combination of physiological and physical descriptions to quantify the rates of planktonic interactions. Physical descriptions include, for example, the diffusion of nutrients to phytoplankton cells and the encounter rate of predators and prey. The link between physical and biogeochemical processes in both models is expressed by the advection-diffusion of the non-conservative tracers. The similarities in the mathematical formulation of the biogeochemical processes in the two models are exploited to determine the parameter set for the biomechanical model that best fits the parameter set used in the first model. Three years of integration have been carried out for each model to reach the so called perpetual year run for biogeochemical conditions. Outputs from both models are averaged monthly and then compared to remote sensing images obtained from sensor MERIS for chlorophyll.

Modelling coupled physical-biogeochemical processes in ice-covered oceans

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.

The effect of abrupt climatic warming on biogeochemical cycling and N2O emissions in a terrestrial ecosystem

The large, rapid increase in atmospheric N2O concentrations that occurred concurrent with the abrupt warming at the end of the Last Glacial period might have been the result of a reorganization in global biogeochemical cycles. To explore the sensitivity of nitrogen cycling in terrestrial ecosystems to abrupt warming, we combined a scenario of climate and vegetation composition change based on multiproxy data for the Oldest Dryas–Bølling abrupt warming event at Gerzensee, Switzerland, with a biogeochemical model that simulates terrestrial N uptake and release, including N2O emissions. As for many central European sites, the pollen record at the Gerzensee is remarkable for the abundant presence of the symbiotic nitrogen fixer Hippophaë rhamnoides (L.) during the abrupt warming that also marks the beginning of primary succession on immature glacial soils. Here we show that without additional nitrogen fixation, climate change results in a significant increase of N2O emissions of approximately factor 3.4 (from 6.4 ± 1.9 to 21.6 ± 5.9 mg N2O–N m− 2 yr− 1). Each additional 1000 mg m− 2 yr− 1 of nitrogen added to the ecosystem through N-fixation results in additional N2O emissions of 1.6 mg N2O–N m− 2 yr− 1 for the time with maximum H. rhamnoides coverage. Our results suggest that local reactions of emissions to abrupt climate change could have been considerably faster than the overall atmospheric concentration changes observed in polar ice. Nitrogen enrichment of soils due to the presence of symbiotic N-fixers during early primary succession not only facilitates the establishment of vegetation on soils in their initial stage of development, but can also have considerable influence on biogeochemical cycles and the release of reactive nitrogen trace gases to the atmosphere.

Biogeochemical response of Tagus Estuary to climate change : a modelling study

Estuaries are highly dynamic systems which may be modified in a climate change context. These changes can affect the biogeochemical cycles. Among the major impacts of climate change, the increasing rainfall events and sea level rise can be considered. This study aims to research the impact of those events in biogeochemical dynamics in the Tagus Estuary, which is the largest and most important estuary along the Portuguese coast. In this context a 2D biophysical model (MOHID) was implemented, validated and explored, through comparison with in-situ data. In order to study the impact of extreme rainfall events, which can be characterized by an high increase in freshwater inflow, three scenarios were set by changing the inputs from the main tributaries, Tagus and Sorraia Rivers. A realistic scenario considering one day of Tagus and Sorraia River extreme discharge, a scenario considering one day of single extreme discharge of the Tagus River and finally one considering the extreme runoff just from Sorraia River. For the mean sea level rise, two scenarios were also established. The first with the actual mean sea level value and the second considering an increase of 0.42 m. For the extreme rainfall events simulations, the results suggest that the biogeochemical characteristics of the Tagus Estuary are mainly influenced by Tagus River discharge. For sea level rise scenario, the results suggest a dilution in nutrient concentrations and an increase in Chl-a in specific areas.For both scenarios, the suggested increase in Chl-a concentration for specific estuarine areas, under the tested scenarios, can lead to events that promote an abnormal growth of phytoplankton (blooms) causing the water quality to drop and the estuary to face severe quality issues risking all the activities that depend on it.

Deep chlorophyll maximum and upper ocean structure interactions: Case of the Guinea Thermal Dome

Deep Chlorophyll Maximum (DCM) modifies the upper ocean heat capture distribution and thus impacts water column temperature and stratification, as well as biogeochemical processes. This energetical role of the DCM is assessed using a 1 m-resolution 1D physical-biogeochemical model of the upper ocean, using climatological forcing conditions of the Guinea Dome (GD). This zone has been chosen among others because a strong and shallow DCM is present all year round. The results show that the DCM warms the seasonal thermocline by +2 degrees C in September/October and causes an increase of heat transfer from below into the mixed layer (ML) by vertical diffusion and entrainment, leading to a ML warming of about 0.3 degrees C in October. In the permanent thermocline, temperature decreases by up to 2 degrees C. The result is a stratification increase of the water column by 0.3 degrees C m(-1) which improves the thermocline realism when compared with observations. At the same time, the heating associated with the DCM is responsible for an increase of nitrate (+300%, 0.024 mu M), chlorophyll (+50%, 0.02 mu g l(-1)) and primary production (+45%: 10 mg C m(-2) day(-1)) in the ML during the entrainment period of October. The considered concentrations are small but this mechanism could be potentially important to give a better explanation of why there is a significant amount of nitrate in the ML. The mechanisms associated with the DCM presence, no matter which temperature or biogeochemical tracers are concerned, are likely to occur in a wide range of tropical or subpolar regions; in these zones a pronounced DCM is present at least episodically at shallow or moderate depths. These results can be generalized to other thermal dome regions where relatively similar physical and biogeochemical structures are encountered. After testing different vertical resolutions (10 m, 5 m, 2.5 m, 1 m and 0.5 m), we show that using at least a 1 to vertical resolution model is mandatory to assess the energetical importance of the DCM.

Modelling growth dynamics and toxin production in Ostreopsis cf. ovata

The benthic dinoflagellate O. ovata represents a serious threat for human health and for the ecology of its blooming areas: thanks to its toxicity this microalga has been responsible for several cases of human intoxication and mass mortalities of benthic invertebrates. Although the large number of studies on this dinoflagellate, the mechanisms underpinning O. ovata growth and toxin production are still far to be fully understood. In this work we have enriched the dataset on this species by carrying out a new experiment on an Adriatic O. cf. ovata strain. Data from this experiment (named Beta) and from another comparable experiment previously conducted on the same strain (named Alpha), revealed some interesting aspects of this dinoflagellate: it is able to grow also in a condition of strong intracellular nutrient deficiency (C:P molar ratio > 400; C:N > 25), reaching extremely low values of chlorophyll-a to carbon ratio (0.0004). Was also found a significant inverse relationships (r > -0.7) between cellular toxin to carbon and cellular nutrient to carbon ratios of experiment Alpha. In the light of these result, we hypothesized that in O. cf. ovata nutrient-stress conditions (intended as intracellular nutrient deficiency) can cause: i) an increase in toxin production; ii) a strong decrease in chlorophyll-a synthesis; iii) a lowering of metabolism associated with the formation of a sort of resting stage. We then used a modelling approach to test and critically evaluate these hypotheses in a mechanistic way: newly developed formulation describing toxin production and fate, and ad hoc changes in the already existent formulations describing chlorophyll synthesis, rest respiration, and mortality, have been incorporated in a simplified version of the European Regional Seas Ecosystem Model (ERSEM), together with a new ad hoc parameterization. The adapted model was able to accurately reproduce many of the trends observed in the Alpha experiment, allowing us to support our hypotheses. Instead the simulations of the experiment Beta were not fully satisfying in quantitative terms. We explained this gap with the presumed different physiological behaviors between the algae of the two experiments, due to the different pre-experimental periods of acclimation: the model was not able to reproduce acclimation processes in its simulations of the experiment Beta. Thus we attempt to simulate the acclimation of the algae to nutrient-stress conditions by manual intervention on some parameters of nutrient-stress thresholds, but we received conflicting results. Further studies are required to shed light on this interesting aspect. In this work we also improve the range of applicability of a state of the art marine biogeochemical model (ERSEM) by implementing in it an ecological relevant process such as the production of toxic compounds.

Modeling the marine aragonite cycle: changes under rising carbon dioxide and its role in shallow water CaCO3 dissolution

The marine aragonite cycle has been included in the global biogeochemical model PISCES to study the role of aragonite in shallow water CaCO3 dissolution. Aragonite production is parameterized as a function of mesozooplankton biomass and aragonite saturation state of ambient waters. Observation-based estimates of marine carbonate production and dissolution are well reproduced by the model and about 60% of the combined CaCO3 water column dissolution from aragonite and calcite is simulated above 2000 m. In contrast, a calcite-only version yields a much smaller fraction. This suggests that the aragonite cycle should be included in models for a realistic representation of CaCO3 dissolution and alkalinity. For the SRES A2 CO2 scenario, production rates of aragonite are projected to notably decrease after 2050. By the end of this century, global aragonite production is reduced by 29% and total CaCO3 production by 19% relative to pre-industrial. Geographically, the effect from increasing atmospheric CO2, and the subsequent reduction in saturation state, is largest in the subpolar and polar areas where the modeled aragonite production is projected to decrease by 65% until 2100.

A Census of Eddy Activities in the South China Sea During 1993-2007

Numerous mesoscale eddies occur each year in the South China Sea (SCS), but their statistical characteristics are still not well documented. A Pacific basin-wide three dimensional physical-biogeochemical model has been developed and the result in the SCS subdomain is used to quantify the eddy activities during the period of 1993-2007. The modeled results are compared with a merged and gridded satellite product of sea level anomaly by using the same eddy identification and tracking method. On average, there are about 32.9 +/- 2.4 eddies predicted by the model and 32.8 +/- 3.4 eddies observed by satellite each year, and about 52% of them are cyclonic eddies. The radius of these eddies ranges from about 46.5 to 223.5 km, with a mean value of 87.4 km. More than 70% of the eddies have a radius smaller than 100 km. The mean area covered by these eddies each year is around 160,170 km(2), equivalent to 9.8% of the SCS area with water depths greater than 1000 m. Linear relationships are found between eddy lifetime and eddy magnitude and between eddy vertical extent and eddy magnitude, showing that strong eddies usually last longer and penetrate deeper than weak ones. Interannual variations in eddy numbers and the total eddy-occupied area indicate that eddy activities in the SCS do not directly correspond to the El Nino-Southern Oscillation events. The wind stress curls are thought to be an important but not the only mechanism of eddy genesis in the SCS.

Modeling Responses of Diatom Productivity and Biogenic Silica Export to Iron Enrichment in the Equatorial Pacific Ocean

Using a three-dimensional physical-biogeochemical model, we have investigated the modeled responses of diatom productivity and biogenic silica export to iron enrichment in the equatorial Pacific, and compared the model simulation with in situ (IronEx II) iron fertilization results. In the eastern equatorial Pacific, an area of 540,000 km(2) was enhanced with iron by changing the photosynthetic efficiency and silicate and nitrogen uptake kinetics of phytoplankton in the model for a period of 20 days. The vertically integrated Chl a and primary production increased by about threefold 5 days after the start of the experiment, similar to that observed in the IronEx II experiment. Diatoms contribute to the initial increase of the total phytoplankton biomass, but decrease sharply after 10 days because of mesozooplankton grazing. The modeled surface nutrients (silicate and nitrate) and TCO(2) anomaly fields, obtained from the difference between the "iron addition'' and "ambient'' (without iron) concentrations, also agreed well with the IronEx II observations. The enriched patch is tracked with an inert tracer similar to the SF6 used in the IronEx II. The modeled depth-time distribution of sinking biogenic silica (BSi) indicates that it would take more than 30 days after iron injection to detect any significant BSi export out of the euphotic zone. Sensitivity studies were performed to establish the importance of fertilized patch size, duration of fertilization, and the role of mesozooplankton grazing. A larger size of the iron patch tends to produce a broader extent and longer-lasting phytoplankton blooms. Longer duration prolongs phytoplankton growth, but higher zooplankton grazing pressure prevents significant phytoplankton biomass accumulation. With the same treatment of iron fertilization in the model, lowering mesozooplankton grazing rate generates much stronger diatom bloom, but it is terminated by Si(OH)(4) limitation after the initial rapid increase. Increasing mesozooplankton grazing rate, the diatom increase due to iron addition stays at minimum level, but small phytoplankton tend to increase. The numerical model experiments demonstrate the value of ecosystem modeling for evaluating the detailed interaction between biogeochemical cycle and iron fertilization in the equatorial Pacific.

Physical and Biological Controls on the Latitudinal Asymmetry of Surface Nutrients and pCO(2) in the Central and Eastern Equatorial Pacific

Surface nutrients and dissolved inorganic carbon (DIC) in the central (CEP) and eastern equatorial Pacific (EEP) show much higher concentrations to the south than to the north of the equator. In this study, the physical and biological controls on this asymmetry are investigated using a coupled physical-biogeochemical model. Two numerical experiments are conducted to examine the effects of asymmetrical photosynthetic efficiency (a) due to asymmetrical iron supply about the equator. The experiment with asymmetrical photosynthesis produces improved results as compared with historical observations. A nitrate budget analysis suggests that in the EEP the divergence of upwelling waters controls the surface nitrate asymmetry with additional contribution from the South Equatorial Current (SEC) carrying nutrient-rich Peru upwelling water. The changes of a affect the surface nitrate distribution but not the overall asymmetry. The SEC further carries excess nitrate to the west and thus extends the asymmetry in the east to the CEP. In the CEP, however, stronger northward than southward transport tends to reduce the nitrate asymmetry, while the asymmetrical photosynthesis would help to maintain it. Similar processes also control the distributions of surface silicate and DIC in the equatorial Pacific, which is also affected by the air-sea CO(2) exchange. The asymmetrical photosynthesis influences the distribution of surface DIC, pCO(2), and the air-sea CO(2) flux, by redistributing about 20% CO(2) flux from the north to the south of the equator. Owing to the adjustment of air-sea CO(2) flux, however, the net surface DIC change is smaller than the direct change associated with primary production.

Modeled uncertainties in marine N2O emissions with links to source files (52 MB, zipped)

The ocean is responsible for up to a third of total global nitrous oxide (N2O) emissions, but uncertainties in emission rates of this potent greenhouse gas are high (>100%). Here we use a marine biogeochemical model to assess six major uncertainties in estimates of N2O production, thereby providing guidance in how future studies may most effectively reduce uncertainties in current and future marine N2O emissions. Potential surface N2O production from nitrification causes the largest uncertainty in N2O emissions (estimated up to ~1.6 Tg N/yr, or 48% of modeled values), followed by the unknown oxygen concentration at which N2O production switches to N2O consumption (0.8 Tg N/yr, or 24% of modeled values). Other uncertainties are minor, cumulatively changing regional emissions by <15%. If production of N2O by surface nitrification could be ruled out in future studies, uncertainties in marine N2O emissions would be halved.

Particle camera and settling chamber measurements at site PC (GeoB11834-3) and SC (GeoB12914-4) off Cape Blanc/Mauritania

Particles sinking out of the euphotic zone are important vehicles of carbon export from the surface ocean. Most of the particles produce heavier aggregates by coagulating with each other before they sink. We implemented an aggregation model into the biogeochemical model of Regional Oceanic Modelling System (ROMS) to simulate the distribution of particles in the water column and their downward transport in the Northwest African upwelling region. Accompanying settling chamber, sediment trap and particle camera measurements provide data for model validation. In situ aggregate settling velocities measured by the settling chamber were around 55 m d**-1. Aggregate sizes recorded by the particle camera hardly exceeded 1 mm. The model is based on a continuous size spectrum of aggregates, characterised by the prognostic aggregate mass and aggregate number concentration. Phytoplankton and detritus make up the aggregation pool, which has an averaged, prognostic and size dependent sinking. Model experiments were performed with dense and porous approximations of aggregates with varying maximum aggregate size and stickiness as well as with the inclusion of a disaggregation term. Similar surface productivity in all experiments has been generated in order to find the best combination of parameters that produce measured deep water fluxes. Although the experiments failed to represent surface particle number spectra, in the deep water some of them gave very similar slope and spectrum range as the particle camera observations. Particle fluxes at the mesotrophic sediment trap site off Cape Blanc (CB) have been successfully reproduced by the porous experiment with disaggregation term when particle remineralisation rate was 0.2 d**-1. The aggregation-disaggregation model improves the prediction capability of the original biogeochemical model significantly by giving much better estimates of fluxes for both upper and lower trap. The results also point to the need for more studies to enhance our knowledge on particle decay and its variation and to the role that stickiness play in the distribution of vertical fluxes.