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Sample records for coastal biogeochemical modelling

  1. An offline unstructured biogeochemical model (UBM) for complex estuarine and coastal environments

    SciTech Connect

    Kim, Tae Yun; Khangaonkar, Tarang

    2012-05-01

    Due to increased pollutant loads and water use from coastal development and population growth, occurrences of low-dissolved oxygen and "hypoxic zones" have increased. Reports of fish kills and water quality impairment are also becoming more frequent in many coastal waters. Water quality managers and regulatory agencies rely on numerical modeling tools to quantify the relative contributions of anthropogenic and "natural" pollutant loads (nutrients and biochemical oxygen demand) on dissolved oxygen levels and use the results for remedial activities and source control. The ability to conduct seasonlong simulations with sufficient nearshore resolution is therefore a key requirement. Mesh flexibility and the ability to increase site specific resolution without disturbing the larger domain setup and calibration are critical. The objective of this effort was to develop a robust biogeochemical model suitable for simulation of water quality dynamics including dissolved oxygen in complex coastal environments with multiple tidal channels, tidal flats, and density-driven circulation using unstructured-grid formulation. This paper presents an offline unstructured biogeochemical model that uses the Finite Volume Coastal Ocean Model (FVCOM) discretization of the study domain and the corresponding hydrodynamic solution to drive biogeochemical kinetics based on a water quality model CE-QUAL-ICM. In this paper, the linkage between selected hydrodynamic and water quality models is subjected to several scalar transport and biogeochemical module tests (plume transport and dilution, BOD/DO sag, and phytoplankton/nutrients reaction), and results are compared to their analytical solutions as part of model validation. A preliminary application of the biogeochemical model with a year-long simulation of Hood Canal basin in Puget Sound, USA, is presented as an example and a test of the tool in a real estuary setting. The model reproduced the dynamics and seasonal variations in the

  2. Use of a coastal biogeochemical model to select environmental monitoring sites

    NASA Astrophysics Data System (ADS)

    Wild-Allen, Karen; Thompson, Peter A.; Volkman, John K.; Parslow, John

    2011-10-01

    A method for the spatial selection of sites for a coastal environmental monitoring system is described. The study was completed in southeastern Tasmania, Australia, but the method can be applied in all regions with validated biogeochemical models. A 3-dimensional coupled hydrodynamic, sediment and biogeochemical model with high spatial and temporal resolution was validated against observations collected throughout 2002 and found to capture the essential features of the biogeochemical dynamics of the system. The model was used to predict the possible quantitative environmental impact of a projected increase in fish farming activity in the region. Integrated impacts of fish farm waste on labile nitrogen, phosphorus, chlorophyll and dissolved oxygen concentrations in the water column were spatially ranked to identify the most likely places to detect environmental change due to fish farming activities. Priority sites were found to be grouped in the Huon Estuary and northern part of the D'Entrecasteaux Channel consistent with the residual northward current in the region. The final monitoring program synthesized model and field understanding to ensure adequate spatial and temporal sampling of the region.

  3. Introducing mixotrophy into a biogeochemical model describing an eutrophied coastal ecosystem: The Southern North Sea

    NASA Astrophysics Data System (ADS)

    Ghyoot, Caroline; Lancelot, Christiane; Flynn, Kevin J.; Mitra, Aditee; Gypens, Nathalie

    2017-04-01

    Most biogeochemical/ecological models divide planktonic protists between phototrophs (phytoplankton) and heterotrophs (zooplankton). However, a large number of planktonic protists are able to combine several mechanisms of carbon and nutrient acquisition. Not representing these multiple mechanisms in biogeochemical/ecological models describing eutrophied coastal ecosystems can potentially lead to different conclusions regarding ecosystem functioning, especially regarding the success of harmful algae, which are often reported as mixotrophic. This modelling study investigates, for the first time, the implications for trophic dynamics of including 3 contrasting forms of mixotrophy, namely osmotrophy (using alkaline phosphatase activity, APA), non-constitutive mixotrophy (acquired phototrophy by microzooplankton) and also constitutive mixotrophy. The application is in the Southern North Sea, an ecosystem that faced, between 1985 and 2005, a significant increase in the nutrient supply N:P ratio (from 31 to 81 mole N:P). The comparison with a traditional model shows that, when the winter N:P ratio in the Southern North Sea is above 22 molN molP-1 (as occurred from mid-1990s), APA allows a 3 to 32% increase of annual gross primary production (GPP). In result of the higher GPP, the annual sedimentation increases as well as the bacterial production. By contrast, APA does not affect the export of matter to higher trophic levels because the increased GPP is mainly due to Phaeocystis colonies, which are not grazed by copepods. The effect of non-constitutive mixotrophy depends on light and affects the ecosystem functioning in terms of annual GPP, transfer to higher trophic levels, sedimentation, and nutrient remineralisation. Constitutive mixotrophy in nanoflagellates appears to have little influence on this ecosystem functioning. An important conclusion from this work is that different forms of mixotrophy have different impacts on system dynamics and it is thus important to

  4. Introducing mixotrophy into a biogeochemical model describing an eutrophied coastal ecosystem: The Southern North Sea

    NASA Astrophysics Data System (ADS)

    Ghyoot, Caroline; Lancelot, Christiane; Flynn, Kevin J.; Mitra, Aditee; Gypens, Nathalie

    2017-09-01

    Most biogeochemical/ecological models divide planktonic protists between phototrophs (phytoplankton) and heterotrophs (zooplankton). However, a large number of planktonic protists are able to combine several mechanisms of carbon and nutrient acquisition. Not representing these multiple mechanisms in biogeochemical/ecological models describing eutrophied coastal ecosystems can potentially lead to different conclusions regarding ecosystem functioning, especially regarding the success of harmful algae, which are often reported as mixotrophic. This modelling study investigates the implications for trophic dynamics of including 3 contrasting forms of mixotrophy, namely osmotrophy (using alkaline phosphatase activity, APA), non-constitutive mixotrophy (acquired phototrophy by microzooplankton) and also constitutive mixotrophy. The application is in the Southern North Sea, an ecosystem that faced, between 1985 and 2005, a significant increase in the nutrient supply N:P ratio (from 31 to 81 mol N:P). The comparison with a traditional model shows that, when the winter N:P ratio in the Southern North Sea is above 22 molN molP-1 (as occurred from mid-1990s), APA allows a 3-32% increase of annual gross primary production (GPP). In result of the higher GPP, the annual sedimentation increases as well as the bacterial production. By contrast, APA does not affect the export of matter to higher trophic levels because the increased GPP is mainly due to Phaeocystis colonies, which are not grazed by copepods. Under high irradiance, non-constitutive mixotrophy appreciably increases annual GPP, transfer to higher trophic levels, sedimentation, and nutrient remineralisation. In this ecosystem, non-constitutive mixotrophy is also observed to have an indirect stimulating effect on diatoms. Constitutive mixotrophy in nanoflagellates appears to have little influence on this ecosystem functioning. An important conclusion from this work is that contrasting forms of mixotrophy have different

  5. Development of a 3D coupled physical-biogeochemical model for the Marseille coastal area (NW Mediterranean Sea): what complexity is required in the coastal zone?

    PubMed

    Fraysse, Marion; Pinazo, Christel; Faure, Vincent Martin; Fuchs, Rosalie; Lazzari, Paolo; Raimbault, Patrick; Pairaud, Ivane

    2013-01-01

    Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period of 5 years (2007-2011). The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model.

  6. Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone?

    PubMed Central

    Fraysse, Marion; Pinazo, Christel; Faure, Vincent Martin; Fuchs, Rosalie; Lazzari, Paolo; Raimbault, Patrick; Pairaud, Ivane

    2013-01-01

    Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period of 5 years (2007–2011). The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model. PMID:24324589

  7. Coastal-zone biogeochemical dynamics under global warming

    SciTech Connect

    Mackenzie, F.T.; Ver, L.M.; Lerman, A.

    2000-03-01

    The coastal zone, consisting of the continental shelves to a depth of 200 meters, including bays, lagoons, estuaries, and near-shore banks, is an environment that is strongly affected by its biogeochemical and physical interactions with reservoirs in the adjacent domains of land, atmosphere, open ocean, and marine sediments. Because the coastal zone is smaller in volume and area coverage relative to the open ocean, it traditionally has been studied as an integral part of the global oceans. In this paper, the authors show by numerical modeling that it is important to consider the coastal zone as an entity separate from the open ocean in any assessment of future Earth-system response under human perturbation. Model analyses for the early part of the 21st century suggest that the coastal zone plays a significant modifying role in the biogeochemical dynamics of the carbon cycle and the nutrient cycles coupled to it. This role is manifested in changes in primary production, storage, and/or export of organic matter, its remineralization, and calcium carbonate precipitation--all of which determine the state of the coastal zone with respect to exchange of CO{sub 2} with the atmosphere. Under a scenario of future reduced or complete cessation of the thermohaline circulation (THC) of the global oceans, coastal waters become an important sink for atmospheric CO{sub 2}, as opposed to the conditions in the past and present, when coastal waters are believed to be a source of CO{sub 2} to the atmosphere. Profound changes in coastal-zone primary productivity underscore the important role of phosphorus as a limiting nutrient. In addition, calculations indicate that the saturation state of coastal waters with respect to carbonate minerals will decline by {approximately}15% by the year 2030. Any future slowdown in the THC of the oceans will increase slightly the rate of decline in saturation state.

  8. Using annually-resolved bivalve records and biogeochemical models to understand and predict climate impacts in coastal oceans

    NASA Astrophysics Data System (ADS)

    Holmes, Sarah

    2017-04-01

    It is more important than ever to study the oceans and especially the shelf seas, which are disproportionately productive, sustaining over 90% of global fisheries . The economic and societal significance of these shallow oceans, as the interface through which society interacts with the marine environment, makes them highly relevant to the decisions of policy-makers and stakeholders. These decision-makers rely upon empirical data informed by consistent and extensive monitoring and assessment from experts in the field, yet long-term, spatially-extensive datasets of the marine environment do not exist or are of poor quality. Modelling the shelf seas with biogeochemical models can provide valuable data, allowing scientists to look at both past and future scenarios to estimate ecosystem response to change. In particular, the European Regional Sea Ecosystem Model or ERSEM combines not only the complex hydrographical aspects of the North West European shelf, but also vast numbers of biological and chemical parameters. Though huge efforts across the modelling community are invested into developing and ultimately increasing the reliability of models such as the ERSEM, this is typically achieved by looking at relationships with aforementioned observed datasets, restricting model accuracy and our understanding of ecosystem processes. It is for this reason that proxy data of the marine environment is so valuable. Of all marine proxies available, sclerochronology, the study of the growth bands on long-lived marine molluscs, is the only proven to provide novel, high resolution, multi-centennial, annually-resolved, absolutely-dated archives of past ocean environment, analogous to dendrochronology. For the first time, this PhD project will combine the proxy data of sclerochronology with model hindcast data from the ERSEM with the aim to better understand the North West European shelf sea environment and potentially improve predictions of future climate change in this region and

  9. Biogeochemical classification of South Florida's estuarine and coastal waters.

    PubMed

    Briceño, Henry O; Boyer, Joseph N; Castro, Joffre; Harlem, Peter

    2013-10-15

    South Florida's watersheds have endured a century of urban and agricultural development and disruption of their hydrology. Spatial characterization of South Florida's estuarine and coastal waters is important to Everglades' restoration programs. We applied Factor Analysis and Hierarchical Clustering of water quality data in tandem to characterize and spatially subdivide South Florida's coastal and estuarine waters. Segmentation rendered forty-four biogeochemically distinct water bodies whose spatial distribution is closely linked to geomorphology, circulation, benthic community pattern, and to water management. This segmentation has been adopted with minor changes by federal and state environmental agencies to derive numeric nutrient criteria. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Scaling analysis of biogeochemical parameters in coastal waters

    NASA Astrophysics Data System (ADS)

    Zongo, Sylvie; Schmitt, François

    2010-05-01

    Monitoring data are very useful for rapidly providing quality controlled measurements of many environmental aquatic, and thus understanding the spatio-temporal structure which governs the dynamics. We consider here the long time biogeochemical time series from automatic continuous monitoring. These biogeochemical time series from in Eastern English Channel: coastal waters, estuarine waters and river waters. In the first analysis, we consider data from the MAREL system (Automatic monitoring network): MAREL Carnot buoy that is situated in the coastal waters of Boulogne-sur-mer with data from the Honfleur MAREL buoy (an estuarine station in the bay of Seine). Marel system is based on the deployment of data buoys having marine water analysis capabilities on an automated mode. It is equipped with high performance technologies for water analysis and real time data transmission and record many parameters at fixed locations: temperature, dissolved Oxygen (DO), pH, chlorophyll a (Chla), salinity with high frequency resolution (10 or 20 minutes). We consider also the data from Wimereux river off Boulogne-sur mer. Two sets of data were recorded in the river Wimereux in downstream and upstream using a temperature, dissolved oxygen, turbidity and salinity sensors. This monitoring provided an approach of spatial temporal functional dynamism, with these two zones: the first is represented by downstream related to hydrodynamic marine; the second is related to the upstream flow waters. All these time series reveal large fluctuations at many time scales. The large number of data provided by the sensors enables the estimation of Fourier spectral analysis, in order to consider the dominant frequencies associated to the dynamics. This shows the impact of turbulence and of the tidal cycle on the high variability of these parameters. These spectra show quite nice scaling regimes which are compared to the one of temperature, as a reference turbulent passive scalar.

  11. Eutrophication-induced acidification of coastal waters in the northern Gulf of Mexico: Insights into origin and processes from a coupled physical-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Laurent, Arnaud; Fennel, Katja; Cai, Wei-Jun; Huang, Wei-Jen; Barbero, Leticia; Wanninkhof, Rik

    2017-01-01

    Nutrient inputs from the Mississippi/Atchafalaya River system into the northern Gulf of Mexico promote high phytoplankton production and lead to high respiration rates. Respiration coupled with water column stratification results in seasonal summer hypoxia in bottom waters on the shelf. In addition to consuming oxygen, respiration produces carbon dioxide (CO2), thus lowering the pH and acidifying bottom waters. Here we present a high-resolution biogeochemical model simulating this eutrophication-driven acidification and investigate the dominant underlying processes. The model shows the recurring development of an extended area of acidified bottom waters in summer on the northern Gulf of Mexico shelf that coincides with hypoxic waters. Not reported before, acidified waters are confined to a thin bottom boundary layer where the production of CO2 by benthic metabolic processes is dominant. Despite a reduced saturation state, acidified waters remain supersaturated with respect to aragonite.

  12. Modelling the global coastal ocean.

    PubMed

    Holt, Jason; Harle, James; Proctor, Roger; Michel, Sylvain; Ashworth, Mike; Batstone, Crispian; Allen, Icarus; Holmes, Robert; Smyth, Tim; Haines, Keith; Bretherton, Dan; Smith, Gregory

    2009-03-13

    Shelf and coastal seas are regions of exceptionally high biological productivity, high rates of biogeochemical cycling and immense socio-economic importance. They are, however, poorly represented by the present generation of Earth system models, both in terms of resolution and process representation. Hence, these models cannot be used to elucidate the role of the coastal ocean in global biogeochemical cycles and the effects global change (both direct anthropogenic and climatic) are having on them. Here, we present a system for simulating all the coastal regions around the world (the Global Coastal Ocean Modelling System) in a systematic and practical fashion. It is based on automatically generating multiple nested model domains, using the Proudman Oceanographic Laboratory Coastal Ocean Modelling System coupled to the European Regional Seas Ecosystem Model. Preliminary results from the system are presented. These demonstrate the viability of the concept, and we discuss the prospects for using the system to explore key areas of global change in shelf seas, such as their role in the carbon cycle and climate change effects on fisheries.

  13. Integrating turbulent flow, biogeochemical, and poromechanical processes in rippled coastal sediment (Invited)

    NASA Astrophysics Data System (ADS)

    Cardenas, M. B.; Cook, P. L.; Jiang, H.; Traykovski, P.

    2010-12-01

    Coastal sediments are the locus of multiple coupled processes. Turbulent flow associated with waves and currents induces porewater flow through sediment leading to fluid exchange with the water column. This porewater flow is determined by the hydraulic and elastic properties of the sediment. Porewater flow also ultimately controls biogeochemical reactions in the sediment whose rates depend on delivery of reactants and export of products. We present results from numerical modeling studies directed at integrating these processes with the goal of shedding light on these complex environments. We show how denitrification rates inside ripples are largest at intermediate permeability which represents the optimal balance of reactant delivery and anoxic conditions. It is clear that nutrient cycling and distribution within the sediment is strongly dependent on the character of the multidimensional flow field inside of sediment. More recent studies illustrate the importance of the elastic properties of the saturated sediment on modulating fluid exchange between the water column and the sediment when pressure fluctuations along the sediment-water interface occur at the millisecond scale. Pressure fluctuations occur at this temporal scale due to turbulence and associated shedding of vortices due to the ripple geometry. This suggests that biogeochemical cycling may also be affected by these high-frequency elastic effects. Future studies should be directed towards this and should take advantage of modeling tools such as those we present.

  14. Coastal Modeling System

    DTIC Science & Technology

    2015-11-04

    and Hydrology - Coastal Community of Practice (CoP) as a Preferred model for Coastal Engineering and Coastal Navigation studies. The work unit...Coastal Inlets Research Program Coastal Modeling System The work unit develops the Coastal Modeling System (CMS) and conducts basic research to... models for simulations of waves, hydrodynamics, salinity and sediment transport, and morphology change. The CMS was identified by the USACE Hydraulics

  15. Biogeochemical processes in model estuaries

    NASA Astrophysics Data System (ADS)

    Church, Thomas M.

    Sixty researchers met to evaluate the effects of global change on estuaries and to improve estuarine modeling at the Second International Symposium on the Biogeochemistry of Model Estuaries, held April 15-19, 1991, at Jekyll Island, Ga. The importance of successful sampling in evaluating chemical fluxes and establishing records of estuarine change was articulated, as was the need for tracer tools for improved modeling. The symposium was sponsored by the National Science Foundation, National Oceanic and Atmospheric Administration, and the Department of Energy.Participants discussed particles and sedimentology, trace elements and metals, organic chemistry, and nutrient cycling of estuarine processes. Four days of presentations were followed by a half-day of discussion on advances in these topics and the overall goal of assessing estuarine processes in global change. What follows is a synopsis of this discussion.

  16. The Anthropogenic Effects of Hydrocarbon Inputs to Coastal Seas: Are There Potential Biogeochemical Impacts?

    NASA Astrophysics Data System (ADS)

    Anderson, M. R.; Rivkin, R. B.

    2016-02-01

    Petroleum hydrocarbon discharges related to fossil fuel exploitation have the potential to alter microbial processes in the upper ocean. While the ecotoxicological effects of such inputs are commonly evaluated, the potential for eutrophication from the constituent organic and inorganic nutrients has been largely ignored. Hydrocarbons from natural seeps and anthropogenic sources represent a measurable source of organic carbon for surface waters. The most recent (1989-1997) estimate of average world-wide input of hydrocarbons to the sea is 1.250 x 1012 g/yr ≈ 1.0 x 1012g C/year. Produced water from offshore platforms is the largest waste stream from oil and gas exploitation and contributes significant quantities of inorganic nutrients such as N, P and Fe. In coastal areas where such inputs are a significant source of these nutrients, model studies show the potential to shift production toward smaller cells and net heterotrophy. The consequences of these nutrient sources for coastal systems and semi enclosed seas are complex and difficult to predict, because (1) there is a lack of comprehensive data on inputs and in situ concentrations and (2) the is no conceptual or quantitative framework to consider their effects on ocean biogeochemical processes. Here we use examples from the North Sea (produced water discharges 1% total riverine input and NH4 3% of the annual riverine nitrogen load), the South China Sea (total petroleum hydrocarbons = 10-1750 μg/l in offshore waters), and the Gulf of Mexico (seeps = 76-106 x 109 gC/yr, Macondo blowout 545 x 109 gC) to demonstrate how hydrocarbon and produced water inputs can influence basin scale biogeochemical and ecosystem processes and to propose a framework to consider these effects on larger scales.

  17. Biogeochemical modeling at mass extinction boundaries

    NASA Technical Reports Server (NTRS)

    Rampino, M. R.; Caldeira, K. G.

    1991-01-01

    The causes of major mass extinctions is a subject of considerable interest to those concerned with the history and evolution of life on earth. The primary objectives of the proposed plan of research are: (1) to develop quantitative time-dependent biogeochemical cycle models, coupled with an ocean atmosphere in order to improve the understanding of global scale physical, chemical, and biological processes that control the distribution of elements important for life at times of mass extinctions; and (2) to develop a comprehensive data base of the best available geochemical, isotopic, and other relevant geologic data from sections across mass extinction boundaries. These data will be used to constrain and test the biogeochemical model. These modeling experiments should prove useful in: (1) determining the possible cause(s) of the environmental changes seen at bio-event boundaries; (2) identifying and quantifying little-known feedbacks among the oceans, atmosphere, and biosphere; and (3) providing additional insights into the possible responses of the earth system to perturbations of various timescales. One of the best known mass extinction events marks the Cretaceous/Tertiary (K/T) boundary (66 Myr ago). Data from the K/T boundary are used here to constrain a newly developed time-dependent biogeochemical cycle model that is designed to study transient behavior of the earth system. Model results predict significant fluctuations in ocean alkalinity, atmospheric CO2, and global temperatures caused by extinction of calcareous plankton and reduction in the sedimentation rates of pelagic carbonates and organic carbon. Oxygen-isotome and other paleoclimatic data from K/T time provide some evidence that such climatic fluctuations may have occurred, but stabilizing feedbacks may have acted to reduce the ocean alkalinity and carbon dioxide fluctuations.

  18. Biogeochemical responses of shallow coastal lagoons to Climate Change

    NASA Astrophysics Data System (ADS)

    Brito, A.; Newton, A.; Tett, P.; Fernandes, T.

    2009-04-01

    The importance of climate change and global warming in the near future is becoming consensual within the scientific community (e.g. Kerr et al., 2008; Lloret et al., 2008). The surface temperature and sea level have increased during the last few years in the northern hemisphere (IPCC, 2007). Predictions for future changes include an increase of surface temperature and sea level for Europe. Moreover, the global warming phenomenon will also change the hydrological cycle and increase precipitation in northern and central Europe (IPCC, 2007). Sea level rise already threatens to overwhelm some lagoons, such as Venice and Moroccan lagoons (Snoussi et al., 2008). Shallow coastal lagoons are some of the most vulnerable systems that will be impacted by these changes (Eisenreich, 2005). Environmental impacts on coastal lagoons include an increase of water turbidity and therefore light attenuation. If these effects are strong enough, the lighted bottoms of shallow lagoons may loose a significant part of the benthic algal community. These communities are highly productive and are essential to control nutrient dynamics of the system by uptaking large amounts of nutrients both from the water column and from the sediments. A decrease in benthic algal communities and photosynthetic oxygen production will also contribute to increasing the vulnerability of the lagoons to hypoxia and anoxia. The flux of nutrients such as phosphate from the sediments may increase dramatically, further disrupting the nutrient balance and condition and promoting cyanobacterial blooms. Microbial activity is temperature dependent, therefore, the increase of temperature will increase the concentrations of ammonium within sediments. The release of phosphate and silicate will also increase with temperature. Coastal lagoons are valuable ecosystems and may be severely impacted, both ecologically and economically, by global change. Shallow coastal lagoons should be considered as sentinel systems and should be

  19. Coastal Modeling System

    DTIC Science & Technology

    2014-09-04

    Coastal Inlets Research Program Coastal Modeling System The work unit develops the Coastal Modeling System ( CMS ) and conducts basic research to...further understanding of sediment transport under mixed forcing from waves and currents. The CMS is a suite of coupled two- dimensional numerical...models for simulating waves, hydrodynamics, salinity and sediment transport, and morphology change. The CMS was identified by the USACE Hydraulics and

  20. Biogeochemical Transport and Reaction Model (BeTR) v1

    SciTech Connect

    TANG, JINYUN

    2016-04-18

    The Biogeochemical Transport and Reaction Model (BeTR) is a F90 code that enables reactive transport modeling in land modules of earth system models (e.g. CESM, ACME). The code adopts the Objective-Oriented-Design, and allows users to plug in their own biogeochemical (BGC) formulations/codes, and compare them to other existing BGC codes in those ESMs. The code takes information of soil physics variables, such as variables, such as temperature, moisture, soil density profile; water flow, etc., from a land model to track the movement of different chemicals in presence of biogeochemical reactions.

  1. Biogeochemical responses to nutrient inputs in a Cuban coastal lagoon: runoff, anthropogenic, and groundwater sources.

    PubMed

    González-De Zayas, R; Merino-Ibarra, M; Soto-Jiménez, M F; Castillo-Sandoval, F S

    2013-12-01

    Laguna Larga, a coastal lagoon in central Cuba, has been heavily altered by tourism infrastructure construction and sewage disposal. We hypothesize that this has decreased the circulation and caused eutrophication of the lagoon. To assess this, 12 bimonthly samplings were carried out in 2007-2008. Temperature, salinity, oxygen, nutrients and nitrogen, and phosphorous fractions (inorganic, organic, and total) were determined. Water and salt budgets, as well as biogeochemical fluxes of nitrogen and phosphorus were calculated using the LOICZ budget model for the three sections of the lagoon identified by morphological constrains and salinity patterns. Laguna Larga is a choked lagoon with restricted water circulation, low exchange, and high residence times that vary significantly along its sections. Residence time was estimated to be 0.1-0.7 years for the inner section and 1-9 days for the outer one. High levels of total nitrogen (annual means 126-137 μM, peaks up to 475 μM) and phosphorus (2.5-4.4 μM, peaks up to 14.5 μM) are evidence of eutrophication of Laguna Larga. During 2007, an average precipitation year, Laguna Larga exported water (703 m(3) d(-1)) and was a source of nitrogen (9.026 mmol m(-2) d(-1)) and phosphorus (0.112 mmol m(-2) d(-1)) to the adjacent sea. δ(15)N determinations in the seagrass Thalassia testudinum (-1.83 to +3.02 ‰) differed significantly between sites in the lagoon and offshore reference sites located W of the inlet, but were similar to those located E of the inlet. δ(15)N determinations in the seaweed Penicillus dumetosus (+1.02 to +4.2) did not show significant differences.

  2. Using Stable Isotope Analysis to Determine Zooplankton Trophic Response to the Biogeochemical Gradient in a Coastal Tributary

    EPA Science Inventory

    The goal of our research is to identify energy inputs that support lower food web production in a coastal tributary using the biogeochemical gradient that arises from the mixing of river and Great Lake water. We characterized the food web along the lower 35 km of the St. Louis Ri...

  3. Using Stable Isotope Analysis to Determine Zooplankton Trophic Response to the Biogeochemical Gradient in a Coastal Tributary

    EPA Science Inventory

    The goal of our research is to identify energy inputs that support lower food web production in a coastal tributary using the biogeochemical gradient that arises from the mixing of river and Great Lake water. We characterized the food web along the lower 35 km of the St. Louis Ri...

  4. Biogeochemical processes and buffering capacity concurrently affect acidification in a seasonally hypoxic coastal marine basin

    NASA Astrophysics Data System (ADS)

    Hagens, M.; Slomp, C. P.; Meysman, F. J. R.; Seitaj, D.; Harlay, J.; Borges, A. V.; Middelburg, J. J.

    2014-11-01

    Coastal areas are impacted by multiple natural and anthropogenic processes and experience stronger pH fluctuations than the open ocean. These variations can weaken or intensify the ocean acidification signal induced by increasing atmospheric pCO2. The development of eutrophication-induced hypoxia intensifies coastal acidification, since the CO2 produced during respiration decreases the buffering capacity of the hypoxic bottom water. To assess the combined ecosystem impacts of acidification and hypoxia, we quantified the seasonal variation in pH and oxygen dynamics in the water column of a seasonally stratified coastal basin (Lake Grevelingen, the Netherlands). Monthly water column chemistry measurements were complemented with estimates of primary production and respiration using O2 light-dark incubations, in addition to sediment-water fluxes of dissolved inorganic carbon (DIC) and total alkalinity (TA). The resulting dataset was used to set up a proton budget on a seasonal scale. Temperature-induced seasonal stratification combined with a high community respiration was responsible for the depletion of oxygen in the bottom water in summer. The surface water showed strong seasonal variation in process rates (primary production, CO2 air-sea exchange), but relatively small seasonal pH fluctuations (0.46 units on the total hydrogen ion scale). In contrast, the bottom water showed less seasonality in biogeochemical rates (respiration, sediment-water exchange), but stronger pH fluctuations (0.60 units). This marked difference in pH dynamics could be attributed to a substantial reduction in the acid-base buffering capacity of the hypoxic bottom water in the summer period. Our results highlight the importance of acid-base buffering in the pH dynamics of coastal systems and illustrate the increasing vulnerability of hypoxic, CO2-rich waters to any acidifying process.

  5. Biogeochemical processes and buffering capacity concurrently affect acidification in a seasonally hypoxic coastal marine basin

    NASA Astrophysics Data System (ADS)

    Hagens, M.; Slomp, C. P.; Meysman, F. J. R.; Seitaj, D.; Harlay, J.; Borges, A. V.; Middelburg, J. J.

    2015-03-01

    Coastal areas are impacted by multiple natural and anthropogenic processes and experience stronger pH fluctuations than the open ocean. These variations can weaken or intensify the ocean acidification signal induced by increasing atmospheric pCO2. The development of eutrophication-induced hypoxia intensifies coastal acidification, since the CO2 produced during respiration decreases the buffering capacity in any hypoxic bottom water. To assess the combined ecosystem impacts of acidification and hypoxia, we quantified the seasonal variation in pH and oxygen dynamics in the water column of a seasonally stratified coastal basin (Lake Grevelingen, the Netherlands). Monthly water-column chemistry measurements were complemented with estimates of primary production and respiration using O2 light-dark incubations, in addition to sediment-water fluxes of dissolved inorganic carbon (DIC) and total alkalinity (TA). The resulting data set was used to set up a proton budget on a seasonal scale. Temperature-induced seasonal stratification combined with a high community respiration was responsible for the depletion of oxygen in the bottom water in summer. The surface water showed strong seasonal variation in process rates (primary production, CO2 air-sea exchange), but relatively small seasonal pH fluctuations (0.46 units on the total hydrogen ion scale). In contrast, the bottom water showed less seasonality in biogeochemical rates (respiration, sediment-water exchange), but stronger pH fluctuations (0.60 units). This marked difference in pH dynamics could be attributed to a substantial reduction in the acid-base buffering capacity of the hypoxic bottom water in the summer period. Our results highlight the importance of acid-base buffering in the pH dynamics of coastal systems and illustrate the increasing vulnerability of hypoxic, CO2-rich waters to any acidifying process.

  6. Biogeochemical response of tropical coastal systems to present and past environmental change

    NASA Astrophysics Data System (ADS)

    Jennerjahn, Tim C.

    2012-08-01

    Global climate and environmental change affect the biogeochemistry and ecology of aquatic systems mostly due to a combination of natural and anthropogenic factors. The latter became more and more important during the past few thousand years and particularly during the 'Anthropocene'. However, although they are considered important in this respect as yet much less is known from tropical than from high latitude coasts. Tropical coasts receive the majority of river inputs into the ocean, they harbor a variety of diverse ecosystems and a majority of the population lives there and economically depends on their natural resources. This review delineates the biogeochemical response of coastal systems to environmental change and the interplay of natural and anthropogenic control factors nowadays and in the recent geological past with an emphasis on tropical regions. Weathering rates are higher in low than in high latitude regions with a maximum in the SE Asia/Western Pacific region. On a global scale the net effect of increasing erosion due to deforestation and sediment retention behind dams is a reduced sediment input into the oceans during the Anthropocene. However, an increase was observed in the SE Asia/Western Pacific region. Nitrogen and phosphorus inputs into the ocean have trebled between the 1970s and 1990s due to human activities. As a consequence of increased nutrient inputs and a change in the nutrient mix excessive algal blooms and changes in the phytoplankton community composition towards non-biomineralizing species have been observed in many regions. This has implications for foodwebs and biogeochemical cycles of coastal seas including the release of greenhouse gases. Examples from tropical coasts with high population density and extensive agriculture, however, display deviations from temperate and subtropical regions in this respect. According to instrumental records and observations the present-day biogeochemical and ecological response to environmental

  7. Wastewater injection, aquifer biogeochemical reactions, and resultant groundwater N fluxes to coastal waters: Kā'anapali, Maui, Hawai'i.

    PubMed

    Fackrell, Joseph K; Glenn, Craig R; Popp, Brian N; Whittier, Robert B; Dulai, Henrietta

    2016-09-15

    We utilize N and C species concentration data along with δ(15)N values of NO3(-) and δ(13)C values of dissolved inorganic C to evaluate the stoichiometry of biogeochemical reactions (mineralization, nitrification, anammox, and denitrification) occurring within a subsurface wastewater plume that originates as treated wastewater injection and enters the coastal waters of Maui as submarine groundwater discharge. Additionally, we compare wastewater effluent time-series data, injection rates, and treatment history with submarine spring discharge time-series data. We find that heterotrophic denitrification is the primary mechanism of N loss within the groundwater plume and that chlorination for pathogen disinfection suppresses microbial activity in the aquifer responsible for N loss, resulting in increased coastal ocean N loading. Replacement of chlorination with UV disinfection may restore biogeochemical reactions responsible for N loss within the aquifer and return N-attenuating conditions in the effluent plume, reducing N loading to coastal waters.

  8. Coupling a terrestrial biogeochemical model to the common land model

    SciTech Connect

    Shi, Xiaoying; Mao, Jiafu; Wang, Yingping; Dai, Yongjiu; Tang, Xuli

    2011-01-01

    A terrestrial biogeochemical model (CASACNP) was coupled to a land surface model (the Common Land Model, CoLM) to simulate the dynamics of carbon substrate in soil and its limitation on soil respiration. The combined model, CoLM-CASACNP, was able to predict long-term carbon sources and sinks that CoLM alone could not. The coupled model was tested using measurements of belowground respiration and surface fluxes from two forest ecosystems. The combined model simulated reasonably well the diurnal and seasonal variations of net ecosystem carbon exchange, as well as seasonal variation in the soil respiration rate of both the forest sites chosen for this study. However, the agreement between model simulations and actual measurements was poorer under dry conditions. The model should be tested against more measurements before being applied globally to investigate the feedbacks between the carbon cycle and climate change.

  9. Arctic Coastal Erosion Modeling

    NASA Astrophysics Data System (ADS)

    Ravens, T. M.; Jones, B.; Zhang, J.; Tweedie, C. E.; Erikson, L. H.; Gibbs, A.; Richmond, B. M.

    2011-12-01

    A process-based coastal erosion/shoreline change model has been developed for Arctic coastal bluffs subject to niche erosion/block collapse. The model explicitly accounts for many environmental/geographic variables including: water temperature, water level, wave height, and bluff height. The model was originally developed for a small coastal segment near Drew Point, Beaufort Sea, Alaska. This coastal setting has experienced a dramatic increase in erosion since the early 2000's. The bluffs at this site are 3-4 m tall and consist of ice-wedge bounded blocks of fine-grained sediments cemented by ice-rich permafrost and capped with a thin organic layer. The bluffs are typically fronted by a narrow (~ 5 m wide) beach or none at all. During a storm surge, the sea contacts the base of the bluff and a niche is formed through thermal and mechanical erosion. The niche grows both vertically and laterally and eventually undermines the bluff, leading to block failure or collapse. The fallen block is then eroded both thermally and mechanically by waves and currents, which must occur before a new niche forming episode may begin. The model has been calibrated based on shoreline change data at Drew Point for two time periods: 1979-2002 and 2002-2007. Measured and modeled shoreline change rates were about 8 m/yr and 16 m/yr, for the earlier and later periods, respectively. In this paper, this work is extended to include modeling and measurement of coastal erosion at Drew Point on an annual basis for the period 2007-2010. In addition, the model is applied at three other Arctic coastal locations - Elson Lagoon, Cape Halkett, and Barter Island - where niche erosion/block collapse prevails.

  10. Exploring the long-term and interannual variability of biogeochemical variables in coastal areas by means of a data assimilation approach

    NASA Astrophysics Data System (ADS)

    Ciavatta, Stefano; Pastres, Roberto

    2011-02-01

    Dynamic Harmonic Regression (DHR) models are applied here to the investigation of the interannual changes in the trend and seasonality of biogeochemical variables monitored in coastal areas. A DHR model can be regarded as a time-series component model, where the phases and amplitudes of the seasonal component, as well as the trend, are parameters that vary with time, reflecting relevant changes in the evolution of the biogeochemical variables. The model parameters and their confidence bounds are estimated by data assimilation algorithms, i.e. the Kalman filter and the Fixed Interval smoother. The DHR model structure is here identified by a preliminary spectral analysis and a subsequent minimization of the Bayesian Information Criterion, thus avoiding subjective choices of the frequencies in the seasonal component. The methodology was applied to the investigation of the long-term and interannual variability of ammonia, nitrate, orthophosphate and chlorophyll-a monitored monthly in the lagoon of Venice (Italy) during the years 1986-2008. It was found that the long-term evolutions of the biogeochemical variables were characterized by non-linear patterns and by statistically significant changes in the trend. The seasonal cycles of all the variables were characterized by a marked interannual variability. In particular, the changes in the seasonality of chlorophyll and nitrate were significantly related to the changes in the seasonality of water temperature at the study site and of nutrient concentrations in river discharges, respectively. These results indicate that the methodology could be a sound alternative to more traditional approaches for investigating the impacts of changes in environmental and anthropogenic forcings on the evolution of biogeochemical variables in coastal areas.

  11. Model for Coastal Restoration

    SciTech Connect

    Thom, Ronald M.; Judd, Chaeli

    2007-07-27

    Successful restoration of wetland habitats depends on both our understanding of our system and our ability to characterize it. By developing a conceptual model, looking at different spatial scales and integrating diverse data streams: GIS datasets and NASA products, we were able to develop a dynamic model for site prioritization based on both qualitative and quantitative relationships found in the coastal environment.

  12. Incorporating nitrogen fixing cyanobacteria in the global biogeochemical model HAMOCC

    NASA Astrophysics Data System (ADS)

    Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina

    2015-04-01

    Nitrogen fixation by marine diazotrophs plays a fundamental role in the oceanic nitrogen and carbon cycle as it provides a major source of 'new' nitrogen to the euphotic zone that supports biological carbon export and sequestration. Since most global biogeochemical models include nitrogen fixation only diagnostically, they are not able to capture its spatial pattern sufficiently. Here we present the incorporation of an explicit, dynamic representation of diazotrophic cyanobacteria and the corresponding nitrogen fixation in the global ocean biogeochemical model HAMOCC (Hamburg Ocean Carbon Cycle model), which is part of the Max Planck Institute for Meteorology Earth system model (MPI-ESM). The parameterization of the diazotrophic growth is thereby based on available knowledge about the cyanobacterium Trichodesmium spp., which is considered as the most significant pelagic nitrogen fixer. Evaluation against observations shows that the model successfully reproduces the main spatial distribution of cyanobacteria and nitrogen fixation, covering large parts of the tropical and subtropical oceans. Besides the role of cyanobacteria in marine biogeochemical cycles, their capacity to form extensive surface blooms induces a number of bio-physical feedback mechanisms in the Earth system. The processes driving these interactions, which are related to the alteration of heat absorption, surface albedo and momentum input by wind, are incorporated in the biogeochemical and physical model of the MPI-ESM in order to investigate their impacts on a global scale. First preliminary results will be shown.

  13. Adapting to life: ocean biogeochemical modelling and adaptive remeshing

    NASA Astrophysics Data System (ADS)

    Hill, J.; Popova, E. E.; Ham, D. A.; Piggott, M. D.; Srokosz, M.

    2013-11-01

    An outstanding problem in biogeochemical modelling of the ocean is that many of the key processes occur intermittently at small scales, such as the sub-mesoscale, that are not well represented in global ocean models. As an example, state-of-the-art models give values of primary production approximately two orders of magnitude lower than those observed in the ocean's oligotrophic gyres, which cover a third of the Earth's surface. This is partly due to their failure to resolve sub-mesoscale phenomena, which play a significant role in nutrient supply. Simply increasing the resolution of the models may be an inefficient computational solution to this problem. An approach based on recent advances in adaptive mesh computational techniques may offer an alternative. Here the first steps in such an approach are described, using the example of a~simple vertical column (quasi 1-D) ocean biogeochemical model. We present a novel method of simulating ocean biogeochemical behaviour on a vertically adaptive computational mesh, where the mesh changes in response to the biogeochemical and physical state of the system throughout the simulation. We show that the model reproduces the general physical and biological behaviour at three ocean stations (India, Papa and Bermuda) as compared to a high-resolution fixed mesh simulation and to observations. The simulations capture both the seasonal and inter-annual variations. The use of an adaptive mesh does not increase the computational error, but reduces the number of mesh elements by a factor of 2-3, so reducing computational overhead. We then show the potential of this method in two case studies where we change the metric used to determine the varying mesh sizes in order to capture the dynamics of chlorophyll at Bermuda and sinking detritus at Papa. We therefore demonstrate adaptive meshes may provide a~suitable numerical technique for simulating seasonal or transient biogeochemical behaviour at high spatial resolution whilst minimising

  14. Adapting to life: ocean biogeochemical modelling and adaptive remeshing

    NASA Astrophysics Data System (ADS)

    Hill, J.; Popova, E. E.; Ham, D. A.; Piggott, M. D.; Srokosz, M.

    2014-05-01

    An outstanding problem in biogeochemical modelling of the ocean is that many of the key processes occur intermittently at small scales, such as the sub-mesoscale, that are not well represented in global ocean models. This is partly due to their failure to resolve sub-mesoscale phenomena, which play a significant role in vertical nutrient supply. Simply increasing the resolution of the models may be an inefficient computational solution to this problem. An approach based on recent advances in adaptive mesh computational techniques may offer an alternative. Here the first steps in such an approach are described, using the example of a simple vertical column (quasi-1-D) ocean biogeochemical model. We present a novel method of simulating ocean biogeochemical behaviour on a vertically adaptive computational mesh, where the mesh changes in response to the biogeochemical and physical state of the system throughout the simulation. We show that the model reproduces the general physical and biological behaviour at three ocean stations (India, Papa and Bermuda) as compared to a high-resolution fixed mesh simulation and to observations. The use of an adaptive mesh does not increase the computational error, but reduces the number of mesh elements by a factor of 2-3. Unlike previous work the adaptivity metric used is flexible and we show that capturing the physical behaviour of the model is paramount to achieving a reasonable solution. Adding biological quantities to the adaptivity metric further refines the solution. We then show the potential of this method in two case studies where we change the adaptivity metric used to determine the varying mesh sizes in order to capture the dynamics of chlorophyll at Bermuda and sinking detritus at Papa. We therefore demonstrate that adaptive meshes may provide a suitable numerical technique for simulating seasonal or transient biogeochemical behaviour at high vertical resolution whilst minimising the number of elements in the mesh. More

  15. Climate-Biogeochemical Coupling in an Antarctic Coastal Ecosystem: Chlorophyll, Nutrient, and Bacterial Production

    NASA Astrophysics Data System (ADS)

    Kim, H.; Doney, S. C.; Iannuzzi, R. A.; Meredith, M. P.; Martinson, D. G.; Ducklow, H. W.

    2016-02-01

    The regional climate and oceanic variability along the West Antarctic Peninsula (WAP) are affected by teleconnections of the El Niño-Southern Oscillation (ENSO) and the Southern Annular Mode (SAM), which in turn cause high seasonal and interannual variability of biogeochemical processes, with sea ice as a mediating physical forcing. Here we investigate a link between climate forcing and biogeochemistry using interdecadal (1992-2014) observations during austral spring-summer (October-March) at Palmer Station (64.8°S, 64.1°W). By employing empirical orthogonal function (EOF) and general linear models (GLMs) via stepwise regression, we examined 1) seasonal and interannual variability of phytoplankton bloom (chlorophyll or Chl), bacterial production (BP), and nutrient (N, P, and Si) drawdown and 2) a scenario of climate and physical forcing mechanisms shaping the variability. Results showed that season-long growth of phytoplankton causes 30% of N, P variability. This variability was predicted by increased water column stability as result of both spring sea ice melt under winter El Niño/-SAM and increased wind forcing due to a +SAM phase in the spring. In contrast, early spring diatom blooms, which cause 20% of Si variability, were predicted by early spring retreat of sea ice. High BP (3H-leucine incorporation) years also appeared under an increased water column stability setting and co-occured with positive Chl anomaly years, demonstrating a close phytoplankton-bacterial coupling, presumably due to consumption of phytoplankton-derived organic matter. Future works focus on quantifying impacts of pure physical processes (e.g. sea ice, meteoric melt fractions, UCDW intrusion) on these biogeochemical parameters using optimal multiparameter (OMP) analysis with salinity and δ18O endmembers. By demonstrating controls of large-scale climate forcing on key biological variables, our findings may provide a better understanding for predicting ecological and biogeochemical

  16. Ecological, biogeochemical and salinity changes in coastal lakes and wetlands over the last 200 years

    NASA Astrophysics Data System (ADS)

    Roberts, Lucy; Holmes, Jonathan; Horne, David

    2016-04-01

    Shallow lakes provide extensive ecosystem services and are ecologically important aquatic resources supporting a diverse flora and fauna. In marginal-marine areas, where such lakes are subjected to the multiple pressures of coastal erosion, sea level rise, increasing sea surface temperature and increasing frequency and intensity of storm surges, environments are complex and unstable. They are characterised by physico-chemical variations due to climatic (precipitation/evaporation cycles) and dynamic factors (tides, currents, freshwater drainage and sea level changes). Combined with human activity in the catchment these processes can alter the salinity, habitat and ecology of coastal fresh- to brackish water ecosystems. In this study the chemical and biological stability of coastal lakes forming the Upper Thurne catchment in the NE of the Norfolk Broads, East Anglia, UK are seriously threatened by long-term changes in salinity resulting from storm surges, complex hydrogeology and anthropogenic activity in the catchment. Future management decisions depend on a sound understanding of the potential ecological impacts, but such understanding is limited by short-term observations and measurements. This research uses palaeolimnological approaches, which can be validated and calibrated with historical records, to reconstruct changes in the aquatic environment on a longer time scale than can be achieved by observations alone. Here, salinity is quantitatively reconstructed using the trace-element geochemistry (Sr/Ca and Mg/Ca) of low Mg-calcite shells of Ostracoda (microscopic bivalved crustaceans) and macrophyte and macroinvertebrate macrofossil remains are used as a proxy to assess ecological change in response to variations in salinity. δ13C values of Cladocera (which are potentially outcompeted by the mysid Neomysis integer with increasing salinity and eutrophication) can be used to reconstruct carbon cycling and energy pathways in lake food webs, which alongside

  17. Simulating aggregate dynamics in ocean biogeochemical models

    NASA Astrophysics Data System (ADS)

    Jackson, George A.; Burd, Adrian B.

    2015-04-01

    The dynamics of elements in the water column is complex, depending on multiple biological and physical processes operating at very different physical scales. Coagulation of particulate material is important for transforming particles and moving them in the water column. Mechanistic models of coagulation processes provide a means to predict these processes, help interpret observations, and provide insight into the processes occurring. However, most model applications have focused on describing simple marine systems and mechanisms. We argue that further model development, in close collaboration with field and experimental scientists, is required in order to extend the models to describe the large-scale elemental distributions and interactions being studied as part of GEOTRACES. Models that provide a fundamental description of trace element-particle interactions are required as are experimental tests of the mechanisms involved and the predictions arising from models. However, a comparison between simple and complicated models of aggregation and trace metal provides a means for understanding the implications of simplifying assumptions and providing guidance as to which simplifications are needed.

  18. Coarsening of physics for biogeochemical model in NEMO

    NASA Astrophysics Data System (ADS)

    Bricaud, Clement; Le Sommer, Julien; Madec, Gurvan; Deshayes, Julie; Chanut, Jerome; Perruche, Coralie

    2017-04-01

    Ocean mesoscale and submesoscale turbulence contribute to ocean tracer transport and to shaping ocean biogeochemical tracers distribution. Representing adequately tracer transport in ocean models therefore requires to increase model resolution so that the impact of ocean turbulence is adequately accounted for. But due to supercomputers power and storage limitations, global biogeochemical models are not yet run routinely at eddying resolution. Still, because the "effective resolution" of eddying ocean models is much coarser than the physical model grid resolution, tracer transport can be reconstructed to a large extent by computing tracer transport and diffusion with a model grid resolution close to the effective resolution of the physical model. This observation has motivated the implementation of a new capability in NEMO ocean model (http://www.nemo-ocean.eu/) that allows to run the physical model and the tracer transport model at different grid resolutions. In a first time, we present results obtained with this new capability applied to a synthetic age tracer in a global eddying model configuration. In this model configuration, ocean dynamic is computed at ¼° resolution but tracer transport is computed at 3/4° resolution. The solution obtained is compared to 2 reference setup ,one at ¼° resolution for both physics and passive tracer models and one at 3/4° resolution for both physics and passive tracer model. We discuss possible options for defining the vertical diffusivity coefficient for the tracer transport model based on information from the high resolution grid. We describe the impact of this choice on the distribution and one the penetration of the age tracer. In a second time we present results obtained by coupling the physics with the biogeochemical model PISCES. We look at the impact of this methodology on some tracers distribution and dynamic. The method described here can found applications in ocean forecasting, such as the Copernicus Marine

  19. Modeling the biogeochemical seasonal cycle in the Strait of Gibraltar

    NASA Astrophysics Data System (ADS)

    Ramírez-Romero, E.; Vichi, M.; Castro, M.; Macías, J.; Macías, D.; García, C. M.; Bruno, M.

    2014-11-01

    A physical-biological coupled model was used to estimate the effect of the physical processes at the Strait of Gibraltar over the biogeochemical features of the Atlantic Inflow (AI) towards the Mediterranean Sea. This work was focused on the seasonal variation of the biogeochemical patterns in the AI and the role of the Strait; including primary production and phytoplankton features. As the physical model is 1D (horizontal) and two-layer, different integration methods for the primary production in the Biogeochemical Fluxes Model (BFM) have been evaluated. An approach based on the integration of a production-irradiance function was the chosen method. Using this Plankton Functional Type model (BFM), a simplified phytoplankton seasonal cycle in the AI was simulated. Main results included a principal bloom in spring dominated by nanoflagellates, whereas minimum biomass (mostly picophytoplankton) was simulated during summer. Physical processes occurring in the Strait could trigger primary production and raise phytoplankton biomass (during spring and autumn), mainly due to two combined effects. First, in the Strait a strong interfacial mixing (causing nutrient supply to the upper layer) is produced, and, second, a shoaling of the surface Atlantic layer occurs eastward. Our results show that these phenomena caused an integrated production of 105 g C m- 2 year- 1 in the eastern side of the Strait, and would also modify the proportion of the different phytoplankton groups. Nanoflagellates were favored during spring/autumn while picophytoplankton is more abundant in summer. Finally, AI could represent a relevant source of nutrients and biomass to Alboran Sea, fertilizing the upper layer of this area with 4.95 megatons nitrate year- 1 (79.83 gigamol year- 1) and 0.44 megatons C year- 1. A main advantage of this coupled model is the capability of solving relevant high-resolution processes as the tidal forcing without expensive computing requirements, allowing to assess the

  20. A hierarchy of ocean biogeochemical comprehensiveness for Earth System Modeling

    NASA Astrophysics Data System (ADS)

    Dunne, J. P.

    2016-12-01

    As Earth System Models mature towards more quantitative explanations of ocean carbon cycle interactions and are applied to an increasingly diverse array of living marine resource communities, the draw towards biogeochemical and ecological comprehensiveness intensifies. However, this draw to comprehensiveness must also be balanced with the added cost of handling additional tracers. One way that GFDL has addressed this constraint is by developing a series of biogeochemical modules based on the 30 tracer TOPAZ formulation used in GFDL's CMIP5 contribution in both simplifying the biogeochemistry down to the 6 tracer BLING formulation and 3 tracer mini-BLING formulation, and in the other direction improving on ecosystem comprehensiveness with the 33 tracer COBALT formulation. We discuss the comparative advantages and disadvantages along this continuum of complexity in terms of both biogeochemical and ecological fidelity and applicability. We also discuss a related approach to separate out other modules for ideal age, 14C, CFCs, SF6, Argon and other tracer suites, allowing use to run an array of experimental designs to suite different needs.

  1. Biogeochemical metabolic modeling of methanogenesis by Methanosarcina barkeri

    NASA Astrophysics Data System (ADS)

    Jensvold, Z. D.; Jin, Q.

    2015-12-01

    Methanogenesis, the biological process of methane production, is the final step of natural organic matter degradation. In studying natural methanogenesis, important questions include how fast methanogenesis proceeds and how methanogens adapt to the environment. To address these questions, we propose a new approach - biogeochemical reaction modeling - by simulating the metabolic networks of methanogens. Biogeochemical reaction modeling combines geochemical reaction modeling and genome-scale metabolic modeling. Geochemical reaction modeling focuses on the speciation of electron donors and acceptors in the environment, and therefore the energy available to methanogens. Genome-scale metabolic modeling predicts microbial rates and metabolic strategies. Specifically, this approach describes methanogenesis using an enzyme network model, and computes enzyme rates by accounting for both the kinetics and thermodynamics. The network model is simulated numerically to predict enzyme abundances and rates of methanogen metabolism. We applied this new approach to Methanosarcina barkeri strain fusaro, a model methanogen that makes methane by reducing carbon dioxide and oxidizing dihydrogen. The simulation results match well with the results of previous laboratory experiments, including the magnitude of proton motive force and the kinetic parameters of Methanosarcina barkeri. The results also predict that in natural environments, the configuration of methanogenesis network, including the concentrations of enzymes and metabolites, differs significantly from that under laboratory settings.

  2. Surrogate-Based Optimization of Biogeochemical Transport Models

    NASA Astrophysics Data System (ADS)

    Prieß, Malte; Slawig, Thomas

    2010-09-01

    First approaches towards a surrogate-based optimization method for a one-dimensional marine biogeochemical model of NPZD type are presented. The model, developed by Oschlies and Garcon [1], simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column and is driven by ocean circulation data. A key issue is to minimize the misfit between the model output and given observational data. Our aim is to reduce the overall optimization cost avoiding expensive function and derivative evaluations by using a surrogate model replacing the high-fidelity model in focus. This in particular becomes important for more complex three-dimensional models. We analyse a coarsening in the discretization of the model equations as one way to create such a surrogate. Here the numerical stability crucially depends upon the discrete stepsize in time and space and the biochemical terms. We show that for given model parameters the level of grid coarsening can be choosen accordingly yielding a stable and satisfactory surrogate. As one example of a surrogate-based optimization method we present results of the Aggressive Space Mapping technique (developed by John W. Bandler [2, 3]) applied to the optimization of this one-dimensional biogeochemical transport model.

  3. Benthic biogeochemical cycling of mercury in two contaminated northern Adriatic coastal lagoons

    NASA Astrophysics Data System (ADS)

    Covelli, Stefano; Emili, Andrea; Acquavita, Alessandro; Koron, Neža; Faganeli, Jadran

    2011-10-01

    Previous research recognized most of the Northern Adriatic coastal lagoon environments as contaminated by mercury (Hg) from multiple anthropogenic sources. Among them, the Pialassa Baiona (P.B.) Lagoon, located near the city of Ravenna (Italy), received between 100 and 200 tons of Hg, generated by an acetaldehyde factory in the period 1957-1977. Further east, the Grado Lagoon has been mainly affected by a long-term Hg input from the Idrija mine (western Slovenia) through the Isonzo River since the 16th century. Hg cycling at the sediment-water interface (SWI) of the two lagoons was investigated and compared by means of an in situ benthic chamber, estimating diffusive Hg and Methyl-Hg fluxes in the summer season. Major chemical features in porewaters (Fe, Mn, H 2S, dissolved inorganic (DIC) and organic carbon (DOC), nutrients) and in the solid phase (C org, N and S) were also explored to understand the general biogeochemical conditions of the system in response to benthic respiration. The daily integrated flux for the methylated Hg form was extremely low in P.B. Lagoon, accounting for only 7% of the corresponding flux calculated for the Grado Lagoon. Despite a higher sedimentary Hg content in the P.B. Lagoon (14.4-79.0 μg g -1) compared to the Grado Lagoon (10.7-12.5 μg g -1), the in situ fluxes of Hg in the two experimental sites appeared similar. A selective sequential extraction procedure was applied to the solid phase, showing that the stable crystalline mineral phase cinnabar (HgS) is the predominant Hg fraction (about 50%) in the Grado Lagoon surface sediments. Conversely, Hg mobilization and sequestration in the P.B. Lagoon is related to the extremely anoxic redox conditions of the system where the intense sulfate reduction, by the release of sulfur and the formation of sulfides, limits the metal recycling at the SWI and its availability for methylation processes. Thus, the environmental conditions at the SWI in the P.B. Lagoon seem to represent a natural

  4. Coastal Surveillance Baseline Model Development

    DTIC Science & Technology

    2015-02-27

    These sensors were defined using basic unclassified information from several different sources [15] [16] [17]. DRDC CORA Task #185 Coastal ...unclassified information from several different sources [19] [20] [21]. DRDC CORA Task #185 Coastal Surveillance Baseline Model Development 27 February...Task #185 Coastal Surveillance Baseline Model Development 27 February 2015 – 27 – 5758-001 Version 01 platform from a couple of different perspectives

  5. Modelling benthic biophysical drivers of ecosystem structure and biogeochemical response

    NASA Astrophysics Data System (ADS)

    Stephens, Nicholas; Bruggeman, Jorn; Lessin, Gennadi; Allen, Icarus

    2016-04-01

    The fate of carbon deposited at the sea floor is ultimately decided by biophysical drivers that control the efficiency of remineralisation and timescale of carbon burial in sediments. Specifically, these drivers include bioturbation through ingestion and movement, burrow-flushing and sediment reworking, which enhance vertical particulate transport and solute diffusion. Unfortunately, these processes are rarely satisfactorily resolved in models. To address this, a benthic model that explicitly describes the vertical position of biology (e.g., habitats) and biogeochemical processes is presented that includes biological functionality and biogeochemical response capturing changes in ecosystem structure, benthic-pelagic fluxes and biodiversity on inter-annual timescales. This is demonstrated by the model's ability to reproduce temporal variability in benthic infauna, vertical pore water nutrients and pelagic-benthic solute fluxes compared to in-situ data. A key advance is the replacement of bulk parameterisation of bioturbation by explicit description of the bio-physical processes responsible. This permits direct comparison with observations and determination of key parameters in experiments. Crucially, the model resolves the two-way interaction between sediment biogeochemistry and ecology, allowing exploration of the benthic response to changing environmental conditions, the importance of infaunal functional traits in shaping benthic ecological structure and the feedback the resulting bio-physical processes exert on pore water nutrient profiles. The model is actively being used to understand shelf sea carbon cycling, the response of the benthos to climatic change, food provision and other societal benefits.

  6. A model simulation of biogeochemical conditions along the British Columbia Continental Shelf

    NASA Astrophysics Data System (ADS)

    Peña, Angelica; Fine, Isaac; Masson, Diane

    2017-04-01

    The British Columbia shelf is at the northern end of the California Current System and is influenced by summer coastal upwelling, mesoscale eddies, and freshwater inputs. A regional coupled circulation-biogeochemical (ROMS) model of this region has been developed to gain a better understanding of the potential impact of climate variability and change on lower trophic levels and the biogeochemistry of the region. A first step to address the impacts of climate variability on marine ecosystem is to develop biophysical models that simulate the present ecosystem state in relation to the climate record and can be used to examine the influence of different forcing acting, at different scales, on ecological processes. This talk will will evaluate the capability of the model to reproduce observations and to respond to main episodic events (seasonal cycle and El Niño events).

  7. Biogeochemical impact of submarine ground water discharge on coastal surface sands of the southern Baltic Sea

    NASA Astrophysics Data System (ADS)

    Donis, Daphne; Janssen, Felix; Liu, Bo; Wenzhöfer, Frank; Dellwig, Olaf; Escher, Peter; Spitzy, Alejandro; Böttcher, Michael E.

    2017-04-01

    This study evaluates the effect of submarine ground water discharge (SGD) on biogeochemical processes of sandy sediments of Hel Bight (Poland) in the shallow southern Baltic Sea, using stirred benthic chambers combined to seepage meters, deep pore water profiles and a reactive transport model. The main impacts of fresh anoxic groundwater seepage are due to (1) the efflux of methane; (2) the efflux of phosphate and silicate; (3) the efflux of dissolved organic carbon (DOC) of aquifer origin. Methane from SGD is assumed to be only slightly oxidized within the sediments and potentially reach the atmosphere at a maximum rate of 30 mmol CH4 m-2 d-1. Silicate and phosphate supplied by SGD promote a seep-site net community production rate that is more than twice as compared to adjacent non seeping sites (70 and 30 mmol C m-2 d-1 respectively). However, oxygen uptake rates at the seep site during the night (30 mmol O2 m-2 d-1) are lower than those observed at the reference sites (50 mmol O2 m-2 d-1). We hypothesize that autogenic, relatively labile DOC is available at the reference site, leading to higher oxygen uptake rates as compared to the seep sites where it is being replaced by less reactive DOC originating from the ground water.

  8. Tidal Marsh Outwelling of Dissolved Organic Matter and Resulting Temporal Variability in Coastal Water Optical and Biogeochemical Properties

    NASA Technical Reports Server (NTRS)

    Tzortziou, Maria; Neale, Patrick J.; Megonigal, J. Patrick; Butterworth, Megan; Jaffe, Rudolf; Yamashita, Youhei

    2010-01-01

    Coastal wetlands are highly dynamic environments at the land-ocean interface where human activities, short-term physical forcings and intense episodic events result in high biological and chemical variability. Long being recognized as among the most productive ecosystems in the world, tidally-influenced coastal marshes are hot spots of biogeochemical transformation and exchange. High temporal resolution observations that we performed in several marsh-estuarine systems of the Chesapeake Bay revealed significant variability in water optical and biogeochemical characteristics at hourly time scales, associated with tidally-driven hydrology. Water in the tidal creek draining each marsh was sampled every hour during several semi-diurnal tidal cycles using ISCO automated samplers. Measurements showed that water leaving the marsh during ebbing tide was consistently enriched in dissolved organic carbon (DOC), frequently by more than a factor of two, compared to water entering the marsh during flooding tide. Estimates of DOC fluxes showed a net DOC export from the marsh to the estuary during seasons of both low and high biomass of marsh vegetation. Chlorophyll amounts were typically lower in the water draining the marsh, compared to that entering the marsh during flooding tide, suggesting that marshes act as transformers of particulate to dissolved organic matter. Moreover, detailed optical and compositional analyses demonstrated that marshes are important sources of optically and chemically distinctive, relatively complex, high molecular weight, aromatic-rich and highly colored dissolved organic compounds. Compared to adjacent estuarine waters, marsh-exported colored dissolved organic matter (CDOM) was characterized by considerably stronger absorption (more than a factor of three in some cases), larger DOC-specific absorption, lower exponential spectral slope, larger fluorescence signal, lower fluorescence per unit absorbance, and higher fluorescence at visible wavelengths

  9. Biogeochemical versus ecological consequences of modeled ocean physics

    NASA Astrophysics Data System (ADS)

    Clayton, Sophie; Dutkiewicz, Stephanie; Jahn, Oliver; Hill, Christopher; Heimbach, Patrick; Follows, Michael J.

    2017-06-01

    We present a systematic study of the differences generated by coupling the same ecological-biogeochemical model to a 1°, coarse-resolution, and 1/6°, eddy-permitting, global ocean circulation model to (a) biogeochemistry (e.g., primary production) and (b) phytoplankton community structure. Surprisingly, we find that the modeled phytoplankton community is largely unchanged, with the same phenotypes dominating in both cases. Conversely, there are large regional and seasonal variations in primary production, phytoplankton and zooplankton biomass. In the subtropics, mixed layer depths (MLDs) are, on average, deeper in the eddy-permitting model, resulting in higher nutrient supply driving increases in primary production and phytoplankton biomass. In the higher latitudes, differences in winter mixed layer depths, the timing of the onset of the spring bloom and vertical nutrient supply result in lower primary production in the eddy-permitting model. Counterintuitively, this does not drive a decrease in phytoplankton biomass but results in lower zooplankton biomass. We explain these similarities and differences in the model using the framework of resource competition theory, and find that they are the consequence of changes in the regional and seasonal nutrient supply and light environment, mediated by differences in the modeled mixed layer depths. Although previous work has suggested that complex models may respond chaotically and unpredictably to changes in forcing, we find that our model responds in a predictable way to different ocean circulation forcing, despite its complexity. The use of frameworks, such as resource competition theory, provides a tractable way to explore the differences and similarities that occur. As this model has many similarities to other widely used biogeochemical models that also resolve multiple phytoplankton phenotypes, this study provides important insights into how the results of running these models under different physical conditions

  10. Tracing biogeochemical subsidies from glacier runoff into Alaska's coastal marine food webs.

    PubMed

    Arimitsu, Mayumi L; Hobson, Keith A; Webber, D'Arcy N; Piatt, John F; Hood, Eran W; Fellman, Jason B

    2017-08-21

    Nearly half of the freshwater discharge into the Gulf of Alaska originates from landscapes draining glacier runoff, but the influence of the influx of riverine organic matter on the trophodynamics of coastal marine food webs is not well understood. We quantified the ecological impact of riverine organic matter subsidies to glacier-marine habitats by developing a multi-trophic level Bayesian three-isotope mixing model. We utilized large gradients in stable (δ(13) C, δ(15) N, δ(2) H) and radiogenic (Δ(14) C) isotopes that trace riverine and marine organic matter sources as they are passed from lower to higher trophic levels in glacial-marine habitats. We also compared isotope ratios between glacial-marine and more oceanic habitats. Based on isotopic measurements of potential baseline sources, ambient water and tissues of marine consumers, estimates of the riverine organic matter source contribution to upper trophic-level species including fish and seabirds ranged from 12-44%. Variability in resource use among similar taxa corresponded to variation in species distribution and life histories. For example, riverine organic matter assimilation by the glacier-nesting seabirds Kittlitz's murrelet (Brachyramphus brevirostris) was greater than that of the forest-nesting marbled murrelet (B. marmoratus). The particulate and dissolved organic carbon in glacial runoff and near surface coastal waters was aged (12100 to 1500 years BP (14) C-age) but dissolved inorganic carbon and biota in coastal waters were young (530 years BP (14) C-age to modern). Thus terrestrial-derived subsidies in marine food webs were primarily composed of young organic matter sources released from glacier ecosystems and their surrounding watersheds. Stable isotope compositions also revealed a divergence in food web structure between glacial-marine and oceanic sites. This work demonstrates linkages between terrestrial and marine ecosystems, and facilitates a greater understanding of how climate

  11. Parameterization of biogeochemical sediment-water fluxes using in situ measurements and a diagenetic model

    NASA Astrophysics Data System (ADS)

    Laurent, A.; Fennel, K.; Wilson, R.; Lehrter, J.; Devereux, R.

    2016-01-01

    Diagenetic processes are important drivers of water column biogeochemistry in coastal areas. For example, sediment oxygen consumption can be a significant contributor to oxygen depletion in hypoxic systems, and sediment-water nutrient fluxes support primary productivity in the overlying water column. Moreover, nonlinearities develop between bottom water conditions and sediment-water fluxes due to loss of oxygen-dependent processes in the sediment as oxygen becomes depleted in bottom waters. Yet, sediment-water fluxes of chemical species are often parameterized crudely in coupled physical-biogeochemical models, using simple linear parameterizations that are only poorly constrained by observations. Diagenetic models that represent sediment biogeochemistry are available, but rarely are coupled to water column biogeochemical models because they are computationally expensive. Here, we apply a method that efficiently parameterizes sediment-water fluxes of oxygen, nitrate and ammonium by combining in situ measurements, a diagenetic model and a parameter optimization method. As a proof of concept, we apply this method to the Louisiana Shelf where high primary production, stimulated by excessive nutrient loads from the Mississippi-Atchafalaya River system, promotes the development of hypoxic bottom waters in summer. The parameterized sediment-water fluxes represent nonlinear feedbacks between water column and sediment processes at low bottom water oxygen concentrations, which may persist for long periods (weeks to months) in hypoxic systems such as the Louisiana Shelf. This method can be applied to other systems and is particularly relevant for shallow coastal and estuarine waters where the interaction between sediment and water column is strong and hypoxia is prone to occur due to land-based nutrient loads.

  12. Biogeochemical Modeling of the Second Rise of Atmospheric Oxygen

    NASA Astrophysics Data System (ADS)

    Smith, M.; Catling, D. C.; Claire, M.

    2014-12-01

    The second rise of atmospheric oxygen (~600 Ma) marked an increase of atmospheric pO2 from a poorly constrained value of 0.1% < pO2 < 10% of present atmospheric level (PAL) in the early and mid Proterozoic to >10%PAL1. The event is important because it ushered in the modern era of animal life. To understand the evolution of Earth's habitability, it is therefore key to understand the cause of this 2nd rise. Here, we quantitatively examine possible causes for the 2nd rise of oxygen. We use a biogeochemical box model2 originally developed to calculate the oxygen evolution before and after the 1st rise of oxygen (~2.4 Ga). The Claire et al. (2006) model calculates the evolution of atmospheric oxygen and methane given production and loss fluxes associated with the oxygen, carbon, and iron cycles. Because the model was unable to drive pO2 to end-Proterozoic levels, the authors suggested that another buffer, such as sulfur, is needed to explain the 2nd rise of oxygen. The sulfur and oxygen cycles are tied through various biogeochemical interactions; therefore, once sulfur (as sulfate) began to accumulate in Proterozoic oceans, it likely began to heavily influence the oxygen cycle. We have added a sulfur biogeochemical cycle to this model, enabling exploration of mechanisms that buffer pO2 at intermediate levels in the Proterozoic and fail to do so in the Phanerozoic. Preliminary results show evolution of oxygen and methane that are consistent with geologic proxies. However, the model-generated 2nd rise of oxygen is dependent upon sulfur fluxes that have uncertain magnitudes, so we will present the sensitivity of our results to model assumptions while constraining scenarios for the 2nd rise of atmospheric O2. In the future, we will also integrate isotopic fractionation effects, which will allow comparison with isotopic data from sedimentary sulfides, carbonates, and organic carbon. 1Canfield, C., 2014, Treatise on Geochemistry, 197 2Claire, M.W., et al., 2006, Geobiology

  13. Chesapeake Bay nitrogen fluxes derived from a land-estuarine ocean biogeochemical modeling system: Model description, evaluation, and nitrogen budgets.

    PubMed

    Feng, Yang; Friedrichs, Marjorie A M; Wilkin, John; Tian, Hanqin; Yang, Qichun; Hofmann, Eileen E; Wiggert, Jerry D; Hood, Raleigh R

    2015-08-01

    The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001-2005 was conducted to quantify the Chesapeake Bay nitrogen budget. The 5 year simulation was characterized by large riverine inputs of nitrogen (154 × 10(9) g N yr(-1)) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 10(9) g N yr(-1)) and buried (46 × 10(9) g N yr(-1)) within the estuarine system. A positive net annual ecosystem production for the bay further contributed to a large advective export of organic nitrogen to the shelf (91 × 10(9) g N yr(-1)) and negligible inorganic nitrogen export. Interannual variability was strong, particularly for the riverine nitrogen fluxes. In years with higher than average riverine nitrogen inputs, most of this excess nitrogen (50-60%) was exported from the bay as organic nitrogen, with the remaining split between burial, denitrification, and inorganic export to the coastal ocean. In comparison to previous simulations using generic shelf biogeochemical model formulations inside the estuary, the estuarine biogeochemical model described here produced more realistic and significantly greater exports of organic nitrogen and lower exports of inorganic nitrogen to the shelf.

  14. Chesapeake Bay nitrogen fluxes derived from a land‐estuarine ocean biogeochemical modeling system: Model description, evaluation, and nitrogen budgets

    PubMed Central

    Friedrichs, Marjorie A. M.; Wilkin, John; Tian, Hanqin; Yang, Qichun; Hofmann, Eileen E.; Wiggert, Jerry D.; Hood, Raleigh R.

    2015-01-01

    Abstract The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land‐estuarine‐ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within‐estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite‐derived data, and a simulation using environmental conditions for 2001–2005 was conducted to quantify the Chesapeake Bay nitrogen budget. The 5 year simulation was characterized by large riverine inputs of nitrogen (154 × 109 g N yr−1) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 109 g N yr−1) and buried (46 × 109 g N yr−1) within the estuarine system. A positive net annual ecosystem production for the bay further contributed to a large advective export of organic nitrogen to the shelf (91 × 109 g N yr−1) and negligible inorganic nitrogen export. Interannual variability was strong, particularly for the riverine nitrogen fluxes. In years with higher than average riverine nitrogen inputs, most of this excess nitrogen (50–60%) was exported from the bay as organic nitrogen, with the remaining split between burial, denitrification, and inorganic export to the coastal ocean. In comparison to previous simulations using generic shelf biogeochemical model formulations inside the estuary, the estuarine biogeochemical model described here produced more realistic and significantly greater exports of organic nitrogen and lower exports of inorganic nitrogen to the shelf. PMID:27668137

  15. A method to efficiently apply a biogeochemical model to a landscape.

    Treesearch

    Robert E. Kennedy; David P. Turner; Warren B. Cohen; Michael. Guzy

    2006-01-01

    Biogeochemical models offer an important means of understanding carbon dynamics, but the computational complexity of many models means that modeling all grid cells on a large landscape is computationally burdensome. Because most biogeochemical models ignore adjacency effects between cells, however, a more efficient approach is possible. Recognizing that spatial...

  16. Using Existing Coastal Models To Address Ocean Acidification Modeling Needs: An Inside Look at Several East and Gulf Coast Regions

    NASA Astrophysics Data System (ADS)

    Jewett, E.

    2013-12-01

    Ecosystem forecast models have been in development for many US coastal regions for decades in an effort to understand how certain drivers, such as nutrients, freshwater and sediments, affect coastal water quality. These models have been used to inform coastal management interventions such as imposition of total maximum daily load allowances for nutrients or sediments to control hypoxia, harmful algal blooms and/or water clarity. Given the overlap of coastal acidification with hypoxia, it seems plausible that the geochemical models built to explain hypoxia and/or HABs might also be used, with additional terms, to understand how atmospheric CO2 is interacting with local biogeochemical processes to affect coastal waters. Examples of existing biogeochemical models from Galveston, the northern Gulf of Mexico, Tampa Bay, West Florida Shelf, Pamlico Sound, Chesapeake Bay, and Narragansett Bay will be presented and explored for suitability for ocean acidification modeling purposes.

  17. Biogeochemical and Optical Analysis of Coastal DOM for Satellite Retrieval of Terrigenous DOM in the U.S. Middle Atlantic Bight

    NASA Technical Reports Server (NTRS)

    Mannino, A.; Dyda, R. Y.; Hernes, P. J.; Hooker, Stan; Hyde, Kim; Novak, Mike

    2012-01-01

    Estuaries and coastal ocean waters experience a high degree of variability in the composition and concentration of particulate and dissolved organic matter (DOM) as a consequence of riverine/estuarine fluxes of terrigenous DOM, sediments, detritus and nutrients into coastal waters and associated phytoplankton blooms. Our approach integrates biogeochemical measurements (elemental content, molecular analyses), optical properties (absorption) and remote sensing to examine terrestrial DOM contributions into the U.S. Middle Atlantic Bight (MAB). We measured lignin phenol composition, DOC and CDOM absorption within the Chesapeake and Delaware Bay mouths, plumes and adjacent coastal ocean waters to derive empirical relationships between CDOM and biogeochemical measurements for satellite remote sensing application. Lignin ranged from 0.03 to 6.6 ug/L between estuarine and outer shelf waters. Our results demonstrate that satellite-derived CDOM is useful as a tracer of terrigenous DOM in the coastal ocean

  18. Biogeochemical cycling in terrestrial ecosystems - Modeling, measurement, and remote sensing

    NASA Technical Reports Server (NTRS)

    Peterson, D. L.; Matson, P. A.; Lawless, J. G.; Aber, J. D.; Vitousek, P. M.

    1985-01-01

    The use of modeling, remote sensing, and measurements to characterize the pathways and to measure the rate of biogeochemical cycling in forest ecosystems is described. The application of the process-level model to predict processes in intact forests and ecosystems response to disturbance is examined. The selection of research areas from contrasting climate regimes and sites having a fertility gradient in that regime is discussed, and the sites studied are listed. The use of remote sensing in determining leaf area index and canopy biochemistry is analyzed. Nitrous oxide emission is investigated by using a gas measurement instrument. Future research projects, which include studying the influence of changes on nutrient cycling in ecosystems and the effect of pollutants on the ecosystems, are discussed.

  19. Complexity, accuracy and practical applicability of different biogeochemical model versions

    NASA Astrophysics Data System (ADS)

    Los, F. J.; Blaas, M.

    2010-04-01

    The construction of validated biogeochemical model applications as prognostic tools for the marine environment involves a large number of choices particularly with respect to the level of details of the .physical, chemical and biological aspects. Generally speaking, enhanced complexity might enhance veracity, accuracy and credibility. However, very complex models are not necessarily effective or efficient forecast tools. In this paper, models of varying degrees of complexity are evaluated with respect to their forecast skills. In total 11 biogeochemical model variants have been considered based on four different horizontal grids. The applications vary in spatial resolution, in vertical resolution (2DH versus 3D), in nature of transport, in turbidity and in the number of phytoplankton species. Included models range from 15 year old applications with relatively simple physics up to present state of the art 3D models. With all applications the same year, 2003, has been simulated. During the model intercomparison it has been noticed that the 'OSPAR' Goodness of Fit cost function (Villars and de Vries, 1998) leads to insufficient discrimination of different models. This results in models obtaining similar scores although closer inspection of the results reveals large differences. In this paper therefore, we have adopted the target diagram by Jolliff et al. (2008) which provides a concise and more contrasting picture of model skill on the entire model domain and for the entire period of the simulations. Correctness in prediction of the mean and the variability are separated and thus enhance insight in model functioning. Using the target diagrams it is demonstrated that recent models are more consistent and have smaller biases. Graphical inspection of time series confirms this, as the level of variability appears more realistic, also given the multi-annual background statistics of the observations. Nevertheless, whether the improvements are all genuine for the particular

  20. Traceable components of terrestrial carbon storage capacity in biogeochemical models.

    PubMed

    Xia, Jianyang; Luo, Yiqi; Wang, Ying-Ping; Hararuk, Oleksandra

    2013-07-01

    Biogeochemical models have been developed to account for more and more processes, making their complex structures difficult to be understood and evaluated. Here, we introduce a framework to decompose a complex land model into traceable components based on mutually independent properties of modeled biogeochemical processes. The framework traces modeled ecosystem carbon storage capacity (Xss ) to (i) a product of net primary productivity (NPP) and ecosystem residence time (τE ). The latter τE can be further traced to (ii) baseline carbon residence times (τ'E ), which are usually preset in a model according to vegetation characteristics and soil types, (iii) environmental scalars (ξ), including temperature and water scalars, and (iv) environmental forcings. We applied the framework to the Australian Community Atmosphere Biosphere Land Exchange (CABLE) model to help understand differences in modeled carbon processes among biomes and as influenced by nitrogen processes. With the climate forcings of 1990, modeled evergreen broadleaf forest had the highest NPP among the nine biomes and moderate residence times, leading to a relatively high carbon storage capacity (31.5 kg cm(-2) ). Deciduous needle leaf forest had the longest residence time (163.3 years) and low NPP, leading to moderate carbon storage (18.3 kg cm(-2) ). The longest τE in deciduous needle leaf forest was ascribed to its longest τ'E (43.6 years) and small ξ (0.14 on litter/soil carbon decay rates). Incorporation of nitrogen processes into the CABLE model decreased Xss in all biomes via reduced NPP (e.g., -12.1% in shrub land) or decreased τE or both. The decreases in τE resulted from nitrogen-induced changes in τ'E (e.g., -26.7% in C3 grassland) through carbon allocation among plant pools and transfers from plant to litter and soil pools. Our framework can be used to facilitate data model comparisons and model intercomparisons via tracking a few traceable components for all terrestrial carbon

  1. Coastal Modeling System: Dredging Module

    DTIC Science & Technology

    2016-06-01

    spacing. Wave data from Wave Information Study (WIS) station 63401 (WIS 2014) were used for input to the wave model. a. b. Figure 1 . (a...ERDC/CHL CHETN-I-90 June 2016 Approved for public release; distribution is unlimited. Coastal Modeling System : Dredging Module by Chris Reed and...within the U.S. Army Corps of Engineers (USACE) Coastal Modeling System (CMS). The DM simulates one or more dredging operations during a CMS

  2. Biogeochemical modelling of the tropical Pacific Ocean. II: Iron biogeochemistry

    NASA Astrophysics Data System (ADS)

    Christian, J. R.; Verschell, M. A.; Murtugudde, R.; Busalacchi, A. J.; McClain, C. R.

    A coupled physical-biogeochemical model of the tropical Pacific Ocean with simultaneous iron and nitrogen limitation was developed to study questions of iron biogeochemistry, its effects on upper ocean production, and ultimately the biogeochemical cycles of the other elements. The model results suggest that iron limitation is ubiquitous in the equatorial Pacific, and extends further west than is generally believed unless there are significant inputs of geothermal iron at quite shallow depths. Most model parameters (e.g., iron solubility, scavenging rates, Fe : N ratios) must be near the limit of their generally accepted range of values in order to prevent elevated surface nitrate concentrations from spreading further into the warm pool than is observed. Transport of geothermal iron in the equatorial undercurrent (EUC) provides a possible mechanism for limiting surface nitrate in the warm pool, but the source must be near the upper boundary of the EUC to provide iron to the surface west of the dateline. Accumulations of ammonium in the western Pacific appear to result from the exhaustion of iron in upwelled water before nitrogen. The realism of the simulation is limited primarily by lack of information about the abundance and distribution of dissolved iron; the assumption of constant Fe : N ratios and the magnitude, distribution and solubility of the aeolian iron flux are also important sources of uncertainty. The sensitivity of the simulation to the way that iron is initialized in the western Pacific thermocline emphasizes the importance of the equatorial undercurrent throughout the tropical Pacific and the need for iron observations in this region.

  3. Biogeochemical cycling during Late Cretcaeous OAE2 - the modelling perspective

    NASA Astrophysics Data System (ADS)

    Floegel, S.; Oschlies, A.; Poulsen, C. J.; Wallmann, K. J.

    2012-12-01

    Cretaceous anoxic events may have been triggered by massive volcanic CO2 degassing as large igneous provinces (LIPs) were emplaced on the seafloor. Here, we present a comprehensive modeling study to decipher the marine biogeochemical consequences of enhanced volcanic CO2 emissions. A biogeochemical box model has been developed for transient model runs with time-dependent volcanic CO2 forcing. The box model considers continental weathering processes, marine export production, degradation processes in the water column, the rain of particles to the seafloor, benthic fluxes of dissolved species across the seabed, and burial of particulates in marine sediments. The ocean is represented by twenty-seven boxes. To estimate horizontal and vertical fluxes between boxes, a coupled ocean-atmosphere general circulation model (AOGCM) is run to derive the circulation patterns of the global ocean under Late Cretaceous boundary conditions. The AOGCM modeling predicts a strong thermohaline circulation and intense ventilation in the Late Cretaceous oceans under high pCO2 values. With an appropriate choice of parameter values such as the continental input of phosphorus, the model produces ocean anoxia at low to mid latitudes and changes in marine δ13C that are consistent with geological data such as the well established δ13C curve. The spread of anoxia is supported by an increase in riverine phosphorus fluxes under high pCO2 and a decrease in phosphorus burial efficiency in marine sediments under low oxygen conditions in ambient bottom waters. Here, we suggest that an additional mechanism might contribute to anoxia, an increase in the C:P ratio of marine plankton which is induced by high pCO2 values. According to our AOGCM model results, an intensively ventilated Cretaceous ocean turns anoxic only if the C:P ratio of marine organic particles exported into the deep ocean is allowed to increase under high pCO2 conditions. Being aware of the uncertainties such as diagenesis, this

  4. A 3-D variational assimilation scheme in coupled transport-biogeochemical models: Forecast of Mediterranean biogeochemical properties.

    PubMed

    Teruzzi, Anna; Dobricic, Srdjan; Solidoro, Cosimo; Cossarini, Gianpiero

    2014-01-01

    [1] Increasing attention is dedicated to the implementation of suitable marine forecast systems for the estimate of the state of the ocean. Within the framework of the European MyOcean infrastructure, the pre-existing short-term Mediterranean Sea biogeochemistry operational forecast system has been upgraded by assimilating remotely sensed ocean color data in the coupled transport-biogeochemical model OPATM-BFM using a 3-D variational data assimilation (3D-VAR) procedure. In the present work, the 3D-VAR scheme is used to correct the four phytoplankton functional groups included in the OPATM-BFM in the period July 2007 to September 2008. The 3D-VAR scheme decomposes the error covariance matrix using a sequence of different operators that account separately for vertical covariance, horizontal covariance, and covariance among biogeochemical variables. The assimilation solution is found in a reduced dimensional space, and the innovation for the biogeochemical variables is obtained by the sequential application of the covariance operators. Results show a general improvement in the forecast skill, providing a correction of the basin-scale bias of surface chlorophyll concentration and of the local-scale spatial and temporal dynamics of typical bloom events. Further, analysis of the assimilation skill provides insights into the functioning of the model. The computational costs of the assimilation scheme adopted are low compared to other assimilation techniques, and its modular structure facilitates further developments. The 3D-VAR scheme results especially suitable for implementation within a biogeochemistry operational forecast system.

  5. Sustainable Management of Coastal Environments Through Coupled Terrestrial-Coastal Ocean Models

    NASA Astrophysics Data System (ADS)

    Lohrenz, S. E.; Cai, W.; Tian, H.; He, R.; Xue, Z.; Fennel, K.; Hopkinson, C.; Howden, S. D.

    2012-12-01

    Changing climate and land use practices have the potential to dramatically alter coupled hydrologic-biogeochemical processes and associated movement of water, carbon and nutrients through various terrestrial reservoirs into rivers, estuaries, and coastal ocean waters. Consequences of climate- and land use-related changes will be particularly evident in large river basins and their associated coastal outflow regions. The large spatial extent of such systems necessitates a combination of satellite observations and model-based approaches coupled with targeted ground-based site studies to adequately characterize relationships among climate forcing (e.g., wind, precipitation, temperature, solar radiation, humidity, extreme weather), land use practice/land cover change, and transport of materials through watersheds and, ultimately, to coastal regions. Here, we describe a NASA Interdisciplinary Science project that employs an integrated suite of models in conjunction with remotely sensed as well as targeted in situ observations with the objectives of describing processes controlling fluxes on land and their coupling to riverine, estuarine and ocean ecosystems. The objectives of this effort are to 1) assemble and evaluate long term datasets for the assessment of impacts of climate variability, extreme weather events, and land use practices on transport of water, carbon and nitrogen within terrestrial systems and the delivery of materials to waterways and rivers; 2) using the Mississippi River as a testbed, develop and evaluate an integrated suite of models to describe linkages between terrestrial and riverine systems, transport of carbon and nutrients in the Mississippi river and its tributaries, and associated cycling of carbon and nutrients in coastal ocean waters; and 3) evaluate uncertainty in model products and parameters and identify areas where improved model performance is needed through model refinement and data assimilation. The effort employs the Dynamic Land

  6. Hyporheic flow and transport processes: mechanisms, models, and biogeochemical implications

    USGS Publications Warehouse

    Boano, Fulvio; Harvey, Judson W.; Marion, Andrea; Packman, Aaron I.; Revelli, Roberto; Ridolfi, Luca; Anders, Wörman

    2014-01-01

    Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed."

  7. Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications

    NASA Astrophysics Data System (ADS)

    Boano, F.; Harvey, J. W.; Marion, A.; Packman, A. I.; Revelli, R.; Ridolfi, L.; Wörman, A.

    2014-12-01

    Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed.

  8. Coastal modelling for flood defence.

    PubMed

    Battjes, Jurjen A; Gerritsen, Herman

    2002-07-15

    This paper reviews practices and trends in hydrodynamic and statistical analyses and modelling in the Netherlands with regard to the risk of coastal flooding. We restrict ourselves to the physical phenomena of tides, storm surges and wind waves. We first give a brief outline of established policy in the Netherlands regarding accepted levels of risk of flooding, and current changes therein. This is followed by a summary of a statistical reanalysis of historical storm-surge data combined with numerical hydrodynamic modelling, aimed at improved estimates of probabilities of occurrence of extreme water levels along the Dutch coast. Recent developments concerning the physical and numerical modelling of inundation of low-lying areas are presented. State-of-the-art modelling of wind waves in coastal areas is also reviewed. Research issues in the area of coastal modelling for flood defence are indicated.

  9. [A biogeochemical model for the Gulf of Nicoya, Costa Rica].

    PubMed

    Tabash Blanco, Farid A

    2007-03-01

    In agreement with the Broecker and Penn two-boxes model, I generated a biogeochemical balance model for the Gulf of Nicoya (Guanacaste, Costa Rica) using two nutrient reservoirs: surface water and deep water. The mixing zone was located at a depth of 20 m. There is a balance between surface waters descending to the bottom and upwelling waters that carry nutrients and other chemical elements to the surface. The main source of nitrogen (nitrate), was the outlet of the Tempisque and Tárcoles rivers. The Gulf of Nicoya is a net source of Dissolved Inorganic Nitrogen (DIN) with an availability rate of 87 x 10(3) mol day(-1) in the dry season and 3044 x 10(3) mol day(-1)in the rainy season. Dissolved Inorganic Phosphate (DIP) was estimated in 27 mol day(-1) in the dry season and 207 mol day(-1) in the rainy season. The dynamics of these biolimited nutrients, in relation to runoff seasonal variations, fits the biological processes reported for the gulf, for example, for variations in primary productivity levels, and maturity and reproduction seasons for species with short and long life cycles.

  10. The dynamics of coastal models

    USGS Publications Warehouse

    Hearn, Clifford J.

    2008-01-01

    Coastal basins are defined as estuaries, lagoons, and embayments. This book deals with the science of coastal basins using simple models, many of which are presented in either analytical form or Microsoft Excel or MATLAB. The book introduces simple hydrodynamics and its applications, from the use of simple box and one-dimensional models to flow over coral reefs. The book also emphasizes models as a scientific tool in our understanding of coasts, and introduces the value of the most modern flexible mesh combined wave-current models. Examples from shallow basins around the world illustrate the wonders of the scientific method and the power of simple dynamics. This book is ideal for use as an advanced textbook for graduate students and as an introduction to the topic for researchers, especially those from other fields of science needing a basic understanding of the basic ideas of the dynamics of coastal basins.

  11. Adsorption behavior of Sudan I-IV on a coastal soil and their forecasted biogeochemical cycles.

    PubMed

    Teng, Yong; Zhou, Qixing

    2017-04-01

    Sudan I-IV as synthetic azo dyes have been concerned worldwide and ever caused a panic on food safety because of illegal addition into foodstuffs. In the past decades, various methods are being developed to identify and determine Sudan dyes in foodstuffs. However, relevant studies about their biogeochemical behaviors and potential environmental effects are rarely reported, although it is of great importance and necessity accounting for their potential environmental contamination from various sources. In this work, the experimental studies on adsorption behavior of Sudan I-IV acting on soil (10, 25, 50, 75, and 100 mg/L) were carried out, and their transport in soil compartments and between soil-water, and air-soil interfaces were discussed. Results showed that the amount of Sudan I-IV adsorbed on soil increased accordingly with the increasing concentration of Sudan dyes in aqueous solution, and Sudan II and IV were more likely adsorbed on the tested soils than Sudan I and III based on their maximum adsorption amount. However, for Sudan I, III, and IV, in some high concentrations (under the treatment of 75 mg/L for Sudan III, 100 mg/L for Sudan I and IV), the adsorption was significantly increased, and then came back to the "normal" level (under the treatment of 100 mg/L for Sudan III). It is expected that relevant researches on their biogeochemical behaviors in soil compartments, and between soil-water and air-soil interfaces would be concerned and addressed.

  12. Biogeochemical modeling of tundra recovery following thermal erosion of permafrost

    NASA Astrophysics Data System (ADS)

    Pearce, A. R.; Rastetter, E. B.; Bowden, W. B.

    2011-12-01

    We simulate the biogeochemical recovery of tundra from a thermal erosion disturbance using the Multiple Element Limitation model (MEL) and compare model results with soil organic matter and nutrient chemistry measurements collected across a chronosequence of thermal erosion features. Thermal erosion of permafrost initially depletes the tundra of much of its vegetation and shallow soil organic matter. However, several decades later, there is often little distinguishing these scars from the surrounding undisturbed tundra. As thermal erosion features become more abundant on the arctic landscape, we desire to understand how the pools of carbon and nutrients rebuild after these disturbances. MEL is a plot-scale, process-based model that optimizes the acquisition of eight resources (light, water, CO2, PO4, NH4, NO3, DON and N-fixation) by vegetation based on how much of each is required and the effort needed to acquire it. Model output includes pool sizes of carbon, nitrogen and phosphorus in vegetation, litter, young soil organic matter and old soil organic matter and the fluxes among these pools over time. This calibration of MEL, operating on a daily timestep, was created with published data collected at or near the Toolik Field Station (Toolik Lake, AK, USA) from moist acidic tussock tundra sites. We corroborate our calibration with data from plot manipulations (N and P fertilization, greenhouse, and shade house) performed as part of the NSF Arctic LTER project. The initial conditions for the recovery simulations reflect post-failure observations of some of the variation in soil organic matter, and soil and water nutrient chemistry. With sufficient nutrients from residual soil or supplied in soil water from upslope, the model indicates that vegetation can recover within several decades, but recovery of C and nutrients lost from soils may take hundreds of years.

  13. A quantitative model of the biogeochemical transport of iodine

    NASA Astrophysics Data System (ADS)

    Weng, H.; Ji, Z.; Weng, J.

    2010-12-01

    Iodine deficiency disorders (IDD) are among the world’s most prevalent public health problems yet preventable by dietary iodine supplements. To better understand the biogeochemical behavior of iodine and to explore safer and more efficient ways of iodine supplementation as alternatives to iodized salt, we studied the behavior of iodine as it is absorbed, accumulated and released by plants. Using Chinese cabbage as a model system and the 125I tracing technique, we established that plants uptake exogenous iodine from soil, most of which are transported to the stem and leaf tissue. The level of absorption of iodine by plants is dependent on the iodine concentration in soil, as well as the soil types that have different iodine-adsorption capacity. The leaching experiment showed that the remainder soil content of iodine after leaching is determined by the iodine-adsorption ability of the soil and the pH of the leaching solution, but not the volume of leaching solution. Iodine in soil and plants can also be released to the air via vaporization in a concentration-dependent manner. This study provides a scientific basis for developing new methods to prevent IDD through iodized vegetable production.

  14. Nitrous Oxide Emissions from Biofuel Crops and Parameterization in the EPIC Biogeochemical Model

    EPA Science Inventory

    This presentation describes year 1 field measurements of N2O fluxes and crop yields which are used to parameterize the EPIC biogeochemical model for the corresponding field site. Initial model simulations are also presented.

  15. Nitrous Oxide Emissions from Biofuel Crops and Parameterization in the EPIC Biogeochemical Model

    EPA Science Inventory

    This presentation describes year 1 field measurements of N2O fluxes and crop yields which are used to parameterize the EPIC biogeochemical model for the corresponding field site. Initial model simulations are also presented.

  16. A 3-D variational assimilation scheme in coupled transport-biogeochemical models: Forecast of Mediterranean biogeochemical properties

    PubMed Central

    Teruzzi, Anna; Dobricic, Srdjan; Solidoro, Cosimo; Cossarini, Gianpiero

    2014-01-01

    [1] Increasing attention is dedicated to the implementation of suitable marine forecast systems for the estimate of the state of the ocean. Within the framework of the European MyOcean infrastructure, the pre-existing short-term Mediterranean Sea biogeochemistry operational forecast system has been upgraded by assimilating remotely sensed ocean color data in the coupled transport-biogeochemical model OPATM-BFM using a 3-D variational data assimilation (3D-VAR) procedure. In the present work, the 3D-VAR scheme is used to correct the four phytoplankton functional groups included in the OPATM-BFM in the period July 2007 to September 2008. The 3D-VAR scheme decomposes the error covariance matrix using a sequence of different operators that account separately for vertical covariance, horizontal covariance, and covariance among biogeochemical variables. The assimilation solution is found in a reduced dimensional space, and the innovation for the biogeochemical variables is obtained by the sequential application of the covariance operators. Results show a general improvement in the forecast skill, providing a correction of the basin-scale bias of surface chlorophyll concentration and of the local-scale spatial and temporal dynamics of typical bloom events. Further, analysis of the assimilation skill provides insights into the functioning of the model. The computational costs of the assimilation scheme adopted are low compared to other assimilation techniques, and its modular structure facilitates further developments. The 3D-VAR scheme results especially suitable for implementation within a biogeochemistry operational forecast system. PMID:26213670

  17. Biogeochemical Modeling of the Second Rise of Oxygen

    NASA Astrophysics Data System (ADS)

    Smith, M. L.; Catling, D.; Claire, M.; Zahnle, K.

    2014-03-01

    The rise of atmospheric oxygen set the tempo for the evolution of complex life on Earth. Oxygen levels are thought to have increased in two broad steps: one step occurred in the Archean ~ 2.45 Ga (the Great Oxidation Event or GOE), and another step occured in the Neoproterozoic ~750-580 Ma (the Neoprotoerozoic Oxygenation Event or NOE). During the NOE, oxygen levels increased from ~1-10% of the present atmospheric level (PAL) (Holland, 2006), to ~15% PAL in the late Neoproterozoic, to ~100% PAL later in the Phanerozoic. Complex life requires O2, so this transition allowed complex life to evolve. We seek to understand what caused the NOE. To explore causes for the NOE, we build upon the biogeochemical model of Claire et al. (2006), which calculates the redox evolution of the atmosphere, ocean, biosphere, and crust in the Archean through to the early Proterozoic. In this model, the balance between oxygenconsuming and oyxgen-producing fluxes evolves over time such that at ~2.4 Ga, the rapidly acting sources of oxygen outweigh the rapidly-acting sinks. Or, in other words, at ~2.4 Ga, the flux of oxygen from organic carbon burial exceeds the sinks of oxygen from reaction with reduced volcanic and metamoprphic gases. The model is able to drive oxygen levels to 1-10% PAL in the Proterozoic; however, the evolving redox fluxes in the model cannot explain how oxygen levels pushed above 1-10% in the late Proterozoic. The authors suggest that perhaps another buffer, such as sulfur, is needed to describe Proterozoic and Phanerozoic redox evolution. Geologic proxies show that in the Proterozoic, up to 10% of the deep ocean may have been sulfidic. With this ocean chemistry, the global sulfur cycle would have worked differently than it does today. Because the sulfur and oxygen cycles interact, the oxygen concentration could have permanently changed due to an evolving sulfur cycle (in combination with evolving redox fluxes associated with other parts of the oxygen cycle and carbon

  18. The general ensemble biogeochemical modeling system (GEMS) and its applications to agriculture systems in the United States

    USDA-ARS?s Scientific Manuscript database

    The General Ensemble Biogeochemical Modeling System (GEMS) was developed for a proper integration of well-established ecosystem biogeochemical models with various spatial databases to simulate biogeochemical cycles over large areas. Major driving variables include land cover and land use, climate, s...

  19. Mechanisms driving estuarine water quality: A 3D biogeochemical model for informed management

    NASA Astrophysics Data System (ADS)

    Wild-Allen, Karen; Skerratt, Jenny; Whitehead, Jason; Rizwi, Farhan; Parslow, John

    2013-12-01

    Estuaries are amongst the most productive marine ecosystems of the world but are also some of the most degraded due to coastal urban development. Sparse sampling of complex interactions between estuarine physics, sediment transport, chemistry, and biology limits understanding of the processes controlling estuarine water quality and confounds active management. We use a 3D coupled hydrodynamic, sediment and biogeochemical model to identify the key mechanisms driving fine-scale fluctuations in water quality in a temperate micro-tidal salt wedge estuary [Derwent Estuary, Tasmania]. Model results are dynamically consistent with relatively sparse monitoring data collected over a seasonal cycle and are considered to be a plausible hypothesis of sub-monitoring scale processes occurring in the estuary. The model shows enhanced mixing of nutrients across the pycnocline downstream of the salt wedge front that supports a persistent phytoplankton bloom. The length and flow regime of the estuary results in nutrient recycling and retention in the estuarine circulation driving a decline in bottom water dissolved oxygen in the mid- and upper-reaches. A budget analysis of modelled nitrogen suggests high levels of denitrification are critical to the maintenance of existing water quality. Active estuarine management focused on the improvement of bottom water dissolved oxygen for ecological health reasons must either concurrently reduce anthropogenic nitrogen loads or be sure to maintain high levels of microbial denitrification for net water quality improvement.

  20. Response of phytoplankton and enhanced biogeochemical activity to an episodic typhoon event in the coastal waters of Japan

    NASA Astrophysics Data System (ADS)

    Tsuchiya, Kenji; Kuwahara, Victor S.; Yoshiki, Tomoko M.; Nakajima, Ryota; Shimode, Shinji; Kikuchi, Tomohiko; Toda, Tatsuki

    2017-07-01

    Daily field surveys were conducted at a coastal-shelf station in Sagami Bay, Japan after the passage of typhoon Malou in 2010 to evaluate the after-effect of a typhoon passage on the physical-chemical environment, phytoplankton bloom formation and microbial processes within and below the euphotic layer. The passage of Malou induced an abrupt decrease in salinity and increased loading of nutrients to the euphotic layer. Dinoflagellates dominated the phytoplankton community at the surface, whereas diatoms dominated below the surface just after the passage of Malou. Four days later, the dominant dinoflagellate taxa at the surface changed from Protoperidinium spp. to Prorocentrum spp. and Ceratium spp., indicating a dinoflagellate community succession from heterotrophic to autotrophic functional groups. Five days after passage, the dominant phytoplankton taxa shifted from dinoflagellates to diatom groups of Chaetoceros spp. and Cerataulina spp. throughout the water column. Below the euphotic layer, there were increases in diatom frustules, mainly composed of Chaetoceros spp. and Cerataulina spp., bacterial abundance and NH4+ concentrations. Diatom carbon biomass contributed to approximately half of particulate organic carbon (POC) below the euphotic layer, suggesting a significant contribution of diatoms to POC sinking flux after the passage of a typhoon. Bacterial abundance was positively correlated to both phaeopigment concentrations (p < 0.01) and NH4+ concentrations (p < 0.01), suggesting bacterial growth was associated with zooplankton grazing and remineralization of NH4+. The results suggest that the passage of a typhoon could significantly affect biogeochemical activities within and below the euphotic layer in temperate coastal waters.

  1. CALIBRATION OF SUBSURFACE BATCH AND REACTIVE-TRANSPORT MODELS INVOLVING COMPLEX BIOGEOCHEMICAL PROCESSES

    EPA Science Inventory

    In this study, the calibration of subsurface batch and reactive-transport models involving complex biogeochemical processes was systematically evaluated. Two hypothetical nitrate biodegradation scenarios were developed and simulated in numerical experiments to evaluate the perfor...

  2. CALIBRATION OF SUBSURFACE BATCH AND REACTIVE-TRANSPORT MODELS INVOLVING COMPLEX BIOGEOCHEMICAL PROCESSES

    EPA Science Inventory

    In this study, the calibration of subsurface batch and reactive-transport models involving complex biogeochemical processes was systematically evaluated. Two hypothetical nitrate biodegradation scenarios were developed and simulated in numerical experiments to evaluate the perfor...

  3. Biogeochemical characterization of MC252 oil:sand aggregates on a coastal headland beach.

    PubMed

    Urbano, Marilany; Elango, Vijaikrishnah; Pardue, John H

    2013-12-15

    MC252 oil:sand aggregates, termed surface residue balls (SRBs), were sampled for physical, chemical and microbial characteristics from different tidal zones on a coastal headland beach in Louisiana, USA. Supratidal SRBs were smaller, had low moisture content, and salinities that were <2 ppt. Intertidal SRBs were hypersaline and had higher N and sulfate concentrations, consistent with regular tidal inundation. Crude oil components were highest in the intertidal "oil mat" SRBs with C1- and C2-phenanthrenes, C2- and C3-dibenzothiophenes comprising the majority of the PAH concentrations. In the other SRB categories, PAHs and alkanes were depleted and profiles were skewed toward higher molecular weight compounds. Oxygen microelectrode measurements demonstrated that saturated O2 is present immediately after wetting, but O2 consumption in the interior of the aggregate occurs after a few days. Microbial populations varied with position on the beach but sequences similar to known PAH-degrading taxa (Mycobacterium sp. and Stenotrophomonas sp.) were observed.

  4. Biogeochemical Radiocabon analysis of the Gulf Oil Spill: Sediments, Plankton and Coastal Fauna

    NASA Astrophysics Data System (ADS)

    Chanton, J.; Cherrier, J.; Sarkadee-Adoo, J.; Joye, S. B.; Hollander, D. J.; Graham, W.; Brunner, C. A.; Bosman, S.; Mickel, A.

    2012-12-01

    The Gulf Oil Spill injected a unique tracer into the Gulf of Mexico, radiocarbon-free fossil organic matter. Most Gulf organic matter is fixed at the surface with a modern radiocarbon (14C) content. We have traced the input of petro-carbon into the Gulf by following input of radiocarbon dead organic matter into the sediments and fauna. Surface ocean organic production and measured oil are separated by 5-7‰ in stable carbon isotope (d13C) space, while in radiocarbon (D14C) space, these two potential sources are separated by more than 1000‰. Thus radiocarbon provides a more sensitive tracer by which to infer possible introduction of Macondo oil into the food web and sediments. We measured D14C and δ13C in plankton collected from within 100km of the spill site as well as in coastal and offshore DIC (Dissolved Inorganic Carbon) to constrain surface production values. On average, plankton values were depleted in 14C relative to surface DIC and we found a significant linear correlation between D14C and δ13C in plankton. Our results support the findings of petro-carbon entering the food web, but infer that methane input may be important. We have also mapped the distribution of radiocarbon in surficial sediments on the seafloor and which show a plume of radiocarbon depleted organic matter to the SW of the well head. Fauna show distinct radiocarbon depletions in Louisiana coastal embayments relative to Florida estuaries.igure 1. Seafloor radiocarbon map

  5. Coastal Modeling System (CMS) Users Manuel

    DTIC Science & Technology

    1992-08-01

    AD-A268 830 , INSTRUCTION REPORT CERC-91-1 COASTAL MODELING SYSTEM ( CMS ) USER’S MANUAL by Mary A. Cialone, David J. Mark, Lucia W. Chou, David A...THE COASTAL MODELING SYSTEM USER’S MANUAL Supplement 1 Issued August 1992 Enclosed are additions and corrections to the Coastal Modeling System ( CMS ...COVERED1 August 1992 Supplement I to September 1991 Manual 4. TITLE AND SUBTITLE S. FUNDING NUMBERS Coastal Modeling System ( CMS ) User’s Manual WU

  6. Inconsistent Strategies to Spin up Models in CMIP5: Implications for Ocean Biogeochemical Model Performance Assessment

    NASA Technical Reports Server (NTRS)

    Seferian, Roland; Gehlen, Marion; Bopp, Laurent; Resplandy, Laure; Orr, James C.; Marti, Olivier; Dunne, John P.; Christian, James R.; Doney, Scott C.; Ilyina, Tatiana; Romanou, Anastasia

    2015-01-01

    During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were made to systematically assess the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. In routine assessments model historical hindcasts were compared with available modern biogeochemical observations. However, these assessments considered neither how close modeled biogeochemical reservoirs were to equilibrium nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESMs) contributes to model-to-model differences in the simulated fields. We take advantage of a 500-year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and holds when confronted with a larger ensemble of CMIP5 models. This shows that drift has implications for performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to- model uncertainty. This requires more attention in future model intercomparison exercises in order to provide quantitatively more correct ESM results on marine biogeochemistry and carbon cycle feedbacks.

  7. Inconsistent strategies to spin up models in CMIP5: implications for ocean biogeochemical model performance assessment

    NASA Astrophysics Data System (ADS)

    Séférian, R.; Gehlen, M.; Bopp, L.; Resplandy, L.; Orr, J. C.; Marti, O.; Dunne, J. P.; Christian, J. R.; Doney, S. C.; Ilyina, T.; Lindsay, K.; Halloran, P.; Heinze, C.; Segschneider, J.; Tjiputra, J.

    2015-10-01

    During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were carried out on the systematic assessment of the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. Mean-state assessments routinely compared model hindcasts to available modern biogeochemical observations. However, these assessments considered neither the extent of equilibrium in modeled biogeochemical reservoirs nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESM) contribute to model-to-model differences in the simulated fields. We take advantage of a 500 year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and is consistent when confronted against a larger ensemble of CMIP5 models. This shows that drift has implications on their performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to-model uncertainty. This requires more attention in future model intercomparison exercices in order to provide realistic ESM results on marine biogeochemistry and carbon cycle feedbacks.

  8. Inconsistent strategies to spin up models in CMIP5: implications for ocean biogeochemical model performance assessment

    NASA Astrophysics Data System (ADS)

    Séférian, Roland; Gehlen, Marion; Bopp, Laurent; Resplandy, Laure; Orr, James C.; Marti, Olivier; Dunne, John P.; Christian, James R.; Doney, Scott C.; Ilyina, Tatiana; Lindsay, Keith; Halloran, Paul R.; Heinze, Christoph; Segschneider, Joachim; Tjiputra, Jerry; Aumont, Olivier; Romanou, Anastasia

    2016-05-01

    During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were made to systematically assess the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. In routine assessments model historical hindcasts were compared with available modern biogeochemical observations. However, these assessments considered neither how close modeled biogeochemical reservoirs were to equilibrium nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESMs) contributes to model-to-model differences in the simulated fields. We take advantage of a 500-year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and holds when confronted with a larger ensemble of CMIP5 models. This shows that drift has implications for performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to-model uncertainty. This requires more attention in future model intercomparison exercises in order to provide quantitatively more correct ESM results on marine biogeochemistry and carbon cycle feedbacks.

  9. Inconsistent Strategies to Spin up Models in CMIP5: Implications for Ocean Biogeochemical Model Performance Assessment

    NASA Technical Reports Server (NTRS)

    Seferian, Roland; Gehlen, Marion; Bopp, Laurent; Resplandy, Laure; Orr, James C.; Marti, Olivier; Dunne, John P.; Christian, James R.; Doney, Scott C.; Ilyina, Tatiana; hide

    2015-01-01

    During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were made to systematically assess the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. In routine assessments model historical hindcasts were compared with available modern biogeochemical observations. However, these assessments considered neither how close modeled biogeochemical reservoirs were to equilibrium nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESMs) contributes to model-to-model differences in the simulated fields. We take advantage of a 500-year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and holds when confronted with a larger ensemble of CMIP5 models. This shows that drift has implications for performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to- model uncertainty. This requires more attention in future model intercomparison exercises in order to provide quantitatively more correct ESM results on marine biogeochemistry and carbon cycle feedbacks.

  10. Biogeochemical Insights into B-Vitamins in the Coastal Marine Sediments of San Pedro Basin, CA

    NASA Astrophysics Data System (ADS)

    Monteverde, D.; Berelson, W.; Baronas, J. J.; Sanudo-Wilhelmy, S. A.

    2015-12-01

    Coastal marine sediments support a high abundance of mircoorganisms which play key roles in the cycling of nutrients, trace metals, and carbon, yet little is known about many of the cofactors essential for their growth, such as the B-vitamins. The suite of B-vitamins (B1, B2, B6, B7, B12) are essential across all domains of life for both primary and secondary metabolism. Therefore, studying sediment concentrations of B-vitamins can provide a biochemical link between microbial processes and sediment geochemistry. Here we present B-vitamin pore water concentrations from suboxic sediment cores collected in September 2014 from San Pedro Basin, a silled, low oxygen, ~900 m deep coastal basin in the California Borderlands. We compare the B-vitamin concentrations (measured via LCMS) to a set of geochemical profiles including dissolved Fe (65-160 μM), dissolved Mn (30-300 nM), TCO2, solid phase organic carbon, and δ13C. Our results show high concentrations (0.8-3nM) of biotin (B7), commonly used for CO2 fixation as a cofactor in carboxylase enzymes. Thiamin (B1) concentrations were elevated (20-700nM), consistent with previous pore water measurements showing sediments could be a source of B1 to the ocean. Cobalamin (B12), a cofactor required for methyl transfers in methanogens, was also detected in pore waters (~4-40pM). The flavins (riboflavin [B2] and flavin mononucleotide[FMN]), molecules utilized in external electron transfer, showed a distinct increase with depth (10-90nM). Interestingly, the flavin profiles showed an inverse trend to dissolved Fe (Fe decreases with depth) providing a potential link to culture experiments which have shown extracellular flavin release to be a common trait in some metal reducers. As some of the first B-vitamin measurements made in marine sediments, these results illustrate the complex interaction between the microbial community and surrounding geochemical environment and provide exciting avenues for future research.

  11. A skill assessment of the biogeochemical model REcoM2 coupled to the finite element sea-ice ocean model (FESOM 1.3)

    NASA Astrophysics Data System (ADS)

    Schourup-Kristensen, V.; Sidorenko, D.; Wolf-Gladrow, D. A.; Völker, C.

    2014-07-01

    In coupled ocean-biogeochemical models, the choice of numerical schemes in the ocean circulation component can have a large influence on the distribution of the biological tracers. Biogeochemical models are traditionally coupled to ocean general circulation models (OGCMs), which are based on dynamical cores employing quasi regular meshes, and therefore utilize limited spatial resolution in a global setting. An alternative approach is to use an unstructured-mesh ocean model, which allows variable mesh resolution. Here, we present initial results of a coupling between the Finite Element Sea-ice Ocean Model (FESOM) and the biogeochemical model REcoM2, with special focus on the Southern Ocean. Surface fields of nutrients, chlorophyll a and net primary production were compared to available data sets with focus on spatial distribution and seasonal cycle. The model produced realistic spatial distributions, especially regarding net primary production and chlorophyll a, whereas the iron concentration became too low in the Pacific Ocean. The modelled net primary production was 32.5 Pg C yr-1 and the export production 6.1 Pg C yr-1. This is lower than satellite-based estimates, mainly due to the excessive iron limitation in the Pacific along with too little coastal production. Overall, the model performed better in the Southern Ocean than on the global scale, though the assessment here is hindered by the lower availability of observations. The modelled net primary production was 3.1 Pg C yr-1 in the Southern Ocean and the export production 1.1 Pg C yr-1. All in all, the combination of a circulation model on an unstructured grid with an ocean biogeochemical model shows similar performance to other models at non-eddy-permitting resolution. It is well suited for studies of the Southern Ocean, but on the global scale deficiencies in the Pacific Ocean would have to be taken into account.

  12. Simulation of land-atmosphere gaseous exchange using a coupled land surface-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Gu, C.; Riley, W. J.; Perez, T. J.; Pan, L.

    2009-12-01

    It is important to develop and evaluate biogeochemical models that on the one hand represent vegetation and soil dynamics and on the other hand provide energy and water fluxes in a temporal resolution suitable for biogeochemical processes. In this study, we present a consistent coupling between a common land surface model (CLM3.0) and a recently developed biogeochemical model (TOUGHREACT-N). The model TOUGHREACT-N (TR-N) is one of the few process-based models that simulate green house gases fluxes by using an implicit scheme to solve the diffusion equations governing soil heat and water fluxes. By coupling with CLM3.0, we have significantly improved TR-N by including realistic representations of surface water, energy, and momentum exchanges, through the use of improved formulations for soil evaporation, plant transpiration, vegetation growth, and plant nitrogen uptake embedded in CLM3.0. The coupled CLMTR-N model is a first step for a full coupling of land surface and biogeochemical processes. The model is evaluated with measurements of soil temperature, soil water content, and N2O and N2 gaseous emission data from fallow, corn, and forest sites in Venezuela. The results demonstrate that the CLMTR-N model simulates realistic diurnal variation of soil temperature, soil water content, and N gaseous fluxes. For example, mean differences between predicted and observed midday near-surface soil water content were 8, 11, and 4 % in July, August, and September. The sensitivity of the biogeochemical processes and resulting N emissions to variation in environmental drivers is high, which indicates the need to calculate biogeochemical processes in, at least, two hourly time steps using dynamically updated (rather than daily averaged) soil environmental conditions. The development in CLMTR-N of such a complex representation of processes will allow us to characterize relevant processes and simplifications appropriate for regional to global-scale coupled biogeochemical and

  13. Study of the Tagus estuarine plume using coupled hydro and biogeochemical models

    NASA Astrophysics Data System (ADS)

    Vaz, Nuno; Leitão, Paulo C.; Juliano, Manuela; Mateus, Marcos; Dias, João. Miguel; Neves, Ramiro

    2010-05-01

    Plumes of buoyant water produced by inflow from rivers and estuaries are common on the continental shelf. Buoyancy associated with estuarine waters is a key mediating factor in the transport and transformation of dissolved and particulate materials in coastal margins. The offshore displacement of the plume is influenced greatly by the local alongshore wind, which will tend to advect the plume either offshore or onshore, consistently with the Ekman transport. Other factor affecting the propagation of an estuarine plume is the freshwater inflow on the landward boundary. In this paper, a coupled three-dimensional ocean circulation and biogeochemical model with realistic high and low frequency forcing is used to get insight on how the Tagus River plume responds to wind and freshwater discharge during winter and spring. A nesting approach based on the MOHID numerical system was implemented for the Tagus estuary near shelf. Realistic hindcast simulations were performed, covering a period from January to June 2007. Model results were evaluated using in-situ and satellite imagery data. The numerical model was implemented using a three level nesting model. The model domain includes the whole Portuguese coast, the Tagus estuary near shelf and the Tagus River estuary, using a realistic coastline and bottom topography. River discharge and wind forcing are considered as landward and surface boundary conditions, respectively. Initial ocean stratification is from the MERCATOR solution. Ambient shelf conditions include tidal motion. As a prior validation, models outputs of salinity and water temperature were compared to available data (January 30th and May 30th, 2007) and were found minor differences between model outputs and data. On January 30th, outside the estuary, the model results reveal a stratified water column, presenting salinity stratification of the order of 3-4. The model also reproduces the hydrography for the May 30th observations. In May, near the Tagus mouth

  14. Quantifying Hydro-biogeochemical Model Sensitivity in Assessment of Climate Change Effect on Hyporheic Zone Processes

    NASA Astrophysics Data System (ADS)

    Song, X.; Chen, X.; Dai, H.; Hammond, G. E.; Song, H. S.; Stegen, J.

    2016-12-01

    The hyporheic zone is an active region for biogeochemical processes such as carbon and nitrogen cycling, where the groundwater and surface water mix and interact with each other with distinct biogeochemical and thermal properties. The biogeochemical dynamics within the hyporheic zone are driven by both river water and groundwater hydraulic dynamics, which are directly affected by climate change scenarios. Besides that, the hydraulic and thermal properties of local sediments and microbial and chemical processes also play important roles in biogeochemical dynamics. Thus for a comprehensive understanding of the biogeochemical processes in the hyporheic zone, a coupled thermo-hydro-biogeochemical model is needed. As multiple uncertainty sources are involved in the integrated model, it is important to identify its key modules/parameters through sensitivity analysis. In this study, we develop a 2D cross-section model in the hyporheic zone at the DOE Hanford site adjacent to Columbia River and use this model to quantify module and parametric sensitivity on assessment of climate change. To achieve this purpose, We 1) develop a facies-based groundwater flow and heat transfer model that incorporates facies geometry and heterogeneity characterized from a field data set, 2) derive multiple reaction networks/pathways from batch experiments with in-situ samples and integrate temperate dependent reactive transport modules to the flow model, 3) assign multiple climate change scenarios to the coupled model by analyzing historical river stage data, 4) apply a variance-based global sensitivity analysis to quantify scenario/module/parameter uncertainty in hierarchy level. The objectives of the research include: 1) identifing the key control factors of the coupled thermo-hydro-biogeochemical model in the assessment of climate change, and 2) quantify the carbon consumption in different climate change scenarios in the hyporheic zone.

  15. The Water, Energy, and Biogeochemical Model (WEBMOD): A TOPMODEL application developed within the Modular Modeling System

    NASA Astrophysics Data System (ADS)

    Webb, R. M.; Wolock, D. M.; Linard, J. I.; Wieczorek, M. E.

    2004-12-01

    Process-based flow and transport simulation models can help increase understanding of how hydrologic flow paths affect biogeochemical mixing and reactions in watersheds. This presentation describes the Water, Energy, and Biogeochemical Model (WEBMOD), a new model designed to simulate water and chemical transport in both pristine and agricultural watersheds. WEBMOD simulates streamflow using TOPMODEL algorithms and also simulates irrigation, canopy interception, snowpack, and tile-drain flow; these are important processes for successful multi-year simulations of agricultural watersheds. In addition, the hydrologic components of the model are linked to the U.S. Geological Survey's (USGS) geochemical model PHREEQC such that solute chemistry for the hillslopes and streams also are computed. Model development, execution, and calibration take place within the USGS Modular Modeling System. WEBMOD is being validated at ten research watersheds. Five of these watersheds are nearly pristine and comprise the USGS Water, Energy, and Biogeochemical Budget (WEBB) Program field sites: Loch Vale, Colorado; Trout Lake, Wisconsin; Sleepers River, Vermont; Panola Mountain, Georgia; and the Luquillo Experimental Forest, Puerto Rico. The remaining five watersheds contain intensely cultivated fields being studied by USGS National Water Quality Assessment Program: Merced River, California; Granger Drain, Washington; Maple Creek, Nebraska; Sugar Creek, Indiana; and Morgan Creek, Delaware. Model calibration improved understanding of observed variations in soil moisture, solute concentrations, and stream discharge at the five WEBB watersheds and is now being set up to simulate the processes at the five agricultural watersheds that are now ending their first year of data collection.

  16. Modelling of transport and biogeochemical processes in pollution plumes: literature review and model development

    NASA Astrophysics Data System (ADS)

    Brun, Adam; Engesgaard, Peter

    2002-01-01

    A literature survey shows how biogeochemical (coupled organic and inorganic reaction processes) transport models are based on considering the complete biodegradation process as either a single- or as a two-step process. It is demonstrated that some two-step process models rely on the Partial Equilibrium Approach (PEA). The PEA assumes the organic degradation step, and not the electron acceptor consumption step, is rate limiting. This distinction is not possible in one-step process models, where consumption of both the electron donor and acceptor are treated kinetically. A three-dimensional, two-step PEA model is developed. The model allows for Monod kinetics and biomass growth, features usually included only in one-step process models. The biogeochemical part of the model is tested for a batch system with degradation of organic matter under the consumption of a sequence of electron acceptors. A second paper [J. Hydrol. 256 (2002) 230-249], reports the application of the model to a field study of biogeochemical transport processes in a landfill plume in Denmark (Vejen).

  17. Improving National Capability in Biogeochemical Flux Modelling: the UK Environmental Virtual Observatory (EVOp)

    NASA Astrophysics Data System (ADS)

    Johnes, P.; Greene, S.; Freer, J. E.; Bloomfield, J.; Macleod, K.; Reaney, S. M.; Odoni, N. A.

    2012-12-01

    The best outcomes from watershed management arise where policy and mitigation efforts are underpinned by strong science evidence, but there are major resourcing problems associated with the scale of monitoring needed to effectively characterise the sources rates and impacts of nutrient enrichment nationally. The challenge is to increase national capability in predictive modelling of nutrient flux to waters, securing an effective mechanism for transferring knowledge and management tools from data-rich to data-poor regions. The inadequacy of existing tools and approaches to address these challenges provided the motivation for the Environmental Virtual Observatory programme (EVOp), an innovation from the UK Natural Environment Research Council (NERC). EVOp is exploring the use of a cloud-based infrastructure in catchment science, developing an exemplar to explore N and P fluxes to inland and coastal waters in the UK from grid to catchment and national scale. EVOp is bringing together for the first time national data sets, models and uncertainty analysis into cloud computing environments to explore and benchmark current predictive capability for national scale biogeochemical modelling. The objective is to develop national biogeochemical modelling capability, capitalising on extensive national investment in the development of science understanding and modelling tools to support integrated catchment management, and supporting knowledge transfer from data rich to data poor regions, The AERC export coefficient model (Johnes et al., 2007) has been adapted to function within the EVOp cloud environment, and on a geoclimatic basis, using a range of high resolution, geo-referenced digital datasets as an initial demonstration of the enhanced national capacity for N and P flux modelling using cloud computing infrastructure. Geoclimatic regions are landscape units displaying homogenous or quasi-homogenous functional behaviour in terms of process controls on N and P cycling

  18. Spatial and temporal variability of nutrient impacts to a coastal biogeochemical systems driven by river water from cultivated land areas

    NASA Astrophysics Data System (ADS)

    Minagawa, M.; Usui, T.; Miura, Y.; Nagao, S.; Irino, T.; Kudo, I.; Suzuki, K.

    2006-12-01

    Tokachi plain, located in eastern Hokkaido, Japan, has been reclaimed in the last 200 years mainly for farming. Despite the relatively lower population density, 33 p/km2 , drastic increase of nitrate concentration both in the underground water and river water has been observed and it has been paid attention from conservation of health and environmental. On the other side, the nitrogen outflow into the river estuary plays an important role in the coastal production and usage for offshore ecosystem too. To elucidate the biogeochemical role of such nutrient from land nutrients for the marine biological activity, we carried out intensive field work for three years from April 2003 to Dec 2005. We observed temporal change of nutrients (NO3, NO2, NH4, PO4, SiO4), Chl.a, POC, and PON in Tokachi River water and offshore seawater. Stable isotope analyses has been done for POC, PN, sediment trap particles and surface sediments. Field observations in the coast were performed from 4.6 to 37 km offshore of the estuary around Tokachi River seasonally in 2003 and March 2005. River water samples were also collected in lower reaches of the Tokachi R. C and N isotope analysis of surface sediments clearly showed the direct contribution of organic matter originated from land plants into offshore sediments. On the other hand, CN isotopes, C/N, and POC/Chl.a in POM indicated that POM in seawater was mostly of marine origin except in surface water near the river mouth. POC concentration in surface water was highest in May, which is due to rising of river discharge and bloom condition in spring. Annual fluxes of DIN increased at the periods of spring snowmelt and heavy rainfall in autumn. Based on the observed nutrient flux and applying Redfield ratio, we estimated that riverine nutrients can potentially correspond to 37% of annual primary production of 143 gC/m2/yr reported in the Oyashio Water (Kasai, 2000), respectively.

  19. [The biogeochemical cycle of methane in the coastal zone and littoral of the Kandalaksha Bay of the White Sea].

    PubMed

    Savvichev, A S; Rusanov, I I; Iusupov, S K; Pimenov, N V; Lein, A Iu; Ivanov, M V

    2004-01-01

    Microbiological and biogeochemical investigations of the processes of methane production (MP) and methane oxidation (MO) in the coastal waters and littoral of the Kandalaksha Bay of the White Sea were carried out. The studies were conducted in the coastal zones and in the water areas of the Kandalaksha Preserve, Moscow University White Sea Biological Station, and Zoological Institute (RAS) Biological Station in August, 1999, 2000, and 2001 and in March, 2001. The rate of CO2 assimilation in the shallow and littoral sediments was 35-27800 microg C/(dm3 day) in summer and 32.8-88.9 microg C/(dm3 day) in winter. The maximal rates of MP were observed in the littoral sediments in the zone of macrophyte decomposition, in local depressions, and in the estuary of a freshwater creak (up to 113 microl/(dm3 day)). The maximal level of MO was observed in the shallow estuarine sediments (up to 2450 microl/(dm3 day)). During the winter season, at the temperature of -0.5 to 0.5 degrees C, the MP rate in the littoral sediments was 0.02-0.3 microl/(dm3 day), while MO rate was 0.06-0.7 microl/(dm3 day). The isotopic data obtained indicate that the C(org) of the mats and of the upper sediment layers is enriched with the heavy 13C isotope by 1-4 per thousand as compared to the C(org) of the suspension, comprised on 33.5-34.3% of phytoplankton. A striking difference was found between the levels of methane emission by the typical littoral microlanscapes. In fine sediments, the average emission was 675 microl CH4/(m2 day), in the stormy discharge stretch sediments it was 1670 microl CH4/(m2 day), and under the stones and in silted pits, 1370 microl CH4/(m2 day). The calculation performed with consideration of the microlandscape areas with a high production allowed the CH4 production of 1 km2 of the littoral to be estimated as 192-300 1 CH4/(km2 day).

  20. Water-table height and microtopography control biogeochemical cycling in an Arctic coastal tundra ecosystem

    NASA Astrophysics Data System (ADS)

    Lipson, D. A.; Zona, D.; Raab, T. K.; Bozzolo, F.; Mauritz, M.; Oechel, W. C.

    2012-01-01

    Drained thaw lake basins (DTLB's) are the dominant land form of the Arctic Coastal Plain in northern Alaska. The presence of continuous permafrost prevents drainage and so water tables generally remain close to the soil surface, creating saturated, suboxic soil conditions. However, ice wedge polygons produce microtopographic variation in these landscapes, with raised areas such as polygon rims creating more oxic microenvironments. The peat soils in this ecosystem store large amounts of organic carbon which is vulnerable to loss as arctic regions continue to rapidly warm, and so there is great motivation to understand the controls over microbial activity in these complex landscapes. Here we report the effects of experimental flooding, along with seasonal and spatial variation in soil chemistry and microbial activity in a DTLB. The flooding treatment generally mirrored the effects of natural landscape variation in water-table height due to microtopography. The flooded portion of the basin had lower dissolved oxygen, lower oxidation-reduction potential (ORP) and higher pH, as did lower elevation areas throughout the entire basin. Similarly, soil pore water concentrations of organic carbon and aromatic compounds were higher in flooded and low elevation areas. Dissolved ferric iron (Fe(III)) concentrations were higher in low elevation areas and responded to the flooding treatment in low areas, only. The high concentrations of soluble Fe(III) in soil pore water were explained by the presence of siderophores, which were much more concentrated in low elevation areas. All the aforementioned variables were correlated, showing that Fe(III) is solubilized in response to anoxic conditions. Dissolved carbon dioxide (CO2) and methane (CH4) concentrations were higher in low elevation areas, but showed only subtle and/or seasonally dependent effects of flooding. In anaerobic laboratory incubations, more CH4 was produced by soils from low and flooded areas, whereas anaerobic CO2

  1. Relocatable Coastal Modeling System

    DTIC Science & Technology

    2016-06-07

    Pacific Ocean, in “Data Assimilation in Meteorology and Oceanography: Theory and Practice”, edited by Michael Ghil, M. Kimito, and others, published by...the Japan Meteorology Society. Harding, J., D.N. Fox, M.R. Carnes, R.C. Rhodes, 1998: “NRL Ocean Modeling and Assimilation Demonstration System

  2. Simple parameter estimation for complex models — Testing evolutionary techniques on 3-dimensional biogeochemical ocean models

    NASA Astrophysics Data System (ADS)

    Mattern, Jann Paul; Edwards, Christopher A.

    2017-01-01

    Parameter estimation is an important part of numerical modeling and often required when a coupled physical-biogeochemical ocean model is first deployed. However, 3-dimensional ocean model simulations are computationally expensive and models typically contain upwards of 10 parameters suitable for estimation. Hence, manual parameter tuning can be lengthy and cumbersome. Here, we present four easy to implement and flexible parameter estimation techniques and apply them to two 3-dimensional biogeochemical models of different complexities. Based on a Monte Carlo experiment, we first develop a cost function measuring the model-observation misfit based on multiple data types. The parameter estimation techniques are then applied and yield a substantial cost reduction over ∼ 100 simulations. Based on the outcome of multiple replicate experiments, they perform on average better than random, uninformed parameter search but performance declines when more than 40 parameters are estimated together. Our results emphasize the complex cost function structure for biogeochemical parameters and highlight dependencies between different parameters as well as different cost function formulations.

  3. Calibrating a global three-dimensional biogeochemical ocean model (MOPS-1.0)

    NASA Astrophysics Data System (ADS)

    Kriest, Iris; Sauerland, Volkmar; Khatiwala, Samar; Srivastav, Anand; Oschlies, Andreas

    2017-01-01

    Global biogeochemical ocean models contain a variety of different biogeochemical components and often much simplified representations of complex dynamical interactions, which are described by many ( ≈ 10 to ≈ 100) parameters. The values of many of these parameters are empirically difficult to constrain, due to the fact that in the models they represent processes for a range of different groups of organisms at the same time, while even for single species parameter values are often difficult to determine in situ. Therefore, these models are subject to a high level of parametric uncertainty. This may be of consequence for their skill with respect to accurately describing the relevant features of the present ocean, as well as their sensitivity to possible environmental changes. We here present a framework for the calibration of global biogeochemical ocean models on short and long timescales. The framework combines an offline approach for transport of biogeochemical tracers with an estimation of distribution algorithm (Covariance Matrix Adaption Evolution Strategy, CMA-ES). We explore the performance and capability of this framework by five different optimizations of six biogeochemical parameters of a global biogeochemical model, simulated over 3000 years. First, a twin experiment explores the feasibility of this approach. Four optimizations against a climatology of observations of annual mean dissolved nutrients and oxygen determine the extent to which different setups of the optimization influence model fit and parameter estimates. Because the misfit function applied focuses on the large-scale distribution of inorganic biogeochemical tracers, parameters that act on large spatial and temporal scales are determined earliest, and with the least spread. Parameters more closely tied to surface biology, which act on shorter timescales, are more difficult to determine. In particular, the search for optimum zooplankton parameters can benefit from a sound knowledge of

  4. Analyzing the ecosystem carbon and hydrologic characteristics of forested wetland using a biogeochemical process model

    Treesearch

    Jianbo Cui; Changsheng Li; Carl Trettin

    2005-01-01

    A comprehensive biogeochemical model, Wetland-DNDC, was applied to analyze the carbon and hydrologic characteristics of forested wetland ecosystem at Minnesota (MN) and Florida (FL) sites. The model simulates the flows of carbon, energy, and water in forested wetlands. Modeled carbon dynamics depends on physiological plant factors, the size of plant pools,...

  5. Dynamic modeling of nitrogen losses in river networks unravels the coupled effects of hydrological and biogeochemical processes

    USGS Publications Warehouse

    Alexander, R.B.; Böhlke, J.K.; Boyer, E.W.; David, M.B.; Harvey, J.W.; Mulholland, P.J.; Seitzinger, S.P.; Tobias, C.R.; Tonitto, C.; Wollheim, W.M.

    2009-01-01

    The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal in the river networks of two watersheds having widely differing levels of nitrate enrichment but nearly identical discharges. Stream denitrification is estimated by regression as a nonlinear function of nitrate concentration, streamflow, and temperature, using more than 300 published measurements from a variety of US streams. These relations are used in the stream transport model to characterize nitrate dynamics related to denitrification at a monthly time scale in the stream reaches of the two watersheds. Results indicate that the nitrate removal efficiency of streams, as measured by the percentage of the stream nitrate flux removed via denitrification per unit length of channel, is appreciably reduced during months with high discharge and nitrate flux and increases during months of low-discharge and flux. Biogeochemical factors, including land use, nitrate inputs, and stream concentrations, are a major control on reach-scale denitrification, evidenced by the disproportionately lower nitrate removal efficiency in streams of the highly nitrate-enriched watershed as compared with that in similarly sized streams in the less nitrate-enriched watershed. Sensitivity analyses reveal that these important biogeochemical factors and physical hydrological factors contribute nearly

  6. Marine biogeochemical responses to the North Atlantic Oscillation in a coupled climate model

    NASA Astrophysics Data System (ADS)

    Patara, Lavinia; Visbeck, Martin; Masina, Simona; Krahmann, Gerd; Vichi, Marcello

    2011-07-01

    In this study a coupled ocean-atmosphere model containing interactive marine biogeochemistry is used to analyze interannual, lagged, and decadal marine biogeochemical responses to the North Atlantic Oscillation (NAO), the dominant mode of North Atlantic atmospheric variability. The coupled model adequately reproduces present-day climatologies and NAO atmospheric variability. It is shown that marine biogeochemical responses to the NAO are governed by different mechanisms according to the time scale considered. On interannual time scales, local changes in vertical mixing, caused by modifications in air-sea heat, freshwater, and momentum fluxes, are most relevant in influencing phytoplankton growth through light and nutrient limitation mechanisms. At subpolar latitudes, deeper mixing occurring during positive NAO winters causes a slight decrease in late winter chlorophyll concentration due to light limitation and a 10%-20% increase in spring chlorophyll concentration due to higher nutrient availability. The lagged response of physical and biogeochemical properties to a high NAO winter shows some memory in the following 2 years. In particular, subsurface nutrient anomalies generated by local changes in mixing near the American coast are advected along the North Atlantic Current, where they are suggested to affect downstream chlorophyll concentration with 1 year lag. On decadal time scales, local and remote mechanisms act contemporaneously in shaping the decadal biogeochemical response to the NAO. The slow circulation adjustment, in response to NAO wind stress curl anomalies, causes a basin redistribution of heat, freshwater, and biogeochemical properties which, in turn, modifies the spatial structure of the subpolar chlorophyll bloom.

  7. Modeling biogeochemical cycles in Chesapeake Bay with a coupled physical biological model

    NASA Astrophysics Data System (ADS)

    Xu, Jiangtao; Hood, Raleigh R.

    2006-08-01

    In this paper we describe the development and validation of a relatively simple biogeochemical model of Chesapeake Bay. This model consists of a 3-dimensional, prognostic hydrodynamic model that is coupled to an NPZD-type open ocean ecosystem model, which has been modified by adding additional compartments and parameterizations of biogeochemical processes that are important in estuarine systems. These modifications include an empirical optical model for predicting the diffuse attenuation coefficient Kd, compartments for representing oxygen and suspended sediment concentrations, and parameterizations of phosphorus limitation, denitrification, and seasonal changes in ecosystem structure and temperature effects. To show the overall performance of the coupled physical-biological model, the modeled dissolved inorganic nitrogen, phytoplankton, dissolved oxygen, total suspended solids and light attenuation coefficient in 1995 (a dry year) and 1996 (a very wet year) are examined and compared with observations obtained from the Chesapeake Bay Program. We demonstrate that this relatively simple model is capable of producing the general distribution of each field (both the mean and variability) in the main stem of the Bay. And the model is robust enough to generate reasonable results under both wet and dry conditions. Some significant discrepancies are also observed, such as overestimation of phytoplankton concentrations in shoal regions and overestimation of oxygen concentrations in deep channels, which reveal some deficiencies in the model formulation. Some potential improvements and remedies are suggested. Sensitivity studies on selected parameters are also reported.

  8. A skill assessment of the biogeochemical model REcoM2 coupled to the Finite Element Sea Ice-Ocean Model (FESOM 1.3)

    NASA Astrophysics Data System (ADS)

    Schourup-Kristensen, V.; Sidorenko, D.; Wolf-Gladrow, D. A.; Völker, C.

    2014-11-01

    In coupled biogeochmical-ocean models, the choice of numerical schemes in the ocean circulation component can have a large influence on the distribution of the biological tracers. Biogeochemical models are traditionally coupled to ocean general circulation models (OGCMs), which are based on dynamical cores employing quasi-regular meshes, and therefore utilize limited spatial resolution in a global setting. An alternative approach is to use an unstructured-mesh ocean model, which allows variable mesh resolution. Here, we present initial results of a coupling between the Finite Element Sea Ice-Ocean Model (FESOM) and the biogeochemical model REcoM2 (Regulated Ecosystem Model 2), with special focus on the Southern Ocean. Surface fields of nutrients, chlorophyll a and net primary production (NPP) were compared to available data sets with a focus on spatial distribution and seasonal cycle. The model produces realistic spatial distributions, especially regarding NPP and chlorophyll a, whereas the iron concentration becomes too low in the Pacific Ocean. The modelled NPP is 32.5 Pg C yr-1 and the export production 6.1 Pg C yr-1, which is lower than satellite-based estimates, mainly due to excessive iron limitation in the Pacific along with too little coastal production. The model performs well in the Southern Ocean, though the assessment here is hindered by the lower availability of observations. The modelled NPP is 3.1 Pg C yr-1 in the Southern Ocean and the export production 1.1 Pg C yr-1. All in all, the combination of a circulation model on an unstructured grid with a biogeochemical-ocean model shows similar performance to other models at non-eddy-permitting resolution. It is well suited for studies of the Southern Ocean, but on the global scale deficiencies in the Pacific Ocean would have to be taken into account.

  9. Assimilation of Sea Color Data Into A Three Dimensional Biogeochemical Model: Sensitivity Experiments

    NASA Astrophysics Data System (ADS)

    Echevin, V.; Levy, M.; Memery, L.

    The assimilation of two dimensional sea color data fields into a 3 dimensional coupled dynamical-biogeochemical model is performed using a 4DVAR algorithm. The biogeochemical model includes description of nitrates, ammonium, phytoplancton, zooplancton, detritus and dissolved organic matter. A subset of the biogeochemical model poorly known parameters (for example,phytoplancton growth, mortality,grazing) are optimized by minimizing a cost function measuring misfit between the observations and the model trajectory. Twin experiments are performed with an eddy resolving model of 5 km resolution in an academic configuration. Starting from oligotrophic conditions, an initially unstable baroclinic anticyclone splits into several eddies. Strong vertical velocities advect nitrates into the euphotic zone and generate a phytoplancton bloom. Biogeochemical parameters are perturbed to generate surface pseudo-observations of chlorophyll,which are assimilated in the model in order to retrieve the correct parameter perturbations. The impact of the type of measurement (quasi-instantaneous, daily mean, weekly mean) onto the retrieved set of parameters is analysed. Impacts of additional subsurface measurements and of errors in the circulation are also presented.

  10. Coastal ocean and shelf-sea biogeochemical cycling of trace elements and isotopes: lessons learned from GEOTRACES

    NASA Astrophysics Data System (ADS)

    Charette, Matthew A.; Lam, Phoebe J.; Lohan, Maeve C.; Kwon, Eun Young; Hatje, Vanessa; Jeandel, Catherine; Shiller, Alan M.; Cutter, Gregory A.; Thomas, Alex; Boyd, Philip W.; Homoky, William B.; Milne, Angela; Thomas, Helmuth; Andersson, Per S.; Porcelli, Don; Tanaka, Takahiro; Geibert, Walter; Dehairs, Frank; Garcia-Orellana, Jordi

    2016-11-01

    Continental shelves and shelf seas play a central role in the global carbon cycle. However, their importance with respect to trace element and isotope (TEI) inputs to ocean basins is less well understood. Here, we present major findings on shelf TEI biogeochemistry from the GEOTRACES programme as well as a proof of concept for a new method to estimate shelf TEI fluxes. The case studies focus on advances in our understanding of TEI cycling in the Arctic, transformations within a major river estuary (Amazon), shelf sediment micronutrient fluxes and basin-scale estimates of submarine groundwater discharge. The proposed shelf flux tracer is 228-radium (T1/2 = 5.75 yr), which is continuously supplied to the shelf from coastal aquifers, sediment porewater exchange and rivers. Model-derived shelf 228Ra fluxes are combined with TEI/ 228Ra ratios to quantify ocean TEI fluxes from the western North Atlantic margin. The results from this new approach agree well with previous estimates for shelf Co, Fe, Mn and Zn inputs and exceed published estimates of atmospheric deposition by factors of approximately 3-23. Lastly, recommendations are made for additional GEOTRACES process studies and coastal margin-focused section cruises that will help refine the model and provide better insight on the mechanisms driving shelf-derived TEI fluxes to the ocean. This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.

  11. Coastal ocean and shelf-sea biogeochemical cycling of trace elements and isotopes: lessons learned from GEOTRACES

    PubMed Central

    Lam, Phoebe J.; Lohan, Maeve C.; Kwon, Eun Young; Hatje, Vanessa; Shiller, Alan M.; Cutter, Gregory A.; Thomas, Alex; Milne, Angela; Thomas, Helmuth; Andersson, Per S.; Porcelli, Don; Tanaka, Takahiro; Geibert, Walter; Dehairs, Frank; Garcia-Orellana, Jordi

    2016-01-01

    Continental shelves and shelf seas play a central role in the global carbon cycle. However, their importance with respect to trace element and isotope (TEI) inputs to ocean basins is less well understood. Here, we present major findings on shelf TEI biogeochemistry from the GEOTRACES programme as well as a proof of concept for a new method to estimate shelf TEI fluxes. The case studies focus on advances in our understanding of TEI cycling in the Arctic, transformations within a major river estuary (Amazon), shelf sediment micronutrient fluxes and basin-scale estimates of submarine groundwater discharge. The proposed shelf flux tracer is 228-radium (T1/2 = 5.75 yr), which is continuously supplied to the shelf from coastal aquifers, sediment porewater exchange and rivers. Model-derived shelf 228Ra fluxes are combined with TEI/ 228Ra ratios to quantify ocean TEI fluxes from the western North Atlantic margin. The results from this new approach agree well with previous estimates for shelf Co, Fe, Mn and Zn inputs and exceed published estimates of atmospheric deposition by factors of approximately 3–23. Lastly, recommendations are made for additional GEOTRACES process studies and coastal margin-focused section cruises that will help refine the model and provide better insight on the mechanisms driving shelf-derived TEI fluxes to the ocean. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’.

  12. Hierarchical framework for coupling a biogeochemical trace gas model to a general circulation model

    SciTech Connect

    Miller, N.L.; Foster, I.T.

    1994-04-01

    A scheme is described for the computation of terrestrial biogeochemical trace gas fluxes in the context of a general circulation model. This hierarchical system flux scheme (HSFS) incorporates five major components: (1) a general circulation model (GCM), which provides a medium-resolution (i.e., 1{degrees} by 1{degrees}) simulation of the atmospheric circulation; (2) a procedure for identifying regions of defined homogeneity of surface type within GCM grid cells; (3) a set of surface process models, to be run within each homogeneous region, which include a biophysical model, the Biosphere Atmospheric Transfer Scheme (BATS), and a biogeochemical model (BGCM); (4) an interpolation/integration system that transfers information between the GCM and surface process models with finer resolution; and (5) an interactive data array based on a geographic information system (GIS), which provides land characteristic information via the interpolator. The goals of this detailed investigation are to compute the local and global sensitivities of trace gas fluxes to GCM and BATS variables, the effects of trace gas fluxes on global climate, and the effects of global climate on specific biomes.

  13. Use of combined biogeochemical model approaches and empirical data to assess critical loads of nitrogen

    Treesearch

    Mark Fenn; Charles Driscoll; Quingtao Zhou; Leela Rao; Thomas Meixner; Edith Allen; Fengming Yuan; Timothy Sullivan

    2015-01-01

    Empirical and dynamic biogeochemical modelling are complementary approaches for determining the critical load (CL) of atmospheric nitrogen (N) or other constituent deposition that an ecosystem can tolerate without causing ecological harm. The greatest benefits are obtained when these approaches are used in combination. Confounding environmental factors can complicate...

  14. Towards coupled physical-biogeochemical models of the ocean carbon cycle

    NASA Technical Reports Server (NTRS)

    Rintoul, Stephen R.

    1992-01-01

    The purpose of this review is to discuss the critical gaps in our knowledge of ocean dynamics and biogeochemical cycles. It is assumed that the ultimate goal is the design of a model of the earth system that can predict the response to changes in the external forces driving climate.

  15. Inconsistent strategies to spin up models in CMIP5: implications for ocean biogeochemical model performance assessment

    NASA Astrophysics Data System (ADS)

    Seferian, R.; Gehlen, M.; Bopp, L.; Resplandy, L.; Orr, J. C.; Marti, O.

    2016-12-01

    During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were made to systematically assess the skills of Earth system models against available modern observations. However, most of these skill-assessment approaches can be considered as "blind" given that they were applied without considering models' specific characteristics and treat models a priori as independent of observations. Indeed, since these models are typically initialized from observations, the spin-up procedure (e.g. the length of time for which the model has been run since initialization, and therefore the degree to which it has approached it's own equilibrium) has the potential to exert a significant control over the skill-assessment metrics calculated for each model. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESM) contributes to model-to-model differences in the simulated fields. We focus on the amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) as a function of spin-up duration in a dedicated 500-year-long spin-up simulation performed with IPSL-CM5A-LR as well as an ensemble of 24 CMIP5 ESMs. We demonstrate that a relationship between spin-up duration and skill-assessment metrics emerges from the results of a single model and holds when confronted with a larger ensemble of CMIP5 models. This shows that drift in biogeochemical fields has implications for performance assessment in addition to possibly influence estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to-model uncertainty. This requires more attention in future model intercomparison exercises in order to provide quantitatively more correct ESM results on marine biogeochemistry and carbon cycle feedbacks.

  16. Coupling Isotopic Fractionation to Multiple-Continuum Reactive Transport Models of Biogeochemical Systems

    NASA Astrophysics Data System (ADS)

    Sonnenthal, E. L.; Wanner, C.

    2014-12-01

    Stable isotopic systems often show an unexpected range in observed fractionation factors associated with biogeochemical systems. In particular, the ranges in such isotopic systems as Cr, Ca, Li, and C have often been attributed to kinetic effects as well as different biogeochemical mechanisms. Reactive transport models developed to capture the sub-micron-scale transport and reaction processes within the macroscale system (e.g., biofilm to cm-scale) have been successful in simulating the biogeochemical processes associated with bacterial growth and the resultant changes in pore-fluid chemistry and redox conditions. Once such multicontinuum reactive transport models are extended to include equilibrium and kinetic isotopic fractionation, diffusive transport, and fluid-gas equilibria, it becomes possible to quantitatively interpret the isotopic changes observed in experimental and natural or engineered biogeochemical systems. We combine a solid-solution approach for isotopic substitution in minerals with the multiple-continuum reactive-transport approach to interpret the effective fractionation factor observed in experimental systems. Although such systems often have poorly constrained inputs (such as the equilibrium fractionation factor and many of the parameters associated with bacterial growth), by combining several independent contraints on reaction rates (such as lactate consumption, 13C/12C and 87Sr/86Sr in calcite), the range of possible interpretations can often be greatly narrowed. Here we present examples of the modeling approaches and their application to experimental systems to examine why the observed fractionation factors are often different from the theoretical values.

  17. Impact of model resolution on biogeochemical tracers concentration in the tropical Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Duteil, Olaf; Boening, Claus; Oschlies, Andreas

    2014-05-01

    Representing correctly the distribution of biogeochemical tracers in the interior ocean, such as oxygen or phosphate, is hampered by large biases in the representation of circulation in the coarse resolution models. Here we assess the oxygen and phosphate budget in two configurations of a coupled circulation biogeochemical model (NEMO - NPZD), focusing on the Atlantic Ocean. These two configurations have been integrated using realistic atmospheric forcings for the period 1948-2007. While a coarse (0.5°) configuration displays the common bias of too low oxygen associated with too high phosphate concentration, particularly at intermediate depth in the eastern side of the basin, the values are closer to the observations in an eddying (0.1°) configuration. The improvement in the representation of oxygen and phosphate is traced to a stronger transport by a more realistic representation of the equatorial and off-equatorial undercurrents. The biogeochemical fluxes are less sensitive to the current strength as the phytoplankton growth is mainly limited by the available light in the two configurations. This study emphasizes the need of high resolution models to tackle coupled biogeochemical problematics, such as the extension of oxygen minimum zones or variability in the eastern boundary upwelling system productivity.

  18. Rejecting hydro-biogeochemical model structures by multi-criteria evaluation

    NASA Astrophysics Data System (ADS)

    Houska, Tobias; Kraft, Philipp; Liebermann, Ralf; Klatt, Steffen; Kraus, David; Haas, Edwin; Santabarbara, Ignacio; Kiese, Ralf; Butterbach-Bahl, Klaus; Müller, Christoph; Breuer, Lutz

    2017-04-01

    This work presents a novel way for assessing and comparing different hydro-biogeochemical model structures and their performances. We used the LandscapeDNDC modelling framework to set up four models of different complexity, considering two soil-biogeochemical and two hydrological modules. The performance of each model combination was assessed using long-term (8 years) data and applying different thresholds, considering multiple criteria and objective functions. Our results show that each model combination had its strength for particular criteria. However, only 0.01% of all model runs passed the complete rejectionist framework. In contrast, our comparatively applied assessments of single thresholds, as frequently used in other studies, lead to a much higher acceptance rate of 40 to 70%. Therefore, our study indicates that models can be right for the wrong reasons, i.e., matching GHG emissions while at the same time failing to simulate other criteria such as soil moisture or plant biomass dynamics.

  19. Patterns and Trends of Primary Production, Inorganic Carbon and Oxygen and Their Ecosystem Impacts in a Regional Biogeochemical Ocean Model for Atlantic Canada

    NASA Astrophysics Data System (ADS)

    Fennel, K.; Rutherford, K. E.; Kuhn, A. M.; Zhang, W.; Brennan, C. E.; Zhang, R.

    2016-12-01

    Representing coastal oceans in global biogeochemical models is a challenge, yet the ecosystems in these regions are most vulnerable to the combined stressors of ocean warming, deoxygenation, acidification, eutrophication and fishing. Coastal regions also have large air-sea fluxes of CO2, making them an important but poorly quantified component of the global carbon cycle, and are the most relevant for human activities. Regional model applications that are nested within large-scale or global models are necessary for detailed studies of coastal regions. We present results from such a regional biogeochemical model for the northwestern North Atlantic shelves and adjacent deep ocean of Atlantic Canada. The model is an implementation of the Regional Ocean Modeling System (ROMS) and includes an NPZD-type nitrogen cycle model with explicit representation of dissolved oxygen and inorganic carbon. The region is at the confluence of the Gulf Stream and Labrador Current making it highly dynamic, a challenge for analysis and prediction, and prone to large changes. Historically a rich fishing ground, coastal ecosystems in Atlantic Canada have undergone dramatic changes including the collapse of several economically important fish stocks and the listing of many species as threatened or endangered. Furthermore it is unclear whether the region is a net source or sink of atmospheric CO2 with estimates of the size and direction of the net air-sea CO2 flux remaining controversial. We will discuss simulated patterns of primary production, inorganic carbon fluxes and oxygen trends in the context of circulation features and shelf residence times for the present ocean state and present future projections.

  20. Biogeochemical Controls on Biodegradation of MC252 Oil:Sand Aggregates on a Rapidly Eroding Coastal Headland Beach

    NASA Astrophysics Data System (ADS)

    Pardue, J.; Elango, V.; Urbano, M.; Lemelle, K.

    2012-12-01

    The research described below was conducted on Fourchon Beach, a coastal headland consisting of nine miles of fairly pristine sandy beaches and dunes, backed by wetlands and tidal channels, located between Belle Pass tidal inlet on the west and Elmer's Island on the east in Lafourche Parish, Louisiana. MC252 oil first arrived in large quantities on Fourchon Beach on or around May 20, 2010. A unique oil form created under these conditions was an aggregate of sand and emulsified oil, typically 0.1-10 cm in diameter, termed small surface residue balls (SSRBs). The work from this project made critical measurements on the factors controlling biodegradability of these SSRB aggregates. SSRB aggregates were sampled across transects perpendicular to the beach from the intertidal to the supratidal. Areas in the supratidal that were sampled initially were set aside for research purposes and not altered by any clean-up activities. Chemical composition of SSRBs was measured including concentrations of n-alkanes, PAHs, hopanes, nutrients (nitrate, nitrite, ammonium and orthophosphate measured on water extracts of SSRBs), and electron acceptor concentrations (O2 microprofiles measured on intact SSRBs and sulfate). Physical characterization of the SSRBs including length and area dimensions, mass, density, porosity, moisture content, and salinity using standard methods. Microbial characterization of SSRBs was also conducted using denaturing gradient gel electrophoresis and sequencing of dominant bands. SSRBs were sampled from various locations across the beach profile deposited by 2 significant tropical events in 2010; Hurricane Alex and TS Bonnie, and one event in 2011, TS Lee. Sampling focused on comparing and contrasting impacts of biogeochemistry on weathering of oil stranded in three beach microenvironments; supratidal surface; subtidal subsurface which is permanently inundated and intertidal subsurface samples which are intermittently inundated. The three types of oil are

  1. Particle Tracking Model (PTM) with Coastal Modeling System (CMS)

    DTIC Science & Technology

    2015-11-04

    Coastal Inlets Research Program Particle Tracking Model (PTM) with Coastal Modeling System (CMS) The Particle Tracking Model (PTM) is a Lagrangian...resuspension in coastal, estuarine and river environments. Local sediment particle sources include dredging, placement sites, inflows, and vessel...propeller wash. The PTM calculates pathways and fate of neutrally buoyant or sediment particles under wave and hydrodynamic conditions. Calculations

  2. ANALYTICAL ELEMENT MODELING OF COASTAL AQUIFERS

    EPA Science Inventory

    Four topics were studied concerning the modeling of groundwater flow in coastal aquifers with analytic elements: (1) practical experience was obtained by constructing a groundwater model of the shallow aquifers below the Delmarva Peninsula USA using the commercial program MVAEM; ...

  3. ANALYTICAL ELEMENT MODELING OF COASTAL AQUIFERS

    EPA Science Inventory

    Four topics were studied concerning the modeling of groundwater flow in coastal aquifers with analytic elements: (1) practical experience was obtained by constructing a groundwater model of the shallow aquifers below the Delmarva Peninsula USA using the commercial program MVAEM; ...

  4. High resolution modelling of the biogeochemical processes in the eutrophic Loire River (France)

    NASA Astrophysics Data System (ADS)

    Minaudo, Camille; Moatar, Florentina; Curie, Florence; Gassama, Nathalie; Billen, Gilles

    2016-04-01

    A biogeochemical model was developed, coupling a physically based water temperature model (T-NET) with a semi-mechanistic biogeochemical model (RIVE, used in ProSe and Riverstrahler models) in order to assess at a fine temporal and spatial resolution the biogeochemical processes in the eutrophic Middle Loire hydrosystem (≈10 000 km², 3361 river segments). The code itself allows parallelized computing, which decreased greatly the calculation time (5 hours for simulating 3 years hourly). We conducted a daily survey during the period 2012-2014 at 2 sampling stations located in the Middle Loire of nutrients, chlorophyll pigments, phytoplankton and physic-chemical variables. This database was used as both input data (upstream Loire boundary) and validation data of the model (basin outlet). Diffuse and non-point sources were assessed based on a land cover analysis and WWTP datasets. The results appeared very sensible to the coefficients governing the dynamic of suspended solids and of phosphorus (sorption/desorption processes) within the model and some parameters needed to be estimated numerically. Both the Lagrangian point of view and fluxes budgets at the seasonal and event-based scale evidenced the biogeochemical functioning of the Loire River. Low discharge levels set up favorable physical conditions for phytoplankton growth (long water travel time, limited water depth, suspended particles sedimentation). Conversely, higher discharge levels highly limited the phytoplankton biomass (dilution of the colony, washing-out, limited travel time, remobilization of suspended sediments increasing turbidity), and most biogeochemical species were basically transferred downstream. When hydrological conditions remained favorable for phytoplankton development, P-availability was the critical factor. However, the model evidenced that most of the P in summer was recycled within the water body: on one hand it was assimilated by the algae biomass, and on the other hand it was

  5. Modelling physical and biogeochemical state of the Mediterranean Sea under contemporary and future climate

    NASA Astrophysics Data System (ADS)

    Solidoro, Cosimo; Lazzari, Paolo; Cossarini, Gianpiero; Melaku Canu, Donata; Lovato, Tomas; Vichi, Marcello

    2014-05-01

    A validated 3D coupled transport-biogeochemical model is used to assess the impact of future climatic and management scenarios on biogeochemical and ecological properties of the Mediterranean Sea. Results are discussed in term of temporal and spatial distribution of parameters and indicators related to the carbonate system and the cycles of carbon and inorganic nutrients through dissolved and particulate phases, as simulated by a multi nutrient multi plankton numerical model under current and future conditions. Simulations span the period 2000-2040 and are performed by forcing a three-dimensional off-line coupled eco-hydrodynamical model (BFM and OPA-tracer model, http://bfm-community.eu/) with marine circulation fields produced by ad hoc implementation of the NEMO modelling system and with river input of nutrient and freshwater computed in recent European fp7 projects. The model properly describes available experimental information on contemporary seasonal dynamic and spatial distribution at the basin and sub-basin scale of major biogeochemical parameters, as well as primary production and carbon fluxes at the air-ocean interface. Model projections suggest that future Mediterranean sea will be globally warmer, more productive, and more acidic, but with significant space variability. The relative importance of different biotic and abiotic parameters in defining such a change is explored through several numerical experiments. Potential implications in terms of ecological and higher trophic level organisms dynamics are explored as well, by integrating niche properties of selected organisms and suggestions provided by food web models.

  6. Stochastic estimation of biogeochemical parameters from Globcolour ocean colour satellite data in a North Atlantic 3D ocean coupled physical-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Doron, Maéva; Brasseur, Pierre; Brankart, Jean-Michel; Losa, Svetlana N.; Melet, Angélique

    2013-05-01

    Biogeochemical parameters remain a major source of uncertainty in coupled physical-biogeochemical models of the ocean. In a previous study (Doron et al., 2011), a stochastic estimation method was developed to estimate a subset of biogeochemical model parameters from surface phytoplankton observations. The concept was tested in the context of idealised twin experiments performed with a 1/4° resolution model of the North Atlantic ocean. The method was based on ensemble simulations describing the model response to parameter uncertainty. The statistical estimation process relies on nonlinear transformations of the estimated space to cope with the non-Gaussian behaviour of the resulting joint probability distribution of the model state variables and parameters. In the present study, the same method is applied to real ocean colour observations, as delivered by the sensors SeaWiFS, MERIS and MODIS embarked on the satellites OrbView-2, Envisat and Aqua respectively. The main outcome of the present experiments is a set of regionalised biogeochemical parameters. The benefit is quantitatively assessed with an objective norm of the misfits, which automatically adapts to the different ecological regions. The chlorophyll concentration simulated by the model with this set of optimally derived parameters is closer to the observations than the reference simulation using uniform values of the parameters. In addition, the interannual and seasonal robustness of the estimated parameters is tested by repeating the same analysis using ocean colour observations from several months and several years. The results show the overall consistency of the ensemble of estimated parameters, which are also compared to the results of an independent study.

  7. Assessing Error in Modelled Ocean Carbon Uptake Resulting From Uncertainty in Biogeochemical Parameters

    NASA Astrophysics Data System (ADS)

    Scott, V.; Kettle, H.; Merchant, C. J.; Hankin, R. K.

    2008-12-01

    Estimates of the air-sea CO2 flux produced by ocean biogeochemical models are uncertain due to poorly constrained model parameters. Here, we present the results of an analysis into the biochemical parameters that influence air-sea CO2 flux, and the error that results from uncertainties in these parameters in GCMs. A sensitivity analysis is performed on the Hadley centre Ocean Carbon Cycle (HadOCC) NPZD biogeochemical model used in the HadCM3 GCM. This uses a 1D test bed with forcing from different locations and identifies the parameters that control phytoplankton growth, formation of calcite and the sinking of organic matter to have greatest effect on the calculated air-sea CO2 flux. These parameters are tuned to data at sites with very different biochemical cycles and are then used to explore the resulting error in global ocean carbon fluxes within GCMs.

  8. Biogeochemical modelling of dissolved oxygen in a changing ocean.

    PubMed

    Andrews, Oliver; Buitenhuis, Erik; Le Quéré, Corinne; Suntharalingam, Parvadha

    2017-09-13

    Secular decreases in dissolved oxygen concentration have been observed within the tropical oxygen minimum zones (OMZs) and at mid- to high latitudes over the last approximately 50 years. Earth system model projections indicate that a reduction in the oxygen inventory of the global ocean, termed ocean deoxygenation, is a likely consequence of on-going anthropogenic warming. Current models are, however, unable to consistently reproduce the observed trends and variability of recent decades, particularly within the established tropical OMZs. Here, we conduct a series of targeted hindcast model simulations using a state-of-the-art global ocean biogeochemistry model in order to explore and review biases in model distributions of oceanic oxygen. We show that the largest magnitude of uncertainty is entrained into ocean oxygen response patterns due to model parametrization of pCO2-sensitive C : N ratios in carbon fixation and imposed atmospheric forcing data. Inclusion of a pCO2-sensitive C : N ratio drives historical oxygen depletion within the ocean interior due to increased organic carbon export and subsequent remineralization. Atmospheric forcing is shown to influence simulated interannual variability in ocean oxygen, particularly due to differences in imposed variability of wind stress and heat fluxes.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

  9. Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

    NASA Astrophysics Data System (ADS)

    Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

    2013-12-01

    Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

  10. Application of modified Patankar schemes to stiff biogeochemical models for the water column

    NASA Astrophysics Data System (ADS)

    Burchard, Hans; Deleersnijder, Eric; Meister, Andreas

    2005-12-01

    In this paper, we apply recently developed positivity preserving and conservative Modified Patankar-type solvers for ordinary differential equations to a simple stiff biogeochemical model for the water column. The performance of this scheme is compared to schemes which are not unconditionally positivity preserving (the first-order Euler and the second- and fourth-order Runge-Kutta schemes) and to schemes which are not conservative (the first- and second-order Patankar schemes). The biogeochemical model chosen as a test ground is a standard nutrient-phytoplankton-zooplankton-detritus (NPZD) model, which has been made stiff by substantially decreasing the half saturation concentration for nutrients. For evaluating the stiffness of the biogeochemical model, so-called numerical time scales are defined which are obtained empirically by applying high-resolution numerical schemes. For all ODE solvers under investigation, the temporal error is analysed for a simple exponential decay law. The performance of all schemes is compared to a high-resolution high-order reference solution. As a result, the second-order modified Patankar-Runge-Kutta scheme gives a good agreement with the reference solution even for time steps 10 times longer than the shortest numerical time scale of the problem. Other schemes do either compute negative values for non-negative state variables (fully explicit schemes), violate conservation (the Patankar schemes) or show low accuracy (all first-order schemes).

  11. Modeling biogeochemical processes of phosphorus for global food supply.

    PubMed

    Dumas, Marion; Frossard, Emmanuel; Scholz, Roland W

    2011-08-01

    Harvests of crops, their trade and consumption, soil erosion, fertilization and recycling of organic waste generate fluxes of phosphorus in and out of the soil that continuously change the worldwide spatial distribution of total phosphorus in arable soils. Furthermore, due to variability in the properties of the virgin soils and the different histories of agricultural practices, on a planetary scale, the distribution of total soil phosphorus is very heterogeneous. There are two key relationships that determine how this distribution and its change over time affect crop yields. One is the relationship between total soil phosphorus and bioavailable soil phosphorus and the second is the relationship between bioavailable soil phosphorus and yields. Both of these depend on environmental variables such as soil properties and climate. We propose a model in which these relationships are described probabilistically and integrated with the dynamic feedbacks of P cycling in the human ecosystem. The model we propose is a first step towards evaluating the large-scale effects of different nutrient management scenarios. One application of particular interest is to evaluate the vulnerability of different regions to an increased scarcity in P mineral fertilizers. Another is to evaluate different regions' deficiency in total soil phosphorus compared with the level at which they could sustain their maximum potential yield without external mineral inputs of phosphorus but solely by recycling organic matter to close the nutrient cycle.

  12. Global patterns of nitrogen limitation: confronting two global biogeochemical models with observations.

    PubMed

    Thomas, R Quinn; Zaehle, Sönke; Templer, Pamela H; Goodale, Christine L

    2013-10-01

    Projections of future changes in land carbon (C) storage using biogeochemical models depend on accurately modeling the interactions between the C and nitrogen (N) cycles. Here, we present a framework for analyzing N limitation in global biogeochemical models to explore how C-N interactions of current models compare to field observations, identify the processes causing model divergence, and identify future observation and experiment needs. We used a set of N-fertilization simulations from two global biogeochemical models (CLM-CN and O-CN) that use different approaches to modeling C-N interactions. On the global scale, net primary productivity (NPP) in the CLM-CN model was substantially more responsive to N fertilization than in the O-CN model. The most striking difference between the two models occurred for humid tropical forests, where the CLM-CN simulated a 62% increase in NPP at high N addition levels (30 g N m(-2) yr(-1)), while the O-CN predicted a 2% decrease in NPP due to N fertilization increasing plant respiration more than photosynthesis. Across 35 temperate and boreal forest sites with field N-fertilization experiments, we show that the CLM-CN simulated a 46% increase in aboveground NPP in response to N, which exceeded the observed increase of 25%. In contrast, the O-CN only simulated a 6% increase in aboveground NPP at the N-fertilization sites. Despite the small response of NPP to N fertilization, the O-CN model accurately simulated ecosystem retention of N and the fate of added N to vegetation when compared to empirical (15) N tracer application studies. In contrast, the CLM-CN predicted lower total ecosystem N retention and partitioned more losses to volatilization than estimated from observed N budgets of small catchments. These results point to the need for model improvements in both models in order to enhance the accuracy with which global C-N cycle feedbacks are simulated.

  13. Coastal erosion problem, modelling and protection

    NASA Astrophysics Data System (ADS)

    Yılmaz, Nihal; Balas, Lale; İnan, Asu

    2015-09-01

    Göksu Delta, located in the south of Silifke County of Mersin on the coastal plain formed by Göksu River, is one of the Specially Protected Areas in Turkey. Along the coastal area of the Delta, coastline changes at significant rates are observed, concentrating especially at four regions; headland of İncekum, coast of Paradeniz Lagoon, river mouth of Göksu and coast of Altınkum. The coast of Paradeniz Lagoon is suffering significantly from erosion and the consequent coastal retreating problem. Therefore, the narrow barrier beach which separates Paradeniz Lagoon from the Mediterranean Sea is getting narrower, creating a risk of uniting with the sea, thus causing the disappearance of the Lagoon. The aim of this study was to understand the coastal transport processes along the coastal area of Göksu Delta to determine the coastal sediment transport rates, and accordingly, to propose solutions to prevent the loss of coastal lands in the Delta. To this end, field measurements of currents and sediment grain sizes were carried out, and wind climate, wave climate, circulation patterns and longshore sediment transport rates were numerically modeled by HYDROTAM-3D, which is a three dimensional hydrodynamic transport model. Finally, considering its special importance as an environmentally protected region, some coastal structures of gabions were proposed as solutions against the coastal erosion problems of the Delta. The effects of proposed structures on future coastline changes were also modeled, and the coastlines predicted for the year 2017 are presented and discussed in the paper.

  14. The distribution of soil phosphorus for global biogeochemical modeling

    DOE PAGES

    Yang, Xiaojuan; Post, Wilfred M.; Thornton, Peter E.; ...

    2013-04-16

    We discuss that phosphorus (P) is a major element required for biological activity in terrestrial ecosystems. Although the total P content in most soils can be large, only a small fraction is available or in an organic form for biological utilization because it is bound either in incompletely weathered mineral particles, adsorbed on mineral surfaces, or, over the time of soil formation, made unavailable by secondary mineral formation (occluded). In order to adequately represent phosphorus availability in global biogeochemistry–climate models, a representation of the amount and form of P in soils globally is required. We develop an approach that buildsmore » on existing knowledge of soil P processes and databases of parent material and soil P measurements to provide spatially explicit estimates of different forms of naturally occurring soil P on the global scale. We assembled data on the various forms of phosphorus in soils globally, chronosequence information, and several global spatial databases to develop a map of total soil P and the distribution among mineral bound, labile, organic, occluded, and secondary P forms in soils globally. The amount of P, to 50cm soil depth, in soil labile, organic, occluded, and secondary pools is 3.6 ± 3, 8.6 ± 6, 12.2 ± 8, and 3.2 ± 2 Pg P (Petagrams of P, 1 Pg = 1 × 1015g) respectively. The amount in soil mineral particles to the same depth is estimated at 13.0 ± 8 Pg P for a global soil total of 40.6 ± 18 Pg P. The large uncertainty in our estimates reflects our limited understanding of the processes controlling soil P transformations during pedogenesis and a deficiency in the number of soil P measurements. In spite of the large uncertainty, the estimated global spatial variation and distribution of different soil P forms presented in this study will be useful for global biogeochemistry models that include P as a limiting element in biological production by providing initial estimates of the available soil P for plant

  15. The distribution of soil phosphorus for global biogeochemical modeling

    SciTech Connect

    Yang, Xiaojuan; Post, Wilfred M.; Thornton, Peter E.; Jain, Atul

    2013-04-16

    We discuss that phosphorus (P) is a major element required for biological activity in terrestrial ecosystems. Although the total P content in most soils can be large, only a small fraction is available or in an organic form for biological utilization because it is bound either in incompletely weathered mineral particles, adsorbed on mineral surfaces, or, over the time of soil formation, made unavailable by secondary mineral formation (occluded). In order to adequately represent phosphorus availability in global biogeochemistry–climate models, a representation of the amount and form of P in soils globally is required. We develop an approach that builds on existing knowledge of soil P processes and databases of parent material and soil P measurements to provide spatially explicit estimates of different forms of naturally occurring soil P on the global scale. We assembled data on the various forms of phosphorus in soils globally, chronosequence information, and several global spatial databases to develop a map of total soil P and the distribution among mineral bound, labile, organic, occluded, and secondary P forms in soils globally. The amount of P, to 50cm soil depth, in soil labile, organic, occluded, and secondary pools is 3.6 ± 3, 8.6 ± 6, 12.2 ± 8, and 3.2 ± 2 Pg P (Petagrams of P, 1 Pg = 1 × 1015g) respectively. The amount in soil mineral particles to the same depth is estimated at 13.0 ± 8 Pg P for a global soil total of 40.6 ± 18 Pg P. The large uncertainty in our estimates reflects our limited understanding of the processes controlling soil P transformations during pedogenesis and a deficiency in the number of soil P measurements. In spite of the large uncertainty, the estimated global spatial variation and distribution of different soil P forms presented in this study will be useful for global biogeochemistry models that include P as a limiting element in biological production by providing initial estimates of the available soil P for

  16. Modeling the Natural Biogeochemical Cycle of Mercury in the Global Ocean

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Jaegle, L.; Thompson, L.; Emerson, S. R.; Deutsch, C. A.; Trossman, D. S.; Shao, A.

    2012-12-01

    The ocean plays an important role in the biogeochemical cycling of mercury (Hg) because of its large reservoir mass and re-emission flux via evasion. The currently available Hg models, including 2D slab, 1D column and 0D box model cannot fully resolve the marine Hg cycle because of the lack of the proper spatial resolution. In this work, we have implemented Hg biogeochemistry in a state-of-the-art 3D offline ocean tracer model (OFFTRAC). OFFTRAC simulates the evolution of three Hg species (Hg0aq, HgIIaq and HgPaq), which are diffused and advected in the ocean. Hg0aq and HgII aq are interconverted in the surface ocean via parameterized photochemical and biological redox processes. The partitioning between HgIIaq and HgPaq depends on the local levels of particulate organic carbon (POC). The sinking of HgPaq is parameterized by coupling with the nutrient phosphorous cycle simulated in OFFTRAC. The reduction of HgIIaq to Hg0aq in the anaerobic subsurface water is proportional to the remineralizaiton of POC. OFFTRAC is coupled to a global simulation of the natural atmospheric Hg cycle in the GEOS-Chem chemical transport model. The GEOS-Chem simulation includes a geogenic source and provides the atmospheric deposition flux of HgII to the ocean and atmospheric Hg0 concentrations. The riverine input of Hg is calculated based on the climatological monthly mean fresh water discharge from continental to ocean and the average soil concentrations near the river mouth. The results show that the riverine input enhances Hg concentrations at surface by a factor of 2-3 near large river mouths and nearby coastal regions. The riverine input approximately doubles surface Hg concentration over the Arctic because of the small basin volume. In the deep ocean, which is not influenced by anthropogenic emissions, the model results (1.1±0.3 pM) generally agree with the observed present-day total Hg concentration profiles (1.4±0.9 pM). In the surface ocean, observations show average total Hg

  17. Data assimilation of physical and chlorophyll a observations in the California Current System using two biogeochemical models

    NASA Astrophysics Data System (ADS)

    Mattern, Jann Paul; Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2017-01-01

    Biogeochemical numerical models coupled to physical ocean circulation models are commonly combined with data assimilation in order to improve the models' state or parameter estimates. Yet much still needs to be learned about important aspects of biogeochemical data assimilation, such as the effect of model complexity and the importance of more realistic model formulations on assimilation results. In this study, 4D-Var-based state estimation is applied to two biogeochemical ocean models: a simple NPZD model with 4 biogeochemical variables (including 1 phytoplankton, 1 zooplankton) and the more complex NEMURO model, containing 11 biogeochemical variables (including 2 phytoplankton, 3 zooplankton). Both models are coupled to a 3-dimensional physical ocean circulation model of the U.S. west coast based on the Regional Ocean Modelling System (ROMS). Chlorophyll satellite observations and physical observations are assimilated into the model, yielding substantial improvements in state estimates for the observed physical and biogeochemical variables in both model formulations. In comparison to the simpler NPZD model, NEMURO shows a better overall fit to the observations. The assimilation also results in small improvements for simulated nitrate concentrations in both models and no apparent degradation of the output for other unobserved variables. The forecasting skill of the biogeochemical models is strongly linked to model performance without data assimilation: for both models, the improved fit obtained through assimilation degrades at similar relative rates, but drops to different absolute levels. Despite the better performance of NEMURO in our experiments, the choice of model and desired level of complexity should depend on the model application and the data available for assimilation.

  18. Modeling biogeochemical processes in subterranean estuaries: Effect of flow dynamics and redox conditions on submarine groundwater discharge of nutrients

    NASA Astrophysics Data System (ADS)

    Spiteri, Claudette; Slomp, Caroline P.; Tuncay, Kagan; Meile, Christof

    2008-02-01

    A two-dimensional density-dependent reactive transport model, which couples groundwater flow and biogeochemical reactions, is used to investigate the fate of nutrients (NO3-, NH4+, and PO4) in idealized subterranean estuaries representing four end-members of oxic/anoxic aquifer and seawater redox conditions. Results from the simplified model representations show that the prevalent flow characteristics and redox conditions in the freshwater-seawater mixing zone determine the extent of nutrient removal and the input of nitrogen and phosphorus to coastal waters. At low to moderate groundwater velocities, simultaneous nitrification and denitrification can lead to a reversal in the depth of freshwater NO3- and NH4+-PO4 plumes, compared to their original positions at the landward source. Model results suggest that autotrophic denitrification pathways with Fe2+ or FeS2 may provide an important, often overlooked link between nitrogen and phosphorus biogeochemistry through the precipitation of iron oxides and subsequent binding of phosphorus. Simulations also highlight that deviations of nutrient data from conservative mixing curves do not necessarily indicate nutrient removal.

  19. Nitrous oxide emissions from cropland: A procedure for calibrating the DayCent biogeochemical model using inverse modelling

    USDA-ARS?s Scientific Manuscript database

    DayCent is a biogeochemical model of intermediate complexity widely used to simulate greenhouse gases (GHG), soil organic carbon (SOC) and nutrients in crop, grassland, forest and savannah ecosystems. Although this model has been applied to a wide range of ecosystems, it is still typically parameter...

  20. Integrating remotely sensed land cover observations and a biogeochemical model for estimating forest ecosystem carbon dynamics

    USGS Publications Warehouse

    Liu, J.; Liu, S.; Loveland, T.R.; Tieszen, L.L.

    2008-01-01

    Land cover change is one of the key driving forces for ecosystem carbon (C) dynamics. We present an approach for using sequential remotely sensed land cover observations and a biogeochemical model to estimate contemporary and future ecosystem carbon trends. We applied the General Ensemble Biogeochemical Modelling System (GEMS) for the Laurentian Plains and Hills ecoregion in the northeastern United States for the period of 1975-2025. The land cover changes, especially forest stand-replacing events, were detected on 30 randomly located 10-km by 10-km sample blocks, and were assimilated by GEMS for biogeochemical simulations. In GEMS, each unique combination of major controlling variables (including land cover change history) forms a geo-referenced simulation unit. For a forest simulation unit, a Monte Carlo process is used to determine forest type, forest age, forest biomass, and soil C, based on the Forest Inventory and Analysis (FIA) data and the U.S. General Soil Map (STATSGO) data. Ensemble simulations are performed for each simulation unit to incorporate input data uncertainty. Results show that on average forests of the Laurentian Plains and Hills ecoregion have been sequestrating 4.2 Tg C (1 teragram = 1012 gram) per year, including 1.9 Tg C removed from the ecosystem as the consequences of land cover change. ?? 2008 Elsevier B.V.

  1. Biogeochemical Modeling of Ureolytically-Driven Calcium Carbonate Precipitation for Contaminant Immobilization

    NASA Astrophysics Data System (ADS)

    Smith, R. W.; Fujita, Y.; Taylor, J. L.

    2008-12-01

    Radionuclide and metal contaminants such as strontium-90 are present beneath U.S. Department of Energy (DOE) lands in both the groundwater (e.g., 100-N area at Hanford, WA) and vadose zone (e.g., Idaho Nuclear Technology and Engineering Center at the Idaho National Laboratory [INL]). Manipulation of in situ biogeochemical conditions to induce immobilization of these contaminants is a promising remediation approach that could yield significant risk and cost benefits to DOE. However, the effective design and interpretation of such field remediation activities requires the availability of numerical tools to model the biogeochemical processes underlying the remediation strategy. We are evaluating the use of microbial urea hydrolysis coupled to calcite precipitation as a means for the cost effective in situ stabilization of trace inorganic contaminants in groundwater and vadose zone systems. The approach relies upon the activity of indigenous ureolytic bacteria to hydrolyze introduced urea and causing an increase in pH and alkalinity, thereby accelerating calcium carbonate precipitation. The precipitation reaction results in the co- precipitation of trace metals and is sustained by the release of cations (both calcium and trace metals) from the aquifer matrix via exchange reactions involving the ammonium ions produced by urea hydrolysis. We have developed and parameterized a mixed kinetic-equilibrium reaction model using the Geochemist's Workbench computer code. Simulation results based on laboratory- and field-scale studies demonstrate the importance of transient events in systems with geochemical fluxes as well as of the coupling of biogeochemical processes.

  2. A global biogeochemical mass balance model for vanadium

    SciTech Connect

    Hope, B.K.

    1995-12-31

    Vanadium is a major trace metal in fossil fuels and combustion of these materials provides a significant source of vanadium in the environment. Close correlation exists between atmospheric vanadium concentration and fuel consumption, so that atmospheric vanadium pentoxide has been used as an indicator of human industrial activity. Little vanadium is retained in refined oil products, and vanadium contamination occurs as fallout from refining operations and burning of residual oils. This is the major cause for the approximate doubling of the environmental flux of vanadium as a result of human activity; other sources are products of coal combustion, leachates, and effluents from mining and milling of uranium and titanium. It was estimated in 1975 that the injection of vanadium into the atmosphere from anthropogenic sources equaled the input from natural sources. Such evidence that environmental levels of vanadium are increasing has raised concern over the injection of vanadium into the atmosphere from anthropogenic sources. A simple global mass balance model was developed to demonstrate the influence of anthropogenic vanadium on the global distribution of this trace metal. Vanadium in particulate emissions owing to man`s industrial activities were estimated to comprise {approx} 53% of total atmosphere vanadium loading and exceeded natural continental or volcanogenic dust by only a narrow margin. Oceanic deposition of vanadium adhering to anthropogenic particles was estimated to comprise {approx} 5% of total ocean vanadium loading. There is no suggestion that these inputs of anthropogenic vanadium pose a significant global environmental threat. It is entirely possible, however, that anthropogenic vanadium inputs could pose an environmental hazard given a more restricted area and a specific set of unfavorable circumstances.

  3. Coupled modeling of transport and biogeochemical processes in aquifers - Model requirements, strength and limitations

    NASA Astrophysics Data System (ADS)

    Mayer, K.

    2003-12-01

    Microbially mediated geochemical changes in aquifers may trigger a series of secondary reactions that include aqueous and surface complexation, ion exchange, and mineral dissolution-precipitation. Due to the coupled nature and the multitude of processes involved it is often difficult to identify the reactions controlling the system's overall evolution. Numerical models can be a useful component for identifying gaps and inconsistencies in conceptual models and for performing a more quantitative investigation of these systems. Suitable computer codes must allow for a general description of transport and reaction processes to facilitate the investigation of site-specific conditions. In recent years significant advances have been made in terms of model generality and applicability. Major advances include the consideration of mass balance equations for reactants and reaction products, the integration of biodegradation and thermodynamic models, and the development of novel approaches for simulating biogeochemical processes and reactive transport under variably saturated conditions. MIN3P is one of the codes capable of simulating coupled biogeochemical and hydrological processes on an increasingly mechanistic level. The simulation of column experiments and a hypothetical case study at the field scale illustrate how reactive transport modeling can be used. Modeling column experiments can be particularly fruitful, because detailed data can be collected to support the mechanistic approach. However, analysis of conceptual models is also beneficial on the field scale. The case study considered here describes natural attenuation of a petroleum hydrocarbon spill in an unconfined aquifer by multiple electron acceptors. The simulations also consider geochemical reactions triggered by contaminant degradation including the re-oxidation of reaction products during transport away from the source area. Comparing the results to contaminant plumes described in the literature suggests

  4. Inverse Modeling of Coastal Tides

    DTIC Science & Technology

    1999-09-30

    data in the tidal band. We have concluded that understanding this discrepancy and developing assimilation methods for baroclinic tides will require...Alexandre Kurapov to develop practical assimilation methods for coastal HF radar data. REFERENCES Bennett, A.F., B.S. Chua, and L.M. Leslie, Generalized

  5. Inverse Modeling of Coastal Tides

    DTIC Science & Technology

    1998-01-01

    produced. We are also working with Profs. J. Allen and R. Miller on developing practical assimilation methods for the coastal problem. REFERENCES...40, 81--108, 1997. Egbert, G.D. and A.F. Bennett, Data assimilation methods for ocean tides, in Modern approaches to data assimilation in ocean

  6. Development of Advanced Eco-hydrologic and Biogeochemical Coupling Model to Constrain Missing Role of Inland Waters on Boundless Biogeochemical Cycle

    NASA Astrophysics Data System (ADS)

    Nakayama, T.; Maksyutov, S. S.

    2016-12-01

    Inland waters including rivers, lakes, and groundwater are suggested to act as a transport pathway for water and dissolved substances, and play some role in continental biogeochemical cycling (Cole et al., 2007; Battin et al., 2009). The authors have developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (Nakayama, 2014, 2015, etc.), which includes feedback between hydrologic-geomorphic-ecological processes. In this study, NICE was further developed to couple with various biogeochemical cycle models in biosphere, those for water quality in aquatic ecosystems, and those for carbon weathering, etc. (NICE-BGC) (Nakayama, accepted). The new model incorporates connectivity of the biogeochemical cycle accompanied by hydrologic cycle between surface water and groundwater, hillslopes and river networks, and other intermediate regions. The model also includes reaction between inorganic and organic carbons, and its relation to nitrogen and phosphorus in terrestrial-aquatic continuum. The model results of CO2 evasion to the atmosphere, sediment storage, and carbon transport to the ocean (DOC, POC, and DIC flux) were reasonably in good agreement with previous compiled data. The model also showed carbon budget in major river basins and in each continent in global scale. In order to decrease uncertainty about carbon cycle, it became clear the previous empirical estimation by compiled data should be extended to this process-oriented model and higher resolution data to further clarify mechanistic interplay between inorganic and organic carbon and its relationship to nitrogen and phosphorus in terrestrial-aquatic linkages. NICE-BGC would play important role to re-evaluate greenhouse gas budget of the biosphere, and to bridge gap between top-down and bottom-up approaches (Battin et al., 2009; Regnier et al., 2013).

  7. Modeling seawater intrusion and the associated reactive solute transport in fractured coastal aquifers

    NASA Astrophysics Data System (ADS)

    Nick, Hamid M.; Regnier, Pierre; Thullner, Martin

    2013-04-01

    In coastal aquifers seawater and terrestrial water get into contact and the reactive mixing between these water bodies controls the water quality of submarine groundwater discharge. The rates of such mixing controlled reactions are depending not only on the properties of the reactive species but also on the density driven flow dynamics and the resulting transport patterns. A prediction of these flow and transport processes and thus of the fate of reactive species is specifically challenged in fracture aquifers as it depends on the focusing of the flow and the local balance of viscous and gravitational forces. To study the influence of fractures on mixing and reactive transport in coastal aquifers we present a reactive discrete fracture and matrix (DFM) model using unstructured spatially adaptively refined finite-element meshes. This model is developed by coupling the Complex System Modelling Platform (CSMP++) utilizing a hybrid FEFV scheme, and a Biogeochemical Reaction Network Simulator (BRNS) capable of solving for kinetically and thermodynamically constrained biogeochemical reactions [1]. The model is applied to simulate the reactive transport in fracture networks embedded in a permeable rock matrix. For virtual coastal aquifers, different fracture data sets are employed to study the effect of fractures and their characteristics on the reactive mixing between fresh water and seawater in coastal aquifers. Obtained results show that the presence of fractures enhances reactive mixing for most cases due to the combined effect of fracture induced flow channeling and dispersion. The magnitude of this effect depends highly on fracture density, spacing and orientation. Furthermore the results indicate that reactive mixing in fractured aquifers is not well described using an effective parameterization of a homogeneous aquifer setup. This suggests that structural information on the fracture network is needed for a sufficient description of reactive transport processes in

  8. Rosenbrock methods in biogeochemical modelling - A comparison to Runge-Kutta methods and modified Patankar schemes

    NASA Astrophysics Data System (ADS)

    Schippmann, Bianca; Burchard, Hans

    Modelling biogeochemical processes in the surface ocean is still a difficult task due to the challenge to identify the most convenient integration scheme for the reaction terms. The scheme is expected to deal with the model characteristics of positivity and conservativity as well as with the different time scales involved, which occur e.g., whenever photochemical reactions take place in the water column. This paper presents a numerical comparison of the Rosenbrock methods, ROS3 and ROS4, often used for solving chemical reactions, to the explicit fourth-order Runge-Kutta method and the unconditionally positive modified Patankar schemes. Following their successful application in air chemistry, we here test the hypothesis that the Rosenbrock methods are an optimal choice for marine biogeochemical modelling in terms of efficiency and accuracy. In this study the schemes are compared in terms of runtime and accuracy and are applied to two test cases of different complexity: a zero-dimensional nutrient-phytoplankton-detritus (NPD)-type model and a one-dimensional nutrient-phytoplankton-zooplankton-detritus (NPZD)-type model. Applying the Rosenbrock methods to the simple NPD model shows their advantage over the other applied methods. They give the most accurate results of all solvers, especially for large step sizes, in less computing time due to their semi-implicitness and adaptive step sizing. On the contrary, for the one-dimensional NPZD model problem this is only the case in comparison to the Runge-Kutta solver, while their performance is worse than that of the second-order modified Patankar scheme. They need longer runtimes than the latter ones in order to achieve similarly accurate results. However, the modified Patankar schemes are not conservative if the system reactions contain more than one source compound. Thus, for more complex marine biogeochemical problems, it is recommended to apply the Rosenbrock methods while for simpler models the use of the second

  9. Reduced-Order Biogeochemical Flux Model for High-Resolution Multi-Scale Biophysical Simulations

    NASA Astrophysics Data System (ADS)

    Smith, Katherine; Hamlington, Peter; Pinardi, Nadia; Zavatarelli, Marco

    2017-04-01

    Biogeochemical tracers and their interactions with upper ocean physical processes such as submesoscale circulations and small-scale turbulence are critical for understanding the role of the ocean in the global carbon cycle. These interactions can cause small-scale spatial and temporal heterogeneity in tracer distributions that can, in turn, greatly affect carbon exchange rates between the atmosphere and interior ocean. For this reason, it is important to take into account small-scale biophysical interactions when modeling the global carbon cycle. However, explicitly resolving these interactions in an earth system model (ESM) is currently infeasible due to the enormous associated computational cost. As a result, understanding and subsequently parameterizing how these small-scale heterogeneous distributions develop and how they relate to larger resolved scales is critical for obtaining improved predictions of carbon exchange rates in ESMs. In order to address this need, we have developed the reduced-order, 17 state variable Biogeochemical Flux Model (BFM-17) that follows the chemical functional group approach, which allows for non-Redfield stoichiometric ratios and the exchange of matter through units of carbon, nitrate, and phosphate. This model captures the behavior of open-ocean biogeochemical systems without substantially increasing computational cost, thus allowing the model to be combined with computationally-intensive, fully three-dimensional, non-hydrostatic large eddy simulations (LES). In this talk, we couple BFM-17 with the Princeton Ocean Model and show good agreement between predicted monthly-averaged results and Bermuda testbed area field data (including the Bermuda-Atlantic Time-series Study and Bermuda Testbed Mooring). Through these tests, we demonstrate the capability of BFM-17 to accurately model open-ocean biochemistry. Additionally, we discuss the use of BFM-17 within a multi-scale LES framework and outline how this will further our understanding

  10. Reduced-Order Biogeochemical Flux Model for High-Resolution Multi-Scale Biophysical Simulations

    NASA Astrophysics Data System (ADS)

    Smith, K.; Hamlington, P.; Pinardi, N.; Zavatarelli, M.; Milliff, R. F.

    2016-12-01

    Biogeochemical tracers and their interactions with upper ocean physical processes such as submesoscale circulations and small-scale turbulence are critical for understanding the role of the ocean in the global carbon cycle. These interactions can cause small-scale spatial and temporal heterogeneity in tracer distributions which can, in turn, greatly affect carbon exchange rates between the atmosphere and interior ocean. For this reason, it is important to take into account small-scale biophysical interactions when modeling the global carbon cycle. However, explicitly resolving these interactions in an earth system model (ESM) is currently infeasible due to the enormous associated computational cost. As a result, understanding and subsequently parametrizing how these small-scale heterogeneous distributions develop and how they relate to larger resolved scales is critical for obtaining improved predictions of carbon exchange rates in ESMs. In order to address this need, we have developed the reduced-order, 17 state variable Biogeochemical Flux Model (BFM-17). This model captures the behavior of open-ocean biogeochemical systems without substantially increasing computational cost, thus allowing the model to be combined with computationally-intensive, fully three-dimensional, non-hydrostatic large eddy simulations (LES). In this talk, we couple BFM-17 with the Princeton Ocean Model and show good agreement between predicted monthly-averaged results and Bermuda testbed area field data (including the Bermuda-Atlantic Time Series and Bermuda Testbed Mooring). Through these tests, we demonstrate the capability of BFM-17 to accurately model open-ocean biochemistry. Additionally, we discuss the use of BFM-17 within a multi-scale LES framework and outline how this will further our understanding of turbulent biophysical interactions in the upper ocean.

  11. Linking sediment structure, hydrological functioning and biogeochemical cycling in disturbed coastal saltmarshes and implications for vegetation development

    NASA Astrophysics Data System (ADS)

    Spencer, Kate; Harvey, Gemma; James, Tempest; Simon, Carr; Michelle, Morris

    2014-05-01

    Saltmarsh restoration undoubtedly provides environmental enhancement, with vegetation quickly re-establishing following the breach of sea walls and subsequent tidal inundation of previously defended areas. Yet evidence increasingly suggests that the restored saltmarshes do not have the same biological characteristics as their natural counterparts (Mossman et al. 2012) and this may be in part be due to physicochemical parameters at the site including anoxia and poor drainage. Hence, restored saltmarshes may not offer the range and quality of ecosystem services anticipated. These environments will have been 'disturbed' by previous land use and there is little understanding of the impacts of this disturbance on the wider hydrogeomorphic and biogeochemical functioning in restored saltmarshes and the implications for saltmarsh vegetation development. This study examines linkages between physical sediment characteristics, sediment structure (using X-ray microtomography), sub-surface hydrology (using pressure transducers and time series analysis), and sediment and porewater geochemistry (major and trace elements, major anions) in sediment cores collected from undisturbed saltmarshes and those restored by de-embankment. Sub-surface sediments in restored saltmarshes have lower organic matter content, lower moisture content and higher bulk density than undisturbed sites. Using X-ray tomography a clear horizon can be observed which separates relict agricultural soils at depth with less dense and structureless sediments deposited since de-embankment. Ratios of open to closed pore space suggest that while undisturbed saltmarshes have the highest porosity, restored saltmarshes have larger void spaces, but limited pore connectivity. Sub-surface hydrological response to tidal flooding was subdued in the restored compared to the undisturbed site, suggesting that porewater flow may be impeded. Time series analysis indicated that flow pathways differ in restored saltmarsh sediments

  12. Implementation ambiguity: The fifth element long lost in uncertainty budgets for land biogeochemical modeling

    NASA Astrophysics Data System (ADS)

    Tang, J.; Riley, W. J.

    2015-12-01

    Previous studies have identified four major sources of predictive uncertainty in modeling land biogeochemical (BGC) processes: (1) imperfect initial conditions (e.g., assumption of preindustrial equilibrium); (2) imperfect boundary conditions (e.g., climate forcing data); (3) parameterization (type I equifinality); and (4) model structure (type II equifinality). As if that were not enough to cause substantial sleep loss in modelers, we propose here a fifth element of uncertainty that results from implementation ambiguity that occurs when the model's mathematical description is translated into computational code. We demonstrate the implementation ambiguity using the example of nitrogen down regulation, a necessary process in modeling carbon-climate feedbacks. We show that, depending on common land BGC model interpretations of the governing equations for mineral nitrogen, there are three different implementations of nitrogen down regulation. We coded these three implementations in the ACME land model (ALM), and explored how they lead to different preindustrial and contemporary land biogeochemical states and fluxes. We also show how this implementation ambiguity can lead to different carbon-climate feedback estimates across the RCP scenarios. We conclude by suggesting how to avoid such implementation ambiguity in ESM BGC models.

  13. Benthic-Pelagic Coupling in Biogeochemical and Climate Models: Existing Approaches, Recent developments and Roadblocks

    NASA Astrophysics Data System (ADS)

    Arndt, Sandra

    2016-04-01

    Marine sediments are key components in the Earth System. They host the largest carbon reservoir on Earth, provide the only long term sink for atmospheric CO2, recycle nutrients and represent the most important climate archive. Biogeochemical processes in marine sediments are thus essential for our understanding of the global biogeochemical cycles and climate. They are first and foremost, donor controlled and, thus, driven by the rain of particulate material from the euphotic zone and influenced by the overlying bottom water. Geochemical species may undergo several recycling loops (e.g. authigenic mineral precipitation/dissolution) before they are either buried or diffuse back to the water column. The tightly coupled and complex pelagic and benthic process interplay thus delays recycling flux, significantly modifies the depositional signal and controls the long-term removal of carbon from the ocean-atmosphere system. Despite the importance of this mutual interaction, coupled regional/global biogeochemical models and (paleo)climate models, which are designed to assess and quantify the transformations and fluxes of carbon and nutrients and evaluate their response to past and future perturbations of the climate system either completely neglect marine sediments or incorporate a highly simplified representation of benthic processes. On the other end of the spectrum, coupled, multi-component state-of-the-art early diagenetic models have been successfully developed and applied over the past decades to reproduce observations and quantify sediment-water exchange fluxes, but cannot easily be coupled to pelagic models. The primary constraint here is the high computation cost of simulating all of the essential redox and equilibrium reactions within marine sediments that control carbon burial and benthic recycling fluxes: a barrier that is easily exacerbated if a variety of benthic environments are to be spatially resolved. This presentation provides an integrative overview of

  14. Modeling Coastal Vulnerability through Space and Time

    PubMed Central

    2016-01-01

    Coastal ecosystems experience a wide range of stressors including wave forces, storm surge, sea-level rise, and anthropogenic modification and are thus vulnerable to erosion. Urban coastal ecosystems are especially important due to the large populations these limited ecosystems serve. However, few studies have addressed the issue of urban coastal vulnerability at the landscape scale with spatial data that are finely resolved. The purpose of this study was to model and map coastal vulnerability and the role of natural habitats in reducing vulnerability in Jamaica Bay, New York, in terms of nine coastal vulnerability metrics (relief, wave exposure, geomorphology, natural habitats, exposure, exposure with no habitat, habitat role, erodible shoreline, and surge) under past (1609), current (2015), and future (2080) scenarios using InVEST 3.2.0. We analyzed vulnerability results both spatially and across all time periods, by stakeholder (ownership) and by distance to damage from Hurricane Sandy. We found significant differences in vulnerability metrics between past, current and future scenarios for all nine metrics except relief and wave exposure. The marsh islands in the center of the bay are currently vulnerable. In the future, these islands will likely be inundated, placing additional areas of the shoreline increasingly at risk. Significant differences in vulnerability exist between stakeholders; the Breezy Point Cooperative and Gateway National Recreation Area had the largest erodible shoreline segments. Significant correlations exist for all vulnerability (exposure/surge) and storm damage combinations except for exposure and distance to artificial debris. Coastal protective features, ranging from storm surge barriers and levees to natural features (e.g. wetlands), have been promoted to decrease future flood risk to communities in coastal areas around the world. Our methods of combining coastal vulnerability results with additional data and across multiple time

  15. Modeling Coastal Vulnerability through Space and Time.

    PubMed

    Hopper, Thomas; Meixler, Marcia S

    2016-01-01

    Coastal ecosystems experience a wide range of stressors including wave forces, storm surge, sea-level rise, and anthropogenic modification and are thus vulnerable to erosion. Urban coastal ecosystems are especially important due to the large populations these limited ecosystems serve. However, few studies have addressed the issue of urban coastal vulnerability at the landscape scale with spatial data that are finely resolved. The purpose of this study was to model and map coastal vulnerability and the role of natural habitats in reducing vulnerability in Jamaica Bay, New York, in terms of nine coastal vulnerability metrics (relief, wave exposure, geomorphology, natural habitats, exposure, exposure with no habitat, habitat role, erodible shoreline, and surge) under past (1609), current (2015), and future (2080) scenarios using InVEST 3.2.0. We analyzed vulnerability results both spatially and across all time periods, by stakeholder (ownership) and by distance to damage from Hurricane Sandy. We found significant differences in vulnerability metrics between past, current and future scenarios for all nine metrics except relief and wave exposure. The marsh islands in the center of the bay are currently vulnerable. In the future, these islands will likely be inundated, placing additional areas of the shoreline increasingly at risk. Significant differences in vulnerability exist between stakeholders; the Breezy Point Cooperative and Gateway National Recreation Area had the largest erodible shoreline segments. Significant correlations exist for all vulnerability (exposure/surge) and storm damage combinations except for exposure and distance to artificial debris. Coastal protective features, ranging from storm surge barriers and levees to natural features (e.g. wetlands), have been promoted to decrease future flood risk to communities in coastal areas around the world. Our methods of combining coastal vulnerability results with additional data and across multiple time

  16. Assimilating GlobColour ocean colour data into a pre-operational physical-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Ford, D. A.; Edwards, K. P.; Lea, D.; Barciela, R. M.; Martin, M. J.; Demaria, J.

    2012-02-01

    As part of the GlobColour project, daily chlorophyll-a observations, derived using remotely sensed ocean colour data from the MERIS, MODIS and SeaWiFS sensors, are produced. The ability of these products to be assimilated into a pre-operational global coupled physical-biogeochemical model has been tested, on both a hindcast and near-real-time basis, and the impact on the system assessed. The assimilation was found to immediately and significantly improve the bias, root mean square error and correlation of modelled surface chlorophyll concentration compared to the GlobColour observations, an improvement which was sustained throughout the year and in every ocean basin. Errors against independent in situ chlorophyll observations were also reduced, both at and beneath the ocean surface. However the model fit to in situ observations was not consistently better than that of climatology, due to errors in the underlying model. The assimilation scheme used is multivariate, updating all biogeochemical model state variables at all depths. Consistent changes were found in the other model variables, with reduced errors against in situ observations of nitrate and pCO2, and evidence of improved representation of zooplankton concentration. Annual mean surface fields of nutrients, alkalinity and carbon variables remained of similar quality compared to climatology. The near-real-time GlobColour products were found to be sufficiently reliable for operational purposes, and of benefit to both operational-style systems and reanalyses.

  17. Parameter estimation and uncertainty quantification in a biogeochemical model using optimal experimental design methods

    NASA Astrophysics Data System (ADS)

    Reimer, Joscha; Piwonski, Jaroslaw; Slawig, Thomas

    2016-04-01

    The statistical significance of any model-data comparison strongly depends on the quality of the used data and the criterion used to measure the model-to-data misfit. The statistical properties (such as mean values, variances and covariances) of the data should be taken into account by choosing a criterion as, e.g., ordinary, weighted or generalized least squares. Moreover, the criterion can be restricted onto regions or model quantities which are of special interest. This choice influences the quality of the model output (also for not measured quantities) and the results of a parameter estimation or optimization process. We have estimated the parameters of a three-dimensional and time-dependent marine biogeochemical model describing the phosphorus cycle in the ocean. For this purpose, we have developed a statistical model for measurements of phosphate and dissolved organic phosphorus. This statistical model includes variances and correlations varying with time and location of the measurements. We compared the obtained estimations of model output and parameters for different criteria. Another question is if (and which) further measurements would increase the model's quality at all. Using experimental design criteria, the information content of measurements can be quantified. This may refer to the uncertainty in unknown model parameters as well as the uncertainty regarding which model is closer to reality. By (another) optimization, optimal measurement properties such as locations, time instants and quantities to be measured can be identified. We have optimized such properties for additional measurement for the parameter estimation of the marine biogeochemical model. For this purpose, we have quantified the uncertainty in the optimal model parameters and the model output itself regarding the uncertainty in the measurement data using the (Fisher) information matrix. Furthermore, we have calculated the uncertainty reduction by additional measurements depending on time

  18. A new implementation of the Biogeochemical Flux Model in sea ice

    NASA Astrophysics Data System (ADS)

    Tedesco, L.; Vichi, M.

    2009-04-01

    The Biogeochemical Flux Model (BFM) is a direct descendent of the European Regional Seas Ecosystem Model (ERSEM) and it has been widely used and validated among the scientific community. The BFM view of the of the marine ecosystem is based upon the recognition that the major ecological functions of producers, decomposers and consumers and their specific trophic interactions can be expressed in terms of material flows of basic elements. The concentration and characteristics of organic and inorganic compounds are thus seen under a stoichiometrical perspective. This functional approach brings to the definition of Chemical Functional Families (CFF) and Living Functional Groups (LFG). The BFM is thus a set of biogeochemical equations describing the cycling of carbon, the macro-nutrients and oxygen through the lower trophic levels of marine ecosystems. A Sea-Ice system has now been implemented in the BFM and the new BFM-SI consists of three new LFG (sea ice algae, heterotrophic zooplankton, bacterioplankton), one new non-living organic functional group (sea ice DOM and POM) and two new inorganic functional groups: dissolved gases (sea ice CO2 and O2) and four nutrients (sea ice PO4, NH3, NO3 and SiO4). The innovative approach consists in simulating the biogeochemistry of the sea ice Biologically-Active-Layer (BAL), where the majority of the biomass (bottom communities) concentrates. The BFM-SI requires the physical properties of the BAL in order to be able to simulate the physiological and ecological response of the biological community to the physical environment. This is currently done by using an Enhanced 1-D thermo-halodynamic Sea Ice Model (ESIM2), developed to be suitable for biogeochemical studies. Since the biogeochemistry of sea ice is largely unknown, the BFM-SI is a useful tool that allow us to test hypotheses on the functioning of the sea ice ecosystem. By initially setting the sea ice community as having the same characteristics than the pelagic community

  19. Use of Combined Biogeochemical Model Approaches and Empirical Data to Assess Critical Loads of Nitrogen

    SciTech Connect

    Fenn, Mark E.; Driscoll, Charles; Zhou, Qingtao; Rao, Leela E.; Meixner, Tom; Allen, Edith B.; Yuan, Fengming; Sullivan, Timothy J.

    2015-01-01

    Empirical and dynamic biogeochemical modelling are complementary approaches for determining the critical load (CL) of atmospheric nitrogen (N) or other constituent deposition that an ecosystem can tolerate without causing ecological harm. The greatest benefits are obtained when these approaches are used in combination. Confounding environmental factors can complicate the determination of empirical CLs across depositional gradients, while the experimental application of N amendments for estimating the CL does not realistically mimic the effects of chronic atmospheric N deposition. Biogeochemical and vegetation simulation models can provide CL estimates and valuable ecosystem response information, allowing for past and future scenario testing with various combinations of environmental factors, pollutants, pollutant control options, land management, and ecosystem response parameters. Even so, models are fundamentally gross simplifications of the real ecosystems they attempt to simulate. Empirical approaches are vital as a check on simulations and CL estimates, to parameterize models, and to elucidate mechanisms and responses under real world conditions. In this chapter, we provide examples of empirical and modelled N CL approaches in ecosystems from three regions of the United States: mixed conifer forest, desert scrub and pinyon- juniper woodland in California; alpine catchments in the Rocky Mountains; and lakes in the Adirondack region of New York state.

  20. Accelerated parameter identification in a 3D marine biogeochemical model using surrogate-based optimization

    NASA Astrophysics Data System (ADS)

    Prieß, M.; Piwonski, J.; Koziel, S.; Oschlies, A.; Slawig, T.

    2013-08-01

    We present the application of the Surrogate-based Optimization (SBO) method on a parameter identification problem for a 3-D biogeochemical model. SBO is a method for acceleration of optimization processes when the underlying model itself is of very high computational complexity. In these cases, coupled simulation runs require large amounts of computer time, where optimization runs may become unfeasible even with high-performance hardware. As a consequence, the key idea of SBO is to replace the original and computationally expensive (high-fidelity) model by a so-called surrogate, which is created from a less accurate but computationally cheaper (low-fidelity) model and a suitable correction approach to increase its accuracy. To date, the SBO approach has been widely and successfully used in engineering applications and also for parameter identification in a 1-D marine ecosystem model of NPZD type. In this paper, we apply the approach onto a two-component biogeochemical model. The model is spun-up into a steady seasonal cycle via the Transport Matrix Approach. The low-fidelity model we use consists of a reduced number of spin-up iterations (several decades instead of millennia used for the original model). A multiplicative correction operator is further exploited to extrapolate the rather inaccurate low-fidelity model onto the original one. This corrected model builds our surrogate. We validate this SBO method by twin-experiments that use synthetic observations generated by the original model. We motivate our choice of the low-fidelity model and the multiplicative correction and discuss the computational advantage of SBO in comparison to an expensive parameter optimization in the context of the high-fidelity model. The proposed SBO technique is shown to yield a solution close to the target at a significant gain of computational efficiency. Without further regularization techniques, the method is able to identify most model parameters. The method is simple to

  1. Impact of operational model nesting approaches and inherent errors for coastal simulations

    NASA Astrophysics Data System (ADS)

    Brown, Jennifer M.; Norman, Danielle L.; Amoudry, Laurent O.; Souza, Alejandro J.

    2016-11-01

    A region of freshwater influence (ROFI) under hypertidal conditions is used to demonstrate inherent problems for nested operational modelling systems. Such problems can impact the accurate simulation of freshwater export within shelf seas, so must be considered in coastal ocean modelling studies. In Liverpool Bay (our UK study site), freshwater inflow from 3 large estuaries forms a coastal front that moves in response to tides and winds. The cyclic occurrence of stratification and remixing is important for the biogeochemical cycles, as nutrient and pollutant loaded freshwater is introduced into the coastal system. Validation methods, using coastal observations from fixed moorings and cruise transects, are used to assess the simulation of the ROFI, through improved spatial structure and temporal variability of the front, as guidance for best practise model setup. A structured modelling system using a 180 m grid nested within a 1.8 km grid demonstrates how compensation for error at the coarser resolution can have an adverse impact on the nested, high resolution application. Using 2008, a year of typical calm and stormy periods with variable river influence, the sensitivities of the ROFI dynamics to initial and boundary conditions are investigated. It is shown that accurate representation of the initial water column structure is important at the regional scale and that the boundary conditions are most important at the coastal scale. Although increased grid resolution captures the frontal structure, the accuracy in frontal position is determined by the offshore boundary conditions and therefore the accuracy of the coarser regional model.

  2. The General Ensemble Biogeochemical Modeling System (GEMS) and its applications to agricultural systems in the United States: Chapter 18

    USGS Publications Warehouse

    Liu, Shuguang; Tan, Zhengxi; Chen, Mingshi; Liu, Jinxun; Wein, Anne; Li, Zhengpeng; Huang, Shengli; Oeding, Jennifer; Young, Claudia; Verma, Shashi B.; Suyker, Andrew E.; Faulkner, Stephen P.

    2012-01-01

    The General Ensemble Biogeochemical Modeling System (GEMS) was es in individual models, it uses multiple site-scale biogeochemical models to perform model simulations. Second, it adopts Monte Carlo ensemble simulations of each simulation unit (one site/pixel or group of sites/pixels with similar biophysical conditions) to incorporate uncertainties and variability (as measured by variances and covariance) of input variables into model simulations. In this chapter, we illustrate the applications of GEMS at the site and regional scales with an emphasis on incorporating agricultural practices. Challenges in modeling soil carbon dynamics and greenhouse emissions are also discussed.

  3. Incorporating a prognostic representation of marine nitrogen fixers into the global ocean biogeochemical model HAMOCC

    NASA Astrophysics Data System (ADS)

    Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina D.; Stemmler, Irene

    2017-03-01

    Nitrogen (N2) fixation is a major source of bioavailable nitrogen to the euphotic zone, thereby exerting an important control on ocean biogeochemical cycling. This paper presents the incorporation of prognostic N2 fixers into the HAMburg Ocean Carbon Cycle model (HAMOCC), a component of the Max Planck Institute Earth System Model (MPI-ESM). Growth dynamics of N2 fixers in the model are based on physiological characteristics of the cyanobacterium Trichodesmium. The applied temperature dependency confines diazotrophic growth and N2 fixation to the tropical and subtropical ocean roughly between 40°S and 40°N. Simulated large-scale spatial patterns compare well with observations, and the global N2 fixation rate of 135.6 Tg N yr-1 is within the range of current estimates. The vertical distribution of N2 fixation also matches well the observations, with a major fraction of about 85% occurring in the upper 20 m. The observed seasonal variability at the stations BATS and ALOHA is reasonably reproduced, with highest fixation rates in northern summer/fall. Iron limitation was found to be an important factor in controlling the simulated distribution of N2 fixation, especially in the Pacific Ocean. The new model component considerably improves the representation of present-day N2 fixation in HAMOCC. It provides the basis for further studies on the role of diazotrophs in global biogeochemical cycles, as well as on the response of N2 fixation to changing environmental conditions.

  4. Isotope data improve the predictive capabilities of a marine biogeochemical model

    NASA Astrophysics Data System (ADS)

    Van Engeland, T.; De Kluijver, A.; Soetaert, K.; Meysman, F. J. R.; Middelburg, J. J.

    2012-07-01

    Mesocosm experiments combined with biogeochemical modeling provide a powerful research tool to better understand marine ecosystem processes. Using an extended Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) model, we investigated the added value of stable isotope tracer additions to constrain biogeochemical transformations within a mesocosm experiment that was designed to study ocean acidification effects on the marine ecosystem. Markov-Chain Monte-Carlo simulations revealed that even when isotope data were available for the majority of the components, not all parameters in the model could be constrained by calibration. However, when isotope tracer data were deliberately excluded from the calibration, the overparameterisation was even stronger. More specifically, it led to unconstrained fluxes through the zooplankton and detritus compartment, and different relative contributions of these two compartments to phytoplankton biomass loss produced equally plausible results. It is concluded that model uncertainty due to overparameterisation can be considerably reduced by explicitly resolving stable isotope dynamics. Therefore, this mesocosm experiment has benefitted substantially from isotope tracer additions to unravel carbon cycling under varying CO2 regimes.

  5. Investigating the initial stages of soil formation in glacier forefields using the new biogeochemical model: SHIMMER

    NASA Astrophysics Data System (ADS)

    Bradley, James; Anesio, Alexandre; Arndt, Sandra; Sabacka, Marie; Barker, Gary; Benning, Liane; Blacker, Joshua; Singarayer, Joy; Tranter, Martyn; Yallop, Marian

    2016-04-01

    Glaciers and ice sheets in Polar and alpine regions are retreating in response to recent climate warming, exposing terrestrial ecosystems that have been locked under the ice for thousands of years. Exposed soils exhibit successional characteristics that can be characterised using a chronosequence approach. Decades of empirical research in glacier forefields has shown that soils are quickly colonised by microbes which drive biogeochemical cycling of elements and affect soil properties including nutrient concentrations, carbon fluxes and soil stability (Bradley et al, 2014). The characterisation of these soils is important for our understanding of the cycling of organic matter under extreme environmental and nutrient limiting conditions, and their potential contribution to global biogeochemical cycles. This is particularly important as these new areas will become more geographically expansive with continued ice retreat. SHIMMER (Soil biogeocHemIcal Model of Microbial Ecosystem Response) (Bradley et al, 2015) is a new mathematical model that simulates biogeochemical and microbial dynamics in glacier forefields. The model captures, explores and predicts the growth of different microbial groups (classified by function), and the associated cycling of carbon, nitrogen and phosphorus along a chronosequence. SHIMMER improves typical soil model formulations by including explicit representation of microbial dynamics, and those processes which are shown to be important for glacier forefields. For example, we categorise microbial groups by function to represent the diversity of soil microbial communities, and include the different metabolic needs and physiological pathways of microbial organisms commonly found in glacier forefields (e.g. microbes derived from underneath the glacier, typical soil bacteria, and microbes that can fix atmospheric nitrogen and assimilate soil nitrogen). Here, we present data from a study where we integrated modelling using SHIMMER with empirical

  6. Dramatic variability of the carbonate system of the coastal ocean is regulated by physical and biogeochemical processes on multiple timescales

    NASA Astrophysics Data System (ADS)

    Johnson, Z. I.; Hunt, D.

    2013-12-01

    Increased atmospheric carbon dioxide (CO2) from anthropogenic sources is acidifying marine environments with potentially dramatic implications for the physical, chemical and biological functioning of these ecosystems. If current trends continue, mean ocean pH is expected to decrease by ~0.2 units over the next ~50 years. Yet, at the same time there is substantial spatial and temporal variability in pH and other carbon system parameters in the ocean resulting in regions that already exceed long term projected pH changes, suggesting that short-term variability is an important layer of complexity on top of long term acidification. Thus, in order to develop predictions of future climate change impacts including ocean acidification, there is a critical need to characterize the natural range and variability of the marine CO2 system and the mechanisms responsible for this variability. Here we examine pH and dissolved inorganic carbon (DIC) variability at time intervals spanning 1 hour to >1 year in a dynamic coastal marine system to quantify variability of the carbon system at multiple time scales. Daily and seasonal variability of the carbon system is largely driven by temperature, alkalinity and the balance between primary production and respiration, but high frequency variability (hours to days) is further influenced by water mass movement (e.g. tides) and stochastic events (e.g. storms). Both annual variability (~0.3 units) and diurnal variability (~0.1 units) in coastal ocean acidity are similar in magnitude to long term projections associated with increasing atmospheric CO2 and their drivers highlight the importance of characterizing the complete carbonate system (and not just pH). Short term variability of ocean carbon parameters may already exert significant pressure on some coastal marine ecosystems with implications for ecology, biogeochemistry and evolution and this shorter term variability layers additive effects and complexity, including extreme values, on

  7. Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Jones, Emlyn M.; Baird, Mark E.; Mongin, Mathieu; Parslow, John; Skerratt, Jenny; Lovell, Jenny; Margvelashvili, Nugzar; Matear, Richard J.; Wild-Allen, Karen; Robson, Barbara; Rizwi, Farhan; Oke, Peter; King, Edward; Schroeder, Thomas; Steven, Andy; Taylor, John

    2016-12-01

    Skillful marine biogeochemical (BGC) models are required to understand a range of coastal and global phenomena such as changes in nitrogen and carbon cycles. The refinement of BGC models through the assimilation of variables calculated from observed in-water inherent optical properties (IOPs), such as phytoplankton absorption, is problematic. Empirically derived relationships between IOPs and variables such as chlorophyll-a concentration (Chl a), total suspended solids (TSS) and coloured dissolved organic matter (CDOM) have been shown to have errors that can exceed 100 % of the observed quantity. These errors are greatest in shallow coastal regions, such as the Great Barrier Reef (GBR), due to the additional signal from bottom reflectance. Rather than assimilate quantities calculated using IOP algorithms, this study demonstrates the advantages of assimilating quantities calculated directly from the less error-prone satellite remote-sensing reflectance (RSR). To assimilate the observed RSR, we use an in-water optical model to produce an equivalent simulated RSR and calculate the mismatch between the observed and simulated quantities to constrain the BGC model with a deterministic ensemble Kalman filter (DEnKF). The traditional assumption that simulated surface Chl a is equivalent to the remotely sensed OC3M estimate of Chl a resulted in a forecast error of approximately 75 %. We show this error can be halved by instead using simulated RSR to constrain the model via the assimilation system. When the analysis and forecast fields from the RSR-based assimilation system are compared with the non-assimilating model, a comparison against independent in situ observations of Chl a, TSS and dissolved inorganic nutrients (NO3, NH4 and DIP) showed that errors are reduced by up to 90 %. In all cases, the assimilation system improves the simulation compared to the non-assimilating model. Our approach allows for the incorporation of vast quantities of remote-sensing observations

  8. Exploring the Influence of Topography on Belowground C Processes Using a Coupled Hydrologic-Biogeochemical Model

    NASA Astrophysics Data System (ADS)

    Shi, Y.; Davis, K. J.; Eissenstat, D. M.; Kaye, J. P.; Duffy, C.; Yu, X.; He, Y.

    2014-12-01

    Belowground carbon processes are affected by soil moisture and soil temperature, but current biogeochemical models are 1-D and cannot resolve topographically driven hill-slope soil moisture patterns, and cannot simulate the nonlinear effects of soil moisture on carbon processes. Coupling spatially-distributed physically-based hydrologic models with biogeochemical models may yield significant improvements in the representation of topographic influence on belowground C processes. We will couple the Flux-PIHM model to the Biome-BGC (BBGC) model. Flux-PIHM is a coupled physically-based land surface hydrologic model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model. Because PIHM is capable of simulating lateral water flow and deep groundwater, Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as the land surface heterogeneities caused by topography. The coupled Flux-PIHM-BBGC model will be tested at the Susquehanna/Shale Hills critical zone observatory (SSHCZO). The abundant observations, including eddy covariance fluxes, soil moisture, groundwater level, sap flux, stream discharge, litterfall, leaf area index, above ground carbon stock, and soil carbon efflux, make SSHCZO an ideal test bed for the coupled model. In the coupled model, each Flux-PIHM model grid will couple a BBGC cell. Flux-PIHM will provide BBGC with soil moisture and soil temperature information, while BBGC provides Flux-PIHM with leaf area index. Preliminary results show that when Biome- BGC is driven by PIHM simulated soil moisture pattern, the simulated soil carbon is clearly impacted by topography.

  9. A new biogeochemical model to simulate regional scale carbon emission from lakes, ponds and wetlands

    NASA Astrophysics Data System (ADS)

    Bayer, Tina; Brakebusch, Matthias; Gustafsson, Erik; Beer, Christian

    2016-04-01

    Small aquatic systems are receiving increasing attention for their role in global carbon cycling. For instance, lakes and ponds in permafrost are net emitters of carbon to the atmosphere, and their capacity to process and emit carbon is significant on a landscape scale, with a global flux of 8-103 Tg methane per year which amounts to 5%-30% of all natural methane emissions (Bastviken et al 2011). However, due to the spatial and temporal highly localised character of freshwater methane emissions, fluxes remain poorly qualified and are difficult to upscale based on field data alone. While many models exist to model carbon cycling in individual lakes and ponds, we perceived a lack of models that can work on a larger scale, over a range of latitudes, and simulate regional carbon emission from a large number of lakes, ponds and wetlands. Therefore our objective was to develop a model that can simulate carbon dioxide and methane emission from freshwaters on a regional scale. Our resulting model provides an additional tool to assess current aquatic carbon emissions as well as project future responses to changes in climatic drivers. To this effect, we have combined an existing large-scale hydrological model (the Variable Infiltration Capacity Macroscale Hydrologic Model (VIC), Liang & Lettenmaier 1994), an aquatic biogeochemical model (BALTSEM, Savchuk et al., 2012; Gustafsson et al., 2014) and developed a new methane module for lakes. The resulting new process-based biogeochemical model is designed to model aquatic carbon emission on a regional scale, and to perform well in high-latitude environments. Our model includes carbon, oxygen and nutrient cycling in lake water and sediments, primary production and methanogenesis. Results of calibration and validation of the model in two catchments (Torne-Kalix in Northern Sweden and of a large arctic river catchment) will be presented.

  10. Characterizing biogeochemical processes in the hyporheic zone using flume experiments and reactive transport modeling

    NASA Astrophysics Data System (ADS)

    Quick, A. M.; Reeder, W. J.; Farrell, T. B.; Feris, K. P.; Tonina, D.; Benner, S. G.

    2015-12-01

    The hyporheic zones of streams are hotspots of biogeochemical cycling, where reactants from surface water and groundwater are continually brought into contact with microbial populations on the surfaces of stream sediments and reaction products are removed by hyporheic flow and degassing. Using large flume experiments we have documented the complex redox dynamics associated with dune-scale hyporheic flow. Observations, coupled with reactive transport modeling, provide insight into how flow dictates spatio-temporal distribution of redox reactions and the associated consumption and production of reactants and products. Dune hyporheic flow was experimentally produced by maintaining control over flow rates, slopes, sediment grain size, bedform geomorphology, and organic carbon content. An extensive in-situ monitoring array combined with sampling events over time elucidated redox-sensitive processes including constraints on the spatial distribution and magnitude of aerobic respiration, organic carbon consumption, sulfide deposition, and denitrification. Reactive transport modeling reveals further insight into the influence of system geometry and reaction rate. As an example application of the model, the relationship between residence times and reaction rates may be used to generate Damköhler numbers that are related to biogeochemical processes, such as the potential of streambed morphology and nitrate loading to influence production of the greenhouse gas nitrous oxide via incomplete denitrification.

  11. Modeling carbon cycle responses to tree mortality: linking microbial and biogeochemical changes

    NASA Astrophysics Data System (ADS)

    Moore, D. J.; Trahan, N. A.; Dynes, E. L.; Zobitz, J. M.; Gallery, R.

    2013-12-01

    Amid a worldwide increase in tree mortality, mountain pine beetles (Dendroctonus ponderosae Hopkins) have killed billions of trees from Mexico to Alaska in the last 13 years. This mortality is predicted to influence important carbon, water and energy balance feedbacks on the Earth system. We studied changes in soil biogeochemical cycling and microbial community structure after tree mortality. We show, using a decade long chronosequence, that tree mortality causes no increase in total respiration from local to watershed scales, with corresponding changes in biogeochemical pools of nitrogen and phosphorus. We also found comparable declines in both gross primary productivity and respiration suggesting little change in net flux. We tested the mechanisms controlling these patterns using an ecosystem model; contrasting a simplified microbial subroutine with a 'dead soil' model. We coupled our modeling work with direct measurements of microbial biomass, enzyme kinetics and community structure. The transitory recovery of respiration 6-7 years after mortality was associated with increased microbial biomass, increased incorporation of leaf litter carbon into soil organic matter, and was followed by a secondary decline in respiration during years 8-10. Our findings are consistent with the mechanism of reduced input of new carbon causing a decline in microbial biomass rather than an increased output of older carbon.

  12. Entropy of biogeochemical compartment models: complexity and information content as a tool for model development

    NASA Astrophysics Data System (ADS)

    Metzler, Holger; Sierra, Carlos A.

    2017-04-01

    Most soil organic matter decomposition models consist of a number of compartments describing the dynamics of substrate and microbial biomass pools. The fluxes of mass between the compartments are usually described by a system of ordinary differential equations, in which the number of compartments and the connections among them define the complexity of the model and the number of biological processes that need to be described. With this approach, it is difficult to determine the level of detail that is required to describe a given system, and it is also difficult to compare models against each other due to large differences in their level of complexity. Here, we propose entropy as a tool to determine the level of complexity required to describe a biogeochemical system and to compare the information content of different models. Instead of entire masses on bulk soil level, we look at such models from the point of view of a single particle on the molecular level. This particle enters the system, cycles through it, and leaves it at some point later in time, thereby following a path through the system. We think of this path as a particular stochastic process, a Markov renewal process. If we consider this path as a random variable in a path space, its Shannon information entropy describes its information content, i.e. how much we learn when we observe the entire path of a particle traveling through the system. In other words, it tells us how hard it is to predict this path and thus how much we do not know about what is going to happen to one single particle. The entropy as a measure of model complexity can help us to decide whether a model is not complex enough to represent the information that we have about a system or whether it is too complex. The concept of maximum entropy provides a powerful tool to develop unbiased models, i.e. models that contain the exact amount of information that we have about the system. In addition, differences between a soil organic matter

  13. The UK Earth System Models Marine Biogeochemical Evaluation Toolkit, BGC-val

    NASA Astrophysics Data System (ADS)

    de Mora, Lee

    2017-04-01

    The Biogeochemical Validation toolkit, BGC-val, is a model and grid independent python-based marine model evaluation framework that automates much of the validation of the marine component of an Earth System Model. BGC-val was initially developed to be a flexible and extensible system to evaluate the spin up of the marine UK Earth System Model (UKESM). However, the grid-independence and flexibility means that it is straightforward to adapt the BGC-val framework to evaluate other marine models. In addition to the marine component of the UKESM, this toolkit has been adapted to compare multiple models, including models from the CMIP5 and iMarNet inter-comparison projects. The BGC-val toolkit produces multiple levels of analysis which are presented in a simple to use interactive html5 document. Level 1 contains time series analyses, showing the development over time of many important biogeochemical and physical ocean metrics, such as the Global primary production or the Drake passage current. The second level of BGC-val is an in-depth spatial analyses of a single point in time. This is a series of point to point comparison of model and data in various regions, such as a comparison of Surface Nitrate in the model vs data from the world ocean atlas. The third level analyses are specialised ad-hoc packages to go in-depth on a specific question, such as the development of Oxygen minimum zones in the Equatorial Pacific. In additional to the three levels, the html5 document opens with a Level 0 table showing a summary of the status of the model run. The beta version of this toolkit is available via the Plymouth Marine Laboratory Gitlab server and uses the BSD 3 clause license.

  14. How to `Elk-test' biogeochemical models in a data rich world? (Invited)

    NASA Astrophysics Data System (ADS)

    Reichstein, M.; Ciais, P.; Seneviratne, S. I.; Carvalhais, N.; Dalmonech, D.; Jung, M.; Luo, Y.; Mahecha, M. D.; Moffat, A. M.; Tomelleri, E.; Zaehle, S.

    2010-12-01

    Process-oriented biogeochemical models are a primary tool that has been used to project future states of climate and ecosystems in the earth system in response to anthropogenic and other forcing, and receive tremendous attention also in the context us the planned assessment report AR5 by the IPCC. However, model intercomparison and data-model comparison studies indicate large uncertainties regarding predictions of global interactions between atmosphere and biosphere. Rigorous scientific testing of these models is essential but very challenging, largely because neither it is technically and ethically possible to perform global earth-scale experiments, nor do we have replicate Earths for hypothesis testing. Hence, model evaluations have to rely on monitoring data such as ecological observation networks, global remote sensing or short-term and small-scale experiments. Here, we critically examine strategies of how model evaluations have been performed with a particular emphasis on terrestrial ecosystems. Often weak ‘validations’ are being presented which do not take advantage of all the relevant information in the observed data, but also apparent falsifications are made, that are hampered by a confusion of system processes with system behavior. We propose that a stronger integration of recent advances in pattern-oriented and system-oriented methodologies will lead to more satisfying earth system model evaluation and development, and show a few enlightening examples from terrestrial biogeochemical modeling and other disciplines. Moreover it is crucial to take advantage of the multidimensional nature of arising earth observation data sets which should be matched by models simultaneously, instead of relying on univariate simple comparisons. A new critical model evaluation is needed to improve future IPCC assessments in order to reduce uncertainties by distinguishing plausible simulation trajectories from fairy tales.

  15. A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

    NASA Astrophysics Data System (ADS)

    Shapiro, B.; Jin, Q.

    2015-12-01

    Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

  16. In Situ Biostimulation at a Former Uranium Mill Tailings Site: Multicomponent Biogeochemical Reactive Transport Modeling

    NASA Astrophysics Data System (ADS)

    Yabusaki, S.; Fang, Y.; Long, P.

    2005-12-01

    In situ biostimulation at a Former Uranium Mill Tailings Site: Multicomponent Biogeochemical Reactive Transport Modeling Field experiments conducted at a former uranium mill tailings site in western Colorado are being used to investigate microbially mediated immobilization of uranium as a potential future remediation option for such sites. While the general principle of biostimulating microbial communities to reduce aqueous hexavalent uranium to immobile uraninite has been demonstrated in the laboratory and field, the ability to predictably engineer long lasting immobilization will require a more complete understanding of field-scale processes and properties. For this study, numerical simulation of the flow field, geochemical conditions, and micriobial communities is used to interpret field-scale biogeochemical reactive transport observed during experiments performed in 2002 to 2004. One key issue is identifying bioavailable Fe(III) oxide, which is the principal electron acceptor utilized by the acetate- oxidizing Geobacter sp. These organisms are responsible for uranium bioreduction that results in the removal of sufficient U(VI) to lower uranium groundwater concentrations to at or near applicable standards. The depletion of bioavailable Fe(III) leads to succession by sulfate reducers that are considerably less effective at uranium bioreduction. An important modeling consideration are the abiotic reactions (e.g., mineral precipitation and dissolution, aqueous and surface complexation) involving the Fe(II) and sulfide produced during biostimulation. These components, strongly associated with the solid phases, may play an important role in the evolving reactivity of the mineral surfaces that are likely to impact long-term uranium immobilization.

  17. Empirical approaches to more accurately predict benthic-pelagic coupling in biogeochemical ocean models

    NASA Astrophysics Data System (ADS)

    Dale, Andy; Stolpovsky, Konstantin; Wallmann, Klaus

    2016-04-01

    The recycling and burial of biogenic material in the sea floor plays a key role in the regulation of ocean chemistry. Proper consideration of these processes in ocean biogeochemical models is becoming increasingly recognized as an important step in model validation and prediction. However, the rate of organic matter remineralization in sediments and the benthic flux of redox-sensitive elements are difficult to predict a priori. In this communication, examples of empirical benthic flux models that can be coupled to earth system models to predict sediment-water exchange in the open ocean are presented. Large uncertainties hindering further progress in this field include knowledge of the reactivity of organic carbon reaching the sediment, the importance of episodic variability in bottom water chemistry and particle rain rates (for both the deep-sea and margins) and the role of benthic fauna. How do we meet the challenge?

  18. Geoelectrical measurement and modeling of biogeochemical breakthrough behavior during microbial activity

    USGS Publications Warehouse

    Slater, L.D.; Day-Lewis, F. D.; Ntarlagiannis, D.; O'Brien, M.; Yee, N.

    2009-01-01

    We recorded bulk electrical conductivity (??b) along a soil column during microbially-mediated selenite oxyanion reduction. Effluent fluid electrical conductivity and early time ??b were modeled according to classic advectivedispersive transport of the nutrient medium. However, ??b along the column exhibited strongly bimodal breakthrough which cannot be explained by changes in the electrical conductivity of the pore fluid. We model the anomalous breakthrough by adding a conduction path in parallel with the fluid phase, with a time dependence described by a microbial population-dynamics model. We incorporate a delay time to show that breakthrough curves along the column satisfy the same growth model parameters and offer a possible explanation based on biomass-limited growth that is delayed with distance from influent of the nutrient medium. Although the mechanism causing conductivity enhancement in the presence of biomass is uncertain, our results strongly , suggest that biogeochemical breakthrough curves have been captured in geoelectrical datasets. Copyright 2009 by the American Geophysical Union.

  19. Pathways for arsenic from sediments to groundwater to streams: Biogeochemical processes in the Inner Coastal Plain, New Jersey, USA

    USGS Publications Warehouse

    Barringer, Julia L.; Mumford, Adam; Young, Lily Y.; Reilly, Pamela A.; Bonin, Jennifer L.; Rosman, Robert

    2010-01-01

    The Cretaceous and Tertiary sediments that underlie the Inner Coastal Plain of New Jersey contain the arsenic-rich mineral glauconite. Streambed sediments in two Inner Coastal Plain streams (Crosswicks and Raccoon Creeks) that traverse these glauconitic deposits are enriched in arsenic (15–25 mg/kg), and groundwater discharging to the streams contains elevated levels of arsenic (>80 μg/L at a site on Crosswicks Creek) with arsenite generally the dominant species. Low dissolved oxygen, low or undetectable levels of nitrate and sulfate, detectable sulfide concentrations, and high concentrations of iron and dissolved organic carbon (DOC) in the groundwater indicate that reducing environments are present beneath the streambeds and that microbial activity, fueled by the DOC, is involved in releasing arsenic and iron from the geologic materials. In groundwater with the highest arsenic concentrations at Crosswicks Creek, arsenic respiratory reductase gene (arrA) indicated the presence of arsenic-reducing microbes. From extracted DNA, 16s rRNA gene sequences indicate the microbial community may include arsenic-reducing bacteria that have not yet been described. Once in the stream, iron is oxidized and precipitates as hydroxide coatings on the sediments. Arsenite also is oxidized and co-precipitates with or is sorbed to the iron hydroxides. Consequently, dissolved arsenic concentrations are lower in streamwater than in the groundwater, but the arsenic contributed by groundwater becomes part of the arsenic load in the stream when sediments are suspended during high flow. A strong positive relation between concentrations of arsenic and DOC in the groundwater samples indicates that any process—natural or anthropogenic—that increases the organic carbon concentration in the groundwater could stimulate microbial activity and thus increase the amount of arsenic that is released from the geologic materials.

  20. Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models

    SciTech Connect

    Sarmiento, Jorge L.; Gnanadesikan, Anand; Gruber, Nicolas; Jin, Xin; Armstrong, Robert

    2007-06-21

    This final report summarizes research undertaken collaboratively between Princeton University, the NOAA Geophysical Fluid Dynamics Laboratory on the Princeton University campus, the State University of New York at Stony Brook, and the University of California, Los Angeles between September 1, 2000, and November 30, 2006, to do fundamental research on ocean iron fertilization as a means to enhance the net oceanic uptake of CO2 from the atmosphere. The approach we proposed was to develop and apply a suite of coupled physical-ecological-biogeochemical models in order to (i) determine to what extent enhanced carbon fixation from iron fertilization will lead to an increase in the oceanic uptake of atmospheric CO2 and how long this carbon will remain sequestered (efficiency), and (ii) examine the changes in ocean ecology and natural biogeochemical cycles resulting from iron fertilization (consequences). The award was funded in two separate three-year installments: September 1, 2000 to November 30, 2003, for a project entitled “Ocean carbon sequestration by fertilization: An integrated biogeochemical assessment.” A final report was submitted for this at the end of 2003 and is included here as Appendix 1; and, December 1, 2003 to November 30, 2006, for a follow-on project under the same grant number entitled “Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models.” This report focuses primarily on the progress we made during the second period of funding subsequent to the work reported on in Appendix 1. When we began this project, we were thinking almost exclusively in terms of long-term fertilization over large regions of the ocean such as the Southern Ocean, with much of our focus being on how ocean circulation and biogeochemical cycling would interact to control the response to a given fertilization scenario. Our research on these types of scenarios, which was carried out largely during the

  1. Numerical modeling of watershed-scale radiocesium transport coupled with biogeochemical cycling in forests

    NASA Astrophysics Data System (ADS)

    Mori, K.; Tada, K.; Tawara, Y.; Tosaka, H.; Ohno, K.; Asami, M.; Kosaka, K.

    2015-12-01

    Since the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident, intensive monitoring and modeling works on radionuclide transfer in environment have been carried out. Although Cesium (Cs) concentration has been attenuating due to both physical and environmental half-life (i.e., wash-off by water and sediment), the attenuation rate depends clearly on the type of land use and land cover. In the Fukushima case, studying the migration in forest land use is important for predicting the long-term behavior of Cs because most of the contaminated region is covered by forests. Atmospheric fallout is characterized by complicated behavior in biogeochemical cycle in forests which can be described by biotic/abiotic interactions between many components. In developing conceptual and mathematical model on Cs transfer in forest ecosystem, defining the dominant components and their interactions are crucial issues (BIOMASS, 1997-2001). However, the modeling of fate and transport in geosphere after Cs exports from the forest ecosystem is often ignored. An integrated watershed modeling for simulating spatiotemporal redistribution of Cs that includes the entire region from source to mouth and surface to subsurface, has been recently developed. Since the deposited Cs can migrate due to water and sediment movement, the different species (i.e., dissolved and suspended) and their interactions are key issues in the modeling. However, the initial inventory as source-term was simplified to be homogeneous and time-independent, and biogeochemical cycle in forests was not explicitly considered. Consequently, it was difficult to evaluate the regionally-inherent characteristics which differ according to land uses, even if the model was well calibrated. In this study, we combine the different advantages in modeling of forest ecosystem and watershed. This enable to include more realistic Cs deposition and time series of inventory can be forced over the land surface. These processes are integrated

  2. Modelling the biogeochemical cycle of silicon in soils using the reactive transport code MIN3P

    NASA Astrophysics Data System (ADS)

    Gerard, F.; Mayer, K. U.; Hodson, M. J.; Meunier, J.

    2006-12-01

    We investigated the biogeochemical cycling of Si in an acidic brown soil covered by a coniferous forest (Douglas fir) based on a comprehensive data set and reactive transport modelling. Both published and original data enable us to make up a conceptual model on which the development of a numerical model is based. We modified the reactive transport code MIN3P, which solves thermodynamic and kinetic reactions coupled with vadose zone flow and solute transport. Simulations were performed for a one-dimensional heterogeneous soil profile and were constrained by observed data including daily soil temperature, plant transpiration, throughfall, and dissolved Si in solutions collected beneath the organic layer. Reactive transport modelling was first used to test the validity of the hypothesis that a dynamic balance between Si uptake by plants and release by weathering controls aqueous Si-concentrations. We were able to calibrate the model quite accurately by stepwise adjustment of the relevant parameters. The capability of the model to predict Si-concentrations was good. Mass balance calculations indicate that only 40% of the biogeochemical cycle of Si is controlled by weathering and that about 60% of Si-cycling is related to biological processes (i.e. Si uptake by plants and dissolution of biogenic Si). Such a large contribution of biological processes was not anticipated considering the temperate climate regime, but may be explained by the high biomass productivity of the planted coniferous species. The large contribution of passive Si-uptake by vegetation permits the conservation of seasonal concentration variations caused by temperature-induced weathering, although the modelling suggests that the latter process was of lesser importance relative to biological Si-cycling.

  3. Biogeochemical mass balances in a turbid tropical reservoir. Field data and modelling approach

    NASA Astrophysics Data System (ADS)

    Phuong Doan, Thuy Kim; Némery, Julien; Gratiot, Nicolas; Schmid, Martin

    2014-05-01

    The turbid tropical Cointzio reservoir, located in the Trans Mexican Volcanic Belt (TMVB), behaves as a warm monomictic water body (area = 6 km2, capacity 66 Mm3, residence time ~ 1 year). It is strategic for the drinking water supply of the city of Morelia, capital of the state of Michoacán, and for downstream irrigation during the dry season. This reservoir is a perfect example of a human-impacted system since its watershed is mainly composed of degraded volcanic soils and is subjected to high erosion processes and agricultural loss. The reservoir is threatened by sediment accumulation and nutrients originating from untreated waters in the upstream watershed. The high content of very fine clay particles and the lack of water treatment plants lead to serious episodes of eutrophication (up to 70 μg chl. a L-1), high levels of turbidity (Secchi depth < 30 cm) and a long period of anoxia (from May to October). Based on intensive field measurements in 2009 (deposited sediment, benthic chamber, water vertical profiles, reservoir inflow and outflow) we determined suspended sediment (SS), carbon (C), nitrogen (N) and phosphorus (P) mass balances. Watershed SS yields were estimated at 35 t km2 y-1 of which 89-92 % were trapped in the Cointzio reservoir. As a consequence the reservoir has already lost 25 % of its initial storage capacity since its construction in 1940. Nutrient mass balances showed that 50 % and 46 % of incoming P and N were retained by sedimentation, and mainly eliminated through denitrification respectively. Removal of C by 30 % was also observed both by sedimentation and through gas emission. To complete field data analyses we examined the ability of vertical one dimensional (1DV) numerical models (Aquasim biogeochemical model coupled with k-ɛ mixing model) to reproduce the main biogeochemical cycles in the Cointzio reservoir. The model can describe all the mineralization processes both in the water column and in the sediment. The values of the

  4. Oceanic biogeochemical characteristic maps identified with holistic use of satellite, model and data

    NASA Astrophysics Data System (ADS)

    Bruun, John; Allen, Icarus; Vichi, Marcello; Somerfield, Paul; Samuelsen, Annette; Racault, Marie-Fanny; Waldron, Howard; Monteiro, Pedro; McKiver, William; Bellerby, Richard; Thomalla, Sandy; Lygre, Kjetil; Moiseev, Denis; Johannessen, Johnny; Brewin, Robert; Butenschön, Momme; Jeansson, Emil; Vines, Aleksander; Heard, Jessica

    2014-05-01

    Ocean province level plankton community exhibit heterogeneity across Arctic, Nordic, Atlantic Gyre and Southern Ocean provinces. GreenSeas research is an international FP7 consortium that includes Arctic, Atlantic and Southern Ocean based research teams who are analysing the planktonic ecosystem. We are looking at how the planktonic ecosystem responds to environmental and climate change. Using Earth Observation monitoring data we report new results on identifying generic plankton characteristics observable at a province level, and also touch on spatial and temporal trends that are evident using a holistic analysis framework. Using advanced statistical methods this framework compares and combines Earth Observation information together with an in-situ Oceanic plankton Analytical Database and up to 40 year ocean general circulation biogeochemical model (OGCBM) time series of the equivalent plankton and sea-state measures of this system. Specifically, we outline the use of the GreenSeas Analytical Database, which is a harmonised set of Oceanic in-situ plankton and sea-state measures covering different cruises and time periods. The Analytical Database information ranges from plankton community,primary production, nutrient cycling to physical sea state temperature and salinity measures. The combined analysis utilises current, 10 year+ Earth Observations of ocean colour and sea surface temperature metrics and interprets these together with biogeochemical model outputs from PELAGOS, ERSEM & NORWECOM model runs to help identify planktonic based biomes. Generic planktonic characteristic maps that are equivalently observable in both the Earth Observations and numerical models are reported on. Both ocean surface and sub-surface signals are analysed together with relevant Analytical Database biome extracts. We present the current results of this inter-comparison & discuss challenges of identifying the province level plankton dominance with the satellite, model and data. In

  5. One-dimensional model for biogeochemical interactions and permeability reduction in soils during leachate permeation.

    PubMed

    Singhal, Naresh; Islam, Jahangir

    2008-02-19

    This paper uses the findings from a column study to develop a reactive model for exploring the interactions occurring in leachate-contaminated soils. The changes occurring in the concentrations of acetic acid, sulphate, suspended and attached biomass, Fe(II), Mn(II), calcium, carbonate ions, and pH in the column are assessed. The mathematical model considers geochemical equilibrium, kinetic biodegradation, precipitation-dissolution reactions, bacterial and substrate transport, and permeability reduction arising from bacterial growth and gas production. A two-step sequential operator splitting method is used to solve the coupled transport and biogeochemical reaction equations. The model gives satisfactory fits to experimental data and the simulations show that the transport of metals in soil is controlled by multiple competing biotic and abiotic reactions. These findings suggest that bioaccumulation and gas formation, compared to chemical precipitation, have a larger influence on hydraulic conductivity reduction.

  6. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

    PubMed Central

    Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

  7. Marine regime shifts in ocean biogeochemical models: a case study in the Gulf of Alaska

    NASA Astrophysics Data System (ADS)

    Beaulieu, Claudie; Cole, Harriet; Henson, Stephanie; Yool, Andrew; Anderson, Tom; de Mora, Lee; Buitenhuis, Erik T.; Butenschön, Momme; Totterdell, Ian J.; Icarus Allen, J.

    2016-08-01

    Regime shifts have been reported in many marine ecosystems, and are often expressed as an abrupt change occurring in multiple physical and biological components of the system. In the Gulf of Alaska, a regime shift in the late 1970s was observed, indicated by an abrupt increase in sea surface temperature and major shifts in the catch of many fish species. A thorough understanding of the extent and mechanisms leading to such regime shifts is challenged by data paucity in time and space. We investigate the ability of a suite of ocean biogeochemistry models of varying complexity to simulate regime shifts in the Gulf of Alaska by examining the presence of abrupt changes in time series of physical variables (sea surface temperature and mixed-layer depth), nutrients and biological variables (chlorophyll, primary productivity and plankton biomass) using change-point analysis. Our results show that some ocean biogeochemical models are capable of simulating the late 1970s shift, manifested as an abrupt increase in sea surface temperature followed by an abrupt decrease in nutrients and biological productivity. Models from low to intermediate complexity simulate an abrupt transition in the late 1970s (i.e. a significant shift from one year to the next) while the transition is smoother in higher complexity models. Our study demonstrates that ocean biogeochemical models can successfully simulate regime shifts in the Gulf of Alaska region. These models can therefore be considered useful tools to enhance our understanding of how changes in physical conditions are propagated from lower to upper trophic levels.

  8. Assimilating GlobColour ocean colour data into a pre-operational physical-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Ford, D. A.; Edwards, K. P.; Lea, D.; Barciela, R. M.; Martin, M. J.; Demaria, J.

    2012-09-01

    As part of the GlobColour project, daily chlorophyll a observations, derived using remotely sensed ocean colour data from the MERIS, MODIS and SeaWiFS sensors, are produced. The ability of these products to be assimilated into a pre-operational global coupled physical-biogeochemical model has been tested, on both a hindcast and near-real-time basis, and the impact on the system assessed. The assimilation was found to immediately and considerably improve the bias, root mean square error and correlation of modelled surface chlorophyll concentration compared to the GlobColour observations, an improvement which was sustained throughout the year and in every ocean basin. Errors against independent in situ chlorophyll observations were also reduced, both at and beneath the ocean surface. However, the model fit to in situ observations was not consistently better than that of climatology, due to errors in the underlying model. The assimilation scheme used is multivariate, updating all biogeochemical model state variables at all depths. The other variables were not degraded by the assimilation, with annual mean surface fields of nutrients, alkalinity and carbon variables remaining of similar quality compared to climatology. There was evidence of improved representation of zooplankton concentration, and reduced errors were seen against in situ observations of nitrate and pCO2, but too few observations were available to conclude about global model skill. The near-real-time GlobColour products were found to be sufficiently reliable for operational purposes, and of benefit to both operational-style systems and reanalyses.

  9. Evaluation of Boundless Biogeochemical Cycle through Development of Process-Based Eco-Hydrological and Biogeochemical Cycle Model to Incorporate Terrestrial-Aquatic Continuum

    NASA Astrophysics Data System (ADS)

    Nakayama, T.; Maksyutov, S. S.

    2014-12-01

    Inland water might act as important transport pathway for continental biogeochemical cycle although its contribution has remained uncertain yet due to a paucity of data (Battin et al. 2009). The author has developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (Nakayama, 2008a-b, 2010, 2011a-b, 2012a-c, 2013; Nakayama and Fujita, 2010; Nakayama and Hashimoto, 2011; Nakayama and Shankman, 2013a-b; Nakayama and Watanabe, 2004, 2006, 2008a-b; Nakayama et al., 2006, 2007, 2010, 2012), which incorporates surface-groundwater interactions, includes up- and down-scaling processes between local-regional-global scales, and can simulate iteratively nonlinear feedback between hydrologic-geomorphic-ecological processes. Because NICE incorporates 3-D groundwater sub-model and expands from previous 1- or 2-D or steady state, the model can simulate the lateral transport pronounced at steeper-slope or riparian/floodplain with surface-groundwater connectivity. River discharge and groundwater level simulated by NICE agreed reasonably with those in previous researches (Niu et al., 2007; Fan et al., 2013) and extended to clarify lateral subsurface also has important role on global hydrologic cycle (Nakayama, 2011b; Nakayama and Shankman, 2013b) though the resolution was coarser. NICE was further developed to incorporate biogeochemical cycle including reaction between inorganic and organic carbons in terrestrial and aquatic ecosystems. The missing role of carbon cycle simulated by NICE, for example, CO2 evasion from inland water (global total flux was estimated as about 1.0 PgC/yr), was relatively in good agreement in that estimated by empirical relation using previous pCO2 data (Aufdenkampe et al., 2011; Laruelle et al., 2013). The model would play important role in identification of greenhouse gas balance of the biosphere and spatio-temporal hot spots, and bridging gap between top-down and bottom-up approaches (Cole et al. 2007; Frei et al. 2012).

  10. Simulating temporal variations of nitrogen losses in river networks with a dynamic transport model unravels the coupled effects of hydrological and biogeochemical processes

    SciTech Connect

    Mulholland, Patrick J; Alexander, Richard; Bohlke, John; Boyer, Elizabeth; Harvey, Judson; Seitzinger, Sybil; Tobias, Craig; Tonitto, Christina; Wollheim, Wilfred

    2009-01-01

    The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal in the river networks of two watersheds having widely differing levels of nitrate enrichment but nearly identical discharges. Stream denitrification is estimated by regression as a nonlinear function of nitrate concentration, streamflow, and temperature, using more than 300 published measurements from a variety of US streams. These relations are used in the stream transport model to characterize nitrate dynamics related to denitrification at a monthly time scale in the stream reaches of the two watersheds. Results indicate that the nitrate removal efficiency of streams, as measured by the percentage of the stream nitrate flux removed via denitrification per unit length of channel, is appreciably reduced during months with high discharge and nitrate flux and increases during months of low-discharge and flux. Biogeochemical factors, including land use, nitrate inputs, and stream concentrations, are a major control on reach-scale denitrification, evidenced by the disproportionately lower nitrate removal efficiency in streams of the highly nitrate-enriched watershed as compared with that in similarly sized streams in the less nitrate-enriched watershed. Sensitivity analyses reveal that these important biogeochemical factors and physical hydrological factors contribute nearly

  11. Biogeochemical and Hydrological Controls on Mercury and Methylmercury in First Order Coastal Plain Watersheds of the Chesapeake Bay

    NASA Astrophysics Data System (ADS)

    Heyes, A.; Gilmour, C. C.; Bell, J. T.; Butera, D.; McBurney, A. W.

    2015-12-01

    Over the past 7 years we made use of the long-term research site at the Smithsonian Environmental Research Center (SERC) in central Maryland to study the fluxes of mercury (Hg) and methylmercury (MeHg) in three small first-order mid-Atlantic coastal plain watersheds. One watershed is entirely forested, one watershed is primarily agriculture with a forested stream buffer, and one watershed is mixed land use but contains a beaver produced wetland pond. Our initial goals were to assess watershed Hg yields in the mid-Atlantic and to establish a baseline prior to implementation of Hg emissions controls. All three studied watersheds produced relatively high yields of Hg, with the greatest yield coming from the forested watershed. Our initial evaluation of three watersheds showed that MeHg production and flux could also be high, but varied dramatically among watersheds and across years and seasons. During each year we observed episodic MeHg production in the spring and sometimes during prolonged high-flow storm events in the fall. The observed spring maxima of MeHg release coincided with development of anoxia in riparian groundwater. MeHg accumulation in riparian groundwater began once nitrate was depleted and either iron accumulation or sulfate depletion of groundwater began. We propose the presence of nitrate was modulating MeHg production through the suppression of sulfate and iron reducers and perhaps methanogens. As sulfate is not limiting in any of the watersheds owing to the sediments marine origin, we hypothesize the depletion of nitrate allows sulfate reducing bacteria to now utilize available carbon. Although wetlands are generally thought of as the primary zones of MeHg production in watersheds, shallow riparian groundwaters very close to the stream appear to play that role in SERC Coastal Plain watersheds. We hypothesize that the balance between nitrate, sulfate and other microbial electron acceptors in watersheds is a major control on MeHg production. Land

  12. Modelling the biogeochemical cycle of silicon in soils: Application to a temperate forest ecosystem

    NASA Astrophysics Data System (ADS)

    Gérard, F.; Mayer, K. U.; Hodson, M. J.; Ranger, J.

    2008-02-01

    We investigated the biogeochemical cycling of silicon (Si) in an acidic brown soil covered by a coniferous forest (Douglas fir). Based on published and original data, we constructed a conceptual model and used a modified version of the reactive transport code MIN3P for model testing and quantification purposes. The model was first calibrated and further validated with respect to biomass data and Si-concentrations in capillary solutions, which were collected monthly over several years by means of suction-cup lysimeters placed at different soil depths. Following sensitivity tests, the model was calibrated quite accurately (limited to a 10% concentration error) by the adjustment of kinetic constants, longitudinal dispersion, and apparent activation energy for K-feldspar dissolution. Calibrated parameter values were constrained by ranges reported in the literature, when available. Mass balance calculations indicate that an average of 60% of the biogeochemical cycle of Si was controlled by biological processes (i.e. Si-uptake and dissolution of phytoliths). Sensitivity analyses suggest that no more than 55% of the Si-cycle is controlled by weathering of primary silicates. Such a large contribution of biological turnover to Si-cycling may be explained by the combined effects of a relatively large Si-content in the litter fall (i.e. specifically in the needles) and high biomass productivity of the coniferous species considered. In addition to potential implications for the global Si cycle, this investigation raises several fundamental questions concerning the nature of Si-uptake mechanisms and physiological use of Si by trees in natural systems.

  13. Marine regime shifts in ocean biogeochemical models: a case study in the Gulf of Alaska

    NASA Astrophysics Data System (ADS)

    Beaulieu, C.; Cole, H.; Henson, S.; Yool, A.; Anderson, T. R.; de Mora, L.; Buitenhuis, E. T.; Butenschön, M.; Totterdell, I. J.; Allen, J. I.

    2015-08-01

    Regime shifts have been reported in many marine ecosystems, and are often expressed as an abrupt change occurring in multiple physical and biological components of the system. In the Gulf of Alaska, a regime shift in the late 1970s was observed, indicated by an abrupt increase in sea surface temperature and major shifts in the catch of many fish species. This late 1970s regime shift in the Gulf of Alaska was followed by another shift in the late 1980s, not as pervasive as the 1977 shift, but which nevertheless did not return to the prior state. A thorough understanding of the extent and mechanisms leading to such regime shifts is challenged by data paucity in time and space. We investigate the ability of a suite of ocean biogeochemistry models of varying complexity to simulate regime shifts in the Gulf of Alaska by examining the presence of abrupt changes in time series of physical variables (sea surface temperature and mixed layer depth), nutrients and biological variables (chlorophyll, primary productivity and plankton biomass) using change-point analysis. Our study demonstrates that ocean biogeochemical models are capable of simulating the late 1970s shift, indicating an abrupt increase in sea surface temperature forcing followed by an abrupt decrease in nutrients and biological productivity. This predicted shift is consistent among all the models, although some of them exhibit an abrupt transition (i.e. a significant shift from one year to the next), whereas others simulate a smoother transition. Some models further suggest that the late 1980s shift was constrained by changes in mixed layer depth. Our study demonstrates that ocean biogeochemical can successfully simulate regime shifts in the Gulf of Alaska region, thereby providing better understanding of how changes in physical conditions are propagated from lower to upper trophic levels through bottom-up controls.

  14. PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies

    NASA Astrophysics Data System (ADS)

    Aumont, O.; Ethé, C.; Tagliabue, A.; Bopp, L.; Gehlen, M.

    2015-08-01

    PISCES-v2 (Pelagic Interactions Scheme for Carbon and Ecosystem Studies volume 2) is a biogeochemical model which simulates the lower trophic levels of marine ecosystems (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbon and of the main nutrients (P, N, Fe, and Si). The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. There are 24 prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton size classes (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod-quota formalism. On the one hand, stoichiometry of C / N / P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicon quotas are variable and the growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting, for instance, the complexity of iron chemistry or the description of particulate organic materials. So far, PISCES-v2 has been coupled to the Nucleus for European Modelling of the Ocean (NEMO) and Regional Ocean Modeling System (ROMS) systems. A full description of PISCES-v2 and of its optional functionalities is provided here. The results of a quasi-steady-state simulation are presented and evaluated against diverse observational and satellite-derived data. Finally, some of the new functionalities of PISCES-v2 are tested in a series of sensitivity experiments.

  15. Variable reactivity of particulate organic matter in a global ocean biogeochemical model

    NASA Astrophysics Data System (ADS)

    Aumont, Olivier; van Hulten, Marco; Roy-Barman, Matthieu; Dutay, Jean-Claude; Éthé, Christian; Gehlen, Marion

    2017-05-01

    The marine biological carbon pump is dominated by the vertical transfer of particulate organic carbon (POC) from the surface ocean to its interior. The efficiency of this transfer plays an important role in controlling the amount of atmospheric carbon that is sequestered in the ocean. Furthermore, the abundance and composition of POC is critical for the removal of numerous trace elements by scavenging, a number of which, such as iron, are essential for the growth of marine organisms, including phytoplankton. Observations and laboratory experiments have shown that POC is composed of numerous organic compounds that can have very different reactivities. However, this variable reactivity of POC has never been extensively considered, especially in modelling studies. Here, we introduced in the global ocean biogeochemical model NEMO-PISCES a description of the variable composition of POC based on the theoretical reactivity continuum model proposed by Boudreau and Ruddick (1991). Our model experiments show that accounting for a variable lability of POC increases POC concentrations in the ocean's interior by 1 to 2 orders of magnitude. This increase is mainly the consequence of a better preservation of small particles that sink slowly from the surface. Comparison with observations is significantly improved both in abundance and in size distribution. Furthermore, the amount of carbon that reaches the sediments is increased by more than a factor of 2, which is in better agreement with global estimates of the sediment oxygen demand. The impact on the major macronutrients (nitrate and phosphate) remains modest. However, iron (Fe) distribution is strongly altered, especially in the upper mesopelagic zone as a result of more intense scavenging: vertical gradients in Fe are milder in the upper ocean, which appears to be closer to observations. Thus, our study shows that the variable lability of POC can play a critical role in the marine

  16. Study of the plankton ecosystem variability using a coupled hydrodynamics biogeochemical modelling in the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Kessouri, Fayçal; Ulses, Caroline; Estournel, Claude; Marsaleix, Patrick

    2015-04-01

    The Mediterranean Sea presents a wide variety of trophic regimes since the large and intense spring bloom of the North-Western Mediterranean Sea (NWMS) that follows winter convection to the extreme oligotrophic regions of the South-eastern basin. The Mediterranean Sea displays a strong time variability revealing its high sensitivity to climate and anthropic pressures. In this context, it is crucial to develop tools allowing to understand the evolution of the Mediterranean hydrology and marine ecosystem as a response to external forcing. Numerical coupled hydrodynamic and biogeochemical modelling carefully calibrated in the different regions of the basin is the only tool that can answer this question. However, this important step of calibration is particularly difficult because of the lack of coherent sets of data describing the seasonal evolution of the main parameters characterizing the physical and biogeochemical environment in the different sub-basins. The chlorophyll satellite data from 4km MODIS products, a multiple in situ data from MerMEX MOOSE and DEWEX cruises and Bio-Argo floats from NAOS project are believed to be an opportunity to strongly improve the realism of ecosystem models. The model is a 3D coupled simulation using NemoMed12 for hydrodynamics and ECO 3MS for biogeochemistry and covers the whole Mediterranean Sea and runs at 1/12°. The relevant variables mentioned are phytoplankton, organic and inorganic matters faced to water masses dynamics, over ten years since summer 2003. After a short validation, we will expose two topics: First, through this coupling we quantify the nutrients fluxes across the Mediterranean straits over the years. For example, we found an annual net average around 150 Giga moles NO3 per year at Gibraltar, where we expect low annual fluctuations. In contrast, the Strait of Sicily shows greater annual variability going from 70 to 92 Giga moles NO3 per year. All the fluxes are resumed in a detailed diagram of the transport

  17. Coastal Modeling System Advanced Topics

    DTIC Science & Technology

    2012-06-18

    is the CMS? Integrated wave, current, and morphology change model in the Surface-water Modeling System (SMS). Why CMS? Operational at 10...Coupled with spectral wave model (CMS-Wave)  Wave-current interactions  Inline sediment transport and morphology change  Non-equilibrium...Easy to setup  Telescoping grid: Efficient and flexible  Solver options  Implicit: Tidal flow, long-term morphology change. ~10 min

  18. Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, S.; Hickman, A. E.; Jahn, O.; Gregg, W. W.; Mouw, C. B.; Follows, M. J.

    2015-02-01

    We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemical-ecosystem in a dynamic three-dimensional physical framework. The radiative transfer component resolves spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (the phytoplankton community, detrital particles, and coloured dissolved organic matter, CDOM). The model is evaluated against in situ observed and satellite derived products. In particular we compare to concurrently measured biogeochemical, ecosystem and optical data along a north-south transect of the Atlantic Ocean. The simulation captures the patterns and magnitudes of these data, and estimates surface upwelling irradiance analogous to that observed by ocean colour satellite instruments. We conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, and the crucial feedbacks between the light field and the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at short wavelengths and in more productive waters, phytoplankton absorption is especially important at the deep chlorophyll a (Chl a) maximum, and absorption by water molecules is relatively most important in the highly oligotrophic gyres. Sensitivity experiments in which absorption by any of the optical constituents was increased led to a decrease in the size of the oligotrophic regions of the subtropical gyres: lateral nutrient supplies were enhanced as a result of decreasing high latitude productivity. Scattering does not as strongly affect the ecosystem and biogeochemistry fields within the water column but is important for setting the surface upwelling irradiance, and hence sea surface reflectance. Having a model capable of capturing bio-optical feedbacks will be important for

  19. Modeling the Oxygen Cycle in the Equatorial Pacific: Regulation of Physical and Biogeochemical Processes

    NASA Astrophysics Data System (ADS)

    Wang, X.; Murtugudde, R. G.; Zhang, D.

    2016-12-01

    Photosynthesis and respiration are important processes in all ecosystems on the Earth, in which carbon and oxygen are the two main elements. However, the oxygen cycle has received much less attention (relative to the carbon cycle) despite its big role in the earth system. Oxygen is a sensitive indicator of physical and biogeochemical processes in the ocean thus a key parameter for understanding the ocean's ecosystem and biogeochemistry. The Oxygen-Minimum-Zone (OMZ), often seen below 200 m, is a profound feature in the world oceans. There has been evidence of OMZ expansion over the past few decades in the tropical oceans. Climate models project that there would be a continued decline in dissolved oxygen (DO) and an expansion of the tropical OMZs under future warming conditions, which is of great concern because of the implications for marine organisms. We employ a validated three-dimensional model that simulates physical transport (circulation and vertical mixing), biological processes (O2 production and consumption) and ocean-atmosphere O2 exchange to quantify various sources and sinks of DO over 1980-2015. We show how we use observational data to improve our model simulation. Then we assess the spatial and temporal variability in simulated DO in the tropical Pacific Ocean, and explore the impacts of physical and biogeochemical processes on the DO dynamics, with a focus on the MOZ. Our analyses indicate that DO in the OMZ has a positive relationship with the 13ºC isotherm depth and a negative relationship with the concentration of dissolved organic material.

  20. Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment

    NASA Astrophysics Data System (ADS)

    Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.; Murray, Christopher J.; Ward, Andy L.; Dayvault, Richard D.; Waichler, Scott R.; Newcomer, Darrell R.; Spane, Frank A.; Long, Philip E.

    2011-11-01

    Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted

  1. Technical Note: A generic law-of-the-minimum flux limiter for simulating substrate limitation in biogeochemical models

    NASA Astrophysics Data System (ADS)

    Tang, J. Y.; Riley, W. J.

    2015-08-01

    We present a generic flux limiter to account for mass limitations from an arbitrary number of substrates in a biogeochemical reaction network. The flux limiter is based on the observation that substrate (e.g., nitrogen, phosphorus) limitation in biogeochemical models can be represented as to ensure mass conservative and non-negative numerical solutions to the governing ordinary differential equations. Application of the flux limiter includes two steps: (1) formulate the biogeochemical processes with a matrix of stoichiometric coefficients and (2) apply Liebig's law of the minimum using the dynamic stoichiometric relationship of the reactants. This approach contrasts with the ad hoc down-regulation approaches that are implemented in many existing models (such as CLM4.5 and the ACME (Accelerated Climate Modeling for Energy) Land Model (ALM)) of carbon and nutrient interactions, which are error prone when adding new processes, even for experienced modelers. Through an example implementation with a Century-like decomposition model that includes carbon, nitrogen, and phosphorus, we show that our approach (1) produced almost identical results to that from the ad hoc down-regulation approaches under non-limiting nutrient conditions; and (2) properly resolved the negative solutions under substrate-limited conditions where the simple clipping approach failed; and (3) successfully avoided the potential conceptual ambiguities that are implied by those ad hoc down-regulation approaches. We expect our approach will make future biogeochemical models easier to improve and more robust.

  2. Technical Note: A generic law-of-the-minimum flux limiter for simulating substrate limitation in biogeochemical models

    NASA Astrophysics Data System (ADS)

    Tang, J. Y.; Riley, W. J.

    2016-02-01

    We present a generic flux limiter to account for mass limitations from an arbitrary number of substrates in a biogeochemical reaction network. The flux limiter is based on the observation that substrate (e.g., nitrogen, phosphorus) limitation in biogeochemical models can be represented as to ensure mass conservative and non-negative numerical solutions to the governing ordinary differential equations. Application of the flux limiter includes two steps: (1) formulation of the biogeochemical processes with a matrix of stoichiometric coefficients and (2) application of Liebig's law of the minimum using the dynamic stoichiometric relationship of the reactants. This approach contrasts with the ad hoc down-regulation approaches that are implemented in many existing models (such as CLM4.5 and the ACME (Accelerated Climate Modeling for Energy) Land Model (ALM)) of carbon and nutrient interactions, which are error prone when adding new processes, even for experienced modelers. Through an example implementation with a CENTURY-like decomposition model that includes carbon, nitrogen, and phosphorus, we show that our approach (1) produced almost identical results to that from the ad hoc down-regulation approaches under non-limiting nutrient conditions, (2) properly resolved the negative solutions under substrate-limited conditions where the simple clipping approach failed, (3) successfully avoided the potential conceptual ambiguities that are implied by those ad hoc down-regulation approaches. We expect our approach will make future biogeochemical models easier to improve and more robust.

  3. Technical Note: A generic law-of-the-minimum flux limiter for simulating substrate limitation in biogeochemical models

    SciTech Connect

    Tang, J. Y.; Riley, W. J.

    2016-02-05

    We present a generic flux limiter to account for mass limitations from an arbitrary number of substrates in a biogeochemical reaction network. The flux limiter is based on the observation that substrate (e.g., nitrogen, phosphorus) limitation in biogeochemical models can be represented as to ensure mass conservative and non-negative numerical solutions to the governing ordinary differential equations. Application of the flux limiter includes two steps: (1) formulation of the biogeochemical processes with a matrix of stoichiometric coefficients and (2) application of Liebig's law of the minimum using the dynamic stoichiometric relationship of the reactants. This approach contrasts with the ad hoc down-regulation approaches that are implemented in many existing models (such as CLM4.5 and the ACME (Accelerated Climate Modeling for Energy) Land Model (ALM)) of carbon and nutrient interactions, which are error prone when adding new processes, even for experienced modelers. Through an example implementation with a CENTURY-like decomposition model that includes carbon, nitrogen, and phosphorus, we show that our approach (1) produced almost identical results to that from the ad hoc down-regulation approaches under non-limiting nutrient conditions, (2) properly resolved the negative solutions under substrate-limited conditions where the simple clipping approach failed, (3) successfully avoided the potential conceptual ambiguities that are implied by those ad hoc down-regulation approaches. We expect our approach will make future biogeochemical models easier to improve and more robust.

  4. Biogeochemical Protocols and Diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)

    NASA Technical Reports Server (NTRS)

    Orr, James C.; Najjar, Raymond G.; Aumont, Olivier; Bopp, Laurent; Bullister, John L.; Danabasoglu, Gokhan; Doney, Scott C.; Dunne, John P.; Dutay, Jean-Claude; Graven, Heather; hide

    2017-01-01

    The Ocean Model Intercomparison Project (OMIP) focuses on the physics and biogeochemistry of the ocean component of Earth system models participating in the sixth phase of the Coupled Model Intercomparison Project (CMIP6). OMIP aims to provide standard protocols and diagnostics for ocean models, while offering a forum to promote their common assessment and improvement. It also offers to compare solutions of the same ocean models when forced with reanalysis data (OMIP simulations) vs. when integrated within fully coupled Earth system models (CMIP6). Here we detail simulation protocols and diagnostics for OMIP's biogeochemical and inert chemical tracers. These passive-tracer simulations will be coupled to ocean circulation models, initialized with observational data or output from a model spin-up, and forced by repeating the 1948-2009 surface fluxes of heat, fresh water, and momentum. These so-called OMIP-BGC simulations include three inert chemical tracers (CFC-11, CFC-12, SF [subscript] 6) and biogeochemical tracers (e.g., dissolved inorganic carbon, carbon isotopes, alkalinity, nutrients, and oxygen). Modelers will use their preferred prognostic BGC model but should follow common guidelines for gas exchange and carbonate chemistry. Simulations include both natural and total carbon tracers. The required forced simulation (omip1) will be initialized with gridded observational climatologies. An optional forced simulation (omip1-spunup) will be initialized instead with BGC fields from a long model spin-up, preferably for 2000 years or more, and forced by repeating the same 62-year meteorological forcing. That optional run will also include abiotic tracers of total dissolved inorganic carbon and radiocarbon, CTabio and 14CTabio, to assess deep-ocean ventilation and distinguish the role of physics vs. biology. These simulations will be forced by observed atmospheric histories of the three inert gases and CO2 as well as carbon isotope ratios of CO2. OMIP-BGC simulation

  5. Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)

    NASA Astrophysics Data System (ADS)

    Orr, James C.; Najjar, Raymond G.; Aumont, Olivier; Bopp, Laurent; Bullister, John L.; Danabasoglu, Gokhan; Doney, Scott C.; Dunne, John P.; Dutay, Jean-Claude; Graven, Heather; Griffies, Stephen M.; John, Jasmin G.; Joos, Fortunat; Levin, Ingeborg; Lindsay, Keith; Matear, Richard J.; McKinley, Galen A.; Mouchet, Anne; Oschlies, Andreas; Romanou, Anastasia; Schlitzer, Reiner; Tagliabue, Alessandro; Tanhua, Toste; Yool, Andrew

    2017-06-01

    The Ocean Model Intercomparison Project (OMIP) focuses on the physics and biogeochemistry of the ocean component of Earth system models participating in the sixth phase of the Coupled Model Intercomparison Project (CMIP6). OMIP aims to provide standard protocols and diagnostics for ocean models, while offering a forum to promote their common assessment and improvement. It also offers to compare solutions of the same ocean models when forced with reanalysis data (OMIP simulations) vs. when integrated within fully coupled Earth system models (CMIP6). Here we detail simulation protocols and diagnostics for OMIP's biogeochemical and inert chemical tracers. These passive-tracer simulations will be coupled to ocean circulation models, initialized with observational data or output from a model spin-up, and forced by repeating the 1948-2009 surface fluxes of heat, fresh water, and momentum. These so-called OMIP-BGC simulations include three inert chemical tracers (CFC-11, CFC-12, SF6) and biogeochemical tracers (e.g., dissolved inorganic carbon, carbon isotopes, alkalinity, nutrients, and oxygen). Modelers will use their preferred prognostic BGC model but should follow common guidelines for gas exchange and carbonate chemistry. Simulations include both natural and total carbon tracers. The required forced simulation (omip1) will be initialized with gridded observational climatologies. An optional forced simulation (omip1-spunup) will be initialized instead with BGC fields from a long model spin-up, preferably for 2000 years or more, and forced by repeating the same 62-year meteorological forcing. That optional run will also include abiotic tracers of total dissolved inorganic carbon and radiocarbon, CTabio and 14CTabio, to assess deep-ocean ventilation and distinguish the role of physics vs. biology. These simulations will be forced by observed atmospheric histories of the three inert gases and CO2 as well as carbon isotope ratios of CO2. OMIP-BGC simulation protocols are

  6. Mechanistic site-based emulation of a global ocean biogeochemical model for parametric analysis and calibration

    NASA Astrophysics Data System (ADS)

    Hemmings, J. C. P.; Challenor, P. G.; Yool, A.

    2014-09-01

    Biogeochemical ocean circulation models used to investigate the role of plankton ecosystems in global change rely on adjustable parameters to compensate for missing biological complexity. In principle, optimal parameter values can be estimated by fitting models to observational data, including satellite ocean colour products such as chlorophyll that achieve good spatial and temporal coverage of the surface ocean. However, comprehensive parametric analyses require large ensemble experiments that are computationally infeasible with global 3-D simulations. Site-based simulations provide an efficient alternative but can only be used to make reliable inferences about global model performance if robust quantitative descriptions of their relationships with the corresponding 3-D simulations can be established. The feasibility of establishing such a relationship is investigated for an intermediate complexity biogeochemistry model (MEDUSA) coupled with a widely-used global ocean model (NEMO). A site-based mechanistic emulator is constructed for surface chlorophyll output from this target model as a function of model parameters. The emulator comprises an array of 1-D simulators and a statistical quantification of the uncertainty in their predictions. The unknown parameter-dependent biogeochemical environment, in terms of initial tracer concentrations and lateral flux information required by the simulators, is a significant source of uncertainty. It is approximated by a mean environment derived from a small ensemble of 3-D simulations representing variability of the target model behaviour over the parameter space of interest. The performance of two alternative uncertainty quantification schemes is examined: a direct method based on comparisons between simulator output and a sample of known target model "truths" and an indirect method that is only partially reliant on knowledge of target model output. In general, chlorophyll records at a representative array of oceanic sites

  7. PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies

    NASA Astrophysics Data System (ADS)

    Aumont, O.; Ethé, C.; Tagliabue, A.; Bopp, L.; Gehlen, M.

    2015-02-01

    PISCES-v2 is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbon and of the main nutrients (P, N, Fe, and Si). The model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod-Quota formalism: on one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. So far, PISCES-v2 has been coupled to the NEMO and ROMS systems. A full description of PISCES-v2 and of its optional functionalities is provided here. The results of a quasi-steady state simulation are presented and evaluated against diverse observational and satellite-derived data. Finally, some of the new functionalities of PISCES-v2 are tested in a series of sensitivity experiments.

  8. Data and Model Uncertainties associated with Biogeochemical Groundwater Remediation and their impact on Decision Analysis

    NASA Astrophysics Data System (ADS)

    Pandey, S.; Vesselinov, V. V.; O'Malley, D.; Karra, S.; Hansen, S. K.

    2016-12-01

    Models and data are used to characterize the extent of contamination and remediation, both of which are dependent upon the complex interplay of processes ranging from geochemical reactions, microbial metabolism, and pore-scale mixing to heterogeneous flow and external forcings. Characterization is wrought with important uncertainties related to the model itself (e.g. conceptualization, model implementation, parameter values) and the data used for model calibration (e.g. sparsity, measurement errors). This research consists of two primary components: (1) Developing numerical models that incorporate the complex hydrogeology and biogeochemistry that drive groundwater contamination and remediation; (2) Utilizing novel techniques for data/model-based analyses (such as parameter calibration and uncertainty quantification) to aid in decision support for optimal uncertainty reduction related to characterization and remediation of contaminated sites. The reactive transport models are developed using PFLOTRAN and are capable of simulating a wide range of biogeochemical and hydrologic conditions that affect the migration and remediation of groundwater contaminants under diverse field conditions. Data/model-based analyses are achieved using MADS, which utilizes Bayesian methods and Information Gap theory to address the data/model uncertainties discussed above. We also use these tools to evaluate different models, which vary in complexity, in order to weigh and rank models based on model accuracy (in representation of existing observations), model parsimony (everything else being equal, models with smaller number of model parameters are preferred), and model robustness (related to model predictions of unknown future states). These analyses are carried out on synthetic problems, but are directly related to real-world problems; for example, the modeled processes and data inputs are consistent with the conditions at the Los Alamos National Laboratory contamination sites (RDX and

  9. Biogeochemical modelling vs. tree-ring data - comparison of forest ecosystem productivity estimates

    NASA Astrophysics Data System (ADS)

    Zorana Ostrogović Sever, Maša; Barcza, Zoltán; Hidy, Dóra; Paladinić, Elvis; Kern, Anikó; Marjanović, Hrvoje

    2017-04-01

    Forest ecosystems are sensitive to environmental changes as well as human-induce disturbances, therefore process-based models with integrated management modules represent valuable tool for estimating and forecasting forest ecosystem productivity under changing conditions. Biogeochemical model Biome-BGC simulates carbon, nitrogen and water fluxes, and it is widely used for different terrestrial ecosystems. It was modified and parameterised by many researchers in the past to meet the specific local conditions. In this research, we used recently published improved version of the model Biome-BGCMuSo (BBGCMuSo), with multilayer soil module and integrated management module. The aim of our research is to validate modelling results of forest ecosystem productivity (NPP) from BBGCMuSo model with observed productivity estimated from an extensive dataset of tree-rings. The research was conducted in two distinct forest complexes of managed Pedunculate oak in SE Europe (Croatia), namely Pokupsko basin and Spačva basin. First, we parameterized BBGCMuSo model at a local level using eddy-covariance (EC) data from Jastrebarsko EC site. Parameterized model was used for the assessment of productivity on a larger scale. Results of NPP assessment with BBGCMuSo are compared with NPP estimated from tree ring data taken from trees on over 100 plots in both forest complexes. Keywords: Biome-BGCMuSo, forest productivity, model parameterization, NPP, Pedunculate oak

  10. Insights into biogeochemical cycling from a soil evolution model and long-term chronosequences

    NASA Astrophysics Data System (ADS)

    Johnson, M. O.; Gloor, M.; Kirkby, M. J.; Lloyd, J.

    2014-12-01

    Despite the importance of soil processes for global biogeochemical cycles, our capability for predicting soil evolution over geological timescales is poorly constrained. We attempt to probe our understanding and predictive capability of this evolutionary process by developing a mechanistic soil evolution model, based on an existing model framework, and comparing the predictions with observations from soil chronosequences in Hawaii. Our soil evolution model includes the major processes of pedogenesis: mineral weathering, percolation of rainfall, leaching of solutes, surface erosion, bioturbation, the effects of vegetation in terms of organic matter input and nutrient cycling and can be applied to various bedrock compositions and climates. The specific properties the model simulates over timescales of tens to hundreds of thousand years are, soil depth, vertical profiles of elemental composition, soil solution pH and organic carbon distribution. We demonstrate with this model the significant role that vegetation plays in accelerating the rate of weathering and hence soil profile development. Comparisons with soils that have developed on Hawaiian basalts reveal a remarkably good agreement with Na, Ca and Mg profiles suggesting that the model captures well the key components of soil formation. Nevertheless, differences between modelled and observed K and P are substantial. The fact that these are important plant nutrients suggests that a process likely missing from our model is the active role of vegetation in selectively acquiring nutrients. This study therefore indirectly indicates the valuable role that vegetation can play in accelerating the weathering and thus release of these globally important nutrients into the biosphere.

  11. Insights into biogeochemical cycling from soil evolution model and long-term chronosequences

    NASA Astrophysics Data System (ADS)

    Johnson, M. O.; Gloor, M.; Kirkby, M. J.; Lloyd, J.

    2014-04-01

    Despite the importance of soil processes for global biogeochemical cycles, our capability for predicting soil evolution over geological timescales is poorly constrained. We attempt to probe our understanding and predictive capability of this evolutionary process by developing a mechanistic soil evolution model, based on an existing model framework, and comparing the predictions with observations from soil chronosequences in Hawaii. Our soil evolution model includes the major processes of pedogenesis: mineral weathering, percolation of rainfall, leaching of solutes, surface erosion, bioturbation and vegetation interactions and can be applied to various bedrock compositions and climates. The specific properties the model simulates over timescales of tens to hundreds of thousand years are, soil depth, vertical profiles of elemental composition, soil solution pH and organic carbon distribution. We demonstrate with this model the significant role that vegetation plays in accelerating the rate of weathering and hence soil profile development. Comparisons with soils that have developed on Hawaiian basalts reveal a remarkably good agreement with Na, Ca and Mg profiles suggesting that the model captures well the key components of soil formation. Nevertheless, differences between modelled and observed K and P are substantial. The fact that these are important plant nutrients suggests that a process likely missing from our model is the active role of vegetation in selectively acquiring nutrients. This study therefore indirectly indicates the valuable role that vegetation can play in accelerating the weathering and thus release of these globally important nutrients into the biosphere.

  12. Climate and biogeochemical sensitivity at ocean model resolutions of 100 km and 10 km

    NASA Astrophysics Data System (ADS)

    Dunne, J. P.; Galbraith, E. D.; Anderson, W.; Dufour, C. O.; Griffies, S. M.; Sarmiento, J. L.; Slater, R.; Winton, M.

    2016-02-01

    One of the representational aspirations driving current Earth System Model development is to capture the global ocean mesoscale (i.e. ocean weather) in coupled carbon-climate. The present study explores a the role of ocean model resolution (100 km and 10 km) on baseline physical and biogeochemical simulation characteristics and their response to climate change. We find the high resolution model to improve the representation of boundary currents and mesoscale phenomena, and to eliminate fictitious current structures that plague the coarse resolution models. Along with these expected improvements of smaller scales however, we also find a general lack of improvement in many of the large scale biases. With respect to sensitivity, we find the high resolution model to restrict ocean heat uptake towards the surface ocean and to exhibit somewhat less structure at the regional scale than the coarse resolution model. We find similarly more uniform patterns of carbon uptake and biogeochemicel response at high resolution consistent with a greater tendency in the high resolution model to accommodate change in the major current structures, and suggesting that some of the highly regional structure observed among CMIP5 models is due to their inability to represent the role of the mesoscale on the regional scale.

  13. Development of Advanced Eco-hydrologic and Biogeochemical Coupling Model to Re-evaluate Greenhouse Gas Budget of Biosphere

    NASA Astrophysics Data System (ADS)

    Nakayama, T.; Maksyutov, S. S.

    2015-12-01

    Inland waters including rivers, lakes, and groundwater are suggested to act as a transport pathway for water and dissolved substances, and play some role in continental biogeochemical cycling (Cole et al., 2007; Battin et al., 2009). The authors have developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (2014, 2015, etc.), which includes feedback between hydrologic-geomorphic-ecological processes. In this study, NICE was further developed to couple with various biogeochemical cycle models in biosphere, those for water quality in aquatic ecosystems, and those for carbon weathering. The NICE-biogeochemical coupling model incorporates connectivity of the biogeochemical cycle accompanied by hydrologic cycle between surface water and groundwater, hillslopes and river networks, and other intermediate regions. The model also includes reaction between inorganic and organic carbons, and its relation to nitrogen and phosphorus in terrestrial-aquatic continuum. The coupled model showed to improve the accuracy of inundation stress mechanism such as photosynthesis and primary production, which attributes to improvement of CH4 flux in wetland sensitive to fluctuations of shallow groundwater. The model also simulated CO2 evasion from inland water in global scale, and was relatively in good agreement in empirical relation (Aufdenkampe et al., 2011) which has relatively an uncertainty in the calculated flux because of pCO2 data missing in some region and effect of small tributaries, etc. Further, the model evaluated how the expected CO2 evasion might change as inland waters become polluted with nutrients and eutrophication increases from agriculture and urban areas (Pacheco et al., 2013). This advanced eco-hydrologic and biogeochemical coupling model would play important role to re-evaluate greenhouse gas budget of the biosphere, and to bridge gap between top-down and bottom-up approaches (Battin et al., 2009; Regnier et al., 2013).

  14. Accounting for intrapopulation variability in biogeochemical models using agent-based methods.

    PubMed

    Hellweger, Ferdi L; Kianirad, Ehsan

    2007-04-15

    Present biogeochemical models typically use a lumped-system (population-level) modeling (LSM) approach that assumes average properties of a population within a control volume. For modern models that formulate phytoplankton growth as a nonlinear function of the internal nutrient (e.g., Droop kinetics), this averaging assumption can introduce a significant error. Agent-based (individual-based) modeling (ABM) is an alternative approach that does not make the assumption of average properties. This paper presents a new agent-based phytoplankton model called iAlgae. The model is contrasted to a conventional lumped-system model, constructed based on identical underlying sub-models of nutrient uptake (including luxury uptake) and growth (cell quota, Droop model). The two models are validated against laboratory data and applied to a realistic scenario, consisting of a point source nutrient discharge into a river. For the realistic scenario, the ABM-predicted phytoplankton bloom is significantly lower than the LSM-predicted one, which is due to the intrapopulation distribution in cell quotas (due to different life histories of individuals) and nonlinearity of the growth rate model. In the ABM, a fraction of the population accumulates nutrients in excess of their immediate growth requirement (luxury uptake), leaving less for the remainder. Because the model is nonlinear, this results in a suboptimal (from a population perspective) utilization of nutrient and a lower population-level growth rate, compared to the case of no intrapopulation variability assumed by the LSM model. In general, the ABM and LSM approaches can produce significantly different results when incompletely mixed conditions lead to intrapopulation variability in cell properties (i.e., cell quota) and the model equations are nonlinear.

  15. IIASA`s climate-vegetation-biogeochemical cycle module as a part of an integrated model for climate change

    SciTech Connect

    Ganopolski, A.V.; Jonas, M.; Krabec, J.; Olendrzynski, K.; Petoukhov, V.K.; Venevsky, S.V.

    1994-12-31

    The main objective of this study is the development of a hierarchy of coupled climate biosphere models with a full description of the global biogeochemical cycles. These models are planned for use as the core of a set of integrated models of climate change and they will incorporate the main elements of the Earth system (atmosphere, hydrosphere, pedosphere and biosphere) linked with each other (and eventually with the antroposphere) through the fluxes of heat, momentum, water and through the global biogeochemical cycles of carbon and nitrogen. This set of integrated models can be considered to fill the gap between highly simplified integrated models of climate change and very sophisticated and computationally expensive coupled models, developed on the basis of general circulation models (GCMs). It is anticipated that this range of integrated models will be an effective tool for investigating the broad spectrum of problems connected with the coexistence of human society and biosphere.

  16. Exploring a microbial ecosystem approach to modeling deep ocean biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Zakem, E.; Follows, M. J.

    2014-12-01

    Though microbial respiration of organic matter in the deep ocean governs ocean and atmosphere biogeochemistry, it is not represented mechanistically in current global biogeochemical models. We seek approaches that are feasible for a global resolution, yet still reflect the enormous biodiversity of the deep microbial community and its associated metabolic pathways. We present a modeling framework grounded in thermodynamics and redox reaction stoichiometry that represents diverse microbial metabolisms explicitly. We describe a bacterial/archaeal functional type with two parameters: a growth efficiency representing the chemistry underlying a bacterial metabolism, and a rate limitation given by the rate of uptake of each of the necessary substrates for that metabolism. We then apply this approach to answer questions about microbial ecology. As a start, we resolve two dominant heterotrophic respiratory pathways- reduction of oxygen and nitrate- and associated microbial functional types. We combine these into an ecological model and a two-dimensional ocean circulation model to explore the organization, biogeochemistry, and ecology of oxygen minimum zones. Intensified upwelling and lateral transport conspire to produce an oxygen minimum at mid-depth, populated by anaerobic denitrifiers. This modeling approach should ultimately allow for the emergence of bacterial biogeography from competition of metabolisms and for the incorporation of microbial feedbacks to the climate system.

  17. Biogeochemical cycling in an organic-rich coastal marine basin: 11. The sedimentary cycling of dissolved, free amino acids

    SciTech Connect

    Burdige, D.J.; Martens, C.S. )

    1990-11-01

    In the anoxic sediments of Cape Lookout Bight, NC, concentrations of total dissolved free amino acids (TDFAAs) are highest near the sediment-water interface, and decrease to non-zero, asymptotic concentrations at depths greater than 20 cm. TDFAAs in the overlying waters are <1 {mu}M. Dissolved free amino acid (DFAA) profiles often show a secondary subsurface maximum in the region between the 1 and 5 mM sulfate isopleths. This phenomenon appears to be related to the transition in the sediments of this region from sulfate reduction to methanogenesis. A steady-state diagenetic model which quantifies the processes affecting DFAAs in these sediments yields rates of DFAA production and consumption that agree reasonably well with independent estimates of these quantities in Cape Lookout Bight and other anoxic marine sediments. The combined results of modelling pore water DFAA and sedimentary amino acid profiles indicate that significant exchange of amino acids occurs between the sediments and pore waters. These results demonstrate that the biogeochemistry of dissolved free amino acids in the pore waters of Cape Lookout Bight sediments is dominated by internal transformations (i.e. production from sedimentary amino acids, microbial remineralization, and reincorporation back into the sediments). There is some uncertainty in the magnitude of the flux of DFAAs across the sediment-water interface, although it appears to be of secondary importance when compared to the other sedimentary processes affecting DFAAs.

  18. Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume.

    PubMed

    van Breukelen, Boris M; Griffioen, Jasper; Röling, Wilfred F M; van Verseveld, Henk W

    2004-06-01

    The biogeochemical processes governing leachate attenuation inside a landfill leachate plume (Banisveld, the Netherlands) were revealed and quantified using the 1D reactive transport model PHREEQC-2. Biodegradation of dissolved organic carbon (DOC) was simulated assuming first-order oxidation of two DOC fractions with different reactivity, and was coupled to reductive dissolution of iron oxide. The following secondary geochemical processes were required in the model to match observations: kinetic precipitation of calcite and siderite, cation exchange, proton buffering and degassing. Rate constants for DOC oxidation and carbonate mineral precipitation were determined, and other model parameters were optimized using the nonlinear optimization program PEST by means of matching hydrochemical observations closely (pH, DIC, DOC, Na, K, Ca, Mg, NH4, Fe(II), SO4, Cl, CH4, saturation index of calcite and siderite). The modelling demonstrated the relevance and impact of various secondary geochemical processes on leachate plume evolution. Concomitant precipitation of siderite masked the act of iron reduction. Cation exchange resulted in release of Fe(II) from the pristine anaerobic aquifer to the leachate. Degassing, triggered by elevated CO2 pressures caused by carbonate precipitation and proton buffering at the front of the plume, explained the observed downstream decrease in methane concentration. Simulation of the carbon isotope geochemistry independently supported the proposed reaction network.

  19. Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume

    NASA Astrophysics Data System (ADS)

    van Breukelen, Boris M.; Griffioen, Jasper; Röling, Wilfred F. M.; van Verseveld, Henk W.

    2004-06-01

    The biogeochemical processes governing leachate attenuation inside a landfill leachate plume (Banisveld, the Netherlands) were revealed and quantified using the 1D reactive transport model PHREEQC-2. Biodegradation of dissolved organic carbon (DOC) was simulated assuming first-order oxidation of two DOC fractions with different reactivity, and was coupled to reductive dissolution of iron oxide. The following secondary geochemical processes were required in the model to match observations: kinetic precipitation of calcite and siderite, cation exchange, proton buffering and degassing. Rate constants for DOC oxidation and carbonate mineral precipitation were determined, and other model parameters were optimized using the nonlinear optimization program PEST by means of matching hydrochemical observations closely (pH, DIC, DOC, Na, K, Ca, Mg, NH 4, Fe(II), SO 4, Cl, CH 4, saturation index of calcite and siderite). The modelling demonstrated the relevance and impact of various secondary geochemical processes on leachate plume evolution. Concomitant precipitation of siderite masked the act of iron reduction. Cation exchange resulted in release of Fe(II) from the pristine anaerobic aquifer to the leachate. Degassing, triggered by elevated CO 2 pressures caused by carbonate precipitation and proton buffering at the front of the plume, explained the observed downstream decrease in methane concentration. Simulation of the carbon isotope geochemistry independently supported the proposed reaction network.

  20. Rhizosphere Processes Are Quantitatively Important Components of Terrestrial Biogeochemical Cycles: Data & Models

    NASA Astrophysics Data System (ADS)

    Finzi, A.

    2016-12-01

    The rhizosphere is a hot spot and hot moment for biogeochemical cycles. Microbial activity, extracellular enzyme activity and element cycles are greatly enhanced by root derived carbon inputs. As such the rhizosphere may be an important driver of ecosystem responses to global changes such as rising temperatures and atmospheric CO2 concentrations. Empirical research on the rhizosphere is extensive but extrapolation of rhizosphere processes to large spatial and temporal scales is largely uninterrogated. Using a combination of field studies, meta-analysis and numerical models we have found good reason to think that scaling is possible. In this talk I discuss the results of this research and focus on the results of a new modeling effort that explicitly links root distribution and architecture with a model of microbial physiology to assess the extent to which rhizosphere processes may affect ecosystem responses to global change. Results to date suggest that root inputs of C and possibly nutrients (ie, nitrogen) impact the fate of new C inputs to the soil (ie, accumulation or loss) in response to warming and enhanced productivity at elevated CO2. The model also provides qualitative guidance on incorporating the known effects of ectomycorrhizal fungi on decomposition and rates of soil C and N cycling.

  1. Variably Saturated Flow and Multicomponent Biogeochemical Reactive Transport Modeling of a Uranium Bioremediation Field Experiment

    SciTech Connect

    Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.; Murray, Christopher J.; Ward, Anderson L.; Dayvault, Richard; Waichler, Scott R.; Newcomer, Darrell R.; Spane, Frank A.; Long, Philip E.

    2011-11-01

    Field experiments at a former uranium mill tailings site have identified the potential for stimulating indigenous bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. This effectively removes uranium from solution resulting in groundwater concentrations below actionable standards. Three-dimensional, coupled variably-saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport rates and biogeochemical reaction rates that determine the location and magnitude of key reaction products. A comprehensive reaction network, developed largely through previous 1-D modeling studies, was used to simulate the impacts on uranium behavior of pulsed acetate amendment, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. A principal challenge is the mechanistic representation of biologically-mediated terminal electron acceptor process (TEAP) reactions whose products significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. In general, these simulations of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado confirmed previously identified behaviors including (1) initial dominance by iron reducing bacteria that concomitantly reduce aqueous U(VI), (2) sulfate reducing bacteria that become dominant after {approx}30 days and outcompete iron reducers for the acetate electron donor, (3) continuing iron-reducer activity and U(VI) bioreduction during dominantly sulfate reducing conditions, and (4) lower apparent U(VI) removal from groundwater during dominantly sulfate reducing conditions. New knowledge on simultaneously active metal and sulfate reducers has been

  2. Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, S.; Hickman, A. E.; Jahn, O.; Gregg, W. W.; Mouw, C. B.; Follows, M. J.

    2015-07-01

    We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemical-ecosystem component in a dynamic three-dimensional physical framework. The radiative transfer component resolves the penetration of spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (different phytoplankton functional types; detrital particles; and coloured dissolved organic matter, CDOM). The model is evaluated against in situ-observed and satellite-derived products. In particular we compare to concurrently measured biogeochemical, ecosystem, and optical data along a meridional transect of the Atlantic Ocean. The simulation captures the patterns and magnitudes of these data, and estimates surface upwelling irradiance analogous to that observed by ocean colour satellite instruments. We find that incorporating the different optically important constituents explicitly and including spectral irradiance was crucial to capture the variability in the depth of the subsurface chlorophyll a (Chl a) maximum. We conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, as well as the crucial feedbacks between the light field, the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at attenuating light at short wavelengths and in more productive waters, phytoplankton absorption is relatively more important at the subsurface Chl a maximum, and water molecules have the greatest contribution when concentrations of other constituents are low, such as in the oligotrophic gyres. Scattering had less effect on attenuation, but since it is important for the amount and type of upwelling irradiance, it is crucial for setting sea surface reflectance. Strikingly, sensitivity experiments in which absorption by any of the

  3. A cost-efficient biogeochemical model for estuaries: a case-study of a funnel-shaped system

    NASA Astrophysics Data System (ADS)

    Volta, Chiara; Arndt, Sandra; Regnier, Pierre

    2013-04-01

    The hydrodynamics exerts an important influence on the biogeochemical functioning of estuarine systems. Comparative studies have long recognized this tight coupling and, for instance, have attempted to correlate key estuarine biogeochemical processes to simple hydrodynamic properties, such as the residence time or the tidal forcing. Yet, these correlations fail to resolve the estuarine spatio-temporal variability and do not provide powerful means to disentangle the complex interplay of multiple reaction and transport processes. In this context, reaction-transport models (RTMs) are useful tools to resolve the variability inherent to the estuarine environment. They ideally complement field observations, because their integrative power provides the required extrapolation means for a system-scale analysis over the entire spectrum of changing forcing conditions, including the long-term response to land-use and climate changes. However, RTM simulations are associated with high computational costs, especially when the biogeochemical dynamics are to be resolved on a regional or global scale. Furthermore, specific data requirements, such as boundary conditions or bathymetric and geometric information may limit their applicability. Here, a generic one-dimensional RTM approach which relies on idealized geometries to support the estuarine physics is used to quantify the biogeochemical dynamics. The model is cost-efficient and requires only a limited number of readily available input data. The approach is applied to a case-study of a funnel-shaped estuary (The Scheldt, BE/NL) and is tested by comparing integrative measures of the estuarine biogeochemical functioning (e.g. Net Ecosystem Metabolism, integrated CO2 fluxes) with those derived from observations (Frankignoulle et al., 1996, 1998) and highly-resolved model simulations (Vanderborght et al., 2002; Arndt et al., 2009). The method provides a robust quantitative tool to carry sensitivity and uncertainty analyses and to

  4. Impact of urban effluents on summer hypoxia in the highly turbid Gironde Estuary, applying a 3D model coupling hydrodynamics, sediment transport and biogeochemical processes

    NASA Astrophysics Data System (ADS)

    Lajaunie-Salla, Katixa; Wild-Allen, Karen; Sottolichio, Aldo; Thouvenin, Bénédicte; Litrico, Xavier; Abril, Gwenaël

    2017-10-01

    Estuaries are increasingly degraded due to coastal urban development and are prone to hypoxia problems. The macro-tidal Gironde Estuary is characterized by a highly concentrated turbidity maximum zone (TMZ). Field observations show that hypoxia occurs in summer in the TMZ at low river flow and a few days after the spring tide peak. In situ data highlight lower dissolved oxygen (DO) concentrations around the city of Bordeaux, located in the upper estuary. Interactions between multiple factors limit the understanding of the processes controlling the dynamics of hypoxia. A 3D biogeochemical model was developed, coupled with hydrodynamics and a sediment transport model, to assess the contribution of the TMZ and the impact of urban effluents through wastewater treatment plants (WWTPs) and sewage overflows (SOs) on hypoxia. Our model describes the transport of solutes and suspended material and the biogeochemical mechanisms impacting oxygen: primary production, degradation of all organic matter (i.e. including phytoplankton respiration, degradation of river and urban watershed matter), nitrification and gas exchange. The composition and the degradation rates of each variable were characterized by in situ measurements and experimental data from the study area. The DO model was validated against observations in Bordeaux City. The simulated DO concentrations show good agreement with field observations and satisfactorily reproduce the seasonal and neap-spring time scale variations around the city of Bordeaux. Simulations show a spatial and temporal correlation between the formation of summer hypoxia and the location of the TMZ, with minimum DO centered in the vicinity of Bordeaux. To understand the contribution of the urban watershed forcing, different simulations with the presence or absence of urban effluents were compared. Our results show that in summer, a reduction of POC from SO would increase the DO minimum in the vicinity of Bordeaux by 3% of saturation. Omitting

  5. Analyzing Glacial-Interglacial Ocean Biogeochemical States in the MPI-Earth System Model

    NASA Astrophysics Data System (ADS)

    Heinze, M.; Ilyina, T.

    2015-12-01

    There is still little consensus about the mechanisms causing the glacial - interglacial variationsin atmospheric CO2 concentrations of around 100 ppm. Some of those mechanisms aredriven by alterations in ocean biogeochemical cycles. Hence, it is crucial to understand oceanbiogeochemistry dynamics during glacial-interglacial transitions. Within the German nationalclimate modeling initiative PalMod, aiming at simulating a full glacial cycle (135k - today) intransient mode with a state-of-the-art Earth System Model (ESM), we address the oceanbiogeochemistry cycles using a comprehensive modeling approach. In order to set up themodel we start with ocean only simulations, which are based on the 3-D ocean generalcirculation model MPIOM coupled to the ocean biogeochemistry model HAMOCC.Atmospheric forcing data is derived from a fully coupled LGM simulation including theatmosphere general circulation model ECHAM6. This setup provides us a sophisticatedrepresentation of the ocean biogeochemistry during the LGM without using any kind of datarestoring,to be consistent with the biological, chemical and physical dynamics of the model.We analyze alterations in ocean biogeochemistry during the LGM in comparison to a preindustrialcontrol climate. We discuss and quantify the changes in ocean biogeochemicalcycles between these two states, as well as possible implications for carbon transfer due tochanges in ocean dynamics. In the next steps we will use the ocean biogeochemistry model aspart of the fully coupled MPI-ESM. Our results aim at improving the understanding of glacial- interglacial changes in atmospheric CO2, especially in terms of marine carbon sequestrationand release. The presented work contributes to developing comprehensive ESMs, which arecapable of simulating the climate evolution and the variability during the last glacial cycle.

  6. Water Quality Modeling System for Coastal Archipelagos

    NASA Astrophysics Data System (ADS)

    Tuomi, L.; Miettunen, E.; Lukkari, K.; Puttonen, I.; Ropponen, J.; Tikka, K.; Piiparinen, J.; Lignell, R.

    2016-02-01

    Coastal seas are encountering pressures from eutrophication, fishing, ship emissions and coastal construction. Sustainable development and use of these areas require science-based guidance with high quality data and efficient tools. Our study area, the Archipelago Sea, is located in the northern part of the semi-enclosed and brackish water Baltic Sea. It is a shallow, topographically heterogeneous and eutrophic sub-basin, covered with thousands of small islands and islets. The catchment area is 8950 km2and has ca. 500 000 inhabitants. We are developing a modeling system that can be used by local authorities and in ministry level decision making to evaluate the environmental impacts that may result from decisions and changes made both in the watershed and in the coastal areas. The modeling system consists of 3D hydrodynamic model COHERENS and water quality model FICOS, both applied to the area with high spatial resolution. Models use river discharge and nutrient loading data supplied by watershed model VEMALA and include loading from multiple point sources located in the Archipelago Sea. An easy-to-use interface made specifically to answer the end-user needs, includes possibility to modify the nutrient loadings and perform model simulations to selected areas and time periods. To ensure the quality and performance of the modeling system, comprehensive measurement dataset including hydrographic, nutrient, chlorophyll-a and bottom sediment data, was gathered based on monitoring and research campaigns previously carried out in the Archipelago Sea. Verification showed that hydrodynamic model was able to simulate surface temperature and salinity fields and their seasonal variation with good accuracy in this complex area. However, the dynamics of the deeper layers need to be improved, especially in areas that have sharp bathymetric gradients. The preliminary analysis of the water quality model results showed that the model was able to reproduce the basic characteristics of

  7. Hydrodynamics and spatial zonation of the Capo Peloro coastal system (Sicily) through 3-D numerical modeling

    NASA Astrophysics Data System (ADS)

    Ferrarin, Christian; Bergamasco, Alessandro; Umgiesser, Georg; Cucco, Andrea

    2013-05-01

    Since advection and diffusion are the main physical processes that influence the cleaning capacity of coastal transitional waters, the 3-D spatial distribution of the water renewal times was used to delineate a physically-based zonation scheme. The temporal and spatial variations of the hydrodynamics are assessed using a validated three dimensional hydrodynamic finite element model. The developed methodology was applied to the Cape Peloro system, a coastal protected area located in the Messina Strait (Italy) consisting of two connected small brackish basins: the shallow Lake Ganzirri and the deep meromictic Lake Faro. The hydrodynamics of the two coastal lakes shows strong seasonal and spatial variation. The 3-D distribution of the water renewal times suggests a horizontal partition of the Lake Ganzirri into two sub-basins and a vertical zonation of the Lake Faro, with the mixolimnion extending till 10 m depth and the presence of a persistent bottom stagnant layer. The derived physically-based zonation scheme helps in explaining the highly heterogeneous spatial distribution of many biogeochemical variables in the Cape Peloro coastal system.

  8. Nitrogen transfers off Walvis Bay: a 3-D coupled physical/biogeochemical modeling approach in the Namibian upwelling system

    NASA Astrophysics Data System (ADS)

    Gutknecht, E.; Dadou, I.; Marchesiello, P.; Cambon, G.; Le Vu, B.; Sudre, J.; Garçon, V.; Machu, E.; Rixen, T.; Kock, A.; Flohr, A.; Paulmier, A.; Lavik, G.

    2013-06-01

    Eastern boundary upwelling systems (EBUS) are regions of high primary production often associated with oxygen minimum zones (OMZs). They represent key regions for the oceanic nitrogen (N) cycle. By exporting organic matter (OM) and nutrients produced in the coastal region to the open ocean, EBUS can play an important role in sustaining primary production in subtropical gyres. However, losses of fixed inorganic N through denitrification and anammox processes take place in oxygen depleted environments such as EBUS, and can potentially mitigate the role of these regions as a source of N to the open ocean. EBUS can also represent a considerable source of nitrous oxide (N2O) to the atmosphere, affecting the atmospheric budget of N2O. In this paper a 3-D coupled physical/biogeochemical model (ROMS/BioEBUS) is used to investigate the N budget in the Namibian upwelling system. The main processes linked to EBUS and associated OMZs are taken into account. The study focuses on the northern part of the Benguela upwelling system (BUS), especially the Walvis Bay area (between 22° S and 24° S) where the OMZ is well developed. Fluxes of N off the Walvis Bay area are estimated in order to understand and quantify (1) the total N offshore export from the upwelling area, representing a possible N source that sustains primary production in the South Atlantic subtropical gyre; (2) export production and subsequent losses of fixed N via denitrification and anammox under suboxic conditions (O2 < 25 mmol O2 m-3); and (3) the N2O emission to the atmosphere in the upwelling area. In the mixed layer, the total N offshore export is estimated as 8.5 ± 3.9 × 1010 mol N yr-1 at 10° E off the Walvis Bay area, with a mesoscale contribution of 20%. Extrapolated to the whole BUS, the coastal N source for the subtropical gyre corresponds to 0.1 ± 0.04 mol N m-2 yr-1. This N flux represents a major source of N for the gyre compared with other N sources, and contributes 28% of the new primary

  9. A general paradigm to model reaction-based biogeochemical processes in batch systems

    NASA Astrophysics Data System (ADS)

    Fang, Yilin; Yeh, Gour-Tsyh; Burgos, William D.

    2003-04-01

    This paper presents the development and illustration of a numerical model of reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions. The objective is to provide a general paradigm for modeling reactive chemicals in batch systems, with expectations that it is applicable to reactive chemical transport problems. The unique aspects of the paradigm are to simultaneously (1) facilitate the segregation (isolation) of linearly independent kinetic reactions and thus enable the formulation and parameterization of individual rates one reaction by one reaction when linearly dependent kinetic reactions are absent, (2) enable the inclusion of virtually any type of equilibrium expressions and kinetic rates users want to specify, (3) reduce problem stiffness by eliminating all fast reactions from the set of ordinary differential equations governing the evolution of kinetic variables, (4) perform systematic operations to remove redundant fast reactions and irrelevant kinetic reactions, (5) systematically define chemical components and explicitly enforce mass conservation, (6) accomplish automation in decoupling fast reactions from slow reactions, and (7) increase the robustness of numerical integration of the governing equations with species switching schemes. None of the existing models to our knowledge has included these scopes simultaneously. This model (BIOGEOCHEM) is a general computer code to simulate biogeochemical processes in batch systems from a reaction-based mechanistic standpoint, and is designed to be easily coupled with transport models. To make the model applicable to a wide range of problems, programmed reaction types include aqueous complexation, adsorption-desorption, ion-exchange, oxidation-reduction, precipitation-dissolution, acid-base reactions, and microbial mediated reactions. In addition, user-specified reaction types can be programmed into the model. Any reaction can be treated as fast/equilibrium or slow

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

    NASA Astrophysics Data System (ADS)

    Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

    2015-08-01

    SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of 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 model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps 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. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently

  11. Parameter optimization and uncertainty analysis for a biogeochemical model using local and genetic algorithms

    NASA Astrophysics Data System (ADS)

    Slawig, Thomas; Rückelt, Johannes; Sauerland, Volkmar; Srivastav, Anand; Ward, Ben

    2010-05-01

    Methods and results for parameter optimization and uncertainty analysis for a one dimensional marine biogeochemical model of NPZD type developed by Schartau and Oschlies are presented. The model simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column and is driven by ocean data. For the optimization, we use two strategies: At first, a genetic algorithm combined with a local search method. Secondly, a gradient-based quasi-newton SQP method to identify parameters and fit them to given observational data. For the SQP method, we use gradients generated by a source transformation tool for Automatic/Algorithmic Differentiation (AD). The algorithm is designed in a flexible way: The local method is a freely available code that can be replaced by other methods offering the same features, e.g. treatment of box constarints. Both optimization methods are parallized and can be viewed as instances of a hybrid, mixed evolutionary and deterministic optimization algorithm. We compare the performance of both approaches. Moreover, we present an uncertainty analysis of the optimized parameters with respect to Gaussian perturbed observations. Here, an ensemble of perturbed observations is taken as target or desired state for the optimization. After the optimization is applied, the distribution of the optimal parameters shows the dependenc of the parameters with respect to uncertainty in the observations.

  12. Impact of satellite data assimilation in a coupled physical-biogeochemical model of the North Atlantic

    NASA Astrophysics Data System (ADS)

    Berline, L.; Brankart, J.-M.; Brasseur, P.

    The general objective of this work is to examine how the assimilation of data in a circulation model can improve the biological response simulated by a coupled physical-ecosystem model. In this work, the focus will be on the impact of altimetric, SST and SSS data assimilation in an eddy-permitting coupled model of the North Atlantic. The physical model is a z-coordinate, rigid lid, primitive-equation model based on the OPA code [Madec et al, 1998]. The horizontal resolution is 1/3° and there are 43 vertical levels with refinement near the surface. The biogeochemical model is the P3ZD biogeochemical model [Aumont et al., 1998] that describes the cycling of carbon, silica and calcium. The simulations are performed using realistic forcings during 1998. The assimilation method is based on a Kalman filter with reduced order error covariance matrix, known as the SEEK filter [ Pham et al., 1998]. The sequential scheme has been modified recently using the concept of "incremental analysis update" to enforce temporal continuity of the assimilation run. In order to evaluate how the assimilation can improve the representation of the biological fields, comparisons are made between free runs and simulations with assimilation. A first comparison with the assimilation run obtained using the scheme developed by Testut et al. [2003] indicates the excessive supply of nutrients in the euphotic zone through spurious mixing and advection mechanisms. This can be partly attributed to several factors, e.g. the statistical method which is unable to maintain the model constraint of hydrostatic stability, the discontinuous nature of the sequential algorithm, or the lack of consistent corrections between the physical and biological components of the state vector. Several variants of the assimilation algorithm are implemented in order to improve the representation of the model dynamics and its subsequent impact on the biological variables. A comparison between the assimilation runs obtained

  13. Systemic vulnerability model for coastal erosion processes

    NASA Astrophysics Data System (ADS)

    Greco, M.; Martino, G.; Guariglia, A.

    2010-09-01

    Many coastal areas constitute an extraordinary environmental worth and economic value resource continuously exposed to an unceasing transformation due to climatic and anthropic factors. The pressure factor overloads carry out an amplification of environmental degradation and economic rent decrease of these territories producing a disruption of normal and anticipated community growth. This paper copes with coastal erosion problem by a systemic vulnerability model application and environmental indicators approach. Through the definition of an original indicator depending on the observed annual rate of coastal erosion and wave climate parameters, such an approach allow scenario generation and it is useful and powerful planning and management tool. The model has been applied on the test case of Ionian Coast of Basilicata Region located in the southern part of Italy, in the middle of Mediterranean basin. The littoral area is constituted of sandy shores of about 50 km length and 5 river deltas take place. Looking at the shoreline in terms of displacements, a shift of a coastal part is a function of grain size characteristics of the shore sands and of the wave climate. Therefore the selected index taking into account the energy stress affecting the shore area, characterizing the territorial system state and finalized to vulnerability estimation, is defined through the maximum annual erosion,tE, and the surface-wave parameters (H,T) corresponding to the wave-generated bottom orbital velocities higher than critical velocity matches with the bottom incipient transport condition. The resulting coefficient ? (? = tE? ? gH2-?T) is obviously dimensionless and represents the part of the available power in the seas, dissipated by erosion processes. If ? increases, the system integrity decreases and the system vulnerability increases. Available data, in terms of topographic/bathymetric information referred to the period 1873-2008, were utilized to derive tE by the use of a GIS

  14. Net greenhouse gas balance in response to nitrogen enrichment: perspectives from a coupled biogeochemical model.

    PubMed

    Lu, Chaoqun; Tian, Hanqin

    2013-02-01

    Increasing reactive nitrogen (N) input has been recognized as one of the important factors influencing climate system through affecting the uptake and emission of greenhouse gases (GHG). However, the magnitude and spatiotemporal variations of N-induced GHG fluxes at regional and global scales remain far from certain. Here we selected China as an example, and used a coupled biogeochemical model in conjunction with spatially explicit data sets (including climate, atmospheric CO2 , O3 , N deposition, land use, and land cover changes, and N fertilizer application) to simulate the concurrent impacts of increasing atmospheric and fertilized N inputs on balance of three major GHGs (CO2 , CH4 , and N2 O). Our simulations showed that these two N enrichment sources in China decreased global warming potential (GWP) through stimulating CO2 sink and suppressing CH4 emission. However, direct N2 O emission was estimated to offset 39% of N-induced carbon (C) benefit, with a net GWP of three GHGs averaging -376.3 ± 146.4 Tg CO2  eq yr(-1) (the standard deviation is interannual variability of GWP) during 2000-2008. The chemical N fertilizer uses were estimated to increase GWP by 45.6 ± 34.3 Tg CO2  eq yr(-1) in the same period, and C sink was offset by 136%. The largest C sink offset ratio due to increasing N input was found in Southeast and Central mainland of China, where rapid industrial development and intensively managed crop system are located. Although exposed to the rapidly increasing N deposition, most of the natural vegetation covers were still showing decreasing GWP. However, due to extensive overuse of N fertilizer, China's cropland was found to show the least negative GWP, or even positive GWP in recent decade. From both scientific and policy perspectives, it is essential to incorporate multiple GHGs into a coupled biogeochemical framework for fully assessing N impacts on climate changes. © 2012 Blackwell Publishing Ltd.

  15. High Resolution Net Ecosystem Metabolism in a Complex Estuary, Evaluated by Biogeochemical Modeling.

    NASA Astrophysics Data System (ADS)

    Llebot, C.; Spitz, Y. H.; Baptista, A. M.

    2016-02-01

    The net ecosystem metabolism (NEM) has been widely used to assess the metabolism of a body of water, indicating if it is net autotrophic (positive NEM) or net heterotrophic (negative NEM) by calculating the gross primary production minus community respiration in the system. Even though many techniques have been used to calculate NEM, it is extremely challenging in stratified, dynamic systems, especially at highly resolved temporal and spatial scales. Here we present the use of a biogeochemical model for the calculation of NEM in the Columbia River estuary (CRE), a river-dominated estuary located on the West Coast of the United States characterized by very short residence times. The Bioreactor Model developed for this study is an adaptation of the Spitz et al (2001) model to an estuarine ecosystem, and is coupled to the unstructured- grid finite element SELFE circulation model. It simulates two groups of phytoplankton (marine and freshwater), two groups of zooplankton (meso and micro), dissolved inorganic nutrients, oxygen and an explicit microbial loop. A simple benthos is coupled to the water column model. The results reveal that the water column of the CRE is net autotrophic during most of the year, while the respiration is concentrated in the benthos. When taking into account the water column and the benthos together, the CRE alternates temporally and spatially between net autotrophy and net heterotrophy. The hotspots for net heterotrophy are the estuarine turbidity maxima region, and the marine lateral bays, while net autotrophy is associated with freshwater. The river flow and concentration of chlorophyll in the river control the timing and location of the boundaries between net autotrophic and net heterotrophic regions. Overall, integrating over space and time, the CRE is, like most estuaries, a net heterotrophic system.

  16. Land Cover Change Effects on Hydrological and Biogeochemical Functions in the Mekong River Basin: Insights From Macro-Scale Hydrologic and Biogeochemical Models.

    NASA Astrophysics Data System (ADS)

    Costa-Cabral, M. C.; Richey, J. E.; Goteti, G.; Lettenmaier, D. P.; Snidvongs, A.

    2004-12-01

    Concerns with the high rates of deforestation in the tropics include the possible impacts on species diversity, hydrologic response, biogeochemical cycles and water quality, topsoil erosion, atmosphere chemistry, and land surface-atmosphere interactions affecting climate. Our work is concerned with hydrologic response and stream biogeochemistry under the monsoonal climate of Southeast Asia. How are the different components of the terrestrial hydrological cycle affected by changes in land cover, such as conversion of forest to agricultural land? Field observations have confirmed local hydrologic effects; but how do localized changes in land cover affect the streamflow at a distance downstream? How does land cover affect the flow response to rainstorms? How does it affect dry season flows? What are the main implications for stream biogeochemistry? Finally, how might each of these effects turn out under altered climate conditions, such as higher average temperature and modified precipitation patterns? We apply the macro-scale Variable Infiltration Capacity (VIC) model to the Mekong basin (795,000 sq.km) in Southeast Asia at a resolution of 5 arc-minutes (roughly, 9 km), using climate forcing from 1979-2004, long-term stream-flow records, historical land cover, and hypothetical land cover and climate scenarios. We consider not only the replacement of forest cover with permanent agriculture, but also the often prevalent but little studied deforestation for swidden cultivation, succeeded by secondary regrowth. Field studies and a simple model attempt to capture effects on stream biogeochemistry. While soil-vegetation-atmosphere transfer schemes (SVATS) have recently been incorporated into GCMs, use of such models to study the impacts on the hydrologic response of river basins has been limited, particularly in the humid tropics.

  17. Technical Note: A generic law-of-the-minimum flux limiter for simulating substrate limitation in biogeochemical models

    DOE PAGES

    Tang, J. Y.; Riley, W. J.

    2016-02-05

    We present a generic flux limiter to account for mass limitations from an arbitrary number of substrates in a biogeochemical reaction network. The flux limiter is based on the observation that substrate (e.g., nitrogen, phosphorus) limitation in biogeochemical models can be represented as to ensure mass conservative and non-negative numerical solutions to the governing ordinary differential equations. Application of the flux limiter includes two steps: (1) formulation of the biogeochemical processes with a matrix of stoichiometric coefficients and (2) application of Liebig's law of the minimum using the dynamic stoichiometric relationship of the reactants. This approach contrasts with the ad hoc down-regulationmore » approaches that are implemented in many existing models (such as CLM4.5 and the ACME (Accelerated Climate Modeling for Energy) Land Model (ALM)) of carbon and nutrient interactions, which are error prone when adding new processes, even for experienced modelers. Through an example implementation with a CENTURY-like decomposition model that includes carbon, nitrogen, and phosphorus, we show that our approach (1) produced almost identical results to that from the ad hoc down-regulation approaches under non-limiting nutrient conditions, (2) properly resolved the negative solutions under substrate-limited conditions where the simple clipping approach failed, (3) successfully avoided the potential conceptual ambiguities that are implied by those ad hoc down-regulation approaches. We expect our approach will make future biogeochemical models easier to improve and more robust.« less

  18. DRINK: a biogeochemical source term model for low level radioactive waste disposal sites.

    PubMed

    Humphreys, P; McGarry, R; Hoffmann, A; Binks, P

    1997-07-01

    Interactions between element chemistry and the ambient geochemistry play a significant role in the control of radionuclide migration in the geosphere. These same interactions influence radionuclide release from near surface, low level radioactive waste, disposal sites once physical containment has degraded. In situations where LLW contains significant amounts of metal and organic materials such as cellulose, microbial degradation in conjunction with corrosion can significantly perturb the ambient geochemistry. These processes typically produce a transition from oxidising to reducing conditions and can influence radionuclide migration through changes in both the dominant radionuclide species and mineral phases. The DRINK (DRIgg Near field Kinetic) code is a biogeochemical transport code designed to simulate the long term evolution of the UK low level radioactive waste disposal site at Drigg. Drigg is the UK's principal solid low level radioactive waste disposal site and has been receiving waste since 1959. The interaction between microbial activity, the ambient geochemistry and radionuclide chemistry is central to the DRINK approach with the development of the ambient pH, redox potential and bulk geochemistry being directly influenced by microbial activity. This paper describes the microbial aspects of the code, site data underpinning the microbial model, the microbiology/chemistry interface and provides an example of the code in action.

  19. Quantification of terrestrial ecosystem carbon dynamics in the conterminous United States combining a process-based biogeochemical model and MODIS and AmeriFlux data

    USDA-ARS?s Scientific Manuscript database

    Satellite remote sensing provides continuous temporal and spatial information of terrestrial ecosystems. Using these remote sensing data and eddy flux measurements and biogeochemical models, such as the Terrestrial Ecosystem Model (TEM), should provide a more adequate quantification of carbon dynami...

  20. Regional impacts of iron-light colimitation in a global biogeochemical model

    NASA Astrophysics Data System (ADS)

    Galbraith, E. D.; Gnanadesikan, A.; Dunne, J. P.; Hiscock, M. R.

    2009-07-01

    Laboratory and field studies have revealed that iron has multiple roles in phytoplankton physiology, with particular importance for light-harvesting cellular machinery. However, although iron-limitation is explicitly included in numerous biogeochemical/ecosystem models, its implementation varies, and its effect on the efficiency of light harvesting is often ignored. Given the complexity of the ocean environment, it is difficult to predict the consequences of applying different iron limitation schemes. Here we explore the interaction of iron and nutrient cycles using a new, streamlined model of ocean biogeochemistry. Building on previously published parameterizations of photoadaptation and export production, the Biogeochemistry with Light Iron Nutrients and Gasses (BLING) model is constructed with only three explicit tracers but including macronutrient and micronutrient limitation, light limitation, and an implicit treatment of community structure. The structural simplicity of this computationally inexpensive model allows us to clearly isolate the global effects of iron availability on maximum light-saturated photosynthesis rates from those of photosynthetic efficiency. We find that the effect on light-saturated photosynthesis rates is dominant, negating the importance of photosynthetic efficiency in most regions, especially the cold waters of the Southern Ocean. The primary exceptions to this occur in iron-rich regions of the Northern Hemisphere, where high light-saturated photosynthesis rates cause photosynthetic efficiency to play a more important role. Additionally, we speculate that the small phytoplankton dominating iron-limited regions tend to have relatively high photosynthetic efficiency, such that iron-limitation has less of a deleterious effect on growth rates than would be expected from short-term iron addition experiments.

  1. Modeling oxygen depletion forced by acetate discharge in the coastal waters of the North Sea

    NASA Astrophysics Data System (ADS)

    Ilinskaya, Alisa; Yakushev, Evgeny; Nøst, Ole-Anders; Pakhomova, Svetlana

    2017-04-01

    Consequences of discharge of acetate produced during the production of X-ray contrast agents in the coastal waters of the Norwegian coast of the North Sea were analyzed with a set of mathematical models. The baseline seasonal variability of temperature, salinity, advection and turbulence were calculated with the Finite Volume Community Ocean Model (FVCOM) applied to the Southern coast of Norway. These data were used to force a vertical 2-Dimensional Benthic-Pelagic transport model (2DBP) coupled via Framework for Aquatic Biogeochemical Models (FABM) with a biogeochemical model OxyDep, considering phytoplankton, heterotrophs, nutrient, dissolved organic matter, particulate organic matter, and dissolved oxygen (DO). Acetate was considered as a chemical oxygen depletion substrate leading to the decrease of oxygen concentrations. We simulated seasonal variability at a 10 km long vertical transect with a spatial resolution of 50 m horizontally and approximately 2 m vertically. These calculations reproduced local minimum in the vertical DO distributions in 2 km distance from the discharge point, that corresponded to the observations. We conducted numerical experiments on the effects of doubling of the acetate discharge and on formation of acetate complexes.

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

    NASA Astrophysics Data System (ADS)

    Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

    2015-10-01

    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.

  3. Improving the physics of a coupled physical biogeochemical model of the North Atlantic through data assimilation: Impact on the ecosystem

    NASA Astrophysics Data System (ADS)

    Berline, Léo; Brankart, Jean-Michel; Brasseur, Pierre; Ourmières, Yann; Verron, Jacques

    2007-01-01

    Several studies on coupled physical-biogeochemical models have shown that major deficiencies in the biogeochemical fields arise from the deficiencies in the physical flow fields. This paper examines the improvement of the physics through data assimilation, and the subsequent impact on the ecosystem response in a coupled model of the North Atlantic. Sea surface temperature and sea surface height data are assimilated with a sequential method based on the SEEK filter adapted to the coupling needs. The model domain covers the Atlantic from 20°S to 70°N at eddy-permitting resolution. The biogeochemical model is a NPZD-DOM model based on the P3ZD formulation. The results of an annual assimilated simulation are compared with an annual free simulation. With assimilation, the representation of the mixed layer depth is significantly improved in mid latitudes, even though the mixed layer depth is generally overestimated compared to the observations. The representation of the mean and variance of the currents is also significantly improved. The nutrient input in the euphotic zone is used to assess the data assimilation impact on the ecosystem. Data assimilation results in a 50% reduction of the input due to vertical mixing in mid-latitudes, and in a four- to six-fold increase of the advective fluxes in mid-latitudes and subtropics. Averaged zonally, the net impact is a threefold increase for the subtropical gyre, and a moderate (20-30%) decrease at mid and high latitudes. Surface chlorophyll concentration increases along the subtropical gyre borders, but little changes are detected at mid and high latitudes. An increase of the primary production appears along the Gulf Stream path, but it represents only 12% on average for mid and high latitudes. In the subtropical gyre centre, primary production is augmented but stays underestimated (20% of observations). These experiments show the benefits of physical data assimilation in coupled physical-biogeochemical applications.

  4. Glacial-interglacial variability in ocean oxygen and phosphorus in a global biogeochemical model

    NASA Astrophysics Data System (ADS)

    Palastanga, V.; Slomp, C. P.; Heinze, C.

    2012-04-01

    The importance of particulate organic carbon and phosphorus (P) delivered from shelves on open ocean productivity, oxygen, and reactive P burial during glacial times has been assessed using a biogeochemical ocean model of the carbon (C), P and iron cycles. The model shows that in simulations of the Last Glacial Maximum (LGM) without any inputs of terrigenous material from shelves there is a moderate increase in productivity (+5 %) and mean deep water oxygen (+29 %) relative to the preindustrial simulation. However, when the input of terrigenous particulate organic C and P is considered as an additional forcing in the LGM simulation, ocean productivity increases by 46 %, mean deep water oxygen concentration decreases by 20 %, and the global rate of reactive P burial is 3 times over the preindustrial value. The associated pattern of negative oxygen anomalies at 1000 m induces a deepening of the Atlantic and Indian Ocean oxygen minimum (OMZ), while in the Pacific Ocean the OMZ is shifted to the eastern basin north of the Equator relative to preindustrial times. In addition, negative trends in oxygen extend globally below 2000 m depth, though their magnitude is rather weak, and in particular bottom waters remain above suboxic levels. Changes in dust deposition can be responsible for positive trends in reactive P burial as simulated at the LGM in open ocean regions, notably over the Southwest Atlantic and Northwest Pacific; on the other hand, inputs of terrigenous material from shelves cause an increase in P burial over the continental slope and rise regions which accounts for 47 % of the total reactive P burial change. Although the glacial-interglacial trends in P burial in our model compare well with the available observations, this study highlights the need of much more core records of C and P in open ocean settings.

  5. Modeling and water quality assessment during realisation of the coastal projects in Sochi region (Black sea coast of Russia)

    NASA Astrophysics Data System (ADS)

    Prokhoda-Shumskikh, L.

    2012-04-01

    Sochi region is the unique subtropical resort on the Black Sea coast of Russia. Nowadays due to Sochi is the capital of the Olympic game 2014, the government of the Russian Federation accepts the special federal program of Black Sea coast development. Program foresees the existing and creation of new coastal recreational and touristic complexes along the Russian Black Sea coast, such as complex of yacht harbors, water centers (aqua-centers), network of port localities and etc. These coastal projects are different, but the main problems of the environmental impact assessment are the same. The environmental impact and the relative damage should be assessed at the stage of construction as well as at the stage of operation. The key problem for the recreation coastal zone is water quality management. The port localities network as example is considered. To increase the accuracy and informative of forecasts for the coastal zone conditions the system-dynamic model has been developed, what allows to estimate the quality of the sea water, including that in the semi-enclosed coastal water areas with the limited water exchange. The model of water quality in the coastal zone includes the equations of deposit concentration changes and chemical substances evolution in the studied areas. The model incorporates joint description of cycles of two biogenic elements - nitrogen and phosphorus. The system is completely defined by the biogeochemical reactions. The sizes of such water areas allow the applying the full mixing and zero-dimensional models of water quality. The circulation of water inside the area is taken into account additionally. Water exchange in the semi-enclosed coastal water areas is defined by the discharge through the open parts of area border. The novelty of the offered model is its adaptation to the specific conditions of semi-enclosed coastal water areas. At the same time, the model contains details of the biogeochemical processes to complete modelling of the

  6. Robust Modeling of Greenhouse Gas (GHG) Fluxes from Coastal Wetland Ecosystems

    NASA Astrophysics Data System (ADS)

    Abdul-Aziz, O. I.; Ishtiaq, K. S.

    2014-12-01

    Many critical wetland biogeochemical processes are still largely unknown or poorly understood at best. Yet, available models for predicting wetland greenhouse gas (GHG) fluxes (e.g., CO2, CH4, and N2O) are generally mechanistic in nature. This knowledge gap leads to inappropriate process descriptions or over-parameterizations in existing mechanistic models, which often fail to provide accurate and robust predictions across time and space. We developed a systematic data-analytics and informatics method to identify the dominant controls and quantify the relative linkages of wetland GHG fluxes in relation to various hydro-climatic, sea level, biogeochemical and ecological drivers. The method was applied to data collected from 2012-14 through an extensive field campaign from different blue carbon sites of Waquoit Bay, MA. Multivariate pattern recognition techniques of principal component and factor analyses were employed to identify the dominant controls of wetland GHG fluxes; classifying and grouping process variables based on their similarity and interrelation patterns. Power-law based partial least squares regression models were developed to quantify the relative linkages of major GHGs with different process drivers and stressors, as well as to achieve site-specific predictions of GHG fluxes. Wetland biogeochemical similitude and scaling laws were also investigated to unravel emergent patterns and organizing principles of wetland GHG fluxes. The research findings will guide the development of parsimonious empirical to appropriate mechanistic models for spatio-temporally robust predictions of GHGs fluxes and carbon sequestration from coastal wetland ecosystems. The research is part of two current projects funded by the National Oceanic and Atmospheric Administration and the National Science Foundation; focusing on wetland data collections, knowledge formation, formulation of robust GHGs prediction models, and development of ecological engineering tools.

  7. Water, Energy, and Biogeochemical Model (WEBMOD), user’s manual, version 1

    USGS Publications Warehouse

    Webb, Richard M.T.; Parkhurst, David L.

    2017-02-08

    The Water, Energy, and Biogeochemical Model (WEBMOD) uses the framework of the U.S. Geological Survey (USGS) Modular Modeling System to simulate fluxes of water and solutes through watersheds. WEBMOD divides watersheds into model response units (MRU) where fluxes and reactions are simulated for the following eight hillslope reservoir types: canopy; snowpack; ponding on impervious surfaces; O-horizon; two reservoirs in the unsaturated zone, which represent preferential flow and matrix flow; and two reservoirs in the saturated zone, which also represent preferential flow and matrix flow. The reservoir representing ponding on impervious surfaces, currently not functional (2016), will be implemented once the model is applied to urban areas. MRUs discharge to one or more stream reservoirs that flow to the outlet of the watershed. Hydrologic fluxes in the watershed are simulated by modules derived from the USGS Precipitation Runoff Modeling System; the National Weather Service Hydro-17 snow model; and a topography-driven hydrologic model (TOPMODEL). Modifications to the standard TOPMODEL include the addition of heterogeneous vertical infiltration rates; irrigation; lateral and vertical preferential flows through the unsaturated zone; pipe flow draining the saturated zone; gains and losses to regional aquifer systems; and the option to simulate baseflow discharge by using an exponential, parabolic, or linear decrease in transmissivity. PHREEQC, an aqueous geochemical model, is incorporated to simulate chemical reactions as waters evaporate, mix, and react within the various reservoirs of the model. The reactions that can be specified for a reservoir include equilibrium reactions among water; minerals; surfaces; exchangers; and kinetic reactions such as kinetic mineral dissolution or precipitation, biologically mediated reactions, and radioactive decay. WEBMOD also simulates variations in the concentrations of the stable isotopes deuterium and oxygen-18 as a result of

  8. Three-dimensional approach using two coupled models for description of hydrological and biogeochemical processes at the catchment scale

    NASA Astrophysics Data System (ADS)

    Plesca, Ina; Kraft, Philipp; Haas, Edwin; Klatt, Steffen; Butterbach-Bahl, Klaus; Frede, Hans-Georg; Breuer, Lutz

    2014-05-01

    Hydrological and biogeochemical transport through changing landscapes has been well described during the past years in literature. However, the uncertainties of combined water quality and water quantity models are still challenging, both due to a lack in process understanding as well to spatiotemporal heterogeneity of environmental conditions driving the processes. In order to reduce the uncertainty in water quality and runoff predictions at the catchment scale, a variety of different model approaches from empirical-conceptual to fully physical and process based models have been developed. In this study we present a new modelling approach for the investigation of hydrological processes and nutrient cycles, with a focus on nitrogen in a small catchment from Hessen, Germany. A hydrological model based on the model toolbox Catchment Modelling Framework (CMF) has been coupled with the process based biogeochemical model LandscapeDNDC. States, fluxes and parameters are exchanged between the models at high temporal and spatial resolution using the Python scripting language in order to obtain a 3-dimensional model application. The transport of water and nutrients through the catchment is modelled using a 3D Richards/Darcy approach for subsurface fluxes, a kinematic wave approach for surface runoff and a Penman-Monteith based calculation of evapotranspiration. Biogeochemical processes are modelled by Landscape-DNDC, including plant growth and biomass allocation, organic matter mineralisation, nitrification, denitrification and associated nitrous oxide emissions. The interactions and module connectivity between the two coupled models, as well as the model application on a 3.7 km² catchment with the runoff results and nitrogen quantification will be presented in this study.

  9. Development of an advanced eco-hydrologic and biogeochemical coupling model aimed at clarifying the missing role of inland water in the global biogeochemical cycle

    NASA Astrophysics Data System (ADS)

    Nakayama, Tadanobu

    2017-04-01

    Recent research showed that inland water including rivers, lakes, and groundwater may play some role in carbon cycling, although its contribution has remained uncertain due to limited amount of reliable data available. In this study, the author developed an advanced model coupling eco-hydrology and biogeochemical cycle (National Integrated Catchment-based Eco-hydrology (NICE)-BGC). This new model incorporates complex coupling of hydrologic-carbon cycle in terrestrial-aquatic linkages and interplay between inorganic and organic carbon during the whole process of carbon cycling. The model could simulate both horizontal transports (export from land to inland water 2.01 ± 1.98 Pg C/yr and transported to ocean 1.13 ± 0.50 Pg C/yr) and vertical fluxes (degassing 0.79 ± 0.38 Pg C/yr, and sediment storage 0.20 ± 0.09 Pg C/yr) in major rivers in good agreement with previous researches, which was an improved estimate of carbon flux from previous studies. The model results also showed global net land flux simulated by NICE-BGC (-1.05 ± 0.62 Pg C/yr) decreased carbon sink a little in comparison with revised Lund-Potsdam-Jena Wetland Hydrology and Methane (-1.79 ± 0.64 Pg C/yr) and previous materials (-2.8 to -1.4 Pg C/yr). This is attributable to CO2 evasion and lateral carbon transport explicitly included in the model, and the result suggests that most previous researches have generally overestimated the accumulation of terrestrial carbon and underestimated the potential for lateral transport. The results further implied difference between inverse techniques and budget estimates suggested can be explained to some extent by a net source from inland water. NICE-BGC would play an important role in reevaluation of greenhouse gas budget of the biosphere, quantification of hot spots, and bridging the gap between top-down and bottom-up approaches to global carbon budget.

  10. Assessment of the GHG Reduction Potential from Energy Crops Using a Combined LCA and Biogeochemical Process Models: A Review

    PubMed Central

    Jiang, Dong; Hao, Mengmeng; Wang, Qiao; Huang, Yaohuan; Fu, Xinyu

    2014-01-01

    The main purpose for developing biofuel is to reduce GHG (greenhouse gas) emissions, but the comprehensive environmental impact of such fuels is not clear. Life cycle analysis (LCA), as a complete comprehensive analysis method, has been widely used in bioenergy assessment studies. Great efforts have been directed toward establishing an efficient method for comprehensively estimating the greenhouse gas (GHG) emission reduction potential from the large-scale cultivation of energy plants by combining LCA with ecosystem/biogeochemical process models. LCA presents a general framework for evaluating the energy consumption and GHG emission from energy crop planting, yield acquisition, production, product use, and postprocessing. Meanwhile, ecosystem/biogeochemical process models are adopted to simulate the fluxes and storage of energy, water, carbon, and nitrogen in the soil-plant (energy crops) soil continuum. Although clear progress has been made in recent years, some problems still exist in current studies and should be addressed. This paper reviews the state-of-the-art method for estimating GHG emission reduction through developing energy crops and introduces in detail a new approach for assessing GHG emission reduction by combining LCA with biogeochemical process models. The main achievements of this study along with the problems in current studies are described and discussed. PMID:25045736

  11. Assessment of the GHG reduction potential from energy crops using a combined LCA and biogeochemical process models: a review.

    PubMed

    Jiang, Dong; Hao, Mengmeng; Fu, Jingying; Wang, Qiao; Huang, Yaohuan; Fu, Xinyu

    2014-01-01

    The main purpose for developing biofuel is to reduce GHG (greenhouse gas) emissions, but the comprehensive environmental impact of such fuels is not clear. Life cycle analysis (LCA), as a complete comprehensive analysis method, has been widely used in bioenergy assessment studies. Great efforts have been directed toward establishing an efficient method for comprehensively estimating the greenhouse gas (GHG) emission reduction potential from the large-scale cultivation of energy plants by combining LCA with ecosystem/biogeochemical process models. LCA presents a general framework for evaluating the energy consumption and GHG emission from energy crop planting, yield acquisition, production, product use, and postprocessing. Meanwhile, ecosystem/biogeochemical process models are adopted to simulate the fluxes and storage of energy, water, carbon, and nitrogen in the soil-plant (energy crops) soil continuum. Although clear progress has been made in recent years, some problems still exist in current studies and should be addressed. This paper reviews the state-of-the-art method for estimating GHG emission reduction through developing energy crops and introduces in detail a new approach for assessing GHG emission reduction by combining LCA with biogeochemical process models. The main achievements of this study along with the problems in current studies are described and discussed.

  12. High-resolution mineralogical characterization and biogeochemical modeling of uranium reaction pathways at the FRC

    SciTech Connect

    Chen Zhu

    2006-06-15

    High-Resolution Mineralogical Characterization and Biogeochemical Modeling of Uranium Reduction Pathways at the Oak Ridge Field-Research Center (FRC) Chen Zhu, Indiana University, David R. Veblen, Johns Hopkins University We have successfully completed a proof-of-concept, one-year grant on a three-year proposal from the former NABIR program, and here we seek additional two-year funding to complete and publish the research. Using a state-of-the-art 300-kV, atomic resolution, Field Emission Gun Transmission Electron Microscope (TEM), we have successfully identified three categories of mineral hosts for uranium in contaminated soils: (1) iron oxides; (2) mixed manganese-iron oxides; and (3) uranium phosphates. Method development using parallel electron energy loss spectroscopy (EELS) associated with the TEM shows great promise for characterizing the valence states of immobilized U during bioremediation. We have also collected 27 groundwater samples from two push-pull field biostimulation tests, which form two time series from zero to approximately 600 hours. The temporal evolution in major cations, anions, trace elements, and the stable isotopes 34S, 18O in sulfate, 15N in nitrate, and 13C in dissolved inorganic carbon (DIC) clearly show that biostimulation resulted in reduction of nitrate, Mn(IV), Fe(III), U(VI), sulfate, and Tc(VII), and these reduction reactions were intimately coupled with a complex network of inorganic reactions evident from alkalinity, pH, Na, K, Mg, and Ca concentrations. From these temporal trends, apparent zero order rates were regressed. However, our extensive suite of chemical and isotopic data sets, perhaps the first and only comprehensive data set available at the FRC, show that the derived rates from these field biostimulation experiments are composite and lump-sum rates. There were several reactions that were occurring at the same time but were masked by these pseudo-zero order rates. A reaction-path model comprising a total of nine

  13. Using satellite-derived backscattering coefficients in addition to chlorophyll data to constrain a simple marine biogeochemical model

    NASA Astrophysics Data System (ADS)

    Kettle, H.

    2009-08-01

    Biogeochemical models of the ocean carbon cycle are frequently validated by, or tuned to, satellite chlorophyll data. However, ocean carbon cycle models are required to accurately model the movement of carbon, not chlorophyll, and due to the high variability of the carbon to chlorophyll ratio in phytoplankton, chlorophyll is not a robust proxy for carbon. Using inherent optical property (IOP) inversion algorithms it is now possible to also derive the amount of light backscattered by the upper ocean (bb) which is related to the amount of particulate organic carbon (POC) present. Using empirical relationships between POC and bb, a 1-D marine biogeochemical model is used to simulate bb at 490 nm thereby allowing the model to be compared with both remotely-sensed chlorophyll or bb data. Here I investigate the possibility of using bb in conjunction with chlorophyll data to help constrain the parameters in a simple 1-D NPZD model. The parameters of the biogeochemical model are tuned with a genetic algorithm, so that the model is fitted to either chlorophyll data or to both chlorophyll and bb data at three sites in the Atlantic with very different characteristics. Several inherent optical property (IOP) algorithms are available for estimating bb, three of which are used here. The effect of the different bb datasets on the behaviour of the tuned model is examined to ascertain whether the uncertainty in bb is significant. The results show that the addition of bb data does not consistently alter the same model parameters at each site and in fact can lead to some parameters becoming less well constrained, implying there is still much work to be done on the mechanisms relating chlorophyll to POC and bb within the model. However, this study does indicate that including bb data has the potential to significantly effect the modelled mixed layer detritus and that uncertainties in bb due to the different IOP algorithms are not particularly significant.

  14. HYDROBIOGEOCHEM: A coupled model of HYDROlogic transport and mixed BIOGEOCHEMical kinetic/equilibrium reactions in saturated-unsaturated media

    SciTech Connect

    Yeh, G.T.; Salvage, K.M.; Gwo, J.P.; Zachara, J.M.; Szecsody, J.E.

    1998-07-01

    The computer program HYDROBIOGEOCHEM is a coupled model of HYDROlogic transport and BIOGEOCHEMical kinetic and/or equilibrium reactions in saturated/unsaturated media. HYDROBIOGEOCHEM iteratively solves the two-dimensional transport equations and the ordinary differential and algebraic equations of mixed biogeochemical reactions. The transport equations are solved for all aqueous chemical components and kinetically controlled aqueous species. HYDROBIOGEOCHEM is designed for generic application to reactive transport problems affected by both microbiological and geochemical reactions in subsurface media. Input to the program includes the geometry of the system, the spatial distribution of finite elements and nodes, the properties of the media, the potential chemical and microbial reactions, and the initial and boundary conditions. Output includes the spatial distribution of chemical and microbial concentrations as a function of time and space, and the chemical speciation at user-specified nodes.

  15. Use of remotely-sensed observations and a data assimilating marine biogeochemical model to determine water quality on the Great Barrier Reef.

    NASA Astrophysics Data System (ADS)

    Baird, Mark; Jones, Emlyn; Wozniak, Monika; Mongin, Mathieu; Skerratt, Jennifer; Margvelashvilli, Nugzar; Wild-Allen, Karen; Robson, Barbara; Rizwi, Farhan; Schroeder, Thomas; Steven, Andy

    2017-04-01

    The health of the Great Barrier Reef is presently assessed using the water column concentration of chlorophyll and suspended solids, and measured light penetration. Quantifying these water column properties over 2,000 km of often cloud-covered, sparsely sampled, and highly variable coastal waters is problematic. To provide the best estimate of water quality, we assimilating satellite remote-sensing reflectance (the ratio of water-leaving radiance versus water-entering irradiance) using an in-water optical model to produce an equivalent simulated remote-sensing reflectance, and calculate the mis-match between the observed and simulated quantities to constrain a complex biogeochemical model (eReefs) with a Deterministic Ensemble Kalman Filter (DEnKF). We compare the water quality properties of the data assimilating model with in-situ observations, as well as with withheld remote-sensed observations. As a final step, we consider whether withheld observations can be combined with the data-assimilation generated chlorophyll fields to provide the best estimate of the chlorophyll concentration given all the available information.

  16. Decision Support Model for Optimal Management of Coastal Gate

    NASA Astrophysics Data System (ADS)

    Ditthakit, Pakorn; Chittaladakorn, Suwatana

    2010-05-01

    The coastal areas are intensely settled by human beings owing to their fertility of natural resources. However, at present those areas are facing with water scarcity problems: inadequate water and poor water quality as a result of saltwater intrusion and inappropriate land-use management. To solve these problems, several measures have been exploited. The coastal gate construction is a structural measure widely performed in several countries. This manner requires the plan for suitably operating coastal gates. Coastal gate operation is a complicated task and usually concerns with the management of multiple purposes, which are generally conflicted one another. This paper delineates the methodology and used theories for developing decision support modeling for coastal gate operation scheduling. The developed model was based on coupling simulation and optimization model. The weighting optimization technique based on Differential Evolution (DE) was selected herein for solving multiple objective problems. The hydrodynamic and water quality models were repeatedly invoked during searching the optimal gate operations. In addition, two forecasting models:- Auto Regressive model (AR model) and Harmonic Analysis model (HA model) were applied for forecasting water levels and tide levels, respectively. To demonstrate the applicability of the developed model, it was applied to plan the operations for hypothetical system of Pak Phanang coastal gate system, located in Nakhon Si Thammarat province, southern part of Thailand. It was found that the proposed model could satisfyingly assist decision-makers for operating coastal gates under various environmental, ecological and hydraulic conditions.

  17. Regional impacts of iron-light colimitation in a global biogeochemical model

    NASA Astrophysics Data System (ADS)

    Galbraith, E. D.; Gnanadesikan, A.; Dunne, J. P.; Hiscock, M. R.

    2010-03-01

    Laboratory and field studies have revealed that iron has multiple roles in phytoplankton physiology, with particular importance for light-harvesting cellular machinery. However, although iron-limitation is explicitly included in numerous biogeochemical/ecosystem models, its implementation varies, and its effect on the efficiency of light harvesting is often ignored. Given the complexity of the ocean environment, it is difficult to predict the consequences of applying different iron limitation schemes. Here we explore the interaction of iron and nutrient cycles in an ocean general circulation model using a new, streamlined model of ocean biogeochemistry. Building on previously published parameterizations of photoadaptation and export production, the Biogeochemistry with Light Iron Nutrients and Gasses (BLING) model is constructed with only four explicit tracers but including macronutrient and micronutrient limitation, light limitation, and an implicit treatment of community structure. The structural simplicity of this computationally-inexpensive model allows us to clearly isolate the global effect that iron availability has on maximum light-saturated photosynthesis rates vs. the effect iron has on photosynthetic efficiency. We find that the effect on light-saturated photosynthesis rates is dominant, negating the importance of photosynthetic efficiency in most regions, especially the cold waters of the Southern Ocean. The primary exceptions to this occur in iron-rich regions of the Northern Hemisphere, where high light-saturated photosynthesis rates allow photosynthetic efficiency to play a more important role. In other words, the ability to efficiently harvest photons has little effect in regions where light-saturated growth rates are low. Additionally, we speculate that the phytoplankton cells dominating iron-limited regions tend to have relatively high photosynthetic efficiency, due to reduced packaging effects. If this speculation is correct, it would imply that

  18. Modeling Biogeochemical Reactive Transport in Fractured Granites: Implications for the Performance of a Deep Geological Repository

    NASA Astrophysics Data System (ADS)

    Molinero, J.; Samper, J.; Pedersen, K.; Puigdomenech, I.

    2003-12-01

    Several countries around the world are considering deep repositories in fractured granitic formations for the final disposal of high-level radioactive waste. Evaluating the long term safety of such repositories requires sound conceptual and numerical models which are being developed from data and knowledge gained from in situ experiments carried out at deep underground laboratories such as that of Žsp” in Sweden. One of the key aspects for performance assessment concerns to groundwater redox conditions because: (a) the presence of oxygen will affect to the corrosion of canisters, (b) possible production of hydrogen sulphide from sulphate reduction will also have a negative effect on these metallic containers, and (c) several long-lived radionuclides are much more soluble and mobile under oxidizing conditions. Several projects have been performed at Žsp” to investigate different aspects of the groundwater redox evolution. The vast amount of in situ-generated information has been used in this work to set up coupled hydrobiogeochemical models. Numerical models account for saturated groundwater flow, solute transport by advection, dispersion and molecular diffusion, geochemical reactions involving both the liquid and solid phases, and microbially-catallyzed processes. For the Žsp” site, modelling results provide quantitative support for the following conclusions. (A) At the operational phase of the repository, shallow fresh groundwater could reach the depth of the underground facility. Shallow groundwaters loose dissolved oxygen during the infiltration through soil layers and then, respiration of dissolved organic matter is induced along the flow paths through the reduction of Fe(III)-bearing minerals of the fracture zones. Microbial anaerobic respiration of DOC provides additional reducing capacity at the depth of the tunnel. (B) After repository closure, atmospheric oxygen will remain trapped within the tunnel. Abiotic consumption of this oxygen has been

  19. Simulating anchovy's full life cycle in the northern Aegean Sea (eastern Mediterranean): A coupled hydro-biogeochemical-IBM model

    NASA Astrophysics Data System (ADS)

    Politikos, D.; Somarakis, S.; Tsiaras, K. P.; Giannoulaki, M.; Petihakis, G.; Machias, A.; Triantafyllou, G.

    2015-11-01

    A 3-D full life cycle population model for the North Aegean Sea (NAS) anchovy stock is presented. The model is two-way coupled with a hydrodynamic-biogeochemical model (POM-ERSEM). The anchovy life span is divided into seven life stages/age classes. Embryos and early larvae are passive particles, but subsequent stages exhibit active horizontal movements based on specific rules. A bioenergetics model simulates the growth in both the larval and juvenile/adult stages, while the microzooplankton and mesozooplankton fields of the biogeochemical model provide the food for fish consumption. The super-individual approach is adopted for the representation of the anchovy population. A dynamic egg production module, with an energy allocation algorithm, is embedded in the bioenergetics equation and produces eggs based on a new conceptual model for anchovy vitellogenesis. A model simulation for the period 2003-2006 with realistic initial conditions reproduced well the magnitude of population biomass and daily egg production estimated from acoustic and daily egg production method (DEPM) surveys, carried out in the NAS during June 2003-2006. Model simulated adult and egg habitats were also in good agreement with observed spatial distributions of acoustic biomass and egg abundance in June. Sensitivity simulations were performed to investigate the effect of different formulations adopted for key processes, such as reproduction and movement. The effect of the anchovy population on plankton dynamics was also investigated, by comparing simulations adopting a two-way or a one-way coupling of the fish with the biogeochemical model.

  20. Linking ocean biogeochemical cycles and ecosystem structure and function: results of the complex SWAMCO-4 model

    NASA Astrophysics Data System (ADS)

    Pasquer, Bénédicte; Laruelle, Goulven; Becquevort, Sylvie; Schoemann, Véronique; Goosse, Hugues; Lancelot, Christiane

    2005-01-01

    We present results obtained with SWAMCO-4, a complex model of the marine planktonic system calculating C, N, P, Si, Fe cycling within the upper ocean, the export production and the exchange of CO 2 between the ocean and atmosphere. The model, constrained by physical, chemical and biological (grazing, lysis) controls, explicitly details the dynamics of four relevant phytoplankton functional groups with respect to C, N, P, Si, Fe cycling and climate change. Those are diatoms, pico/nano phytoplankton, coccolithophorids, and Phaeocystis spp. whose growth regulation by light, temperature and nutrients has been obtained based on a comprehensive analysis of literature reviews on these taxonomic groups. The performance of SWAMCO-4 is first evaluated in a 1D physical frame throughout its cross application in provinces with contrasted key species dominance, export production, CO 2 air-sea fluxes and where biogeochemical time-series data are available for model initialisation and comparison of results. These are: (i) the ice-free Southern Ocean Time Series station KERFIX (50°40S, 68°E) for the period 1993-1994 (diatom-dominated); (ii) the sea-ice associated Ross Sea domain (Station S; 76°S, 180°W) of the Antarctic Environment and Southern Ocean Process Study AESOPS in 1996-1997 ( Phaeocystis-dominated); and (iii) the North Atlantic Bloom Experiment NABE (60°N, 20°W) in 1991 (coccolithophorids). We then explore and compare the ocean response to increased atmospheric CO 2 by running SWAMCO-4 at the different locations over the last decade. Results show that at all tested latitudes the prescribed increase of atmospheric CO 2 enhances the carbon uptake by the ocean. However, the amplitude of the predicted atmospheric CO 2 sinks displays large regional and interannual variations due to the actual meteorological forcing that drives the local hydrodynamics. This is particularly true in the marginal ice zone of the Ross Sea (AESOPS) where the magnitude of the predicted annual

  1. Decoupling of arsenic and iron release from ferrihydrite suspension under reducing conditions: a biogeochemical model

    PubMed Central

    Burnol, André; Garrido, Francis; Baranger, Philippe; Joulian, Catherine; Dictor, Marie-Christine; Bodénan, Françoise; Morin, Guillaume; Charlet, Laurent

    2007-01-01

    High levels of arsenic in groundwater and drinking water are a major health problem. Although the processes controlling the release of As are still not well known, the reductive dissolution of As-rich Fe oxyhydroxides has so far been a favorite hypothesis. Decoupling between arsenic and iron redox transformations has been experimentally demonstrated, but not quantitatively interpreted. Here, we report on incubation batch experiments run with As(V) sorbed on, or co-precipitated with, 2-line ferrihydrite. The biotic and abiotic processes of As release were investigated by using wet chemistry, X-ray diffraction, X-ray absorption and genomic techniques. The incubation experiments were carried out with a phosphate-rich growth medium and a community of Fe(III)-reducing bacteria under strict anoxic conditions for two months. During the first month, the release of Fe(II) in the aqueous phase amounted to only 3% to 10% of the total initial solid Fe concentration, whilst the total aqueous As remained almost constant after an initial exchange with phosphate ions. During the second month, the aqueous Fe(II) concentration remained constant, or even decreased, whereas the total quantity of As released to the solution accounted for 14% to 45% of the total initial solid As concentration. At the end of the incubation, the aqueous-phase arsenic was present predominately as As(III) whilst X-ray absorption spectroscopy indicated that more than 70% of the solid-phase arsenic was present as As(V). X-ray diffraction revealed vivianite Fe(II)3(PO4)2.8H2O in some of the experiments. A biogeochemical model was then developed to simulate these aqueous- and solid-phase results. The two main conclusions drawn from the model are that (1) As(V) is not reduced during the first incubation month with high Eh values, but rather re-adsorbed onto the ferrihydrite surface, and this state remains until arsenic reduction is energetically more favorable than iron reduction, and (2) the release of As

  2. Decoupling of arsenic and iron release from ferrihydrite suspension under reducing conditions: a biogeochemical model.

    PubMed

    Burnol, André; Garrido, Francis; Baranger, Philippe; Joulian, Catherine; Dictor, Marie-Christine; Bodénan, Françoise; Morin, Guillaume; Charlet, Laurent

    2007-11-29

    High levels of arsenic in groundwater and drinking water are a major health problem. Although the processes controlling the release of As are still not well known, the reductive dissolution of As-rich Fe oxyhydroxides has so far been a favorite hypothesis. Decoupling between arsenic and iron redox transformations has been experimentally demonstrated, but not quantitatively interpreted. Here, we report on incubation batch experiments run with As(V) sorbed on, or co-precipitated with, 2-line ferrihydrite. The biotic and abiotic processes of As release were investigated by using wet chemistry, X-ray diffraction, X-ray absorption and genomic techniques. The incubation experiments were carried out with a phosphate-rich growth medium and a community of Fe(III)-reducing bacteria under strict anoxic conditions for two months. During the first month, the release of Fe(II) in the aqueous phase amounted to only 3% to 10% of the total initial solid Fe concentration, whilst the total aqueous As remained almost constant after an initial exchange with phosphate ions. During the second month, the aqueous Fe(II) concentration remained constant, or even decreased, whereas the total quantity of As released to the solution accounted for 14% to 45% of the total initial solid As concentration. At the end of the incubation, the aqueous-phase arsenic was present predominately as As(III) whilst X-ray absorption spectroscopy indicated that more than 70% of the solid-phase arsenic was present as As(V). X-ray diffraction revealed vivianite Fe(II)3(PO4)2.8H2O in some of the experiments. A biogeochemical model was then developed to simulate these aqueous- and solid-phase results. The two main conclusions drawn from the model are that (1) As(V) is not reduced during the first incubation month with high Eh values, but rather re-adsorbed onto the ferrihydrite surface, and this state remains until arsenic reduction is energetically more favorable than iron reduction, and (2) the release of As

  3. Modeling potential hydrochemical responses to climate change and rising CO2 at the Hubbard Brook Experimental Forest using a dynamic biogeochemical model (PnET-BGC)

    Treesearch

    Afshin Pourmokhtarian; Charles T. Driscoll; John L. Campbell; Katharine. Hayhoe

    2012-01-01

    Dynamic hydrochemical models are useful tools for understanding and predicting the interactive effects of climate change, atmospheric CO2, and atmospheric deposition on the hydrology and water quality of forested watersheds. We used the biogeochemical model, PnET-BGC, to evaluate the effects of potential future changes in temperature,...

  4. A Unified Multi-scale Model for Cross-Scale Evaluation and Integration of Hydrological and Biogeochemical Processes

    NASA Astrophysics Data System (ADS)

    Liu, C.; Yang, X.; Bailey, V. L.; Bond-Lamberty, B. P.; Hinkle, C.

    2013-12-01

    Mathematical representations of hydrological and biogeochemical processes in soil, plant, aquatic, and atmospheric systems vary with scale. Process-rich models are typically used to describe hydrological and biogeochemical processes at the pore and small scales, while empirical, correlation approaches are often used at the watershed and regional scales. A major challenge for multi-scale modeling is that water flow, biogeochemical processes, and reactive transport are described using different physical laws and/or expressions at the different scales. For example, the flow is governed by the Navier-Stokes equations at the pore-scale in soils, by the Darcy law in soil columns and aquifer, and by the Navier-Stokes equations again in open water bodies (ponds, lake, river) and atmosphere surface layer. This research explores whether the physical laws at the different scales and in different physical domains can be unified to form a unified multi-scale model (UMSM) to systematically investigate the cross-scale, cross-domain behavior of fundamental processes at different scales. This presentation will discuss our research on the concept, mathematical equations, and numerical execution of the UMSM. Three-dimensional, multi-scale hydrological processes at the Disney Wilderness Preservation (DWP) site, Florida will be used as an example for demonstrating the application of the UMSM. In this research, the UMSM was used to simulate hydrological processes in rooting zones at the pore and small scales including water migration in soils under saturated and unsaturated conditions, root-induced hydrological redistribution, and role of rooting zone biogeochemical properties (e.g., root exudates and microbial mucilage) on water storage and wetting/draining. The small scale simulation results were used to estimate effective water retention properties in soil columns that were superimposed on the bulk soil water retention properties at the DWP site. The UMSM parameterized from smaller

  5. Project Summary. ANALYTICAL ELEMENT MODELING OF COASTAL AQUIFERS

    EPA Science Inventory

    Four topics were studied concerning the modeling of groundwater flow in coastal aquifers with analytic elements: (1) practical experience was obtained by constructing a groundwater model of the shallow aquifers below the Delmarva Peninsula USA using the commercial program MVAEM; ...

  6. Project Summary. ANALYTICAL ELEMENT MODELING OF COASTAL AQUIFERS

    EPA Science Inventory

    Four topics were studied concerning the modeling of groundwater flow in coastal aquifers with analytic elements: (1) practical experience was obtained by constructing a groundwater model of the shallow aquifers below the Delmarva Peninsula USA using the commercial program MVAEM; ...

  7. A Spatially Explicit Modeling Approach to Capture the Hydrological Effects on Biogeochemical Processes in a Boreal Watershed

    NASA Astrophysics Data System (ADS)

    Govind, A.; Chen, J.

    2009-05-01

    Current estimates of terrestrial carbon (C) fluxes overlook hydrological controls. A modeling study was conducted to explore the hydrological, ecophysiological and biogeochemical interactions in a humid boreal ecosystem. Several hydro-ecological processes were simulated and validated using field measurements for two years. After gaining confidence in the model's ability and having understood that topographically driven sub-surface baseflow is the main process determining the soil moisture regime in humid boreal ecosystem, its influence on ecophysiological and biogeochemical processes were investigated. Three modeling scenarios were designed that represent strategies that are commonly used in ecological models to represent hydrological controls. These scenarios were: 1) Explicit, where realistic lateral water routing was considered; 2) Implicit, where calculations were based on a bucket-modeling approach; and 3) NoFlow, where the lateral sub-surface flow was turned off in the model. In general, the Implicit scenario overestimated GPP, ET and NEP, as opposed to the Explicit scenario. The NoFlow scenario underestimated GPP and ET but overestimated NEP. The key processes controlling the differences were due to the combined effects of variations in plant physiology, photosynthesis, heterotrophic respiration, autotrophic respiration and nitrogen mineralization; all of which occurred simultaneously in different directions, at different rates, affecting the spatio-temporal distribution of terrestrial C-sources or sinks (NEP). The scientific implication of this work is that regional or global scale terrestrial C estimates could have significant errors if proper hydrological constraints are not considered for modeling ecological and biogeochemical processes due to large topographic variations of the Earth's surface and also because of the non-linear interactions between these processes.

  8. A coastal ocean model with subgrid approximation

    NASA Astrophysics Data System (ADS)

    Walters, Roy A.

    2016-06-01

    A wide variety of coastal ocean models exist, each having attributes that reflect specific application areas. The model presented here is based on finite element methods with unstructured grids containing triangular and quadrilateral elements. The model optimizes robustness, accuracy, and efficiency by using semi-implicit methods in time in order to remove the most restrictive stability constraints, by using a semi-Lagrangian advection approximation to remove Courant number constraints, and by solving a wave equation at the discrete level for enhanced efficiency. An added feature is the approximation of the effects of subgrid objects. Here, the Reynolds-averaged Navier-Stokes equations and the incompressibility constraint are volume averaged over one or more computational cells. This procedure gives rise to new terms which must be approximated as a closure problem. A study of tidal power generation is presented as an example of this method. A problem that arises is specifying appropriate thrust and power coefficients for the volume averaged velocity when they are usually referenced to free stream velocity. A new contribution here is the evaluation of three approaches to this problem: an iteration procedure and two mapping formulations. All three sets of results for thrust (form drag) and power are in reasonable agreement.

  9. A Coupled Ocean General Circulation, Biogeochemical, and Radiative Model of the Global Oceans: Seasonal Distributions of Ocean Chlorophyll and Nutrients

    NASA Technical Reports Server (NTRS)

    Gregg, Watson W.; Busalacchi, Antonio (Technical Monitor)

    2000-01-01

    A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability. and the interactions among three functional phytoplankton groups (diatoms. chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (greater than 1000 km) model chlorophyll results are in overall agreement with CZCS pigments in many global regions. Seasonal variability observed in the CZCS is also represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are generally in conformance although occasional departures are apparent. Model nitrate distributions agree with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicates that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent many aspects of the great diversity of physical, biological, chemical, and radiative environments encountered in the global oceans.

  10. Nitrous oxide emissions from cropland: a procedure for calibrating the DayCent biogeochemical model using inverse modelling

    USGS Publications Warehouse

    Rafique, Rashad; Fienen, Michael N.; Parkin, Timothy B.; Anex, Robert P.

    2013-01-01

    DayCent is a biogeochemical model of intermediate complexity widely used to simulate greenhouse gases (GHG), soil organic carbon and nutrients in crop, grassland, forest and savannah ecosystems. Although this model has been applied to a wide range of ecosystems, it is still typically parameterized through a traditional “trial and error” approach and has not been calibrated using statistical inverse modelling (i.e. algorithmic parameter estimation). The aim of this study is to establish and demonstrate a procedure for calibration of DayCent to improve estimation of GHG emissions. We coupled DayCent with the parameter estimation (PEST) software for inverse modelling. The PEST software can be used for calibration through regularized inversion as well as model sensitivity and uncertainty analysis. The DayCent model was analysed and calibrated using N2O flux data collected over 2 years at the Iowa State University Agronomy and Agricultural Engineering Research Farms, Boone, IA. Crop year 2003 data were used for model calibration and 2004 data were used for validation. The optimization of DayCent model parameters using PEST significantly reduced model residuals relative to the default DayCent parameter values. Parameter estimation improved the model performance by reducing the sum of weighted squared residual difference between measured and modelled outputs by up to 67 %. For the calibration period, simulation with the default model parameter values underestimated mean daily N2O flux by 98 %. After parameter estimation, the model underestimated the mean daily fluxes by 35 %. During the validation period, the calibrated model reduced sum of weighted squared residuals by 20 % relative to the default simulation. Sensitivity analysis performed provides important insights into the model structure providing guidance for model improvement.

  11. Modeled Global vs. Coastal Impacts on 1970 and 2005 Summer Daytime Temperature Trends in Coastal California

    NASA Astrophysics Data System (ADS)

    Habtezion, B. L.; Gonzalez, J.; Bornstein, R. D.

    2010-12-01

    California summertime July to August (JJA) mean monthly air temperatures (1970-2005) were analyzed for two California air basins: South Coast (SoCAB) and the San Francisco Bay Area (SFBA), which extended into the Central Valley (CV). Daily Tmin and Tmax values were used to produce average monthly values and spatial distributions of and Tmax values trends for each air basin. Results showed concurrent cooling in coastal areas and warming at further inland areas. This pattern suggests that the regional-warming of inland areas resulted in increased coastal sea breeze activity. Further investigations by use of mesoscale model simulations with the Regional Atmospheric Modeling System (RAMS) meso-met model with a horizontal grid resolution of 4 km on an inner grid over SoCAB were undertaken to investigate the effects of long-term changes due to green house gas (GHG) warming and land-use land-cover changes on coastal flows. Comparison of simulated present (2000-4) and past climate (1970-4) conditions showed significant increases in sea breeze activity and thus coastal cooling, which supports the observational analysis results that coastal cooling is an indirect “reverse reaction” of GHG warming. The magnitude and location of the simulated and observed coastal-cooling region were in good agreement. Urbanization effects on coastal environment were twofold: increased urban mechanical surface roughness retards sea breeze flows, while urban heat islands (UHIs) enhance them. Significant beneficial societal impacts will result from this observed reverse-reaction to global-warming, especially during UHI-growth periods, include decreased maximum: agricultural production, O3 levels, per-capita energy requirements for cooling, and human thermal-stress levels. Similar “reverse-reaction” effects should be found in other mid-latitude western coastal-regions.

  12. Modeling evapotranspiration based on plant hydraulic theory can predict spatial variability across an elevation gradient and link to biogeochemical fluxes

    NASA Astrophysics Data System (ADS)

    Mackay, D. S.; Frank, J.; Reed, D.; Whitehouse, F.; Ewers, B. E.; Pendall, E.; Massman, W. J.; Sperry, J. S.

    2012-04-01

    In woody plant systems transpiration is often the dominant component of total evapotranspiration, and so it is key to understanding water and energy cycles. Moreover, transpiration is tightly coupled to carbon and nutrient fluxes, and so it is also vital to understanding spatial variability of biogeochemical fluxes. However, the spatial variability of transpiration and its links to biogeochemical fluxes, within- and among-ecosystems, has been a challenge to constrain because of complex feedbacks between physical and biological controls. Plant hydraulics provides an emerging theory with the rigor needed to develop testable hypotheses and build useful models for scaling these coupled fluxes from individual plants to regional scales. This theory predicts that vegetative controls over water, energy, carbon, and nutrient fluxes can be determined from the limitation of plant water transport through the soil-xylem-stomata pathway. Limits to plant water transport can be predicted from measurable plant structure and function (e.g., vulnerability to cavitation). We present a next-generation coupled transpiration-biogeochemistry model based on this emerging theory. The model, TREEScav, is capable of predicting transpiration, along with carbon and nutrient flows, constrained by plant structure and function. The model incorporates tightly coupled mechanisms of the demand and supply of water through the soil-xylem-stomata system, with the feedbacks to photosynthesis and utilizable carbohydrates. The model is evaluated by testing it against transpiration and carbon flux data along an elevation gradient of woody plants comprising sagebrush steppe, mid-elevation lodgepole pine forests, and subalpine spruce/fir forests in the Rocky Mountains. The model accurately predicts transpiration and carbon fluxes as measured from gas exchange, sap flux, and eddy covariance towers. The results of this work demonstrate that credible spatial predictions of transpiration and related

  13. Quantifying the Variability of CH4 Emissions from Pan-Arctic Lakes with Lake Biogeochemical and Landscape Evolution Models

    NASA Astrophysics Data System (ADS)

    Tan, Z.; Zhuang, Q.

    2014-12-01

    Recent studies in the arctic and subarctic show that CH4 emissions from pan-arctic lakes are playing much more significant roles in the regional carbon cycling than previously estimated. Permafrost thawing due to pronounced warming at northern high latitudes affects lake morphology, changing its CH4 emissions. Thermokarst can enlarge the extent of artic lakes, exposing stable ancient carbon buried in the permafrost zone for degradation and changing a previously known carbon sink to a large carbon source. In some areas, the thawing of subarctic discontinuous and isolated permafrost can diminish thermokarst lakes. To date, few models have considered these important hydrological and biogeochemical processes to provide adequate estimation of CH4 emissions from these lakes. To fill this gap, we have developed a process-based climate-sensitive lake biogeochemical model and a landscape evolution model, which have been applied to quantify the state and variability of CH4 emissions from this freshwater system. Site-level experiments show the models are capable to capture the spatial and temporal variability of CH4 emissions from lakes across Siberia and Alaska. With the lake biogeochemical model solely, we estimate that the magnitude of CH4 emissions from lakes is 13.2 Tg yr-1 in the north of 60 ºN at present, which is on the same order of CH4 emissions from northern high-latitude wetlands. The maximum increment is 11.8 Tg CH4 yr-1 by the end of the 21st century when the worst warming scenario is assumed. We expect the landscape evolution model will improve the existing estimates.

  14. Modelling of transport and biogeochemical processes in pollution plumes: Vejen landfill, Denmark

    NASA Astrophysics Data System (ADS)

    Brun, Adam; Engesgaard, Peter; Christensen, Thomas H.; Rosbjerg, Dan

    2002-01-01

    A biogeochemical transport code is used to simulate leachate attenuation, biogeochemical processes, and development of redox zones in a pollution plume downstream of the Vejen landfill in Denmark. Calibration of the degradation parameters resulted in a good agreement with the observed distribution in the plume of a number of species, such as dissolved organic carbon (DOC), Fe 2+, NO 3-, HCO 3-, SO 42-, CH 4, and pH. The simulated redox zones agree with observations confirming that the Fe-reducing zone played an important role in the attenuation of the DOC plume. Effective first-order rate constants for every redox zone were determined giving DOC half-lives ranging from 100 to 1-2 days going from the methanogenic to the aerobic zone. The order of decrease in DOC half-lives from the anaerobic to the aerobic zone corresponds to findings at other landfills.

  15. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

    PubMed

    Ebrahimi, Ali; Or, Dani

    2016-09-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

  16. Modeling the long-term and transient evolution of biogeochemical and isotopic signatures in coal tar-contaminated aquifers

    NASA Astrophysics Data System (ADS)

    D'Affonseca, Fernando Mazo; Prommer, Henning; Finkel, Michael; Blum, Philipp; Grathwohl, Peter

    2011-05-01

    Reactive transport modeling is a critical element in assessing the potential of natural attenuation of groundwater pollutants. In the present study, we developed a comprehensive quantitative model that incorporates the key processes affecting the long-term fate of complex organic compound mixtures released from coal tar-type dense nonaqueous phase liquid sources. The model framework addresses the simulation of the long-term dynamics of source zone depletion, the fate of the released compounds during reactive transport in the groundwater, the evolution of the aquifer's biogeochemical response, in particular its redox conditions, and the redox-dependent carbon isotope fractionation of selected organic compounds. The modeling framework was applied for the interpretation of observed biogeochemical and isotopic data from a well-characterized coal tar-contaminated site in northern Germany. The simulations highlight the diversity of fates of the individual compounds, which result from their widely varying physicochemical characteristics, and also how complex interactions develop over the lifetime of the contamination. The highly transient release of contaminants from the coal tar as pool and as heterogeneously distributed blobs in the source zone triggers continuously changing biogeochemical conditions and isotope signatures. The modeling results illustrate how difficult and uncertain the assessment of contaminant fate can be if the collected data cover only a small time window relative to the transport time scale. This emphasizes the need for a holistic understanding of the governing processes that control the effectiveness of monitored natural attenuation before it is implemented as a passive remediation strategy at nonaqueous phase liquid-contaminated sites.

  17. Relaxation Biodynamics: Experimental Studies and Modeling of Biogeochemical Processes in Northern Terrestrial Ecosystems

    NASA Astrophysics Data System (ADS)

    Panikov, N. S.; Pankratov, T.

    2001-12-01

    Relaxation phenomenon in physics and chemistry stands for delay between the application of an external stress to a system and its response. When an equilibrated nuclear, atomic or molecular system is subjected to an abrupt physical change (sudden rise in temperature or pressure), it takes time for the system to re-equilibrate under the new conditions. This period (relaxation time) can provide a powerful insight into mechanisms of chemical reaction. Our intention is to extend such approach to analysis of the complex biological phenomena related mainly to microbial growth and activity in the soil. We will show how this information can be used for better understanding the biogeochemical processes in northern terrestrial ecosystems such as aerobic and anaerobic decomposition of organic matter, gas (CO2 and CH4) emission to atmosphere, migration and transformation of biogenic elements, etc. The major source of experimental data is laboratory soil incubation under controlled environmental conditions with abrupt changes in one of the key parameters: temperature (including the water-to-ice phase transition), soil moisture, light (illumination of planted soil), supply of organic substrate and mineral nutrients. The state of biological component before and after abrupt changes was followed by continuous recording of gas (CO2, CH4) exchange rate and (in some special experiments), chemical analysis of the soil solution, and the characterization of soil community (microbial and plants biomass, species composition, change of life forms, etc.) The obtained dynamic data were fit to simulation models (sets of differential equations) describing the C- and energy flow through the studied microcosm systems. The comparison of predicted and observed relaxation dynamics allowed us to discard wrong assumptions on the nature of regulatory mechanisms involved in the functioning of the soil community. Finally, the conclusions derived from the lab experiments are projected to field

  18. Modeling the Impact of Biogeochemical Hotspots and Hot Moments on Subsurface Carbon Fluxes from a Flood Plain Site

    NASA Astrophysics Data System (ADS)

    Arora, B.; Spycher, N.; Steefel, C. I.; King, E.; Conrad, M. E.

    2015-12-01

    Biogeochemical hotspots and hot moments are known to account for a high percentage of carbon and nutrient cycling within flood plain environments. To quantify the impact of these hotspots and hot moments on the carbon cycle, a 2D reactive transport model was developed for the saturated-unsaturated zone of a flood plain site in Rifle, CO. Previous studies have identified naturally reduced zones (NRZs) in the saturated zone of the Rifle site to be hotspots and important regions for subsurface biogeochemical cycling. Wavelet analysis of geochemical concentrations at the site suggested that hydrologic and temperature variations are hot moments and exert an important control on biogeochemical conditions in the Rifle aquifer. Here, we describe the development of a reactive transport model that couples hydrologic and biogeochemical processes to microbial functional distributions inferred from site-specific 'omic' data. The model includes microbial contributions from heterotrophic and chemolithoautotrophic processes. We use Monod based formulations to represent biomass formation and consider energy partitioning between catabolic and anabolic processes. We use this model to explore community emergence at the Rifle site and further constrain the extent and rates of nutrient uptake as well as abiotic and biotic reactions using stable carbon isotopes. Results from 2D model simulations with only abiotic reactions predict lower CO2 partial pressures in the unsaturated zone and severely underpredict (~200%) carbon fluxes to the river compared to simulations with chemolithoautotrophic pathways. δ13C-CO2 profiles also point to biotic sources for the locally observed high CO2 concentrations above NRZs. Results further indicate that groundwater carbon fluxes from the Rifle site to the river are underestimated by almost 180% (to 3.3 g m-2 d-1) when temperature fluctuations are ignored in the simulations. Preliminary results demonstrate the emergence of denitrifiers at specific depths

  19. Coastal Ecosystem Integrated Compartment Model (ICM): Modeling Framework

    NASA Astrophysics Data System (ADS)

    Meselhe, E. A.; White, E. D.; Reed, D.

    2015-12-01

    The Integrated Compartment Model (ICM) was developed as part of the 2017 Coastal Master Plan modeling effort. It is a comprehensive and numerical hydrodynamic model coupled to various geophysical process models. Simplifying assumptions related to some of the flow dynamics are applied to increase the computational efficiency of the model. The model can be used to provide insights about coastal ecosystems and evaluate restoration strategies. It builds on existing tools where possible and incorporates newly developed tools where necessary. It can perform decadal simulations (~ 50 years) across the entire Louisiana coast. It includes several improvements over the approach used to support the 2012 Master Plan, such as: additional processes in the hydrology, vegetation, wetland and barrier island morphology subroutines, increased spatial resolution, and integration of previously disparate models into a single modeling framework. The ICM includes habitat suitability indices (HSIs) to predict broad spatial patterns of habitat change, and it provides an additional integration to a dynamic fish and shellfish community model which quantitatively predicts potential changes in important fishery resources. It can be used to estimate the individual and cumulative effects of restoration and protection projects on the landscape, including a general estimate of water levels associated with flooding. The ICM is also used to examine possible impacts of climate change and future environmental scenarios (e.g. precipitation, Eustatic sea level rise, subsidence, tropical storms, etc.) on the landscape and on the effectiveness of restoration projects. The ICM code is publically accessible, and coastal restoration and protection groups interested in planning-level modeling are encouraged to explore its utility as a computationally efficient tool to examine ecosystem response to future physical or ecological changes, including the implementation of restoration and protection strategies.

  20. Biogeochemical Properties of Eddies in the California Current System

    NASA Astrophysics Data System (ADS)

    Chenillat, Fanny; Franks, Peter J. S.; Combes, Vincent

    2016-04-01

    The California Current System (CCS) is a coastal upwelling system characterized by intense mesoscale activity. This mesoscale activity plays a critical role in modulating biological production and exporting coastal biogeochemical materials offshore. To characterize and quantify the ability of mesoscale eddies to affect local and regional planktonic ecosystems in the CCS, we analyzed a 10-year-long physical-biological model simulation - with 5km horizontal resolution - using eddy detection and tracking to isolate the dynamics in cyclonic and anticyclonic eddies. At any given time, ~8% of the model domain was covered by eddies, and this small area belies ~50% of the cross-shelf biological transport. As they propagate westward across the shelf, cyclonic eddies efficiently transport coastal planktonic organisms, and maintain locally elevated production, Anticyclones, on the other hand, have a limited impact on local production.

  1. Hydrodynamic modeling of Singapore's coastal waters: Nesting and model accuracy

    NASA Astrophysics Data System (ADS)

    Hasan, G. M. Jahid; van Maren, Dirk Sebastiaan; Ooi, Seng Keat

    2016-01-01

    The tidal variation in Singapore's coastal waters is influenced by large-scale, complex tidal dynamics (by interaction of the Indian Ocean and the South China Sea) as well as monsoon-driven low frequency variations, requiring a model with large spatial coverage. Close to the shores, the complex topography, influenced by headlands and small islands, requires a high resolution model to simulate tidal dynamics. This can be achieved through direct nesting or multi-scale nesting, involving multiple model grids. In this paper, we investigate the effect of grid resolution and multi-scale nesting on the tidal dynamics in Singapore's coastal waters, by comparing model results with observations using different statistical techniques. The results reveal that the intermediate-scale model is generally sufficiently accurate (equal to or better than the most refined model), but also that the most refined model is only more accurate when nested in the intermediate scale model (requiring multi-scale nesting). This latter is the result of the complex tidal dynamics around Singapore, where the dominantly diurnal tidal currents are decoupled from the semi-diurnal water level variations. Furthermore, different techniques to quantify model accuracy (harmonic analysis, basic statistics and more complex statistics) are inconsistent in determining which model is more accurate.

  2. Integrating 'omic' data and biogeochemical modeling: the key to understanding the microbial regulation of matter cycling in soil

    NASA Astrophysics Data System (ADS)

    Pagel, Holger; Kandeler, Ellen; Seifert, Jana; Camarinha-Silva, Amélia; Kügler, Philipp; Rennert, Thilo; Poll, Christian; Streck, Thilo

    2016-04-01

    Matter cycling in soils and associated soil functions are intrinsically controlled by microbial dynamics. It is therefore crucial to consider functional traits of microorganisms in biogeochemical models. Tremendous advances in 'omic' methods provide a plethora of data on physiology, metabolic capabilities and ecological life strategies of microorganisms in soil. Combined with isotopic techniques, biochemical pathways and transformations can be identified and quantified. Such data have been, however, rarely used to improve the mechanistic representation of microbial dynamics in soil organic matter models. It is the goal of the Young Investigator Group SoilReg to address this challenge. Our general approach is to tightly integrate experiments and biochemical modeling. NextGen sequencing will be applied to identify key functional groups. Active microbial groups will be quantified by measurements of functional genes and by stable isotope probing methods of DNA and proteins. Based on this information a biogeochemical model that couples a mechanistic representation of microbial dynamics with physicochemical processes will be set up and calibrated. Sensitivity and stability analyses of the model as well as scenario simulations will reveal the importance of intrinsic and extrinsic controls of organic matter turnover. We will demonstrate our concept and present first results of two case studies on pesticide degradation and methane oxidation.

  3. Coastal Storm Modeling System (CoSMoS)

    USGS Publications Warehouse

    Barnard, Patrick; Erikson, Li; Foxgrover, Amy; Herdman, Liv; Limber, Patrick W.; O'Neill, Andrea; Vitousek, Sean

    2015-01-01

    The Coastal Storm Modeling System (CoSMoS) makes detailed predictions (meter-scale) over large geographic scales (100s of kilometers) of storm-induced coastal flooding and erosion for both current and future SLR scenarios, as well as long-term shoreline change and cliff retreat. CoSMoS v3.0 for Southern California shows projections for future climate scenarios (sea-level rise and storms) to provide emergency responders and coastal planners with critical storm-hazards information that can be used to increase public safety, mitigate physical damages, and more effectively manage and allocate resources within complex coastal settings. Phase I data for Southern California includes 100-year storm flood hazard information for the coast from the Mexican Border to Pt. Conception. Flood projection data in the initial November release is limited to coastal areas within Los Angeles, San Diego, and Orange counties.

  4. Environmental Drivers of Biogeochemical Variability in the Southern Ross Sea: Results from a 1D Modeling Study

    NASA Astrophysics Data System (ADS)

    Kaufman, D. E.; Friedrichs, M. A.; Smith, W.; Hofmann, E. E.; Hemmings, J. C. P.

    2016-02-01

    Ross Sea phytoplankton, generally dominated by diatoms and Phaeocystis antarctica, play an essential biogeochemical role in this highly biologically productive Southern Ocean region. Although associations between these phytoplankton and environmental factors such as temperature, vertical mixing, and irradiance have been documented, the causal mechanisms among these interactions and extent to which they are modified by altered climatic conditions are poorly understood. To investigate these relationships, data from a 2012 glider deployment are analyzed in conjunction with model experiments performed using a modified version of the multi-component Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification (MEDUSA) run within the Marine Model Optimization Testbed (MarMOT), a one-dimensional data assimilative analysis framework. Specifically, MEDUSA has been adapted for the Ross Sea by including both solitary and colonial forms of P. antarctica and irradiance-Fe interactions. After evaluating model performance with glider observations of chlorophyll and particulate organic carbon, scenario experiments are conducted investigating how the magnitude and phenology of spring and summer phytoplankton are likely to be modified by a future altered climate. In particular, the relative impacts of potential increased water temperatures on phytoplankton productivity will be assessed, through differences in biological rates, increased iron and light availability from melting ice, and increased stratification. Variability in phytoplankton productivity resulting from these effects of warming temperatures are analyzed individually and in combination to evaluate the relative importance of these drivers of change in the biogeochemical environment of the Ross Sea.

  5. Robbing Peter to Pay Paul: Modeling the Dynamic Evolution of the Coastal Carbon Sink Across Multiple Landforms

    NASA Astrophysics Data System (ADS)

    Herbert, E. R.; Walters, D.; Windham-Myers, L.; Kirwan, M. L.

    2016-12-01

    Evaluating the strength and long-term stability of the coastal carbon sink requires a consideration of the spatial evolution of coastal landscapes in both the horizontal and vertical dimensions. We present a model of the transformation and burial of carbon along a bay-marsh-upland forest complex to explore the response of the coastal carbon sink to sea level rise (SLR) and anthropogenic activity. We establish a carbon mass-balance by coupling dynamic biogeochemically-based models of soil carbon burial in aquatic, intertidal, and upland environments with a physically-based model of marsh edge erosion, vertical growth and migration into adjacent uplands. The modeled increase in marsh vertical growth and carbon burial at moderate rates of sea level rise (3-10 mm/yr) is consistent with a synthesis of 219 field measurements of marsh carbon accumulation that show a significant (p<0.0001) positive correlation with local SLR rates. The model suggests that at moderate SLR rates in low topographic relief landscapes, net marsh expansion into upland forest concomitant with increased carbon burial rates are sufficient to mitigate the associated loss of forest carbon stocks. Coastlines with high relief or barriers to wetland migration can become sources of carbon through the erosion of buried carbon stocks, but we show that the recapture of eroded carbon through vertical growth can be an important mechanism for reducing carbon loss. Overall, we show that the coastal carbon balance must be evaluated in a landscape context to account for changes in the size and magnitude of both the stocks and sinks of marsh carbon and for the transfers of carbon between coastal habitats. These results may help inform current efforts to appraise coastal carbon sinks that are beset by issues of landscape heterogeneity and the provenance of buried carbon.

  6. Evaluating Approaches to a Coupled Model for Arctic Coastal Erosion, Infrastructure Risk, and Associated Coastal Hazards

    NASA Astrophysics Data System (ADS)

    Frederick, J. M.; Bull, D. L.; Jones, C.; Roberts, J.; Thomas, M. A.

    2016-12-01

    Arctic coastlines are receding at accelerated rates, putting existing and future activities in the developing coastal Arctic environment at extreme risk. For example, at Oliktok Long Range Radar Site, erosion that was not expected until 2040 was reached as of 2014 (Alaska Public Media). As the Arctic Ocean becomes increasingly ice-free, rates of coastal erosion will likely continue to increase as (a) increased ice-free waters generate larger waves, (b) sea levels rise, and (c) coastal permafrost soils warm and lose strength/cohesion. Due to the complex and rapidly varying nature of the Arctic region, little is known about the increasing waves, changing circulation, permafrost soil degradation, and the response of the coastline to changes in these combined conditions. However, as scientific focus has been shifting towards the polar regions, Arctic science is rapidly advancing, increasing our understanding of complex Arctic processes. Our present understanding allows us to begin to develop and evaluate the coupled models necessary for the prediction of coastal erosion in support of Arctic risk assessments. What are the best steps towards the development of a coupled model for Arctic coastal erosion? This work focuses on our current understanding of Arctic conditions and identifying the tools and methods required to develop an integrated framework capable of accurately predicting Arctic coastline erosion and assessing coastal risk and hazards. We will present a summary of the state-of-the-science, and identify existing tools and methods required to develop an integrated diagnostic and monitoring framework capable of accurately predicting and assessing Arctic coastline erosion, infrastructure risk, and coastal hazards. The summary will describe the key coastal processes to simulate, appropriate models to use, effective methods to couple existing models, and identify gaps in knowledge that require further attention to make progress in our understanding of Arctic coastal

  7. Our evolving conceptual model of the coastal eutrophication problem

    USGS Publications Warehouse

    Cloern, James E.

    2001-01-01

    A primary focus of coastal science during the past 3 decades has been the question: How does anthropogenic nutrient enrichment cause change in the structure or function of nearshore coastal ecosystems? This theme of environmental science is recent, so our conceptual model of the coastal eutrophication problem continues to change rapidly. In this review, I suggest that the early (Phase I) conceptual model was strongly influenced by limnologists, who began intense study of lake eutrophication by the 1960s. The Phase I model emphasized changing nutrient input as a signal, and responses to that signal as increased phytoplankton biomass and primary production, decomposition of phytoplankton-derived organic matter, and enhanced depletion of oxygen from bottom waters. Coastal research in recent decades has identified key differences in the responses of lakes and coastal-estuarine ecosystems to nutrient enrichment. The contemporary (Phase II) conceptual model reflects those differences and includes explicit recognition of (1) system-specific attributes that act as a filter to modulate the responses to enrichment (leading to large differences among estuarine-coastal systems in their sensitivity to nutrient enrichment); and (2) a complex suite of direct and indirect responses including linked changes in: water transparency, distribution of vascular plants and biomass of macroalgae, sediment biogeochemistry and nutrient cycling, nutrient ratios and their regulation of phytoplankton community composition, frequency of toxic/harmful algal blooms, habitat quality for metazoans, reproduction/growth/survival of pelagic and benthic invertebrates, and subtle changes such as shifts in the seasonality of ecosystem functions. Each aspect of the Phase II model is illustrated here with examples from coastal ecosystems around the world. In the last section of this review I present one vision of the next (Phase III) stage in the evolution of our conceptual model, organized around 5

  8. Integration of the DAYCENT Biogeochemical Model within a Multi-Model Framework

    SciTech Connect

    David Muth

    2012-07-01

    Agricultural residues are the largest near term source of cellulosic 13 biomass for bioenergy production, but removing agricultural residues sustainably 14 requires considering the critical roles that residues play in the agronomic system. 15 Determining sustainable removal rates for agricultural residues has received 16 significant attention and integrated modeling strategies have been built to evaluate 17 sustainable removal rates considering soil erosion and organic matter constraints. 18 However the current integrated model does not quantitatively assess soil carbon 19 and long term crop yields impacts of residue removal. Furthermore the current 20 integrated model does not evaluate the greenhouse gas impacts of residue 21 removal, specifically N2O and CO2 gas fluxes from the soil surface. The DAYCENT 22 model simulates several important processes for determining agroecosystem 23 performance. These processes include daily Nitrogen-gas flux, daily carbon dioxide 24 flux from soil respiration, soil organic carbon and nitrogen, net primary productivity, 25 and daily water and nitrate leaching. Each of these processes is an indicator of 26 sustainability when evaluating emerging cellulosic biomass production systems for 27 bioenergy. A potentially vulnerable cellulosic biomass resource is agricultural 28 residues. This paper presents the integration of the DAYCENT model with the 29 existing integration framework modeling tool to investigate additional environment 30 impacts of agricultural residue removal. The integrated model is extended to 31 facilitate two-way coupling between DAYCENT and the existing framework. The 32 extended integrated model is applied to investigate additional environmental 33 impacts from a recent sustainable agricultural residue removal dataset. The 34 integrated model with DAYCENT finds some differences in sustainable removal 35 rates compared to previous results for a case study county in Iowa. The extended 36 integrated model with

  9. Net primary productivity estimates and environmental variables in the Arctic Ocean: An assessment of coupled physical-biogeochemical models

    NASA Astrophysics Data System (ADS)

    Lee, Younjoo J.; Matrai, Patricia A.; Friedrichs, Marjorie A. M.; Saba, Vincent S.; Aumont, Olivier; Babin, Marcel; Buitenhuis, Erik T.; Chevallier, Matthieu; de Mora, Lee; Dessert, Morgane; Dunne, John P.; Ellingsen, Ingrid H.; Feldman, Doron; Frouin, Robert; Gehlen, Marion; Gorgues, Thomas; Ilyina, Tatiana; Jin, Meibing; John, Jasmin G.; Lawrence, Jon; Manizza, Manfredi; Menkes, Christophe E.; Perruche, Coralie; Le Fouest, Vincent; Popova, Ekaterina E.; Romanou, Anastasia; Samuelsen, Annette; Schwinger, Jörg; Séférian, Roland; Stock, Charles A.; Tjiputra, Jerry; Tremblay, L. Bruno; Ueyoshi, Kyozo; Vichi, Marcello; Yool, Andrew; Zhang, Jinlun

    2016-12-01

    The relative skill of 21 regional and global biogeochemical models was assessed in terms of how well the models reproduced observed net primary productivity (NPP) and environmental variables such as nitrate concentration (NO3), mixed layer depth (MLD), euphotic layer depth (Zeu), and sea ice concentration, by comparing results against a newly updated, quality-controlled in situ NPP database for the Arctic Ocean (1959-2011). The models broadly captured the spatial features of integrated NPP (iNPP) on a pan-Arctic scale. Most models underestimated iNPP by varying degrees in spite of overestimating surface NO3, MLD, and Zeu throughout the regions. Among the models, iNPP exhibited little difference over sea ice condition (ice-free versus ice-influenced) and bottom depth (shelf versus deep ocean). The models performed relatively well for the most recent decade and toward the end of Arctic summer. In the Barents and Greenland Seas, regional model skill of surface NO3 was best associated with how well MLD was reproduced. Regionally, iNPP was relatively well simulated in the Beaufort Sea and the central Arctic Basin, where in situ NPP is low and nutrients are mostly depleted. Models performed less well at simulating iNPP in the Greenland and Chukchi Seas, despite the higher model skill in MLD and sea ice concentration, respectively. iNPP model skill was constrained by different factors in different Arctic Ocean regions. Our study suggests that better parameterization of biological and ecological microbial rates (phytoplankton growth and zooplankton grazing) are needed for improved Arctic Ocean biogeochemical modeling.

  10. Arsenic in New Jersey Coastal Plain streams, sediments, and shallow groundwater: effects from different geologic sources and anthropogenic inputs on biogeochemical and physical mobilization processes

    USGS Publications Warehouse

    Barringer, Julia L.; Reilly, Pamela A.; Eberl, Dennis D.; Mumford, Adam C.; Benzel, William M.; Szabo, Zoltan; Shourds, Jennifer L.; Young, Lily Y.

    2013-01-01

    With a history of agriculture in the New Jersey Coastal Plain, anthropogenic inputs of As, such as residues from former pesticide applications in soils, can amplify any geogenic As in runoff. Such inputs contribute to an increased total As load to a stream at high stages of flow. As a result of yet another anthropogenic influence, microbes that reduce and mobilize As beneath the streambeds are stimulated by inputs of dissolved organic carbon (DOC). Although DOC is naturally occurring, anthropogenic contributions from wastewater inputs may deliver increased levels of DOC to subsurface soils and ultimately groundwater. Arsenic concentrations may increase with the increases in pH of groundwater and stream water in developed areas receiving wastewater inputs, as As mobilization caused by pH-controlled sorption and desorption reactions are likely to occur in waters of neutral or alkaline pH (for example, Nimick and others, 1998; Barringer and others, 2007b). Because of the difference in As content of the geologic materials in the two sub-provinces of the Coastal Plain, the amount of As that is mobile in groundwater and stream water is, potentially, substantially greater in the Inner Coastal Plain than in the Outer Coastal Plain. In turn, streams within the Inner and Outer Coastal Plain can receive substantially more As in groundwater discharge from developed areas than from environments where DOC appears to be of natural origin.

  11. Modeling greenhouse gas emissions and nutrient transport in managed arable soils with a fully coupled hydrology-biogeochemical modeling system

    NASA Astrophysics Data System (ADS)

    Haas, Edwin; Klatt, Steffen; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    evapotranspiration is based on Penman-Monteith. Biogeochemical processes are modelled by LandscapeDNDC, including soil microclimate, plant growth and biomass allocation, organic matter mineralisation, nitrification, denitrification, chemodenitrification and methanogenesis producing and consuming soil based greenhouse gases. The model application will present first results of the coupled model to simulate soil based greenhouse gas emissions as well as nitrate discharge from the Yanting catchment. The model application will also present the effects of different management practices (fertilization rates and timings, tilling, residues management) on the redistribution of N surplus within the catchment causing biomass productivity gradients and different levels of indirect N2O emissions along topographical gradients.

  12. Seasonal Distributions of Global Ocean Chlorophyll and Nutrients: Analysis with a Coupled Ocean General Circulation Biogeochemical, and Radiative Model

    NASA Technical Reports Server (NTRS)

    Gregg, Watson W.

    1999-01-01

    A coupled general ocean circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. The model is driven by climatological meteorological conditions, cloud cover, and sea surface temperature. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability, and the interactions among three functional phytoplankton groups (diatoms, chorophytes, and picoplankton) and three nutrient groups (nitrate, ammonium, and silicate). Phytoplankton groups are initialized as homogeneous fields horizontally and vertically, and allowed to distribute themselves according to the prevailing conditions. Basin-scale model chlorophyll results are in very good agreement with CZCS pigments in virtually every global region. Seasonal variability observed in the CZCS is also well represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are also in good conformance, although occasional departures are apparent. Agreement of nitrate distributions with in situ data is even better, including seasonal dynamics, except for the equatorial Atlantic. The good agreement of the model with satellite and in situ data sources indicates that the model dynamics realistically simulate phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization, and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent the great diversity of physical, biological

  13. A model of biogeochemical cycles of carbon, nitrogen and phosphorus including symbiotic nitrogen fixation and phosphatase production.

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Houlton, B.; Field, C. B.

    2006-12-01

    Global climate models have not yet considered the effects of nutrient cycles and limitation when forecasting carbon uptake by the terrestrial biosphere into the future. Using the principle of resource optimization, we here develop a new theory by which C, N and P cycles interact. Our model is able to replicate the observed responses of net primary production to nutrient additions in N-limited, N and P co-limited, and P-limited environments. Our framework identifies a new pathway by which N2 fixers can alter P availability: by investing in N-rich phosphorus liberation enzymes (phosphatases), fixers can greatly accelerate soil P availability and its cycling rates. This is critical for the successive invasion and establishment of N2 fixers into an N limited environment. We conclude that our model can be used to examine nutrient limitation broadly, and thus offers promise for coupling the biogeochemical system of C, N, and P to broader climate-system models.

  14. Establishing a National Coastal Change Model for Scotland

    NASA Astrophysics Data System (ADS)

    Fitton, James; Hansom, Jim; Rennie, Alistair

    2015-04-01

    The Climate Change (Scotland) Act 2009 requires the development of an Adaptation Programme to take forward the risks identified within the UK's Climate Change Risk Assessment (UK-CCRA). The UK-CCRA anticipates increases in sea level, coastal erosion and coastal flooding to increasingly affect Scotland's soft coastlines and the assets found on these coasts. Shoreline Management Plans have been produced for only short sections of the Scottish coast which limits the information available to coastal managers. Consequently a National Coastal Change Assessment (NCCA) has been commissioned by the Scottish Government and is supported by a number of agencies. The assessment aims to create a shared evidence base to support more sustainable coastal and terrestrial planning decisions in the light of a changing climate. The NCCA aims to establish historic coastal change by extracting the georectified coastline position from OS 2nd Edition Country Series maps (1892-1905) and to then compare it to both the 1970's and current coastal position (updated by LiDAR datasets where available) in order to estimate past erosion/accretion rates. Using the historic coastal change rates the coastline position can then be projected into the future, albeit mediated by a Coastal Erosion Susceptibility Model (CESM) whose function is to limit erosion to areas where the hinterland is susceptible to erosion. The CESM is a national GIS assessment at 50 m raster resolution which models the physical susceptibility of the coast. The model uses a range of data (elevation, rockhead elevation, proximity to the coast, wave exposure, sediment accretion, and coastal defences) which are ranked and amalgamated into a single raster dataset reflecting erosion susceptibility. Using the erosion rates combined with a number of socioeconomic datasets, key assets at risk from future coastal erosion can be identified. The NCCA aims to inform existing strategic planning (Shoreline Management Plans, Flood Risk Management

  15. Simulation of glacial ocean biogeochemical tracer and isotope distributions based on the PMIP3 suite of climate models

    NASA Astrophysics Data System (ADS)

    Khatiwala, Samar; Muglia, Juan; Kvale, Karin; Schmittner, Andreas

    2016-04-01

    In the present climate system, buoyancy forced convection at high-latitudes together with internal mixing results in a vigorous overturning circulation whose major component is North Atlantic Deep Water. One of the key questions of climate science is whether this "mode" of circulation persisted during glacial periods, and in particular at the Last Glacial Maximum (LGM; 21000 years before present). Resolving this question is both important for advancing our understanding of the climate system, as well as a critical test of numerical models' ability to reliably simulate different climates. The observational evidence, based on interpreting geochemical tracers archived in sediments, is conflicting, as are simulations carried out with state-of-the-art climate models (e.g., as part of the PMIP3 suite), which, due to the computational cost involved, do not by and large include biogeochemical and isotope tracers that can be directly compared with proxy data. Here, we apply geochemical observations to evaluate the ability of several realisations of an ocean model driven by atmospheric forcing from the PMIP3 suite of climate models to simulate global ocean circulation during the LGM. This results in a wide range of circulation states that are then used to simulate biogeochemical tracer and isotope (13C, 14C and Pa/Th) distributions using an efficient, "offline" computational scheme known as the transport matrix method (TMM). One of the key advantages of this approach is the use of a uniform set of biogeochemical and isotope parameterizations across all the different circulations based on the PMIP3 models. We compare these simulated distributions to both modern observations and data from LGM ocean sediments to identify similarities and discrepancies between model and data. We find, for example, that when the ocean model is forced with wind stress from the PMIP3 models the radiocarbon age of the deep ocean is systematically younger compared with reconstructions. Changes in

  16. Sea Level Rise National Coastal Property Model

    EPA Science Inventory

    The impact of sea level rise on coastal properties depends critically on the human response to the threat, which in turn depends on several factors, including the immediacy of the risk, the magnitude of property value at risk, options for adapting to the threat and the cost of th...

  17. Sea Level Rise National Coastal Property Model

    EPA Science Inventory

    The impact of sea level rise on coastal properties depends critically on the human response to the threat, which in turn depends on several factors, including the immediacy of the risk, the magnitude of property value at risk, options for adapting to the threat and the cost of th...

  18. Simulation of annual biogeochemical cycles of nutrient balance, phytoplankton bloom(s), and DO in Puget Sound using an unstructured grid model

    SciTech Connect

    Khangaonkar, Tarang; Sackmann, Brandon; Long, Wen; Mohamedali, Teizeen; Roberts, Mindy

    2012-08-14

    Nutrient pollution from rivers, nonpoint source runoff, and nearly 100 wastewater discharges is a potential threat to the ecological health of Puget Sound with evidence of hypoxia in some basins. However, the relative contributions of loads entering Puget Sound from natural and anthropogenic sources, and the effects of exchange flow from the Pacific Ocean are not well understood. Development of a quantitative model of Puget Sound is thus presented to help improve our understanding of the annual biogeochemical cycles in this system using the unstructured grid Finite-Volume Coastal Ocean Model framework and the Integrated Compartment Model (CE-QUAL-ICM) water quality kinetics. Results based on 2006 data show that phytoplankton growth and die-off, succession between two species of algae, nutrient dynamics, and dissolved oxygen in Puget Sound are strongly tied to seasonal variation of temperature, solar radiation, and the annual exchange and flushing induced by upwelled Pacific Ocean waters. Concentrations in the mixed outflow surface layer occupying approximately 5–20 m of the upper water column show strong effects of eutrophication from natural and anthropogenic sources, spring and summer algae blooms, accompanied by depleted nutrients but high dissolved oxygen levels. The bottom layer reflects dissolved oxygen and nutrient concentrations of upwelled Pacific Ocean water modulated by mixing with biologically active surface outflow in the Strait of Juan de Fuca prior to entering Puget Sound over the Admiralty Inlet. The effect of reflux mixing at the Admiralty Inlet sill resulting in lower nutrient and higher dissolved oxygen levels in bottom waters of Puget Sound than the incoming upwelled Pacific Ocean water is reproduced. Finally, by late winter, with the reduction in algal activity, water column constituents of interest, were renewed and the system appeared to reset with cooler temperature, higher nutrient, and higher dissolved oxygen waters from the Pacific

  19. Simulation of annual biogeochemical cycles of nutrient balance, phytoplankton bloom(s), and DO in Puget Sound using an unstructured grid model

    NASA Astrophysics Data System (ADS)

    Khangaonkar, Tarang; Sackmann, Brandon; Long, Wen; Mohamedali, Teizeen; Roberts, Mindy

    2012-09-01

    Nutrient pollution from rivers, nonpoint source runoff, and nearly 100 wastewater discharges is a potential threat to the ecological health of Puget Sound with evidence of hypoxia in some basins. However, the relative contributions of loads entering Puget Sound from natural and anthropogenic sources, and the effects of exchange flow from the Pacific Ocean are not well understood. Development of a quantitative model of Puget Sound is thus presented to help improve our understanding of the annual biogeochemical cycles in this system using the unstructured grid Finite-Volume Coastal Ocean Model framework and the Integrated Compartment Model (CE-QUAL-ICM) water quality kinetics. Results based on 2006 data show that phytoplankton growth and die-off, succession between two species of algae, nutrient dynamics, and dissolved oxygen in Puget Sound are strongly tied to seasonal variation of temperature, solar radiation, and the annual exchange and flushing induced by upwelled Pacific Ocean waters. Concentrations in the mixed outflow surface layer occupying approximately 5-20 m of the upper water column show strong effects of eutrophication from natural and anthropogenic sources, spring and summer algae blooms, accompanied by depleted nutrients but high dissolved oxygen levels. The bottom layer reflects dissolved oxygen and nutrient concentrations of upwelled Pacific Ocean water modulated by mixing with biologically active surface outflow in the Strait of Juan de Fuca prior to entering Puget Sound over the Admiralty Inlet. The effect of reflux mixing at the Admiralty Inlet sill resulting in lower nutrient and higher dissolved oxygen levels in bottom waters of Puget Sound than the incoming upwelled Pacific Ocean water is reproduced. By late winter, with the reduction in algal activity, water column constituents of interest, were renewed and the system appeared to reset with cooler temperature, higher nutrient, and higher dissolved oxygen waters from the Pacific Ocean.

  20. Useless arithmetic or useful scientific tools? Evaluation of the current state and future perspectives of aquatic biogeochemical modeling

    NASA Astrophysics Data System (ADS)

    Arhonditsis, G.

    2009-04-01

    What is the capacity of the current models to simulate the dynamics of environmental systems? How carefully do modelers develop their models? Which model features primarily determine our decision to utilize a specific model? How rigorously do we assess what a model can or cannot predict? The first part of my presentation is to answer some of these questions by reviewing the state of aquatic biogeochemical modeling; a research tool that has been extensively used for understanding and quantitatively describing aquatic ecosystems. Mechanistic aquatic biogeochemical models have form the scientific basis for environmental management decisions by providing a predictive link between management actions and ecosystem response; they have provided an important tool for elucidating the interactions between climate variability and plankton communities, and thus for addressing questions regarding the pace and impacts of climate change. The sizable number of aquatic ecosystem modeling studies which successfully passed the scrutiny of the peer-review process along with the experience gained from addressing a breadth of management problems can objectively reveal the systematic biases, methodological inconsistencies, and common misconceptions characterizing the modeling practice in environmental science. My arguments are that (i) models are not always developed in a consistent manner, clearly stated purpose, and predetermined acceptable model performance level, (ii) the potential "customers" select models without properly assessing their technical value, and (iii) oceanic modeling is a dynamic area of the current modeling practice whereas, model application for addressing environmental management issues on a local scale faces challenges as a scientific tool. The second part of my presentation argues that (i) the development of novel methods for rigorously assessing the uncertainty underlying model predictions should be a top priority of the modeling community, and (ii) the model

  1. Multidecadal simulation of coastal fog with a regional climate model

    NASA Astrophysics Data System (ADS)

    O'Brien, Travis A.; Sloan, Lisa C.; Chuang, Patrick Y.; Faloona, Ian C.; Johnstone, James A.

    2013-06-01

    In order to model stratocumulus clouds and coastal fog, we have coupled the University of Washington boundary layer model to the regional climate model, RegCM (RegCM-UW). By comparing fog occurrences observed at various coastal airports in the western United States, we show that RegCM-UW has success at modeling the spatial and temporal (diurnal, seasonal, and interannual) climatology of northern California coastal fog. The quality of the modeled fog estimate depends on whether coast-adjacent ocean or land grid cells are used; for the model runs shown here, the oceanic grid cells seem to be most appropriate. The interannual variability of oceanic northern California summertime fog, from a multi-decadal simulation, has a high and statistically significant correlation with the observed interannual variability ( r = 0.72), which indicates that RegCM-UW is capable of investigating the response of fog to long-term climatological forcing. While RegCM-UW has a number of aspects that would benefit from further investigation and development, RegCM-UW is a new tool for investigating the climatology of coastal fog and the physical processes that govern it. We expect that with appropriate physical parameterizations and moderate horizontal resolution, other climate models should be capable of simulating coastal fog. The source code for RegCM-UW is publicly available, under the GNU license, through the International Centre for Theoretical Physics.

  2. A mass-conserving advection scheme for offline simulation of scalar transport in coastal ocean models

    NASA Astrophysics Data System (ADS)

    Gillibrand, P. A.; Herzfeld, M.

    2016-05-01

    We present a flux-form semi-Lagrangian (FFSL) advection scheme designed for offline scalar transport simulation with coastal ocean models using curvilinear horizontal coordinates. The scheme conserves mass, overcoming problems of mass conservation typically experienced with offline transport models, and permits long time steps (relative to the Courant number) to be used by the offline model. These attributes make the method attractive for offline simulation of tracers in biogeochemical or sediment transport models using archived flow fields from hydrodynamic models. We describe the FFSL scheme, and test it on two idealised domains and one real domain, the Great Barrier Reef in Australia. For comparison, we also include simulations using a traditional semi-Lagrangian advection scheme for the offline simulations. We compare tracer distributions predicted by the offline FFSL transport scheme with those predicted by the original hydrodynamic model, assess the conservation of mass in all cases and contrast the computational efficiency of the schemes. We find that the FFSL scheme produced very good agreement with the distributions of tracer predicted by the hydrodynamic model, and conserved mass with an error of a fraction of one percent. In terms of computational speed, the FFSL scheme was comparable with the semi-Lagrangian method and an order of magnitude faster than the full hydrodynamic model, even when the latter ran in parallel on multiple cores. The FFSL scheme presented here therefore offers a viable mass-conserving and computationally-efficient alternative to traditional semi-Lagrangian schemes for offline scalar transport simulation in coastal models.

  3. Coastal mapping and modelling of Tuktoyaktuk Harbour, Western Arctic, Canada

    NASA Astrophysics Data System (ADS)

    Manson, G. K.

    2015-12-01

    Climate models suggest that sea ice in the Arctic is expected to decrease and that the frequency of storms bringing high waves and storm surges is expected to increase. Reduced sea ice, higher waves, and higher storm surge water levels have implications for coastal infrastructure, nearshore sediment transport, and rates of coastal change. Tuktoyaktuk is an important shipping terminal servicing the petroleum industry and Inuvialuit communities in the western Canadian Arctic. The hydrodynamic model Delft3D is used to model sediment transport in Tuktoyaktuk Harbour and the approaches. For nearshore applications, Delft3D works best with a seamless coastal digital elevation model (DEM). A DEM was constructed from a variety of sources. Terrestrial LiDAR (Light Detection And Ranging) uses an infrared laser to construct a detailed elevation model of the terrestrial coastal zone. Multibeam bathymetry uses arrays of acoustic signals to collect detailed of the subaqueous coastal zone. Bathymetry data, and charts from the Canadian Hydrographic Service supplement the offshore bathymetry. The shoreline is derived from CanCoast, a nationally consistent geospatial database of Canada's marine coasts. The Coastal Information System (CIS) supplements CanCoast and describes coastal geomorphology in local areas. With these data, Delft3D delivered wave, current, and sediment transport data in a common reference frame. When compared to measurements, the model successfully simulates waves and currents. Output from Delft3D was mapped into a Geographic Information System, and combined with other data to help an Arctic community and industries adapt to potential climate-related hazards .

  4. Terrestrial Particulate Organic Matter Degradation in Estuarine and Coastal Areas: Coupling Lipid Tracers and Molecular Tools to Better Understand Deltaic Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Galeron, M. A.; Volkman, J. K.; Rontani, J. F.; Radakovitch, O.; Charriere, B.; Amiraux, R.

    2016-02-01

    Deltaic and coastal areas have been studied extensively worldwide, due to their high economic and ecosystemic value. It was long thought that terrestrial particulate organic matter (TPOM) degraded during river transport was refractory to further degradation upon its arrival at sea. But studies on coastal sediments and in the Mackenzie delta (Canada) showed that, on the contrary, TPOM was undergoing intense degradation upon reaching seawater. In order to generalize these results to worldwide river basins, we propose to trace degradation processes impacting TPOM during in-stream transport as well as coastal distribution. We selected the Rhône River (France) for its differences with the Mackenzie River (latitude, temperature, coastal salinity) and carefully researched lipid tracers to help us pinpoint both the origin of the POM and the degradative processes undergone. Betulin, α-/β-amyrins, dehydroabietic acid, sitosterol and their specific degradation products were selected. While the Rhône delta has been studied for decades, there is very little research on its in-stream processes, and how they can be linked with coastal cycles and fluxes. Coupling new specific lipid tracers especially selected for the monitoring of higher plant degradation and molecular biology tools, we were able to better trace the origin of TPOM transported along the Rhône River, as well as better understand its degradation state in the river, the delta, and upon its arrival at sea. We show here that autoxidation (free radical induced oxidation), long overlooked, is a major degradation process impacting TPOM transported along the Rhone River, and is even more intense upon the arrival of TPOM at sea. Salinity, metal ion desorption, bacterial and biochemical activity are amongst the factors studied as inducers of such an intense degradation. This understanding is crucial if we want a truly extensive knowledge of terrestrial particulate organic matter transport and deposition, as well as

  5. Upwelling and coastal current biases in climate models

    NASA Astrophysics Data System (ADS)

    Chang, P.; Small, J.

    2016-12-01

    The upwelling regions at the eastern edges of the world's subtropical oceans exhibit pronounced SST biases in leading global coupled climate models. Reducing the SST and upwelling biases is important to climate variability and predictability, as well as projections of how coastal ecosystems respond to changing climate, including fishery and other impacts. In the southeastern tropical Atlantic, the wind-stress curl associated with the Benguela atmospheric low-level coastal jet (LLCJ) plays a major role in determining the coastal circulation and the spatial distribution of SST. Realistic representation of the detailed structure of the Benguela LLCJ, including both the double core structure and coastal wind drop-off, is critical to reducing the coastal ocean bias in the southeastern tropical Atlantic and is highly dependent on model resolution. In recent experiments with coupled models, it is found that increasing atmospheric model resolution substantially improves the LLCJ core structure, whilst in order to get a realistic upwelling system, a high-resolution ocean model is also required. Further, coupled feedbacks between SST and wind and cloud are important. Hence, attempting to derive parameterizations to reduce the bias remains a significant challenge in low or standard resolution climate models, as it involves deficiencies in the atmosphere and ocean, and estimation of the feedbacks. However, on the bright side, there is substantial theoretical, numerical, and observational work that can be brought to address the problem. The presentation will hopefully motivate discussion of parameterizations in the light of this work.

  6. Modeling the primary and secondary productions of the southern Benguela upwelling system: A comparative study through two biogeochemical models

    NASA Astrophysics Data System (ADS)

    Koné, V.; Machu, E.; Penven, P.; Andersen, V.; GarçOn, V.; FréOn, P.; Demarcq, H.

    2005-12-01

    A three-dimensional primitive equation model, the Regional Ocean Modeling Systems (ROMS), coupled to two biogeochemical configurations (NPZD and N2P2Z2D2) was used to study the dynamics of the first trophic levels of the pelagic food web in the southern Benguela upwelling system. The domain extends from the Agulhas Bank bordered by the Agulhas Current to 27°S on the west coast of South Africa. The circulation is driven by monthly climatologies of atmospheric forcing fields. The NPZD ecosystem model consists of four state variables: nutrient (nitrate), phytoplankton, zooplankton and detritus. In the N2P2Z2D2 model, ammonium has been added and the three other variables have been divided into small and large organisms or detritus. Both models are able to reproduce the spatio-temporal phytoplankton distribution. Along the west coast, chlorophyll concentrations maxima are associated to surface waters. Westward dominating winds generate the lowest chlorophyll concentrations encountered in winter. The small phytoplankton organisms simulated by the N2P2Z2D2 model are responsible for a weaker chlorophyll inshore/offshore gradient, in closer agreement with observations. Transitions from a regime dominated by new production (high f ratio) to one dominated by regenerated production (low f ratio) happen to be abrupt, underlying the constant competition between small and large organisms with regard to upwelling induced nutrient inputs. On the Agulhas Bank, the summer enrichment is associated with subsurface maxima, while in winter, mixing by storms results in a homogeneous phytoplankton distribution in the water column. Regenerated production plays an important role in maintaining the total phytoplankton growth. Zooplankton biomass reflects the overall patterns of chlorophyll a concentrations with differences between the west coast and the Agulhas Bank, consistent with data, and its distribution exhibits a clear seasonal contrast. The seasonality of small and large zooplankton

  7. Comparison of alternative spatial resolutions in the application of a spatially distributed biogeochemical model over complex terrain

    USGS Publications Warehouse

    Turner, D.P.; Dodson, R.; Marks, D.

    1996-01-01

    Spatially distributed biogeochemical models may be applied over grids at a range of spatial resolutions, however, evaluation of potential errors and loss of information at relatively coarse resolutions is rare. In this study, a georeferenced database at the 1-km spatial resolution was developed to initialize and drive a process-based model (Forest-BGC) of water and carbon balance over a gridded 54976 km2 area covering two river basins in mountainous western Oregon. Corresponding data sets were also prepared at 10-km and 50-km spatial resolutions using commonly employed aggregation schemes. Estimates were made at each grid cell for climate variables including daily solar radiation, air temperature, humidity, and precipitation. The topographic structure, water holding capacity, vegetation type and leaf area index were likewise estimated for initial conditions. The daily time series for the climatic drivers was developed from interpolations of meteorological station data for the water year 1990 (1 October 1989-30 September 1990). Model outputs at the 1-km resolution showed good agreement with observed patterns in runoff and productivity. The ranges for model inputs at the 10-km and 50-km resolutions tended to contract because of the smoothed topography. Estimates for mean evapotranspiration and runoff were relatively insensitive to changing the spatial resolution of the grid whereas estimates of mean annual net primary production varied by 11%. The designation of a vegetation type and leaf area at the 50-km resolution often subsumed significant heterogeneity in vegetation, and this factor accounted for much of the difference in the mean values for the carbon flux variables. Although area wide means for model outputs were generally similar across resolutions, difference maps often revealed large areas of disagreement. Relatively high spatial resolution analyses of biogeochemical cycling are desirable from several perspectives and may be particularly important in the

  8. Multimillennium changes in dissolved oxygen under global warming: results from an AOGCM and offline ocean biogeochemical model

    NASA Astrophysics Data System (ADS)

    Yamamoto, A.; Abe-Ouchi, A.; Shigemitsu, M.; Oka, A.; Takahashi, K.; Ohgaito, R.; Yamanaka, Y.

    2016-12-01

    Long-term oceanic oxygen change due to global warming is still unclear; most future projections (such as CMIP5) are only performed until 2100. Indeed, few previous studies using conceptual models project oxygen change in the next thousands of years, showing persistent global oxygen reduction by about 30% in the next 2000 years, even after atmospheric carbon dioxide stops rising. Yet, these models cannot sufficiently represent the ocean circulation change: the key driver of oxygen change. Moreover, considering serious effect oxygen reduction has on marine life and biogeochemical cycling, long-term oxygen change should be projected for higher validity. Therefore, we used a coupled atmosphere-ocean general circulation model (AOGCM) and an offline ocean biogeochemical model, investigating realistic long-term changes in oceanic oxygen concentration and ocean circulation. We integrated these models for 2000 years under atmospheric CO2 doubling and quadrupling. After global oxygen reduction in the first 500 years, oxygen concentration in deep ocean globally recovers and overshoots, despite surface oxygen decrease and weaker Atlantic Meridional Overturning Circulation. Deep ocean convection in the Weddell Sea recovers and overshoots, after initial cessation. Thus, enhanced deep convection and associated Antarctic Bottom Water supply oxygen-rich surface waters to deep ocean, resulting global deep ocean oxygenation. We conclude that the change in ocean circulation in the Southern Ocean potentially drives millennial-scale oxygenation in the deep ocean; contrary to past reported long-term oxygen reduction and general expectation. In presentation, we will discuss the mechanism of response of deep ocean convection in the Weddell Sea and show the volume changes of hypoxic waters.

  9. Assessing biogeochemical effects and best management practice for a wheat-maize cropping system using the DNDC model

    NASA Astrophysics Data System (ADS)

    Cui, F.; Zheng, X.; Liu, C.; Wang, K.; Zhou, Z.; Deng, J.

    2014-01-01

    Contemporary agriculture is shifting from a single-goal to a multi-goal strategy, which in turn requires choosing best management practice (BMP) based on an assessment of the biogeochemical effects of management alternatives. The bottleneck is the capacity of predicting the simultaneous effects of different management practice scenarios on multiple goals and choosing BMP among scenarios. The denitrification-decomposition (DNDC) model may provide an opportunity to solve this problem. We validated the DNDC model (version 95) using the observations of soil moisture and temperature, crop yields, aboveground biomass and fluxes of net ecosystem exchange of carbon dioxide, methane, nitrous oxide (N2O), nitric oxide (NO) and ammonia (NH3) from a wheat-maize cropping site in northern China. The model performed well for these variables. Then we used this model to simulate the effects of management practices on the goal variables of crop yields, NO emission, nitrate leaching, NH3 volatilization and net emission of greenhouse gases in the ecosystem (NEGE). Results showed that no-till and straw-incorporated practices had beneficial effects on crop yields and NEGE. Use of nitrification inhibitors decreased nitrate leaching and N2O and NO emissions, but they significantly increased NH3 volatilization. Irrigation based on crop demand significantly increased crop yield and decreased nitrate leaching and NH3 volatilization. Crop yields were hardly decreased if nitrogen dose was reduced by 15% or irrigation water amount was reduced by 25%. Two methods were used to identify BMP and resulted in the same BMP, which adopted the current crop cultivar, field operation schedules and full straw incorporation and applied nitrogen and irrigation water at 15 and 25% lower rates, respectively, than the current use. Our study indicates that the DNDC model can be used as a tool to assess biogeochemical effects of management alternatives and identify BMP.

  10. Assessing biogeochemical effects and best management practice for a wheat-maize cropping system using the DNDC model

    NASA Astrophysics Data System (ADS)

    Cui, F.; Zheng, X. H.; Liu, C. Y.; Wang, K.; Zhou, Z. X.; Deng, J.

    2013-05-01

    Contemporary agriculture is shifting from a single-goal to a multi-goal strategy, which in turn requires choosing best management practice (BMP) based on assessment of the biogeochemical effects of management alternatives. The bottleneck is the capacity of predicting the simultaneous effects of different management practice scenarios on multiple goals and choosing BMP among scenarios. The denitrification-decomposition (DNDC) model may provide an opportunity to solve this problem. We validated the DNDC model (version 95) using the observations of soil moisture and temperature, crop yields, aboveground biomass and fluxes of net ecosystem exchange of carbon dioxide, methane, nitrous oxide (N2O), nitric oxide (NO) and ammonia (NH3) from a wheat-maize cropping site in northern China. The model performed well for these variables. Then we used this model to simulate the effects of management practices on the goal variables of crop yields, NO emission, nitrate leaching, NH3 volatilization and net emission of greenhouse gases in the ecosystem (NEGE). Results showed that no-till and straw-incorporated practices had beneficial effects on crop yields and NEGE. Use of nitrification inhibitors decreased nitrate leaching and N2O and NO emissions, but they significantly increased NH3 volatilization. Irrigation based on crop demand significantly increased crop yield and decreased nitrate leaching and NH3 volatilization. Crop yields were hardly decreased if nitrogen dose was reduced by 15% or irrigation water amount was reduced by 25%. Two methods were used to identify BMP and resulted in the same BMP, which adopted the current crop cultivar, field operation schedules and full straw incorporation and applied nitrogen and irrigation water at 15% and 25% lower rates, respectively, than the current use. Our study indicates that the DNDC model can be used as a tool to assess biogeochemical effects of management alternatives and identify BMP.

  11. Temperature Calculations in the Coastal Modeling System

    DTIC Science & Technology

    2017-04-01

    sediment can be controlled by the density-driven flow and mixing. Temperature can alter the water physical environment that impacts marine organisms ...survey station locations. In application of the CMS to the Corrotoman River, a quadtree grid system was developed to discretize the computational...601-634-2840; fax: 601-634-3080) of the U.S. Army Engineer Research and Development Center (ERDC), Coastal and Hydraulics Laboratory (CHL). The CIRP

  12. A correction on coastal heads for groundwater flow models.

    PubMed

    Lu, Chunhui; Werner, Adrian D; Simmons, Craig T; Luo, Jian

    2015-01-01

    We introduce a simple correction to coastal heads for constant-density groundwater flow models that contain a coastal boundary, based on previous analytical solutions for interface flow. The results demonstrate that accurate discharge to the sea in confined aquifers can be obtained by direct application of Darcy's law (for constant-density flow) if the coastal heads are corrected to ((α + 1)/α)hs  - B/2α, in which hs is the mean sea level above the aquifer base, B is the aquifer thickness, and α is the density factor. For unconfined aquifers, the coastal head should be assigned the value hs1+α/α. The accuracy of using these corrections is demonstrated by consistency between constant-density Darcy's solution and variable-density flow numerical simulations. The errors introduced by adopting two previous approaches (i.e., no correction and using the equivalent fresh water head at the middle position of the aquifer to represent the hydraulic head at the coastal boundary) are evaluated. Sensitivity analysis shows that errors in discharge to the sea could be larger than 100% for typical coastal aquifer parameter ranges. The location of observation wells relative to the toe is a key factor controlling the estimation error, as it determines the relative aquifer length of constant-density flow relative to variable-density flow. The coastal head correction method introduced in this study facilitates the rapid and accurate estimation of the fresh water flux from a given hydraulic head measurement and allows for an improved representation of the coastal boundary condition in regional constant-density groundwater flow models.

  13. Simulating Coastal Fog with a Regional Climate Model

    NASA Astrophysics Data System (ADS)

    O'Brien, T. A.; Sloan, L. C.; Chuang, P. Y.; Faloona, I. C.; Rossiter, D. L.

    2011-12-01

    We introduce a new tool for studying the physical processes that control coastal fog. We have coupled the University of Washington (UW) boundary layer model to the International Centre for Theoretical Physics's regional climate model, RegCM v4.0. The UW model explicitly includes physical processes relevant to stratocumulus clouds and coastal fog. The coupling of the UW model to RegCM (RegCM-UW) adds marine stratocumulus clouds (MSc) to RegCM; the modeled MSc compare well with observations of MSc at a variety of temporal scales (from synoptic to decadal). In accord with observations of MSc, the height of the modeled cloud deck (base and top) decreases approaching the coast, such that the MSc are frequently below the 400 m altitude threshold that Johnstone and Dawson (2010) use as a definition of fog. The spatial and temporal variability of modeled coastal fog is generally in accord with the observed spatiotemporal variability. In addition to the good agreement between the modeled interannual variability of northern California coastal fog, the model hindcasts a long-term decline in northern California coastal fog frequency that is statistically significant and statistically indistinguishable from the observed decline. Sensitivity tests show that the modeled coastal fog frequency is controlled strongly by sea surface temperature (SST) in a manner consistent with the Bakun hypothesis; cooler SSTs lead to higher fog frequency and vice-versa. We discuss research-in-progress that aims to elucidate how and why fog has declined in the recent past and how it may change in the future.

  14. Integrated carbon budget models for the Everglades terrestrial-coastal-oceanic gradient: Current status and needs for inter-site comparisons

    Treesearch

    T. G. Troxler; E. Gaiser; J. Barr; J. D. Fuentes; R. Jaffe; D. L. Childers; L. Collado-Vides; V. H. Rivera-Monroy; E. Castaneda-Moya; W. Anderson; R. Chambers; M. Chen; C. Coronado-Molina; S. E. Davis; V. Engel; C. Fitz; J. Fourqurean; T. Frankovich; J. Kominoski; C. Madden; S. L. Malone; S. F. Oberbauer; P. Olivas; J. Richards; C. Saunders; J. Schedlbauer; L. J. Scinto; F. Sklar; T. Smith; J. M. Smoak; G. Starr; R. R. Twilley; K. Whelan

    2013-01-01

    Recent studies suggest that coastal ecosystems can bury significantly more C than tropical forests, indicating that continued coastal development and exposure to sea level rise and storms will have global biogeochemical consequences. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) site provides an excellent subtropical system for examining...

  15. Modeling nutrient retention in the coastal zone of an eutrophic sea - a model study in the Stockholm Archipelago, Sweden

    NASA Astrophysics Data System (ADS)

    Almroth-Rosell, Elin; Edman, Moa; Eilola, Kari; Meier, Markus; Sahlberg, Jörgen

    2016-04-01

    This study shows that the Stockholm archipelago works as a filter for nutrients that enters the coastal zone from land. The filter capacity is high, but not effective enough to take care of all the nutrients that the system receives. At least 65 % and 72 % of the phosphorus (P) and nitrogen (N), respectively, is retained. The multi-basin one dimensional Swedish Coastal zone Model (SCM) that was used is based on the Swedish Coastal and Ocean Biogeochemical model (SCOBI) coupled to the equation solver PROgram for Boundary layers in the Environment (PROBE). An evaluation of model results showed that the nutrient, salinity and temperature dynamics in the SCM model are of good quality. To analyse the results the Stockholm archipelago was divided into three sub-areas: the inner, the intermediate and the outer archipelago. The analysis showed that the highest total amounts of P and N are retained in the outer archipelago where the surface area is largest. The area weighted retention of P and N, however, is highest in the smaller inner archipelago and decreases towards the open sea. A major part of the retention is permanent. For P sediment burial is the only permanent retention mechanism, but for N almost 92 % of the permanent retention is caused by benthic denitrification, less than 8 % by burial, while pelagic denitrification is below 1%. A reduction of the land load of nutrients (P reduced with 13 % and N with 20%) resulted in increased retention capacity of N and P and lowered the transport of N out from the archipelago. About 15 years after the reduction P is imported into the archipelago instead of being exported.

  16. A biogeochemical model for phosphorus and nitrogen cycling in the Eastern Mediterranean Sea. Part 1. Model development, initialization and sensitivity

    NASA Astrophysics Data System (ADS)

    Van Cappellen, P.; Powley, H. R.; Emeis, K.-C.; Krom, M. D.

    2014-11-01

    The Eastern Mediterranean Sea (EMS) is the largest marine basin whose annual primary productivity is limited by phosphorus (P) rather than nitrogen (N). The basin is nearly entirely land-locked and receives substantial external nutrient fluxes, comparable for instance to those of the Baltic Sea. The biological productivity of the EMS, however, is among the lowest observed in the oceans. The water column exhibits very low P and N concentrations with N:P ratios in excess of the Redfield value. These unique biogeochemical features are analyzed using a mass balance model of the coupled P and N cycles in the EMS. The present paper describes the conceptual basis, quantitative implementation and sensitivity of the model. The model is initialized for the year 1950, that is, prior to the large increase in anthropogenic nutrient loading experienced by the EMS during the second half of the 20th century. In the companion paper, the model is used to simulate the P and N cycles during the period 1950-2000. The 1950 model set-up and sensitivity analyses support the following conclusions. Inorganic molar N:P ratios in excess of the 16:1 Redfield value observed in the water column reflect higher-than-Redfield N:P ratios of the external inputs, combined with negligible denitrification. Model simulations imply that the denitrification flux would have to increase by at least a factor of 14, relative to the 1950 flux, in order for the inorganic N:P ratio of the deep waters to approach the Redfield value. The higher

  17. Hawaii and Beyond: Volcanic Islands as Model Systems for Biogeochemical and Human Ecodynamic Research

    NASA Astrophysics Data System (ADS)

    Chadwick, O.

    2012-12-01

    The Hawaiian Islands provide an excellent natural lab for understanding geochemical and ecosystem processes. The most important features are: a) increasing volcano age with distance from the hotspot, b) asymmetric rainfall distribution imposed by the northeasterly trade winds and orographic processes, creating wet windward and dry leeward landscapes, c) an impoverished vegetation assemblage allowing the same species to grow in strongly varying climate and soil conditions, d) the ability to hold topography relatively constant over long time scales by sampling on volcanic shield remnants that are preserved even on the oldest high island, Kauai, and e) a long-term topographic evolution that carves the gently sloping shield surfaces into steep-sided, amphitheater headed, relatively flat floored valleys. Although deeply incised valleys are well represented in Kauai, the later stages of volcanic island evolution are not well expressed in the exposed Hawaiian Islands. Therefore, I also consider examples from the Society and Gambier Islands in French Polynesia to demonstrate the biogeochemical and human ecodynamic impacts of valley expansion and subsidence leading to drowning of all but the highest elevation interfluves. In Hawaii, I and many colleagues have characterized the details of biogeochemical processes such as: a) variations in oxygen isotopes in soil water and soil minerals, b) changing nutrient sources using Sr, Ca, and Mg isotopes, c) mineral - carbon sorption and its implications for carbon storage in soils and for mineral ripening, and d) the development of leaching and redox driven pedogenic thresholds. Here, I address how these biogeochemical features influence human land-use decisions in prehistoric Hawaii and elsewhere in the Pacific. Polynesian radiation into the eastern Pacific occurred rapidly after 1300 y bp. Although they carried with them a kitchen garden each new island presented a different environmental challenge. They were sensitive to

  18. Carbon and nitrogen stock and fluxes in coastal Atlantic Forest of southeast Brazil: potential impacts of climate change on biogeochemical functioning.

    PubMed

    Villela, D M; Mattos, E A de; Pinto, A S; Vieira, S A; Martinelli, L A

    2012-08-01

    The Atlantic Forest is one of the most important biomes of Brazil. Originally covering approximately 1.5 million of km², today this area has been reduced to 12% of its original size. Climate changes may alter the structure and the functioning of this tropical forest. Here we explore how increases in temperature and changes in precipitation distribution could affect dynamics of carbon and nitrogen in coastal Atlantic Forest of the southeast region of Brazil The main conclusion of this article is that the coastal Atlantic Forest has high stocks of carbon and nitrogen above ground, and especially, below ground. An increase in temperature may transform these forests from important carbon sinks to carbon sources by increasing loss of carbon and nitrogen to the atmosphere. However, this conclusion should be viewed with caution because it is based on limited information. Therefore, more studies are urgently needed to enable us to make more accurate predictions.

  19. A dynamic organic soil biogeochemical model for simulating the effects of wildfire on soil environmental conditions and carbon dynamics of black spruce forests

    Treesearch

    Shuhua Yi; A. David McGuire; Eric Kasischke; Jennifer Harden; Kristen Manies; Michelle Mack; Merritt. Turetsky

    2010-01-01

    Ecosystem models have not comprehensively considered how interactions among fire disturbance, soil environmental conditions, and biogeochemical processes affect ecosystem dynamics in boreal forest ecosystems. In this study, we implemented a dynamic organic soil structure in the Terrestrial Ecosystem Model (DOS-TEM) to investigate the effects of fire on soil temperature...

  20. Emergent Archetype Hydrological-Biogeochemical Response Patterns in Heterogeneous Catchments

    NASA Astrophysics Data System (ADS)

    Jawitz, J. W.; Gall, H. E.; Rao, P.

    2013-12-01

    What can spatiotemporally integrated patterns observed in stream hydrologic and biogeochemical signals generated in response to transient hydro-climatic and anthropogenic forcing tell us about the interactions between spatially heterogeneous soil-mediated hydrological and biogeochemical processes? We seek to understand how the spatial structure of solute sources coupled with hydrologic responses affect observed concentration-discharge (C-Q) patterns. These patterns are expressions of the spatiotemporal structure of solute loads exported from managed catchments, and their likely ecological consequences manifested in receiving water bodies (e.g., wetlands, rivers, lakes, and coastal waters). We investigated the following broad questions: (1) How does the correlation between flow-generating areas and biogeochemical source areas across a catchment evolve under stochastic hydro-climatic forcing? (2) What are the feasible hydrologic and biogeochemical responses that lead to the emergence of the observed archetype C-Q patterns? and; (3) What implications do these coupled dynamics have for catchment monitoring and implementation of management practices? We categorize the observed temporal signals into three archetypical C-Q patterns: dilution; accretion, and constant concentration. We introduce a parsimonious stochastic model of heterogeneous catchments, which act as hydrologic and biogeochemical filters, to examine the relationship between spatial heterogeneity and temporal history of solute export signals. The core concept of the modeling framework is considering the types and degree of spatial correlation between solute source zones and flow generating zones, and activation of different portions of the catchments during rainfall events. Our overarching hypothesis is that each of the archetype C-Q patterns can be generated by explicitly linking landscape-scale hydrologic responses and spatial distributions of solute source properties within a catchment. The model

  1. Biogeochemical and Hydrological Heterogeneity and Emergent Archetypical Catchment Response Patterns

    NASA Astrophysics Data System (ADS)

    Jawitz, J. W.; Gall, H. E.; Rao, P. S.

    2014-12-01

    What can stream hydrologic and biogeochemical signals tell us about interactions among spatially heterogeneous hydrological and biogeochemical processes at the catchment-scale? We seek to understand how the spatial structure of solute sources coupled with both stationary and nonstationary hydroclimatic drivers affect observed archetypes of concentration-discharge (C-Q) patterns. These response patterns are the spatially integrated expressions of the spatiotemporal structure of solutes exported from managed catchments, and can provide insight into likely ecological consequences of receiving water bodies (e.g., wetlands, rivers, lakes, and coastal waters). We investigated the following broad questions: (1) How does the spatial correlation between the structure of flow-generating areas and biogeochemical source areas across a catchment evolve under stochastic hydro-climatic forcing? (2) What are the feasible hydrologic and biogeochemical responses that lead to the emergence of archetypical C-Q patterns? and; (3) What implications do these coupled dynamics have for catchment monitoring and implementation of management practices? We categorize the observed temporal signals into three archetypical C-Q patterns: dilution; accretion, and constant concentration. We applied a parsimonious stochastic model of heterogeneous catchments, which act as hydrologic and biogeochemical filters, to examine the relationship between spatial heterogeneity and temporal history of solute export signals. The core concept of the modeling framework is considering the type and degree of spatial correlation between solute source zones and flow generating zones, and activation of different portions of the catchments during rainfall events. Our overarching hypothesis is that each archetype C-Q pattern can be generated by explicitly linking landscape-scale hydrologic responses and spatial distributions of solute source properties within a catchment. We compared observed multidecadal data to

  2. Widespread euxinia in the aftermath of the Lomagundi event: insights from a modeling study of ocean biogeochemical dynamics

    NASA Astrophysics Data System (ADS)

    Ozaki, Kazumi; Tajika, Eiichi

    2015-04-01

    The emergence of strongly sulphidic oceanic waters (euxinia) during the Proterozoic may have affected biological turnover, extinction, and evolution, not only because of its toxicity to eukaryotes but also because of its fundamental role on bioessential trace metal availability. From this point of view, the evidence for euxinic environments in the Lomagundi-Jatuli event (LJE) aftermath (~2.08-2.05 billion years ago) in Gabon and Karelia are notable because their low δ98/95Mo values (less than 0.95o and 0.85o respectively) imply widespread euxinia at that time. The Francevillian Group in Gabon represents the oxic-anoxic/euxinic transitional sequence, implying a fluctuation in the atmospheric redox condition from oxic to relatively reducing, possibly due to the oxidation of substantial amount of organic matter deposited during the LJE. The large positive anomaly of sulphur isotopes and a substantial contraction of marine sulphate reservoir size through the latter part of the LJE also imply a fall in surface oxidation state. Variations of the oxygenation state of the Earth's surface would have caused substantial changes in oceanic chemical composition and, in turn, would surely have impacted the biosphere. However, the nature and dynamics of oceanic biogeochemical cycles for this interval are poorly understood. To unravel cause and effect of the variations of oceanic redox state in the Paleoproteorozoic, we improved the CANOPS model (a 1-D advection-diffusion-reaction marine biogeochemical cycle model), in which coupled C-N-O-P-S marine biogeochemical cycles and a series of redox reactions were adequately taken into account. Through systematic sensitivity experiments we show that a substantial drop in atmospheric oxygen level could cause a widespread euxinia for millions of years, which provides a theoretical explanation consistent with the geological records, such as large positive anomaly of δ34S, low δ98/95Mo, and a decrease in SO4 concentration, in the

  3. Simulating mesoscale coastal evolution for decadal coastal management: A new framework integrating multiple, complementary modelling approaches

    NASA Astrophysics Data System (ADS)

    van Maanen, Barend; Nicholls, Robert J.; French, Jon R.; Barkwith, Andrew; Bonaldo, Davide; Burningham, Helene; Brad Murray, A.; Payo, Andres; Sutherland, James; Thornhill, Gillian; Townend, Ian H.; van der Wegen, Mick; Walkden, Mike J. A.

    2016-03-01

    Coastal and shoreline management increasingly needs to consider morphological change occurring at decadal to centennial timescales, especially that related to climate change and sea-level rise. This requires the development of morphological models operating at a mesoscale, defined by time and length scales of the order 101 to 102 years and 101 to 102 km. So-called 'reduced complexity' models that represent critical processes at scales not much smaller than the primary scale of interest, and are regulated by capturing the critical feedbacks that govern landform behaviour, are proving effective as a means of exploring emergent coastal behaviour at a landscape scale. Such models tend to be computationally efficient and are thus easily applied within a probabilistic framework. At the same time, reductionist models, built upon a more detailed description of hydrodynamic and sediment transport processes, are capable of application at increasingly broad spatial and temporal scales. More qualitative modelling approaches are also emerging that can guide the development and deployment of quantitative models, and these can be supplemented by varied data-driven modelling approaches that can achieve new explanatory insights from observational datasets. Such disparate approaches have hitherto been pursued largely in isolation by mutually exclusive modelling communities. Brought together, they have the potential to facilitate a step change in our ability to simulate the evolution of coastal morphology at scales that are most relevant to managing erosion and flood risk. Here, we advocate and outline a new integrated modelling framework that deploys coupled mesoscale reduced complexity models, reductionist coastal area models, data-driven approaches, and qualitative conceptual models. Integration of these heterogeneous approaches gives rise to model compositions that can potentially resolve decadal- to centennial-scale behaviour of diverse coupled open coast, estuary and inner

  4. Biogeochemical Trends and Their Ecosystem Impacts in Atlantic Canada

    NASA Astrophysics Data System (ADS)

    Fennel, Katja; Rutherford, Krysten; Kuhn, Angela; Zhang, Wenxia; Brennan, Katie; Zhang, Rui

    2017-04-01

    The representation of coastal oceans in global biogeochemical models is a challenge, yet the ecosystems in these regions are most vulnerable to the combined stressors of ocean warming, deoxygenation, acidification, eutrophication and fishing. Coastal regions also have large air-sea fluxes of CO2, making them an important but poorly quantified component of the global carbon cycle, and are the most relevant for human activities. Regional model applications that are nested within large-scale or global models are necessary for detailed studies of coastal regions. We present results from such a regional biogeochemical model for the northwestern North Atlantic shelves and adjacent deep ocean of Atlantic Canada. The model is an implementation of the Regional Ocean Modeling System (ROMS) and includes an NPZD-type nitrogen cycle model with explicit representation of dissolved oxygen and inorganic carbon. The region is at the confluence of the Gulf Stream and Labrador Current making it highly dynamic, a challenge for analysis and prediction, and prone to large changes. Historically a rich fishing ground, coastal ecosystems in Atlantic Canada have undergone dramatic changes including the collapse of several economically important fish stocks and the listing of many species as threatened or endangered. Furthermore it is unclear whether the region is a net source or sink of atmospheric CO2 with estimates of the size and direction of the net air-sea CO2 flux remaining controversial. We will discuss simulated patterns of primary production, inorganic carbon fluxes and oxygen trends in the context of circulation features and shelf residence times for the present ocean state and present future projections.

  5. Modeling Tidal Stream Energy Extraction and its Effects on Transport Processes in a Tidal Channel and Bay System Using a Three-dimensional Coastal Ocean Model

    SciTech Connect

    Yang, Zhaoqing; Wang, Taiping; Copping, Andrea E.

    2013-02-28

    This paper presents a numerical modeling study for simulating in-stream tidal energy extraction and assessing its effects on the hydrodynamics and transport processes in a tidal channel and bay system connecting to coastal ocean. A marine and hydrokinetic (MHK) module was implemented in a three-dimensional (3-D) coastal ocean model using the momentum sink approach. The MHK model was validated with the analytical solutions for tidal channels under one-dimensional (1-D) conditions. Model simulations were further carried out to compare the momentum sink approach with the quadratic bottom friction approach. The effects of 3-D simulations on the vertical velocity profile, maximum extractable energy, and volume flux reduction across the channel were investigated through a series of numerical experiments. 3-D model results indicate that the volume flux reduction at the maximum extractable power predicted by the 1-D analytical model or two-dimensional (2-D) depth-averaged numerical model may be overestimated. Maximum extractable energy strongly depends on the turbine hub height in the water column, and which reaches a maximum when turbine hub height is located at mid-water depth. Far-field effects of tidal turbines on the flushing time of the tidal bay were also investigated. Model results demonstrate that tidal energy extraction has a greater effect on the flushing time than volume flux reduction, which could negatively affect the biogeochemical processes in estuarine and coastal waters that support primary productivity and higher forms of marine life.

  6. The ocean response to volcanic iron fertilisation after the eruption of Kasatochi volcano: a regional scale biogeochemical ocean model study

    NASA Astrophysics Data System (ADS)

    Lindenthal, A.; Langmann, B.; Paetsch, J.; Lorkowski, I.; Hort, M.

    2012-07-01

    In High-Nutrient-Low-Chlorophyll regions, phytoplankton growth is limited by the availability of water soluble iron. Volcanic ash can carry bio-available iron salts on its surface, which may be formed during volcanic eruptions by surface reactions between volcanic gases and ash. The eruption of Kasatochi volcano in August 2008 led to ash deposition into the iron-limited NE Pacific Ocean releasing iron upon contact of volcanic ash with seawater. Atmospheric and oceanic conditions were favourable to generate a massive phytoplankton bloom, which was observed by satellite instruments and in-situ measurements. Here we investigate this event with a regional scale ocean biogeochemical model system to illuminate the ocean response to iron fertilisation by volcanic ash. The results indicate that the added iron triggered an additional phytoplankton bloom in the summer of 2008, which produced a drawdown of carbon dioxide in surface seawater. The simulated development is in good agreement with the available observations.

  7. Stochastic parameterizations of biogeochemical uncertainties in a 1/4° NEMO/PISCES model for probabilistic comparisons with ocean color data

    NASA Astrophysics Data System (ADS)

    Garnier, F.; Brankart, J.-M.; Brasseur, P.; Cosme, E.

    2016-03-01

    In spite of recent advances, biogeochemical models are still unable to represent the full complexity of natural ecosystems. Their formulations are mainly based on empirical laws involving many parameters. Improving biogeochemical models therefore requires to properly characterize model uncertainties and their consequences. Subsequently, this paper investigates the potential of using random processes to simulate some uncertainties of the 1/4° coupled Physical-Biogeochemical NEMO/PISCES model of the North Atlantic ocean. Starting from a deterministic simulation performed with the original PISCES formulation, we propose a generic method based on AR(1) random processes to generate perturbations with temporal and spatial correlations. These perturbations are introduced into the model formulations to simulate 2 classes of uncertainties: the uncertainties on biogeochemical parameters and the uncertainties induced by unresolved scales in the presence of non-linear processes. Using these stochastic parameterizations, a probabilistic version of PISCES is designed and a 60-member ensemble simulation is performed. With respect to the simulation of chlorophyll, the relevance of the probabilistic configuration and the impacts of these stochastic parameterizations are assessed. In particular, it is shown that the ensemble simulation is in good agreement with the SeaWIFS ocean color data. Using these observations, the statistical consistency (reliability) of the ensemble is evaluated with rank histograms. Finally, the benefits expected from the probabilistic description of uncertainties (model error) are discussed in the context of future ocean color data assimilation.

  8. Challenges and potential solutions for European coastal ocean modelling

    NASA Astrophysics Data System (ADS)

    She, Jun; Stanev, Emil

    2017-04-01

    Coastal operational oceanography is a science and technological platform to integrate and transform the outcomes in marine monitoring, new knowledge generation and innovative technologies into operational information products and services in the coastal ocean. It has been identified as one of the four research priorities by EuroGOOS (She et al. 2016). Coastal modelling plays a central role in such an integration and transformation. A next generation coastal ocean forecasting system should have following features: i) being able to fully exploit benefits from future observations, ii) generate meaningful products in finer scales e.g., sub-mesoscale and in estuary-coast-sea continuum, iii) efficient parallel computing and model grid structure, iv) provide high quality forecasts as forcing to NWP and coastal climate models, v) resolving correctly inter-basin and inter-sub-basin water exchange, vi) resolving synoptic variability and predictability in marine ecosystems, e.g., for algae bloom, vi) being able to address critical and relevant issues in coastal applications, e.g., marine spatial planning, maritime safety, marine pollution protection, disaster prevention, offshore wind energy, climate change adaptation and mitigation, ICZM (integrated coastal zone management), the WFD (Water Framework Directive), and the MSFD (Marine Strategy Framework Directive), especially on habitat, eutrophication, and hydrographic condition descriptors. This presentation will address above challenges, identify limits of current models and propose correspondent research needed. The proposed roadmap will address an integrated monitoring-modelling approach and developing Unified European Coastal Ocean Models. In the coming years, a few new developments in European Sea observations can expected, e.g., more near real time delivering on profile observations made by research vessels, more shallow water Argo floats and bio-Argo floats deployed, much more high resolution sea level data from SWOT

  9. Offshore and coastal dispersion (OCD) model. Users guide

    SciTech Connect

    Hanna, S.R.; Schulman, L.L.; Paine, R.J.; Pleim, J.E.

    1984-09-01

    The Offshore and Coastal Dispersion (OCD) model was adapted from the EPA guideline model MPTER to simulate the effect of offshore emissions from point sources in coastal regions. Modifications were made to incorporate overwater plume transport and dispersion as well as changes that occur as the plume crosses the shoreline. Hourly meteorological data are needed from overwater and overland locations. Turbulence intensities are used but are not mandatory. For overwater dispersion, the turbulence intensities are parameterized from boundary-layer similarity relationships if they are not measured. Specifications of emission characteristics and receptor locations are the same as for MPTER; 250 point sources and 180 receptors may be used.

  10. Offshore and coastal dispersion (OCD) model. User's guide

    SciTech Connect

    Hanna, S.R.; Schulman, L.L.; Paine, R.J.; Pleim, J.E.

    1984-09-01

    The Offshore Coastal Dispersion (OCD) model was adapted from the EPA guideline model MPTER to simulate the effect of offshore emissions from point sources in coastal regions. Modifications were made to incorporate overwater plume transport and dispersion as well as changes that occur as the plume crosses the shoreline. Hourly meteorological data are needed from overwater and overland locations. For overwater dispersion, the turbulence intensities are parameterized from boundary layer similarity relationships if they are not measured. A virtual source technique is used to change the rate of plume growth as the overwater plume intercepts the overland internal boundary layer.

  11. Dramatic variability of the carbonate system at a temperate coastal ocean site (Beaufort, North Carolina, USA) is regulated by physical and biogeochemical processes on multiple timescales.

    PubMed

    Johnson, Zackary I; Wheeler, Benjamin J; Blinebry, Sara K; Carlson, Christina M; Ward, Christopher S; Hunt, Dana E

    2013-01-01

    Increasing atmospheric carbon dioxide (CO2) from anthropogenic sources is acidifying marine environments resulting in potentially dramatic consequences for the physical, chemical and biological functioning of these ecosystems. If current trends continue, mean ocean pH is expected to decrease by ~0.2 units over the next ~50 years. Yet, there is also substantial temporal variability in pH and other carbon system parameters in the ocean resulting in regions that already experience change that exceeds long-term projected trends in pH. This points to short-term dynamics as an important layer of complexity on top of long-term trends. Thus, in order to predict future climate change impacts, there is a critical need to characterize the natural range and dynamics of the marine carbonate system and the mechanisms responsible for observed variability. Here, we present pH and dissolved inorganic carbon (DIC) at time intervals spanning 1 hour to >1 year from a dynamic, coastal, temperate marine system (Beaufort Inlet, Beaufort NC USA) to characterize the carbonate system at multiple time scales. Daily and seasonal variation of the carbonate system is largely driven by temperature, alkalinity and the balance between primary production and respiration, but high frequency change (hours to days) is further influenced by water mass movement (e.g. tides) and stochastic events (e.g. storms). Both annual (~0.3 units) and diurnal (~0.1 units) variability in coastal ocean acidity are similar in magnitude to 50 year projections of ocean acidity associated with increasing atmospheric CO2. The environmental variables driving these changes highlight the importance of characterizing the complete carbonate system rather than just pH. Short-term dynamics of ocean carbon parameters may already exert significant pressure on some coastal marine ecosystems with implications for ecology, biogeochemistry and evolution and this shorter term variability layers additive effects and complexity, including

  12. Dramatic Variability of the Carbonate System at a Temperate Coastal Ocean Site (Beaufort, North Carolina, USA) Is Regulated by Physical and Biogeochemical Processes on Multiple Timescales

    PubMed Central

    Johnson, Zackary I.; Wheeler, Benjamin J.; Blinebry, Sara K.; Carlson, Christina M.; Ward, Christopher S.; Hunt, Dana E.

    2013-01-01

    Increasing atmospheric carbon dioxide (CO2) from anthropogenic sources is acidifying marine environments resulting in potentially dramatic consequences for the physical, chemical and biological functioning of these ecosystems. If current trends continue, mean ocean pH is expected to decrease by ~0.2 units over the next ~50 years. Yet, there is also substantial temporal variability in pH and other carbon system parameters in the ocean resulting in regions that already experience change that exceeds long-term projected trends in pH. This points to short-term dynamics as an important layer of complexity on top of long-term trends. Thus, in order to predict future climate change impacts, there is a critical need to characterize the natural range and dynamics of the marine carbonate system and the mechanisms responsible for observed variability. Here, we present pH and dissolved inorganic carbon (DIC) at time intervals spanning 1 hour to >1 year from a dynamic, coastal, temperate marine system (Beaufort Inlet, Beaufort NC USA) to characterize the carbonate system at multiple time scales. Daily and seasonal variation of the carbonate system is largely driven by temperature, alkalinity and the balance between primary production and respiration, but high frequency change (hours to days) is further influenced by water mass movement (e.g. tides) and stochastic events (e.g. storms). Both annual (~0.3 units) and diurnal (~0.1 units) variability in coastal ocean acidity are similar in magnitude to 50 year projections of ocean acidity associated with increasing atmospheric CO2. The environmental variables driving these changes highlight the importance of characterizing the complete carbonate system rather than just pH. Short-term dynamics of ocean carbon parameters may already exert significant pressure on some coastal marine ecosystems with implications for ecology, biogeochemistry and evolution and this shorter term variability layers additive effects and complexity, including

  13. Parameterizing soil emission and atmospheric oxidation-reduction in a model of the global biogeochemical cycle of mercury.

    PubMed

    Kikuchi, Tetsuro; Ikemoto, Hisatoshi; Takahashi, Katsuyuki; Hasome, Hisashi; Ueda, Hiromasa

    2013-01-01

    Using the GEOS-Chem atmosphere-land-ocean coupled mercury model, we studied the significances of two processes, soil emission and atmospheric oxidation-reduction, in the global biogeochemical cycling of mercury and their parametrization to improve model performance. Implementing an empirical equation for soil emission flux (Esoil) including soil mercury concentration, solar radiation, and surface air temperature as parameters enabled the model to reproduce the observed seasonal variations of Esoil, whereas the default setting, which uses only the former two parameters, failed. The modified setting of Esoil also increased the model-simulated atmospheric concentration in the summertime surface layer of the lower- and midlatitudes and improved the model reproducibility for the observations in Japan and U.S. in the same period. Implementing oxidation of atmospheric gaseous elemental mercury (Hg(0)) by ozone with an updated rate constant, as well as the oxidation by bromine atoms (Br) in the default setting, improved the model reproducibility for the dry deposition fluxes observed in Japan. This setting, however, failed to reproduce the observed seasonal variations of atmospheric concentrations in the Arctic sites due to the imbalance between oxidation and reduction, whereas the model with Br as the sole Hg(0) oxidant in the polar atmosphere could capture the variations.

  14. Modeling of carbon cycling and biogeochemical changes during injection and recovery of reclaimed water at Bolivar, South Australia

    NASA Astrophysics Data System (ADS)

    Greskowiak, Janek; Prommer, Henning; Vanderzalm, Joanne; Pavelic, Paul; Dillon, Peter

    2005-10-01

    Managed aquifer recharge is an increasingly popular technique to secure and enhance water supplies. Among a range of recharging techniques, single-well aquifer storage and recovery (ASR) is becoming a common option to either augment drinking water supplies or facilitate reuse of reclaimed water. For the present study a conceptual biogeochemical model for reclaimed water ASR was developed and incorporated into an existing reactive multicomponent transport model. The conceptual and numerical model for carbon cycling includes various forms of organic and inorganic carbon and several reactive processes that transfer carbon within and across different phases. The major geochemical processes considered in the model were microbially mediated redox reactions, driven by the mineralization of organic carbon, mineral dissolution/precipitation, and ion exchange. The numerical model was tested and applied for the analysis of observed data collected during an ASR field experiment at Bolivar, South Australia. The model simulation of this experiment provides a consistent interpretation of the observed hydrochemical changes. The results suggest that during the storage phase, dynamic changes in bacterial mass have a significant influence on the local geochemistry in the vicinity of the injection/extraction well. Farther away from the injection/extraction well, breakthrough of cations is shown to be strongly affected by exchange reactions and, in the case of calcium, by calcite dissolution.

  15. Modeling the Biogeochemical Response of a Flood Plain Aquifer Impacted By Seasonal Temperature and Water Table Variations

    NASA Astrophysics Data System (ADS)

    Arora, B.; Spycher, N.; Molins, S.; Steefel, C. I.

    2014-12-01

    With the overarching goal of understanding the impacts of climate and land use changes on carbon and nutrient cycles, we are developing a reactive transport model that couples hydrologic and biogeochemical processes to microbial functional distributions inferred from site-specific 'omic' data. The objective of the modeling approach is to simulate changes in carbon and nutrient fluxes and aquifer biogeochemistry over longer time periods due to changes in climate and/or land use, while also considering shorter time periods in which water table fluctuations and temperature variations are important. A 2-D reactive transport model has been developed for the unsaturated-saturated zone of the Rifle site, CO, an alluvial aquifer bordering the Colorado River. Modeling efforts focus on the April through September 2013 time frame that corresponds to the spring snow melt event that lead to an approximately 1 meter rise in the water table followed by a gradual lowering over 3 months. Temperature variations of as much as 10ºC are observed at shallow depths (< 1m), while at least some temperature variation (1ºC) occurs as deep as about 7m. A field survey of the microbial populations indicates the presence and activity of chemo(litho)autotrophic bacteria within the saturated zone of the alluvial aquifer. Model simulations are used to quantify the release of carbon dioxide and consumption of oxygen via abiotic pathways and heterotrophic microbial oxidation of reduced species (Fe(II), S(-2)) and minerals (pyrite). Results indicate that the observed oxygen profiles and/or carbon fluxes cannot be matched by considering abiotic reactions alone. The importance of including microbial contributions from chemo(litho)autotrophic processes (e.g., ammonia, sulfur and iron oxidation) is supported by both field observations and model simulations. Important conclusions from the study are to: (1) include microbially-mediated processes and contributions from the unsaturated zone, and (2) account

  16. Benthic processes and coastal aquaculture: merging models and field data at a local scale

    NASA Astrophysics Data System (ADS)

    Brigolin, Daniele; Rabouille, Christophe; Bombled, Bruno; Colla, Silvia; Pastres, Roberto; Pranovi, Fabio

    2016-04-01

    Shellfish farming is regarded as an organic extractive aquaculture activity. However, the production of faeces and pseudofaeces, in fact, leads to a net transfer of organic matter from the water column to the surface sediment. This process, which is expected to locally affect the sediment biogeochemistry, may also cause relevant changes in coastal areas characterized by a high density of farms. In this paper, we present the result of a study recently carried out in the Gulf of Venice (northern Adriatic sea), combining mathematical modelling and field sampling efforts. The work aimed at using a longline mussel farm as an in-situ test-case for modelling the differences in soft sediments biogeochemical processes along a gradient of organic deposition. We used an existing integrated model, allowing to describe biogeochemical fluxes towards the mussel farm and to predict the extent of the deposition area underneath it. The model framework includes an individual-based population dynamic model of the Mediterranean mussel coupled with a Lagrangian deposition model and a 1D benthic model of early diagenesis. The work was articulated in 3 steps: 1) the integrated model allowed to simulate the downward fluxes of organic matter originated by the farm, and the extent of its deposition area; 2) based on the first model application, two stations were localized, at which sediment cores were collected during a field campaign, carried out in June 2015. Measurements included O2 and pH microprofiling, porosity and micro-porosity, Total Organic Carbon, and pore waters NH4, PO4, SO4, Alkalinity, and Dissolved Inorganic Carbon; 3) two distinct early diagenesis models were set-up, reproducing observed field data in the sampled cores. Observed oxygen microprofiles showed a different behavior underneath the farm with respect to the outside reference station. In particular, a remarkable decrease in the oxygen penetration depth, and an increase in the O2 influx calculated from the

  17. An assessment of net primary productivity estimates using coupled physical-biogeochemical/earth system models in the Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Lee, Y. J.; Matrai, P.; Friedrichs, M. A.; Saba, V. S.

    2016-02-01

    Net primary production (NPP) is the major source of energy for the Arctic Ocean (AO) ecosystem, as in most ecosystems. Reproducing current patterns of NPP is essential to understand the physical and biogeochemical controls in the present and the future AO. The Primary Productivity Algorithm Round Robin (PPARR) activity provides a framework to evaluate the skill and sensitivity of NPP as estimated by coupled global/regional climate models and earth system models in the AO. Here we compare results generated from 18 global/regional climate models and three earth system models with observations from a unique pan-Arctic data set (1959-2011) that includes in situ NPP (N=928 stations) and nitrate (N=678 stations). Models results showed a distribution similar to the in situ data distribution, except for the high values of integrated NPP data. Model skill of integrated NPP exhibited little difference as a function of sea ice condition (ice-free vs. ice-covered) and depth (shallow vs. deep), but performance of models varied significantly as a function of seasons. For example, simulated integrated NPP was underestimated in the beginning of the production season (April-June) compared to mid-summer (July and August) and had the highest variability in late summer and early fall (September-October). While models typically underestimated mean NPP, nitrate concentrations were overestimated. Overall, models performed better in reproducing nitrate than NPP in terms of differences in variability. The model performance was similar at all depths within the top 100 m, both in NPP and nitrate. Continual feedback, modification and improvement of the participating models and the resulting increase in model skill are the primary goals of the PPARR-5 AO exercise.

  18. Modeling population dynamics and woody biomass of Alaska coastal forest

    Treesearch

    Randy L. Peterson; Jingjing Liang; Tara M. Barrett

    2014-01-01

    Alaska coastal forest, 6.2 million ha in size, has been managed in the past mainly through clearcutting. Declining harvest and dwindling commercial forest resources over the past 2 decades have led to increased interest in management of young-growth stands and utilization of woody biomass for bioenergy. However, existing models to support these new management systems...

  19. Study of the seasonal cycle of the biogeochemical processes in the Ligurian Sea using a 1D interdisciplinary model

    NASA Astrophysics Data System (ADS)

    Raick, C.; Delhez, E. J. M.; Soetaert, K.; Grégoire, M.

    2005-04-01

    A one-dimensional coupled physical-biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version 1D) developed at the GeoHydrodynamics and Environmental Laboratory (GHER) of the University of Liège. The ecosystem model contains 19 state variables describing the carbon and nitrogen cycles of the pelagic food web. Phytoplankton and zooplankton are both divided in three size-based compartments and the model includes an explicit representation of the microbial loop including bacteria, dissolved organic matter, nano-, and microzooplankton. The internal carbon/nitrogen ratio is assumed variable for phytoplankton and detritus, and constant for zooplankton and bacteria. Silicate is considered as a potential limiting nutrient of phytoplankton's growth. The aggregation model described by Kriest and Evans in (Proc. Ind. Acad. Sci., Earth Planet. Sci. 109 (4) (2000) 453) is used to evaluate the sinking rate of particulate detritus. The model is forced at the air-sea interface by meteorological data coming from the "Côte d'Azur" Meteorological Buoy. The dynamics of atmospheric fluxes in the Mediterranean Sea (DYFAMED) time-series data obtained during the year 2000 are used to calibrate and validate the biological model. The comparison of model results within in situ DYFAMED data shows that although some processes are not represented by the model, such as horizontal and vertical advections, model results are overall in agreement with observations and differences observed can be explained with environmental conditions.

  20. Modeling the fate of nitrogen on the catchment scale using a spatially explicit hydro-biogeochemical simulation system

    NASA Astrophysics Data System (ADS)

    Klatt, S.; Butterbach-Bahl, K.; Kiese, R.; Haas, E.; Kraus, D.; Molina-Herrera, S. W.; Kraft, P.

    2015-12-01

    The continuous growth of the human population demands an equally growing supply for fresh water and food. As a result, available land for efficient agriculture is constantly diminishing which forces farmers to cultivate inferior croplands and intensify agricultural practices, e.g., increase the use of synthetic fertilizers. This intensification of marginal areas in particular will cause a dangerous rise in nitrate discharge into open waters or even drinking water resources. In order to reduce the amount of nitrate lost by surface runoff or lateral subsurface transport, bufferstrips have proved to be a valuable means. Current laws, however, promote rather static designs (i.e., width and usage) even though a multitude of factors, e.g., soil type, slope, vegetation and the nearby agricultural management, determines its effectiveness. We propose a spatially explicit modeling approach enabling to assess the effects of those factors on nitrate discharge from arable lands using the fully distributed hydrology model CMF coupled to the complex biogeochemical model LandscapeDNDC. Such a modeling scheme allows to observe the displacement of dissolved nutrients in both vertical and horizontal directions and serves to estimate both their uptake by the vegetated bufferstrip and loss to the environment. First results indicate a significant reduction of nitrate loss in the presence of a bufferstrip (2.5 m). We show effects induced by various buffer strip widths and plant cover on the nitrate retention.

  1. A model of biogeochemical cycles of carbon, nitrogen, and phosphorus including symbiotic nitrogen fixation and phosphatase production

    NASA Astrophysics Data System (ADS)

    Wang, Y.-P.; Houlton, B. Z.; Field, C. B.

    2007-03-01

    Global climate models have not yet considered the effects of nutrient cycles and limitation when forecasting carbon uptake by the terrestrial biosphere into the future. Using the principle of resource optimization, we here develop a new theory by which C, N, and P cycles interact. Our model is able to replicate the observed responses of net primary production to nutrient additions in N-limited, N- and P-colimited, and P-limited terrestrial environments. Our framework identifies a new pathway by which N2 fixers can alter P availability: By investing in N-rich, phosphorus liberation enzymes (phosphatases), fixers can greatly accelerate soil P availability and P cycling rates. This interaction is critical for the successful invasion and establishment of N2 fixers in an N-limited environment. We conclude that our model can be used to examine nutrient limitation broadly, and thus offers promise for coupling the biogeochemical system of C, N, and P to broader climate-system models.

  2. Modeling the mitigation effect of coastal forests on tsunami

    NASA Astrophysics Data System (ADS)

    Kh'ng, Xin Yi; Teh, Su Yean; Koh, Hock Lye

    2017-08-01

    As we have learned from the 26 Dec 2004 mega Andaman tsunami that killed 250, 000 lives worldwide, tsunami is a devastating natural disaster that can cause severe impacts including immense loss of human lives and extensive destruction of properties. The wave energy can be dissipated by the presence of coastal mangrove forests, which provide some degree of protection against tsunami waves. On the other hand, costly artificial structures such as reinforced walls can substantially diminish the aesthetic value and may cause environmental problems. To quantify the effectiveness of coastal forests in mitigating tsunami waves, an in-house 2-D model TUNA-RP is developed and used to quantify the reduction in wave heights and velocities due to the presence of coastal forests. The degree of reduction varies significantly depending on forest flow-resistant properties such as vegetation characteristics, forest density and forest width. The ability of coastal forest in reducing tsunami wave heights along the west coast of Penang Island is quantified by means of model simulations. Comparison between measured tsunami wave heights for the 2004 Andaman tsunami and 2-D TUNA-RP model simulated values demonstrated good agreement.

  3. A Mechanistically Informed User-Friendly Model to Predict Greenhouse Gas (GHG) Fluxes and Carbon Storage from Coastal Wetlands

    NASA Astrophysics Data System (ADS)

    Abdul-Aziz, O. I.; Ishtiaq, K. S.

    2015-12-01

    We present a user-friendly modeling tool on MS Excel to predict the greenhouse gas (GHG) fluxes and estimate potential carbon sequestration from the coastal wetlands. The dominant controls of wetland GHG fluxes and their relative mechanistic linkages with various hydro-climatic, sea level, biogeochemical and ecological drivers were first determined by employing a systematic data-analytics method, including Pearson correlation matrix, principal component and factor analyses, and exploratory partial least squares regressions. The mechanistic knowledge and understanding was then utilized to develop parsimonious non-linear (power-law) models to predict wetland carbon dioxide (CO2) and methane (CH4) fluxes based on a sub-set of climatic, hydrologic and environmental drivers such as the photosynthetically active radiation, soil temperature, water depth, and soil salinity. The models were tested with field data for multiple sites and seasons (2012-13) collected from the Waquoit Bay, MA. The model estimated the annual wetland carbon storage by up-scaling the instantaneous predicted fluxes to an extended growing season (e.g., May-October) and by accounting for the net annual lateral carbon fluxes between the wetlands and estuary. The Excel Spreadsheet model is a simple ecological engineering tool for coastal carbon management and their incorporation into a potential carbon market under a changing climate, sea level and environment. Specifically, the model can help to determine appropriate GHG offset protocols and monitoring plans for projects that focus on tidal wetland restoration and maintenance.

  4. Integrating "Omics" Data Into A Biogeochemical Model: A New Model Scheme To Predict Climate Feedbacks From Microbial Function In Tropical Ecosystems

    NASA Astrophysics Data System (ADS)

    Song, Y.; Yao, Q.; Wang, G.; Yang, X.; Pan, C.; Johnston, E.; Kim, M.; Konstantinidis, K.; Hazen, T.; Mayes, M. A.

    2016-12-01

    Soil microorganisms and their activities, which play a significant role in regulating carbon (C) and nutrient biogeochemical cycles, are highly responsive to changes in climate. The diversity of microorganisms, however, complicates the explicit representation of microbial and enzymatic processes in biogeochemical or earth system models. Uncertainties in accounting for microbial diversity therefore limits our ability to incorporate microbial functions into models. However, `omics technology provides abundant information to identify the structure and function of the microbial community and strengthens our ability to understand microbially-mediated C and nutrient cycles and their climate feedbacks. We collected soils from control and phosphorus (P) fertilized plots at the Gigante Peninsula long-term fertilization experiment at the Smithsonian Tropical Research Institute in Panama, an ecosystem where P limitation constrains primary productivity and microbial activities. We monitored effects P addition on soil carbon decomposition with respiration measurements and investigated the responsible microbial mechanisms with metagenomics, metatranscriptomics, metaproteomics, and enzyme activity assays. We integrated the P dynamics into the C-N coupled Microbial Enzyme Decomposition (MEND) model. We integrated the `omics data with the new microbially-enabled C-N-P model to examine the mechanistic responses of soil microbial activity and heterotrophic respiration to P availability. Our finding indicates that increases in soil P availability can alter both the abundance and activity of enzymes related to soil carbon decomposition and P mineralization in the tropical soil, leading to increased CO2 emissions to the atmosphere. Integrating the `omics data into the biogeochemical model enabled scaling of complex ecosystem functions from genes to functional groups to enable predictions of microbial controls on C, N and P cycles.

  5. Pore-scale network modeling of microbially induced calcium carbonate precipitation: Insight into scale dependence of biogeochemical reaction rates

    NASA Astrophysics Data System (ADS)

    Qin, Chao-Zhong; Hassanizadeh, S. Majid; Ebigbo, Anozie

    2016-11-01

    The engineering of microbially induced calcium carbonate precipitation (MICP) has attracted much attention in a number of applications, such as sealing of CO2 leakage pathways, soil stabilization, and subsurface remediation of radionuclides and toxic metals. The goal of this work is to gain insight into pore-scale processes of MICP and scale dependence of biogeochemical reaction rates. This will help us develop efficient field-scale MICP models. In this work, we have developed a comprehensive pore-network model for MICP, with geochemical speciation calculated by the open-source PHREEQC module. A numerical pseudo-3-D micromodel as the computational domain was generated by a novel pore-network generation method. We modeled a three-stage process in the engineering of MICP including the growth of biofilm, the injection of calcium-rich medium, and the precipitation of calcium carbonate. A number of test cases were conducted to illustrate how calcite precipitation was influenced by different operating conditions. In addition, we studied the possibility of reducing the computational effort by simplifying geochemical calculations. Finally, the effect of mass transfer limitation of possible carbonate ions in a pore element on calcite precipitation was explored.

  6. Model-based integration and analysis of biogeochemical and isotopic dynamics in a nitrate-polluted pyritic aquifer.

    PubMed

    Zhang, Yan-Chun; Prommer, Henning; Broers, Hans Peter; Slomp, Caroline P; Greskowiak, Janek; van der Grift, Bas; Van Cappellen, Philippe

    2013-09-17

    Leaching of nitrate from agricultural land to groundwater and the resulting nitrate pollution are a major environmental problem worldwide. Its impact is often mitigated in aquifers hosting sufficiently reactive reductants that can promote autotrophic denitrification. In the case of pyrite acting as reductant, however, denitrification is associated with the release of sulfate and often also with the mobilization of trace metals (e.g., arsenic). In this study, reactive transport modeling was used to reconstruct, quantify and analyze the dynamics of the dominant biogeochemical processes in a nitrate-polluted pyrite-containing aquifer and its evolution over the last 50 years in response to changing agricultural practices. Model simulations were constrained by measured concentration depth profiles. Measured (3)H/(3)He profiles were used to support the calibration of flow and conservative transport processes, while the comparison of simulated and measured sulfur isotope signatures acted as additional calibration constraint for the reactive processes affecting sulfur cycling. The model illustrates that denitrification largely prevented an elevated discharge of nitrate to surface waters, while sulfate discharges were significantly increased, peaking around 15 years after the maximum nitrogen inputs.

  7. High-resolution wave and hydrodynamics modelling in coastal areas: operational applications for coastal planning, decision support and assessment

    NASA Astrophysics Data System (ADS)

    Samaras, Achilleas G.; Gaeta, Maria Gabriella; Moreno Miquel, Adrià; Archetti, Renata

    2016-07-01

    Numerical modelling has become an essential component of today's coastal planning, decision support and risk assessment. High-resolution modelling offers an extensive range of capabilities regarding simulated conditions, works and practices and provides with a wide array of data regarding nearshore wave dynamics and hydrodynamics. In the present work, the open-source TELEMAC suite and the commercial software MIKE21 are applied to selected coastal areas of South Italy. Applications follow a scenario-based approach in order to study representative wave conditions in the coastal field; the models' results are intercompared in order to test both their performance and capabilities and are further evaluated on the basis of their operational use for coastal planning and design. A multiparametric approach for the rapid assessment of wave conditions in coastal areas is also presented and implemented in areas of the same region. The overall approach is deemed to provide useful insights on the tested models and the use of numerical models - in general - in the above context, especially considering that the design of harbours, coastal protection works and management practices in the coastal zone is based on scenario-based approaches as well.

  8. Full uncertainty quantification of a regional N2O and NO3 inventory using the biogeochemical model LandscapeDNDC

    NASA Astrophysics Data System (ADS)

    Santabarbara, Ignacio; Haas, Edwin; Klatt, Steffen; Kiese, Ralf; Butterbach-Bahl, Klaus

    2015-04-01

    Numerical simulation models are increasingly used to estimate greenhouse gas emissions at site to regional / national scale and are outlined as the most advanced methodology (Tier 3) in the framework of UNFCCC reporting. Process-based models incorporate the major processes of the carbon and nitrogen cycle of terrestrial ecosystems and are thus thought to be widely applicable at various spatial scales. Regional inventories require high spatial resolution input data on soil properties, climate drivers and management information. The acceptance of model based inventory calculations depends on the assessment of the inventory's uncertainty (model, input data and parameter induced uncertainties). In this study we fully quantify the uncertainty in regional N2O / NO3 inventory predictions from arable soils of Saxony (Germany) using the biogeochemical model LandscapeDNDC. We address model induced uncertainty (MU) by contrasting two different soil biogeochemistry modules in conjunction with two different plant growth descriptions within LandscapeDNDC. Input data induced uncertainty (DU) was addressed by Latin Hyper Cube sampling of soil properties, climate drivers and agricultural management practices. The parameter induced uncertainty (PU) was assessed by using joint parameter distributions for key parameters describing microbial C and N turnover processes as obtained by differenct Bayesian calibration studies for each model configuration. We representatively sampled different parameter vectors from the discrete joint parameter distribution comprising all parameter combinations and used these to calculate individual realizations of the regional inventory. The spatial domain (4042 polygons) was set up with spatially explicit soil and climate information and a region-typical 3-year crop rotation consisting of winter wheat, rapeseed, and winter barley. For the MU, DU and PU we calculated several hundred regional inventories each to assess the individual uncertainty

  9. OCD: The offshore and coastal dispersion model. Volume 2. Appendices

    SciTech Connect

    DiCristofaro, D.C.; Hanna, S.R.

    1989-11-01

    The Offshore and Coastal Dispersion (OCD) Model has been developed to simulate the effect of offshore emissions from point, area, or line sources on the air quality of coastal regions. The OCD model was adapted from the EPA guideline model MPTER (EPA, 1980). Modifications were made to incorporate overwater plume transport and dispersion as well as changes that occur as the plume crosses the shoreline. This is a revised OCD model, the fourth version to date. The volume is an appendices for the OCD documentation, included are three appendices: Appendix A the OCD computer program, Appendix B an Analysis Post-processor, Appendix C Offshore Meteorological data Collection Instrumentation, also included are general References.

  10. Skill assessment of an integrated modeling system for shallow coastal and estuarine ecosystems

    NASA Astrophysics Data System (ADS)

    Sheng, Y. Peter; Kim, Taeyun

    2009-02-01

    The predictive skills of an integrated physical-biogeochemical modeling system (CH3D-IMS) for shallow estuarine and coastal ecosystems are assessed using available field data in the Indian River Lagoon estuarine system, Florida during 1998-2000. The cornerstone of the modeling system is the circulation model CH3D (Curvilinear-grid Hydrodynamics in 3D), which is coupled to models of wave (SMB), sediment transport, water quality (nutrients: N, P, and Si, three phytoplankton species, zooplankton, and dissolved oxygen), light attenuation, and seagrass. To resolve the complex geometry and bathymetry of the estuarine system, the modeling system uses a boundary-fitted non-orthogonal curvilinear grid in the horizontal direction and a terrain-following sigma grid in the vertical direction. While water level and salinity data were collected continuously (at 15-min intervals) at 10 fixed stations, most water quality data were collected at much longer time scales (bi-weekly to quarterly) during ship surveys at more than 30 stations. Sediment-water quality data were collected at 24 stations once in 1998. Model skills for hydrodynamic and water quality simulations are assessed in terms of the absolute relative errors and the relative operating characteristic (ROC) scores. Both methods indicate that the modeling system has skills in simulating water level, salinity, dissolved oxygen, chlorophyll, and dissolved nutrients, with the ROC score between 0.6 and 0.862, indicating skills for most of the variables. Skills for simulating total suspended solids (TSS) and particulate nutrients are lacking, with ROC score and: between 0.5-0.6. Simulated diffuse attenuation coefficient, which depends on TSS, chlorophyll a, and dissolved organic matter, has an ROC of 0.55. Using high frequency time-varying field data collected during two episodic events in the study period, the skills of CH3D-IMS improved significantly for both TSS and particulate nutrients. Model skills for particulate

  11. Full Uncertainty Quantification of a Regional N2O and NO3 Inventory Using the Biogeochemical Model LandscapeDNDC

    NASA Astrophysics Data System (ADS)

    Haas, E.; Santabarbara, I.; Kraus, D.; Klatt, S.; Werner, C.; Kiese, R.; Butterbach-Bahl, K.

    2014-12-01

    Numerical simulation models are increasingly used to estimate greenhouse gas emissions at site to regional / national scale and are outlined as the most advanced methodology (Tier 3) in the framework of UNFCCC reporting. Process-based models incorporate the major processes of the carbon and nitrogen cycle of terrestrial ecosystems and are thus thought to be widely applicable at various spatial scales. Regional inventories require high spatial resolution input data on soil properties, climate drivers and management information. The acceptance of model based inventory calculations depends on the assessment of the inventory's uncertainty (model, input data and parameter induced uncertainties). In this study we fully quantify uncertainty in regional N2O / NO3 inventory predictions from arable soils of Saxony (Germany) using the biogeochemical model LandscapeDNDC. We address model induced uncertainty (MU) by contrasting two different soil biogeochemistry modules in conjunction with two different plant growth descriptions within LandscapeDNDC. Input data induced uncertainty (DU) was addressed by Latin Hyper Cube sampling of soil properties, climate drivers and agricultural management practices. The parameter induced uncertainty (PU) was assessed by using a joint parameter distribution for key parameters describing microbial C and N turnover processes as obtained by a Bayesian calibration study. We representatively sampled different parameter vectors from the discrete joint parameter distribution comprising all parameter combinations and used these to calculate individual realizations of the regional inventory. The spatial domain (4042 polygons) was set up with spatially explicit soil and climate information and a region-typical 3-year crop rotation consisting of winter wheat, rapeseed, and winter barley. For the MU, DU and PU we calculated several hundred regional inventories each to assess the individual uncertainty contributions. For the overall uncertainty

  12. Modeling Biogeochemical-Physical Interactions and Carbon Flux in the Sargasso Sea (Bermuda Atlantic Time-series Study site)

    NASA Technical Reports Server (NTRS)

    Signorini, Sergio R.; McClain, Charles R.; Christian, James R.

    2001-01-01

    An ecosystem-carbon cycle model is used to analyze the biogeochemical-physical interactions and carbon fluxes in the Bermuda Atlantic Time-series Study (BATS) site for the period of 1992-1998. The model results compare well with observations (most variables are within 8% of observed values). The sea-air flux ranges from -0.32 to -0.50 mol C/sq m/yr, depending upon the gas transfer algorithm used. This estimate is within the range (-0.22 to -0.83 mol C/sq m/yr) of previously reported values which indicates that the BATS region is a weak sink of atmospheric CO2. The overall carbon balance consists of atmospheric CO2 uptake of 0.3 Mol C/sq m/yr, upward dissolved inorganic carbon (DIC) bottom flux of 1.1 Mol C/sq m/yr, and carbon export of 1.4 mol C/sq m/yr via sedimentation. Upper ocean DIC levels increased between 1992 and 1996 at a rate of approximately 1.2 (micro)mol/kg/yr, consistent with observations. However, this trend was reversed during 1997-1998 to -2.7 (micro)mol/kg/yr in response to hydrographic changes imposed by the El Nino-La Nina transition, which were manifested in the Sargasso Sea by the warmest SST and lowest surface salinity of the period (1992-1998).

  13. Intercomparison and validation of operational coastal-scale models, the experience of the project MOMAR.

    NASA Astrophysics Data System (ADS)

    Brandini, C.; Coudray, S.; Taddei, S.; Fattorini, M.; Costanza, L.; Lapucci, C.; Poulain, P.; Gerin, R.; Ortolani, A.; Gozzini, B.

    2012-04-01

    The need for regional governments to implement operational systems for the sustainable management of coastal waters, in order to meet the requirements imposed by legislation (e.g. EU directives such as WFD, MSFD, BD and relevant national legislation) often lead to the implementation of coastal measurement networks and to the construction of computational models that surround and describe parts of regional seas without falling in the classic definition of regional/coastal models. Although these operational models may be structured to cover parts of different oceanographic basins, they can have considerable advantages and highlight relevant issues, such as the role of narrow channels, straits and islands in coastal circulation, as both in physical and biogeochemical processes such as in the exchanges of water masses among basins. Two models of this type were made in the context of cross-border European project MOMAR: an operational model of the Tuscan Archipelago sea and one around the Corsica coastal waters, which are both located between the Tyrrhenian and the Algerian-Ligurian-Provençal basins. Although these two models were based on different computer codes (MARS3D and ROMS), they have several elements in common, such as a 400 m resolution, boundary conditions from the same "father" model, and an important area of overlap, the Corsica channel, which has a key role in the exchange of water masses between the two oceanographic basins. In this work we present the results of the comparison of these two ocean forecasting systems in response to different weather and oceanographic forcing. In particular, we discuss aspects related to the validation of the two systems, and a systematic comparison between the forecast/hindcast based on such hydrodynamic models, as regards to both operational models available at larger scale, both to in-situ measurements made by fixed or mobile platforms. In this context we will also present the results of two oceanographic cruises in the

  14. Investigating the Role of Biogeochemical Processes in the Northern High Latitudes on Global Climate Feedbacks Using an Efficient Scalable Earth System Model

    SciTech Connect

    Jain, Atul K.

    2016-09-14

    The overall objectives of this DOE funded project is to combine scientific and computational challenges in climate modeling by expanding our understanding of the biogeophysical-biogeochemical processes and their interactions in the northern high latitudes (NHLs) using an earth system modeling (ESM) approach, and by adopting an adaptive parallel runtime system in an ESM to achieve efficient and scalable climate simulations through improved load balancing algorithms.

  15. Modeling Sediment Transport in Qatar: Application for Coastal Development Planning.

    PubMed

    Yousif, Ruqaiya; Warren, Chris; Ben-Hamadou, Radhouan; Hurevoglu, Sinan

    2017-10-06

    Hydrodynamics and sediment transport are key physical processes contributing to habitat structure within the marine environment. Coastal development that results in the alteration of these processes (e.g., changing water flushing and/or sedimentation rates) can have detrimental impacts on sensitive systems. This is a current relevant issue in Qatar as its coastal regions continue to be developed, not only around the capital of Doha, but in many areas around this Arabian Gulf peninsula. The Northeastern Qatari coast is comprised of diverse and sensitive flora and fauna such as seagrass and macro-algae meadows, coral reefs/patches, turtles and dugongs that tolerate harsh environmental conditions. In the near future, this area may see a rise in anthropogenic activity in the form of coastal development projects. These will add to existing natural stresses, such as high temperature, high salinity and low rates of precipitation. Consequently, there is a need to characterize this area and assess the potential impacts that these anthropogenic activities may have on the region. In this study, a novel sediment transport model is described and used to demonstrate the potential impact of altering hydrodynamics and subsequent sediment transport along the northeastern Qatar near shore marine environment. The developed models will be tested using potential scenarios of future anthropogenic activities forecasted to take place in the area. The results will show the effects on water and sediment behavior, and provide a scientificapproach for key stakeholders to make decisions with respect to the management of the considered coastal zone. Furthermore, it provides a tool / framework that can be utilized in environmental impact assessment and associated hydrodynamic studies along other areas of the Qatari coastal zone. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  16. A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 (KMBM2) for UVic 2.9

    NASA Astrophysics Data System (ADS)

    Nickelsen, L.; Keller, D. P.; Oschlies, A.

    2014-12-01

    Marine biological production and the associated biotic uptake of carbon in many ocean regions depend on the availability of nutrients in the euphotic zone. While large areas are limited by nitrogen and/or phosphorus, the micronutrient iron is considered the main limiting nutrient in the North Pacific, equatorial Pacific and Southern Ocean. Changes in iron availability via changes in atmospheric dust input are discussed to play an important role in glacial/interglacial cycles via climate feedbacks caused by changes in biological ocean carbon sequestration. Although many aspects of the iron cycle remain unknown, its incorporation into marine biogeochemical models is needed to test our current understanding and better constrain its role in the Earth system. In the University of Victoria Earth System Climate Model (UVic) iron limitation in the ocean was, until now, simulated pragmatically with an iron concentration masking scheme that did not allow a consistent interactive response to perturbations of ocean biogeochemistry or iron cycling sensitivity studies. Here, we replace the iron masking scheme with a dynamic iron cycle and compare the results to available observations and the previous marine biogeochemical model. Sensitivity studies are also conducted with the new model to test the importance of considering the variable solubility of iron in dust deposition, the importance of considering high resolution bathymetry for the sediment release of iron, the effect of scaling the sedimentary iron release with temperature and the sensitivity of the iron cycle to a climate change scenario.

  17. DEVELOPING SITE-SPECIFIC MODELS FOR FORECASTING BACTERIA LEVELS AT COASTAL BEACHES

    EPA Science Inventory

    The U.S.Beaches Environmental Assessment and Coastal Health Act of 2000 authorizes studies of pathogen indicators in coastal recreation waters that develop appropriate, accurate, expeditious, and cost-effective methods (including predictive models) for quantifying pathogens in co...

  18. DEVELOPING SITE-SPECIFIC MODELS FOR FORECASTING BACTERIA LEVELS AT COASTAL BEACHES

    EPA Science Inventory

    The U.S.Beaches Environmental Assessment and Coastal Health Act of 2000 authorizes studies of pathogen indicators in coastal recreation waters that develop appropriate, accurate, expeditious, and cost-effective methods (including predictive models) for quantifying pathogens in co...

  19. Modeling potential interactions of acid deposition and climate change at four watersheds in Shenandoah National Park, VA using the dynamic biogeochemical model PnET-BGC

    NASA Astrophysics Data System (ADS)

    Robison, A.; Scanlon, T. M.; Cosby, B. J.; Webb, J. R.; Hayhoe, K.; Galloway, J. N.

    2013-12-01

    The ecological threat imposed by acid deposition on watersheds in the eastern U.S. has, to a certain extent, been alleviated by the passage of the Clean Air Act and subsequent amendments. At the same time, as climate change continues to emerge as a global issue affecting temperature regimes and hydrological cycling among many other variables, new concerns are developing for these watershed ecosystems. Considering that climate change and acid deposition do not influence watersheds independently, there is an opportunity and need to examine both the potential interactions and the impacts of these two biogeochemical drivers. Long-term monitoring of four streams in Shenandoah National Park, VA has provided a favorable setting for analyzing this interaction. Deposition of both sulfur and nitrogen has significantly decreased over the past 30 years in the region. Meanwhile, all four streams have warmed significantly over the past 20-33 years at an average rate of 0.07 oC yr-1, a trend that is closely tied to atmospheric warming rather than changes in hydrology. We applied a dynamic biogeochemical model (PnET-BGC) to these four watersheds to a) investigate how climate change will affect watershed response to reduced acid deposition; b) identify the key processes through which this interaction will be manifested; and c) examine how differences in watershed characteristics (e.g. bedrock and soil properties) affect the response to these two biogeochemical drivers. Included in model application are statistically downscaled climate projections of temperature maximums and minimums, precipitation, and solar radiation. Results will be used to assess the relative impact of these climate variables in regulating stream acid-base status. This study will also provide insight into the future ecological health of these ecosystems, primarily through examination of aquatic habitat suitability based on temperature and acidity.

  20. Automated calibration of a stream solute transport model: Implications for interpretation of biogeochemical parameters

    USGS Publications Warehouse

    Scott, D.T.; Gooseff, M.N.; Bencala, K.E.; Runkel, R.L.

    2003-01-01

    The hydrologic processes of advection, dispersion, and transient storage are the primary physical mechanisms affecting solute transport in streams. The estimation of parameters for a conservative solute transport model is an essential step to characterize transient storage and other physical features that cannot be directly measured, and often is a preliminary step in the study of reactive solutes. Our study used inverse modeling to estimate parameters of the transient storage model OTIS (One dimensional Transport with Inflow and Storage). Observations from a tracer injection experiment performed on Uvas Creek, California, USA, are used to illustrate the application of automated solute transport model calibration to conservative and nonconservative stream solute transport. A computer code for universal inverse modeling (UCODE) is used for the calibrations. Results of this procedure are compared with a previous study that used a trial-and-error parameter estimation approach. The results demonstrated 1) importance of the proper estimation of discharge and lateral inflow within the stream system; 2) that although the fit of the observations is not much better when transient storage is invoked, a more randomly distributed set of residuals resulted (suggesting non-systematic error), indicating that transient storage is occurring; 3) that inclusion of transient storage for a reactive solute (Sr2+) provided a better fit to the observations, highlighting the importance of robust model parameterization; and 4) that applying an automated calibration inverse modeling estimation approach resulted in a comprehensive understanding of the model results and the limitation of input data.

  1. Data-driven models of groundwater salinization in coastal plains

    NASA Astrophysics Data System (ADS)

    Felisa, G.; Ciriello, V.; Antonellini, M.; Di Federico, V.; Tartakovsky, D. M.

    2015-12-01

    Salinization of shallow coastal aquifers is particularly critical for ecosystems and agricultural activities. Management of such aquifers is an open challenge, because predictive models, on which science-based decisions are to be made, often fail to capture the complexity of relevant natural and anthropogenic processes. Complicating matters further is the sparsity of hydrologic and geochemical data that are required to parameterize spatially distributed models of flow and transport. These limitations often undermine the veracity of modeling predictions and raise the question of their utility. As an alternative, we employ data-driven statistical approaches to investigate the underlying mechanisms of groundwater salinization in low coastal plains. A time-series analysis and auto-regressive moving average models allow us to establish dynamic relations between key hydrogeological variables of interest. The approach is applied to the data collected at the phreatic coastal aquifer of Ravenna, Italy. We show that, even in absence of long time series, this approach succeeds in capturing the behavior of this complex system, and provides the basis for making predictions and decisions.

  2. A quantitative assessment of methane cycling in Hikurangi Margin sediments (New Zealand) using geophysical imaging and biogeochemical modeling

    NASA Astrophysics Data System (ADS)

    Luo, Min; Dale, Andrew W.; Haffert, Laura; Haeckel, Matthias; Koch, Stephanie; Crutchley, Gareth; De Stigter, Henko; Chen, Duofu; Greinert, Jens

    2016-12-01

    Takahe seep, located on the Opouawe Bank, Hikurangi Margin, is characterized by a well-defined subsurface seismic chimney structure ˜80,500 m2 in area. Subseafloor geophysical data based on acoustic anomaly layers indicated the presence of gas hydrate and free gas layers within the chimney structure. Reaction-transport modeling was applied to porewater data from 11 gravity cores to constrain methane turnover rates and benthic methane fluxes in the upper 10 m. Model results show that methane dynamics were highly variable due to transport and dissolution of ascending gas. The dissolution of gas (up to 3761 mmol m-2 yr-1) dwarfed the rate of methanogenesis within the simulated sediment column (2.6 mmol m-2 yr-1). Dissolved methane is mainly consumed by anaerobic oxidation of methane (AOM) at the base of the sulfate reduction zone and trapped by methane hydrate formation below it, with maximum rates in the central part of the chimney (946 and 2420 mmol m-2 yr-1, respectively). A seep-wide methane budget was constrained by combining the biogeochemical model results with geophysical data and led to estimates of AOM rates, gas hydrate formation, and benthic dissolved methane fluxes of 3.68 × 104 mol yr-1, 73.85 × 104 mol yr-1, and 1.19 × 104 mol yr-1, respectively. A much larger flux of methane probably escapes in gaseous form through focused bubble vents. The approach of linking geochemical model results with spatial geophysical data put forward here can be applied elsewhere to improve benthic methane turnover rates from limited single spot measurements to larger spatial scales.

  3. The Effects of Chlorophyll Assimilation on Carbon Fluxes in a Global Biogeochemical Model. [Technical Report Series on Global Modeling and Data Assimilation

    NASA Technical Reports Server (NTRS)

    Koster, Randal D. (Editor); Rousseaux, Cecile Severine; Gregg, Watson W.

    2014-01-01

    In this paper, we investigated whether the assimilation of remotely-sensed chlorophyll data can improve the estimates of air-sea carbon dioxide fluxes (FCO2). Using a global, established biogeochemical model (NASA Ocean Biogeochemical Model, NOBM) for the period 2003-2010, we found that the global FCO2 values produced in the free-run and after assimilation were within -0.6 mol C m(sup -2) y(sup -1) of the observations. The effect of satellite chlorophyll assimilation was assessed in 12 major oceanographic regions. The region with the highest bias was the North Atlantic. Here the model underestimated the fluxes by 1.4 mol C m(sup -2) y(sup -1) whereas all the other regions were within 1 mol C m(sup -2) y(sup -1) of the data. The FCO2 values were not strongly impacted by the assimilation, and the uncertainty in FCO2 was not decreased, despite the decrease in the uncertainty in chlorophyll concentration. Chlorophyll concentrations were within approximately 25% of the database in 7 out of the 12 regions, and the assimilation improved the chlorophyll concentration in the regions with the highest bias by 10-20%. These results suggest that the assimilation of chlorophyll data does not considerably improve FCO2 estimates and that other components of the carbon cycle play a role that could further improve our FCO2 estimates.

  4. Modeling of Upwelling/Relaxation Events with the Navy Coastal Ocean Model

    DTIC Science & Technology

    2007-06-26

    2006JC003946, 2007 Art ~IA Modeling of upwelling/relaxation events with the Appro.-’d kor Public Release Navy Coastal Ocean Model Distribution Unlimited Igor...Ocean Data [6] In the present paper, the Navy Coastal Ocean Model Assimilation System [ MODAS ; Fox et. al., 2002], and uses (NCOM) [Rhodes et aL, 2002...dimensional temperature and [7] Models can provide us with additional information salinity observations derived from the MODAS . about circulation patterns

  5. An integrated coastal model for aeolian and hydrodynamic sediment transport

    NASA Astrophysics Data System (ADS)

    Baart, F.; den Bieman, J.; van Koningsveld, M.; Luijendijk, A. P.; Parteli, E. J. R.; Plant, N. G.; Roelvink, J. A.; Storms, J. E. A.; de Vries, S.; van Thiel de Vries, J. S. M.; Ye, Q.

    2012-04-01

    Dunes are formed by aeolian and hydrodynamic processes. Over the last decades numerical models were developed that capture our knowledge of the hydrodynamic transport of sediment near the coast. At the same time others have worked on creating numerical models for aeolian-based transport. Here we show a coastal model that integrates three existing numerical models into one online-coupled system. The XBeach model simulates storm-induced erosion (Roelvink et al., 2009). The Delft3D model (Lesser et al., 2004) is used for long term morphology and the Dune model (Durán et al., 2010) is used to simulate the aeolian transport. These three models were adapted to be able to exchange bed updates in real time. The updated models were integrated using the ESMF framework (Hill et al., 2004), a system for composing coupled modeling systems. The goal of this integrated model is to capture the relevant coastal processes at different time and spatial scales. Aeolian transport can be relevant during storms when the strong winds are generating new dunes, but also under relative mild conditions when the dunes are strengthened by transporting sand from the intertidal area to the dunes. Hydrodynamic transport is also relevant during storms, when high water in combination with waves can cause dunes to avalanche and erode. While under normal conditions the hydrodynamic transport can result in an onshore transport of sediment up to the intertidal area. The exchange of sediment in the intertidal area is a dynamic interaction between the hydrodynamic transport and the aeolian transport. This dynamic interaction is particularly important for simulating dune evolution at timescales longer than individual storm events. The main contribution of the integrated model is that it simulates the dynamic exchange of sediment between aeolian and hydrodynamic models in the intertidal area. By integrating the numerical models, we hope to develop a model that has a broader scope and applicability than

  6. A coupled hydrologic and biogeochemical model for assessing watershed responses to climate and land use

    EPA Science Inventory

    This seminar for Oregon State University’s Water Resources Graduate Program will describe the use of a spatially-distributed ecohydrological model, VELMA, for quantifying how alternative land use and climate scenarios affect tradeoffs among important ecosystem services. Sp...

  7. A coupled hydrologic and biogeochemical model for assessing watershed responses to climate and land use

    EPA Science Inventory

    This seminar for Oregon State University’s Water Resources Graduate Program will describe the use of a spatially-distributed ecohydrological model, VELMA, for quantifying how alternative land use and climate scenarios affect tradeoffs among important ecosystem services. Sp...

  8. Parameter sensitivity and identifiability for a biogeochemical model of hypoxia in the northern Gulf of Mexico

    EPA Science Inventory

    Local sensitivity analyses and identifiable parameter subsets were used to describe numerical constraints of a hypoxia model for bottom waters of the northern Gulf of Mexico. The sensitivity of state variables differed considerably with parameter changes, although most variables ...

  9. Contribution of subsurface chlorophyll maxima to primary production in the coastal Beaufort Sea (Canadian Arctic): A model assessment

    NASA Astrophysics Data System (ADS)

    Martin, Johannie; Dumont, Dany; Tremblay, Jean-Éric

    2013-11-01

    Previous comprehensive investigations of the Canadian Arctic revealed that subsurface chlorophyll maxima (SCM) are widespread and long-lived structures that can contribute significantly to daily primary production in the water column. However, estimating the annual contribution of SCM to production with in situ or remote-sensing approaches is challenging in the high Arctic. For this reason and to estimate the impacts of fluctuating or changing environmental conditions on SCM, a numerical approach combining a turbulence model and an ecosystem model was implemented for the coastal Beaufort Sea. An ensemble analysis of simulations suggested that SCM contribute 65-90% of total annual primary production and that this proportion is weakly affected by ice regime, winter nitrogen (N) concentration, parameter values determining phytoplankton growth and decay or the physical forcing imposed, all varying within realistic values. Due to the persistent association between the SCM and the shallow nitracline, the pelagic ecosystem of the coastal Beaufort Sea is apparently characterized by a high ratio of new to total production, contrasting with the common assumption that oligotrophic systems are predominantly supported by recycled N and regenerated production. This study demonstrated that the use of a simple model in combination with in situ data leads to novel insights into biogeochemical processes that are otherwise very difficult to measure and track.

  10. Adaptive Unstructured Grid Generation for Modeling of Coastal Margins

    DTIC Science & Technology

    1999-09-30

    Baptista and Edward Myers have developed models for predicting and mapping tsunami inundation of the Oregon and Washington coasts from Cascadia Subduction ...Protection of the Portuguese Coastal Zone , sponsored in the Portuguese side by FCT - Fundação para a Ciência e Tecnologia. The FCT project will, in... Zone and remote earthquakes. The research is sponsored by NOAA and DOGAMI. The analysis of energy conservation as an error norm (Myers and Baptista

  11. Long-term Morphological Modeling at Coastal Inlets

    DTIC Science & Technology

    2015-05-15

    the tidal shoals. In this study, model results are presented for a 10-year simulation of an idealized inlet and bay system with dimensions similar to...Introduction Coastal barrier-inlet systems are relatively short and narrow channels connecting the open ocean with sheltered bays, lagoons , or...of tidal flow, waves, and morphology at barrier-inlet systems extend over a wide range of temporal and spatial scales. Thus, the prediction of the

  12. Beyond The Blueprint: Development Of Genome-Informed Trait-Based Models For Prediction Of Microbial Dynamics And Biogeochemical Rates

    NASA Astrophysics Data System (ADS)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Johnson, J. N.; Bouskill, N.; Hug, L. A.; Thomas, B. C.; Castelle, C. J.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.

    2014-12-01

    -guild trait variability amongst other parameters and are using this model to explore abiotic controls on community emergence and impact on rates of reactions that contribute to the cycling of carbon across biogeochemical gradients from the soil to the subsurface.

  13. Analyzing early exo-Earths with a coupled atmosphere biogeochemical model

    NASA Astrophysics Data System (ADS)

    Gebauer, Stefanie; Grenfell, John Lee; Stock, Joachim; Lehmann, Ralph; Godolt, Mareike; von Paris, Philip; Rauer, Heike

    2017-04-01

    Investigating Earth-like extrasolar planets with atmospheric models is a central focus in planetary science. Taking the development of Earth as a reference for Earth-like planets we investigate interactions between the atmosphere, planetary surface and organisms. The Great Oxidation Event (GOE) is related to feedbacks between these three. Its origin and controlling mechanisms are not well defined - requiring interdisciplinary, coupled models. We present results from our newly-developed Coupled Atmosphere Biogeochemistry (CAB) model which is unique in the literature. Applying a unique tool (Pathway Analysis Program), ours is the first quantitative analysis of catalytic cycles governing O2 in early Earth's atmosphere near the GOE. Complicated oxidation pathways play a key role in destroying O2 whereas in the upper atmosphere, most O2 is formed abiotically via CO2 photolysis.

  14. Assessment of global nitrogen pollution in rivers using an integrated biogeochemical modeling framework.

    PubMed

    He, Bin; Kanae, Shinjiro; Oki, Taikan; Hirabayashi, Yukiko; Yamashiki, Yosuke; Takara, Kaoru

    2011-04-01

    This study has analyzed the global nitrogen loading of rivers resulting from atmospheric deposition, direct discharge, and nitrogenous compounds generated by residential, industrial, and agricultural sources. Fertilizer use, population distribution, land cover, and social census data were used in this study. A terrestrial nitrogen cycle model with a 24-h time step and 0.5° spatial resolution was developed to estimate nitrogen leaching from soil layers in farmlands, grasslands, and natural lands. The N-cycle in this model includes the major processes of nitrogen fixation, nitrification, denitrification, immobilization, mineralization, leaching, and nitrogen absorption by vegetation. The previously developed Total Runoff Integrating Pathways network was used to analyze nitrogen transport from natural and anthropogenic sources through river channels, as well as the collecting and routing of nitrogen to river mouths by runoff. Model performance was evaluated through nutrient data measured at 61 locations in several major world river basins. The dissolved inorganic nitrogen concentrations calculated by the model agreed well with the observed data and demonstrate the reliability of the proposed model. The results indicate that nitrogen loading in most global rivers is proportional to the size of the river basin. Reduced nitrate leaching was predicted for basins with low population density, such as those at high latitudes or in arid regions. Nitrate concentration becomes especially high in tropical humid river basins, densely populated basins, and basins with extensive agricultural activity. On a global scale, agriculture has a significant impact on the distribution of nitrogenous compound pollution. The map of nitrate distribution indicates that serious nitrogen pollution (nitrate concentration: 10-50 mg N/L) has occurred in areas with significant agricultural activities and small precipitation surpluses. Analysis of the model uncertainty also suggests that the nitrate

  15. Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms

    NASA Astrophysics Data System (ADS)

    Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; Yang, Ziming; Graham, David E.; Gu, Baohua; Painter, Scott L.; Thornton, Peter E.

    2016-09-01

    Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe the observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.

  16. Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms

    DOE PAGES

    Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; ...

    2016-09-12

    Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe themore » observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.« less

  17. Natural biogeochemical cycle of mercury in a global three-dimensional ocean tracer model

    NASA Astrophysics Data System (ADS)

    Zhang, Yanxu; Jaeglé, Lyatt; Thompson, LuAnne

    2014-05-01

    We implement mercury (Hg) biogeochemistry in the offline global 3-D ocean tracer model (OFFTRAC) to investigate the natural Hg cycle, prior to any anthropogenic input. The simulation includes three Hg tracers: dissolved elemental (Hg0aq), dissolved divalent (HgIIaq), and particle-bound mercury (HgPaq). Our Hg parameterization takes into account redox chemistry in ocean waters, air-sea exchange of Hg0, scavenging of HgIIaq onto sinking particles, and resupply of HgIIaq at depth by remineralization of sinking particles. Atmospheric boundary conditions are provided by a global simulation of the natural atmospheric Hg cycle in the GEOS-Chem model. In the surface ocean, the OFFTRAC model predicts global mean concentrations of 0.16 pM for total Hg, partitioned as 80% HgIIaq, 14% Hg0aq, and 6% HgPaq. Total Hg concentrations increase to 0.38 pM in the thermocline/intermediate waters (between the mixed layer and 1000 m depth) and 0.82 pM in deep waters (below 1000 m), reflecting removal of Hg from the surface to the subsurface ocean by particle sinking followed by remineralization at depth. Our model predicts that Hg concentrations in the deep North Pacific Ocean (>2000 m) are a factor of 2-3 higher than in the deep North Atlantic Ocean. This is the result of cumulative input of Hg from particle remineralization as deep waters transit from the North Atlantic to the North Pacific on their ~2000 year journey. The model is able to reproduce the relatively uniform concentrations of total Hg observed in the old deep waters of the North Pacific Ocean (observations: 1.2 ± 0.4 pM; model: 1.1 ± 0.04 pM) and Southern Ocean (observations: 1.1 ± 0.2 pM; model: 0.8 ± 0.02 pM). However, the modeled concentrations are factors of 5-6 too low compared to observed concentrations in the surface ocean and in the young water masses of the deep North Atlantic Ocean. This large underestimate for these regions implies a factor of 5-6 anthropogenic enhancement in Hg concentrations.

  18. Development and evaluation of the offshore and coastal dispersion model

    SciTech Connect

    Hanna, S.R.; Schulman, L.L.; Paine, R.J.; Pleim, J.E.; Baer, M.

    1985-10-01

    The Offshore and Coastal Dispersion (OCD) model has been developed for the Minerals Management Service (MMS) to determine the impact of offshore and onshore emissions from point sources on the air quality of coastal regions. Constructed on the framework of the EPA guideline model MPTER, the OCD model incorporates overwater plume transport and dispersion as well as changes that occur as the plume crosses the shoreline. Hourly meteorological data are needed from both offshore and onshore locations, including wind direction and speed, mixing height, overwater air temperature and relative humidity, and the sea surface temperature. Observed turbulence intensities are preferred by the model but are not mandatory. Dispersion coefficients are proportional to turbulence intensities. A virtual source technique is used to change the rate of plume growth as the overwater plume intercepts the overland internal boundary layer. The continuous shoreline fumigation case is treated using an approach suggested by Deardorff and Willis. Calculation of plume reflection from elevated terrain follows the Rough Terrain Dispersion Model (RTDM). The OCD model and the modified EPA model used as an interim model for overwater applications by the MMS were tested with measurements from three offshore tracer experiments. The OCD model was shown to be a clear improvement over the EPA model and was officially approved by the MMS in March 1985.

  19. A Hierarchical Bayesian Model for Estimating Remediation-induced Biogeochemical Transformations Using Spectral Induced Polarization Data: Development and Application to the Contaminated DOE Rifle (CO) Site

    NASA Astrophysics Data System (ADS)

    Chen, J.; Hubbard, S. S.; Williams, K. H.; Tuglus, C.; Flores-Orozco, A.; Kemna, A.

    2010-12-01

    Although in-situ bioremediation is often considered as a key approach for subsurface environmental remediation, monitoring induced biogeochemical processes, needed to evaluate the efficacy of the treatments, is challenging over field relevant scales. In this study, we develop a hierarchical Bayesian model that builds on our previous framework for estimating biogeochemical transformations using geochemical and geophysical data obtained from laboratory column experiments. The new Bayesian model treats the induced biogeochemical transformations as both spatial and temporal (rather than just temporal) processes and combines time-lapse borehole ‘point’ geochemical measurements with inverted surface- or crosshole-based spectral induced polarization (SIP) data. This model consists of three levels of statistical sub-models: (1) data model (or likelihood function), which provides links between the biogeochemical end-products and geophysical attributes, (2) process model, which describes the spatial and temporal variability of biogeochemical properties in the disturbed subsurface systems, and (3) parameter model, which describes the prior distributions of various parameters and initial conditions. The joint posterior probability distribution is explored using Markov Chain Monte Carlo sampling methods to obtain the spatial and temporal distribution of the hidden parameters. We apply the developed Bayesian model to the datasets collected from the uranium-contaminated DOE Rifle site for estimating the spatial and temporal distribution of remediation-induced end products. The datasets consist of time-lapse wellbore aqueous geochemical parameters (including Fe(II), sulfate, sulfide, acetate, uranium, chloride, and bromide concentrations) and surface SIP data collected over 13 frequencies (ranging from 0.065Hz to 256Hz). We first perform statistical analysis on the multivariate data to identify possible patterns (or ‘diagnostic signatures’) of bioremediation, and then we

  20. Coupling AVHRR imagery with biogeochemical models of methane emission from rice crops

    NASA Astrophysics Data System (ADS)

    Paliouras, Eleni Joyce

    2000-10-01

    Rice is a staple food source for much of the world and most of it is grown in paddies which remain flooded for a large part of the growing season. This anaerobic environment is ideal for the activities of methanogenic bacteria, that are responsible for the production of methane gas, some of which is released into the atmosphere. In order to better understand the role that rice cropping plays in the levels of atmospheric methane, several models have been developed to predict the methane flux from the paddies. These models generally utilize some type of nominal plant growth curve based on one or two pieces of ground truth data. Ideally, satellite data could be used instead to provide these models with an estimate of biomass change over the growing season, eliminating the need for related ground truth. A technique proposed to accomplish this is presented here, and results that demonstrate its success when applied to rice cropping areas of Texas are discussed. Also presented is a method for utilizing satellite data to map rice cropping areas that could eventually aid in a scheme for populating a GIS-type database with information on exact rice cropping areas. Such a database could then be directly tied to the methane emission models to obtain flux estimates for extensive regional areas.

  1. Modeling the effects of coastal wind- and wind-stress curl-driven upwellings on plankton dynamics in the Southern California current system

    NASA Astrophysics Data System (ADS)

    Macías, D.; Franks, P. J. S.; Ohman, M. D.; Landry, M. R.

    2012-06-01

    We use a Nitrogen-Phytoplankton-Zooplankton-Detritus (NPZD) biogeochemical model implemented in a time-dependent box model scheme to simulate the temporal dynamics of the pelagic ecosystem in the Southern California Current System (SCCS). The model was forced by winds, sea surface temperature and light. Nutrient inputs to the modeled box were driven by coastal upwelling or upwelling due to wind-stress curl in order to assess the importance of each process in the temporal dynamics of the SCCS ecosystem. Model results were compared to the CalCOFI dataset, both in terms of climatological annual cycles and actual values. This comparison led to modifications of the basic model structure to better represent the coastal ecosystem, particularly phytoplankton growth and zooplankton mortality terms. Wind-stress curl-induced upwelling was found to be significant only in the offshore regions while coastal upwelling better represented the dynamics of the inshore areas. The two upwelling mechanisms work in synchrony, however, to bring nutrients to surface waters during the same time periods. Finally, the effect of low-frequency perturbations, such as those associated with the ENSO and NPGO, were assessed by comparing model results and data. Since the NPGO cycle largely impacts the SCCS through modifications of upwelling-favorable winds, its effects were well represented in the model results. In contrast, ENSO responses were poorly captured in the simulations because such perturbations alter the system by changing surface water mass distributions via mechanisms that were not included in the model forcing.

  2. Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales.

    PubMed

    Bridgham, Scott D; Cadillo-Quiroz, Hinsby; Keller, Jason K; Zhuang, Qianlai

    2013-05-01

    Understanding the dynamics of methane (CH4 ) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2 ) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr(-1) , which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry

  3. Modeling of Natural Coastal Hazards in Puerto Rico in Support of Emergency Management and Coastal Planning

    NASA Astrophysics Data System (ADS)

    Mercado, A., Jr.

    2015-12-01

    The island of Puerto Rico is not only located in the so-called Caribbean hurricane alley, but is also located in a tsunami prone region. And both phenomena have affected the island. For the past few years we have undergone the task of upgrading the available coastal flood maps due to storm surges and tsunamis. This has been done taking advantage of new Lidar-derived, high resolution, topography and bathymetry and state-of-the-art models (MOST for tsunamis and ADCIRC/SWAN for storm surges). The tsunami inundation maps have been converted to evacuation maps. In tsunamis we are also working in preparing hazard maps due to tsunami currents inside ports, bays, and marinas. The storm surge maps include two scenarios of sea level rise: 0.5 and 1.0 m above Mean High Water. All maps have been adopted by the Puerto Rico State Emergency Management Agency, and are publicly available through the Internet. It is the purpose of this presentation to summarize how it has been done, the spin-off applications they have generated, and how we plan to improve coastal flooding predictions.

  4. Kinetic Modeling of Biogeochemical Processes in Subsurface Environments: Coupling Transport, Microbial Metabolism and Geochemistry

    NASA Astrophysics Data System (ADS)

    Wang, Y.

    2002-12-01

    Microbial reactions play an important role in regulating pore water chemistry (e.g., pH and Eh) as well as secondary mineral distribution in many subsurface systems and therefore directly control trace metal migration and recycling in those systems. In this paper, we present a multicomponent kinetic model that explicitly accounts for the coupling of microbial metabolism, microbial population dynamics, advective/dispersive transport of chemical species, aqueous speciation, and mineral precipitation/dissolution in porous geologic media. A modification to the traditional microbial growth kinetic equation is proposed, to account for the likely achievement of quasi-steady state biomass accumulations in natural environments. A scale dependence of microbial reaction rates is derived based on both field observations and the scaling analysis of reactive transport equations. As an example, we use the model to simulate a subsurface contaminant migration scenario, in which a water flow containing both uranium and a complexing organic ligand is recharged into an oxic carbonate aquifer. The model simulation shows that Mn and Fe oxyhydroxides may vary significantly along a flow path. The simulation also shows that uranium (VI) can be reduced and therefore immobilized in the anoxic zone created by microbial degradation. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy (US DOE) under Contract DE-AC04-94AL85000.

  5. Modeling tidal circulation in coastal seas

    SciTech Connect

    Spaulding, M.L.; Beauchamp, C.H.

    1983-01-01

    The two-dimensional vertically averaged hydrodynamic equations solved by V.V. Leenderstee's multi-operational finite difference scheme have been used to study tidal circulation in Long Island Sound, Block Island Sound, Rhode Island Sound, and Buzzards Bay (located along the southern New England coastline). Using data on tidal elevation along the model open boundaries as input, a series of simulations have been performed to calibrate the model by varying bottom friction and topography. Comparison of predicted tidal range, high and low tidal phase lag, and tidal currents to observed values shows excellent agreement and clearly illustrates the standing wave character of the tide in Long Island Sound. Significant improvements in predicting tidal dynamics in the study region require additional information on the frequency composition and shape of the tidal wave entering the area and refinement of the grid system at the entrance to Long Island Sound.

  6. SENEQUE: a multi-scaling GIS interface to the Riverstrahler model of the biogeochemical functioning of river systems.

    PubMed

    Ruelland, Denis; Billen, Gilles; Brunstein, Daniel; Garnier, Josette

    2007-04-01

    The Riverstrahler model describes the biogeochemical functioning of an entire river system, from 100 to 100,000 km(2) or more, taking into account the constraints set by the morphology of the drainage network, the meteorological/hydrological conditions, and the inputs of material from point and non-point sources in the watershed. This tool has been applied for research purpose to several river systems differing in terms of hydrological regime and anthropogenic influences. In order to improve its capabilities and its generic dimension, as well as to develop a user-friendly interface allowing its transfer to non-specialist users including managers, the model has been coupled to a GIS interface. This gives the user the possibility to visualize the available geospatial database, to select the best geographical representation of the drainage network, to automatically prepare the corresponding input files required for the model, to pilot the model calculation and to visualize the results. The coupling with a GIS interface has considerably improved the capabilities of the Riverstrahler model. The code of the model is now entirely generic and can be run on any river system for which a suitable database is available. Its spatial resolution can be adapted to the requirement of the relevant problem, from the highest level, where each elementary watershed is individualized, to the lower level, where the whole basin is idealized as one basin with tributaries of each order having the same characteristics. As an illustration of the new potentialities offered by the coupling of Riverstrahler with a GIS through the SENEQUE interface, the results of a same modeling scenario are compared at different spatial resolutions. For the first time, with on-line coupling to a geodatabase, the effect of increasing the spatial resolution of the drainage network representation on the performance of the Riverstrahler model has been examined. At the outlet of the basin, the water quality results

  7. Impact of climate change on ecological quality indicators and biogeochemical fluxes in the Baltic sea: a multi-model ensemble study.

    PubMed

    Meier, H E Markus; Müller-Karulis, Bärbel; Andersson, Helén C; Dieterich, Christian; Eilola, Kari; Gustafsson, Bo G; Höglund, Anders; Hordoir, Robinson; Kuznetsov, Ivan; Neumann, Thomas; Ranjbar, Zohreh; Savchuk, Oleg P; Schimanke, Semjon

    2012-09-01

    Multi-model ensemble simulations using three coupled physical-biogeochemical models were performed to calculate the combined impact of projected future climate change and plausible nutrient load changes on biogeochemical cycles in the Baltic Sea. Climate projections for 1961-2099 were combined with four nutrient load scenarios ranging from a pessimistic business-as-usual to a more optimistic case following the Helsinki Commission's (HELCOM) Baltic Sea Action Plan (BSAP). The model results suggest that in a future climate, water quality, characterized by ecological quality indicators like winter nutrient, summer bottom oxygen, and annual mean phytoplankton concentrations as well as annual mean Secchi depth (water transparency), will be deteriorated compared to present conditions. In case of nutrient load reductions required by the BSAP, water quality is only slightly improved. Based on the analysis of biogeochemical fluxes, we find that in warmer and more anoxic waters, internal feedbacks could be reinforced. Increased phosphorus fluxes out of the sediments, reduced denitrification efficiency and increased nitrogen fixation may partly counteract nutrient load abatement strategies.

  8. Mapping and modeling the biogeochemical cycling of turf grasses in the United States.

    PubMed

    Milesi, Cristina; Running, Steven W; Elvidge, Christopher D; Dietz, John B; Tuttle, Benjamin T; Nemani, Ramakrishna R

    2005-09-01

    Turf grasses are ubiquitous in the urban landscape of the United States and are often associated with various types of environmental impacts, especially on water resources, yet there have been limited efforts to quantify their total surface and ecosystem functioning, such as their total impact on the continental water budget and potential net ecosystem exchange (NEE). In this study, relating turf grass area to an estimate of fractional impervious surface area, it was calculated that potentially 163,800 km2 (+/- 35,850 km2) of land are cultivated with turf grasses in the continental United States, an area three times larger than that of any irrigated crop. Using the Biome-BGC ecosystem process model, the growth of warm-season and cool-season turf grasses was modeled at a number of sites across the 48 conterminous states under different management scenarios, simulating potential carbon and water fluxes as if the entire turf surface was to be managed like a well-maintained lawn. The results indicate that well-watered and fertilized turf grasses act as a carbon sink. The potential NEE that could derive from the total surface potentially under turf (up to 17 Tg C/yr with the simulated scenarios) would require up to 695 to 900 liters of water per person per day, depending on the modeled water irrigation practices, suggesting that outdoor water conservation practices such as xeriscaping and irrigation with recycled waste-water may need to be extended as many municipalities continue to face increasing pressures on freshwater.

  9. Spatial Modeling in The Coastal Area of East Java Province

    NASA Astrophysics Data System (ADS)

    Fadlilah Kurniawati, Ummi

    2017-07-01

    The existence of gaps that occur between regions, shows that it is a reasonable process considering that each region has different initial endowment factors. The first step that can be done to controll disparity is know what is the benchmark of the gap. The revenue growth indicator is one of benchmark for measuring regional disparities. The regional output is represented by the gross domestic regional income per capita. Concerning the phenomenon of regional disparity, East Java Province is concentrated in the north-south part, especially in coastal areas is an early indication of the gap. This is what prompted the analysis of predictor factors affecting the disparity in East Java Coastal Areas through a spatial modeling approach. Spatial modeling is done on the consideration that there are different local characteristics or potentials in each regency / city. Factors Economic growth, social factors, and physical development factors are the main factors in this study will be described in derived variables to obtain a clear picture of the influence of each factor to the disparity that occurred in the Coastal Region of East Java Province.

  10. Reconstructing paleo-ocean silicon chemistry and ecology during Last Glacial Maximum, a biogeochemical cycle modeling approach

    NASA Astrophysics Data System (ADS)

    Li, D. D.; Lerman, A.; Mackenzie, F. T.

    2012-12-01

    It has been established by a number of investigators that opal content and Si-C isotope studies in the marine sediments reveal information about paleooceanography and the impact on silicic acid utilization by marine autotrophes (diatoms, silicoflagellates) and heterotrophes (radiolarians) during the Last Glacial Maximum (LGM). Opal, as an amorphous form of SiO2, formed by marine Si-secreting organisms, has been used as a proxy to indicate chemical ocean evolution, paleoproductivity and temperature variations in the paleoenvironment and regional ocean water biogeochemical studies, both on million- and thousand-year scales. Here, we are using a model of the global silicon biogeochemical cycle to understand and reconstruct evolutionary history of the paleobiogeochemical cycle and paleoenvironment since LGM. The model is process-driven, temperature-driven, and land-ocean-sediment coupled with specific marine Si-secreting organisms that represent different trophic levels and physiological mechanisms. Specifically, Si utilization by marine silicoflagellates and radiolarians are each about 5% of that of ubiquitous marine diatoms. Available marine reactive Si is controlled by variation of diatom bioproduction that represents 5% of the total marine primary productivity (Si/C Redfield ratio in the marine organic matter is ~0.13, which is an order of magnitude higher than ratio in land organic matter). River input of Si is controlled by chemical weathering of silicate rocks and biocyling of land plant phytoliths. Decreasing dissolved and particulate Si input from land and less favorable climatic condition into LGM diminished the primary production of marine diatoms. However, because radiolarians favor deep-water habitat, where a higher level of DSi is found and that is less affected by temperature changes, a peak of relative abundance is usually observed in sedimentary record during LGM. Given that opal formation fractionated seawater δ30Si (1‰) and enriched seawater with

  11. Estimates of fire emissions from an active deforestation region in the southern Amazon based on satellite data and biogeochemical modelling

    NASA Astrophysics Data System (ADS)

    van der Werf, G. R.; Morton, D. C.; Defries, R. S.; Giglio, L.; Randerson, J. T.; Collatz, G. J.; Kasibhatla, P. S.

    2008-09-01

    Tropical deforestation contributes to the build-up of atmospheric carbon dioxide in the atmosphere. Within the deforestation process, fire is frequently used to eliminate biomass in preparation for agricultural use. Quantifying these deforestation-induced fire emissions represents a challenge, and current estimates are only available at coarse spatial resolution with large uncertainty. Here we developed a biogeochemical model using remote sensing observations of plant productivity, fire activity, and deforestation rates to estimate emissions for the Brazilian state of Mato Grosso during 2001 2005. Our model of DEforestation CArbon Fluxes (DECAF) runs at 250-m spatial resolution with a monthly time step to capture spatial and temporal heterogeneity in fire dynamics in our study area within the "arc of deforestation", the southern and eastern fringe of the Amazon tropical forest where agricultural expansion is most concentrated. Fire emissions estimates from our modelling framework were on average 90 Tg C year-1, mostly stemming from fires associated with deforestation (74%) with smaller contributions from fires from conversions of Cerrado or pastures to cropland (19%) and pasture fires (7%). In terms of carbon dynamics, about 80% of the aboveground living biomass and litter was combusted when forests were converted to pasture, and 89% when converted to cropland because of the highly mechanized nature of the deforestation process in Mato Grosso. The trajectory of land use change from forest to other land uses often takes more than one year, and part of the biomass that was not burned in the dry season following deforestation burned in consecutive years. This led to a partial decoupling of annual deforestation rates and fire emissions, and lowered interannual variability in fire emissions. Interannual variability in the region was somewhat dampened as well because annual emissions from fires following deforestation and from maintenance fires did not covary, although

  12. Estimates of fire emissions from an active deforestation region in the southern Amazon based on satellite data and biogeochemical modelling

    NASA Astrophysics Data System (ADS)

    van der Werf, G. R.; Morton, D. C.; Defries, R. S.; Giglio, L.; Randerson, J. T.; Collatz, G. J.; Kasibhatla, P. S.

    2009-02-01

    Tropical deforestation contributes to the build-up of atmospheric carbon dioxide in the atmosphere. Within the deforestation process, fire is frequently used to eliminate biomass in preparation for agricultural use. Quantifying these deforestation-induced fire emissions represents a challenge, and current estimates are only available at coarse spatial resolution with large uncertainty. Here we developed a biogeochemical model using remote sensing observations of plant productivity, fire activity, and deforestation rates to estimate emissions for the Brazilian state of Mato Grosso during 2001-2005. Our model of DEforestation CArbon Fluxes (DECAF) runs at 250-m spatial resolution with a monthly time step to capture spatial and temporal heterogeneity in fire dynamics in our study area within the ''arc of deforestation'', the southern and eastern fringe of the Amazon tropical forest where agricultural expansion is most concentrated. Fire emissions estimates from our modelling framework were on average 90 Tg C year-1, mostly stemming from fires associated with deforestation (74%) with smaller contributions from fires from conversions of Cerrado or pastures to cropland (19%) and pasture fires (7%). In terms of carbon dynamics, about 80% of the aboveground living biomass and litter was combusted when forests were converted to pasture, and 89% when converted to cropland because of the highly mechanized nature of the deforestation process in Mato Grosso. The trajectory of land use change from forest to other land uses often takes more than one year, and part of the biomass that was not burned in the dry season following deforestation burned in consecutive years. This led to a partial decoupling of annual deforestation rates and fire emissions, and lowered interannual variability in fire emissions. Interannual variability in the region was somewhat dampened as well because annual emissions from fires following deforestation and from maintenance fires did not covary, although

  13. Predicting coastal cliff erosion using a Bayesian probabilistic model

    USGS Publications Warehouse

    Hapke, Cheryl J.; Plant, Nathaniel G.

    2010-01-01

    Regional coastal cliff retreat is difficult to model due to the episodic nature of failures and the along-shore variability of retreat events. There is a growing demand, however, for predictive models that can be used to forecast areas vulnerable to coastal erosion hazards. Increasingly, probabilistic models are being employed that require data sets of high temporal density to define the joint probability density function that relates forcing variables (e.g. wave conditions) and initial conditions (e.g. cliff geometry) to erosion events. In this study we use a multi-parameter Bayesian network to investigate correlations between key variables that control and influence variations in cliff retreat processes. The network uses Bayesian statistical methods to estimate event probabilities using existing observations. Within this framework, we forecast the spatial distribution of cliff retreat along two stretches of cliffed coast in Southern California. The input parameters are the height and slope of the cliff, a descriptor of material strength based on the dominant cliff-forming lithology, and the long-term cliff erosion rate that represents prior behavior. The model is forced using predicted wave impact hours. Results demonstrate that the Bayesian approach is well-suited to the forward modeling of coastal cliff retreat, with the correct outcomes forecast in 70–90% of the modeled transects. The model also performs well in identifying specific locations of high cliff erosion, thus providing a foundation for hazard mapping. This approach can be employed to predict cliff erosion at time-scales ranging from storm events to the impacts of sea-level rise at the century-scale.

  14. Soil Biogeochemical Properties and Erosion Source Prediction Model Summary for the Buffalo Bayou Watershed, Houston, Texas

    NASA Astrophysics Data System (ADS)

    Ahmed, I.

    2015-12-01

    We draw conclusions on the research output and findings from a 4-year multidisciplinary USDA-CBG collaborative program in sustainable integrated monitoring of soil organic carbon (SOC) loss prediction via erosion. The underlying method uses the state-of-the-art stable isotope science of sediment tracing under uncertain hydrologic influences. The research finds are rooted in the (i) application of Bayesian Markov Chain Monte Carlo statistical models to assess the relationship between rainfall-runoff and soil erosion in space and time, (ii) capture of the episodic nature of rainfall events and its role in the spatial distribution of SOC loss from water erosion, (iii) stable isotope composition guided fingerprinting (source and quantity) of eroded soil, and (iv) the creation of an integrated watershed scale statistical soil loss monitoring model driven by spatial and temporal correlation of flow and stable isotope composition. The research theme was successfully applied on the urbanized Buffalo Bayou Watershed in Houston, Texas. The application brought to light novel future research conceptual outlines which will also be discussed in this deliverable to the AGU meeting. These include but not limited to: regional rainfall cluster research, physics of muddy river-bank soil and suspended sediment interaction, and friction & mobility that together make up the plasticity of soil aggregates that control erosion processes and landscape changes in a riparian corridor. References: Ahmed, I., Karim, A., Boutton, T.W., and Strom, K.B. (2013a). "Monitoring Soil Organic Carbon Loss from Erosion Using Stable Isotopes." Proc., Soil Carbon Sequestration, International Conference, May 26-29, Reykjavik, Iceland. Ahmed, I, Bouttom, T.W., Strom, K. B., Karim, A., and Irvin-Smith, N. (2013b). "Soil carbon distribution and loss monitoring in the urbanized Buffalo Bayou watershed, Houston, Texas." Proc., 4th Annual All Investigators Meeting of the North American Carbon Program, February 4

  15. Toward a Predictive Model of Arctic Coastal Retreat in a Warming Climate, Beaufort Sea, Alaska

    DTIC Science & Technology

    2012-09-30

    quantify the environmental drivers of rapid coastal erosion in the Arctic, and to begin developing predictive models of future rates of coastal erosion ...wave) energy in driving coastal erosion in the Arctic. We are combining high-resolution observations of coastline retreat with meteorological and...content, ice-wedge polygon spacing, and the thermal properties of bluff materials; 2) time-lapse photography to observe coastal erosion processes in

  16. Modeling physical and biogeochemical controls over carbon accumulation in a boreal forest soil

    USGS Publications Warehouse

    Carrasco, J.J.; Neff, J.C.; Harden, J.W.

    2006-01-01

    Boreal soils are important to the global C cycle owing to large C stocks, repeated disturbance from fire, and the potential for permafrost thaw to expose previously stable, buried C. To evaluate the primary mechanisms responsible for both short- and long-term C accumulation in boreal soils, we developed a multi-isotope (12,14C) Soil C model with dynamic soil layers that develop through time as soil organic matter burns and reaccumulates. We then evaluated the mechanisms that control organic matter turnover in boreal regions including carbon input rates, substrate recalcitrance, soil moisture and temperature, and the presence of historical permafrost to assess the importance of these factors in boreal C accumulation. Results indicate that total C accumulation is controlled by the rate of carbon input, decomposition rates, and the presence of historical permafrost. However, unlike more temperate ecosystems, one of the key mechanisms involved in C preservation in boreal soils examined here is the cooling of subsurface soil layers as soil depth increases rather than increasing recalcitrance in subsurface soils. The propagation of the 14C bomb spike into soils also illustrates the importance of historical permafrost and twentieth century warming in contemporary boreal soil respiration fluxes. Both 14C and total C simulation data also strongly suggest that boreal SOM need not be recalcitrant to accumulate; the strong role of soil temperature controls on boreal C accumulation at our modeling test site in Manitoba, Canada, indicates that carbon in the deep organic soil horizons is probably relatively labile and thus subject to perturbations that result from changing climatic conditions in the future. Copyright 2006 by the American Geophysical Union.

  17. Atmosphere-ocean ozone exchange: A global modeling study of biogeochemical, atmospheric, and waterside turbulence dependencies

    NASA Astrophysics Data System (ADS)

    Ganzeveld, L.; Helmig, D.; Fairall, C. W.; Hare, J.; Pozzer, A.

    2009-12-01

    The significance of the removal of tropospheric ozone by the oceans, covering ˜2/3 of the Earth's surface, has only been addressed in a few studies involving water tank, aircraft, and tower flux measurements. On the basis of results from these few observations of the ozone dry deposition velocity (VdO3), atmospheric chemistry models generally apply an empirical, constant ocean uptake rate of 0.05 cm s-1. This value is substantially smaller than the atmospheric turbulent transport velocity for ozone. On the other hand, the uptake is higher than expected from the solubility of ozone in clean water alone, suggesting that there is an enhancement in oceanic ozone uptake, e.g., through a chemical destruction mechanism. We present an evaluation of a global-scale analysis with a new mechanistic representation of atmosphere-ocean ozone exchange. The applied atmosphere chemistry-climate model includes not only atmospheric but also waterside turbulence and the role of waterside chemical loss processes as a function of oceanic biogeochemistry. The simulations suggest a larger role of biogeochemistry in tropical and subtropical ozone oceanic uptake with a relative small temporal variability, whereas in midlatitude and high-latitude regions, highly variable ozone uptake rates are expected because of the stronger influence of waterside turbulence. Despite a relatively large range in the explicitly calculated ocean uptake rate, there is a surprisingly small sensitivity of simulated Marine Boundary Layer ozone concentrations compared to the sensitivity for the commonly applied constant ocean uptake approach. This small sensitivity points at compensating effects through inclusion of the process-based ocean uptake mechanisms to consider variability in oceanic O3 deposition consistent with that in atmospheric and oceanic physical, chemical, and biological processes.

  18. Particle Tracking Model (PTM) with Coastal Modeling System (CMS)

    DTIC Science & Technology

    2014-10-31

    applications of CMS-PTM include Long Island Sound, Connecticut; Shinnecock Inlet, New York; Ocean City, Maryland; Poplar Island, Maryland; Cape Fear ...load and bed load, and deposition and resuspension in coastal, estuarine and river environments. Local sediment particle sources include dredging

  19. Probabilistic Downscaling of Remote Sensing Data with Applications for Multi-Scale Biogeochemical Flux Modeling

    PubMed Central

    Stoy, Paul C.; Quaife, Tristan

    2015-01-01

    Upscaling ecological information to larger scales in space and downscaling remote sensing observations or model simulations to finer scales remain grand challenges in Earth system science. Downscaling often involves inferring subgrid information from coarse-scale data, and such ill-posed problems are classically addressed using regularization. Here, we apply two-dimensional Tikhonov Regularization (2DTR) to simulate subgrid surface patterns for ecological applications. Specifically, we test the ability of 2DTR to simulate the spatial statistics of high-resolution (4 m) remote sensing observations of the normalized difference vegetation index (NDVI) in a tundra landscape. We find that the 2DTR approach as applied here can capture the major mode of spatial variability of the high-resolution information, but not multiple modes of spatial variability, and that the Lagrange multiplier (γ) used to impose the condition of smoothness across space is related to the range of the experimental semivariogram. We used observed and 2DTR-simulated maps of NDVI to estimate landscape-level leaf area index (LAI) and gross primary productivity (GPP). NDVI maps simulated using a γ value that approximates the range of observed NDVI result in a landscape-level GPP estimate that differs by ca 2% from those created using observed NDVI. Following findings that GPP per unit LAI is lower near vegetation patch edges, we simulated vegetation patch edges using multiple approaches and found that simulated GPP declined by up to 12% as a result. 2DTR can generate random landscapes rapidly and can be applied to disaggregate ecological information and compare of spatial observations against simulated landscapes. PMID:26067835

  20. Probabilistic Downscaling of Remote Sensing Data with Applications for Multi-Scale Biogeochemical Flux Modeling.

    PubMed

    Stoy, Paul C; Quaife, Tristan

    2015-01-01

    Upscaling ecological information to larger scales in space and downscaling remote sensing observations or model simulations to finer scales remain grand challenges in Earth system science. Downscaling often involves inferring subgrid information from coarse-scale data, and such ill-posed problems are classically addressed using regularization. Here, we apply two-dimensional Tikhonov Regularization (2DTR) to simulate subgrid surface patterns for ecological applications. Specifically, we test the ability of 2DTR to simulate the spatial statistics of high-resolution (4 m) remote sensing observations of the normalized difference vegetation index (NDVI) in a tundra landscape. We find that the 2DTR approach as applied here can capture the major mode of spatial variability of the high-resolution information, but not multiple modes of spatial variability, and that the Lagrange multiplier (γ) used to impose the condition of smoothness across space is related to the range of the experimental semivariogram. We used observed and 2DTR-simulated maps of NDVI to estimate landscape-level leaf area index (LAI) and gross primary productivity (GPP). NDVI maps simulated using a γ value that approximates the range of observed NDVI result in a landscape-level GPP estimate that differs by ca 2% from those created using observed NDVI. Following findings that GPP per unit LAI is lower near vegetation patch edges, we simulated vegetation patch edges using multiple approaches and found that simulated GPP declined by up to 12% as a result. 2DTR can generate random landscapes rapidly and can be applied to disaggregate ecological information and compare of spatial observations against simulated landscapes.

  1. Development of advanced process-based model towards evaluation of boundless biogeochemical cycles in terrestrial-aquatic continuum

    NASA Astrophysics Data System (ADS)

    Nakayama, Tadanobu; Maksyutov, Shamil

    2014-05-01

    Recent research shows inland water may play some role in continental biogeochemical cycling though its contribution has remained uncertain due to a paucity of data (Battin et al. 2009). The author has developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (Nakayama, 2008a-b, 2010, 2011a-b, 2012a-c, 2013; Nakayama and Fujita, 2010; Nakayama and Hashimoto, 2011; Nakayama and Shankman, 2013a-b; Nakayama and Watanabe, 2004, 2006, 2008a-b; Nakayama et al., 2006, 2007, 2010, 2012), which incorporates surface-groundwater interactions, includes up- and down-scaling processes between local, regional and global scales, and can simulate iteratively nonlinear feedback between hydrologic, geomorphic, and ecological processes. In this study, NICE was extended to evaluate global hydrologic cycle by using various global datasets. The simulated result agreed reasonably with that in the previous research (Fan et al., 2013) and extended to clarify further eco-hydrological process in global scale. Then, NICE was further developed to incorporate the biogeochemical cycle including the reaction between inorganic and organic carbons (DOC, POC, DIC, pCO2, etc.) in the biosphere (terrestrial and aquatic ecosystems including surface water and groundwater). The model simulated the carbon cycle, for example, CO2 evasion from inland water in global scale, which is relatively in good agreement in that estimated by empirical relation using the previous pCO2 data (Aufdenkampe et al., 2011; Global River Chemistry Database, 2013). This simulation system would play important role in identification of full greenhouse gas balance of the biosphere and spatio-temporal hot spots in boundless biogeochemical cycle (Cole et al. 2007; Frei et al. 2012). References; Aufdenkampe, A.K., et al., Front. Ecol. Environ., doi:10.1890/100014, 2011. Battin, T.J., et al., Nat. Geosci., 2, 598-600, 2009. Cole, J.J. et al., Ecosystems, doi:10.1007/s10021-006-9013-8, 2007. Fan, Y. et al

  2. A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 for UVic 2.9

    NASA Astrophysics Data System (ADS)

    Nickelsen, L.; Keller, D. P.; Oschlies, A.

    2015-05-01

    Marine biological production as well as the associated biotic uptake of carbon in many ocean regions depends on the availability of nutrients in the euphotic zone. While large areas are limited by nitrogen and/or phosphorus, the micronutrient iron is considered the main limiting nutrient in the North Pacific, equatorial Pacific and Southern Ocean. Changes in iron availability via changes in atmospheric dust input are discussed to play an important role in glacial-interglacial cycles via climate feedbacks caused by changes in biological ocean carbon sequestration. Although many aspects of the iron cycle remain unknown, its incorporation into marine biogeochemical models is needed to test our current understanding and better constrain its role in the Earth system. In the University of Victoria Earth System Climate Model (UVic) iron limitation in the ocean was, until now, simulated pragmatically with an iron concentration masking scheme that did not allow a consistent interactive response to perturbations of ocean biogeochemistry or iron cycling sensitivity studies. Here, we replace the iron masking scheme with a dynamic iron cycle and compare the results to available observations and the previous marine biogeochemical model. Sensitivity studies are also conducted with the new model to test the sensitivity of the model to parameterized iron ligand concentrations, the importance of considering the variable solubility of iron in dust deposition, the importance of considering high-resolution bathymetry for the sediment release of iron, the effect of scaling the sedimentary iron release with temperature and the sensitivity of the iron cycle to a climate change scenario.

  3. FORWARD AND INVERSE BIO-GEOCHEMICAL MODELING OF MICROBIALLY INDUCED PRECIPITATION IN 0.5M COLUMNAR EXPERIMENTS

    NASA Astrophysics Data System (ADS)

    Barkouki, T. H.; Martinez, B.; Mortensen, B.; Dejong, J.; Weathers, T. S.; Spycher, N.; Ginn, T. R.; Fujita, Y.; Smith, R. W.

    2009-12-01

    Subsurface contamination by metals and radionuclides threatens water supplies and ecosystem health at sites worldwide. One potential solution is immobilization in calcite where mineral precipitation is induced in situ by microbially-mediated ureolysis. Specifically, immobile aerobic biophases (cells or enzymes) mediate the conversion of urea to ammonium and carbonate, raising pH and promoting calcite precipitation. Divalent species such as strontium (including 90Sr, a common radionuclide contaminant) can co-precipitate, resulting in in situ immobilization. In waters that are saturated with respect to calcite, this represents a long-term sequestration mechanism. Calcite precipitation also enables control of mechanical properties of the medium through the cementation of particles thus increasing the shear strength and stiffness, while decreasing the permeability and compressibility. Challenges in application include design of the injectate aqueous chemistry (e.g., calcium, carbonate, urea, pH buffer, microbial nutrients) and selection of injection rates in order to control the timing and rate of calcite precipitation to generate the desired spatial distribution. Modeling ultimately requires incorporation of comprehensive reaction networks into transport simulators for non-uniform flow. To develop an