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  • 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles  (25)
  • 1
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2017-04-04
    Description: A 1-D model system, consisting of the 1-D version of the Princeton Ocean Model (POM) coupled with the European Regional Seas Ecosystem Model (ERSEM) has been applied to a sub-basin of the Baltic Proper, the Bornholm basin. The model has been forced with 3h meteorological data for the period 1979-1990, producing a 12-year hindcast validated with datasets from the Baltic Environmental Database for the same period. The model results demonstrate the model to hindcast the time-evolution of the physical structure very well, confirming the view of the open Baltic water column as a three layer system of surface, intermediate and bottom waters. Comparative analyses of modelled hydrochemical components with respect to the independent data have shown that the long-term system behaviour of the model is within the observed ranges. Also primary production processes, deduced from oxygen (over)saturation are hindcast correctly over the entire period and the annual net primary production is within the observed range. The largest mismatch with observations is found in simulating the biogeochemistry of the Baltic intermediate waters. Modifications in the structure of the model (addition of fast-sinking detritus and polysaccharide dynamics) have shown that the nutrient dynamics are linked to the quality and dimensions of the organic matter produced in the euphotic zone, highlighting the importance of the residence time of the organic matter within the microbial foodweb in the intermediate waters. Experiments with different scenarios of riverine nutrient loads, assessed in the limits of a 1-D setup, have shown that the external input of organic matter makes the open Baltic model more heterotrophic. The characteristics of the inputs also drive the dynamics of nitrogen in the bottom layers leading either to nitrate accumulation (when the external sources are inorganic), or to coupled nitrification-denitrification (under strong organic inputs). The model indicates the permanent stratification to be the main feature of the system as regulator of carbon and nutrient budgets. The model predicts that most of the carbon produced in the euphotic zone is also consumed in the water column and this enhances the importance of heterotrophic benthic processes as final closure of carbon and nutrient cycles in the open Baltic.
    Description: Supported by a Marie Curie Research Training Grant (MAS3-CT97-5050) and by the Italian Ministry for Environment and Territory
    Description: Published
    Description: 79-100
    Description: open
    Keywords: ERSEM ; ecosystem modelling ; open Baltic ; 03. Hydrosphere::03.04. Chemical and biological::03.04.99. General or miscellaneous ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 3
    Publication Date: 2017-04-04
    Description: Currently biogeochemical models of the global ocean focus on simulating the coupling between prevalent physical conditions and the biogeochemical processes with the underlying assumption that coherent biological properties are a direct (or modulated) response to physics. This is one possible biogeographic characterisation of the pelagic environment, since biogeochemistry represents only one aspect of marine ecosystems. Several models are currently capable of simulating the chlorophyll distribution observed from space, though an objective validation with respect to relevant ecosystem properties is still lacking. In this paper we analyse the results of one of the most comprehensive models of ocean biogeochemistry with an emphasis on biogeographic validation sensu Longhurst (Ecological Geography of the Sea, 2007, 2nd edition, Academic Press). A set of multivariate statistical tools, Multi Dimensional Scaling (MDS) and Principal Components Analysis (PCA), are used to verify the existence of pre-defined biogeographic provinces and their statistical significance. The MDS ordination indicates that the given provinces are recognizable in the model on the basis of the selected variables. Analysis of Similarity (ANOSIM) shows that the provinces are statistically separable and they can be more easily distinguished in terms of their environmental features rather than their biology. The underlying relationships between the physical and biological properties are investigated through correlation analyses, thus providing some insights on how the model reproduces features characteristic of the various regions. Satellite chlorophyll data have been used to demonstrate external validation at the biogeographic level. The a priori provinces as characterised by chlorophyll values cannot be statistically separated in either the data or the model. It is likely this is related to the arbitrary choice of province boundaries, which are not necessarily the same as those derivable from non-interpolated SeaWiFS data. The PCA comparison of modelled and observed chlorophyll demonstrated some objective skill in the model as it generally captures the dominant mode of the data, although severe mismatch was identified in certain regions by visual comparison (Indian and Southern Oceans). The model also overestimated seasonal variability compared to the data. The method shows promise for helping overcome problems with model verification due to undersampling of most ocean biogeochemical variables.
    Description: EUR-OCEANS, CMCC
    Description: Submitted
    Description: 1-51
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: open
    Keywords: Biogeochemical model ; global ocean ; general circulation ; ERSEM ; PELAGOS ; BFM ; biogeography ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: manuscript
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  • 4
    Publication Date: 2017-04-04
    Description: The set of equations for global ocean biogeochemistry deterministic models have been formulated in a comprehensive and unified form in order to use them in numerical simulations of the marine ecosystem for climate change studies (PELAGOS, PELAgic biogeochemistry for Global Ocean Simulations). The fundamental approach stems from the representation of marine trophic interactions and major biogeochemical cycles introduced in the European Regional Seas Ecosystem Model (ERSEM). Our theoretical formulation revisits and generalizes the stoichiometric approach of ERSEM by defining the state variables as Chemical Functional Families (CFF). CFFs are further subdivided into living, non-living and inorganic components. Living CFFs are the basis for the definition of Living Functional Groups, the biomass-based functional prototype of the real organisms. Both CFFs and LFGs are theoretical constructs which allow us to relate measurable properties of marine biogeochemistry to the state variables used in deterministic models. This approach is sufficiently generic that may be used to describe other existing biomass-based ecosystem model.
    Description: Published
    Description: 89-109
    Description: JCR Journal
    Description: reserved
    Keywords: Marine biogeochemistry ; Biomass-based ecosystem model ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 5
    Publication Date: 2017-04-04
    Description: Abstract Several biogeochemical data have been collected in the last 10 years of Italian activity in Antarctica (ABIOCLEAR, ROSSMIZE, BIOSESO-I/II). A comprehensive 1-D biogeochemical model was implemented as a tool to link observations with processes and to investigate the mechanisms that regulate the flux of biogenic material through the water column. The model is ideally located at station B (175^{o}E - 74^{o}S) and was set up to reproduce the seasonal cycle of phytoplankton and organic matter fluxes as forced by the dominant water column physics over the period 1990-2001. Austral spring-summer bloom conditions are assessed by comparing simulated nutrient drawdown, primary production rates, bacterial respiration and biomass with the available observations. The simulated biogenic fluxes of carbon, nitrogen and silica have been compared with the fluxes derived from sediment traps data. The model reproduces quite well the magnitude of the biogenic fluxes, expecially those observed in the bottom sediment trap, but the peaks are delayed in time. Sensitivity experiments have shown that the characterization of detritus, the choice of the sinking velocity and the degradation rates are crucial for the timing and magnitude of the vertical fluxes. An increase of velocity leads to a shift towards observation but also to an overestimation of the deposition flux which can be counteracted by higher bacterial remineralization rates. Model results suggest that observed fluxes could be explained by the size-distribution and quality of the locally-produced biogenic material. It is hypothesized that the bottom sediment trap collects material originated from rapid sinking of particles and also from previous years production periods, likely modulated by advective and aggregation mechanisms which are still not resolved by the model.
    Description: Acknowledgements This research was supported by the Italian projects BIOSESO I and II, funded by the Progetto Nazionale di Ricerca in Antartide initiative. MV was partly funded by the Italian project VECTOR for the adaptation of the BFM to the Ross Sea. P. Ruardij (NIOZ) is acknowledged for the availability of the OpenSesame simulation package.
    Description: Submitted
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: open
    Keywords: Numerical model ; BFM ; Antarctica ; Ross Sea ; Biogeochemistry model ; 02. Cryosphere::02.04. Sea ice::02.04.01. Atmosphere/sea ice/ocean interaction ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: manuscript
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  • 6
    Publication Date: 2017-04-04
    Description: A fully prognostic 1-D thermodynamic model, functional for studies of sea-ice biogeochemistry is developed to better understand the physical processes and the interactions between the environment and the sea-ice ecosystem. The physical model is capable of simulating seasonal changes of snow and ice thickness. Particular attention is paid to reproduce the snow-ice and the superimposed ice formation which play important roles in the dynamics of sea ice algae. The assessment of the model capabilities is done in 1979--1993 at four different stations in the Baltic Sea. A sensitivity analysis stresses the importance of adequate surface forcing functions to properly simulate the onset of sea ice. Our results show that thickness of the ice layers and timing of the melting are in good agreement with the observed data and confirm that one of the key variables in modelling sea-ice thermodynamics is the snow layer and its metamorphism.
    Description: This study is supported by the VECTOR project, funded by the Italian Ministry of the University and the Scientific Research. Collaboration with the Finnish Institute of Marine Research has started thanks to the “Marco Polo” scholarship awarded by the University of Bologna to the first author and it is going on in the framework of EUROceans, Network of Excellence. NCEP Reanalysis and ECMWF data have been provided by the NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, from their Web site at http://www.cdc.noaa.gov/. The observed snow and ice thickness data have been provided by the Ice Service at the Finnish Institute of Marine Research. We are particularly grateful to Ari Seinä for support with the observations.
    Description: Unpublished
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: open
    Keywords: sea-ice ; biogeochemistry ; numerical model ; BFM ; 02. Cryosphere::02.02. Glaciers::02.02.05. Ice dynamics ; 02. Cryosphere::02.02. Glaciers::02.02.07. Ocean/ice interaction ; 02. Cryosphere::02.04. Sea ice::02.04.01. Atmosphere/sea ice/ocean interaction ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: manuscript
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  • 7
    Publication Date: 2017-04-04
    Description: This paper presents a long-term time series (1986–2005) of hydrological and biogeochemical data, both published and unpublished. Data were collected in the north-western area of the Adriatic Sea, at two stations that are considered hydrodynamically and trophically different. The time series have been statistically and graphically analysed on a monthly scale in order to study the annual climatologies, links between the concentrations of chlorophyll-a and the variability in the environment, trophic differences between the two areas and chlorophyll-a trends over time. Basically, the two areas have similar hydrological features, yet they present significant differences in the amount of nutrient inputs: these are in fact higher at the coastal site, which is characterized by a prevalence of surface blooms, while they are lower at the offshore station, which is mainly affected by blooms at intermediate depths. Nonetheless, throughout the whole water column, chlorophyll-a concentrations are only slightly different. Both areas are affected by riverine discharge, though chlorophyll-a concentrations are also driven strongly by the seasonal cycle at the station closer to the coast. Results show that the two stations are not trophically different, although some controlling factors, such as zooplankton grazing in one case and light attenuation in the other, may further regulate the growth of phytoplankton. In both cases no significant trends are detected in either the average chlorophyll-a values or in dispersion of the data, in contrast with significant trends in temperature and salinity.
    Description: Data from 1999 to date have been collected in the framework of the EU programs INTERREG II and INTERREG III Italia-Slovenia. We thank the ISMAR colleagues for having taken part in most of the data collection and also for critical contributions to the manuscript. L. Tedesco, M. Vichi and G. Socal acknowledge support from the Italian project VECTOR. We are grateful to three anonymous referees for their critical comments, which helped us to improve the manuscript. R. King is acknowledged for the language review of this paper and the Editor (E. Boss) for his continued support during the editorial process.
    Description: Published
    Description: 673-687
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: Adriatic Sea ; biogeochemistry ; time-series ; climate variability ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.03. Chemistry of waters ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2012-02-03
    Description: The study presented in this thesis is principally meant to analyze the genericity of a deterministic, comprehensive marine ecosystem model in combination with various refined representations of hydrodynamical processes, and to evaluate the potential predictability skills of this combined modelling system with specific applications in two rather different coastal basins. This objective has been realized by first developing a modular coupling interface between the Princeton Ocean Model (POM) and the European Regional Seas Ecosystem Model (ERSEM), called High-Resolution OpenSESAME POM ERSEM (HiROPE). Secondly, this model framework, embedding a composite of 'complex' conceptual principles of the functioning of the main biogeochemical processes, has been applied to substantially different marine systems, the Baltic proper and the northern Adriatic Sea. The generic biological first principles of the ERSEM ecosystem model have been throughly controlled for consistency, and a suitable mathematical syntax has been defined in order to accomodate the various biogeochemical cycles of the resolved elements. The model has been specifically applied in the chosen basins with different temporal and spatial resolutions: a one-dimensional (vertical, 1D-V), climatological implementation in the northern Adriatic Sea; a 1D-V implementation in the Baltic proper with realistic forcing functions in the period 1979-1991 and a fully three-dimensional, high-frequency realistic implementation in the northern Adriatic Sea (October 1995). General conclusions are that the representation of hydrodynamical variability, the definition and resolution of boundary processes, the introduction of new source terms or the implementation of new biological state variables, affect the predictability of the system behavior more than the utilization of incomplete initial conditions of biological variables in a complex comprehensive ecosystem model.
    Description: TMR Marie Curie Grant (MAS3-CT97-5050) Ministero dell'Ambiente e del Territorio
    Description: Published
    Description: open
    Keywords: ERSEM ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.02. Equatorial and regional oceanography ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: thesis
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  • 9
    Publication Date: 2017-04-04
    Description: This paper presents a global ocean implementation of a multi-component model of marine pelagic biogeochemistry coupled on-line with an ocean general circulation model forced with climatological surface fields (PELAgic biogeochemistry for Global Ocean Simulations, PELAGOS). The final objective is the inclusion of this model as a component in an Earth System model for climate studies. The pelagic model is based on a functional stoichiometric representation of marine biogeochemical cycles and allows simulating the dynamics of C, N, P, Si, O and Fe taking into account the variation of their elemental ratios in the functional groups. The model also includes a parameterization of variable chlorophyll:carbon ratio in phytoplankton, carrying chl as a prognostic variable. The first part of the paper analyzes the contribution of non-local advective-diffusive terms and local vertical processes to the simulated chl distributions. The comparison of the three experiments shows that the mean chl distribution at higher latitudes is largely determined by mixing processes, while vertical advection dominates the distribution in the equatorial upwelling regions. Horizontal advective and diffusive processes are necessary mechanisms for the shape of chl distribution in the sub-tropical Pacific. In the second part, the results have been compared with existing datasets of satellite-derived chlorophyll, surface nutrients, estimates of phytoplankton community composition and primary production data. The agreement is reasonable both in terms of the spatial distribution of annual means and seasonal variability in different dynamical oceanographic regions. Results indicate that some of the model biases in chl and surface nutrients distributions can be related to deficiencies in the simulation of physical processes such as advection and mixing. Other discrepancies are attributed to inadequate parameterizations of phytoplankton functional groups. The model has skill in reproducing the overall distribution of large and small phytoplankton but tends to underestimate diatoms in the northern higher latitudes and overestimate nanophytoplankton with respect to picoautotrophs in oligotrophic regions. The performance of the model is discussed in the context of its use in climate studies and an approach for improving the parameterization of functional groups in deterministic models is outlined.
    Description: EU projects: ENSAMBLES [project no. GOCE-CT-2003-505539] DYNAMITE [project no. 00393(GOCE)]
    Description: Submitted
    Description: open
    Keywords: ecosystem model ; OPA ; ERSEM ; PELAGOS ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.03. Physical::03.03.02. General circulation ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.02. Carbon cycling ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: manuscript
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  • 10
    Publication Date: 2017-04-04
    Description: The response of phytoplankton growth to iron supply and its modulation by large scale circulation and tropical instability waves (TIWs) in the eastern equatorial Pacific has been investigated with an ocean biogeochemistry model. This process study shows that iron can be efficiently advected from the New Guinea shelf through the Equatorial Undercurrent (EUC) to the eastern Pacific. In this region phytoplankton production is enhanced when an additional source of iron is applied in the New Guinea shelf and advected in the model by the EUC. In the eastern Pacific, phytoplankton variability is linked to TIWs activity, as revealed by a wavelet analysis of the total autotrophic carbon. The net local effect of the waves on phytoplankton can be either positive or negative depending on several fac- tors. In some cases the effect of the waves is to enhance iron availability in the euphotic zone leading to a net local increase of phytoplankton biomass, provided that the iron nu- tricline is sufficiently shallow to be reached by the wave vertical scale. In these cases it is also suggested that local maxima of phytoplankton observed in moorings off equator are sustained by advected iron and subsequent local production instead of being the result of concentration mechanisms.
    Description: This work was partly funded by the EU DYNAMITE project
    Description: Submitted
    Description: 1-38
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: open
    Keywords: biogeochemical model ; BFM ; PELAGOS ; tropical instability waves ; iron ; equatorial Pacific ; 03. Hydrosphere::03.01. General::03.01.02. Equatorial and regional oceanography ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: manuscript
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