Science.gov

Sample records for surface-subsurface biogeochemical coupling

  1. Quantifying the surface-subsurface biogeochemical coupling during the VERTIGO ALOHA and K2 studies

    SciTech Connect

    Boyd, P.W.; Gall, M.P.; Silver, M.W.; Bishop, J.K.B.; Coale, Susan L.; Bidigare, Robert R.

    2008-02-25

    A central question addressed by the VERTIGO (VERtical Transport In the Global Ocean) study was 'What controls the efficiency of particle export between the surface and subsurface ocean'? Here, we present data from sites at ALOHA (N Central Pacific Gyre) and K2 (NW subarctic Pacific) on phytoplankton processes, and relate them via a simple planktonic foodweb model, to subsurface particle export (150-500 m). Three key factors enable quantification of the surface-subsurface coupling: a sampling design to overcome the temporal lag and spatial displacement between surface and subsurface processes; data on the size-partitioning of Net Primary Production (NPP) and subsequent transformations prior to export; estimates of the ratio of algal- to faecal-mediated vertical export flux. At ALOHA, phytoplankton were characterized by low stocks, NPP, F{sub v}/F{sub m} (N-limited), and were dominated by picoplankton. The HNLC waters at K2 were characterized by both two-fold changes in NPP and floristic shifts (high to low proportion of diatoms) between deployment 1 and 2. Prediction of export exiting the euphotic zone was based on size-partitioning of NPP, a copepod-dominated foodweb and a ratio of 0.2 (ALOHA) and 0.1 (K2) for algal:faecal particle flux. Predicted export was 20-22 mg POC m{sup -2} d{sup -1} at ALOHA (i.e. 10-11% NPP (0-125 m); 1.1-1.2 x export flux at 150 m (E{sub 150}). At K2, export was 111 mg C m{sup -2} d{sup -1} (21% NPP (0-50 m); 1.8 x E{sub 150}) and 33 mg POC m{sup -2} d{sup -1} (11% NPP, 0-55 m); 1.4 x E{sub 150}) for deployments 1 and 2, respectively. This decrease in predicted export at K2 matches the observed trend for E{sub 150}. Also, the low attenuation of export flux from 60 to 150 m is consistent with that between 150 to 500 m. This strong surface-subsurface coupling suggests that phytoplankton productivity and floristics play a key role at K2 in setting export flux, and moreover that pelagic particle transformations by grazers strongly influence

  2. Quantifying the surface subsurface biogeochemical coupling during the VERTIGO ALOHA and K2 studies

    NASA Astrophysics Data System (ADS)

    Boyd, Philip W.; Gall, Mark P.; Silver, Mary W.; Coale, Susan L.; Bidigare, Robert R.; Bishop, James L. K. B.

    2008-07-01

    A central question addressed by the VERtical Transport In the Global Ocean (VERTIGO) study was 'What controls the efficiency of particle export between the surface and subsurface ocean'? Here, we present data from sites at ALOHA (N Central Pacific Gyre) and K2 (NW subarctic Pacific) on phytoplankton processes, and relate them via a simple planktonic foodweb model, to subsurface particle export (150-500 m). Three key factors enable quantification of the surface-subsurface coupling: a sampling design to overcome the temporal lag and spatial displacement between surface and subsurface processes; data on the size partitioning of net primary production (NPP) and subsequent transformations prior to export; estimates of the ratio of algal- to faecal-mediated vertical export flux. At ALOHA, phytoplankton were characterized by low stocks, NPP, Fv/ Fm (N-limited), and were dominated by picoplankton. The HNLC waters at K2 were characterized by both two-fold changes in NPP and floristic shifts (high to low proportion of diatoms) between deployment 1 and 2. Prediction of export exiting the euphotic zone was based on size partitioning of NPP, a copepod-dominated foodweb and a ratio of 0.2 (ALOHA) and 0.1 (K2) for algal:faecal particle flux. Predicted export was 20-22 mg POC m -2 d -1 at ALOHA (i.e. 10-11% NPP (0-125 m); 1.1-1.2×export flux at 150 m ( E150). At K2, export was 111 mg C m -2 d -1 (21% NPP (0-50 m); 1.8× E150) and 33 mg POC m -2 d -1 (11% NPP, 0-55 m); 1.4× E150) for deployments 1 and 2, respectively. This decrease in predicted export at K2 matches the observed trend for E150. Also, the low attenuation of export flux from 60 to 150 m is consistent with that between 150 and 500 m. This strong surface-subsurface coupling suggests that phytoplankton productivity and floristics play a key role at K2 in setting export flux, and moreover that pelagic particle transformations by grazers strongly influence to what extent sinking particles are further broken down in the

  3. Optimization of a catchment-scale coupled surface-subsurface hydrological model using pilot points

    NASA Astrophysics Data System (ADS)

    Danapour, Mehrdis; Stisen, Simon; Lajer Højberg, Anker

    2016-04-01

    Transient coupled surface-subsurface models are usually complex and contain a large amount of spatio-temporal information. In the traditional calibration approach, model parameters are adjusted against only few spatially aggregated observations of discharge or individual point observations of groundwater head. However, this approach doesn't enable an assessment of spatially explicit predictive model capabilities at the intermediate scale relevant for many applications. The overall objectives of this project is to develop a new model calibration and evaluation framework by combining distributed model parameterization and regularization with new types of objective functions focusing on optimizing spatial patterns rather than individual points or catchment scale features. Inclusion of detailed observed spatial patterns of hydraulic head gradients or relevant information obtained from remote sensing data in the calibration process could allow for a better representation of spatial variability of hydraulic properties. Pilot Points as an alternative to classical parameterization approaches, introduce great flexibility when calibrating heterogeneous systems without neglecting expert knowledge (Doherty, 2003). A highly parameterized optimization of complex distributed hydrological models at catchment scale is challenging due to the computational burden that comes with it. In this study the physically-based coupled surface-subsurface model MIKE SHE is calibrated for the 8,500 km2 area of central Jylland (Denmark) that is characterized by heterogeneous geology and considerable groundwater flow across topographical catchment boundaries. The calibration of the distributed conductivity fields is carried out with a pilot point-based approach, implemented using the PEST parameter estimation tool. To reduce the high number of calibration parameters, PEST's advanced singular value decomposition combined with regularization was utilized and a reduction of the model's complexity was

  4. Modelling the effects of tides and storm surges on coastal aquifers using a coupled surface-subsurface approach.

    PubMed

    Yang, Jie; Graf, Thomas; Herold, Maria; Ptak, Thomas

    2013-06-01

    Coastal aquifers are complex hydrologic systems because many physical processes interact: (i) variably saturated flow, (ii) spatial-temporal fluid density variations, (iii) tidal fluctuations, (iv) storm surges overtopping dykes, and (v) surface runoff of storm water. The HydroGeoSphere model is used to numerically simulate coastal flow dynamics, assuming a fully coupled surface-subsurface approach, accounting for all processes listed above. The diffusive wave approximation of the St. Venant equation is used to describe surface flow. Surface flow and salt transport are fully coupled with subsurficial variably saturated, variable-density flow and salt transport through mathematical terms that represent exchange of fluid mass and solute mass, respectively. Tides and storm surges induce a time-variant head that is applied to nodes of the surface domain. The approach is applied to real cases of tide and storm surge events. Tide simulation results confirm the existence of a recirculating zone, forming beneath the upper part of the intertidal zone. By monitoring the exchange fluid flux rates through the beach, it was found that the major inflow to the aquifer takes place at the upper part of the intertidal zone, which explains the formation of the recirculating zone. The recirculating zone is forming particularly during rising tide. Results from a storm surge simulation show that plume fingers develop below the flooded land surface. Natural remediation by seaward flowing freshwater is relatively slow, such that reducing the salt concentration in the aquifer down to drinking water standards takes up to 10 years.

  5. Progress Towards Coupled Simulation of Surface/Subsurface Hydrologic Processes and Terrestrial Ecosystem Dynamics Using the Community Models PFLOTRAN and CLM

    NASA Astrophysics Data System (ADS)

    Mills, R. T.; Bisht, G.; Karra, S.; Hoffman, F. M.; Hammond, G. E.; Kumar, J.; Painter, S.; Thornton, P. E.; Lichtner, P. C.

    2012-12-01

    Accurately simulating regional water cycle dynamics is challenging because of strong soil moisture-rainfall feedbacks and large uncertainties associated with vegetation and energy interactions. Earth system models of today cannot accurately capture such interactions, because current-generation land surface models (LSMs) 1) do not explicitly represent the fine-scale spatial variability of topography, soils, and vegetation that play a significant role in determining the response of hydrologic states (soil moisture) and fluxes (interception, infiltration, runoff, evapotranspiration) and 2) over-simplify or completely omit some key physical processes, such as lateral flow of water and heat, surface-subsurface interactions, realistic groundwater-vadose zone interactions, and freeze-thaw dynamics. Capturing such processes is critically important for predicting regional precipitation, vegetation productivity, and the disposition of carbon stored in potentially vulnerable permafrost under scenarios of climate change. Towards this end, we have added coupled surface water-groundwater interactions to the the open-source, massively parallel flow and reactive transport model PFLOTRAN, and have been developing a framework for coupling PFLOTRAN with the Community Land Model (CLM). PFLOTRAN is an open-source (LGPL-licensed) code -- with a growing community of users -- developed for simulation of multiscale, multiphase, multicomponent subsurface flow and reactive transport problems on machines ranging from laptops to leadership-class supercomputers. It has been applied in studies of contaminant fate and transport, geologic CO2 sequestration, and geothermal energy production, among others, and has been run using up to 262,144 processor cores on Jaguar, the Cray XK6 supercomputer at Oak Ridge National Laboratory. We have recently added a surface flow component in PFLOTRAN that is integrated with the subsurface. The underlying solver framework employed allows significant flexibility

  6. Ensemble Kalman Filter vs Particle Filter in a Physically Based Coupled Model of Surface-Subsurface Flow (Invited)

    NASA Astrophysics Data System (ADS)

    Putti, M.; Camporese, M.; Pasetto, D.

    2010-12-01

    Data assimilation (DA) has recently received growing interest by the hydrological modeling community due to its capability to merge observations into model prediction. Among the many DA methods available, the Ensemble Kalman Filter (EnKF) and the Particle Filter (PF) are suitable alternatives for applications to detailed physically-based hydrological models. For each assimilation period, both methods use a Monte Carlo approach to approximate the state probability distribution (in terms of mean and covariance matrix) by a finite number of independent model trajectories, also called particles or realizations. The two approaches differ in the way the filtering distribution is evaluated. EnKF implements the classical Kalman filter, optimal only for linear dynamics and Gaussian error statistics. Particle filters, instead, use directly the recursive formula of the sequential Bayesian framework and approximate the posterior probability distributions by means of appropriate weights associated to each realization. We use the Sequential Importance Resampling (SIR) technique, which retains only the most probable particles, in practice the trajectories closest in a statistical sense to the observations, and duplicates them when needed. In contrast to EnKF, particle filters make no assumptions on the form of the prior distribution of the model state, and convergence to the true state is ensured for large enough ensemble size. In this study EnKF and PF have been implemented in a physically based catchment simulator that couples a three-dimensional finite element Richards equation solver with a finite difference diffusion wave approximation based on a digital elevation data for surface water dynamics. We report on the retrieval performance of the two schemes using a three-dimensional tilted v-catchment synthetic test case in which multi-source observations are assimilated (pressure head, soil moisture, and streamflow data). The comparison between the results of the two approaches

  7. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies.

    PubMed

    Stegen, James C; Konopka, Allan; McKinley, James P; Murray, Chris; Lin, Xueju; Miller, Micah D; Kennedy, David W; Miller, Erin A; Resch, Charles T; Fredrickson, Jim K

    2016-07-29

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies-oxidized, reduced, and transition-within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness-the number of microbial taxa-was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  8. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    SciTech Connect

    Stegen, James C.; Konopka, Allan; McKinely, Jim; Murray, Christopher J.; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-07-29

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, diversity, and community composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial diversity—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  9. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    PubMed Central

    Stegen, James C.; Konopka, Allan; McKinley, James P.; Murray, Chris; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-01-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions. PMID:27469056

  10. Characterization of Coupled Hydrologic-Biogeochemical Processes Using Geophysical Data

    SciTech Connect

    Hubbard, Susan

    2005-06-01

    Biogeochemical and hydrological processes are naturally coupled and variable over a wide range of spatial and temporal scales. Many remediation approaches also induce dynamic transformations in natural systems, such as the generation of gases, precipitates and biofilms. These dynamic transformations are often coupled and can reduce the hydraulic conductivity of the geologic materials, making it difficult to introduce amendments or to perform targeted remediation. Because it is difficult to predict these transformations, our ability to develop effective and sustainable remediation conditions at contaminated sites is often limited. Further complicating the problem is the inability to collect the necessary measurements at a high enough spatial resolution yet over a large enough volume for understanding field-scale transformations.

  11. 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.

  12. Electric currents couple spatially separated biogeochemical processes in marine sediment.

    PubMed

    Nielsen, Lars Peter; Risgaard-Petersen, Nils; Fossing, Henrik; Christensen, Peter Bondo; Sayama, Mikio

    2010-02-25

    Some bacteria are capable of extracellular electron transfer, thereby enabling them to use electron acceptors and donors without direct cell contact. Beyond the micrometre scale, however, no firm evidence has previously existed that spatially segregated biogeochemical processes can be coupled by electric currents in nature. Here we provide evidence that electric currents running through defaunated sediment couple oxygen consumption at the sediment surface to oxidation of hydrogen sulphide and organic carbon deep within the sediment. Altering the oxygen concentration in the sea water overlying the sediment resulted in a rapid (<1-h) change in the hydrogen sulphide concentration within the sediment more than 12 mm below the oxic zone, a change explicable by transmission of electrons but not by diffusion of molecules. Mass balances indicated that more than 40% of total oxygen consumption in the sediment was driven by electrons conducted from the anoxic zone. A distinct pH peak in the oxic zone could be explained by electrochemical oxygen reduction, but not by any conventional sets of aerobic sediment processes. We suggest that the electric current was conducted by bacterial nanowires combined with pyrite, soluble electron shuttles and outer-membrane cytochromes. Electrical communication between distant chemical and biological processes in nature adds a new dimension to our understanding of biogeochemistry and microbial ecology.

  13. Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Co-Metabolism

    SciTech Connect

    Rick Colwell; Corey Radtke; Mark Delwiche; Deborah Newby; Lynn Petzke; Mark Conrad; Eoin Brodie; Hope Lee; Bob Starr; Dana Dettmers; Ron Crawford; Andrzej Paszczynski; Nick Bernardini; Ravi Paidisetti; Tonia Green

    2006-06-01

    Chlorinated solvent wastes (e.g., trichloroethene or TCE) often occur as diffuse subsurface plumes in complex geological environments where coupled processes must be understood in order to implement remediation strategies. Monitored natural attenuation (MNA) warrants study as a remediation technology because it minimizes worker and environment exposure to the wastes and because it costs less than other technologies. However, to be accepted MNA requires different ?lines of evidence? indicating that the wastes are effectively destroyed. We are studying the coupled biogeochemical processes that dictate the rate of TCE co-metabolism first in the medial zone (TCE concentration: 1,000 to 20,000 ?g/L) of a plume at the Idaho National Laboratory?s Test Area North (TAN) site and then at Paducah or the Savannah River Site. We will use flow-through in situ reactors (FTISR) to investigate the rate of methanotrophic co-metabolism of TCE and the coupling of the responsible biological processes with the dissolved methane flux and groundwater flow velocity. TCE co-metabolic rates at TAN are being assessed and interpreted in the context of enzyme activity, gene expression, and cellular inactivation related to intermediates of TCE co-metabolism. By determining the rate of TCE co-metabolism at different groundwater flow velocities, we will derive key modeling parameters for the computational simulations that describe the attenuation, and thereby refine such models while assessing the contribution of microbial co-metabolism relative to other natural attenuation processes. This research will strengthen our ability to forecast the viability of MNA at DOE and other sites contaminated with chlorinated hydrocarbons.

  14. Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Co-Metabolism

    SciTech Connect

    Colwell, Frederick; Radtke, Corey; Newby, Deborah; Delwiche, Mark; Crawf, Ronald L.; Paszczynski, Andrzej; Strap, Janice; Conrad, Mark; Brodic, Eoin; Starr, Robert; Lee, Hope

    2006-04-05

    Chlorinated solvent wastes (e.g., trichloroethene or TCE) often occur as diffuse subsurface plumes in complex geological environments where coupled processes must be understood in order to implement remediation strategies. Monitored natural attenuation (MNA) warrants study as a remediation technology because it minimizes worker and environment exposure to the wastes and because it costs less than other technologies. However, to be accepted MNA requires 'lines of evidence' indicating that the wastes are effectively destroyed. Our research will study the coupled biogeochemical processes that dictate the rate of TCE co-metabolism in contaminated aquifers first at the Idaho National Laboratory and then at Paducah or the Savannah River Site, where natural attenuation of TCE is occurring. We will use flow-through in situ reactors to investigate the rate of methanotrophic co-metabolism of TCE and the coupling of the responsible biological processes with the dissolved methane flux and groundwater flow velocity. We will use new approaches (e.g., stable isotope probing, enzyme activity probes, real-time reverse transcriptase polymerase chain reaction, proteomics) to assay the TCE co-metabolic rates, and interpret these rates in the context of enzyme activity, gene expression, and cellular inactivation related to intermediates of TCE co-metabolism. By determining the rate of TCE co-metabolism at different methane concentrations and groundwater flow velocities, we will derive key modeling parameters for the computational simulations that describe the attenuation, and thereby refine such models while assessing the contribution of microbial relative to other natural attenuation processes. This research will strengthen our ability to forecast the viability of MNA at DOE and other sites that are contaminated with chlorinated hydrocarbons.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Silicon and zinc biogeochemical cycles coupled through the Southern Ocean

    NASA Astrophysics Data System (ADS)

    Vance, Derek; Little, Susan H.; de Souza, Gregory F.; Khatiwala, Samar; Lohan, Maeve C.; Middag, Rob

    2017-02-01

    Zinc is vital for the physiology of oceanic phytoplankton. The striking similarity of the depth profiles of zinc to those of silicate suggests that the uptake of both elements into the opaline frustules of diatoms, and their regeneration from these frustules, should be coupled. However, the zinc content of diatom opal is negligible, and zinc is taken up into and regenerated from the organic parts of diatom cells. Thus, since opaline frustules dissolve deep in the water column while organic material is regenerated in the shallow subsurface ocean, there is little reason to expect the observed close similarity between zinc and silicate, and the dissimilarity between zinc and phosphate. Here we combine observations with simulations using a three-dimensional model of ocean circulation and biogeochemistry to show that the coupled distribution of zinc and silicate, as well as the decoupling of zinc and phosphate, can arise in the absence of mechanistic links between the uptake of zinc and silicate, and despite contrasting regeneration length scales. Our simulations indicate that the oceanic zinc distribution is, in fact, a natural result of the interaction between ocean biogeochemistry and the physical circulation through the Southern Ocean hub. Our analysis demonstrates the importance of uptake stoichiometry in controlling ocean biogeochemistry, and the utility of global-scale elemental covariation in the ocean in understanding these controls.

  20. Integrated Surface/subsurface flow modeling in PFLOTRAN

    SciTech Connect

    Painter, Scott L

    2016-10-01

    Understanding soil water, groundwater, and shallow surface water dynamics as an integrated hydrological system is critical for understanding the Earth’s critical zone, the thin outer layer at our planet’s surface where vegetation, soil, rock, and gases interact to regulate the environment. Computational tools that take this view of soil moisture and shallow surface flows as a single integrated system are typically referred to as integrated surface/subsurface hydrology models. We extend the open-source, highly parallel, subsurface flow and reactive transport simulator PFLOTRAN to accommodate surface flows. In contrast to most previous implementations, we do not represent a distinct surface system. Instead, the vertical gradient in hydraulic head at the land surface is neglected, which allows the surface flow system to be eliminated and incorporated directly into the subsurface system. This tight coupling approach leads to a robust capability and also greatly simplifies implementation in existing subsurface simulators such as PFLOTRAN. Successful comparisons to independent numerical solutions build confidence in the approximation and implementation. Example simulations of the Walker Branch and East Fork Poplar Creek watersheds near Oak Ridge, Tennessee demonstrate the robustness of the approach in geometrically complex applications. The lack of a robust integrated surface/subsurface hydrology capability had been a barrier to PFLOTRAN’s use in critical zone studies. This work addresses that capability gap, thus enabling PFLOTRAN as a community platform for building integrated models of the critical zone.

  1. 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

  2. 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.

  3. 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.

  4. Advances in Coupling of Kinetics and Molecular Scale Tools to Shed Light on Soil Biogeochemical Processes

    SciTech Connect

    Sparks, Donald

    2014-09-02

    Biogeochemical processes in soils such as sorption, precipitation, and redox play critical roles in the cycling and fate of nutrients, metal(loid)s and organic chemicals in soil and water environments. Advanced analytical tools enable soil scientists to track these processes in real-time and at the molecular scale. Our review focuses on recent research that has employed state-of-the-art molecular scale spectroscopy, coupled with kinetics, to elucidate the mechanisms of nutrient and metal(loid) reactivity and speciation in soils. We found that by coupling kinetics with advanced molecular and nano-scale tools major advances have been made in elucidating important soil chemical processes including sorption, precipitation, dissolution, and redox of metal(loids) and nutrients. Such advances will aid in better predicting the fate and mobility of nutrients and contaminants in soils and water and enhance environmental and agricultural sustainability.

  5. Effects of ozone-vegetation coupling on surface ozone air quality via biogeochemical and meteorological feedbacks

    NASA Astrophysics Data System (ADS)

    Sadiq, Mehliyar; Tai, Amos P. K.; Lombardozzi, Danica; Martin, Maria Val

    2017-02-01

    Tropospheric ozone is one of the most hazardous air pollutants as it harms both human health and plant productivity. Foliage uptake of ozone via dry deposition damages photosynthesis and causes stomatal closure. These foliage changes could lead to a cascade of biogeochemical and biogeophysical effects that not only modulate the carbon cycle, regional hydrometeorology and climate, but also cause feedbacks onto surface ozone concentration itself. In this study, we implement a semi-empirical parameterization of ozone damage on vegetation in the Community Earth System Model to enable online ozone-vegetation coupling, so that for the first time ecosystem structure and ozone concentration can coevolve in fully coupled land-atmosphere simulations. With ozone-vegetation coupling, present-day surface ozone is simulated to be higher by up to 4-6 ppbv over Europe, North America and China. Reduced dry deposition velocity following ozone damage contributes to ˜ 40-100 % of those increases, constituting a significant positive biogeochemical feedback on ozone air quality. Enhanced biogenic isoprene emission is found to contribute to most of the remaining increases, and is driven mainly by higher vegetation temperature that results from lower transpiration rate. This isoprene-driven pathway represents an indirect, positive meteorological feedback. The reduction in both dry deposition and transpiration is mostly associated with reduced stomatal conductance following ozone damage, whereas the modification of photosynthesis and further changes in ecosystem productivity are found to play a smaller role in contributing to the ozone-vegetation feedbacks. Our results highlight the need to consider two-way ozone-vegetation coupling in Earth system models to derive a more complete understanding and yield more reliable future predictions of ozone air quality.

  6. 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

  7. 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.

  8. 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

  9. 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?

  10. Skill assessment of the coupled physical-biogeochemical operational Mediterranean Forecasting System

    NASA Astrophysics Data System (ADS)

    Cossarini, Gianpiero; Clementi, Emanuela; Salon, Stefano; Grandi, Alessandro; Bolzon, Giorgio; Solidoro, Cosimo

    2016-04-01

    The Mediterranean Monitoring and Forecasting Centre (Med-MFC) is one of the regional production centres of the European Marine Environment Monitoring Service (CMEMS-Copernicus). Med-MFC operatively manages a suite of numerical model systems (3DVAR-NEMO-WW3 and 3DVAR-OGSTM-BFM) that provides gridded datasets of physical and biogeochemical variables for the Mediterranean marine environment with a horizontal resolution of about 6.5 km. At the present stage, the operational Med-MFC produces ten-day forecast: daily for physical parameters and bi-weekly for biogeochemical variables. The validation of the coupled model system and the estimate of the accuracy of model products are key issues to ensure reliable information to the users and the downstream services. Product quality activities at Med-MFC consist of two levels of validation and skill analysis procedures. Pre-operational qualification activities focus on testing the improvement of the quality of a new release of the model system and relays on past simulation and historical data. Then, near real time (NRT) validation activities aim at the routinely and on-line skill assessment of the model forecast and relays on the NRT available observations. Med-MFC validation framework uses both independent (i.e. Bio-Argo float data, in-situ mooring and vessel data of oxygen, nutrients and chlorophyll, moored buoys, tide-gauges and ADCP of temperature, salinity, sea level and velocity) and semi-independent data (i.e. data already used for assimilation, such as satellite chlorophyll, Satellite SLA and SST and in situ vertical profiles of temperature and salinity from XBT, Argo and Gliders) We give evidence that different variables (e.g. CMEMS-products) can be validated at different levels (i.e. at the forecast level or at the level of model consistency) and at different spatial and temporal scales. The fundamental physical parameters temperature, salinity and sea level are routinely validated on daily, weekly and quarterly base

  11. 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

    into the watershed simulator GETFLOWS coupled with biogeochemical cycling in forests. We present brief a overview of the simulator and an application for reservoir basin.

  12. 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).

  13. 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.

  14. 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

  15. Modeling Nitrogen Cycle at the Surface-Subsurface Water Interface

    NASA Astrophysics Data System (ADS)

    Marzadri, A.; Tonina, D.; Bellin, A.

    2011-12-01

    Anthropogenic activities, primarily food and energy production, have altered the global nitrogen cycle, increasing reactive dissolved inorganic nitrogen, Nr, chiefly ammonium NH4+ and nitrate NO3-, availability in many streams worldwide. Increased Nr promotes biological activity often with negative consequences such as water body eutrophication and emission of nitrous oxide gas, N2O, an important greenhouse gas as a by-product of denitrification. The hyporheic zone may play an important role in processing Nr and returning it to the atmosphere. Here, we present a process-based three-dimensional semi-analytical model, which couples hyporheic hydraulics with biogeochemical reactions and transport equations. Transport is solved by means of particle tracking with negligible local dispersion and biogeochemical reactions modeled by linearized Monod's kinetics with temperature dependant reaction rate coefficients. Comparison of measured and predicted N2O emissions from 7 natural stream shows a good match. We apply our model to gravel bed rivers with alternate bar morphology to investigate the role of hyporheic hydraulic, depth of alluvium, relative availability of stream concentration of NO3- and NH4+ and water temperature on nitrogen gradients within the sediment. Our model shows complex concentration dynamics, which depend on hyporheic residence time distribution and consequently on streambed morphology, within the hyporheic zone. Nitrogen gas emissions from the hyporheic zone increase with alluvium depth in large low-gradient streams but not in small steep streams. On the other hand, hyporheic water temperature influences nitrification/denitrification processes mainly in small-steep than large low-gradient streams, because of the long residence times, which offset the slow reaction rates induced by low temperatures in the latter stream. The overall conclusion of our analysis is that river morphology has a major impact on biogeochemical processes such as nitrification

  16. 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.

  17. 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

  18. 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.

  19. Prospecting for natural attenuation: Coupled geophysical-biogeochemical studies at DOE's Rifle IFRC site

    NASA Astrophysics Data System (ADS)

    Williams, K. H.; Kukkadapu, R. K.; Long, P. E.; Flores Orozco, A.; Kemna, A.

    2011-12-01

    Research activities at the Rifle Integrated Field Research Challenge (IFRC) site in Rifle, Colorado (USA) are designed to integrate geochemical, biological, and hydrological studies to enhance our understanding of subsurface uranium mobility. While much of the research activities at the site have focused on stimulating subsurface microbial activity through acetate amendment, there is growing interest in the role that natural biogeochemical processes play in constraining uranium mobility in the aquifer. Such processes constitute a form of natural uranium attenuation in the subsurface and are inferred to result from elevated concentrations of natural organic matter associated with alluvial sediments. Referred to as naturally reduced zones (NRZ's), they are characterized by the presence of reduced and/or magnetic mineral phases (e.g. FeS, FeS2, and Fe3O4), elevated Fe(II), and refractory organic carbon compounds (e.g. roots, twigs, and cones). Elevated rates of microbial activity associated with NRZ's and their mineralogical makeup act to sequester uranium from groundwater at levels higher that background alluvium. Their unique composition within a matrix of relatively oxidized, low-bioactivity sediments constitutes a potential target for a variety of exploration geophysical techniques, such as induced polarization and magnetic susceptibility. Both methods have been successfully applied at the Rifle IFRC site to delineate the ubiquity and extent of NRZ's across the floodplain. Sediments recovered from drilling targets identified through the use of exploration geophysical techniques have identified elevated uranium concentrations associated with both magnetite and framboid pyrite; however, the extent to which such minerals are the direct product of in situ microbial activity remains unknown. While diverse, the microbial community composition of NRZ's suggest dominance by fermentative organisms capable of degrading lignitic carbon to low molecular weight organic

  20. 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.

  1. 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.

  2. 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

  3. Coupled Hydrological and Biogeochemical Controls on Methylmercury Production and Export from a Boreal Wetland

    NASA Astrophysics Data System (ADS)

    Heyes, A.; Krabbenhoft, D. P.; Branfireun, B. A.; Gilmour, C. C.; Mitchell, C. P.; Tate, M. T.; Richardson, M.

    2007-12-01

    Through long-term addition of a mercury (Hg) stable isotope to a wetland, we have begun to unravel the complexity of Hg and methylmercury (MeHg) cycling in a Boreal wetland. As part of the METAALICUS project being conducted at the Experimental Lakes Area, the lake 658 wetland was annually amended from 2001-2006 with a mercury isotope at a level approximately 5 times the annual anthropogenic deposition. However, wetlands not only receive Hg directly from atmospheric deposition, but also from upland runoff and from adjacent water bodies during periods of inundation. As METAALICUS is a whole watershed experiment, both the adjacent lake and uplands were each amended with a different mercury isotope. This has allowed us to study the cycling of Hg within the wetland in a watershed context. What is clear from this integrated approach is Hg cycling is dependent on the complex interplay of hydrodynamic and biogeochemical factors which will form the focus of this presentation. The Lake 658 wetland is classified as a basin oligotrophic swamp, and is surrounded on three sides by steeply sloping uplands and on the fourth by a lake. The morphology of the wetland causes large portions of the wetland to be hydrologically disconnected for long periods during dry periods in the summer and by ice in winter. When flow occurs, it is along defined channels rather than by sheet flow, which is partially an artifact of the basin morphology. Thus, wetland form influences the wetland volume that contributes to Hg and MeHg export. The majority of the Hg isotope added to the wetland has been retained in the vegetation and upper few centimeters of peat, with less than 1% exported despite the substantial export of both inorganic ambient Hg and MeHg. As little newly deposited Hg, represented by the amended isotope has been exported, we hypothesize that Hg export from wetlands is strongly coupled to decomposition and the fate of dissolved organic carbon which binds both Hg and MeHg. While MeHg is

  4. 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.

  5. Robust Representation of Integrated Surface-subsurface Hydrology at Watershed Scales

    NASA Astrophysics Data System (ADS)

    Painter, S. L.; Tang, G.; Collier, N.; Jan, A.; Karra, S.

    2015-12-01

    A representation of integrated surface-subsurface hydrology is the central component to process-rich watershed models that are emerging as alternatives to traditional reduced complexity models. These physically based systems are important for assessing potential impacts of climate change and human activities on groundwater-dependent ecosystems and water supply and quality. Integrated surface-subsurface models typically couple three-dimensional solutions for variably saturated flow in the subsurface with the kinematic- or diffusion-wave equation for surface flows. The computational scheme for coupling the surface and subsurface systems is key to the robustness, computational performance, and ease-of-implementation of the integrated system. A new, robust approach for coupling the subsurface and surface systems is developed from the assumption that the vertical gradient in head is negligible at the surface. This tight-coupling assumption allows the surface flow system to be incorporated directly into the subsurface system; effects of surface flow and surface water accumulation are represented as modifications to the subsurface flow and accumulation terms but are not triggered until the subsurface pressure reaches a threshold value corresponding to the appearance of water on the surface. The new approach has been implemented in the highly parallel PFLOTRAN (www.pflotran.org) code. Several synthetic examples and three-dimensional examples from the Walker Branch Watershed in Oak Ridge TN demonstrate the utility and robustness of the new approach using unstructured computational meshes. Representation of solute transport in the new approach is also discussed. Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC0500OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid

  6. 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.

  7. 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.

  8. Biogeochemical Transformation Pathways through the Land-water Geosphere

    NASA Astrophysics Data System (ADS)

    Destouni, G.; Asokan, S. M.; Augustsson, A.; Balfors, B.; Bring, A.; Jaramillo, F.; Jarsjo, J.; Johansson, E.; Juston, J.; Levi, L.; Olofsson, B.; Prieto, C.; Quin, A.; Åström, M. E.; Cvetkovic, V.

    2014-12-01

    Water on land undergoes and participates in many biogeochemical exchanges and changes. A bits-and-pieces approach to these may miss essential aspects of change propagation and transformation by land-water through different segments of the Earth system. This paper proposes a conceptualization of the entire land-water geosphere as a scale-free catchment-wise organised system (Figure 1), emphasizing four key new system aspects compared to traditional hydrosphere/water cycle view: i) distinction of coastal divergent in addition to traditional convergent catchments; ii) physical and social-ecological system coupling through four main nodal zones/interfaces (surface, subsurface, coastal, observation); iii) flow-transport pathways as system coupling agents; iv) multiple interactions with the anthroposphere as integral system parts. Utilizing this conceptualization, we identify distinct patterns of direct anthropogenic change in large-scale water and waterborne nutrient fluxes, emerging across different parts of the world. In general, its embedment directly in the anthroposphere/technosphere makes land-water a key geosphere for understanding and monitoring human-driven biogeochemical changes. Further progress in system-level understanding of such changes requires studies of land-water as a continuous yet structured geosphere following the proposed spatiotemporal pathways of change propagation-transformation.

  9. Autonomous Studies of Coupled Physical-Biogeochemical Processes- Lessons from NAB08 and Prospects for the Future

    NASA Astrophysics Data System (ADS)

    Lee, Craig; D'Asaro, Eric; Perry, Mary Jane

    2013-04-01

    Motivated by the increasing application of autonomous sensors to physical, biological and biogeochemical investigations at the submesoscale, we examine techniques developed during the 2008 North Atlantic Bloom Experiment (NAB08), review successes, failures, and lessons learned, and offer perspectives on how these approaches might evolve in response to near-term shifts in scientific goals and technological advances. NAB08 exploited the persistence of autonomous platforms coupled with the extensive capabilities of a ship-based sampling program to investigate the patch-scale physics, biogeochemistry and community dynamics of a spring phytoplankton bloom. Autonomous platforms (Seagliders following a heavily-instrumented Lagrangian float) collected measurements in a quasi-Lagrangian frame, beginning before bloom initiation and extending well past its demise. This system of autonomous instruments resolved variability at the patch scale while also providing the persistence needed to follow bloom evolution. Biological and biogeochemical measurements were conducted from R/V Knorr during the bloom. An aggressive protocol for sensor calibration and proxy building bridged the ship-based and autonomous efforts, leveraging the intensive but sparse ship-based measurements onto the much more numerous autonomous observations. The combination of sampling in the patch-following frame, persistent, autonomous surveys and focused, aggressive calibration and proxy building produced robust, quantitative estimates of physical and biogeochemical processes. For example, budgets of nitrate, dissolved oxygen and particulate organic carbon (POC) following the patch were used to estimate net community production (NCP) and apparent POC export. Net community production was 805 mmol C?m-2 during the main bloom, with apparent POC export of 564 mmol C?m-2 and 282 mmol C?m-2 lost due to net respiration (70%) and apparent export (30%) on the day following bloom termination. Thus, POC export of roughly

  10. 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

  11. Coupling between Pentachlorophenol Dechlorination and Soil Redox As Revealed by Stable Carbon Isotope, Microbial Community Structure, and Biogeochemical Data.

    PubMed

    Xu, Yan; He, Yan; Zhang, Qian; Xu, Jianming; Crowley, David

    2015-05-05

    Carbon isotopic analysis and molecular-based methods were used in conjunction with geochemical data sets to assess the dechlorination of pentachlorophenol (PCP) when coupled to biogeochemical processes in a mangrove soil having no prior history of anthropogenic contamination. The PCP underwent 96% dechlorination in soil amended with acetate, compared to 21% dehalogenation in control soil. Carbon isotope analysis of residual PCP demonstrated an obvious enrichment of 13C (εC, -3.01±0.1%). Molecular and statistical analyses demonstrated that PCP dechlorination and Fe(III) reduction were synergistically combined electron-accepting processes. Microbial community analysis further suggested that enhanced dechlorination of PCP during Fe(III) reduction was mediated by members of the multifunctional family of Geobacteraceae. In contrast, PCP significantly suppressed the growth of SO4(2-) reducers, which, in turn, facilitated the production of CH4 by diversion of electrons from SO4(2-) reduction to methanogenesis. The integrated data regarding stoichiometric alterations in this study gives direct evidence showing PCP, Fe(III), and SO4(2-) reduction, and CH4 production are coupled microbial processes during changes in soil redox.

  12. Coupled biogeochemical cycles in riparian zones with contrasting hydrogeomorphic characteristics in the US Midwest

    NASA Astrophysics Data System (ADS)

    Liu, X.

    2012-12-01

    In this study we aims to understand what drives the fate and transport of multiple contaminants sensitive to soil redox condition across hydrogeomorphic (HGM) gradient and evaluate overall biogeochemical functions of riparian zones regarding those contaminants. We conducted monthly field work for 19 consecutive months from November 2009 to May 2011 at three study sites representative for main HGM types at the US Midwest. We collected the parameters from different sources which include field parameters, such as topography, water table depth, oxidation reduction potential (ORP) and dissolved oxygen (DO), and groundwater chemistry, such as NH4+, NO3-, PO43-, SO42-, CI- , and Hg and MeHg. Our results demonstrated that seasonal water table fluctuations and groundwater flows characteristics at three sites are strongly affected by their HGM setting. Specifically, the convergence of quick rise of water table, high ORP and sharp decrease in concentrations of NO3- and SO42 from field edge to stream edge (60-90% at LWD and 90% at WR) in spring after snowmelt and early May, which could be explained by that snow melt and early summer rainfall are major drivers of fluctuations of water table, variations of ORP and transport and transformation of contaminants. Riparian zones removed NO3- and SO42- during high water table but released Mercury in summer at both LWD and WR, and sulfate reduction, ammonia production and MeHg production all occurred when ORP and water tables were low in summer. These results might reflect the strong ORP control on these processes at landscape scale. These findings supported our hypothesis. Other findings however contrast to our hypothesis. For instances, unusual high concentrations of nitrate and Hg at WR suggest that the transport and fate of multiple contaminants relate not only to HGM settings but geographic location and land use. Negligible variations of P concentration in groundwater indicate that the transformation of P is not sensitive to soil

  13. Coupled hydrological and biogeochemical processes controlling variability of nitrogen species in streamflow during autumn in an upland forest

    NASA Astrophysics Data System (ADS)

    Sebestyen, Stephen D.; Shanley, James B.; Boyer, Elizabeth W.; Kendall, Carol; Doctor, Daniel H.

    2014-02-01

    Autumn is a season of dynamic change in forest streams of the northeastern United States due to effects of leaf fall on both hydrology and biogeochemistry. Few studies have explored how interactions of biogeochemical transformations, various nitrogen sources, and catchment flow paths affect stream nitrogen variation during autumn. To provide more information on this critical period, we studied (1) the timing, duration, and magnitude of changes to stream nitrate, dissolved organic nitrogen (DON), and ammonium concentrations; (2) changes in nitrate sources and cycling; and (3) source areas of the landscape that most influence stream nitrogen. We collected samples at higher temporal resolution for a longer duration than typical studies of stream nitrogen during autumn. This sampling scheme encompassed the patterns and extremes that occurred during base flow and stormflow events of autumn. Base flow nitrate concentrations decreased by an order of magnitude from 5.4 to 0.7 µmol L-1 during the week when most leaves fell from deciduous trees. Changes to rates of biogeochemical transformations during autumn base flow explained the low nitrate concentrations; in-stream transformations retained up to 72% of the nitrate that entered a stream reach. A decrease of in-stream nitrification coupled with heterotrophic nitrate cycling were primary factors in the seasonal nitrate decline. The period of low nitrate concentrations ended with a storm event in which stream nitrate concentrations increased by 25-fold. In the ensuing weeks, peak stormflow nitrate concentrations progressively decreased over closely spaced, yet similarly sized events. Most stormflow nitrate originated from nitrification in near-stream areas with occasional, large inputs of unprocessed atmospheric nitrate, which has rarely been reported for nonsnowmelt events. A maximum input of 33% unprocessed atmospheric nitrate to the stream occurred during one event. Large inputs of unprocessed atmospheric nitrate show

  14. Coupled hydrological and biogeochemical processes controlling variability of nitrogen species in streamflow during autumn in an upland forest

    USGS Publications Warehouse

    Sebestyen, Stephen D.; Shanley, James B.; Boyer, Elizabeth W.; Kendall, Carol; Doctor, Daniel H.

    2014-01-01

    Autumn is a season of dynamic change in forest streams of the northeastern United States due to effects of leaf fall on both hydrology and biogeochemistry. Few studies have explored how interactions of biogeochemical transformations, various nitrogen sources, and catchment flow paths affect stream nitrogen variation during autumn. To provide more information on this critical period, we studied (1) the timing, duration, and magnitude of changes to stream nitrate, dissolved organic nitrogen (DON), and ammonium concentrations; (2) changes in nitrate sources and cycling; and (3) source areas of the landscape that most influence stream nitrogen. We collected samples at higher temporal resolution for a longer duration than typical studies of stream nitrogen during autumn. This sampling scheme encompassed the patterns and extremes that occurred during base flow and stormflow events of autumn. Base flow nitrate concentrations decreased by an order of magnitude from 5.4 to 0.7 µmol L−1 during the week when most leaves fell from deciduous trees. Changes to rates of biogeochemical transformations during autumn base flow explained the low nitrate concentrations; in-stream transformations retained up to 72% of the nitrate that entered a stream reach. A decrease of in-stream nitrification coupled with heterotrophic nitrate cycling were primary factors in the seasonal nitrate decline. The period of low nitrate concentrations ended with a storm event in which stream nitrate concentrations increased by 25-fold. In the ensuing weeks, peak stormflow nitrate concentrations progressively decreased over closely spaced, yet similarly sized events. Most stormflow nitrate originated from nitrification in near-stream areas with occasional, large inputs of unprocessed atmospheric nitrate, which has rarely been reported for nonsnowmelt events. A maximum input of 33% unprocessed atmospheric nitrate to the stream occurred during one event. Large inputs of unprocessed atmospheric nitrate

  15. Final Progress Report: Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Cometabolism

    SciTech Connect

    Crawford, Ronald L; Paszczynski, Andrzej J

    2010-02-19

    spectrometry and genomic analyses using RT-PCR to characterize these enzyme systems. UI’s specific objectives were to develop the proteomics and genomic tools to assess the presence of the methane monooxygenase (MMO) proteins in the aquifers under study and relate this to the enumeration of methanotrophic microorganisms. We targeted the identification of both sMMO and pMMO. We believe that the copper level in the TAN aquifer is most likely suppressing the expression of sMMO and mediates the higher levels of pMMO expression. Hence our investigations included the identification of both forms of MMOs, and we expected a higher concentration of pMMO proteins in TAN samples. The amounts of these proteins present were correlated with numbers of methanotrophs determined by us and other members of the research team using PCR-based methods. In summary, to accomplish our objectives we applied environmental proteomics techniques to monitor proteins that are involved in the co-metabolic degradation of trichloroethylene (TCE) in groundwater of the INL TAN site on Department of Energy ands of near Idaho Falls, ID USA. To acquire peptides sequences information we used an ultra performance chromatography (UPLC) system coupled with QToF Premiere nano-electrospray tandem quadropole-time of flight mass spectrometer. Our goal was to identify signature peptides of methane monooxygenases (MMOs) within methanotrophic bacteria that are active in cometabolic degradation of TCE. We developed a new method for extracting total proteins from environmental planktonic and/or biofilm samples that involve a new time course cell lysis and protein extraction method in combination with chromatographic separation of peptide and tandem mass spectrometry sequencing. The techniques resulted in successful extraction and identification of MMO-based peptides from both pure cultures and TAN site samples. The work confirmed the importance of mathonotrophs in the co-metabolic removal of TCE from the TAN site aquifer.

  16. 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.

  17. 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.

  18. Assimilation of SeaWiFS chlorophyll data into a 3D-coupled physical-biogeochemical model applied to a freshwater-influenced coastal zone

    NASA Astrophysics Data System (ADS)

    Fontana, Clément; Grenz, Christian; Pinazo, Christel; Marsaleix, Patrick; Diaz, Frédéric

    2009-06-01

    In order to predict eutrophication events in coastal areas we tested an assimilation scheme based on sequential data assimilation of SeaWiFS chlorophyll data into a coupled 3D physical-biogeochemical model. The area investigated is a semi-enclosed estuarine system (Gulf of Fos-North-western Mediterranean Sea) closely linked to the Rhone River delta. This system is subjected to episodic eutrophication caused by certain hydrodynamic conditions and intermittent nutrient inputs. The 3D hydrodynamic model Symphonie was coupled to the biogeochemical modelling platform Eco3M. Surface chlorophyll concentrations were derived from SeaWiFS data using the OC5 algorithm and were sequentially assimilated using a singular evolutive extended Kalman filter. Assimilation efficiency was evaluated through an independent in situ data set collected during a field survey that took place in May 2001 (ModelFos cruise). An original approach was used in constructing the state vector and the observation vector. By assimilating pseudo-salinity extracted from the model biogeochemical dynamics in both open sea and plume region were respected. We proved that substantial improvements were made in short-term forecasts by integrating such satellite-estimated chlorophyll maps. We showed that missing freshwater inputs could be corrected to a certain extent by the assimilation process. Simulated concentrations of surface chlorophyll and other basic components of the pelagic ecosystem such as nitrates were improved by assimilating surface chlorophyll maps. Finally we showed the coherent spatial behaviour of the filter over the whole modelled domain.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. Final Report DE-SC0006997; PI Sharp; Coupled Biological and Micro-XAS/XRF Analysis of In Situ Uranium Biogeochemical Processes

    SciTech Connect

    Sharp, Jonathan O.

    2016-03-30

    Project Overview: The impact of the original seed award was substantially increased by leveraging a postdoctoral fellowship (Marie Curie Postdoctoral Fellowship) and parallel funds from (A) synergistic project supported by NSF and (B) with DOE collaborators (PI’s Ranville and Williams) as well as no-cost extension that greatly increased the impact and publications associated with the project. In aligning with SBR priorities, the project’s focus was extended more broadly to explore coupled biogeochemical analysis of metal (im)mobilization processes beyond uranium with a foundation in integrating microbial ecology with geochemical analyses. This included investigations of arsenic and zinc during sulfate reducing conditions in addition to direct microbial reduction of metals. Complimentary work with NSF funding and collaborative DOE interactions further increased the project scope to investigate metal (im)mobilization coupled to biogeochemical perturbations in forest ecosystems with an emphasis on coupled carbon and metal biogeochemistry. In total, the project was highly impactful and resulted in 9 publications and directly supported salary/tuition for 3 graduate students at various stages of their academic careers as well as my promotion to Associate Professor. In going forward, findings provided inspiration for a two subsequent proposals with collaborators at Lawrence Berkeley Laboratory and others that are currently in review (as of March 2016).

  4. Efficient Use of Prior Information to Calibrate the Gridded Surface Subsurface Hydrologic Analysis (GSSHA) Hydrology Model

    DTIC Science & Technology

    2014-09-01

    Gridded Surface Subsurface Hydrologic Analysis (GSSHA) Hydrology Model by Brian E. Skahill and Charles W. Downer PURPOSE: The purpose of this... Hydrologic Analysis (GSSHA) model. These new capabilities enable the incorporation of soft data, or prior information (i.e., extra observations which...traditional hydrologic simulation models (viz., lumped and semidistributed model structures). Such models have the potential to predict with greater

  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. Development, testing and application of DrainFlow: A fully distributed integrated surface-subsurface flow model for drainage study

    NASA Astrophysics Data System (ADS)

    Shokri, Ali; Bardsley, William Earl

    2016-06-01

    Hydrological and hydrogeological investigation of drained land is a complex and integrated procedure. The scale of drainage studies may vary from a high-resolution small scale project through to comprehensive catchment or regional scale investigations. This wide range of scales and integrated system behaviour poses a significant challenge for the development of suitable drainage models. Toward meeting these requirements, a fully distributed coupled surface-subsurface flow model titled DrainFlow has been developed and is described. DrainFlow includes both the diffusive wave equation for surface flow components (overland flow, open drain, tile drain) and Richard's equation for saturated/unsaturated zones. To overcome the non-linearity problem created from switching between wet and dry boundaries, a smooth transitioning technique is introduced to buffer the model at tile drains and at interfaces between surface and subsurface flow boundaries. This gives a continuous transition between Dirichlet and Neumann boundary conditions. DrainFlow is tested against five well-known integrated surface-subsurface flow benchmarks. DrainFlow as applied to some synthetic drainage study examples is quite flexible for changing all or part of the model dimensions as required by problem complexity, problem scale, and data availability. This flexibility enables DrainFlow to be modified to allow for changes in both scale and boundary conditions, as often encountered in real-world drainage studies. Compared to existing drainage models, DrainFlow has the advantage of estimating actual infiltration directly from the partial differential form of Richard's equation rather than through analytical or empirical infiltration approaches like the Green and Ampt equation.

  7. Integrated Modeling Analysis on Surface-Subsurface Water Interaction and Impact on Riparian Vegetation under Climate Change Scenarios

    NASA Astrophysics Data System (ADS)

    Bhattarai, M. P.; Acharya, K.; Chen, L.

    2010-12-01

    Primary objective of this study is to investigate the impact of climate change on riparian vegetation especially Tamarisk, an invasive riparian species widely spread along the lower Virgin River corridor. The lower Virgin River basin is located in Nevada, Utah and Arizona and the study area is approximately 4,500 sq. km. Our prevailing hypothesis is that the climate change will likely alter evapotranspiration (ET) and recharge/discharge pattern of surface-subsurface flow system creating a new moisture distribution profile in unsaturated zone and potentially altering existing ecosystem structure. The Hydrogeosphere, a fully integrated surface and subsurface flow model developed by Groundwater Simulations Group, University of Waterloo is used for the study. The model is able to perform fully coupled simulation of surface-subsurface flow with 2D representation of surface regime and 3D for unsaturated/saturated subsurface flow. The study area has 8 stratigraphic layers, which are further divided into 21 layers. The model is calibrated to produce steady state hydraulic head based on long term precipitation, ET and stream hydrograph. The steady-state result is then used as initial condition to run transient simulation for the year 2008 and 2009. Bias corrected and downscaled WCRP CMIP3 climate projections data for three scenarios will be used to predict the soil moisture distribution within unsaturated zone. Results of present and future climate conditions will be analyzed to investigate if the local hydrology favors Tamarisk in a long run or provides favorable conditions for native species such as Cottonwood and Willows.

  8. Significant Findings: Seasonal Distributions of Global Ocean Chlorophyll and Nutrients With a Coupled Ocean General Circulation, Biogeochemical, and Radiative Model. 2; Comparisons With Satellite and In Situ Data

    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 were 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 (>1000 km) model chlorophyll seasonal distributions were statistically positively correlated with CZCS chlorophyll in 10 of 12 major oceanographic regions, and with SeaWiFS in all 12. Notable disparities in magnitudes occurred, however, in the tropical Pacific, the spring/summer bloom in the Antarctic, autumn in the northern high latitudes, and during the southwest monsoon in the North Indian Ocean. Synoptic scale (100-1000 km) comparisons of satellite and in situ data exhibited broad agreement, although occasional departures were apparent. Model nitrate distributions agreed 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 indicated that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on basin and synoptic scales.

  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. 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.

  11. A Conceptual Model of Coupled Biogeochemical and Hydrogeological Processes Affected by In Situ Cr(VI) Bioreduction in Groundwater at Hanford 100H Site

    NASA Astrophysics Data System (ADS)

    Faybishenko, B.; Long, P. E.; Hazen, T. C.; Hubbard, S. S.; Williams, K. H.; Peterson, J. E.; Chen, J.; Volkova, E. V.; Newcomer, D. R.; Resch, C. T.; Cantrell, K.; Conrad, M. S.; Brodie, E. L.; Joyner, D. C.; Borglin, S. E.; Chakraborty, R. C.

    2007-05-01

    The overall objective of this presentation is to demonstrate a conceptual multiscale, multidomain model of coupling of biogeochemical and hydrogeological processes during bioremediation of Cr(VI) contaminated groundwater at Hanford 100H site. A slow release polylactate, Hydrogen Release Compound (HRCTM), was injected in Hanford sediments to stimulate immobilization of Cr(VI). The HRC injection induced a 2-order-of- magnitude increase in biomass and the onset of reducing biogeochemical conditions [e.g., redox potential decreased from +240 to -130 mV and dissolved oxygen (DO) was completely removed]. A three-well system, comprised of an injection well and upgradient and downgradient monitoring wells, was used for conducting the in situ biostimulation, one regional flow (no-pumping) tracer test, and five pumping tests along with the Br-tracer injection. Field measurements were conducted using a Br ion-selective electrode and a multiparameter flow cell to collect hourly data on temperature, pH, redox potential, electrical conductivity, and DO. Groundwater sampling was conducted by pumping through specially designed borehole water samplers. Cross-borehole radar tomography and seismic measurements were carried out to assess the site background lithological heterogeneity and the migration pathways of HRC byproducts through groundwater after the HRC injection. Several alternative approaches, including conventional and fractional advective dispersion equations and geostatistical analysis, were used to characterize hydraulic and biogeochemical transport parameters. The results of a joint inversion of cross-borehole geophysical tomography and flow-rate measurements in boreholes indicate the presence of a bimodal distribution of hydraulic conductivity for Hanford sediments. The Br- concentration double-peak BTCs curves indicate that HRC injection caused an increase in the tracer travel time (mainly in the low-permeability zone) over the period of observations of about 2 years

  12. Potential for real-time understanding of coupled hydrologic and biogeochemical processes in stream ecosystems: Future integration of telemetered data with process models for glacial meltwater streams

    NASA Astrophysics Data System (ADS)

    McKnight, Diane M.; Cozzetto, Karen; Cullis, James D. S.; Gooseff, Michael N.; Jaros, Christopher; Koch, Joshua C.; Lyons, W. Berry; Neupauer, Roseanna; Wlostowski, Adam

    2015-08-01

    While continuous monitoring of streamflow and temperature has been common for some time, there is great potential to expand continuous monitoring to include water quality parameters such as nutrients, turbidity, oxygen, and dissolved organic material. In many systems, distinguishing between watershed and stream ecosystem controls can be challenging. The usefulness of such monitoring can be enhanced by the application of quantitative models to interpret observed patterns in real time. Examples are discussed primarily from the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. Although the Dry Valley landscape is barren of plants, many streams harbor thriving cyanobacterial mats. Whereas a daily cycle of streamflow is controlled by the surface energy balance on the glaciers and the temporal pattern of solar exposure, the daily signal for biogeochemical processes controlling water quality is generated along the stream. These features result in an excellent outdoor laboratory for investigating fundamental ecosystem process and the development and validation of process-based models. As part of the McMurdo Dry Valleys Long-Term Ecological Research project, we have conducted field experiments and developed coupled biogeochemical transport models for the role of hyporheic exchange in controlling weathering reactions, microbial nitrogen cycling, and stream temperature regulation. We have adapted modeling approaches from sediment transport to understand mobilization of stream biomass with increasing flows. These models help to elucidate the role of in-stream processes in systems where watershed processes also contribute to observed patterns, and may serve as a test case for applying real-time stream ecosystem models.

  13. Significant Findings: Tracking the SeaWiFS Record with a Coupled Physical/Biogeochemical/Radiative Model of the Global Oceans

    NASA Technical Reports Server (NTRS)

    Watson, Gregg W.

    2000-01-01

    The Sea-Viewing Wide Field-of-view Sensor (SeaWiFS) has observed 2.5 years of routine global chlorophyll observations from space. The mission was launched into a record El Nino event, which eventually gave way to one of the most intensive and longest-lasting La Nina events ever recorded. The SeaWiFS chlorophyll record captured the response of ocean phytoplankton to these significant events in the tropical Indo-Pacific basins, but also indicated significant interannual variability unrelated to the El Nino/La Nina events. This included large variability in the North Atlantic and Pacific basins, in the North Central and equatorial Atlantic, and milder patterns in the North Central Pacific. This SeaWiFS record was tracked with a coupled physical/biogeochemical/radiative model of the global oceans using near-real-time forcing data such as wind stresses, sea surface temperatures, and sea ice. This provided an opportunity to offer physically and biogeochemically meaningful explanations of the variability observed in the SeaWiFS data set, since the causal mechanisms and interrelationships of the model are completely understood. The coupled model was able to represent the seasonal distributions of chlorophyll during the SeaWiFS era, and was capable of differentiating among the widely different processes and dynamics occurring in the global oceans. The model was also reasonably successful in representing the interannual signal, especially when it was large, such as, the El Nino and La Nina events in the tropical Pacific and Indian Oceans. The model provided different phytoplankton group responses for the different events in these regions: diatoms were predominant in the tropical Pacific during the La Nina but other groups were predominant during El Nino. The opposite condition occurred in the tropical Indian Ocean. Both situations were due to the different responses of the basins to El Nino. The interannual variability in the North Atlantic, which was exhibited in Sea

  14. One-Dimensional Coupled Ecosystem-Carbon Flux Model for the Simulation of Biogeochemical Parameters at Ocean Weather Station P

    NASA Technical Reports Server (NTRS)

    Signorini, S.; McClain, C.; Christian, J.; Wong, C. S.

    2000-01-01

    In this Technical Publication, we describe the model functionality and analyze its application to the seasonal and interannual variations of phytoplankton, nutrients, pCO2 and CO2 concentrations in the eastern subarctic Pacific at Ocean Weather Station P (OWSP, 50 deg. N 145 deg. W). We use a verified one-dimensional ecosystem model, coupled with newly incorporated carbon flux and carbon chemistry components, to simulate 22 years (1958-1980) of pCO2 and CO2 variability at Ocean Weather Station P (OWS P). This relatively long period of simulation verifies and extends the findings of previous studies using an explicit approach for the biological component and realistic coupling with the carbon flux dynamics. The slow currents and the horizontally homogeneous ocean in the subarctic Pacific make OWS P one of the best available candidates for modeling the chemistry of the upper ocean in one dimension. The chlorophyll and ocean currents composite for 1998 illustrates this premise. The chlorophyll concentration map was derived from SeaWiFS data and the currents are from an OGCM simulation (from R. Murtugudde).

  15. Data assimilation in a coupled physical-biogeochemical model of the California current system using an incremental lognormal 4-dimensional variational approach: Part 3-Assimilation in a realistic context using satellite and in situ observations

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    A fully coupled physical and biogeochemical ocean data assimilation system is tested in a realistic configuration of the California Current System using the Regional Ocean Modeling System. In situ measurements for sea surface temperature and salinity as well as satellite observations for temperature, sea level and chlorophyll are used for the year 2000. Initial conditions of the combined physical and biogeochemical state are adjusted at the start of each 3-day assimilation cycle. Data assimilation results in substantial reduction of root-mean-square error (RMSE) over unconstrained model output. RMSE for physical variables is slightly lower when assimilating only physical variables than when assimilating both physical variables and surface chlorophyll. Surface chlorophyll RMSE is lowest when assimilating both physical variables and surface chlorophyll. Estimates of subsurface, nitrate and chlorophyll show modest improvements over the unconstrained model run relative to independent, unassimilated in situ data. Assimilation adjustments to the biogeochemical initial conditions are investigated within different regions of the California Current System. The incremental, lognormal 4-dimensional data assimilation method tested here represents a viable approach to coupled physical biogeochemical state estimation at practical computational cost.

  16. Budget of organic carbon in the North-Western Mediterranean open sea over the period 2004-2008 using 3-D coupled physical-biogeochemical modeling

    NASA Astrophysics Data System (ADS)

    Ulses, C.; Auger, P.-A.; Soetaert, K.; Marsaleix, P.; Diaz, F.; Coppola, L.; Herrmann, M. J.; Kessouri, F.; Estournel, C.

    2016-09-01

    A 3-D hydrodynamic-biogeochemical coupled model has been used to estimate a budget of organic carbon and its interannual variability over the 5 year period 2004-2008 in the North-Western Mediterranean Open Sea (NWMOS). The comparison of its results with in situ and satellite observations reveals that the timing and the magnitude of the convection and bloom processes during the study period, marked by contrasted atmospheric conditions, are reasonably well reproduced by the model. Model outputs show that the amount of nutrients annually injected into the surface layer is clearly linked to the intensity of the events of winter convection. During cold winters, primary production is reduced by intense mixing events but then spectacularly increases when the water column restratifies. In contrast, during mild winters, the primary production progressively and continuously increases, sustained by moderate new production followed by regenerated production. Overall, interannual variability in the annual primary production is low. The export in subsurface and at middepth is however affected by the intensity of the convection process, with annual values twice as high during cold winters than during mild winters. Finally, the estimation of a global budget of organic carbon reveals that the NWMOS acts as a sink for the shallower areas and as a source for the Algerian and Balearic subbasins.

  17. A Conceptual model of coupled biogeochemical and hydrogeologicalprocesses affected by in situ Cr(VI) bioreduction in groundwater atHanford 100H Site

    SciTech Connect

    Faybishenko, B.; Long, P.E.; Hazen, T.C.; Hubbard, S.S.; Williams, K.H.; Peterson, J.E.; Chen, J.; Volkova, E.V.; Newcomer, D.R.; Resch, C.T.; Cantrell, K.; Conrad, M.S.; Brodie, E.L.; Joyner, D.C.; Borglin, S.E.; Chakraborty, R.C.

    2006-09-06

    The overall objective of this presentation is to demonstratea conceptual multiscale, multidomain model of coupling of biogeochemicaland hydrogeological processes during bioremediation of Cr(VI)contaminated groundwater at Hanford 100H site. A slow releasepolylactate, Hydrogen Release Compound (HRCTM), was injected in Hanfordsediments to stimulate immobilization of Cr(VI). The HRC injectioninduced a 2-order-of-magnitude increase in biomass and the onset ofreducing biogeochemical conditions [e.g., redox potential decreased from+240 to -130 mV and dissolved oxygen (DO) was completely removed]. Athree-well system, comprised of an injection well and upgradient anddowngradient monitoring wells, was used for conducting the in situbiostimulation, one regional flow (no-pumping) tracer test, and fivepumping tests along with the Br-tracer injection. Field measurements wereconducted using a Br ion-selective electrode and a multiparameter flowcell to collect hourly data on temperature, pH, redox potential,electrical conductivity, and DO. Groundwater sampling was conducted bypumping through specially designed borehole water samplers.Cross-borehole radar tomography and seismic measurements were carried outto assess the site background lithological heterogeneity and themigration pathways of HRC byproducts through groundwater after the HRCinjection.

  18. The Role of Biogeochemical Cycling of Atmosphere-surface Exchangeable Pollutants (ASEPs) in the Dynamic Coupled Human-Natural ASEP System

    NASA Astrophysics Data System (ADS)

    Perlinger, J. A.; Urban, N. R.; Obrist, D.; Wu, S.

    2014-12-01

    Thousands of toxic pollutants that we term "atmosphere-surface exchangeable pollutants", or ASEPs, pass readily in both directions between the atmosphere and environmental surfaces and exhibit three characteristic tendencies when emitted to the environment: resistance to rapid degradation, accumulation in organic-rich biotic and abiotic surface reservoirs, and semivolatility causing re-emission to the atmosphere. ASEPs are emitted into the environment in part or in total through human activities, are transported and processed in the environment, and often deposited in locations distant from their original use or release. This characteristic separation of use and harm limits the capacity of communities affected by ASEPs to mitigate them. Incomplete understanding of the dynamic behavior of these pollutants in the environment has resulted in efforts to regulate them that do not fully protect human and ecosystem health from risks. To demonstrate this characteristic separation of use and harm, we compare and contrast the role that biogeochemical cycling plays in the dynamic coupled human-natural ASEP system for polycyclic aromatic hydrocarbons, polychlorinated biphenyl compounds, and mercury. We highlight remobilization effects related to land use and climate change, and demonstrate the ecosystem service provided by natural organic matter through sequestration of ASEPs in terrestrial environments.

  19. Integrated surface/subsurface permafrost thermal hydrology: Model formulation and proof-of-concept simulations

    DOE PAGES

    Painter, Scott L.; Coon, Ethan T.; Atchley, Adam L.; ...

    2016-08-11

    The need to understand potential climate impacts and feedbacks in Arctic regions has prompted recent interest in modeling of permafrost dynamics in a warming climate. A new fine-scale integrated surface/subsurface thermal hydrology modeling capability is described and demonstrated in proof-of-concept simulations. The new modeling capability combines a surface energy balance model with recently developed three-dimensional subsurface thermal hydrology models and new models for nonisothermal surface water flows and snow distribution in the microtopography. Surface water flows are modeled using the diffusion wave equation extended to include energy transport and phase change of ponded water. Variation of snow depth in themore » microtopography, physically the result of wind scour, is also modeled heuristically with a diffusion wave equation. The multiple surface and subsurface processes are implemented by leveraging highly parallel community software. Fully integrated thermal hydrology simulations on the tilted open book catchment, an important test case for integrated surface/subsurface flow modeling, are presented. Fine-scale 100-year projections of the integrated permafrost thermal hydrological system on an ice wedge polygon at Barrow Alaska in a warming climate are also presented. Finally, these simulations demonstrate the feasibility of microtopography-resolving, process-rich simulations as a tool to help understand possible future evolution of the carbon-rich Arctic tundra in a warming climate.« less

  20. Integrated surface/subsurface permafrost thermal hydrology: Model formulation and proof-of-concept simulations

    SciTech Connect

    Painter, Scott L.; Coon, Ethan T.; Atchley, Adam L.; Berndt, Markus; Garimella, Rao; Moulton, J. David; Svyatskiy, Daniil; Wilson, Cathy J.

    2016-08-11

    The need to understand potential climate impacts and feedbacks in Arctic regions has prompted recent interest in modeling of permafrost dynamics in a warming climate. A new fine-scale integrated surface/subsurface thermal hydrology modeling capability is described and demonstrated in proof-of-concept simulations. The new modeling capability combines a surface energy balance model with recently developed three-dimensional subsurface thermal hydrology models and new models for nonisothermal surface water flows and snow distribution in the microtopography. Surface water flows are modeled using the diffusion wave equation extended to include energy transport and phase change of ponded water. Variation of snow depth in the microtopography, physically the result of wind scour, is also modeled heuristically with a diffusion wave equation. The multiple surface and subsurface processes are implemented by leveraging highly parallel community software. Fully integrated thermal hydrology simulations on the tilted open book catchment, an important test case for integrated surface/subsurface flow modeling, are presented. Fine-scale 100-year projections of the integrated permafrost thermal hydrological system on an ice wedge polygon at Barrow Alaska in a warming climate are also presented. Finally, these simulations demonstrate the feasibility of microtopography-resolving, process-rich simulations as a tool to help understand possible future evolution of the carbon-rich Arctic tundra in a warming climate.

  1. Integrated surface/subsurface permafrost thermal hydrology: Model formulation and proof-of-concept simulations

    NASA Astrophysics Data System (ADS)

    Painter, Scott L.; Coon, Ethan T.; Atchley, Adam L.; Berndt, Markus; Garimella, Rao; Moulton, J. David; Svyatskiy, Daniil; Wilson, Cathy J.

    2016-08-01

    The need to understand potential climate impacts and feedbacks in Arctic regions has prompted recent interest in modeling of permafrost dynamics in a warming climate. A new fine-scale integrated surface/subsurface thermal hydrology modeling capability is described and demonstrated in proof-of-concept simulations. The new modeling capability combines a surface energy balance model with recently developed three-dimensional subsurface thermal hydrology models and new models for nonisothermal surface water flows and snow distribution in the microtopography. Surface water flows are modeled using the diffusion wave equation extended to include energy transport and phase change of ponded water. Variation of snow depth in the microtopography, physically the result of wind scour, is modeled phenomenologically with a diffusion wave equation. The multiple surface and subsurface processes are implemented by leveraging highly parallel community software. Fully integrated thermal hydrology simulations on the tilted open book catchment, an important test case for integrated surface/subsurface flow modeling, are presented. Fine-scale 100 year projections of the integrated permafrost thermal hydrological system on an ice wedge polygon at Barrow Alaska in a warming climate are also presented. These simulations demonstrate the feasibility of microtopography-resolving, process-rich simulations as a tool to help understand possible future evolution of the carbon-rich Arctic tundra in a warming climate.

  2. Surface-subsurface model for a dimer-dimer catalytic reaction: a Monte Carlo simulation study

    NASA Astrophysics Data System (ADS)

    Khan, K. M.; Albano, E. V.

    2002-02-01

    The surface-subsurface model for a dimer-dimer reaction of the type A2 + 2B2→2AB2 has been studied through Monte Carlo simulation via a model based on the lattice gas non-thermal Langmuir-Hinshelwood mechanism, which involves the precursor motion of the B2 molecule. The motion of precursors is considered on the surface as well as in the subsurface. The most interesting feature of this model is that it yields a steady reactive window, which is separated by continuous and discontinuous irreversible phase transitions. The phase diagram is qualitatively similar to the well known Ziff, Gulari and Barshad (ZGB) model. The width of the window depends upon the mobility of precursors. The continuous transition disappears when the mobility of the surface precursors is extended to the third-nearest neighbourhood. The dependence of production rate on partial pressure of B2 dimer is predicted by simple mathematical equations in our model.

  3. Data assimilation in a coupled physical-biogeochemical model of the California Current System using an incremental lognormal 4-dimensional variational approach: Part 1-Model formulation and biological data assimilation twin experiments

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    A quadratic formulation for an incremental lognormal 4-dimensional variational assimilation method (incremental L4DVar) is introduced for assimilation of biogeochemical observations into a 3-dimensional ocean circulation model. L4DVar assumes that errors in the model state are lognormally rather than Gaussian distributed, and implicitly ensures that state estimates are positive definite, making this approach attractive for biogeochemical variables. The method is made practical for a realistic implementation having a large state vector through linear assumptions that render the cost function quadratic and allow application of existing minimization techniques. A simple nutrient-phytoplankton-zooplankton-detritus (NPZD) model is coupled to the Regional Ocean Modeling System (ROMS) and configured for the California Current System. Quadratic incremental L4DVar is evaluated in a twin model framework in which biological fields only are in error and compared to G4DVar which assumes Gaussian distributed errors. Five-day assimilation cycles are used and statistics from four years of model integration analyzed. The quadratic incremental L4DVar results in smaller root-mean-squared errors and better statistical agreement with reference states than G4DVar while maintaining a positive state vector. The additional computational cost and implementation effort are trivial compared to the G4DVar system, making quadratic incremental L4DVar a practical and beneficial option for realistic biogeochemical state estimation in the ocean.

  4. Biogeochemical control of the coupled CO2-O 2 system of the Baltic Sea: a review of the results of Baltic-C.

    PubMed

    Omstedt, Anders; Humborg, Christoph; Pempkowiak, Janusz; Perttilä, Matti; Rutgersson, Anna; Schneider, Bernd; Smith, Benjamin

    2014-02-01

    Past, present, and possible future changes in the Baltic Sea acid-base and oxygen balances were studied using different numerical experiments and a catchment-sea model system in several scenarios including business as usual, medium scenario, and the Baltic Sea Action Plan. New CO2 partial pressure data provided guidance for improving the marine biogeochemical model. Continuous CO2 and nutrient measurements with high temporal resolution helped disentangle the biogeochemical processes. These data and modeling indicate that traditional understandings of the nutrient availability-organic matter production relationship do not necessarily apply to the Baltic Sea. Modeling indicates that increased nutrient loads will not inhibit future Baltic Sea acidification; instead, increased mineralization and biological production will amplify the seasonal surface pH cycle. The direction and magnitude of future pH changes are mainly controlled by atmospheric CO2 concentration. Apart from decreasing pH, we project a decreasing calcium carbonate saturation state and increasing hypoxic area.

  5. French Guiana Fluidized Muds: Predominant Sulfur Transformation Pathways and Prokaryotic Players in a Coupled System of Carbon-Sulfur-Metal Biogeochemical Cycling.

    NASA Astrophysics Data System (ADS)

    Luzan, T.; Chistoserdov, A. Y.; Aller, J. Y.; Aller, R. C.

    2008-12-01

    The fluidized mud ecosystem off French Guiana coast is a unique and globally important sedimentary environment characterized by intense physical reworking and rapid turnover of major biogeochemical elements. Here we assess the major pathways of carbon cycling focusing on the transformation of sulfur species and major prokaryotic participants. The depth distribution of organic carbon oxidation rates was determined for ~100 cm long cores collected off the French Guiana coast. Total organic carbon oxidation rates inferred from accumulation of inorganic carbon during a 3-6 month incubation series were elevated at the surface and decreased with depth. A similar incubation approach was applied for estimation of ferric reduction|oxidation rates. Short- chain fatty acid degradation rates and dark carbon dioxide rates were determined with 14C radiolabeled acetate and carbon dioxide, respectively, which both decreased with depth. The rates for sulfate and elemental sulfur transformation pathways were determined using 35S radiolabeled sulfur species with and without the presence of molybdate. Proposed microbially-mediated biogeochemical pathways were confirmed by MPN measurements of sulfate-, sulfur- and iron-reducing heterotrophic bacteria. Autotrophic bacteria were less numerous and their numbers did not directly correlate with rates of specific biogeochemical pathways. With most carbon oxidation accounted for by sulfur species - and ferric iron respiration, corresponding microbial groups may play a significant role in regulation of the net balance of organic carbon mineralization. Experimental results imply that auto- and heterotrophy likely coexist simultaneously and, thus participate in the internal carbon cycling in this environment.

  6. Spatio-temporal surface-subsurface water exchanges: from the local to the watershed scale

    NASA Astrophysics Data System (ADS)

    Rivière, Agnès; Flipo, Nicolas; Mouhri, Amer; Ansart, Patrick; Baudin, Aurélien; Berrhouma, Asma; Bodet, Ludovic; Cocher, Emmanuel; Cucchi, Karina; Durand, Véronique; Flageul, Sébastien; de Fouquet, Chantal; Goblet, Patrick; Hovhannissian, Gaghik; Jost, Anne; Pasquet, Sylvain; Rejiba, Fayçal; Rubin, Yoram; Tallec, Gaëlle; Mouchel, Jean-Marie

    2016-04-01

    Understanding the temporal and spatial variations of the surface-subsurface water exchanges is a prerequisite to achieve sustainable water use in basin. The concept of nested stream-aquifer interfaces (Flipo et al., 2014) is used to simulate the variation of the spatio-temporal surface-subsurface exchanges at the watershed scale from LOcal MOnitoring Stations (LOMOSs) measurements of the stream-aquifer exchanges. This method is applied along the stream network of the Avenelles basin. The Avenelles basin (46 km2) is located 70 km east from Paris. The basin is composed of a multi-layer aquifer system which consists of two limestone aquifers: the Brie aquifer (Oligocene) and the Champigny aquifer (Eocene) separated by a clayey aquitard. The meandering river is shallow, connected with the Brie aquifer in its upstream part and the Champigny aquifer in its downstream part. A high-frequency hydrologic monitoring network was deployed on the basin from 1960. The network measures water levels and water temperatures in the aquifers, and in-stream discharge rates. Five LOMOSs have been operating since 2012 along the stream-network (two upstream, two intermediate, and one downstream site) to monitor spatio-temporal stream-aquifer exchanges over years. LOMOSs are composed of one or two shallow piezometers to monitor the temperature and the hydraulic head variations in the aquifers, two hyporheic zone (HZ) temperature profiles located close to each river bank and one water level and temperature monitoring system in the river. A local 2D thermo-hydro model is used to determine hydrogeological and thermal properties of the aquifer and the HZ by inversion and to quantify the stream-aquifer exchanges at the local scale. We performed a pseudo 3D hydro(geo)logical simulation, over 23 years, at the Avenelles basin scale by the used of CAWAQS modelling platform. The CAWAQS platform is composed of four spatially distributed modules (Surface, Sub-surface, River and Groundwater

  7. Improving surface-subsurface water budgeting using high resolution satellite imagery applied on a brownfield.

    PubMed

    Dujardin, J; Batelaan, O; Canters, F; Boel, S; Anibas, C; Bronders, J

    2011-01-15

    The estimation of surface-subsurface water interactions is complex and highly variable in space and time. It is even more complex when it has to be estimated in urban areas, because of the complex patterns of the land-cover in these areas. In this research a modeling approach with integrated remote sensing analysis has been developed for estimating water fluxes in urban environments. The methodology was developed with the aim to simulate fluxes of contaminants from polluted sites. Groundwater pollution in urban environments is linked to patterns of land use and hence it is essential to characterize the land cover in a detail. An object-oriented classification approach applied on high-resolution satellite data has been adopted. To assign the image objects to one of the land-cover classes a multiple layer perceptron approach was adopted (Kappa of 0.86). Groundwater recharge has been simulated using the spatially distributed WetSpass model and the subsurface water flow using MODFLOW in order to identify and budget water fluxes. The developed methodology is applied to a brownfield case site in Vilvoorde, Brussels (Belgium). The obtained land use map has a strong impact on the groundwater recharge, resulting in a high spatial variability. Simulated groundwater fluxes from brownfield to the receiving River Zenne were independently verified by measurements and simulation of groundwater-surface water interaction based on thermal gradients in the river bed. It is concluded that in order to better quantify total fluxes of contaminants from brownfields in the groundwater, remote sensing imagery can be operationally integrated in a modeling procedure.

  8. 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.

  9. 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.

  10. TerrSysMP-PDAF (version 1.0): a modular high-performance data assimilation framework for an integrated land surface-subsurface model

    NASA Astrophysics Data System (ADS)

    Kurtz, Wolfgang; He, Guowei; Kollet, Stefan J.; Maxwell, Reed M.; Vereecken, Harry; Hendricks Franssen, Harrie-Jan

    2016-04-01

    Modelling of terrestrial systems is continuously moving towards more integrated modelling approaches, where different terrestrial compartment models are combined in order to realise a more sophisticated physical description of water, energy and carbon fluxes across compartment boundaries and to provide a more integrated view on terrestrial processes. While such models can effectively reduce certain parameterisation errors of single compartment models, model predictions are still prone to uncertainties regarding model input variables. The resulting uncertainties of model predictions can be effectively tackled by data assimilation techniques, which allow one to correct model predictions with observations taking into account both the model and measurement uncertainties. The steadily increasing availability of computational resources makes it now increasingly possible to perform data assimilation also for computationally highly demanding integrated terrestrial system models. However, as the computational burden for integrated models as well as data assimilation techniques is quite large, there is an increasing need to provide computationally efficient data assimilation frameworks for integrated models that allow one to run on and to make efficient use of massively parallel computational resources. In this paper we present a data assimilation framework for the land surface-subsurface part of the Terrestrial System Modelling Platform (TerrSysMP). TerrSysMP is connected via a memory-based coupling approach with the pre-existing parallel data assimilation library PDAF (Parallel Data Assimilation Framework). This framework provides a fully parallel modular environment for performing data assimilation for the land surface and the subsurface compartment. A simple synthetic case study for a land surface-subsurface system (0.8 million unknowns) is used to demonstrate the effects of data assimilation in the integrated model TerrSysMP and to assess the scaling behaviour of the

  11. Ocean Circulation and Biogeochemical responses to Typhoons

    NASA Astrophysics Data System (ADS)

    Huang, S. M.; Oey, L. Y.; Lin, P. L.; Liu, K. K.

    2014-12-01

    Typhoons produce vertical and horizontal mixing in the ocean and impact biogeochemical response. The goal of this study is to examine the fundamental processes involved in the physical and biogeochemical changes occurring in an ocean basin traversed by a zonally moving typhoon. The study employs an idealized typhoon wind field with varying intensities and translation speeds over a rectangular ocean basin. The model is based on the mpiPOM which is coupled to an NPZD biogeochemical model. The results show north-south asymmetric responses depending on the translation speeds of the typhoon, due to (1) the different intensities of inertial oscillation, (2) mixing caused by symmetric instability, and (3) re-stratification by mixed-layer baroclinic instability along the typhoon track.

  12. Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models: FINAL REPORT of grant Grant No. DE-FG02-04ER63726

    SciTech Connect

    Sarmiento, Jorge L; Gnanadesikan, Anand; Gruber, Nicolas

    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-ecologicalbiogeochemical 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. • 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

  13. An investigation on the surface/subsurface defects in potassium dihydrogen phosphate crystals after fly-cutting

    NASA Astrophysics Data System (ADS)

    Hou, Ning; Zhang, Yong; Zhang, Liangchi; Mylvaganam, Kausala; Wei, Junqi; Zhang, Feihu

    2016-10-01

    Potassium dihydrogen phosphate (KDP) crystals play an important role in the laser ignition facility of inertial confinement fusion (ICF) due to its unique large size and transparency. However, the laser damage threshold (LDT) of KDP crystal components is far below the intrinsic threshold that the band structure of a perfect crystal should provide. It has been considered that the surface/subsurface defects of a KDP component have a significant effect on the low LDT. This paper investigates the surface fogging phenomenon when a KDP is machined by a dry diamond fly-cutting. The subsurface damage was detected with the aid of the grazing incidence X-ray diffraction (GIXD) method. It was found that the subsurface structure changed from the KDP single crystal to a lattice misaligned structure due to the fly-cutting.

  14. Using Coupled Models to Study the Effects of River Discharge on Biogeochemical Cycling and Hypoxia in the Northern Gulf of Mexico

    DTIC Science & Technology

    2009-01-01

    high performance liquid chromatography ( HPLC ) pigment analysis; paniculate organic carbon and nitrogen (POC and PON); dissolved oxygen; dissolved...Ternary plots [4] of the components of total absorption are used to ’ fingerprint ’ water masses using surface ocean color imagery. These techniques... analyze the results from our first coupled model run. In addition to the modifications mentioned above, we arc currently implementing the sediment

  15. Subsurface Uranium Fate and Transport: Integrated Experiments and Modeling of Coupled Biogeochemical Mechanisms of Nanocrystalline Uraninite Oxidation by Fe(III)-(hydr)oxides - Project Final Report

    SciTech Connect

    Peyton, Brent M.; Timothy, Ginn R.; Sani, Rajesh K.

    2013-08-14

    citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO2 reoxidation as Fe(III) oxidizes HS– preferentially over UO2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network.

  16. Evolution of Earth-like Extrasolar Planetary Atmospheres: Assessing the Atmospheres and Biospheres of Early Earth Analog Planets with a Coupled Atmosphere Biogeochemical Model

    NASA Astrophysics Data System (ADS)

    Gebauer, S.; Grenfell, J. L.; Stock, J. W.; Lehmann, R.; Godolt, M.; von Paris, P.; Rauer, H.

    2017-01-01

    Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models. In this work, we present results from our newly developed Coupled Atmosphere Biogeochemistry model in which atmospheric O2 concentrations are fixed to values inferred by geological evidence. Applying a unique tool (Pathway Analysis Program), ours is the first quantitative analysis of catalytic cycles that governed O2 in early Earth's atmosphere near the Great Oxidation Event. Complicated oxidation pathways play a key role in destroying O2, whereas in the upper atmosphere, most O2 is formed abiotically via CO2 photolysis. The O2 bistability found by Goldblatt et al. (2006) is not observed in our calculations likely due to our detailed CH4 oxidation scheme. We calculate increased CH4 with increasing O2 during the Great Oxidation Event. For a given atmospheric surface flux, different atmospheric states are possible; however, the net primary productivity of the biosphere that produces O2 is unique. Mixing, CH4 fluxes, ocean solubility, and mantle/crust properties strongly affect net primary productivity and surface O2 fluxes. Regarding exoplanets, different "states" of O2 could exist for similar biomass output. Strong geological activity could lead to false negatives for life (since our analysis suggests that reducing gases remove O2 that

  17. Numerical simulation of in-situ chemical oxidation (ISCO) and biodegradation of petroleum hydrocarbons using a coupled model for bio-geochemical reactive transport

    NASA Astrophysics Data System (ADS)

    Marin, I. S.; Molson, J. W.

    2013-05-01

    Petroleum hydrocarbons (PHCs) are a major source of groundwater contamination, being a worldwide and well-known problem. Formed by a complex mixture of hundreds of organic compounds (including BTEX - benzene, toluene, ethylbenzene and xylenes), many of which are toxic and persistent in the subsurface and are capable of creating a serious risk to human health. Several remediation technologies can be used to clean-up PHC contamination. In-situ chemical oxidation (ISCO) and intrinsic bioremediation (IBR) are two promising techniques that can be applied in this case. However, the interaction of these processes with the background aquifer geochemistry and the design of an efficient treatment presents a challenge. Here we show the development and application of BIONAPL/Phreeqc, a modeling tool capable of simulating groundwater flow, contaminant transport with coupled biological and geochemical processes in porous or fractured porous media. BIONAPL/Phreeqc is based on the well-tested BIONAPL/3D model, using a powerful finite element simulation engine, capable of simulating non-aqueous phase liquid (NAPL) dissolution, density-dependent advective-dispersive transport, and solving the geochemical and kinetic processes with the library Phreeqc. To validate the model, we compared BIONAPL/Phreeqc with results from the literature for different biodegradation processes and different geometries, with good agreement. We then used the model to simulate the behavior of sodium persulfate (NaS2O8) as an oxidant for BTEX degradation, coupled with sequential biodegradation in a 2D case and to evaluate the effect of inorganic geochemistry reactions. The results show the advantages of a treatment train remediation scheme based on ISCO and IBR. The numerical performance and stability of the integrated BIONAPL/Phreeqc model was also verified.

  18. Monsoon-Driven Biogeochemical Processes in the Arabian Sea

    DTIC Science & Technology

    2005-08-03

    ton-detritus ( NPZD ) ecosystem formulation, Ryabchenko et al. (1998) utilized a more complex ecosystem model that specifically included the microbial...of these observations and the first large- scale physical-biogeochemical modeling attempts, a pre-JGOFS understanding of the Arabian Sea emerged...viewing Wide Field-of-View Sensor ocean color measurements. Analyses of these new data and coupled physical-biogeochemical models have already

  19. Evolution of Earth-like Extrasolar Planetary Atmospheres: Assessing the Atmospheres and Biospheres of Early Earth Analog Planets with a Coupled Atmosphere Biogeochemical Model.

    PubMed

    Gebauer, S; Grenfell, J L; Stock, J W; Lehmann, R; Godolt, M; von Paris, P; Rauer, H

    2017-01-01

    Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models. In this work, we present results from our newly developed Coupled Atmosphere Biogeochemistry model in which atmospheric O2 concentrations are fixed to values inferred by geological evidence. Applying a unique tool (Pathway Analysis Program), ours is the first quantitative analysis of catalytic cycles that governed O2 in early Earth's atmosphere near the Great Oxidation Event. Complicated oxidation pathways play a key role in destroying O2, whereas in the upper atmosphere, most O2 is formed abiotically via CO2 photolysis. The O2 bistability found by Goldblatt et al. ( 2006 ) is not observed in our calculations likely due to our detailed CH4 oxidation scheme. We calculate increased CH4 with increasing O2 during the Great Oxidation Event. For a given atmospheric surface flux, different atmospheric states are possible; however, the net primary productivity of the biosphere that produces O2 is unique. Mixing, CH4 fluxes, ocean solubility, and mantle/crust properties strongly affect net primary productivity and surface O2 fluxes. Regarding exoplanets, different "states" of O2 could exist for similar biomass output. Strong geological activity could lead to false negatives for life (since our analysis suggests that reducing gases remove O2 that

  20. Final Report DE-EE0005380: Assessment of Offshore Wind Farm Effects on Sea Surface, Subsurface and Airborne Electronic Systems

    SciTech Connect

    Ling, Hao; Hamilton, Mark F.; Bhalla, Rajan; Brown, Walter E.; Hay, Todd A.; Whitelonis, Nicholas J.; Yang, Shang-Te; Naqvi, Aale R.

    2013-09-30

    Offshore wind energy is a valuable resource that can provide a significant boost to the US renewable energy portfolio. A current constraint to the development of offshore wind farms is the potential for interference to be caused by large wind farms on existing electronic and acoustical equipment such as radar and sonar systems for surveillance, navigation and communications. The US Department of Energy funded this study as an objective assessment of possible interference to various types of equipment operating in the marine environment where offshore wind farms could be installed. The objective of this project was to conduct a baseline evaluation of electromagnetic and acoustical challenges to sea surface, subsurface and airborne electronic systems presented by offshore wind farms. To accomplish this goal, the following tasks were carried out: (1) survey electronic systems that can potentially be impacted by large offshore wind farms, and identify impact assessment studies and research and development activities both within and outside the US, (2) engage key stakeholders to identify their possible concerns and operating requirements, (3) conduct first-principle modeling on the interactions of electromagnetic signals with, and the radiation of underwater acoustic signals from, offshore wind farms to evaluate the effect of such interactions on electronic systems, and (4) provide impact assessments, recommend mitigation methods, prioritize future research directions, and disseminate project findings. This report provides a detailed description of the methodologies used to carry out the study, key findings of the study, and a list of recommendations derived based the findings.

  1. Identifying biogeochemical processes beneath stormwater infiltration ponds in support of a new best management practice for groundwater protection

    USGS Publications Warehouse

    O'Reilly, Andrew M.; Chang, Ni-Bin; Wanielista, Martin P.; Xuan, Zhemin; Schirmer, Mario; Hoehn, Eduard; Vogt, Tobias

    2011-01-01

     When applying a stormwater infiltration pond best management practice (BMP) for protecting the quality of underlying groundwater, a common constituent of concern is nitrate. Two stormwater infiltration ponds, the SO and HT ponds, in central Florida, USA, were monitored. A temporal succession of biogeochemical processes was identified beneath the SO pond, including oxygen reduction, denitrification, manganese and iron reduction, and methanogenesis. In contrast, aerobic conditions persisted beneath the HT pond, resulting in nitrate leaching into groundwater. Biogeochemical differences likely are related to soil textural and hydraulic properties that control surface/subsurface oxygen exchange. A new infiltration BMP was developed and a full-scale application was implemented for the HT pond. Preliminary results indicate reductions in nitrate concentration exceeding 50% in soil water and shallow groundwater beneath the HT pond.

  2. Modeling greenhouse gas emissions (CO2, N2O, CH4) from managed arable soils with a fully coupled hydrology-biogeochemical modeling system simulating water and nutrient transport and associated carbon and nitrogen cycling at catchment scale

    NASA Astrophysics Data System (ADS)

    Klatt, Steffen; Haas, Edwin; Kraus, David; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Plesca, Ina; Breuer, Lutz; Zhu, Bo; Zhou, Minghua; Zhang, Wei; Zheng, Xunhua; Wlotzka, Martin; Heuveline, Vincent

    2014-05-01

    The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in a small catchment at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the evapotranspiration is based on Penman-Monteith. Biogeochemical processes are modelled by LandscapeDNDC, including soil microclimate, plant growth and biomass allocation

  3. 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.

  4. 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."

  5. Integrated surface-subsurface model to investigate the role of groundwater in headwater catchment runoff generation: A minimalist approach to parameterisation

    NASA Astrophysics Data System (ADS)

    Ala-aho, Pertti; Soulsby, Chris; Wang, Hailong; Tetzlaff, Doerthe

    2017-04-01

    Understanding the role of groundwater for runoff generation in headwater catchments is a challenge in hydrology, particularly so in data-scarce areas. Fully-integrated surface-subsurface modelling has shown potential in increasing process understanding for runoff generation, but high data requirements and difficulties in model calibration are typically assumed to preclude their use in catchment-scale studies. We used a fully integrated surface-subsurface hydrological simulator to enhance groundwater-related process understanding in a headwater catchment with a rich background in empirical data. To set up the model we used minimal data that could be reasonably expected to exist for any experimental catchment. A novel aspect of our approach was in using simplified model parameterisation and including parameters from all model domains (surface, subsurface, evapotranspiration) in automated model calibration. Calibration aimed not only to improve model fit, but also to test the information content of the observations (streamflow, remotely sensed evapotranspiration, median groundwater level) used in calibration objective functions. We identified sensitive parameters in all model domains (subsurface, surface, evapotranspiration), demonstrating that model calibration should be inclusive of parameters from these different model domains. Incorporating groundwater data in calibration objectives improved the model fit for groundwater levels, but simulations did not reproduce well the remotely sensed evapotranspiration time series even after calibration. Spatially explicit model output improved our understanding of how groundwater functions in maintaining streamflow generation primarily via saturation excess overland flow. Steady groundwater inputs created saturated conditions in the valley bottom riparian peatlands, leading to overland flow even during dry periods. Groundwater on the hillslopes was more dynamic in its response to rainfall, acting to expand the saturated area

  6. A hierarchical framework for coupling surface fluxes to atompsheric general circulation models: The homogeneity test

    SciTech Connect

    Miller, N.L.

    1993-01-01

    The atmosphere and the biosphere are inherently coupled to one another. Atmospheric surface state variables such as temperature, winds, water vapor, precipitation, and radiation control biophysical, biogeochemical, and ecological processes at the surface and subsurface. At the same time, surface fluxes of momentum, moisture, heat, and trace gases act as time-dependent boundary conditions providing feedback on atmospheric processes. To understand such phenomena, a coupled set of interactive models is required. Costs are still prohibitive for computing surface/subsurface fluxes directly for medium-resolution atmospheric general circulation models (AGCMs), but a technique has been developed for testing large-scale homogeneity and accessing surface parameterizations and models to reduce this computational cost and maintain accuracy. This modeling system potentially bridges the observed spatial and temporal ranges yet allows the incorporation of necessary details about individual ecological community types or biomes and simulates the net momentum, heat, moisture, and trace gas fluxes. This suite of coupled models is defined here as the hierarchical systems flux scheme (HSFS).

  7. A hierarchical framework for coupling surface fluxes to atompsheric general circulation models: The homogeneity test

    SciTech Connect

    Miller, N.L.

    1993-12-31

    The atmosphere and the biosphere are inherently coupled to one another. Atmospheric surface state variables such as temperature, winds, water vapor, precipitation, and radiation control biophysical, biogeochemical, and ecological processes at the surface and subsurface. At the same time, surface fluxes of momentum, moisture, heat, and trace gases act as time-dependent boundary conditions providing feedback on atmospheric processes. To understand such phenomena, a coupled set of interactive models is required. Costs are still prohibitive for computing surface/subsurface fluxes directly for medium-resolution atmospheric general circulation models (AGCMs), but a technique has been developed for testing large-scale homogeneity and accessing surface parameterizations and models to reduce this computational cost and maintain accuracy. This modeling system potentially bridges the observed spatial and temporal ranges yet allows the incorporation of necessary details about individual ecological community types or biomes and simulates the net momentum, heat, moisture, and trace gas fluxes. This suite of coupled models is defined here as the hierarchical systems flux scheme (HSFS).

  8. Biogeochemical Cycles in Degraded Lands

    NASA Technical Reports Server (NTRS)

    Davidson, Eric A.; Vieira, Ima Celia G.; ReisdeCarvalho, Claudio Jose; DeanedeAbreuSa, Tatiana; deSouzaMoutinho, Paulo R.; Figueiredo, Ricardo O.; Stone, Thomas A.

    2004-01-01

    The objectives of this project were to define and describe the types of landscapes that fall under the broad category of "degraded lands" and to study biogeochemical cycles across this range of degradation found in secondary forests. We define degraded land as that which has lost part of its capacity of renovation of a productive ecosystem, either in the context of agroecosystems or as native communities of vegetation. This definition of degradation permits evaluation of biogeochemical constraints to future land uses.

  9. Biogeochemical Cycles in Degraded Lands

    NASA Technical Reports Server (NTRS)

    Davidson, Eric A.; Vieira, Ima Celia G.; ReisdeCarvalho, Claudio Jose; DeaneDeAbreuSa, Tatiana; deSpozaMoutinho, Paulo R.; Figueiredo, Ricardo O.; Stone, Thomas A.

    2003-01-01

    The objectives of this project were to define and describe the types of landscapes that fall under the broad category of "degraded lands" and to study biogeochemical cycles across this range of degradation found in secondary forests. We define degraded land as that which has lost part of its capacity of renovation of a productive ecosystem, either in the context of agroecosystems or as native communities of vegetation. This definition of degradation permits evaluation of biogeochemical constraints to future land uses.

  10. Surface-subsurface flow modeling: an example of large-scale research at the new NEON user facility

    NASA Astrophysics Data System (ADS)

    Powell, H.; McKnight, D. M.

    2009-12-01

    Climate change is predicted to alter surface-subsurface interactions in freshwater ecosystems. These interactions are hypothesized to control nutrient release at diel and seasonal time scales, which may then exert control over epilithic algal growth rates. The mechanisms underlying shifts in complex physical-chemical-biological patterns can be elucidated by long-term observations at sites that span hydrologic and climate gradients across the continent. Development of the National Ecological Observatory Network (NEON) will provide researchers the opportunity to investigate continental-scale patterns by combining investigator-driven measurements with Observatory data. NEON is a national-scale research platform for analyzing and understanding the impacts of climate change, land-use change, and invasive species on ecology. NEON features sensor networks and experiments, linked by advanced cyberinfrastructure to record and archive ecological data for at least 30 years. NEON partitions the United States into 20 ecoclimatic domains. Each domain hosts one fully instrumented Core Aquatic site in a wildland area and one Relocatable site, which aims to capture ecologically significant gradients (e.g. landuse, nitrogen deposition, urbanization). In the current definition of NEON there are 36 Aquatic sites: 30 streams/rivers and 6 ponds/lakes. Each site includes automated, in-situ sensors for groundwater elevation and temperature; stream flow (discharge and stage); pond water elevation; atmospheric chemistry (Tair, barometric pressure, PAR, radiation); and surface water chemistry (DO, Twater, conductivity, pH, turbidity, cDOM, nutrients). Groundwater and surface water sites shall be regularly sampled for selected chemical and isotopic parameters. The hydrologic and geochemical monitoring design provides basic information on water and chemical fluxes in streams and ponds and between groundwater and surface water, which is intended to support investigator-driven modeling studies

  11. Interactions of Biogeochemical Cycles in Oncoid Microbialites from Cuatro Ciénegas, Mexico

    NASA Astrophysics Data System (ADS)

    Corman, J. R.; Souza, V.; Elser, J. J.

    2010-04-01

    Modern microbialite systems may provide unique opportunities to study the feedbacks that couple or uncouple multiple biogeochemical cycles. Here we present results from a two-week manipulative ecosystem experiment using oncoid microbialites from Cuatro Ciénegas, Mexico.

  12. 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.

  13. Astronomical Forcing of Salt Marsh Biogeochemical Cascades

    NASA Astrophysics Data System (ADS)

    Morris, J. T.; Sundberg, K.

    2008-12-01

    Astronomically forced changes in the hydroperiod of a salt marsh affect the rate of marsh primary production leading to a biogeochemical cascade. For example, salt marsh primary production and biogeochemical cycles in coastal salt marshes are sensitive to the 18.6-year lunar nodal cycle, which alters the tidal amplitude by about 5 cm. For marshes that are perched high in the tidal frame, a relatively small increase in tidal amplitude and flooding lowers sediment salinity and stimulates primary production. Porewater sulfide concentrations are positively correlated with tidal amplitude and vary on the same cycle as primary production. Soluble reactive phosphate and ammonium concentrations in pore water also vary on this 18.6- year cycle. Phosphate likely responds to variation in the reaction of sulfide with iron-phosphate compounds, while the production of ammonium in sediments is coupled to the activity of diazotrophs that are carbon- limited and, therefore, are regulated by primary productivity. Ammonium also would accumulate when sulfides block nitrification. These dependencies work as a positive feedback between primary production and nutrient supply and are predictive of the near-term effects of sea-level rise.

  14. Effects of Privately Owned Land Management Practices on Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Getson, J. M.; Hutyra, L.; Short, A. G.; Templer, P. H.; Kittredge, D.

    2014-12-01

    An increasing fraction of the global population lives in urban settings. Understanding how the human-natural system couple and decouple biogeochemical cycles across urbanization gradients is crucial for human health and environmental sustainability. Natural processes of nutrient deposition, export, uptake, and internal cycling can be disrupted by human activities. Residential landscape management (e.g. composting, leaf litter collection, fertilizer application) interrupts these natural biogeochemical cycles; therefore, it is key to characterize these practices and their impacts. This study looks at private land management practices along a rural to urban gradient in Boston, Massachusetts. We used a mail survey instrument coupled with biogeochemical measurements and remote sensing derived estimates of aboveground biomass to estimate biogeochemical modifications associated with residential landscape management practices. We find parcel size influences management behavior, management practices differ for leaf litter and lawn clippings, and fertilizer application is unrelated to parcel size or degree of urban-ness. These management practices result in nutrient redistribution that differs with residential characteristics.

  15. 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

  16. 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

  17. Biogeochemical Processes in Microbial Ecosystems

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.

    2001-01-01

    The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

  18. Biogeochemical cycling and remote sensing

    NASA Technical Reports Server (NTRS)

    Peterson, D. L.

    1985-01-01

    Research is underway at the NASA Ames Research Center that is concerned with aspects of the nitrogen cycle in terrestrial ecosystems. An interdisciplinary research group is attempting to correlate nitrogen transformations, processes, and productivity with variables that can be remotely sensed. Recent NASA and other publications concerning biogeochemical cycling at global scales identify attributes of vegetation that could be related or explain the spatial variation in biologically functional variables. These functional variables include net primary productivity, annual nitrogen mineralization, and possibly the emission rate of nitrous oxide from soils.

  19. Data assimilation in a coupled physical-biogeochemical model of the California Current System using an incremental lognormal 4-dimensional variational approach: Part 2-Joint physical and biological data assimilation twin experiments

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    Coupled physical and biological data assimilation is performed within the California Current System using model twin experiments. The initial condition of physical and biological variables is estimated using the four-dimensional variational (4DVar) method under the Gaussian and lognormal error distributions assumption, respectively. Errors are assumed to be independent, yet variables are coupled by assimilation through model dynamics. Using a nutrient-phytoplankton-zooplankton-detritus (NPZD) model coupled to an ocean circulation model (the Regional Ocean Modeling System, ROMS), the coupled data assimilation procedure is evaluated by comparing results to experiments with no assimilation and with assimilation of physical data and biological data separately. Independent assimilation of physical (biological) data reduces the root-mean-squared error (RMSE) of physical (biological) state variables by more than 56% (43%). However, the improvement in biological (physical) state variables is less than 7% (13%). In contrast, coupled data assimilation improves both physical and biological components by 57% and 49%, respectively. Coupled data assimilation shows robust performance with varied observational errors, resulting in significantly smaller RMSEs compared to the free run. It still produces the estimation of observed variables better than that from the free run even with the physical and biological model error, but leads to higher RMSEs for unobserved variables. A series of twin experiments illustrates that coupled physical and biological 4DVar assimilation is computationally efficient and practical, capable of providing the reliable estimation of the coupled system with the same and ready to be examined in a realistic configuration.

  20. COUPLING

    DOEpatents

    Frisch, E.; Johnson, C.G.

    1962-05-15

    A detachable coupling arrangement is described which provides for varying the length of the handle of a tool used in relatively narrow channels. The arrangement consists of mating the key and keyhole formations in the cooperating handle sections. (AEC)

  1. The role of macropores and multi-resolution soil survey datasets for distributed surface-subsurface flow modeling

    NASA Astrophysics Data System (ADS)

    Yu, Xuan; Duffy, Christopher; Baldwin, Doug C.; Lin, Henry

    2014-08-01

    Distributed watershed-scale modeling is often used as a framework for exploring the heterogeneity of runoff response and hydrologic performance of the catchment. The objective of this study is to apply this framework to characterizing the impacts of soil hydraulic properties at multiple scales on moisture storage and distributed runoff generation in a forested catchment. The physics-based and fully-coupled Penn State Integrated Hydrologic Model (PIHM) is employed to test a priori and field-measured properties in the modeling of watershed hydrology. PIHM includes an approximate representation of macropore flow that preserves the water holding capacity of the soil matrix while still allowing rapid flow through the macroporous soil under wet conditions. Both phenomena are critical to the overall hydrologic performance of the catchment. Soils data at different scales were identified: Case I STATSGO soils data (uniform or single soil type), Case II STATSGO soils data with macropore effect, and Case III field-based hydropedologic experiment revised distributed soil hydraulic properties and macropore property estimation. Our results showed that the Case I had difficulties in simulating the timing and peakflow of the runoff responses. Case II performed satisfactorily for peakflow at the outlet and internal weir locations. The distributed soils data in Case III demonstrated the model ability of predicting groundwater levels. The analysis suggests the important role of macropore flow to setting the threshold for recharge and runoff response, while still preserving the water holding capability of the soil and plant water availability. The spatial variability in soil hydraulic properties represented by Case III introduces an additional improvement in distributed catchment flow modeling, especially as it relates to subsurface lateral flow. Comparison of the three cases suggests the value of high-resolution soil survey mapping combined with a macropore parameterization can

  2. Ocean fronts drive marine fishery production and biogeochemical cycling

    PubMed Central

    Woodson, C. Brock; Litvin, Steven Y.

    2015-01-01

    Long-term changes in nutrient supply and primary production reportedly foreshadow substantial declines in global marine fishery production. These declines combined with current overfishing, habitat degradation, and pollution paint a grim picture for the future of marine fisheries and ecosystems. However, current models forecasting such declines do not account for the effects of ocean fronts as biogeochemical hotspots. Here we apply a fundamental technique from fluid dynamics to an ecosystem model to show how fronts increase total ecosystem biomass, explain fishery production, cause regime shifts, and contribute significantly to global biogeochemical budgets by channeling nutrients through alternate trophic pathways. We then illustrate how ocean fronts affect fishery abundance and yield, using long-term records of anchovy–sardine regimes and salmon abundances in the California Current. These results elucidate the fundamental importance of biophysical coupling as a driver of bottom–up vs. top–down regulation and high productivity in marine ecosystems. PMID:25624488

  3. Ocean fronts drive marine fishery production and biogeochemical cycling.

    PubMed

    Woodson, C Brock; Litvin, Steven Y

    2015-02-10

    Long-term changes in nutrient supply and primary production reportedly foreshadow substantial declines in global marine fishery production. These declines combined with current overfishing, habitat degradation, and pollution paint a grim picture for the future of marine fisheries and ecosystems. However, current models forecasting such declines do not account for the effects of ocean fronts as biogeochemical hotspots. Here we apply a fundamental technique from fluid dynamics to an ecosystem model to show how fronts increase total ecosystem biomass, explain fishery production, cause regime shifts, and contribute significantly to global biogeochemical budgets by channeling nutrients through alternate trophic pathways. We then illustrate how ocean fronts affect fishery abundance and yield, using long-term records of anchovy-sardine regimes and salmon abundances in the California Current. These results elucidate the fundamental importance of biophysical coupling as a driver of bottom-up vs. top-down regulation and high productivity in marine ecosystems.

  4. 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

  5. Are channels standalone? Analysis of channel to land interactions using a physically-based surface-subsurface processes model with multi-way exchanges

    NASA Astrophysics Data System (ADS)

    Shen, C.; Smithgall, K. M.; Riley, W. J.

    2014-12-01

    Large-scale land surface models commonly assumed that land-channel exchanges are unidirectional, in which the channel network receives runoff, baseflow, sediments, and other materials from land and conveys them to the outlet. The physiographic and geomorphological characteristics of channels, as well as flow conditions, exert no influence on simulated upland dynamics. In this work we study the feedbacks to upland hydrologic and ecosystem states and fluxes provided by channels. We employ a physically-based surface-subsurface processes model (PAWS+CLM) that fully resolves the multi-way interactions between channel flow, overland flow, groundwater, soil water and wetlands. We found notable influences of channels on land surface fluxes, which are explained by the baseflow mechanism and the efficient conveyance mechanism. We systematically quantify the extent of the impact and link channel characteristics to these impacts. Our results indicate that to further improve our understanding of the land-water system, the influence of channels need to be included in integrated models.

  6. Terrestrial biogeochemical cycles: global interactions with the atmosphere and hydrology

    NASA Astrophysics Data System (ADS)

    Schimel, David S.; Kittel, Timothy G. F.; Parton, William J.

    1991-08-01

    Ecosystem scientists have developed a body of theory to predict the behaviour of biogeochemical cycles when exchanges with other ecosystems are small or prescribed. Recent environmental changes make it clear that linkages between ecosystems via atmospheric and hydrological transport have large effects on ecosystem dynamics when considered over time periods of a decade to a century, time scales relevant to contemporary humankind. Our ability to predict behaviour of ecosystems coupled by transport is limited by our ability (1) to extrapolate biotic function to large spatial scales and (2) to measure and model transport. We review developments in ecosystem theory, remote sensing, and geographical information systems (GIS) that support new efforts in spatial modeling. A paradigm has emerged to predict behaviour of ecosystems based on understanding responses to multiple resources (e.g., water, nutrients, light). Several ecosystem models couple primary production to decomposition and nutrient availability using the above paradigm. These models require a fairly small set of environmental variables to simulate spatial and temporal variation in rates of biogeochemical cycling. Simultaneously, techniques for inferring ecosystem behaviour from remotely measured canopy light interception are improving our ability to infer plant activity from satellite observations. Efforts have begun to couple models of transport in air and water to models of ecosystem function. Preliminary work indicates that coupling of transport and ecosystem processes alters the behaviour of earth system components (hydrology, terrestrial ecosystems, and the atmosphere) from that of an uncoupled mode.

  7. Proterozoic ocean redox and biogeochemical stasis

    PubMed Central

    Reinhard, Christopher T.; Planavsky, Noah J.; Robbins, Leslie J.; Partin, Camille A.; Gill, Benjamin C.; Lalonde, Stefan V.; Bekker, Andrey; Konhauser, Kurt O.; Lyons, Timothy W.

    2013-01-01

    The partial pressure of oxygen in Earth’s atmosphere has increased dramatically through time, and this increase is thought to have occurred in two rapid steps at both ends of the Proterozoic Eon (∼2.5–0.543 Ga). However, the trajectory and mechanisms of Earth’s oxygenation are still poorly constrained, and little is known regarding attendant changes in ocean ventilation and seafloor redox. We have a particularly poor understanding of ocean chemistry during the mid-Proterozoic (∼1.8–0.8 Ga). Given the coupling between redox-sensitive trace element cycles and planktonic productivity, various models for mid-Proterozoic ocean chemistry imply different effects on the biogeochemical cycling of major and trace nutrients, with potential ecological constraints on emerging eukaryotic life. Here, we exploit the differing redox behavior of molybdenum and chromium to provide constraints on seafloor redox evolution by coupling a large database of sedimentary metal enrichments to a mass balance model that includes spatially variant metal burial rates. We find that the metal enrichment record implies a Proterozoic deep ocean characterized by pervasive anoxia relative to the Phanerozoic (at least ∼30–40% of modern seafloor area) but a relatively small extent of euxinic (anoxic and sulfidic) seafloor (less than ∼1–10% of modern seafloor area). Our model suggests that the oceanic Mo reservoir is extremely sensitive to perturbations in the extent of sulfidic seafloor and that the record of Mo and chromium enrichments through time is consistent with the possibility of a Mo–N colimited marine biosphere during many periods of Earth’s history. PMID:23515332

  8. The global troposphere - Biogeochemical cycles, chemistry, and remote sensing

    NASA Technical Reports Server (NTRS)

    Levine, J. S.; Allario, F.

    1982-01-01

    The chemical composition of the troposphere is controlled by various biogeochemical cycles that couple the atmosphere with the oceans, the solid earth and the biosphere, and by atmospheric photochemical/chemical reactions. These cycles and reactions are discussed and a number of key questions concerning tropospheric composition and chemistry for the carbon, nitrogen, oxygen and sulfur species are identified. Next, various remote sensing techniques and instruments capable of measuring and monitoring tropospheric species from the ground, aircraft and space to address some of these key questions are reviewed. Future thrusts in remote sensing of the troposphere are also considered.

  9. A generic reaction-based biogeochemical simulator

    SciTech Connect

    Fang, Yilin; Yabusaki, Steven B.; Yeh, Gour T.; C.T. Miller, M.W. Farthing, W.G. Gray, and G.F. Pinder

    2004-06-17

    This paper presents a generic biogeochemical simulator, BIOGEOCHEM. The simulator can read a thermodynamic database based on the EQ3/EQ6 database. It can also read user-specified equilibrium and kinetic reactions (reactions not defined in the format of that in EQ3/EQ6 database) symbolically. BIOGEOCHEM is developed with a general paradigm. It overcomes the requirement in most available reaction-based models that reactions and rate laws be specified in a limited number of canonical forms. The simulator interprets the reactions, and rate laws of virtually any type for input to the MAPLE symbolic mathematical software package. MAPLE then generates Fortran code for the analytical Jacobian matrix used in the Newton-Raphson technique, which are compiled and linked into the BIOGEOCHEM executable. With this feature, the users are exempted from recoding the simulator to accept new equilibrium expressions or kinetic rate laws. Two examples are used to demonstrate the new features of the simulator.

  10. The Southern Ocean biogeochemical divide.

    PubMed

    Marinov, I; Gnanadesikan, A; Toggweiler, J R; Sarmiento, J L

    2006-06-22

    Modelling studies have demonstrated that the nutrient and carbon cycles in the Southern Ocean play a central role in setting the air-sea balance of CO(2) and global biological production. Box model studies first pointed out that an increase in nutrient utilization in the high latitudes results in a strong decrease in the atmospheric carbon dioxide partial pressure (pCO2). This early research led to two important ideas: high latitude regions are more important in determining atmospheric pCO2 than low latitudes, despite their much smaller area, and nutrient utilization and atmospheric pCO2 are tightly linked. Subsequent general circulation model simulations show that the Southern Ocean is the most important high latitude region in controlling pre-industrial atmospheric CO(2) because it serves as a lid to a larger volume of the deep ocean. Other studies point out the crucial role of the Southern Ocean in the uptake and storage of anthropogenic carbon dioxide and in controlling global biological production. Here we probe the system to determine whether certain regions of the Southern Ocean are more critical than others for air-sea CO(2) balance and the biological export production, by increasing surface nutrient drawdown in an ocean general circulation model. We demonstrate that atmospheric CO(2) and global biological export production are controlled by different regions of the Southern Ocean. The air-sea balance of carbon dioxide is controlled mainly by the biological pump and circulation in the Antarctic deep-water formation region, whereas global export production is controlled mainly by the biological pump and circulation in the Subantarctic intermediate and mode water formation region. The existence of this biogeochemical divide separating the Antarctic from the Subantarctic suggests that it may be possible for climate change or human intervention to modify one of these without greatly altering the other.

  11. Simulating spatially distributed catchment response using a fully-integrated surface-subsurface model based on dual calibration with streamflow and evapotranspiration

    NASA Astrophysics Data System (ADS)

    Ala-aho, Pertti; Soulsby, Chris; Wang, Hailong; Tetzlaff, Doerthe

    2016-04-01

    We use above-ground hydrological fluxes (streamflow and evapotranspiration (ET)) to calibrate an integrated hydrological simulator for a headwater catchment located in the Scottish highlands. Our study explores the feasibility of simulating spatially distributed catchment response in a physically based framework whilst having only preliminary data about the subsurface hydrological parameters. Furthermore we investigate the added value of insitu ET data in the calibration process. Transient simulations are performed with a fully integrated surface-subsurface hydrological model HydroGeoSphere and calibration of model parameters is done in PEST framework. In the first calibration step only the stream hydrograph is included using the original time series alongside with log-transformed hydrograph and weekly flow volumes in the objective function. ET is estimated with energy balance technique using above canopy temperatures, humidity and net radiation measured within the catchment. In the second calibration step, the ET time series are introduced in the calibration objective function. Parameter identifiability along with uncertainty in the model output will be examined as a part of the model calibration for both calibration steps. Furthermore, the post-calibration model will allow us to simulate spatially distributed hydrological fluxes and to distinguish between different water sources that make up the stream hydrograph using the hydraulic mixing-cell method. Preliminary simulations have shown that transient and spatially distributed surface water, subsurface water and evaporative fluxes of a headwater catchment can be reproduced in integrated modelling framework using only above-ground hydrological data in model calibration. We hypothesize that the evapotranspiration dataset informs the catchment water budget and water transmission rates and is therefore useful in constraining subsurface hydraulic parameters, such as hydraulic conductivities, which are typically

  12. Cretaceous-Palaeogene experiments in Biogeochemical Resilience

    NASA Astrophysics Data System (ADS)

    Penman, D. E.; Henehan, M. J.; Hull, P. M.; Planavsky, N.; Schmidt, D. N.; Rae, J. W. B.; Thomas, E.; Huber, B. T.

    2015-12-01

    Human activity is altering biogeochemical cycles in the ocean. While ultimately anthropogenic forcings may be brought under control, it is still unclear whether tipping points may exist beyond which human-induced changes to biogeochemical cycles become irreversible. We use the Late Cretaceous and the Cretaceous-Palaeogene (K-Pg) boundary interval as an informative case study. Over this interval, two carbon cycle perturbations (gradual flood basalt volcanism and abrupt bolide impact) occurred within a short time window, allowing us to investigate the resilience of biogeochemical cycles to different pressures applied to the same initial boundary conditions on very different time scales. We demonstrate that relatively gradual emission of CO2 from the Deccan large igneous province was efficiently mitigated within the limits of existing biogeochemical processes. However, the rapid extinction of pelagic calcifying organisms at the K-Pg boundary due to the Chicxulub bolide impact had more profound effects, and caused lasting (> 1 million years) changes to biogeochemical cycles. By combining sedimentological observations with boron isotope-based pH reconstructions over these events, we document two potentially useful partial analogues for best and worst case scenarios for anthropogenic global change. We suggest that if current ocean acidification results in the mass extinction of marine pelagic calcifiers, we may cause profound changes to the Earth system that will persist for 100,000s to millions of years.

  13. Global Change: A Biogeochemical Perspective

    NASA Technical Reports Server (NTRS)

    Mcelroy, M.

    1983-01-01

    A research program that is designed to enhance our understanding of the Earth as the support system for life is described. The program change, both natural and anthropogenic, that might affect the habitability of the planet on a time scale roughly equal to that of a human life is studied. On this time scale the atmosphere, biosphere, and upper ocean are treated as a single coupled system. The need for understanding the processes affecting the distribution of essential nutrients--carbon, nitrogen, phosphorous, sulfur, and water--within this coupled system is examined. The importance of subtle interactions among chemical, biological, and physical effects is emphasized. The specific objectives are to define the present state of the planetary life-support system; to ellucidate the underlying physical, chemical, and biological controls; and to provide the body of knowledge required to assess changes that might impact the future habitability of the Earth.

  14. Improving Intercomparability of Marine Biogeochemical Time Series

    NASA Astrophysics Data System (ADS)

    Benway, Heather M.; Telszewski, Maciej; Lorenzoni, Laura

    2013-04-01

    Shipboard biogeochemical time series represent one of the most valuable tools scientists have to quantify marine elemental fluxes and associated biogeochemical processes and to understand their links to changing climate. They provide the long, temporally resolved data sets needed to characterize ocean climate, biogeochemistry, and ecosystem variability and change. However, to monitor and differentiate natural cycles and human-driven changes in the global oceans, time series methodologies must be transparent and intercomparable when possible. To review current shipboard biogeochemical time series sampling and analytical methods, the International Ocean Carbon Coordination Project (IOCCP; http://www.ioccp.org/) and the Ocean Carbon and Biogeochemistry Program (http://www.us-ocb.org/) convened an international ocean time series workshop at the Bermuda Institute for Ocean Sciences.

  15. Dynamic interactions of ecohydrological and biogeochemical processes in water-stressed environments

    NASA Astrophysics Data System (ADS)

    Wang, L.; Manzoni, S.; Ravi, S.; Riveros-Iregui, D. A.; Caylor, K. K.

    2015-12-01

    Water is the essential reactant, catalyst, or medium for many biogeochemical reactions and flows. The coupling between hydrological and biogeochemical processes is particularly evident in drylands, but also in areas with strong seasonal precipitation patterns or in mesic systems during droughts. Moreover, this coupling is apparent at all levels in the ecosystems - from soil microbial cells to whole plants to landscapes. A holistic approach is essential to fully understand function and processes in water-limited ecosystems and to predict their responses to environmental change. We examine some of the mechanisms responsible for microbial and vegetation responses to moisture inputs in water-limited ecosystems through a synthesis of existing literature and we also summarize the modeling advances in addressing these interactions. This paper focuses on three opportunities to advance coupled hydrological and biogeochemical research: (1) improved quantitative understanding of mechanisms linking hydrological and biogeochemical variations in drylands, (2) experimental and theoretical approaches that describe linkages between hydrology and biogeochemistry (particularly across scales), and (3) the use of these tools and insights to address critical dryland issues of societal relevance.

  16. Temporal dynamics of biogeochemical processes at the Norman Landfill site

    USGS Publications Warehouse

    Arora, Bhavna; Mohanty, Binayak P.; McGuire, Jennifer T.; Cozzarelli, Isabelle M.

    2013-01-01

    The temporal variability observed in redox sensitive species in groundwater can be attributed to coupled hydrological, geochemical, and microbial processes. These controlling processes are typically nonstationary, and distributed across various time scales. Therefore, the purpose of this study is to investigate biogeochemical data sets from a municipal landfill site to identify the dominant modes of variation and determine the physical controls that become significant at different time scales. Data on hydraulic head, specific conductance, δ2H, chloride, sulfate, nitrate, and nonvolatile dissolved organic carbon were collected between 1998 and 2000 at three wells at the Norman Landfill site in Norman, OK. Wavelet analysis on this geochemical data set indicates that variations in concentrations of reactive and conservative solutes are strongly coupled to hydrologic variability (water table elevation and precipitation) at 8 month scales, and to individual eco-hydrogeologic framework (such as seasonality of vegetation, surface-groundwater dynamics) at 16 month scales. Apart from hydrologic variations, temporal variability in sulfate concentrations can be associated with different sources (FeS cycling, recharge events) and sinks (uptake by vegetation) depending on the well location and proximity to the leachate plume. Results suggest that nitrate concentrations show multiscale behavior across temporal scales for different well locations, and dominant variability in dissolved organic carbon for a closed municipal landfill can be larger than 2 years due to its decomposition and changing content. A conceptual framework that explains the variability in chemical concentrations at different time scales as a function of hydrologic processes, site-specific interactions, and/or coupled biogeochemical effects is also presented.

  17. Temporal dynamics of biogeochemical processes at the Norman Landfill site

    NASA Astrophysics Data System (ADS)

    Arora, Bhavna; Mohanty, Binayak P.; McGuire, Jennifer T.; Cozzarelli, Isabelle M.

    2013-10-01

    The temporal variability observed in redox sensitive species in groundwater can be attributed to coupled hydrological, geochemical, and microbial processes. These controlling processes are typically nonstationary, and distributed across various time scales. Therefore, the purpose of this study is to investigate biogeochemical data sets from a municipal landfill site to identify the dominant modes of variation and determine the physical controls that become significant at different time scales. Data on hydraulic head, specific conductance, δ2H, chloride, sulfate, nitrate, and nonvolatile dissolved organic carbon were collected between 1998 and 2000 at three wells at the Norman Landfill site in Norman, OK. Wavelet analysis on this geochemical data set indicates that variations in concentrations of reactive and conservative solutes are strongly coupled to hydrologic variability (water table elevation and precipitation) at 8 month scales, and to individual eco-hydrogeologic framework (such as seasonality of vegetation, surface-groundwater dynamics) at 16 month scales. Apart from hydrologic variations, temporal variability in sulfate concentrations can be associated with different sources (FeS cycling, recharge events) and sinks (uptake by vegetation) depending on the well location and proximity to the leachate plume. Results suggest that nitrate concentrations show multiscale behavior across temporal scales for different well locations, and dominant variability in dissolved organic carbon for a closed municipal landfill can be larger than 2 years due to its decomposition and changing content. A conceptual framework that explains the variability in chemical concentrations at different time scales as a function of hydrologic processes, site-specific interactions, and/or coupled biogeochemical effects is also presented.

  18. Isotopic, petrologic and biogeochemical investigations of banded iron-formations

    NASA Technical Reports Server (NTRS)

    Hayes, J. M.; Kaufman, A. J.; Klein, C.; Studley, S. A.; Baur, M. E.; Walter, M. R.

    1986-01-01

    It is recognized that the first occurrence of banded iron-formations (BIFs) clearly predates biological oxygenation of the atmosphere-hydrosphere system and that their last occurrences extend beyond plausible dates of pervasive biological oxygenation. For this reason, and because enormous quantities of oxidizing power have been sequestered in them, it is widely thought that these massive, but enigmatic, sediments must encode information about the mechanism and timing of the rise of atmospheric O2. By coupling isotopic analyses of iron-formation carbonates with biogeochemical and petrologic investigations, we are studying (1) the mechanism of initial sedimentation of iron; (2) the role of iron in microbially mediated diagenetic processes in fresh iron-formation sediments; and (3) the logical integration of mechanisms of deposition with observed levels of banding. Thus far, it has been shown that (1) carbonates in BIFs of the Hamersley Group of Western Australia are isotopically inhomogenous; (2) the nature and pattern of isotopic ordering is not consistent with a metamorphic origin for the overall depletion of C-13 observed in the carbonates; (3) if biological, the origin of the C-13 depleted carbonate could be either respiratory or fermentative; (4) iron may have been precipitate d as Fe(3+), then reduced to Fe(2+) within the sediment; and (5) sedimentary biogeochemical systems may have been at least partially closed to mass transport of carbonate species.

  19. Biogeochemical redox processes and their impact on contaminant dynamics

    USGS Publications Warehouse

    Borch, Thomas; Kretzschmar, Ruben; Kappler, Andreas; Van Cappellen, Philippe; Ginder-Vogel, Matthew; Campbell, Kate M.

    2010-01-01

    Life and element cycling on Earth is directly related to electron transfer (or redox) reactions. An understanding of biogeochemical redox processes is crucial for predicting and protecting environmental health and can provide new opportunities for engineered remediation strategies. Energy can be released and stored by means of redox reactions via the oxidation of labile organic carbon or inorganic compounds (electron donors) by microorganisms coupled to the reduction of electron acceptors including humic substances, iron-bearing minerals, transition metals, metalloids, and actinides. Environmental redox processes play key roles in the formation and dissolution of mineral phases. Redox cycling of naturally occurring trace elements and their host minerals often controls the release or sequestration of inorganic contaminants. Redox processes control the chemical speciation, bioavailability, toxicity, and mobility of many major and trace elements including Fe, Mn, C, P, N, S, Cr, Cu, Co, As, Sb, Se, Hg, Tc, and U. Redox-active humic substances and mineral surfaces can catalyze the redox transformation and degradation of organic contaminants. In this review article, we highlight recent advances in our understanding of biogeochemical redox processes and their impact on contaminant fate and transport, including future research needs.

  20. Managing biogeochemical cycles to reduce greenhouse gases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This special issue focuses on terrestrial biogeochemical cycles and their roles in determining current continental-scale budgets and future trends in biogenic greenhouse gases (GHGs) for North America. Understanding the current magnitude and forecasting future trajectories of atmospheric GHG concent...

  1. Marginal Ice Zone: Biogeochemical Sampling with Gliders

    DTIC Science & Technology

    2014-09-30

    Figure 3. Map of 2014 IBRV Araon Arctic cruise study area, indicating CTD, XCTD, sea- ice caps , and helicopter...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Marginal Ice Zone: Biogeochemical Sampling with Gliders...distribution of phytoplankton and particulate organic carbon in the Arctic under the ice and in the marginal ice zone, as well as to understand feedbacks

  2. Molecular biogeochemical provinces in the Atlantic Surface Ocean

    NASA Astrophysics Data System (ADS)

    Koch, B. P.; Flerus, R.; Schmitt-Kopplin, P.; Lechtenfeld, O. J.; Bracher, A.; Cooper, W.; Frka, S.; Gašparović, B.; Gonsior, M.; Hertkorn, N.; Jaffe, R.; Jenkins, A.; Kuss, J.; Lara, R. J.; Lucio, M.; McCallister, S. L.; Neogi, S. B.; Pohl, C.; Roettgers, R.; Rohardt, G.; Schmitt, B. B.; Stuart, A.; Theis, A.; Ying, W.; Witt, M.; Xie, Z.; Yamashita, Y.; Zhang, L.; Zhu, Z. Y.; Kattner, G.

    2010-12-01

    One of the most important aspects to understand marine organic carbon fluxes is to resolve the molecular mechanisms which convert fresh, labile biomolecules into semi-labile and refractory dissolved and particulate organic compounds in the ocean. In this interdisciplinary project, which was performed on a cruise with RV Polarstern, we carried out a detailed molecular characterisation of dissolved organic matter (DOM) on a North-South transect in the Atlantic surface ocean in order to relate the data to different biological, climatic, oceanographic, and meteorological regimes as well as to terrestrial input from riverine and atmospheric sources. Our goal was to achieve a high resolution data set for the biogeochemical characterisation of the sources and reactivity of DOM. We applied ultrahigh resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS), nutrient, trace element, amino acid, and lipid analyses and other biogeochemical measurements for 220 samples from the upper water column (0-200m) and eight deep profiles. Various spectroscopic techniques were applied continuously in a constant sample water flow supplied by a fish system and the moon pool. Radiocarbon dating enabled assessing DOC residence time. Bacterial abundance and production provided a metabolic context for the DOM characterization work and pCO2 concentrations. Combining molecular organic techniques and inductively coupled plasma mass spectrometry (ICP-MS) established an important link between organic and inorganic biogeochemical studies. Multivariate statistics, primarily based on FT-ICR-MS data for 220 samples, allowed identifying geographical clusters which matched ecological provinces proposed previously by Longhurst (2007). Our study demonstrated that marine DOM carries molecular information reflecting the “history” of ocean water masses. This information can be used to define molecular biogeochemical provinces and to improve our understanding of element fluxes in

  3. Cumulative Significance of Hyporheic Exchange and Biogeochemical Processing in River Networks

    NASA Astrophysics Data System (ADS)

    Harvey, J. W.; Gomez-Velez, J. D.

    2014-12-01

    Biogeochemical reactions in rivers that decrease excessive loads of nutrients, metals, organic compounds, etc. are enhanced by hydrologic interactions with microbially and geochemically active sediments of the hyporheic zone. The significance of reactions in individual hyporheic flow paths has been shown to be controlled by the contact time between river water and sediment and the intrinsic reaction rate in the sediment. However, little is known about how the cumulative effects of hyporheic processing in large river basins. We used the river network model NEXSS (Gomez-Velez and Harvey, submitted) to simulate hyporheic exchange through synthetic river networks based on the best available models of network topology, hydraulic geometry and scaling of geomorphic features, grain size, hydraulic conductivity, and intrinsic reaction rates of nutrients and metals in river sediment. The dimensionless reaction significance factor, RSF (Harvey et al., 2013) was used to quantify the cumulative removal fraction of a reactive solute by hyporheic processing. SF scales reaction progress in a single pass through the hyporheic zone with the proportion of stream discharge passing through the hyporheic zone for a specified distance. Reaction progress is optimal where the intrinsic reaction timescale in sediment matches the residence time of hyporheic flow and is less efficient in longer residence time hyporheic flow as a result of the decreasing proportion of river flow that is processed by longer residence time hyporheic flow paths. In contrast, higher fluxes through short residence time hyporheic flow paths may be inefficient because of the repeated surface-subsurface exchanges required to complete the reaction. Using NEXSS we found that reaction efficiency may be high in both small streams and large rivers, although for different reasons. In small streams reaction progress generally is dominated by faster pathways of vertical exchange beneath submerged bedforms. Slower exchange

  4. Soil property control of biogeochemical processes beneath two subtropical stormwater infiltration basins

    USGS Publications Warehouse

    O'Reilly, Andrew M.; Wanielista, Martin P.; Chang, Ni-Bin; Harris, Willie G.; Xuan, Zhemin

    2012-01-01

    Substantially different biogeochemical processes affecting nitrogen fate and transport were observed beneath two stormwater infiltration basins in north-central Florida. Differences are related to soil textural properties that deeply link hydroclimatic conditions with soil moisture variations in a humid, subtropical climate. During 2008, shallow groundwater beneath the basin with predominantly clayey soils (median, 41% silt+clay) exhibited decreases in dissolved oxygen from 3.8 to 0.1 mg L-1 and decreases in nitrate nitrogen (NO3-–N) from 2.7 mg L-1 to -1, followed by manganese and iron reduction, sulfate reduction, and methanogenesis. In contrast, beneath the basin with predominantly sandy soils (median, 2% silt+clay), aerobic conditions persisted from 2007 through 2009 (dissolved oxygen, 5.0–7.8 mg L-1), resulting in NO3-–N of 1.3 to 3.3 mg L-1 in shallow groundwater. Enrichment of d15N and d18O of NO3- combined with water chemistry data indicates denitrification beneath the clayey basin and relatively conservative NO3- transport beneath the sandy basin. Soil-extractable NO3-–N was significantly lower and the copper-containing nitrite reductase gene density was significantly higher beneath the clayey basin. Differences in moisture retention capacity between fine- and coarse-textured soils resulted in median volumetric gas-phase contents of 0.04 beneath the clayey basin and 0.19 beneath the sandy basin, inhibiting surface/subsurface oxygen exchange beneath the clayey basin. Results can inform development of soil amendments to maintain elevated moisture content in shallow soils of stormwater infiltration basins, which can be incorporated in improved best management practices to mitigate NO3- impacts.

  5. Soil property control of biogeochemical processes beneath two subtropical stormwater infiltration basins.

    PubMed

    O'Reilly, Andrew M; Wanielista, Martin P; Chang, Ni-Bin; Harris, Willie G; Xuan, Zhemin

    2012-01-01

    Substantially different biogeochemical processes affecting nitrogen fate and transport were observed beneath two stormwater infiltration basins in north-central Florida. Differences are related to soil textural properties that deeply link hydroclimatic conditions with soil moisture variations in a humid, subtropical climate. During 2008, shallow groundwater beneath the basin with predominantly clayey soils (median, 41% silt+clay) exhibited decreases in dissolved oxygen from 3.8 to 0.1 mg L and decreases in nitrate nitrogen (NO-N) from 2.7 mg L to <0.016 mg L, followed by manganese and iron reduction, sulfate reduction, and methanogenesis. In contrast, beneath the basin with predominantly sandy soils (median, 2% silt+clay), aerobic conditions persisted from 2007 through 2009 (dissolved oxygen, 5.0-7.8 mg L), resulting in NO-N of 1.3 to 3.3 mg L in shallow groundwater. Enrichment of δN and δO of NO combined with water chemistry data indicates denitrification beneath the clayey basin and relatively conservative NO transport beneath the sandy basin. Soil-extractable NO-N was significantly lower and the copper-containing nitrite reductase gene density was significantly higher beneath the clayey basin. Differences in moisture retention capacity between fine- and coarse-textured soils resulted in median volumetric gas-phase contents of 0.04 beneath the clayey basin and 0.19 beneath the sandy basin, inhibiting surface/subsurface oxygen exchange beneath the clayey basin. Results can inform development of soil amendments to maintain elevated moisture content in shallow soils of stormwater infiltration basins, which can be incorporated in improved best management practices to mitigate NO impacts.

  6. 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.

  7. BIOGEOCHEMICAL STUDIES OF PHOTOSYNTHETIC MICROBIAL MATS AND THEIR BIOTA

    NASA Technical Reports Server (NTRS)

    DesMarais, David; Discipulo, M.; Turk, K.; Londry, K. L.

    2005-01-01

    Photosynthetic microbial mats offer an opportunity to define holistic functionality at the millimeter scale. At the same time. their biogeochemistry contributes to environmental processes on a planetary scale. These mats are possibly direct descendents of the most ancient biological communities; communities in which oxygenic photosynthesis might have been invented. Mats provide one of the best natural systems to study how microbial populations associate to control dynamic biogeochemical gradients. These are self- sustaining, complete ecosystems in which light energy absorbed over a dial (24 hour) cycle drives the synthesis of spatially-organized, diverse biomass. Tightly-coupled microorganisms in the mat have specialized metabolisms that catalyze transformations of carbon, nitrogen, sulfur, and a host of other elements.

  8. 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.

  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. Biogeochemical Dynamics of Zero-Order Arctic Catchments

    NASA Astrophysics Data System (ADS)

    Harms, T.; Godsey, S.; Jones, J.; Risser, R. R.; Rushlow, C. R.

    2013-12-01

    A significant fraction of arctic catchments underlain by permafrost may be drained by linear flowpaths constituting zero-order channels, which are termed water tracks. Hydrology and biogeochemistry of arctic hillslopes are subject to rapid changes caused by thawing permafrost, changing precipitation regime, and altered vegetation patterns. We investigated coupling of hydrologic and biogeochemical cycles at six water tracks that drain to the Kuparuk River to understand the role of zero-order catchments in delivering solutes to stream networks, and better predict how solute fluxes will respond to changing climate. Peak concentrations of organic solutes occurred during snowmelt, and snowmelt-derived water remained in catchments until mid-summer, indicating that changes in snowpack or timing of melt will induce strong changes in delivery of solutes to stream networks. Further, temporal coherence in solute chemistry between water tracks and the Kuparuk river suggests that water tracks are important contributors of solutes to downstream ecosystems. Solute dynamics during storms follow a flush and dilution pattern indicative of source-limited solute transport. However, the relative difference between minimum and maximum concentrations of dissolved organic carbon and ammonium decreased during successive storms, suggesting decreased availability of these solutes as flowpaths deepen throughout the season. Despite these broad patterns, individual water tracks vary significantly in solute concentrations and storm responses, suggesting that site-level characteristics including sources of water contributing to flow, rates of solute uptake, contributing area, and depth of thaw influence the delivery of solutes from arctic hillslopes to stream networks. Hydrologic and biogeochemical signals potentially propagate from these zero-order catchments to stream networks and coasts, and may contribute to observed long-term changes in solute and freshwater fluxes in arctic river networks.

  11. 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.

  12. Apparatus for Cold, Pressurized Biogeochemical Experiments

    NASA Technical Reports Server (NTRS)

    Amashukeli, Xenia; Pappalardo, Robert T.; Connon, Stephanie A.; Gleeson, Damhnait F.

    2010-01-01

    A laboratory apparatus has been devised as a means of studying plausible biogeochemical reactions under high-pressure, low-temperature aqueous, anaerobic conditions like those conjectured to prevail in a liquid water ocean on Europa (the fourth largest moon of the planet Jupiter). The experiments to be performed by use of this apparatus are intended to enhance understanding of how life (if any) could originate and evolve in the Europa ocean environment. Inasmuch as terrestrial barophilic, psychrophilic organisms that thrive under anaerobic conditions are used in the experiments, the experiments may also contribute to terrestrial biogeochemistry. The apparatus (see figure) includes a bolt-closure reaction vessel secured inside a refrigerator that maintains a temperature of 4 C. Pressurized water is supplied to the interior of the vessel by a hydrostatic pump, which is attached to the vessel via high-pressure fittings. The terrestrial organisms used in the experiments thus far have been several facultative barophilic, psychrophilic stains of Shewanella bacteria. In the experiments, these organisms have been tested for reduction of ferric ion by growing them in the presence of a ferric food source under optimized terrestrial conditions. The short-term goal of these experiments has been to select Shewanella strains that exhibit iron-reduction capability and test their ability to facilitate biogeochemical reduction of iron under temperature and pressure conditions imitating those in Europa s ocean. It is anticipated, that, once growth under Europa-like conditions has been achieved, the selected Shewanella strains will be used to facilitate biogeochemical reactions of sulfate and carbonate with hydrogen gas. Any disequilibrium of the products with the environment would be interpreted as signifying biogenic activity and the possibility of life in Europa s ocean.

  13. Meet the Editor: Global Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Kumar, Mohi

    Meinrat Andreae was named the editor of the AGU's journal Global Biogeochemical Cycles last year.Andreae, director of the biogeochemistry department at the Max Plank Institute for Chemistry (MPIC), located in Mainz, Germany said that he plans to maintain the journal as a resource that highlights the broad spectrum of interdisciplinary themes that showcase the interactions between the biosphere and the geosphere. “Our special niche is in the field of larger-scale, more integrative studies that have global scope,” he explained.

  14. Biogeochemical Cycles of Carbon and Sulfur

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    The elements carbon (C) and sulfur (S) interact with each other across a network of elemental reservoirs that are interconnected by an array of physical, chemical and biological processes. These networks are termed the biogeochemical C and S cycles. The compounds of C are highly important, not only as organic matter, but also as atmospheric greenhouse gases, pH buffers in seawater, oxidation-reduction buffers virtually everywhere, and key magmatic constituents affecting plutonism and volcanism. The element S assumes important roles as an oxidation-reduction partner with C and Fe in biological systems, as a key constituent in magmas and volcanic gases, and as a major influence upon pH in certain environments. This presentation describes the modern biogeochemical C and S cycles. Measurements are described whereby stable isotopes can help to infer the nature and quantitative significance of biological and geological processes involved in the C and S cycles. This lecture also summarizes the geological and climatologic aspects of the ancient C and S cycles, as well as the planetary and extraterrestrial processes that influenced their evolution over millions to billions of years.

  15. The NEON Aquatic Network: Expanding the Availability of Biogeochemical Data

    NASA Astrophysics Data System (ADS)

    Vance, J. M.; Bohall, C.; Fitzgerald, M.; Utz, R.; Parker, S. M.; Roehm, C. L.; Goodman, K. J.; McLaughlin, B.

    2013-12-01

    Aquatic ecosystems are facing unprecedented pressure from climate change and land-use practices. Invasive species, whether plant, animal, insect or microbe present additional threat to aquatic ecosystem services. There are significant scientific challenges to understanding how these forces will interact to affect aquatic ecosystems, as the flow of energy and materials in the environment is driven by multivariate and non-linear biogeochemical cycles. The National Ecological Observatory Network (NEON) will collect and provide observational data across multiple scales. Sites were selected to maximize representation of major North American ecosystems using a multivariate geographic clustering method that partitioned the continental US, AK, HI, and Puerto Rico into 20 eco-climatic domains. The NEON data collection systems and methods are designed to yield standardized, near real-time data subjected to rigorous quality controls prior to public dissemination through an online data portal. NEON will collect data for 30 years to facilitate spatial-temporal analysis of environmental responses and drivers of ecosystem change, ranging from local through continental scales. Here we present the NEON Aquatic Network, a multi-parameter network consisting of a combination of in situ sensor and observational data. This network will provide data to examine biogeochemical, biological, hydrologic and geomorphic metrics at 36 sites, which are a combination of small 1st/2nd order wadeable streams, large rivers and lakes. A typical NEON Aquatic site will host up to two in-stream sensor sets designed to collect near-continuous water quality data (e.g. pH/ORP, temperature, conductivity, dissolved oxygen, CDOM) along with up to 8 shallow groundwater monitoring wells (level, temp., cond.), and a local meteorological station (e.g. 2D wind speed, PAR, barometric pressure, temperature, net radiation). These coupled sensor suites will be complemented by observational data (e.g. water

  16. Reanalysis of biogeochemical properties in the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Cossarini, Gianpiero; Teruzzi, Anna; Salon, Stefano; Solidoro, Cosimo

    2014-05-01

    In the 3D variational (3DVAR) assimilation approach the error covariance matrix can be decomposed in a series of operators. The decomposition makes the 3DVAR particularly suitable for marine biogeochemistry data assimilation, because of the reduced computational costs of the method and its modularity, which allows to define the covariance among the biogeochemical variables in a specific operator. In the present work, the results of 3DVAR assimilation of surface chlorophyll concentration in a multi-annual simulation of the Mediterranean Sea biogeochemistry are presented. The assimilated chlorophyll concentrations are obtained from satellite observations (Volpe et al. 2012). The multi-annual simulation is carried out using the OPATM-BFM model (Lazzari et al. 2012), which describes the low trophic web dynamics and is offline coupled with the MFS physical model (Oddo et al. 2009). In the OPATM-BFM four types of phytoplankton are simulated in terms of their content in carbon, nitrogen, phosphorous, silicon and chlorophyll. In the 3DVAR the error covariance matrix has been decomposed in three different operators, which account for the vertical, the horizontal and the biogeochemical covariance (Teruzzi et al. 2014). The biogeochemical operator propagates the result of the assimilation to the OPATM-BFM variables, providing innovation for the components of the four phytoplankton types. The biogeochemical covariance has been designed supposing that the assimilation preserves the physiological status and the relative abundances of phytoplankton types. Practically, the assimilation preserves the internal quotas of the components for each phytoplankton as long as the optimal growth rate condition are maintained. The quotas preservation is not applied when the phytoplankton is in severe declining growth phase, and the correction provided by the assimilation is set equal to zero. Moreover, the relative abundances among the phytoplankton functional types are preserved. The 3DVAR

  17. 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.

  18. Impacts of mesoscale eddies in the South China Sea on biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Guo, Mingxian; Chai, Fei; Xiu, Peng; Li, Shiyu; Rao, Shivanesh

    2015-09-01

    Biogeochemical cycles associated with mesoscale eddies in the South China Sea (SCS) were investigated. The study was based on a coupled physical-biogeochemical Pacific Ocean model (Regional Ocean Model System-Carbon, Silicate, and Nitrogen Ecosystem, ROMS-CoSiNE) simulation for the period from 1991 to 2008. A total of 568 mesoscale eddies with lifetime longer than 30 days were used in the analysis. Composite analysis revealed that the cyclonic eddies were associated with abundance of nutrients, phytoplankton, and zooplankton while the anticyclonic eddies depressed biogeochemical cycles, which are generally controlled by the eddy pumping mechanism. In addition, diatoms were dominant in phytoplankton species due to the abundance of silicate. Dipole structures of vertical fluxes with net upward motion in cyclonic eddies and net downward motion in anticyclonic eddies were revealed. During the lifetime of an eddy, the evolutions of physical, biological, and chemical structures were not linearly coupled at the eddy core where plankton grew, and composition of the community depended not only on the physical and chemical processes but also on the adjustments by the predator-prey relationship.

  19. 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.

  20. Diel biogeochemical processes in terrestrial waters

    USGS Publications Warehouse

    Compiled and Edited by Nimick, David A.; Gammons, Christopher H.

    2011-01-01

    Many biogeochemical processes in rivers and lakes respond to the solar photocycle and produce persistent patterns of measureable phenomena that exhibit a day-night, or 24-h, cycle. Despite a large body of recent literature, the mechanisms responsible for these diel fluctuations are widely debated, with a growing consensus that combinations of physical, chemical, and biological processes are involved. These processes include streamflow variation, photosynthesis and respiration, plant assimilation, and reactions involving photochemistry, adsorption and desorption, and mineral precipitation and dissolution. Diel changes in streamflow and water properties such as temperature, pH, and dissolved oxygen concentration have been widely recognized, and recently, diel studies have focused more widely by considering other constituents such as dissolved and particulate trace metals, metalloids, rare earth elements, mercury, organic matter, dissolved inorganic carbon (DIC), and nutrients. The details of many diel processes are being studied using stable isotopes, which also can exhibit diel cycles in response to microbial metabolism, photosynthesis and respiration, or changes in phase, speciation, or redox state. In addition, secondary effects that diel cycles might have, for example, on biota or in the hyporheic zone are beginning to be considered. This special issue is composed primarily of papers presented at the topical session "Diurnal Biogeochemical Processes in Rivers, Lakes, and Shallow Groundwater" held at the annual meeting of the Geological Society of America in October 2009 in Portland, Oregon. This session was organized because many of the growing number of diel studies have addressed just a small part of the full range of diel cycling phenomena found in rivers and lakes. This limited focus is understandable because (1) fundamental aspects of many diel processes are poorly understood and require detailed study, (2) the interests and expertise of individual

  1. Biogeochemical Reactions Under Simulated Europa Ocean Conditions

    NASA Astrophysics Data System (ADS)

    Amashukeli, X.; Connon, S. A.; Gleeson, D. F.; Kowalczyk, R. S.; Pappalardo, R. T.

    2007-12-01

    Galileo data have demonstrated the probable presence of a liquid water ocean on Europa, and existence of salts and carbon dioxide in the satellite's surface ice (e.g., Carr et al., 1998; McCord et al., 1999, Pappalardo et al., 1999; Kivelson et al., 2000). Subsequently, the discovery of chemical signatures of extinct or extant life in Europa's ocean and on its surface became a distinct possibility. Moreover, understanding of Europa's potential habitability is now one of the major goals of the Europa Orbiter Flagship mission. It is likely, that in the early stages of Europa's ocean formation, moderately alkaline oceanic sulfate-carbonate species and a magnetite-silicate mantel could have participated in low-temperature biogeochemical sulfur, iron and carbon cycles facilitated by primitive organisms (Zolotov and Shock, 2004). If periodic supplies of fresh rock and sulfate-carbonate ions are available in Europa's ocean, then an exciting prospect exists that life may be present in Europa's ocean today. In our laboratory, we began the study of the plausible biogeochemical reactions under conditions appropriate to Europa's ocean using barophilic psychrophilic organisms that thrive under anaerobic conditions. In the near absence of abiotic synthetic pathways due to low Europa's temperatures, the biotic synthesis may present a viable opportunity for the formation of the organic and inorganic compounds under these extreme conditions. This work is independent of assumptions regarding hydrothermal vents at Europa's ocean floor or surface-derived oxidant sources. For our studies, we have fabricated a high-pressure (5,000 psi) reaction vessel that simulates aqueous conditions on Europa. We were also successful at reviving barophilic psychrophilic strains of Shewanella bacterium, which serve as test organisms in this investigation. Currently, facultative barophilic psychrophilic stains of Shewanella are grown in the presence of ferric food source; the strains exhibiting iron

  2. Global Biology Research Program: Biogeochemical Processes in Wetlands

    NASA Technical Reports Server (NTRS)

    Bartlett, D. S. (Editor)

    1984-01-01

    The results of a workshop examining potential NASA contributions to research on wetland processes as they relate to global biogeochemical cycles are summarized. A wetlands data base utilizing remotely sensed inventories, studies of wetland/atmosphere exchange processes, and the extrapolation of local measurements to global biogeochemical cycling processes were identified as possible areas for NASA support.

  3. Biogeochemical cycling in the Strait of Georgia.

    PubMed

    Johannessen, S C; Macdonald, R W; Burd, B; van Roodselaar, A

    2008-12-01

    The papers in this special issue present the results of a five-year project to study sedimentary biogeochemical processes in the Strait of Georgia, with special emphasis on the near-field of a large municipal outfall. Included in this special issue are overviews of the sedimentology, benthic biology, status of siliceous sponge reefs and distribution of organic carbon in the water column. Other papers address the cycling of contaminants (PCBs, PBDEs) and redox metals in the sediment, a method to map the extent of the influence of municipal effluent from staining on benthic bivalves, and the relationships among geochemical conditions and benthic abundance and diversity. The latter set of papers addresses the role of municipal effluent as a pathway of organic carbon and other contaminants into the Strait of Georgia and the effect of the effluent on benthic geochemistry and biology.

  4. Biogeochemical patchiness at the sea surface

    NASA Astrophysics Data System (ADS)

    Mahadevan, A.; Campbell, J. W.

    2002-10-01

    The surface distributions of many tracers in the ocean are highly correlated in time and space on meso (~100 km) and smaller scales (Figure 1). However, their characteristic scales of variability differ. Some variables like sea surface chlorophyll (Chl) are very fine-scaled or patchy, while others like sea surface temperature (SST) are not. We characterize the patchiness of a distribution quantitatively by the dependence of the variance V on the length scale L as V ~ Lp; smaller p corresponds to greater patchiness. Using scaling and a numerical model we show that patchiness, p, varies with the characteristic response time τ of the tracer to processes that alter its concentration in the upper ocean as p ~ log τ. This suggests that sea surface Chl is more patchy (has smaller p) than SST at mesoscales because the characteristic time scale of phytoplankton growth in response to the availability of nutrients is less than that for the equilibration of temperature in response to heat fluxes. Similarly, sea surface dissolved oxygen (O2) exhibits more fine-scaled variability than total dissolved inorganic carbon (TCO2) because O2 equilibrates with the atmosphere much more rapidly than TCO2. Tracers that are more patchy require higher resolution to model and sample; the sampling or model grid spacing required scales as exp(-1/log τ). The quantitative relationship between p and τ can be used to relate various biogeochemical distributions, particularly to those that are remotely sensed, and to deduce biogeochemical response times of various tracers or plankton species from the characteristics of their distributions in space or time.

  5. Nutrient removal using biosorption activated media: preliminary biogeochemical assessment of an innovative stormwater infiltration basin

    USGS Publications Warehouse

    O'Reilly, Andrew M.; Wanielista, Martin P.; Chang, Ni-Bin; Xuan, Zhemin; Harris, Willie G.

    2012-01-01

    Soil beneath a stormwater infiltration basin receiving runoff from a 22.7 ha predominantly residential watershed in central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop a prototype stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO3-/Cl-) ratios for the shallow groundwater indicate that prior to using BAM, NO3- concentrations were substantially influenced by nitrification or variations in NO3- input. In contrast, for the prototype basin utilizing BAM, NO3-/Cl- ratios indicate minor nitrification and NO3- losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest NO3- losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO43-) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO43-/Cl- ratios for shallow groundwater indicate predominantly minor increases and

  6. Biogeochemical drivers of microbial community convergence across actively retreating glaciers

    SciTech Connect

    Castle, Sarah C.; Nemergut, Diana R.; Grandy, A. Stuart; Leff, Jonathan W.; Graham, Emily B.; Hood, Eran; Schmidt, Steven K.; Wickings, Kyle; Cleveland, Cory C.

    2016-10-01

    The ecological processes that influence biogeographical patterns of microorganisms are actively debated. To investigate how such patterns emerge during ecosystem succession, we examined the biogeochemical drivers of bacterial community assembly in soils over two environmentally distinct, recently deglaciated chronosequences separated by a distance of more than 1,300 kilometers. Our results show that despite different geographic, climatic, and soil chemical and physical characteristics at the two sites, soil bacterial community structure and decomposer function converged during plant succession. In a comparative analysis, we found that microbial communities in early succession soils were compositionally distinct from a group of diverse, mature forest soils, but that the differences between successional soils and mature soils decreased from early to late stages of succession. Differences in bacterial community composition across glacial sites were largely explained by pH. However, successional patterns and community convergence across sites were more consistently related to soil organic carbon and organic matter chemistry, which appeared to be tightly coupled with bacterial community structure across both young and mature soils.

  7. 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

  8. Centimeter-scale characterization of biogeochemical gradients at a wetland-aquifer interface using capillary electrophoresis

    USGS Publications Warehouse

    Baez-Cazull, S.; McGuire, J.T.; Cozzarelli, I.M.; Raymond, A.; Welsh, L.

    2007-01-01

    Steep biogeochemical gradients were measured at mixing interfaces in a wetland-aquifer system impacted by landfill leachate in Norman, Oklahoma. The system lies within a reworked alluvial plain and is characterized by layered low hydraulic conductivity wetland sediments interbedded with sandy aquifer material. Using cm-scale passive diffusion samplers, "peepers", water samples were collected in a depth profile to span interfaces between surface water and a sequence of deeper sedimentary layers. Geochemical indicators including electron acceptors, low-molecular-weight organic acids, base cations, and NH4+ were analyzed by capillary electrophoresis (CE) and field techniques to maximize the small sample volumes available from the centimeter-scale peepers. Steep concentration gradients of biogeochemical indicators were observed at various interfaces including those created at sedimentary boundaries and boundaries created by heterogeneities in organic C and available electron acceptors. At the sediment-water interface, chemical profiles with depth suggest that SO42 - and Fe reduction dominate driven by inputs of organic C from the wetland and availability of electron acceptors. Deeper in the sediments (not associated with a lithologic boundary), a steep gradient of organic acids (acetate maximum 8.8 mM) and NH4+ (maximum 36 mM) is observed due to a localized source of organic matter coupled with the lack of electron acceptor inputs. These findings highlight the importance of quantifying the redox reactions occurring in small interface zones and assessing their role on biogeochemical cycling at the system scale. ?? 2007 Elsevier Ltd. All rights reserved.

  9. 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).

  10. 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.

  11. 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.

  12. Using Observations to Models to Understand the Effects of Irrigation, Groundwater Dynamics, Land Surface/Subsurface Heterogeneity on Land-Atmosphere-Cloud-Interactions: Evidence from the Southern Great Plains

    NASA Astrophysics Data System (ADS)

    Huang, M.; Berg, L. K.; Qian, Y.; Xiao, H.; Gustafson, W. I., Jr.; Liu, Y.

    2015-12-01

    Land-Atmosphere-Cloud Interactions (LACI) are important for a number of physical and biological processes that drive the climate system. Historical and planned observations from the US Department of Energy's Atmospheric Radiation Measurement (ARM) Climate Research Facility Southern Great Plain (SGP) site provide unique opportunities for analyzing local land-atmosphere interactions and serve as metrics for benchmarking model simulated land and atmospheric variables. This region is of particular interest because it has been identified as a "hotspot" of land atmosphere interactions under past, present, and future climate conditions. In this presentation, we will discuss results from several modeling studies integrated with observations that evaluate the impacts of a few selected land surface processes/land model representations on surface energy fluxes, structure of boundary layer turbulence, and hence potentially cloud formation and precipitation, that have shown to be important over the SGP region, including (1) the role of land surface/subsurface heterogeneity in terms of land cover and soil texture that affects the spatial patterns of the soil moisture and surface fluxes, (2) anthropogenic disturbance to the terrestrial hydrological cycle through irrigation as a result of agricultural expansion over the region, and (3) the interactions between soil moisture and groundwater dynamics that alter evapotranspiration and partitioning of the surface energy budget. Future research directions to be explored by the community to better understand LACI will also be discussed.

  13. Searching for Biogeochemical Cycles on Mars

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.

    1997-01-01

    The search for life on Mars clearly benefits from a rigorous, yet broad, definition of life that compels us to consider all possible lines of evidence for a martian biosphere. Recent studies in microbial ecology illustrate that the classic definition of life should be expanded beyond the traditional definition of a living cell. The traditional defining characteristics of life are threefold. First, life is capable of metabolism, that is, it performs chemical reactions that utilize energy and also synthesize its cellular constituents. Second, life is capable of self-replication. Third, life can evolve in order to adapt to environmental changes. An expanded, ecological definition of life also recognizes that life is a community of organisms that must interact with their nonliving environment through processes called biogeochemical cycles. This regenerative processing maintains, in an aqueous conditions, a dependable supply of nutrients and energy for growth. In turn, life can significantly affect those processes that control the exchange of materials between the atmosphere, ocean, and upper crust. Because metabolic processes interact directly with the environment, they can alter their surroundings and thus leave behind evidence of life. For example, organic matter is produced from single-carbon-atom precursors for the biosynthesis of cellular constituents. This leads to a reservoir of reduced carbon in sediments that, in turn, can affect the oxidation state of the atmosphere. The harvesting of chemical energy for metabolism often employs oxidation-reduction reactions that can alter the chemistry and oxidation state of the redox-sensitive elements carbon, sulfur, nitrogen, iron, and manganese. Have there ever been biogeochemical cycles on Mars? Certain key planetary processes can offer clues. Active volcanism provides reduced chemical species that biota can use for organic synthesis. Volcanic carbon dioxide and methane can serve as greenhouse gases. Thus the

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Coupled assimilation for an intermediated coupled ENSO prediction model

    NASA Astrophysics Data System (ADS)

    Zheng, Fei; Zhu, Jiang

    2010-10-01

    The value of coupled assimilation is discussed using an intermediate coupled model in which the wind stress is the only atmospheric state which is slavery to model sea surface temperature (SST). In the coupled assimilation analysis, based on the coupled wind-ocean state covariance calculated from the coupled state ensemble, the ocean state is adjusted by assimilating wind data using the ensemble Kalman filter. As revealed by a series of assimilation experiments using simulated observations, the coupled assimilation of wind observations yields better results than the assimilation of SST observations. Specifically, the coupled assimilation of wind observations can help to improve the accuracy of the surface and subsurface currents because the correlation between the wind and ocean currents is stronger than that between SST and ocean currents in the equatorial Pacific. Thus, the coupled assimilation of wind data can decrease the initial condition errors in the surface/subsurface currents that can significantly contribute to SST forecast errors. The value of the coupled assimilation of wind observations is further demonstrated by comparing the prediction skills of three 12-year (1997-2008) hindcast experiments initialized by the ocean-only assimilation scheme that assimilates SST observations, the coupled assimilation scheme that assimilates wind observations, and a nudging scheme that nudges the observed wind stress data, respectively. The prediction skills of two assimilation schemes are significantly better than those of the nudging scheme. The prediction skills of assimilating wind observations are better than assimilating SST observations. Assimilating wind observations for the 2007/2008 La Niña event triggers better predictions, while assimilating SST observations fails to provide an early warning for that event.

  19. Redox chemistry in the phosphorus biogeochemical cycle

    NASA Astrophysics Data System (ADS)

    Pasek, Matthew A.; Sampson, Jacqueline M.; Atlas, Zachary

    2014-10-01

    The element phosphorus (P) controls growth in many ecosystems as the limiting nutrient, where it is broadly considered to reside as pentavalent P in phosphate minerals and organic esters. Exceptions to pentavalent P include phosphine-PH3-a trace atmospheric gas, and phosphite and hypophosphite, P anions that have been detected recently in lightning strikes, eutrophic lakes, geothermal springs, and termite hindguts. Reduced oxidation state P compounds include the phosphonates, characterized by C-P bonds, which bear up to 25% of total organic dissolved phosphorus. Reduced P compounds have been considered to be rare; however, the microbial ability to use reduced P compounds as sole P sources is ubiquitous. Here we show that between 10% and 20% of dissolved P bears a redox state of less than +5 in water samples from central Florida, on average, with some samples bearing almost as much reduced P as phosphate. If the quantity of reduced P observed in the water samples from Florida studied here is broadly characteristic of similar environments on the global scale, it accounts well for the concentration of atmospheric phosphine and provides a rationale for the ubiquity of phosphite utilization genes in nature. Phosphine is generated at a quantity consistent with thermodynamic equilibrium established by the disproportionation reaction of reduced P species. Comprising 10-20% of the total dissolved P inventory in Florida environments, reduced P compounds could hence be a critical part of the phosphorus biogeochemical cycle, and in turn may impact global carbon cycling and methanogenesis.

  20. Understanding Oceanic Migrations with Intrinsic Biogeochemical Markers

    PubMed Central

    Ramos, Raül; González-Solís, Jacob; Croxall, John P.; Oro, Daniel

    2009-01-01

    Migratory marine vertebrates move annually across remote oceanic water masses crossing international borders. Many anthropogenic threats such as overfishing, bycatch, pollution or global warming put millions of marine migrants at risk especially during their long-distance movements. Therefore, precise knowledge about these migratory movements to understand where and when these animals are more exposed to human impacts is vital for addressing marine conservation issues. Because electronic tracking devices suffer from several constraints, mainly logistical and financial, there is emerging interest in finding appropriate intrinsic markers, such as the chemical composition of inert tissues, to study long-distance migrations and identify wintering sites. Here, using tracked pelagic seabirds and some of their own feathers which were known to be grown at different places and times within the annual cycle, we proved the value of biogeochemical analyses of inert tissue as tracers of marine movements and habitat use. Analyses of feathers grown in summer showed that both stable isotope signatures and element concentrations can signal the origin of breeding birds feeding in distinct water masses. However, only stable isotopes signalled water masses used during winter because elements mainly accumulated during the long breeding period are incorporated into feathers grown in both summer and winter. Our findings shed new light on the simple and effective assignment of marine organisms to distinct oceanic areas, providing new opportunities to study unknown migration patterns of secretive species, including in relation to human-induced mortality on specific populations in the marine environment. PMID:19623244

  1. Redox chemistry in the phosphorus biogeochemical cycle

    PubMed Central

    Pasek, Matthew A.; Sampson, Jacqueline M.; Atlas, Zachary

    2014-01-01

    The element phosphorus (P) controls growth in many ecosystems as the limiting nutrient, where it is broadly considered to reside as pentavalent P in phosphate minerals and organic esters. Exceptions to pentavalent P include phosphine—PH3—a trace atmospheric gas, and phosphite and hypophosphite, P anions that have been detected recently in lightning strikes, eutrophic lakes, geothermal springs, and termite hindguts. Reduced oxidation state P compounds include the phosphonates, characterized by C−P bonds, which bear up to 25% of total organic dissolved phosphorus. Reduced P compounds have been considered to be rare; however, the microbial ability to use reduced P compounds as sole P sources is ubiquitous. Here we show that between 10% and 20% of dissolved P bears a redox state of less than +5 in water samples from central Florida, on average, with some samples bearing almost as much reduced P as phosphate. If the quantity of reduced P observed in the water samples from Florida studied here is broadly characteristic of similar environments on the global scale, it accounts well for the concentration of atmospheric phosphine and provides a rationale for the ubiquity of phosphite utilization genes in nature. Phosphine is generated at a quantity consistent with thermodynamic equilibrium established by the disproportionation reaction of reduced P species. Comprising 10–20% of the total dissolved P inventory in Florida environments, reduced P compounds could hence be a critical part of the phosphorus biogeochemical cycle, and in turn may impact global carbon cycling and methanogenesis. PMID:25313061

  2. Hydrological Perturbations Drive Biogeochemical Processes in Experimental Soil Columns from the Norman Landfill Site

    NASA Astrophysics Data System (ADS)

    Arora, B.; Mohanty, B. P.; McGuire, J. T.

    2010-12-01

    Fate and transport of contaminants in saturated and unsaturated zones is governed by biogeochemical processes that are complex and non-linearly coupled to each other. A fundamental understanding of the interactions between transport and reaction processes is essential to better characterize contaminant movement in the subsurface. The objectives of this study are to: i) develop quantitative relationships between hydrological (initial and boundary conditions, hydraulic conductivity ratio, and soil layering), geochemical (mineralogy, surface area, redox potential, and organic matter) and microbiological factors (MPN) that alter the biogeochemical processes, and ii) characterize the effect of hydrologic perturbations on coupled processes occurring at the column scale. The perturbations correspond to rainfall intensity, duration of wet and dry conditions, and water chemistry (pH). Soils collected from two locations with significantly different geochemistry at the Norman landfill site are used in this study. Controlled flow experiments were conducted on: i) two homogeneous soil columns, ii) a layered soil column, iii) a soil column with embedded clay lenses, and iv) a soil column with embedded clay lenses and one central macropore. Experimental observations showed enhanced biogeochemical activity at the interface of the layered and lensed columns over the texturally homogeneous soil columns. Multivariate statistical analysis showed that the most important processes were microbial reduction of Fe(III) and SO42-, and oxidation of reduced products in the columns. Modeling results from HP1 indicate least redox activity in the homogeneous sand column while the structurally heterogeneous columns utilize oxygen and nitrate from recharge as well as iron sulfide minerals already present in the columns as electron acceptors. Furthermore, the interface of the layered and lensed soil columns acts as a hotspot of biogeochemical activity due to increased transport timescale as a

  3. Climate change effects on watershed hydrological and biogeochemical processes

    EPA Science Inventory

    Projected changes in climate are widely expected to alter watershed processes. However, the extent of these changes is difficult to predict because complex interactions among affected hydrological and biogeochemical processes will likely play out over many decades and spatial sc...

  4. Biogeochemical Processes Regulating the Mobility of Uranium in Sediments

    SciTech Connect

    Belli, Keaton M.; Taillefert, Martial

    2016-07-01

    This book chapters reviews the latest knowledge on the biogeochemical processes regulating the mobility of uranium in sediments. It contains both data from the literature and new data from the authors.

  5. 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.

  6. Restoration of biogeochemical function in mangrove forests

    USGS Publications Warehouse

    McKee, K.L.; Faulkner, P.L.

    2000-01-01

    Forest structure of mangrove restoration sites (6 and 14 years old) at two locations (Henderson Creek [HC] and Windstar [WS]) in southwest Florida differed from that of mixed-basin forests (>50 years old) with which they were once contiguous. However, the younger site (HC) was typical of natural, developing forests, whereas the older site (WS) was less well developed with low structural complexity. More stressful physicochemical conditions resulting from incomplete tidal flushing (elevated salinity) and variable topography (waterlogging) apparently affected plant survival and growth at the WS restoration site. Lower leaf fall and root production rates at the WS restoration site, compared with that at HC were partly attributable to differences in hydroedaphic conditions and structural development. However, leaf and root inputs at each restoration site were not significantly different from that in reference forests within the same physiographic setting. Macrofaunal consumption of tethered leaves also did not differ with site history, but was dramatically higher at HC compared with WS, reflecting local variation in leaf litter processing rates, primarily by snails (Melampus coffeus). Degradation of leaves and roots in mesh bags was slow overall at restoration sites, however, particularly at WS where aerobic decomposition may have been more limited. These findings indicate that local or regional factors such as salinity regime act together with site history to control primary production and turnover rates of organic matter in restoration sites. Species differences in senescent leaf nitrogen content and degradation rates further suggest that restoration sites dominated by Laguncularia racemosa and Rhizophora mangle should exhibit slower recycling of nutrients compared with natural basin forests where Avicennia germinans is more abundant. Structural development and biogeochemical functioning of restored mangrove forests thus depend on a number of factors, but site

  7. Design and performance of subgrade biogeochemical reactors.

    PubMed

    Gamlin, Jeff; Downey, Doug; Shearer, Brad; Favara, Paul

    2017-02-18

    Subgrade biogeochemical reactors (SBGRs), also commonly referred to as in situ bioreactors, are a unique technology for treatment of contaminant source areas and groundwater plume hot spots. SBGRs have most commonly been configured for enhanced reductive dechlorination (ERD) applications for chlorinated solvent treatment. However, they have also been designed for other contaminant classes using alternative treatment media. The SBGR technology typically consists of removal of contaminated soil via excavation or large-diameter augers, and backfill of the soil void with gravel and treatment amendments tailored to the target contaminant(s). In most cases SBGRs include installation of infiltration piping and a low-flow pumping system (typically solar-powered) to recirculate contaminated groundwater through the SBGR for treatment. SBGRs have been constructed in multiple configurations, including designs capable of meeting limited access restrictions at heavily industrialized sites, and at sites with restrictions on surface disturbance due to sensitive species or habitat issues. Typical performance results for ERD applications include 85 to 90 percent total molar reduction of chlorinated volatile organic compounds (CVOCs) near the SBGR and rapid clean-up of adjacent dissolved contaminant source areas. Based on a review of the literature and CH2M's field-scale results from over a dozen SBGRs with a least one year of performance data, important site-specific design considerations include: 1) hydraulic residence time should be long enough for sufficient treatment but not too long to create depressed pH and stagnant conditions (e.g., typically between 10 and 60 days), 2) reactor material should balance appropriate organic mulch as optimal bacterial growth media along with other organic additives that provide bioavailable organic carbon, 3) a variety of native bacteria are important to the treatment process, and 4) biologically mediated generation of iron sulfides along with

  8. Characteristics of the surface-subsurface flow generation and sediment yield to the rainfall regime and land-cover by long-term in-situ observation in the red soil region, Southern China

    NASA Astrophysics Data System (ADS)

    Liu, Yao-Jun; Yang, Jie; Hu, Jian-Min; Tang, Chong-Jun; Zheng, Hai-Jin

    2016-08-01

    Land cover and rainfall regime are two important factors that affect soil erosion. In this paper, three land cover types - grass cover, litter cover and bare land - were employed to analyze surface runoff, subsurface flow and sediment loss processes in relation to the rainfall regimes in the red soil region of China. Five rainfall regimes were classified according to 393 rainfall events via a k-means clustering method based on the rainfall depth, duration and maximum 30-min intensity. The highest surface runoff coefficient and erosion amount were found on bare land in all five rainfall regimes, and the lowest were found on grass cover. The litter cover generated the highest subsurface flow rate, followed by the grass cover; the lowest was on bare land. For grass cover and litter cover plots, rainfall events of rainfall regime IV which had the longest duration, greatest depth and lowest intensity had the highest surface runoff coefficient, soil erosion amount and subsurface flow rate. For bare land, storm rainfall events of rainfall regime V had the highest intensity, lowest depth and duration, had the highest surface runoff coefficient and soil erosion amount, but the lowest subsurface flow rate. The highest subsurface flow rate of bare land happened in rainfall regime IV. Surface cover was urgently needed to reduce soil erosion. When the lands under dense surface cover, more attention should be paid to rainfall events that of long duration, high depth but low in intensity which commonly occurred in spring. The interactions of surface-subsurface flow and its effects on soil erosion and nutrient loss were worth considering in the red soil region.

  9. A General Simulator for Reaction-Based Biogeochemical Processes

    SciTech Connect

    Fang, Yilin; Yabusaki, Steven B.; Yeh, George

    2006-02-01

    As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, passivation of reactive surfaces, dissolution of sorbates), there is a growing need for biogeochemical simulators to flexibly and facilely address new reaction forms and rate laws. This paper presents an approach that accommodates this need to efficiently simulate general biogeochemical processes, while insulating the user from additional code development. The approach allows for the automatic extraction of fundamental reaction stoichiometry and thermodynamics from a standard chemistry database, and the symbolic entry of arbitrarily complex user-specified reaction forms, rate laws, and equilibria. The user-specified equilibrium and kinetic reactions (i.e., reactions not defined in the format of the standardized database) are interpreted by the Maple symbolic mathematical software package. FORTRAN 90 code is then generated by Maple for (1) the analytical Jacobian matrix (if preferred over the numerical Jacobian matrix) used in the Newton-Raphson solution procedure, and (2) the residual functions for user-specified equilibrium expressions and rate laws. Matrix diagonalization eliminates the need to conceptualize the system of reactions as a tableau, while identifying a minimum rank set of basis species with enhanced numerical convergence properties. The newly generated code, which is designed to operate in the BIOGEOCHEM biogeochemical simulator, is then compiled and linked into the BIOGEOCHEM executable. With these features, users can avoid recoding the simulator to accept new equilibrium expressions or kinetic rate laws, while still taking full advantage of the stoichiometry and thermodynamics provided by an existing chemical database. Thus, the approach introduces efficiencies in the specification of biogeochemical reaction networks and eliminates opportunities for mistakes in preparing input files and coding errors. Test problems are used to demonstrate the features of

  10. Mathematical and Computational Modeling of Multiphysics Couplings in the Geosciences

    NASA Astrophysics Data System (ADS)

    Wheeler, M. F.

    2004-12-01

    Multiphysics couplings can happen in different ways. Aĉ_sA,A One may have different physical processes (e.g. flow, transport, reactions) occurring within the same physical domain, or one may have different physical regimes (e.g., surface/subsurface environments, fluid/structure interactions) interacting through interfaces. We will discuss both of these types of multiphysics couplings during this presentation. Of particular interest will be the development of interpolation/projection algorithms for projecting physical quantities from one space/time grid to another, the investigation of mortar and mortar-free methods for coupling multiple physical domains, and the coupling of non-conforming and conforming finite element methods.

  11. Predictability of Biogeochemical Responses in Engineered Watersheds

    NASA Astrophysics Data System (ADS)

    Yaeger, M. A.; Voepel, H. E.; Basu, N. B.; Rao, P. C.; Donner, S. D.; Packman, A. I.

    2009-12-01

    Examining the impacts of large-scale human modifications of watersheds (e.g., land-use intensification for food production; hydrologic modification through extensive tile-drainage, etc.) on the hydrologic and biogeochemical responses, and ecological impacts at various scales has been the focus of monitoring and modeling studies over the past two decades. Complex interactions between hydrology and biogeochemistry and the need to predict responses across scales has led to the development of detailed process-based models that are computationally intensive and calibration-dependent. Our overall hypothesis is that human modifications and intensive management of these watersheds have led to more predictable responses, which are typical of engineered, less-complex systems rather than natural, complex systems. We examined monitoring data for nitrogen, phosphorous, silica and chloride in 25 large watersheds (10,000 km2 to 500,000 km2) in the Mississippi River Basin. This sparse dataset was complemented with nitrogen cycling and hydrology output from a whole-basin terrestrial and aquatic modeling system (IBIS-THMB). These sub-basins have diverse land uses, although agriculture still dominates (from ~30% to ~80%). Despite diversity in soils, geology, rainfall patterns, and land use, a linear relationship was observed between the annual cumulative discharge (Q; m3/yr) and the measured nitrate load (L; kg/yr). The slopes of these linear L-Q plots represent the flow-weighted annual average concentrations (Cf), and a linear L-Q relationship indicates an apparent “chemostatic” response of these large watersheds. Analysis of Mississippi River monitoring data for nitrate and IBIS-THMB simulations revealed that Cf is a strong function of land-use (eg, percent corn) that defines the chemical input function. The scatter around the L-Q plots was small for “endogenous” (generated from internal sources) solutes (eg, silica), intermediate for “hybrid” (contributions from both

  12. Biogeochemical drivers of phosphatase activity in salt marsh sediments

    NASA Astrophysics Data System (ADS)

    Freitas, Joana; Duarte, Bernardo; Caçador, Isabel

    2014-10-01

    Although nitrogen has become a major concern for wetlands scientists dealing with eutrophication problems, phosphorous represents another key element, and consequently its biogeochemical cycling has a crucial role in eutrophication processes. Microbial communities are a central component in trophic dynamics and biogeochemical processes on coastal systems, since most of the processes in sediments are microbial-mediated due to enzymatic action, including the mineralization of organic phosphorus carried out by acid phosphatase activity. In the present work, the authors investigate the biogeochemical sediment drivers that control phosphatase activities. Authors also aim to assess biogeochemical factors' influence on the enzyme-mediated phosphorous cycling processes in salt marshes. Plant rhizosediments and bare sediments were collected and biogeochemical features, including phosphatase activities, inorganic and organic phosphorus contents, humic acids content and pH, were assessed. Acid phosphatase was found to give the highest contribution for total phosphatase activity among the three pH-isoforms present in salt marsh sediments, favored by acid pH in colonized sediments. Humic acids also appear to have an important role inhibiting phosphatase activity. A clear relation of phosphatase activity and inorganic phosphorous was also found. The data presented reinforces the role of phosphatase in phosphorous cycling.

  13. Factors Influencing Phosphorous Cycling in Biogeochemical 'Hot Spots'

    NASA Astrophysics Data System (ADS)

    Saia, S. M.; Walter, M. T.; Buda, A. R.; Carrick, H. J.; Regan, J. M.

    2015-12-01

    Anthropogenic alteration of the phosphorus (P) cycle has led to subsequent soil and water quality issues. For example, P build up in soils due to historic fertilizer application may become biologically available and exacerbate eutrophication and anoxia in nearby water bodies. In the humid Northeastern United States, storm runoff transports P and also stimulates biogeochemical processes, these locations are termed biogeochemical 'hot spots'. Many studies have looked at nitrogen and carbon cycling in biogeochemical hot spots but few have focused on P. We hypothesize the periodic wetting and drying of biogeochemical hot spots promotes a combination of abiotic and biotic processes that influence the mobility of P. To test this hypothesis, we took monthly soil samples (5 cm deep) from May to October in forest, pasture, and cropped land near Ithaca, NY. In-situ measurements taken with each sample included volumetric soil moisture and soil temperature. We also analyzed samples for 'runoff generated' phosphate, nitrate, and sulfate (from 0.01 M CaCl2 extraction), Fe(II), percent organic matter, pH, as well as oxalate extractable and total P, Al, and Fe. We used linear mixed effects models to test how runoff generated phosphate concentrations vary with soil moisture and whether other environmental factors strengthen/weaken this relationship. The knowledge gained from this study will improve our understanding of P cycling in biogeochemical hot spots and can be used to improve the effectiveness of agricultural management practices in the Northeastern United States.

  14. The impacts of climate change and human activities on biogeochemical cycles on the Qinghai-Tibetan Plateau.

    PubMed

    Chen, Huai; Zhu, Qiuan; Peng, Changhui; Wu, Ning; Wang, Yanfen; Fang, Xiuqing; Gao, Yongheng; Zhu, Dan; Yang, Gang; Tian, Jianqing; Kang, Xiaoming; Piao, Shilong; Ouyang, Hua; Xiang, Wenhua; Luo, Zhibin; Jiang, Hong; Song, Xingzhang; Zhang, Yao; Yu, Guirui; Zhao, Xinquan; Gong, Peng; Yao, Tandong; Wu, Jianghua

    2013-10-01

    With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles.

  15. 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

  16. The biogeochemical iron cycle and astrobiology

    NASA Astrophysics Data System (ADS)

    Schröder, Christian; Köhler, Inga; Muller, Francois L. L.; Chumakov, Aleksandr I.; Kupenko, Ilya; Rüffer, Rudolf; Kappler, Andreas

    2016-12-01

    Biogeochemistry investigates chemical cycles which influence or are influenced by biological activity. Astrobiology studies the origin, evolution and distribution of life in the universe. The biogeochemical Fe cycle has controlled major nutrient cycles such as the C cycle throughout geological time. Iron sulfide minerals may have provided energy and surfaces for the first pioneer organisms on Earth. Banded iron formations document the evolution of oxygenic photosynthesis. To assess the potential habitability of planets other than Earth one looks for water, an energy source and a C source. On Mars, for example, Fe minerals have provided evidence for the past presence of liquid water on its surface and would provide a viable energy source. Here we present Mössbauer spectroscopy investigations of Fe and C cycle interactions in both ancient and modern environments. Experiments to simulate the diagenesis of banded iron formations indicate that the formation of ferrous minerals depends on the amount of biomass buried with ferric precursors rather than on the atmospheric composition at the time of deposition. Mössbauer spectra further reveal the mutual stabilisation of Fe-organic matter complexes against mineral transformation and decay of organic matter into CO2. This corresponds to observations of a `rusty carbon sink' in modern sediments. The stabilisation of Fe-organic matter complexes may also aid transport of particulate Fe in the water column while having an adverse effect on the bioavailability of Fe. In the modern oxic ocean, Fe is insoluble and particulate Fe represents an important source. Collecting that particulate Fe yields small sample sizes that would pose a challenge for conventional Mössbauer experiments. We demonstrate that the unique properties of the beam used in synchrotron-based Mössbauer applications can be utilized for studying such samples effectively. Reactive Fe species often occur in amorphous or nanoparticulate form in the environment and

  17. Recent directions taken in water, energy, and biogeochemical budgets research

    USGS Publications Warehouse

    Lins, Harry F.

    1994-01-01

    Understanding and predicting global change is a major scientific focus of the late 20th century. Although atmospheric scientists have made substantial progress in developing models that account for many components of the climate system, significant progress is needed in understanding processes associated with the exchange of water, energy, and carbon between terrestrial systems and the atmosphere.To strengthen terrestrial process research, especially research associated with the interactions of water, energy, gases, nutrients, and vegetation, the U.S. Geological Survey initiated an intensive study of Water, Energy, and Biogeochemical Budgets (WEBB). WEBB is aimed at improving understanding of processes controlling terrestrial water, energy, and biogeochemical fluxes, their interactions, and their relations to climatic variables; and the ability to predict continental water, energy, and biogeochemical budgets over a range of spatial and temporal scales.

  18. Quantifying Linkages between Biogeochemical Processes in a Contaminated Aquifer-Wetland System Using Multivariate Statistics and HP1

    NASA Astrophysics Data System (ADS)

    Arora, B.; Mohanty, B. P.; McGuire, J. T.

    2009-12-01

    Fate and transport of contaminants in saturated and unsaturated zones in the subsurface is controlled by complex biogeochemical processes such as precipitation, sorption-desorption, ion-exchange, redox, etc. In dynamic systems such as wetlands and anaerobic aquifers, these processes are coupled and can interact non-linearly with each other. Variability in measured hydrological, geochemical and microbiological parameters thus corresponds to multiple processes simultaneously. To infer the contributing processes, it is important to eliminate correlations and to identify inter-linkages between factors. The objective of this study is to develop quantitative relationships between hydrological (initial and boundary conditions, hydraulic conductivity ratio, and soil layering), geochemical (mineralogy, surface area, redox potential, and organic matter) and microbiological factors (MPN) that alter the biogeochemical processes at the column scale. Data used in this study were collected from controlled flow experiments in: i) two homogeneous soil columns, ii) a layered soil column, iii) a soil column with embedded clay lenses, and iv) a soil column with embedded clay lenses and one central macropore. The soil columns represent increasing level of soil structural heterogeneity to better mimic the Norman Landfill research site. The Norman Landfill is a closed municipal facility with prevalent organic contamination. The sources of variation in the dataset were explored using multivariate statistical techniques and dominant biogeochemical processes were obtained using principal component analysis (PCA). Furthermore, artificial neural networks (ANN) coupled with HP1 was used to develop mathematical rules identifying different combinations of factors that trigger, sustain, accelerate/decelerate, or discontinue the biogeochemical processes. Experimental observations show that infiltrating water triggers biogeochemical processes in all soil columns. Similarly, slow release of water

  19. Scaling hyporheic exchange and its influence on biogeochemical reactions in aquatic ecosystems

    USGS Publications Warehouse

    O'Connor, B.L.; Harvey, J.W.

    2008-01-01

    Hyporheic exchange and biogeochemical reactions are difficult to quantify because of the range in fluid-flow and sediment conditions inherent to streams, wetlands, and nearshore marine ecosystems. Field measurements of biogeochemical reactions in aquatic systems are impeded by the difficulty of measuring hyporheic flow simultaneously with chemical gradients in sediments. Simplified models of hyporheic exchange have been developed using Darcy's law generated by flow and bed topography at the sediment-water interface. However, many modes of transport are potentially involved (molecular diffusion, bioturbation, advection, shear, bed mobility, and turbulence) with even simple models being difficult to apply in complex natural systems characterized by variable sediment sizes and irregular bed geometries. In this study, we synthesize information from published hyporheic exchange investigations to develop a scaling relationship for estimating mass transfer in near-surface sediments across a range in fluid-flow and sediment conditions. Net hyporheic exchange was quantified using an effective diffusion coefficient (De) that integrates all of the various transport processes that occur simultaneously in sediments, and dimensional analysis was used to scale De to shear stress velocity, roughness height, and permeability that describe fluid-flow and sediment characteristics. We demonstrated the value of the derived scaling relationship by using it to quantify dissolved oxygen (DO) uptake rates on the basis of DO profiles in sediments and compared them to independent flux measurements. The results support a broad application of the De scaling relationship for quantifying coupled hyporheic exchange and biogeochemical reaction rates in streams and other aquatic ecosystems characterized by complex fluid-flow and sediment conditions.

  20. Earth's Early Biosphere and the Biogeochemical Carbon Cycle

    NASA Technical Reports Server (NTRS)

    DesMarais, David

    2004-01-01

    Our biosphere has altered the global environment principally by influencing the chemistry of those elements most important for life, e g., C, N, S, O, P and transition metals (e.g., Fe and Mn). The coupling of oxygenic photosynthesis with the burial in sediments of photosynthetic organic matter, and with the escape of H2 to space, has increased the state of oxidation of the Oceans and atmosphere. It has also created highly reduced conditions within sedimentary rocks that have also extensively affected the geochemistry of several elements. The decline of volcanism during Earth's history reduced the flow of reduced chemical species that reacted with photosynthetically produced O2. The long-term net accumulation of photosynthetic O2 via biogeochemical processes has profoundly influenced our atmosphere and biosphere, as evidenced by the O2 levels required for algae, multicellular life and certain modem aerobic bacteria to exist. When our biosphere developed photosynthesis, it tapped into an energy resource that was much larger than the energy available from oxidation-reduction reactions associated with weathering and hydrothermal activity. Today, hydrothermal sources deliver globally (0.13-1.1)x10(exp l2) mol yr(sup -1) of reduced S, Fe(2+), Mn(2+), H2 and CH4; this is estimated to sustain at most about (0.2-2)xl0(exp 12)mol C yr(sup -1) of organic carbon production by chemautotrophic microorganisms. In contrast, global photosynthetic productivity is estimated to be 9000x10(exp 12) mol C yr(sup -1). Thus, even though global thermal fluxes were greater in the distant geologic past than today, the onset of oxygenic photosynthesis probably increased global organic productivity by some two or more orders of magnitude. This enormous productivity materialized principally because oxygenic photosynthesizers unleashed a virtually unlimited supply of reduced H that forever freed life from its sole dependence upon abiotic sources of reducing power such as hydrothermal emanations

  1. The Coordination and Harmonics of Biogeochemical Cycles in North Inlet, SC Salt Marshes

    NASA Astrophysics Data System (ADS)

    Morris, J. T.

    2015-12-01

    North Inlet is a pristine estuary within a small coastal watershed with minimal surface water input or human impact. North Inlet exchanges its water with the coastal ocean with a turnover time of about 0.5 per day. Its marshes are dominated by the grass Spartina alterniflora. Growth rates of Spartina have been measured monthly on permanent plots in North Inlet since 1984, and concentrations of porewater ammonium and phosphate, and sulfide have been measured monthly over depth (10-100 cm) since 1994. The salt marsh shows pronounced seasonal biogeochemical cycles that are highly correlated. Ammonium, phosphate and sulfide concentrations all peak in August-October and are minimal during February-April. Mean monthly ammonium concentration varies between 42 and 87 μM, phosphate between 3 and 18 μM, and sulfide between 8 and 87 μM. Monthly growth rates of Spartina range from 91 to 111 g dry weight m-2 between April and September. The integrated total aboveground production is 25 mol C m-2 yr-1. The inventories of N and P in porewater are small fractions of what is required to support primary production. Primary production is N-limited and this is consistent with the N:P ratio declining from 14 during early spring to 5 in late summer. There are losses, especially of N, from drainage, denitrification, and export of organic production. These have to be compensated by gains from N fixation, most likely from coupled sulfate reduction. There is also a coupling between sulfide, iron, and phosphorous that appears to conserve P during the winter and generate soluble P during the active growing season. These couplings coordinate the biogeochemical cycles, and this extends to the tidal creeks that are dominated by benthic sources of nutrients.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Editorial: Organic wastes in soils: Biogeochemical and Environmental Aspects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This special issue of Soil Biology and Biochemistry presents papers from the Second General Annual Conference of European Geosciences Union, Session SSS12 Recycling of Organic Wastes in Soils: Biogeochemical and Environmental Issues, held at the Austria Center Vienna, 24-29 April 2005. Session SSS12...

  8. PHOTOREACTIONS IN SURFACE WATERS AND THEIR ROLE IN BIOGEOCHEMICAL CYCLES

    EPA Science Inventory

    During the past decade significant interest has developed in the influence of photochemical reactions on biogeochemical cycles in surface waters of lakes and the sea. A major portion of recent research on these photoreactions has focused on the colored component of dissolved org...

  9. Applying computationally efficient schemes for biogeochemical cycles (ACES4BGC)

    SciTech Connect

    Vertenstein, Mariana

    2016-01-11

    NCAR contributed to the ACES4BGC project through software engineering work on aerosol model implementation, build system and script changes, coupler enhancements for biogeochemical tracers, improvements to the Community Land Model (CLM) code and testing infrastructure, and coordinating and integrating code changes from the various project participants.

  10. 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

  11. The value of automated high-frequency nutrient monitoring in inference of biogeochemical processes, temporal variability and trends

    NASA Astrophysics Data System (ADS)

    Bieroza, Magdalena; Heathwaite, Louise

    2013-04-01

    Stream water quality signals integrate catchment-scale processes responsible for delivery and biogeochemical transformation of the key biotic macronutrients (N, C, P). This spatial and temporal integration is particularly pronounced in the groundwater-dominated streams, as in-stream nutrient dynamics are mediated by the processes occurring within riparian and hyporheic ecotones. In this paper we show long-term high-frequency in-stream macronutrient dynamics from a small agricultural catchment located in the North West England. Hourly in-situ measurements of total and reactive phosphorus (Systea, IT), nitrate (Hach Lange, DE) and physical water quality parameters (turbidity, specific conductivity, dissolved oxygen, temperature, pH; WaterWatch, UK) were carried out on the lowland, gaining reach of the River Leith. High-frequency data show complex non-linear nutrient concentration-discharge relationships. The dominance of hysteresis effects suggests the presence of a temporally varying apportionment of allochthonous and autochthonous nutrient sources. Varying direction, magnitude and dynamics of the hysteretic responses between storm events is driven by the variation in the contributing source areas and shows the importance of the coupling of catchment-scale, in-stream, riparian and hyporheic biogeochemical cycles. The synergistic effect of physical (temperature-driven, the hyporheic exchange controlled by diffusion) and biogeochemical drivers (stream and hyporheic metabolism) on in-stream nutrient concentrations manifests itself in observed diurnal patterns. As inferred from the high-frequency nutrient monitoring, the diurnal dynamics are of the greatest importance under baseflow conditions. Understanding the role and relative importance of these processes can be difficult due to spatial and temporal heterogeneity of the key mechanisms involved. This study shows the importance of in-situ, fine temporal resolution, automated monitoring approaches in providing evidence

  12. 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.

  13. Hybrid Multiscale Simulation of Hydrologic and Biogeochemical Processes in the River-Groundwater Interaction Zone

    NASA Astrophysics Data System (ADS)

    Yang, X.; Scheibe, T. D.; Chen, X.; Hammond, G. E.; Song, X.

    2015-12-01

    The zone in which river water and groundwater mix plays an important role in natural ecosystems as it regulates the mixing of nutrients that control biogeochemical transformations. Subsurface heterogeneity leads to local hotspots of microbial activity that are important to system function yet difficult to resolve computationally. To address this challenge, we are testing a hybrid multiscale approach that couples models at two distinct scales, based on field research at the U. S. Department of Energy's Hanford Site. The region of interest is a 400 x 400 x 20 m macroscale domain that intersects the aquifer and the river and contains a contaminant plume. However, biogeochemical activity is high in a thin zone (mud layer, <1 m thick) immediately adjacent to the river. This microscale domain is highly heterogeneous and requires fine spatial resolution to adequately represent the effects of local mixing on reactions. It is not computationally feasible to resolve the full macroscale domain at the fine resolution needed in the mud layer, and the reaction network needed in the mud layer is much more complex than that needed in the rest of the macroscale domain. Hence, a hybrid multiscale approach is used to efficiently and accurately predict flow and reactive transport at both scales. In our simulations, models at both scales are simulated using the PFLOTRAN code. Multiple microscale simulations in dynamically defined sub-domains (fine resolution, complex reaction network) are executed and coupled with a macroscale simulation over the entire domain (coarse resolution, simpler reaction network). The objectives of the research include: 1) comparing accuracy and computing cost of the hybrid multiscale simulation with a single-scale simulation; 2) identifying hot spots of microbial activity; and 3) defining macroscopic quantities such as fluxes, residence times and effective reaction rates.

  14. 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.

  15. Novel Imaging Techniques, Integrated with Mineralogical, Geochemical and Microbiological Characterization to Determine the Biogeochemical Controls....

    SciTech Connect

    Lloyd, Jonathan R.

    2005-06-01

    Tc(VII) will be reduced and precipitated in FRC sediments under anaerobic conditions in batch experiments (progressive microcosms). The complementary microcosm experiments using low pH/nigh nitrate sediments from 3 (near FW 009) are imminent, with the sediment cores already shipped to Manchester. HYPOTHESIS 2. Tc(VII) reduction and precipitation can be visualized in discrete biogeochemical zones in sediment columns using 99mTc and a gamma-camera. Preliminary experiments testing the use of 99mTc as a radiotracer to address hypotheses 2 and 3 have suggested that the 99mTc associates with Fe(II)-bearing sediments in microcosms and stratified columns containing FRC sediments. Initial proof of concept microcosms containing Fe(II)-bearing, microbially-reduced FRC sediments were spiked with 99mTc and imaged using a gamma-camera. In comparison with oxic controls, 99mTc was significantly partitioned in the solid phase in Fe(III)-reducing sediments in batch experiments. Column experiments using FRC background area soil with stratified biogeochemical zones after stimulation of anaerobic processes through nutrient supplementation, suggested that 99mTc transport was retarded through areas of Fe(III) reduction. HYPOTHESIS 3. Sediment-bound reduced 99mTc can be solubilized by perturbations including oxidation coupled to biological nitrate reduction, and mobilization visualized in real-time using a gamma-camera. Significant progress has been made focusing on the impact of nitrate on the biogeochemical behavior of technetium. Additions of 100 mM nitrate to FRC sediment microcosms, which could potentially compete for electrons during metal reduction, inhibited the reduction of both Fe(III) and Tc(VII) completely. Experiments have also addressed the impact of high nitrate concentrations on Fe(II) and Tc(IV) in pre-reduced sediments, showing no significant resolubilization of Tc with the addition of 25 mM nitrate. A parallel set of experiments addressing the impact of aerobic

  16. Abrupt shifts in ecosystem function and intensification of global biogeochemical cycle driven by hydroclimatic extremes

    NASA Astrophysics Data System (ADS)

    Ma, Xuanlong; Huete, Alfredo; Ponce-Campos, Guillermo; Zhang, Yongguang; Xie, Zunyi; Giovannini, Leandro; Cleverly, James; Eamus, Derek

    2016-04-01

    Amplification of the hydrologic cycle as a consequence of global warming is increasing the frequency, intensity, and spatial extent of extreme climate events globally. The potential influences resulting from amplification of the hydro-climatic cycle, coupled with an accelerating warming trend, pose great concerns on the sustainability of terrestrial ecosystems to sequester carbon, maintain biodiversity, provide ecosystem services, food security, and support human livelihood. Despite the great implications, the magnitude, direction, and carry-over effect of these extreme climate events on ecosystem function, remain largely uncertain. To address these pressing issues, we conducted an observational, interdisciplinary study using satellite retrievals of atmospheric CO2 and photosynthesis (chlorophyll fluorescence), and in-situ flux tower measures of ecosystem-atmosphere carbon exchange, to reveal the shifts in ecosystem function across extreme drought and wet periods. We further determine the factors that govern ecosystem sensitivity to hydroclimatic extremes. We focus on Australia but extended our analyses to other global dryland regions due to their significant role in global biogeochemical cycles. Our results revealed dramatic impacts of drought and wet hydroclimatic extremes on ecosystem function, with abrupt changes in vegetation productivity, carbon uptake, and water-use-efficiency between years. Drought resulted in widespread reductions or collapse in the normal patterns of vegetation growth seasonality such that in many cases there was no detectable phenological cycle during extreme drought years. We further identified a significant increasing trend (p < 0.001) in extreme wet year precipitation amounts over Australia and many other global regions, resulting in an increasing trend in magnitude of the episodic carbon sink pulses coupled to each La Niña-induced wet years. This finding is of global biogeochemical significance, with the consequence of amplifying

  17. Biogeochemical Transformations in the History of the Ocean.

    PubMed

    Lenton, Timothy M; Daines, Stuart J

    2017-01-03

    The ocean has undergone several profound biogeochemical transformations in its 4-billion-year history, and these were an integral part of the coevolution of life and the planet. This review focuses on changes in ocean redox state as controlled by changes in biological activity, nutrient concentrations, and atmospheric O2. Motivated by disparate interpretations of available geochemical data, we aim to show how quantitative modeling-spanning microbial mats, shelf seas, and the open ocean-can help constrain past ocean biogeochemical redox states and show what caused transformations between them. We outline key controls on ocean redox structure and review pertinent proxies and their interpretation. We then apply this quantitative framework to three key questions: How did the origin of oxygenic photosynthesis transform ocean biogeochemistry? How did the Great Oxidation transform ocean biogeochemistry? And how was ocean biogeochemistry transformed in the Neoproterozoic-Paleozoic?

  18. Biogeochemical Transformations in the History of the Ocean

    NASA Astrophysics Data System (ADS)

    Lenton, Timothy M.; Daines, Stuart J.

    2017-01-01

    The ocean has undergone several profound biogeochemical transformations in its 4-billion-year history, and these were an integral part of the coevolution of life and the planet. This review focuses on changes in ocean redox state as controlled by changes in biological activity, nutrient concentrations, and atmospheric O2. Motivated by disparate interpretations of available geochemical data, we aim to show how quantitative modeling—spanning microbial mats, shelf seas, and the open ocean—can help constrain past ocean biogeochemical redox states and show what caused transformations between them. We outline key controls on ocean redox structure and review pertinent proxies and their interpretation. We then apply this quantitative framework to three key questions: How did the origin of oxygenic photosynthesis transform ocean biogeochemistry? How did the Great Oxidation transform ocean biogeochemistry? And how was ocean biogeochemistry transformed in the Neoproterozoic-Paleozoic?

  19. The microbial engines that drive Earth's biogeochemical cycles.

    PubMed

    Falkowski, Paul G; Fenchel, Tom; Delong, Edward F

    2008-05-23

    Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.

  20. Polychlorinated Biphenyls as Probes of Biogeochemical Processes in Rivers

    USGS Publications Warehouse

    Fitzgerald, S.A.; Steuer, J.J.

    1997-01-01

    A field study was conducted to investigate the use of PCB (polychlorinated biphenyl) congener and homolog assemblages as tracers of biogeochemical processes in the Milwaukee and Manitowoc Rivers in southeastern Wisconsin from 1993 to 1995. PCB congeners in the dissolved and suspended particle phases, along with various algal indicators (algal carbon and pigments), were quantitated in the water seasonally. In addition, PCB congener assemblages were determined seasonally in surficial bed sediments. Biogeochemical processes investigated included: determination of the source of suspended particles and bottom sediments by comparison with known Aroclor mixtures, water-solid partitioning, and algal uptake of PCBs. Seasonal differences among the PCB assemblages were observed mainly in the dissolved phase, somewhat less in the suspended particulate phase, and not at all in the bed sediments.

  1. Estimating impacts of lichens and bryophytes on global biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Porada, Philipp; Weber, Bettina; Elbert, Wolfgang; Pöschl, Ulrich; Kleidon, Axel

    2014-02-01

    Lichens and bryophytes may significantly affect global biogeochemical cycles by fixation of nitrogen and biotic enhancement of surface weathering rates. Most of the studies suggesting these effects, however, are either conceptual or rely on upscaling of regional estimates to obtain global numbers. Here we use a different method, based on estimates of net carbon uptake, to quantify the impacts of lichens and bryophytes on biogeochemical cycles at the global scale. We focus on three processes, namely, nitrogen fixation, phosphorus uptake, and chemical weathering. Our estimates have the form of potential rates, which means that we quantify the amount of nitrogen and phosphorus needed by the organisms to build up biomass, also accounting for resorption and leaching of nutrients. Subsequently, we use potential phosphorus uptake on bare ground to estimate chemical weathering by the organisms, assuming that they release weathering agents to obtain phosphorus. The predicted requirement for nitrogen ranges from 3.5 to 34 Tgyr-1 and for phosphorus it ranges from 0.46 to 4.6 Tgyr-1. Estimates of chemical weathering are between 0.058 and 1.1 km3 yr-1 of rock. These values seem to have a realistic order of magnitude, and they support the notion that lichens and bryophytes have the potential to play an important role for biogeochemical cycles.

  2. 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.

  3. 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

  4. 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

    , location and tracer. The high computational effort of a model evaluation was encountered by using the transport matrix method with spatial parallelization, advanced derivative-based optimization algorithms and a cost saving approximation of the derivative. Globalization techniques were used to overcome local minima. Due to a special software interface, coupling of arbitrary water-column biogeochemical models is possible. In the talk, we present the used methods together with results for this exemplary model.

  5. 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

  6. 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

    scale simulations were then used to simulate coupled flow and moisture migration in soils in saturated and unsaturated zones, surface and groundwater exchange, and surface water flow in streams and lakes at the DWP site under dynamic precipitation conditions. Laboratory measurements of soil hydrological and biogeochemical properties are used to parameterize the UMSM at the small scales, and field measurements are used to evaluate the UMSM.

  7. Biogeochemical control of marine productivity in the Mediterranean Sea during the last 50 years

    PubMed Central

    Macias, Diego; Garcia-Gorriz, Elisa; Piroddi, Chiara; Stips, Adolf

    2014-01-01

    The temporal dynamics of biogeochemical variables derived from a coupled 3-D model of the Mediterranean Sea are evaluated for the last 50 years (1960–2010) against independent data on fisheries catch per unit effort (CPUE) for the same time period. Concordant patterns are found in the time series of all of the biological variables (from the model and from fisheries statistics), with low values at the beginning of the series, a later increase, with maximum levels reached at the end of the 1990s, and a posterior stabilization. Spectral analysis of the annual biological time series reveals coincident low-frequency signals in all of them. The first, more energetic signal peaks around the year 2000, while the second, less energetic signal peaks near 1982. Almost identical low-frequency signals are found in the nutrient loads of the rivers and in the integrated nutrient levels in the surface marine ecosystem. Nitrate concentration shows a maximum level in 1998, with a later stabilization to present-day values, coincident with the first low-frequency signal found in the biological series. Phosphate shows maximum concentrations around 1982 and a posterior sharp decline, in concordance with the second low-frequency signal observed in the biological series. That result seems to indicate that the control of marine productivity (plankton to fish) in the Mediterranean is principally mediated through bottom-up processes that could be traced back to the characteristics of riverine discharges. The high sensitivity of CPUE time series to environmental conditions might be another indicator of the overexploitation of this marine ecosystem. Key Points Biogeochemical evolution of the Mediterranean over the past 50 years River nutrient loads drive primary and secondary productions Strong link between low trophic levels and fisheries PMID:26180286

  8. Effects of solar UV radiation and climate change on biogeochemical cycling: Interactions and feedbacks

    SciTech Connect

    Erickson III, David J

    2011-01-01

    Solar UV radiation, climate and other drivers of global change are undergoing significant changes and models forecast that these changes will continue for the remainder of this century. Here we assess the effects of solar UV radiation on biogeochemical cycles and the interactions of these effects with climate change, including feedbacks on climate. Such interactions occur in both terrestrial and aquatic ecosystems. While there is significant uncertainty in the quantification of these effects, they could accelerate the rate of atmospheric CO{sub 2} increase and subsequent climate change beyond current predictions. The effects of predicted changes in climate and solar UV radiation on carbon cycling in terrestrial and aquatic ecosystems are expected to vary significantly between regions. The balance of positive and negative effects on terrestrial carbon cycling remains uncertain, but the interactions between UV radiation and climate change are likely to contribute to decreasing sink strength in many oceanic regions. Interactions between climate and solar UV radiation will affect cycling of elements other than carbon, and so will influence the concentration of greenhouse and ozone-depleting gases. For example, increases in oxygen-deficient regions of the ocean caused by climate change are projected to enhance the emissions of nitrous oxide, an important greenhouse and ozone-depleting gas. Future changes in UV-induced transformations of aquatic and terrestrial contaminants could have both beneficial and adverse effects. Taken in total, it is clear that the future changes in UV radiation coupled with human-caused global change will have large impacts on biogeochemical cycles at local, regional and global scales.

  9. 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.

  10. Global biogeochemical implications of mercury discharges from rivers and sediment burial.

    PubMed

    Amos, Helen M; Jacob, Daniel J; Kocman, David; Horowitz, Hannah M; Zhang, Yanxu; Dutkiewicz, Stephanie; Horvat, Milena; Corbitt, Elizabeth S; Krabbenhoft, David P; Sunderland, Elsie M

    2014-08-19

    Rivers are an important source of mercury (Hg) to marine ecosystems. Based on an analysis of compiled observations, we estimate global present-day Hg discharges from rivers to ocean margins are 27 ± 13 Mmol a(-1) (5500 ± 2700 Mg a(-1)), of which 28% reaches the open ocean and the rest is deposited to ocean margin sediments. Globally, the source of Hg to the open ocean from rivers amounts to 30% of atmospheric inputs. This is larger than previously estimated due to accounting for elevated concentrations in Asian rivers and variability in offshore transport across different types of estuaries. Riverine inputs of Hg to the North Atlantic have decreased several-fold since the 1970s while inputs to the North Pacific have increased. These trends have large effects on Hg concentrations at ocean margins but are too small in the open ocean to explain observed declines of seawater concentrations in the North Atlantic or increases in the North Pacific. Burial of Hg in ocean margin sediments represents a major sink in the global Hg biogeochemical cycle that has not been previously considered. We find that including this sink in a fully coupled global biogeochemical box model helps to balance the large anthropogenic release of Hg from commercial products recently added to global inventories. It also implies that legacy anthropogenic Hg can be removed from active environmental cycling on a faster time scale (centuries instead of millennia). Natural environmental Hg levels are lower than previously estimated, implying a relatively larger impact from human activity.

  11. 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.

  12. 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

  13. Effects of solar UV radiation and climate change on biogeochemical cycling: interactions and feedbacks.

    PubMed

    Zepp, R G; Erickson, D J; Paul, N D; Sulzberger, B

    2011-02-01

    Solar UV radiation, climate and other drivers of global change are undergoing significant changes and models forecast that these changes will continue for the remainder of this century. Here we assess the effects of solar UV radiation on biogeochemical cycles and the interactions of these effects with climate change, including feedbacks on climate. Such interactions occur in both terrestrial and aquatic ecosystems. While there is significant uncertainty in the quantification of these effects, they could accelerate the rate of atmospheric CO(2) increase and subsequent climate change beyond current predictions. The effects of predicted changes in climate and solar UV radiation on carbon cycling in terrestrial and aquatic ecosystems are expected to vary significantly between regions. The balance of positive and negative effects on terrestrial carbon cycling remains uncertain, but the interactions between UV radiation and climate change are likely to contribute to decreasing sink strength in many oceanic regions. Interactions between climate and solar UV radiation will affect cycling of elements other than carbon, and so will influence the concentration of greenhouse and ozone-depleting gases. For example, increases in oxygen-deficient regions of the ocean caused by climate change are projected to enhance the emissions of nitrous oxide, an important greenhouse and ozone-depleting gas. Future changes in UV-induced transformations of aquatic and terrestrial contaminants could have both beneficial and adverse effects. Taken in total, it is clear that the future changes in UV radiation coupled with human-caused global change will have large impacts on biogeochemical cycles at local, regional and global scales.

  14. Using Geochemical Indicators to Distinguish High Biogeochemical Activity in Sediments

    NASA Astrophysics Data System (ADS)

    Kenwell, A. M.; Navarre-Sitchler, A.; Prugue, R.; Spear, J. R.; Williams, K. H.; Maxwell, R. M.

    2014-12-01

    A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This study develops a methodology to predict elevated rates of biogeochemical activity (microbial "hotspots") in subsurface environments by correlating microbial community structure with the spatial distribution of geochemical indicators in subsurface sediments. Statistical hierarchical cluster analyses (HCA) of X-ray fluorescence (XRF), simulated precipitation leachate, bioavailable Fe and Mn, total organic carbon (TOC), microbial community structure, grain size, bulk density and moisture content data were used to identify regions of the subsurface characterized by biogeochemical hotspots and sample characteristics indicative of these hotspots within fluvially-derived aquifer sediments. The methodology has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 33 sediment samples were taken from 8 sediment cores and at the East River 33 soil/sediment samples were collected across and perpendicular to 3 active meanders. The East River watershed exhibits characteristic fluvial progression and serves as a representative example of many headwater catchments with the upper Colorado River basin. Initial clustering revealed that operationally defined hotspots were characterized by high organic carbon, bioavailable iron and dark colors but not necessarily low hydraulic conductivity. Applying the method to identify hotspots in both contaminated and natural floodplain deposits and their associated alluvial aquifers demonstrates the broad applicability of a geochemical indicator based approach.

  15. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Krause, S.

    2015-12-01

    Ecohydrological interfaces, represent the boundaries between water-dependent ecosystems that can alter substantially the fluxes of energy and matter. There is still a critical gap of understanding the organisational principles of the drivers and controls of spatially and temporally variable ecohydrological interface functions. This knowledge gap limits our capacity to efficiently quantify, predict and manage the services provided by complex ecosystems. Many ecohydrological interfaces are characterized by step changes in microbial metabolic activity, steep redox gradients and often even thermodynamic phase shifts, for instance at the interfaces between atmosphere and water or soil matrix and macro-pores interfaces. This paper integrates investigations from point scale microcosm experiments with reach and subcatchment scale tracer experiments and numerical modeling studies to elaborate similarities in the drivers and controls that constitute the enhanced biogeochemical activity of different types of ecohydrologica interfaces across a range of spatial and temporal scales. We therefore combine smart metabolic activity tracers to quantify the impact of bioturbating benthic fauna onto ecosystem respiration and oxygen consumption and investigate at larger scale, how microbial metabolic activity and carbon turnover at the water-sediment interface are controlled by sediment physical and chemical properties as well as water temperatures. Numerical modeling confirmed that experimentally identified hotspots of streambed biogeochemical cycling were controlled by patterns of physical properties such as hydraulic conductivities or bioavailability of organic matter, impacting on residence time distributions and hence reaction times. In contrast to previous research, our investigations thus confirmed that small-scale variability of physical and chemical interface properties had a major impact on biogeochemical processing at the investigated ecohydrological interfaces. Our results

  16. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Krause, Stefan; Lewandowski, Joerg; Hannah, David; McDonald, Karlie; Folegot, Silvia; Baranov, Victor

    2016-04-01

    Ecohydrological interfaces, represent the boundaries between water-dependent ecosystems that can alter substantially the fluxes of energy and matter. There is still a critical gap of understanding the organisational principles of the drivers and controls of spatially and temporally variable ecohydrological interface functions. This knowledge gap limits our capacity to efficiently quantify, predict and manage the services provided by complex ecosystems. Many ecohydrological interfaces are characterized by step changes in microbial metabolic activity, steep redox gradients and often even thermodynamic phase shifts, for instance at the interfaces between atmosphere and water or soil matrix and macro-pores interfaces. This paper integrates investigations from point scale laboratory microcosm experiments with reach and subcatchment scale tracer experiments and numerical modeling studies to elaborate similarities in the drivers and controls that constitute the enhanced biogeochemical activity of different types of ecohydrologica interfaces across a range of spatial and temporal scales. We therefore combine smart metabolic activity tracers to quantify the impact of bioturbating benthic fauna onto ecosystem respiration and oxygen consumption and investigate at larger scale, how microbial metabolic activity and carbon turnover at the water-sediment interface are controlled by sediment physical and chemical properties as well as water temperatures. Numerical modeling confirmed that experimentally identified hotspots of streambed biogeochemical cycling were controlled by patterns of physical properties such as hydraulic conductivities or bioavailability of organic matter, impacting on residence time distributions and hence reaction times. In contrast to previous research, our investigations thus confirmed that small-scale variability of physical and chemical interface properties had a major impact on biogeochemical processing at the investigated ecohydrological interfaces

  17. Nutrient loads exported from managed catchments reveal emergent biogeochemical stationarity

    NASA Astrophysics Data System (ADS)

    Basu, Nandita B.; Destouni, Georgia; Jawitz, James W.; Thompson, Sally E.; Loukinova, Natalia V.; Darracq, Amélie; Zanardo, Stefano; Yaeger, Mary; Sivapalan, Murugesu; Rinaldo, Andrea; Rao, P. Suresh C.

    2010-12-01

    Complexity of heterogeneous catchments poses challenges in predicting biogeochemical responses to human alterations and stochastic hydro-climatic drivers. Human interferences and climate change may have contributed to the demise of hydrologic stationarity, but our synthesis of a large body of observational data suggests that anthropogenic impacts have also resulted in the emergence of effective biogeochemical stationarity in managed catchments. Long-term monitoring data from the Mississippi-Atchafalaya River Basin (MARB) and the Baltic Sea Drainage Basin (BSDB) reveal that inter-annual variations in loads (LT) for total-N (TN) and total-P (TP), exported from a catchment are dominantly controlled by discharge (QT) leading inevitably to temporal invariance of the annual, flow-weighted concentration, $\\overline{Cf = (LT/QT). Emergence of this consistent pattern across diverse managed catchments is attributed to the anthropogenic legacy of accumulated nutrient sources generating memory, similar to ubiquitously present sources for geogenic constituents that also exhibit a linear LT-QT relationship. These responses are characteristic of transport-limited systems. In contrast, in the absence of legacy sources in less-managed catchments, $\\overline{Cf values were highly variable and supply limited. We offer a theoretical explanation for the observed patterns at the event scale, and extend it to consider the stochastic nature of rainfall/flow patterns at annual scales. Our analysis suggests that: (1) expected inter-annual variations in LT can be robustly predicted given discharge variations arising from hydro-climatic or anthropogenic forcing, and (2) water-quality problems in receiving inland and coastal waters would persist until the accumulated storages of nutrients have been substantially depleted. The finding has notable implications on catchment management to mitigate adverse water-quality impacts, and on acceleration of global biogeochemical cycles.

  18. Biogeochemical cycling of Si in a California rice cropping system

    NASA Astrophysics Data System (ADS)

    Seyfferth, A.; Kocar, B. D.; Lee, J.; Fendorf, S.

    2012-12-01

    Silicon is the second most abundant element in the earth's crust, but the number of studies on the biogeochemical cycling of Si does not reflect its environmental ubiquity. While not an "essential" plant nutrient, Si is important for many plants, particularly monocots, for structural integrity and protection against disease and environmental stress. For rice, Si fertilization with N and P increases yield significantly more than N and P alone. While total Si in soil is high, much of this Si is tied up in the crystal lattice of primary and secondary minerals and is only slowly released through chemical weathering. Thus, plant-available Si may be limited particularly in highly weathered soils in humid environments where long-term chemical weathering has lead to desilicification of the soils (e.g., in Southeast Asia where most rice is grown). In such Si-depleted environments, the biocycling of Si through decaying plant litter (i.e., phytoliths) and subsequent plant uptake has proven an important component of the terrestrial biogeochemical cycling of Si. Here, we investigate the dynamics of Si cycling over a two-year period in a rice paddy in Northern California where soil incorporation of harvested rice straw has impacted the terrestrial biogeochemical cycling of Si. We use Ge/Si ratios in pore-waters to infer the contribution of chemical weathering vs. dissolution of plant phytoliths on the plant-available Si pool. We found that the Ge/Si ratios change over the growing and fallow seasons reflecting different rates of Si release through phytolith dissolution and plant uptake.

  19. Remote analysis of biological invasion and biogeochemical change.

    PubMed

    Asner, Gregory P; Vitousek, Peter M

    2005-03-22

    We used airborne imaging spectroscopy and photon transport modeling to determine how biological invasion altered the chemistry of forest canopies across a Hawaiian montane rain forest landscape. The nitrogen-fixing tree Myrica faya doubled canopy nitrogen concentrations and water content as it replaced native forest, whereas the understory herb Hedychium gardnerianum reduced nitrogen concentrations in the forest overstory and substantially increased aboveground water content. This remote sensing approach indicates the geographic extent, intensity, and biogeochemical impacts of two distinct invaders; its wider application could enhance the role of remote sensing in ecosystem analysis and management.

  20. Remote analysis of biological invasion and biogeochemical change

    PubMed Central

    Asner, Gregory P.; Vitousek, Peter M.

    2005-01-01

    We used airborne imaging spectroscopy and photon transport modeling to determine how biological invasion altered the chemistry of forest canopies across a Hawaiian montane rain forest landscape. The nitrogen-fixing tree Myrica faya doubled canopy nitrogen concentrations and water content as it replaced native forest, whereas the understory herb Hedychium gardnerianum reduced nitrogen concentrations in the forest overstory and substantially increased aboveground water content. This remote sensing approach indicates the geographic extent, intensity, and biogeochemical impacts of two distinct invaders; its wider application could enhance the role of remote sensing in ecosystem analysis and management. PMID:15761055

  1. Rivers and Stable Isotopes as Indicators of Biogeochemical Gradients

    NASA Astrophysics Data System (ADS)

    Barth, J. A.

    2005-12-01

    Consideration of processes on very small (microbe) to large (catchment) scales become increasingly important in biogeochemical gradient work. In this context, rivers are ideal indicators of biogeochemical gradients for large continental scales when geochemical- and discharge data are combined for flux evaluations. If these are further combined with isotope measurements, sources and turnover of water and dissolved constituents can be quantified. An example study is the combination of GIS-, discharge- and water stable isotope data on the in Clyde River basin in Scotland. Here we determined transpiration with an annual average of 0.489 km3 a-1. When combining this rate with the water use efficiency, the CO2 uptake of the entire basin yielded an annual net primary production (NPP) of 185.2 g C m-2. Compared to other temperate areas this is about half the NPP than expected, which is most likely caused by the predominant cover of grasslands. Therefore, agricultural and forest vegetation schemes could influence continental water balances on time scales of years to decades. In another study on the Lagan River in N. Ireland, stable isotope methods were applied to evaluate the role of carbonate versus silicate dissolution. Of these two types of weathering only silicate dissolution withdraws atmospheric CO2 to be stored in the continental crust over long time periods. A downstream evolution with increasing pH- and δ13CDIC values revealed carbonate dissolution despite their minor abundance in the catchment of less than 5 %. This dominant carbonate signal on the riverine carbon cycle outlines the capacity of buffering anthropogenic influences and CO2 turnover. It should be even more pronounced in other rivers where carbonates usually occupy a larger proportion of the basin geology. Future biogeochemical gradient work on rivers should apply particulate and dissolved organic constituent fluxes. This includes more refined compound specific isotope work on selected pollutants such

  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. Hydro-biogeochemical Controls on Geophysical Signatures (Invited)

    NASA Astrophysics Data System (ADS)

    Atekwana, E. A.

    2013-12-01

    Geophysical techniques such as seismic, magnetic and electrical techniques have historically played a major role in oil exploration. Their main use has been for delineation basin geometry, structures and hydrocarbon traps and for understanding the subsurface stratigraphy. Their use for investigating microbial processes has only recently been recognized over the last decade resulting in the development of biogeophysics as a frontier research area which bridges the fields of environmental microbiology, biogeochemistry, geomicrobiology. Recent biogeophysical studies have demonstrated the potential of geophysical technologies to (1) probe the presence of microbial cells and biofilms in subsurface geologic media, (2) investigate the interactions between microorganisms and subsurface geologic media, (3) assess biogeochemical transformations, biomineralization, and biogeochemical reaction rates, and (4) investigate the alteration of physical properties of subsurface geologic media induced by microorganisms. The unique properties of geophysical datasets (e.g. non-invasive data acquisition, spatially continuous properties retrieved) make them attractive for probing microbial processes affecting fate and transport of contaminants. This presentation will provide an updated understanding of major controls on geophysical signatures by highlighting some of the important advancements in biogeophysical studies at hydrocarbon contaminated environments. Important challenges that provide an opportunity for further research in this new field will also be examined.

  4. 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.

  5. Long-term biogeochemical impacts of liming the ocean

    NASA Astrophysics Data System (ADS)

    Ilyina, T.; Wolf-Gladrow, D.; Munhoven, G.; Heinze, C.

    2011-12-01

    Fossil fuel CO2 emissions result in large-scale long-term perturbations in seawater chemistry. Oceans take up atmospheric CO2, and several geo-engineering approaches have been suggested to mitigate impacts of CO2 emissions and resulting ocean acidification that are based on this property. One of them is to enhance weathering processes to remove atmospheric CO2. This method involves dissolving rocks (i.e. limestone) or adding strong bases (i.e. calcium hydroxide) in the upper ocean and is termed as liming the oceans. The net effect of this approach is to increase ocean alkalinity, thereby increasing the oceanic capacity to store anthropogenic CO2. Another effect of adding alkalinity would be to drive seawater to higher pH values and thus counteract the ongoing ocean acidification. However, whereas adding bases only alter alkalinity of seawater, dissolution of carbonates perturb both, alkalinity and dissolved inorganic carbon budgets. Thus, on longer time scales, these two methods will likely have different biogeochemical effects in the ocean. Here we test enduring implications of the two approaches for marine carbon cycle using the global ocean biogeochemical model HAMOCC. In our model scenarios we add alkalinity in the amounts proportional to fossil fuel emissions. We compare the long-term effectiveness of the two geo-engineering approaches to decrease atmospheric CO2.

  6. BIOGEOCHEMICAL GRADIENTS AS A FRAMEWORK FOR UNDERSTANDING WASTE SITE EVOLUTION

    SciTech Connect

    Denham, M; Karen Vangelas, K

    2008-10-17

    The migration of biogeochemical gradients is a useful framework for understanding the evolution of biogeochemical conditions in groundwater at waste sites contaminated with metals and radionuclides. This understanding is critical to selecting sustainable remedies and evaluating sites for monitored natural attenuation, because most attenuation mechanisms are sensitive to geochemical conditions such as pH and redox potential. Knowledge of how gradients in these parameters evolve provides insights into the behavior of contaminants with time and guides characterization, remedy selection, and monitoring efforts. An example is a seepage basin site at the Savannah River Site in South Carolina where low-level acidic waste has seeped into groundwater. The remediation of this site relies, in part, on restoring the natural pH of the aquifer by injecting alkaline solutions. The remediation will continue until the pH up-flow of the treatment zone increases to an acceptable value. The time required to achieve this objective depends on the time it takes the trailing pH gradient, the gradient separating the plume from influxing natural groundwater, to reach the treatment zone. Predictions of this length of time will strongly influence long-term remedial decisions.

  7. 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.

  8. Subsurface Biogeochemical Research FY11 Second Quarter Performance Measure

    SciTech Connect

    Scheibe, Timothy D.

    2011-03-31

    The Subsurface Biogeochemical Research (SBR) Long Term Measure for 2011 under the Performance Assessment Rating Tool (PART) measure is to "Refine subsurface transport models by developing computational methods to link important processes impacting contaminant transport at smaller scales to the field scale." The second quarter performance measure is to "Provide a report on computational methods linking genome-enabled understanding of microbial metabolism with reactive transport models to describe processes impacting contaminant transport in the subsurface." Microorganisms such as bacteria are by definition small (typically on the order of a micron in size), and their behavior is controlled by their local biogeochemical environment (typically within a single pore or a biofilm on a grain surface, on the order of tens of microns in size). However, their metabolic activity exerts strong influence on the transport and fate of groundwater contaminants of significant concern at DOE sites, in contaminant plumes with spatial extents of meters to kilometers. This report describes progress and key findings from research aimed at integrating models of microbial metabolism based on genomic information (small scale) with models of contaminant fate and transport in aquifers (field scale).

  9. Biogeochemical fluxes through the Strait of Otranto (Eastern Mediterranean)

    NASA Astrophysics Data System (ADS)

    Civitarese, G.; Gačić, M.; Vetrano, A.; Boldrin, A.; Bregant, D.; Rabitti, S.; Souvermezoglou, E.

    1998-06-01

    A series of seasonal cruises and Eulerian current measurements in the Otranto Strait were carried out to study the biogeochemical characteristics of the strait and to estimate the exchange of water, dissolved and particulate matter between the Adriatic and the Ionian Sea. Analysis of data shows that on an annual scale, the Adriatic Sea exports dissolved nutrients (nitrate and phosphate) to the Ionian, and imports particulate organic carbon and nitrogen. Estimate of the mean annual water flux for the first time based on direct Eulerian current measurements gives value of 0.9 Sv that is appreciably higher than those found in literature. Calculations of the ratio of new and total primary production based on an annual phosphate subsurface export suggest that the trophic status of the Adriatic Sea on the whole is close to that of an oligotrophic sea. From the biogeochemical distributions obtained, an active role for the Adriatic in supporting the well-known N:P ratio anomaly of the Mediterranean is hy pothesized. Further studies are needed to estimate the contribution of the dissolved organic forms to the nutrient exchanges through the strait, and to establish the total budget of N and P in the Adriatic Sea.

  10. Nitrogen and Sulfur Deposition Effects on Forest Biogeochemical Processes.

    NASA Astrophysics Data System (ADS)

    Goodale, C. L.

    2014-12-01

    Chronic atmospheric deposition of nitrogen and sulfur have widely ranging biogeochemical consequences in terrestrial ecosystems. Both N and S deposition can affect plant growth, decomposition, and nitrous oxide production, with sometimes synergistic and sometimes contradictory responses; yet their separate effects are rarely isolated and their interactive biogeochemical impacts are often overlooked. For example, S deposition and consequent acidification and mortality may negate stimulation of plant growth induced by N deposition; decomposition can be slowed by both N and S deposition, though through different mechanisms; and N2O production may be stimulated directly by N and indirectly by S amendments. Recent advances in conceptual models and whole-ecosystem experiments provide novel means for disentangling the impacts of N and S in terrestrial ecosystems. Results from a new whole-ecosystem N x S- addition experiment will be presented in detail, examining differential response of tree and soil carbon storage to N and S additions. These results combine with observations from a broad array of long-term N addition studies, atmospheric deposition gradients, stable isotope tracer studies, and model analyses to inform the magnitude, controls, and stability of ecosystem C storage in response to N and S addition.

  11. Global changes in biogeochemical cycles in response to human activities

    NASA Technical Reports Server (NTRS)

    Moore, Berrien, III; Melillo, Jerry

    1994-01-01

    The main objective of our research was to characterize biogeochemical cycles at continental and global scales in both terrestrial and aquatic ecosystems. This characterization applied to both natural ecosystems and those disturbed by human activity. The primary elements of interest were carbon and nitrogen and the analysis sought to quantify standing stocks and dynamic cycling processes. The translocation of major nutrients from the terrestrial landscape to the atmosphere (via trace gases) and to fluvial systems (via leaching, erosional losses, and point source pollution) were of particular importance to this study. Our aim was to develop the first generation of Earth System Models. Our research was organized around the construction and testing of component biogeochemical models which treated terrestrial ecosystem processes, aquatic nutrient transport through drainage basins, and trace gas exchanges at the continental and global scale. A suite of three complementary models were defined within this construct. The models were organized to operate at a 1/2 degree latitude by longitude level of spatial resolution and to execute at a monthly time step. This discretization afforded us the opportunity to understand the dynamics of the biosphere down to subregional scales, while simultaneously placing these dynamics into a global context.

  12. A flexible numerical component to simulate surface runoff transport and biogeochemical processes through dense vegetation

    NASA Astrophysics Data System (ADS)

    Munoz-Carpena, R.; Perez-Ovilla, O.

    2012-12-01

    Methods to estimate surface runoff pollutant removal using dense vegetation buffers (i.e. vegetative filter strips) usually consider a limited number of factors (i.e. filter length, slope) and are in general based on empirical relationships. When an empirical approach is used, the application of the model is limited to those conditions of the data used for the regression equations. The objective of this work is to provide a flexible numerical mechanistic tool to simulate dynamics of a wide range of surface runoff pollutants through dense vegetation and their physical, chemical and biological interactions based on equations defined by the user as part of the model inputs. A flexible water quality model based on the Reaction Simulation Engine (RSE) modeling component is coupled to a transport module based on the traditional Bubnov -Galerkin finite element method to solve the advection-dispersion-reaction equation using the alternating split-operator technique. This coupled transport-reaction model is linked to the VFSMOD-W (http://abe.ufl.edu/carpena/vfsmod) program to mechanistically simulate mobile and stabile pollutants through dense vegetation based on user-defined conceptual models (differential equations written in XML language as input files). The key factors to consider in the creation of a conceptual model are the components in the buffer (i.e. vegetation, soil, sediments) and how the pollutant interacts with them. The biogeochemical reaction component was tested successfully with laboratory and field scale experiments. One of the major advantages when using this tool is that the pollutant transport and removal thought dense vegetation is related to physical and biogeochemical process occurring within the filter. This mechanistic approach increases the range of use of the model to a wide range of pollutants and conditions without modification of the core model. The strength of the model relies on the mechanistic approach used for simulating the removal of

  13. Biogeochemical responses of the carbon cycle to natural and human perturbations: Past, present, and future

    SciTech Connect

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

    1999-07-01

    In the past three centuries, human perturbations of the environment have affected the biogeochemical behavior of the global carbon cycle and that of the other three nutrient elements closely coupled to carbon: nitrogen, phosphorus, and sulfur. The partitioning of anthropogenic CO{sub 2} among its various sinks in the past, for the present, and for projections into the near future is controlled by the interactions of these four elemental cycles within the major environmental domains of the land, atmosphere, coastal oceanic zone, and open ocean. The authors analyze the past, present, and future behavior of the global carbon cycle using the Terrestrial-Ocean-aTmosphere Ecosystem Model (TOTEM), a unique process-based model of the four global coupled biogeochemical cycles of carbon, nitrogen, phosphorus, and sulfur. They find that during the past 300 yrs, anthropogenic CO{sub 2} was mainly stored in the atmosphere and in the open ocean. Human activities on land caused an enhanced loss of mass from the terrestrial organic matter reservoirs (phytomass and humus) mainly through deforestation and consequently increased humus remineralization, erosion, and transport to the coastal margins by rivers and runoff. Photosynthetic uptake by the terrestrial phytomass was enhanced owing to fertilization by increasing atmospheric CO{sub 2} concentrations and supported by nutrients remineralized from organic matter. TOTEM results indicate that through most of the past 300 yrs, the loss of C from deforestation and other land-use activities was greater than the gain from the enhanced photosynthetic uptake. Since pre-industrial time (since 1700), the net flux of CO{sub 2} from the coastal waters has decreased by 40%, from 0.20 Gt C/yr to 0.12 Gt C/yr. TOTEM analyses of atmospheric CO{sub 2} concentrations for the 21st century were based on the fossil-fuel emission projections of IPCC (business as usual scenario) and of the more restrictive UN 1997 Kyoto Protocol. By the mid-21st century

  14. Enhanced biogeochemical cycling and subsequent reduction of hydraulic conductivity associated with soil-layer interfaces in the vadose zone

    PubMed Central

    Hansen, David J.; McGuire, Jennifer T.; Mohanty, Binayak P.

    2013-01-01

    Biogeochemical dynamics in the vadose zone are poorly understood due to the transient nature of chemical and hydrologic conditions, but are nonetheless critical to understanding chemical fate and transport. This study explored the effects of a soil layer on linked geochemical, hydrological, and microbiological processes. Three laboratory soil columns were constructed: a homogenized medium-grained sand, a homogenized organic-rich loam, and a sand-over-loam layered column. Upward and downward infiltration of water was evaluated during experiments to simulate rising water table and rainfall events respectively. In-situ collocated probes measured soil water content, matric potential, and Eh while water samples collected from the same locations were analyzed for Br−, Cl−, NO3−, SO42−, NH4+, Fe2+, and total sulfide. Compared to homogenous columns, the presence of a soil layer altered the biogeochemistry and water flow of the system considerably. Enhanced biogeochemical cycling was observed in the layered column over the texturally homogeneous soil columns. Enumerations of iron and sulfate reducing bacteria showed 1-2 orders of magnitude greater community numbers in the layered column. Mineral and soil aggregate composites were most abundant near the soil-layer interface; the presence of which, likely contributed to an observed order-of-magnitude decrease in hydraulic conductivity. These findings show that quantifying coupled hydrologic-biogeochemical processes occurring at small-scale soil interfaces is critical to accurately describing and predicting chemical changes at the larger system scale. Findings also provide justification for considering soil layering in contaminant fate and transport models because of its potential to increase biodegradation and/or slow the rate of transport of contaminants. PMID:22031578

  15. Estuarine Biogeochemical Dynamics of Nutrients and Organic Carbon in the Columbia River: Observing Transformations Using a Biogeochemical Sensor Network

    NASA Astrophysics Data System (ADS)

    Needoba, J. A.; Peterson, T. D.; Riseman, S.; Wilkin, M.; Baptista, A. M.

    2015-12-01

    The Columbia River estuary is an ecosystem dominated by both a large river discharge and strong tidal forcing that creates fast currents, intense and variable physical stratification, low water residence times, and large gradients in salinity, temperature and water quality across the river to ocean boundary. Assessing ecosystem function and biogeochemical cycling in this environment is hampered by the inherent variability in both temporal and spatial timescales. In recent years the NSF Science and Technology Center for Coastal Margin Observation and Prediction has established a comprehensive in situ observation network that spans the estuarine gradient and captures variability associated with tides, diel cycles, episodic events, and seasonal changes in the river and ocean end-members. Here we describe the major patterns of variability in nitrate, orthophosphate, fluorescent dissolved organic carbon and related variables that demonstrate the dominant physical forcing and the biogeochemical hotspots within the ecosystem. These hotspots include intertidal lateral bays, the tidal freshwater river, and the estuarine turbidity maxima. Improved understanding of the role of these estuarine hotspots has informed ecosystem stewardship activities related to juvenile salmon survival, hypoxia, and food web structure.

  16. 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.

  17. 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

  18. Linking Soil and Sediment Properties for research on Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Kuhn, N. J.

    2012-04-01

    Conventional perspectives on soil erosion include the on-site damage to soil and reductions in crop yield, as well as the resulting off-site effects on water quality, runoff and sediment loads in rivers. Our evolving understanding of the Earth System has added a new dimension to the role of soil erosion within the global geochemical cycles. First, the relevance of soil as a nutrient and Carbon (C) pool was recognized. Initially, the role of soils in the global C cycle was largely considered to be limited to a vertical exchange of greenhouse house gases (GHG) between vegetation, soil and atmosphere and thus mostly studied by soil scientists, plant ecologists and climatologists. Even Critical Zone research focused mostly on weathering and regolith properties and ignored lateral fluxes of dissolved or particulate organic matter. Since the late 1990s, a wider role of soils in biogeochemical cycles has emerged. Recent estimates place the lateral movement of C between soil and sediment pools in terrestrial ecosystems (including rivers and lakes) at approximately 0.6 to 1.5 Gt per year. Some of the eroded C is replaced by photosynthesis from the atmosphere, but at a cost of additional emissions, for example due to fertilizer production. The long-term fate of the eroded and deposited soil organic matter is subject to an open debate and suffers from a lack of reliable spatial information on lateral C fluxes and its subsequent fate in terrestrial ecosystems. The connection between soil C pool, GHG emissions and erosion illustrates the relevance of surface processes for the C fluxes between Earth's spheres. Accordingly, soil is now considered as mobile system to make accurate predictions about the consequences of global change for terrestrial biogeochemical cycles and climate feedbacks. This expanded perspective on soils as dynamic pool of weathering regolith, sediment, nutrients and C at the interface between the geospheres requires the analysis of relevant soil properties

  19. Linking soil and sediment properties for research on biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Kuhn, Nikolaus J.

    2013-04-01

    Conventional perspectives on soil erosion include the on-site damage to soil and reductions in crop yield, as well as the resulting off-site effects on water quality, runoff and sediment loads in rivers. Our evolving understanding of the Earth System has added a new dimension to the role of soil erosion within the global geochemical cycles. First, the relevance of soil as a nutrient and Carbon (C) pool was recognized. Initially, the role of soils in the global C cycle was largely considered to be limited to a vertical exchange of greenhouse house gases (GHG) between vegetation, soil and atmosphere and thus mostly studied by soil scientists, plant ecologists and climatologists. Even Critical Zone research focused mostly on weathering and regolith properties and ignored lateral fluxes of dissolved or particulate organic matter. Since the late 1990s, a wider role of soils in biogeochemical cycles has emerged. Recent estimates place the lateral movement of C between soil and sediment pools in terrestrial ecosystems (including rivers and lakes) at approximately 0.6 to 1.5 Gt per year. Some of the eroded C is replaced by photosynthesis from the atmosphere, but at a cost of additional emissions, for example due to fertilizer production. The long-term fate of the eroded and deposited soil organic matter is subject to an open debate and suffers from a lack of reliable spatial information on lateral C fluxes and its subsequent fate in terrestrial ecosystems. The connection between soil C pool, GHG emissions and erosion illustrates the relevance of surface processes for the C fluxes between Earth's spheres. Accordingly, soil is now considered as mobile system to make accurate predictions about the consequences of global change for terrestrial biogeochemical cycles and climate feedbacks. This expanded perspective on soils as dynamic pool of weathering regolith, sediment, nutrients and C at the interface between the geospheres requires the analysis of relevant soil properties

  20. 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...

  1. Biogeochemical responses following coral mass spawning on the Great Barrier Reef: pelagic-benthic coupling

    NASA Astrophysics Data System (ADS)

    Wild, C.; Jantzen, C.; Struck, U.; Hoegh-Guldberg, O.; Huettel, M.

    2008-03-01

    This study quantified how the pulse of organic matter from the release of coral gametes triggered a chain of pelagic and benthic processes during an annual mass spawning event on the Australian Great Barrier Reef. Particulate organic matter (POM) concentrations in reef waters increased by threefold to 11-fold the day after spawning and resulted in a stimulation of pelagic oxygen consumption rates that lasted for at least 1 week. Water column microbial communities degraded the organic carbon of gametes of the broadcast-spawning coral Acropora millepora at a rate of >15% h-1, which is about three times faster than the degradation rate measured for larvae of the brooding coral Stylophora pistillata. Stable isotope signatures of POM in the water column reflected the fast transfer of organic matter from coral gametes into higher levels of the food chain, and the amount of POM reaching the seafloor immediately increased after coral spawning and then tailed-off in the next 2 weeks. Short-lasting phytoplankton blooms developed within a few days after the spawning event, indicating a prompt recycling of nutrients released through the degradation of spawning products. These data show the profound effects of coral mass spawning on the reef community and demonstrate the tight recycling of nutrients in this oligotrophic ecosystem.

  2. 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.

  3. Spatial dynamics of biogeochemical processes in the St. Louis River freshwater estuary

    EPA Science Inventory

    In the Great Lakes, river-lake transition zones within freshwater estuaries are hydrologically and biogeochemically dynamic areas that regulate nutrient and energy fluxes between rivers and Great Lakes. The goal of our study was to characterize the biogeochemical properties of th...

  4. Aqueous complexation reactions governing the rate and extent of biogeochemical U(VI) reduction

    SciTech Connect

    Kemner, K.M.; Kelly, S.D.; Brooks, Scott C.; Dong, Wenming; Carroll, Sue; Fredrickson, James K.

    2006-06-01

    The proposed research will elucidate the principal biogeochemical reactions that govern the concentration, chemical speciation, and reactivity of the redox-sensitive contaminant uranium. The results will provide an improved understanding and predictive capability of the mechanisms that govern the biogeochemical reduction of uranium in subsurface environments.

  5. INTERACTIVE EFFECTS OF SOLAR UV RADIATION AND CLIMATE CHANGE ON BIOGEOCHEMICAL CYCLING

    EPA Science Inventory

    This paper assesses research on the interactions of UV radiation (280-400 nm) and global climate change with global biogeochemical cycles at the Earth's surface. The effects of UV-B (280-315 nm), which are dependent on the stratospheric ozone layer, on biogeochemical cycles are o...

  6. 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

  7. Differential leaflet mortality may influence biogeochemical cycling following tropical cyclones.

    PubMed

    Marler, Thomas E; Ferreras, Ulysses

    2014-01-01

    Intensity of tropical cyclones is expected to increase in the coming century, and an improved understanding of their influence on biogeochemical cycles would benefit ecologists and conservationists. We studied the November 2013 Typhoon Haiyan damage to observe that numerous examples of partial leaf necrosis on intact leaves of trees in the Cycadaceae and Arecaceae families resulted, leaving behind a copious amount of arboreal dead leaf material attached to live leaves. The decay process of this form of arboreal litter has not been previously studied. When compared with decay of ground litter or detached litter suspended in the canopy, we predict the decay process of this form of arboreal litter will include increased photooxidation, leaching, and comminution by detritivorous insects and mites; but decreased catabolism of organic molecules by saprophytic organisms.

  8. Andreae is New Editor of Global Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Andreae, Meinrat O.

    2004-10-01

    As the incoming editor of Global Biogeochemical Cycles, I would like to introduce myself and my ideas for the journal to Eos readers and to current and potential GBC authors. I've had a somewhat ``roaming'' scientific evolution, coming from ``straight'' chemistry through hard-rock geochemistry to chemical oceanography, the field in which I did my Ph.D. I taught marine chemistry at Florida State University for a number of years, and developed an interest in ocean/atmosphere interactions and atmospheric chemistry. In 1987 I took on my present job at the Max Planck Institute for Chemistry, in Mainz, Germany, and, after leaving the seacoast, my interests shifted to interactions between the terrestrial biosphere and atmosphere, including the role of vegetation fires. My present focus is on the role of biogenic aerosols and biomass smoke in regulating cloud properties and influencing climate.

  9. Phototrophic bacteria and their role in the biogeochemical sulfur cycle

    NASA Technical Reports Server (NTRS)

    Trueper, H. G.

    1985-01-01

    An essential step that cannot be bypassed in the biogeochemical cycle of sulfur today is dissimilatory sulfate reduction by anaerobic bacteria. The enormous amounts of sulfides produced by these are oxidized again either anaerobically by phototrophic bacteria or aerobically by thiobacilli and large chemotrophic bacteria (Beggiatoa, Thiovulum, etc.). Phototrophic bacteria use sulfide, sulfur, thiosulfate, and sulfite as electron donors for photosynthesis. The most obvious intermediate in their oxidative sulfur metabolism is a long chain polysulfide that appears as so called sulfur globules either inside (Chromatiaceae) or outside (Ectothiorhodospiraceae, Chlorobiaceae, and some of the Rhodospirillaceae) the cells. The assimilation of sulfur compounds in phototrophic bacteria is in principle identical with that of nonphototrophic bacteria. However, the Chlorobiaceae and some of the Chromatiaceae and Rhodospirillaceae, unable to reduce sulfate, rely upon reduced sulfur for biosynthetic purposes.

  10. 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.

  11. Deriving forest fire ignition risk with biogeochemical process modelling☆

    PubMed Central

    Eastaugh, C.S.; Hasenauer, H.

    2014-01-01

    Climate impacts the growth of trees and also affects disturbance regimes such as wildfire frequency. The European Alps have warmed considerably over the past half-century, but incomplete records make it difficult to definitively link alpine wildfire to climate change. Complicating this is the influence of forest composition and fuel loading on fire ignition risk, which is not considered by purely meteorological risk indices. Biogeochemical forest growth models track several variables that may be used as proxies for fire ignition risk. This study assesses the usefulness of the ecophysiological model BIOME-BGC's ‘soil water’ and ‘labile litter carbon’ variables in predicting fire ignition. A brief application case examines historic fire occurrence trends over pre-defined regions of Austria from 1960 to 2008. Results show that summer fire ignition risk is largely a function of low soil moisture, while winter fire ignitions are linked to the mass of volatile litter and atmospheric dryness. PMID:26109905

  12. Isotopic constraints on biogeochemical cycling of copper in the ocean.

    PubMed

    Takano, Shotaro; Tanimizu, Masaharu; Hirata, Takafumi; Sohrin, Yoshiki

    2014-12-05

    Trace elements and their isotopes are being actively studied as powerful tracers in the modern ocean and as proxies for the palaeocean. Although distributions and fractionations have been reported for stable isotopes of dissolved Fe, Cu, Zn and Cd in the ocean, the data remain limited and only preliminary explanations have been given. Copper is of great interest because it is either essential or toxic to organisms and because its distribution reflects both biological recycling and scavenging. Here we present new isotopic composition data for dissolved Cu (δ(65)Cu) in seawater and rainwater. The Cu isotopic composition in surface seawater can be explained by the mixing of rain, river and deep seawater. In deep seawater, δ(65)Cu becomes heavier with oceanic circulation because of preferential scavenging of the lighter isotope ((63)Cu). In addition, we constrain the marine biogeochemical cycling of Cu using a new box model based on Cu concentrations and δ(65)Cu.

  13. The biogeochemical cycle of iron in the ocean

    NASA Astrophysics Data System (ADS)

    Boyd, P. W.; Ellwood, M. J.

    2010-10-01

    Advances in iron biogeochemistry have transformed our understanding of the oceanic iron cycle over the past three decades: multiple sources of iron to the ocean were discovered, including dust, coastal and shallow sediments, sea ice and hydrothermal fluids. This new iron is rapidly recycled in the upper ocean by a range of organisms; up to 50% of the total soluble iron pool is turned over weekly in this way in some ocean regions. For example, bacteria dissolve particulate iron and at the same time release compounds - iron-binding ligands - that complex with iron and therefore help to keep it in solution. Sinking particles, on the other hand, also scavenge iron from solution. The balance between these supply and removal processes determines the concentration of dissolved iron in the ocean. Whether this balance, and many other facets of the biogeochemical cycle, will change as the climate warms remains to be seen.

  14. A GIS approach to conducting biogeochemical research in wetlands

    NASA Technical Reports Server (NTRS)

    Brannon, David P.; Irish, Gary J.

    1985-01-01

    A project was initiated to develop an environmental data base to address spatial aspects of both biogeochemical cycling and resource management in wetlands. Specific goals are to make regional methane flux estimates and site specific water level predictions based on man controlled water releases within a wetland study area. The project will contribute to the understanding of the Earth's biosphere through its examination of the spatial variability of methane emissions. Although wetlands are thought to be one of the primary sources for release of methane to the atmosphere, little is known about the spatial variability of methane flux. Only through a spatial analysis of methane flux rates and the environmental factors which influence such rates can reliable regional and global methane emissions be calculated. Data will be correlated and studied from Landsat 4 instruments, from a ground survey of water level recorders, precipitation recorders, evaporation pans, and supplemental gauges, and from flood gate water release; and regional methane flux estimates will be made.

  15. Reconstructing disturbances and their biogeochemical consequences over multiple timescales

    USGS Publications Warehouse

    McLauchlan, Kendra K.; Higuera, Philip E.; Gavin, Daniel G.; Perakis, Steven S.; Mack, Michelle C.; Alexander, Heather; Battles, John; Biondi, Franco; Buma, Brian; Colombaroli, Daniele; Enders, Sara K.; Engstrom, Daniel R.; Hu, Feng Sheng; Marlon, Jennifer R.; Marshall, John; McGlone, Matt; Morris, Jesse L.; Nave, Lucas E.; Shuman, Bryan; Smithwick, Erica A.H.; Urrego, Dunia H.; Wardle, David A.; Williams, Christopher J.; Williams, Joseph J.

    2014-01-01

    Ongoing changes in disturbance regimes are predicted to cause acute changes in ecosystem structure and function in the coming decades, but many aspects of these predictions are uncertain. A key challenge is to improve the predictability of postdisturbance biogeochemical trajectories at the ecosystem level. Ecosystem ecologists and paleoecologists have generated complementary data sets about disturbance (type, severity, frequency) and ecosystem response (net primary productivity, nutrient cycling) spanning decadal to millennial timescales. Here, we take the first steps toward a full integration of these data sets by reviewing how disturbances are reconstructed using dendrochronological and sedimentary archives and by summarizing the conceptual frameworks for carbon, nitrogen, and hydrologic responses to disturbances. Key research priorities include further development of paleoecological techniques that reconstruct both disturbances and terrestrial ecosystem dynamics. In addition, mechanistic detail from disturbance experiments, long-term observations, and chronosequences can help increase the understanding of ecosystem resilience.

  16. Relating hydraulic conductivity and hyporheic zone biogeochemical processing to conserve and restore river ecosystem services.

    PubMed

    Mendoza-Lera, Clara; Datry, Thibault

    2017-02-01

    River management practices commonly attempt to improve habitat and ecological functioning (e.g. biogeochemical processing or retention of pollutants) by restoring hydrological exchange with the hyporheic zone (i.e. hyporheic flow) in an effort to increase mass transfer of solutes (nutrients, carbon and electron acceptors such as oxygen or nitrate). However, even when hyporheic flow is increased, often no significant changes in biogeochemical processing are detected. Some of these apparent paradox result from the simplistic assumption that there is a direct relationship between hyporheic flow and biogeochemical processing. We propose an alternative conceptual model that hyporheic flow is non-linearly related with biogeochemical processing. Based on the different solute mass transfer and area available for colonization among hydraulic conductivities, we hypothesize that biogeochemical processing in the hyporheic zone follows a Gaussian function depending on hyporheic hydraulic conductivity. After presenting the conceptual model and its domain of application, we discuss the potential implications, notably for river restoration and further hyporheic research.

  17. Biogeochemical evolution of a landfill leachate plume, Norman, Oklahoma

    USGS Publications Warehouse

    Cozzarelli, Isabelle M.; Bohlke, Johnkarl F.; Masoner, Jason R.; Breit, George N.; Lorah, Michelle M.; Tuttle, Michele L.W.; Jaeschke, Jeanne B.

    2011-01-01

    Leachate from municipal landfills can create groundwater contaminant plumes that may last for decades to centuries. The fate of reactive contaminants in leachate-affected aquifers depends on the sustainability of biogeochemical processes affecting contaminant transport. Temporal variations in the configuration of redox zones downgradient from the Norman Landfill were studied for more than a decade. The leachate plume contained elevated concentrations of nonvolatile dissolved organic carbon (NVDOC) (up to 300 mg/L), methane (16 mg/L), ammonium (650 mg/L as N), iron (23 mg/L), chloride (1030 mg/L), and bicarbonate (4270 mg/L). Chemical and isotopic investigations along a 2D plume transect revealed consumption of solid and aqueous electron acceptors in the aquifer, depleting the natural attenuation capacity. Despite the relative recalcitrance of NVDOC to biodegradation, the center of the plume was depleted in sulfate, which reduces the long-term oxidation capacity of the leachate-affected aquifer. Ammonium and methane were attenuated in the aquifer relative to chloride by different processes: ammonium transport was retarded mainly by physical interaction with aquifer solids, whereas the methane plume was truncated largely by oxidation. Studies near plume boundaries revealed temporal variability in constituent concentrations related in part to hydrologic changes at various time scales. The upper boundary of the plume was a particularly active location where redox reactions responded to recharge events and seasonal water-table fluctuations. Accurately describing the biogeochemical processes that affect the transport of contaminants in this landfill-leachate-affected aquifer required understanding the aquifer's geologic and hydrodynamic framework.

  18. Watershed Management and Mercury Biogeochemical Cycling in Lake Zapotlan, Mexico

    NASA Astrophysics Data System (ADS)

    Malczyk, E. A.; Branfireun, B. A.

    2009-05-01

    Lake Zapotlan is an endorheic subtropical eutrophic lake located in Jalisco State, Mexico. The lake supports a small but important local fishery for carp (Cyprinus sp.) and tilapia (Oreochromis sp.) and is an internationally recognized RAMSAR site. Very little research exists in these regions regarding mercury biogeochemical cycling. The lake receives considerable untreated municipal wastewater discharge that is elevated in inorganic total mercury (250-800 ng Hg/L) and organic methylmercury (3-10 ng CH3Hg+/L). The lake is also located on an active fault zone near an active volcano which may cause natural mercury enrichment. To assess a mercury risk to the commercial fishery we investigated the distribution of total inorganic mercury and organic methylmercury in waters, sediments, and fish tissues of the lake, surrounding wetlands, and incoming waters. Although there were high concentrations of inorganic mercury entering the lake in wastewater and seasonal tributary stream flow inputs, average concentrations in lake surface waters (3 ng Hg/L) and sediments (50 ng Hg/gdw) were relatively low. Average concentrations of total inorganic mercury were an order of magnitude higher in water (70 ng Hg/L) and sediment (245 ng Hg/gdw) in wetlands receiving the wastewater discharges. Mercury loading to the main body of the lake is likely reduced by these wetland buffer zones which allow mercury bound to particulate matter to settle out. A similar pattern was seen with respect to methylmercury concentrations. Average concentrations of methylmercury in lake surface water (below detect) and sediment (0.1 ng/gdw) were lower than in impounded wetlands (1 ng CH3Hg+/L, 0.7 ng CH3Hg+/gdw). Mercury concentrations in tilapia (3.5 ng/g) and carp (8 ng/g) from the commercial catch were found to be low in mercury; likely due to a combination of physiological, biogeochemical, and ecological factors.

  19. Drought-induced Changes in Dryland Soil Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Belnap, J.; Darrouzet-Nardi, A.; Duniway, M.; Ferrenberg, S.; Hoover, D. L.; Reed, S.

    2015-12-01

    Approximately 41% of Earth´s terrestrial surface consists of drylands and they are an important biome on all continents. Although dryland biota would be expected to be drought adapted, they can be surprisingly vulnerable to extended dry periods with subsequent consequences for biogeochemical cycles. Biological soil crusts, constituting up to 70% of the living cover in these regions, are important in these cycles. They fix both N and C, providing a significant percentage of regional and global inputs. However, extended drought reduces both types of inputs, as biocrusts are only metabolically active when wet, yet losses continue even when soils are dry. In addition, extended droughts can result in their mortality. The amount of net soil C exchange of biocrusted soils is controversial, but in SE Utah, soil C uptake only occurred when only when soils were wet. As soils are infrequently wet, annual balances were negative during the 2 year study and with future extended droughts or increased temperatures that reduce soil moisture, these losses will become even greater. As with C, N fixation also requires biocrusts be wet and thus inputs decline with extended drought or higher temperatures that both reduce input and result in lichen and cyanobacterial mortality. And similarly, N losses continue even when soils are dry. Loss of biocrust mosses can profoundly alter N cycles. Desert plants are also affected by drought: in plots where experimental drought was imposed, plants had lower photosynthetic rates and higher leaf C:N, which will likely affect productivity and decomposition rates and thus have further impacts on soil biogeochemical cycles.

  20. 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.

  1. 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

  2. Incorporating urban infrastructure into biogeochemical assessment of urban tropical streams in Puerto Rico

    NASA Astrophysics Data System (ADS)

    Potter, J.; McDowell, W. H.; Daley, M. L.; Helton, A. M.

    2012-12-01

    Urban development alters catchment hydrology and the subsequent delivery of solutes to streams and downstream ecosystems. The extent to which the impacts of urban development vary by biome is uncertain, and the impacts are poorly understood in tropical catchments. In a previous study (Helton et al. 2011), downstream changes in nitrogen (N) in the highly urbanized Rio Piedras catchment in Puerto Rico (42% urban land use) were found to be greater than predicted (23%) in a simple river network model that uses land use and in-stream N loss to predict spatial patterns in N fluxes. Here we evaluate the deviations of the biogeochemical patterns in this urban catchment through synoptic sampling of hydrology and water quality collected annually at approximately 40 sites over 8 years (2004 - 2011) coupled with spatial analysis of the urban infrastructure in the catchment. Results indicate that urbanization leads to an increase in most solute concentrations measured (DOC, DON, NH4, PO4), but not NO3. The lack of urban influence on NO3 is inconsistent with findings in other biomes, but consistent with previous studies in Puerto Rico. Conservative tracers (Cl and F) indicate that the source of the organic solutes increase is likely from sewage inputs. We suggest that stream nutrient cycling models that assume topographically driven flow accumulation need to be changed in urban catchments to include different delivery mechanisms such as sewer and water lines, especially in tropical regions where this infrastructure is often inadequate.

  3. 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.

  4. Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions

    PubMed Central

    Lamba, Sanjay; Bera, Soumen; Rashid, Mubasher; Medvinsky, Alexander B.; Acquisti, Claudia; Li, Bai-Lian

    2017-01-01

    Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics. We show that alternative biochemical pathways play a key role in keeping nitrogen conversion and conservation properties invariant in fluctuating environments. Our results indicate that the biochemical network holds inherent adaptive capacity to stabilize ammonium and nitrate availability, and that the bistability in the formation of ammonium is linked to the transient upregulation of the amo-hao mediated nitrification pathway. The bistability is maintained by a pair of complementary subsystems acting as either source or sink type systems in response to soil redox fluctuations. It is further shown how elevated anthropogenic pressure has the potential to break down the stability of the system, altering substantially ammonium and nitrate availability in the soil, with dramatic effects on biodiversity. PMID:28280580

  5. 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.

  6. Biogeochemical and ecosystem responses of the North Atlantic subtropical gyre to atmospheric forcing and climate variability

    NASA Astrophysics Data System (ADS)

    Bates, N. R.; Lomas, M. L.; Johnson, R. J.; Knap, A. H.

    2003-04-01

    Long-term oceanographic time-series near Bermuda and Hawaii have generated new insights about the responses of and interactions between ocean biogeochemistry, ecosystem dynamics, and physical variability of the atmosphere and climate. Over the last 14 years, physical, chemical and biological measurements have been collected each month at the Bermuda Atlantic Time-series Study (BATS) site in the oligotrophic subtropical gyre of the North Atlantic. On seasonal time-scales, complex interactions between physical forcing, nutrient and carbon cycling, and biological community dynamics have been demonstrated. On interannual time-scales, significant coupling has been observed between physical forcing, which is linked to modes of climate variability such as the North Atlantic Oscillation (NAO), and variability of biogeochemical and ecosystem community structure. Much of the variance of temperature, mixed layer depth, nutrient inputs, primary production, and phytoplankton community dynamics appear related to NAO variability. Over the past decade, a shift in the fate of the carbon fixed during primary production has occurred. This change in the partitioning of primary production correlates with changes in phytoplankton community structure and variability in NAO phase. The magnitude and temporal variability of the oceanic sink for atmospheric CO2 in the subtropical gyre also appears linked to NAO variability and it's influence on shallow mode water formation in the northern fringes of the subtropical gyre.

  7. The biogeochemical role of baleen whales and krill in Southern Ocean nutrient cycling.

    PubMed

    Ratnarajah, Lavenia; Bowie, Andrew R; Lannuzel, Delphine; Meiners, Klaus M; Nicol, Stephen

    2014-01-01

    The availability of micronutrients is a key factor that affects primary productivity in High Nutrient Low Chlorophyll (HNLC) regions of the Southern Ocean. Nutrient supply is governed by a range of physical, chemical and biological processes, and there are significant feedbacks within the ecosystem. It has been suggested that baleen whales form a crucial part of biogeochemical cycling processes through the consumption of nutrient-rich krill and subsequent defecation, but data on their contribution are scarce. We analysed the concentration of iron, cadmium, manganese, cobalt, copper, zinc, phosphorus and carbon in baleen whale faeces and muscle, and krill tissue using inductively coupled plasma mass spectrometry. Metal concentrations in krill tissue were between 20 thousand and 4.8 million times higher than typical Southern Ocean HNLC seawater concentrations, while whale faecal matter was between 276 thousand and 10 million times higher. These findings suggest that krill act as a mechanism for concentrating and retaining elements in the surface layer, which are subsequently released back into the ocean, once eaten by whales, through defecation. Trace metal to carbon ratios were also higher in whale faeces compared to whale muscle indicating that whales are concentrating carbon and actively defecating trace elements. Consequently, recovery of the great whales may facilitate the recycling of nutrients via defecation, which may affect productivity in HNLC areas.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  9. 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

  10. 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

  11. Rn as a geochemical tool for estimating residence times in the hyporheic zone and its application to biogeochemical processes

    NASA Astrophysics Data System (ADS)

    Gilfedder, Benjamin; Dörner, Sebastian; Ebertshäuser, Marlene Esther; Glaser, Barbara; Klug, Maria; Pittroff, Marco; Pieruschka, Ines; Waldemer, Carolin

    2014-05-01

    The hyporheic zone is at the interface between groundwater and surface water systems. It is also often a geochemical and redox boundary between typically reduced groundwater and oxic surface water. It experiences dynamic physical and chemical conditions as both groundwater fluxes and surface water levels vary in time and space. This can be particularly important for processes such as biogeochemical processing of nutrients and carbon. There has recently been an increasing focus on coupling residence times of surface water in the hyporheic zone with biogeochemical reactions. While geochemical profiles can be readily measured using established geochemical sampling techniques (e.g. peepers), quantifying surface water residence times and flow paths within the hyporheic zone is more elusive. The nobel gas radon offers a method for quantification of surface water residence times in the hyporheic zone. Radon activities are typically low in surface waters due to degassing to the atmosphere and decay. However once the surface water flows into the hyporheic zone radon accumulates along the flow path due to emanation from the sediments. Using simple analytical equations the water residence time can be calculated based on the difference between measured 222Rn activities and 222Rn activities at secular equilibrium, with a maximum limit of about 20 days (depending on measurement precision). Rn is particularly suited to residence time measurements in the hyporheic zone since it does not require addition of tracers to the stream nor does it require complex simulations and assumptions (such as 1D vertical flow) as for temperature measurements. As part of the biogeochemistry course at the University of Bayreuth, we have investigated the coupling of redox processes and water residence times in the hyporheic zone using 222Rn as a tracer for residence time. Of particular interest were nitrate and sulfate reduction and methane and CO2 production. Measurements were made in a sandy section

  12. 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.

  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. Coupled surface and subsurface flow modeling of natural hillslopes in the Aburrá Valley (Medellín, Colombia)

    NASA Astrophysics Data System (ADS)

    Blessent, Daniela; Barco, Janet; Temgoua, André Guy Tranquille; Echeverrri-Ramirez, Oscar

    2017-03-01

    Numerical results are presented of surface-subsurface water modeling of a natural hillslope located in the Aburrá Valley, in the city of Medellín (Antioquia, Colombia). The integrated finite-element hydrogeological simulator HydroGeoSphere is used to conduct transient variably saturated simulations. The objective is to analyze pore-water pressure and saturation variation at shallow depths, as well as volumes of water infiltrated in the porous medium. These aspects are important in the region of study, which is highly affected by soil movements, especially during the high-rain seasons that occur twice a year. The modeling exercise considers rainfall events that occurred between October and December 2014 and a hillslope that is currently monitored because of soil instability problems. Simulation results show that rainfall temporal variability, mesh resolution, coupling length, and the conceptual model chosen to represent the heterogeneous soil, have a noticeable influence on results, particularly for high rainfall intensities. Results also indicate that surface-subsurface coupled modeling is required to avoid unrealistic increase in hydraulic heads when high rainfall intensities cause top-down saturation of soil. This work is a first effort towards fostering hydrogeological modeling expertise that may support the development of monitoring systems and early landslide warning in a country where the rainy season is often the cause of hydrogeological tragedies associated with landslides, mud flow or debris flow.

  15. Coupled surface and subsurface flow modeling of natural hillslopes in the Aburrá Valley (Medellín, Colombia)

    NASA Astrophysics Data System (ADS)

    Blessent, Daniela; Barco, Janet; Temgoua, André Guy Tranquille; Echeverrri-Ramirez, Oscar

    2016-10-01

    Numerical results are presented of surface-subsurface water modeling of a natural hillslope located in the Aburrá Valley, in the city of Medellín (Antioquia, Colombia). The integrated finite-element hydrogeological simulator HydroGeoSphere is used to conduct transient variably saturated simulations. The objective is to analyze pore-water pressure and saturation variation at shallow depths, as well as volumes of water infiltrated in the porous medium. These aspects are important in the region of study, which is highly affected by soil movements, especially during the high-rain seasons that occur twice a year. The modeling exercise considers rainfall events that occurred between October and December 2014 and a hillslope that is currently monitored because of soil instability problems. Simulation results show that rainfall temporal variability, mesh resolution, coupling length, and the conceptual model chosen to represent the heterogeneous soil, have a noticeable influence on results, particularly for high rainfall intensities. Results also indicate that surface-subsurface coupled modeling is required to avoid unrealistic increase in hydraulic heads when high rainfall intensities cause top-down saturation of soil. This work is a first effort towards fostering hydrogeological modeling expertise that may support the development of monitoring systems and early landslide warning in a country where the rainy season is often the cause of hydrogeological tragedies associated with landslides, mud flow or debris flow.

  16. Connections between physical, optical and biogeochemical processes in the Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Xiu, Peng; Chai, Fei

    2014-03-01

    A new biogeochemical model has been developed and coupled to a three-dimensional physical model in the Pacific Ocean. With the explicitly represented dissolved organic pools, this new model is able to link key biogeochemical processes with optical processes. Model validation against satellite and in situ data indicates the model is robust in reproducing general biogeochemical and optical features. Colored dissolved organic matter (CDOM) has been suggested to play an important role in regulating underwater light field. With the coupled model, physical and biological regulations of CDOM in the euphotic zone are analyzed. Model results indicate seasonal variability of CDOM is mostly determined by biological processes, while the importance of physical regulation manifests in the annual mean terms. Without CDOM attenuating light, modeled depth-integrated primary production is about 10% higher than the control run when averaged over the entire basin, while this discrepancy is highly variable in space with magnitudes reaching higher than 100% in some locations. With CDOM dynamics integrated in physical-biological interactions, a new mechanism by which physical processes affect biological processes is suggested, namely, physical transport of CDOM changes water optical properties, which can further modify underwater light field and subsequently affect the distribution of phytoplankton chlorophyll. This mechanism tends to occur in the entire Pacific basin but with strong spatial variability, implying the importance of including optical processes in the coupled physical-biogeochemical model. If ammonium uptake is sufficient to permit utilization of DOM, that is, UB∗⩾-U{U}/{U}-{(1-r_b)}/{RB}, then bacteria uptake of DOM has the form of FB=(1-r_b){U}/{RB}, bacteria respiration, SB=r_b×U, remineralization by bacteria, EB=UC{UN}/{UC}-{(1-r_b)}/{RB}. If EB > 0, then UB = 0; otherwise, UB = -EB. If there is insufficient ammonium, that is, UB∗<-U{U}/{U}-{(1-r_b)}/{RB}, then

  17. Biogeochemical and hydrological controls on fate and distribution of trace metals in oiled Gulf salt marshes

    NASA Astrophysics Data System (ADS)

    Keevan, J.; Natter, M.; Lee, M.; Keimowitz, A.; Okeke, B.; Savrda, C.; Saunders, J.

    2011-12-01

    carbon source for stimulating sulfate-reducing bacteria. The high sulfur levels, coupled with the low levels of iron, indicate that iron-reducing bacteria are outcompeted by sulfate reducers in oiled salt marshes. Moreover, pore-water pH values show a general increasing trend (ranging from 6.6 to 8.0) with depth, possibly reflecting the combined effects of bacterial sulfate reduction and saltwater intrusion at depth. Despite high levels of trace metals in bulk sediments, concentrations of trace metals dissolved in pore-waters are generally low. It is very likely that high organic matter content and bacterially-mediated sulfate reduction promote metal retention through the formation of sulfide solids. Framboidal pyrites, as well as other sulfides, have been identified, and are currently undergoing XRD, SEM, and EDAX analyses. Continued research is needed to monitor possible re-mobilization of trace metals in changing redox and biogeochemical conditions.

  18. 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

  19. BRIE: The Penn State Biogeochemical Research Initiative for Education

    NASA Astrophysics Data System (ADS)

    Freeman, K. H.; Brantley, S. L.; Brenchley, J.

    2003-12-01

    Few scientists are prepared to address the interdisciplinary challenges of biogeochemical research due to disciplinary differences in vocabulary, technique, and scientific paradigm. Thus scientists and engineers trained in traditional disciplines bring a restricted view to the study of environmental systems, which can limit their ability to exploit new techniques and opportunities for scientific advancement. Although the literature is effusive with enthusiasm for interdisciplinary approaches to biogeochemistry, there remains the basic difficulty of cross-training geological and biological scientists. The NSF-IGERT funded Biogeochemical Research Initiative for Education (BRIE) program at Penn State is specifically designed to break down both disciplinary and institutional barriers and it has fostered cross-disciplinary collaboration and training since 1999. Students and faculty are drawn from environmental engineering, geochemistry, soil science, chemistry and microbiology, and the program is regarded on the Penn State campus as a successful example of how interdisciplinary science can best be promoted. There are currently 23 Ph.D. students funded by the program, with an additional 7 affiliated students. At present, a total of 6 students have completed doctoral degrees, and they have done so within normal timeframes. The program is "discipline-plus," whereby students enroll in traditional disciplinary degree programs, and undertake broad training via 12 credits of graduate coursework in other departments. Students are co-advised by faculty from different disciplines, and engage in interdisciplinary research facilitated by research "credit cards." Funding is available for international research experiences, travel to meetings, and other opportunities for professional development. Students help institutionalize interdisciplinary training by designing and conducting a teaching module that shares their expertise with a class in another department or discipline

  20. Mesoscale Variations of Biogeochemical Properties in the Sargasso Sea

    NASA Technical Reports Server (NTRS)

    McGillicuddy Dennis J., Jr.; Johnson, R.; Siegel, D. A.; Michaels, A. F.; Bates, N. R.; Knap, A. H.

    1999-01-01

    A mesoscale resolution biogeochemical survey was carried out in the vicinity of the US Joint Global Ocean Flux Study Bermuda Atlantic Time-Series Study (BATS) site during the summer of 1996. Real-time nowcasting and forecasting of the flow field facilitated adaptive sampling of several eddy features in the area. Variations in upper ocean nutrient and pigment distributions were largely controlled by vertical isopycnal displacements associated with the mesoscale field. Shoaling density surfaces tended to introduce cold, nutrient-rich water into the euphotic zone, while deepening isopycnals displaced nutrient-depleted water downward. Chlorophyll concentration was generally enhanced in the former case and reduced in the latter. Eddy-induced upwelling at the base of the euphotic zone was affected by features of two different types captured in this survey: (1) a typical mid-ocean cyclone in which doming of the main thermocline raised the near-surface stratification upward; and (2) a mode water eddy composed of a thick lens of 18 C water, which pushed up the seasonal thermocline and depressed the main thermocline. Model hindcasts using all available data provide a four-dimensional context in which to interpret temporal trends at the BATS site and two other locations during the two weeks subsequent to the survey. Observed changes in near-surface structure at the BATS site included shoaling iscpycnals, increased nutrient availability at the base of the euphotic zone, and enhanced chlorophyll concentration within the euphotic zone. These trends are explicable in terms of a newly formed cyclone that impinged upon the site during this time period. These observations reveal that eddy upwelling has a demonstrable impact on the way in which the nitrate-density relationship changes with depth from the aphotic zone into the euphotic zone. A similar transition is present in the BATS record, suggesting that eddy-driven upwelling events are present in the time series of upper ocean

  1. Mesoscale Variations of Biogeochemical Properties in the Sargasso Sea

    NASA Technical Reports Server (NTRS)

    McGillicuddy, D. J.; Johnson, R.; Siegel, D. A.; Michaels, A. F.; Bates, N. R.; Knap, A. H.

    1999-01-01

    A mesoscale resolution biogeochemical survey was carried out in the vicinity of the U.S. Joint Global Ocean Flux Study Bermuda Atlantic Time-series Study (BATS) site during the summer of 1996. Real-time nowcasting and forecasting of the flow field facilitated adaptive sampling of several eddy features in the area. Variations in upper ocean nutrient and pigment distributions were largely controlled by vertical isopycnal displacements associated with the mesoscale field. Shoaling density surfaces tended to introduce cold, nutrient-rich water into the euphotic zone, while deepening isopycnals displaced nutrient-depleted water downward. Chlorophyll concentration was generally enhanced in the former case and reduced in the latter. Eddy-induced upwelling at the base of the euphotic zone was affected by features of two different types captured in this survey-, (1) a typical mid-ocean cyclone in which doming of the main thermocline raised the near-surface stratification upward and (2) a mode water eddy composed of a thick lens of 18C water, which pushed up the seasonal thermocline and depressed the main thermocline. Model hindcasts using all available data provide a four-dimensional context in which to interpret temporal trends at the BATS site and two other locations during the 2 weeks subsequent to the survey. Observed changes in near-surface structure at the BATS site included shoaling isopycnals, increased nutrient availability at the base of the euphotic zone, and enhanced chlorophyll concentration within the cuphotic zone. These trends are explicable in terms of a newly formed cyclone that impinged upon the site during this time period. These observations reveal that eddy upwelling has a demonstrable impact on the way in which the nitrate-density relationship changes with depth from the aphotic zone into the euphotic zone. A similar transition is present in the BATS record, suggesting that eddy-driven upwelling events are present in the time series of upper ocean

  2. Biogeochemical controls on metal behaviour in freshwater environments

    NASA Astrophysics Data System (ADS)

    Warren, Lesley A.; Haack, Elizabeth A.

    2001-08-01

    The biogeochemical controls on metal behaviour in aqueous environments involve complex linkages of biological, principally bacterially driven, and geochemical processes, which occur at both microscopic and macroscopic scales. The framework of aqueous surface chemistry and aquatic geochemistry continues to provide the foundations of the emerging paradigm: (1) metal behaviour (e.g., transport, toxicity, bioaccumulation) is governed by solid-solution reactions; (2) pH, ionic strength, redox potential, the types and concentrations of solution elements, and solid surfaces all interact to determine metal behaviour in any given system; (3) metal sorption reactions show both metal ion and solid surface specificity; (4) sorption reactions are dynamic and reversible; and (5) processes are at sufficient pseudo-equilibrium or dynamic steady state that thermodynamics can be applied to describe such reactions. Reactions controlling metal behaviour are increasingly modelled, with some success, using a variety of geochemical modelling approaches all based on this framework. However, not yet considered in the majority of these thermodynamic treatments of metal dynamics is that these reactions are highly influenced by biological factors, which will affect their location, magnitude and rate. The extent of this influence will be largely driven by microbial ecology, and thus, a fundamental identification and mechanistic understanding of how these factors will drive the geochemistry of a particular system is required. The lack of substantive biogeochemical understanding stems from the fact that the field of environmental microbiology, with its crossover to environmental geochemistry, has only recently begun to receive attention. The developing evidence strongly underscores the impact of bacterial reactions for a number of highly relevant processes related to metal dynamics such as solid solution partitioning, mineral precipitation and dissolution reactions, and intense changes in system

  3. Aqueous Complexation Reactions Governing the Rate and Extent of Biogeochemical U(VI) Reduction

    SciTech Connect

    Scott C. Brooks; Wenming Dong; Sue Carroll; Jim Fredrickson; Ken Kemner; Shelly Kelly

    2006-06-01

    The proposed research will elucidate the principal biogeochemical reactions that govern the concentration, chemical speciation, and reactivity of the redox-sensitive contaminant uranium. The results will provide an improved understanding and predictive capability of the mechanisms that govern the biogeochemical reduction of uranium in subsurface environments. In addition, the work plan is designed to: (1) Generate fundamental scientific understanding on the relationship between U(VI) chemical speciation and its susceptibility to biogeochemical reduction reactions. ? Elucidate the controls on the rate and extent of contaminant reactivity. (2) Provide new insights into the aqueous and solid speciation of U(VI)/U(IV) under representative groundwater conditions.

  4. Aqueous Complexation Reactions Governing the Rate and Extent of Biogeochemical U(VI) Reduction

    SciTech Connect

    Scott C. Brooks; Wenming Dong; Sue Carroll; James K. Fredrickson; Kenneth M. Kemner; Shelly D. Kelly

    2006-06-01

    The proposed research will elucidate the principal biogeochemical reactions that govern the concentration, chemical speciation, and reactivity of the redox-sensitive contaminant uranium. The results will provide an improved understanding and predictive capability of the mechanisms that govern the biogeochemical reduction of uranium in subsurface environments. In addition, the work plan is designed to: (1) Generate fundamental scientific understanding on the relationship between U(VI) chemical speciation and its susceptibility to biogeochemical reduction reactions. (2) Elucidate the controls on the rate and extent of contaminant reactivity. (3) Provide new insights into the aqueous and solid speciation of U(VI)/U(IV) under representative groundwater conditions.

  5. [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.

  6. Biogeochemical effects of seawater restoration to diked salt marshes

    USGS Publications Warehouse

    Portnoy, J.W.; Giblin, A.E.

    1997-01-01

    We conducted greenhouse microcosm experiments to examine the biogeochemical effects of restoring seawater to historically diked Cape Cod salt marshes. Peat cores from both seasonally flooded and drained diked marshes were waterlogged with seawater, and porewater chemistry was subsequently monitored for 21 mo. The addition of seawater to highly organic, seasonally flooded peat caused the death of freshwater wetland plants, 6-8 cm of sediment subsidence, and increased N and P mineralization. Also, sulfides and alkalinity increased 10-fold, suggesting accelerated decomposition by sulfate reduction. Addition of seawater to the low-organic-content acidic peat from the drained marsh increased porewater pH, alkalinity, PO4-P, and Fe(II), which we attribute to the reestablishment of SO4 and Fe(III) mineral reduction. Increased cation exchange contributed to 6-fold increases in dissolved Fe(II) and Al and 60-fold increases in NH4-N within 6 mo of sail-nation. Seawater reintroductions to seasonally flooded diked marshes will cause porewater sulfides to increase, likely reducing the success of revegetation efforts. Sulfide toxicity is of less concern in resalinated drained peats because of the abundance of Fe(II) to precipitate sulfides, and of NH4-N to offset sulfide inhibition of N uptake. Restoration of either seasonally flooded or drained diked marshes could stimulate potentially large nutrient and Fe(II) releases, which could in turn increase primary production and lower oxygen in receiving waters. These findings suggest that tidal restoration be gradual and carefully monitored.

  7. The genomic potential of Marinobacter aquaeolei - A biogeochemical opportunotroph

    NASA Astrophysics Data System (ADS)

    Singer, E.; Webb, E.; Nelson, W.; Heidelberg, J.; Edwards, K. J.

    2009-12-01

    The family of Marinobacter is one of the most ubiquitous in the ocean. Members of this genus are found throughout the water column, in the deep sea, and are often associated with hydrothermal plume particles and marine snow. They are known to degrade hydrocarbons and show some extremophilic lifestyles, such as pyschrophily, oligotrophy and halotolerance. This study has determined the genomic potential of one particular strain - Marinobacter aquaeolei VT8, which relies on a very large set of survival strategies. Isolated from an oil well in Southern Vietnam, M. aquaeolei was known to be a facultative anaerobe with the ability to utilize various carbon sources. Fitting with these observations, genome annotation has revealed: four variations of the TCA cycle, complete pathways of glycolysis and the degradation of more complex hydrocarbons (including octane oxidation and cyclohexanol degradation), alternative phosphorous and nitrogen sources, genes for the use of nitrate and sulfate as electron acceptors as well as complete pathways for sulfite oxidation, denitrification and iron oxidation. The versatility and interrelatedness of these metabolic potentials coin the opportunistic character of M. aquaeolei and help to more completely define the biogeochemical niche of the genus.

  8. Feedbacks between hydrological heterogeneity and bioremediation induced biogeochemical transformations

    SciTech Connect

    Englert, A.; Hubbard, S.S.; Williams, K.H.; Li, L.; Steefel, C.I.

    2009-04-15

    For guiding optimal design and interpretation of in-situ treatments that strongly perturb subsurface systems, knowledge about the spatial and temporal patterns of mass transport and reaction intensities are important. Here, a procedure was developed and applied to time-lapse concentrations of a conservative tracer (bromide), an injected amendment (acetate) and reactive species (iron(II), uranium(VI) and sulfate) associated with two field scale biostimulation experiments, which were conducted successively at the same field location over two years. The procedure is based on a temporal moment analysis approach that relies on a streamtube approximation. The study shows that biostimulated reactions can be considerably influenced by subsurface hydrological and geochemical heterogeneities: the delivery of bromide and acetate and the intensity of the sulfate reduction is interpreted to be predominantly driven by the hydrological heterogeneity, while the intensity of the iron reduction is interpreted to be primarily controlled by the geochemical heterogeneity. The intensity of the uranium(VI) reduction appears to be impacted by both the hydrological and geochemical heterogeneity. Finally, the study documents the existence of feedbacks between hydrological heterogeneity and remediation-induced biogeochemical transformations at the field scale, particularly the development of precipitates that may cause clogging and flow rerouting.

  9. 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.

  10. Dust from southern Africa: rates of emission and biogeochemical properties

    NASA Astrophysics Data System (ADS)

    Bhattachan, A.; D'Odorico, P.; Zobeck, T. M.; Okin, G. S.; Dintwe, K.

    2012-12-01

    The stabilized linear dunefields in the southern Kalahari show signs of reactivation due to reduced vegetation cover owing to drought and/or overgrazing. It has been demonstrated with a laboratory dust generator that the southern Kalahari soils are good emitters of dust and that large-scale dune reactivation can potentially make the region an important dust source in the relatively low-dust Southern Hemisphere. We show that emergence of the southern Kalahari as a new dust source may affect ocean biogeochemistry as the soils are rich in soluble iron and the dust from the southern Kalahari commonly reaches the Southern Ocean. We investigate the biogeochemical properties of the fine fraction of soil from the Kalahari dunes and compare them to those of currently active dust sources such as the Makgadikgadi and the Etosha pans as well as other smaller pans in the region. Using field measurements of sediment fluxes and satellite images, we calculate the rates of dust emission from the southern Kalahari under different land cover scenarios. To assess the reversibility of dune reactivation in the southern Kalahari, we investigate the resilience of dunefield vegetation by looking at changes in soil nutrients, fine soil fractions, and seed bank in areas affected by intense denudation.

  11. First-order exchange coefficient coupling for simulating surface water-groundwater interactions: Parameter sensitivity and consistency with a physics-based approach

    USGS Publications Warehouse

    Ebel, B.A.; Mirus, B.B.; Heppner, C.S.; VanderKwaak, J.E.; Loague, K.

    2009-01-01

    Distributed hydrologic models capable of simulating fully-coupled surface water and groundwater flow are increasingly used to examine problems in the hydrologic sciences. Several techniques are currently available to couple the surface and subsurface; the two most frequently employed approaches are first-order exchange coefficients (a.k.a., the surface conductance method) and enforced continuity of pressure and flux at the surface-subsurface boundary condition. The effort reported here examines the parameter sensitivity of simulated hydrologic response for the first-order exchange coefficients at a well-characterized field site using the fully coupled Integrated Hydrology Model (InHM). This investigation demonstrates that the first-order exchange coefficients can be selected such that the simulated hydrologic response is insensitive to the parameter choice, while simulation time is considerably reduced. Alternatively, the ability to choose a first-order exchange coefficient that intentionally decouples the surface and subsurface facilitates concept-development simulations to examine real-world situations where the surface-subsurface exchange is impaired. While the parameters comprising the first-order exchange coefficient cannot be directly estimated or measured, the insensitivity of the simulated flow system to these parameters (when chosen appropriately) combined with the ability to mimic actual physical processes suggests that the first-order exchange coefficient approach can be consistent with a physics-based framework. Copyright ?? 2009 John Wiley & Sons, Ltd.

  12. Global Biogeochemical Changes at Both Ends of the Proterozoic: Insights from Phosphorites

    NASA Astrophysics Data System (ADS)

    Papineau, D.

    2010-04-01

    The striking similarities in biogeochemical evolution between the Paleo- and Neoproterozoic are discussed in light of the two oldest phosphogenic events in Earth's history and their relations to the step-wise rise of atmospheric oxygen.

  13. SEASONAL VARIATION IN THE BIOGEOCHEMICAL CYCLING OF SESTON IN GRAND TRAVERSE BAY, LAKE MICHIGAN. (R825151)

    EPA Science Inventory

    This study describes the biogeochemical cycling of seston in Grand Traverse Bay, Lake Michigan. Seston was characterized by carbon and nitrogen elemental and isotopic abundances. Fluorescence, temperature, light transmittance, and concentrations of dissolved inorganic nitrogen we...

  14. 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...

  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. Understanding Biogeochemical Transformations Of Trace Elements In Multi Metal-Rich Geomaterials Under Stimulated Redox Conditions

    EPA Science Inventory

    Natural and anthropogenic influences on hydrological conditions can induce periodic or long-term reduced conditions in geologic materials. Such conditions can cause significant impacts on biogeochemical processes of trace elements in subsurface or near surface environments. The...

  17. Diel biogeochemical processes and their effect on the aqueous chemistry of streams: A review

    USGS Publications Warehouse

    Nimick, David A.; Gammons, Christopher H.; Parker, Stephen R.

    2011-01-01

    This review summarizes biogeochemical processes that operate on diel, or 24-h, time scales in streams and the changes in aqueous chemistry that are associated with these processes. Some biogeochemical processes, such as those producing diel cycles of dissolved O2 and pH, were the first to be studied, whereas processes producing diel concentration cycles of a broader spectrum of chemical species including dissolved gases, dissolved inorganic and organic carbon, trace elements, nutrients, stable isotopes, and suspended particles have received attention only more recently. Diel biogeochemical cycles are interrelated because the cyclical variations produced by one biogeochemical process commonly affect another. Thus, understanding biogeochemical cycling is essential not only for guiding collection and interpretation of water-quality data but also for geochemical and ecological studies of streams. Expanded knowledge of diel biogeochemical cycling will improve understanding of how natural aquatic environments function and thus lead to better predictions of how stream ecosystems might react to changing conditions of contaminant loading, eutrophication, climate change, drought, industrialization, development, and other factors.

  18. 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

  19. South Florida wetlands ecosystem; biogeochemical processes in peat

    USGS Publications Warehouse

    Orem, William; ,

    1996-01-01

    The South Florida wetlands ecosystem is an environment of great size and ecological diversity (figs. 1 and 2). The landscape diversity and subtropical setting of this ecosystem provide a habitat for an abundance of plants and wildlife, some of which are unique to South Florida. South Florida wetlands are currently in crisis, however, due to the combined effects of agriculture, urbanization, and nearly 100 years of water management. Serious problems facing this ecosystem include (1) phosphorus contamination producing nutrient enrichment, which is causing changes in the native vegetation, (2) methylmercury contamination of fish and other wildlife, which poses a potential threat to human health, (3) changes in the natural flow of water in the region, resulting in more frequent drying of wetlands, loss of organic soils, and a reduction in freshwater flow to Florida Bay, (4) hypersalinity, massive algal blooms, and seagrass loss in parts of Florida Bay, and (5) a decrease in wildlife populations, especially those of wading birds. This U.S. Geological Survey (USGS) project focuses on the role of organic-rich sediments (peat) of South Florida wetlands in regulating the concentrations and impact of important chemical species in the environment. The cycling of carbon, nitrogen, phosphorus, and sulfur in peat is an important factor in the regulation of water quality in the South Florida wetlands ecosystem. These elements are central to many of the contamination issues facing South Florida wetlands, such as nutrient enrichment, mercury toxicity, and loss of peat. Many important chemical and biological reactions occur in peat and control the fate of chemical species in wetlands. Wetland scientists often refer to these reactions as biogeochemical processes, because they are chemical reactions usually mediated by microorganisms in a geological environment. An understanding of the biogeochemical processes in peat of South Florida wetlands will provide a basis for evaluating the

  20. Silicon biogeochemical processes in a large river (Cauvery, India)

    NASA Astrophysics Data System (ADS)

    Kameswari Rajasekaran, Mangalaa; Arnaud, Dapoigny; Jean, Riotte; Sarma Vedula, V. S. S.; Nittala, S. Sarma; Sankaran, Subramanian; Gundiga Puttojirao, Gurumurthy; Keshava, Balakrishna; Cardinal, Damien

    2016-04-01

    Silicon (Si), one of the key nutrients for diatom growth in ocean, is principally released during silicate weathering on continents and then exported by rivers. Phytoplankton composition is determined by the availability of Si relative to other nutrients, mainly N and P, which fluxes in estuarine and coastal systems are affected by eutrophication due to land use and industrialization. In order to understand the biogeochemical cycle of Si and its supply to the coastal ocean, we studied a tropical monsoonal river from Southern India (Cauvery) and compare it with other large and small rivers. Cauvery is the 7th largest river in India with a basin covering 85626 sq.km. The major part of the basin (˜66%) is covered by agriculture and inhabited by more than 30 million inhabitants. There are 96 dams built across the basin. As a consequence, 80% of the historical discharge is diverted, mainly for irrigation (Meunier et al. 2015). This makes the Cauvery River a good example of current anthropogenic pressure on silicon biogeochemical cycle. We measured amorphous silica contents (ASi) and isotopic composition of dissolved silicon (δ30Si-DSi) in the Cauvery estuary, including freshwater end-member and groundwater as well as along a 670 km transect along the river course. Other Indian rivers and estuaries have also been measured, including some less impacted by anthropogenic pressure. The average Cauvery δ30Si signature just upstream the estuary is 2.21±0.15 ‰ (n=3) which is almost 1‰ heavier than the groundwater isotopic composition (1.38±0.03). The δ30Si-DSi of Cauvery water is also almost 1‰ heavier than the world river supply to the ocean estimated so far and 0.4‰ heavier than other large Indian rivers like Ganges (Frings et al 2015) and Krishna. On the other hand, the smaller watersheds (Ponnaiyar, Vellar, and Penna) adjacent to Cauvery also display heavy δ30Si-DSi. Unlike the effect of silicate weathering, the heavy isotopic compositions in the river

  1. Biogeochemical cycling in terrestrial ecosystems of the Caatinga Biome.

    PubMed

    Menezes, R S C; Sampaio, E V S B; Giongo, V; Pérez-Marin, A M

    2012-08-01

    The biogeochemical cycles of C, N, P and water, the impacts of land use in the stocks and flows of these elements and how they can affect the structure and functioning of Caatinga were reviewed. About half of this biome is still covered by native secondary vegetation. Soils are deficient in nutrients, especially N and P. Average concentrations of total soil P and C in the top layer (0-20 cm) are 196 mg kg(-1) and 9.3 g kg(-1), corresponding to C stocks around 23 Mg ha(-1). Aboveground biomass of native vegetation varies from 30 to 50 Mg ha(-1), and average root biomass from 3 to 12 Mg ha(-1). Average annual productivities and biomass accumulation in different land use systems vary from 1 to 7 Mg ha(-1) year(-1). Biological atmospheric N2 fixation is estimated to vary from 3 to 11 kg N ha(-1) year-1 and 21 to 26 kg N ha(-1) year(-1) in mature and secondary Caatinga, respectively. The main processes responsible for nutrient and water losses are fire, soil erosion, runoff and harvest of crops and animal products. Projected climate changes in the future point to higher temperatures and rainfall decreases. In face of the high intrinsic variability, actions to increase sustainability should improve resilience and stability of the ecosystems. Land use systems based on perennial species, as opposed to annual species, may be more stable and resilient, thus more adequate to face future potential increases in climate variability. Long-term studies to investigate the potential of the native biodiversity or adapted exotic species to design sustainable land use systems should be encouraged.

  2. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

    PubMed

    Roux, Simon; Brum, Jennifer R; Dutilh, Bas E; Sunagawa, Shinichi; Duhaime, Melissa B; Loy, Alexander; Poulos, Bonnie T; Solonenko, Natalie; Lara, Elena; Poulain, Julie; Pesant, Stéphane; Kandels-Lewis, Stefanie; Dimier, Céline; Picheral, Marc; Searson, Sarah; Cruaud, Corinne; Alberti, Adriana; Duarte, Carlos M; Gasol, Josep M; Vaqué, Dolors; Bork, Peer; Acinas, Silvia G; Wincker, Patrick; Sullivan, Matthew B

    2016-09-29

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they

  3. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    NASA Astrophysics Data System (ADS)

    2016-09-01

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where

  4. Biogeochemical indicators of elevated nitrogen deposition in semiarid Mediterranean ecosystems

    PubMed Central

    Ochoa-Hueso, Raúl; Arróniz-Crespo, María; Bowker, Mathew A.; Maestre, Fernando T.; Pérez-Corona, M. Esther; Theobald, Mark R.; Vivanco, Marta G.; Manrique, Esteban

    2015-01-01

    Nitrogen (N) deposition has doubled the natural N inputs received by ecosystems through biological N-fixation and is currently a global problem that is affecting the Mediterranean regions. We evaluated the existing relationships between increased atmospheric N deposition and biogeochemical indicators related to soil chemical factors and cryptogam species across semiarid central, southern and eastern Spain. The cryptogam species studied were the biocrust-forming Pleurochaete squarrosa (moss) and Cladonia foliacea (lichen). Sampling sites were chosen in Quercus coccifera (kermes oak) shrublands and Pinus halepensis (Aleppo pine) forests to cover a range of inorganic N deposition representative of the levels found in the Iberian Peninsula (between 4.4 and 8.1 kg N ha−1 yr−1). We extended the ambient N deposition gradient by including experimental plots to which N had been added for three years at rates of 10, 20 and 50 kg N ha−1 yr−1. Overall, N deposition (extant plus simulated) increased soil inorganic N availability and caused soil acidification. Nitrogen deposition increased phosphomonoesterase (PME) enzyme activity and PME:nitrate reductase (NR) ratio in both species, whereas the NR activity was reduced only in the moss. Responses of PME and NR activities were attributed to an induced N to phosphorus imbalance and to N saturation, respectively. When only considering the ambient N deposition, soil organic C and N contents were positively related to N deposition, a response driven by pine forests. The PME:NR ratios of the moss were better predictors of N deposition rates than PME or NR activities alone in shrublands, whereas no correlation between N deposition and the lichen physiology was observed. We conclude that integrative physiological measurements, such as PME:NR ratios, measured on sensitive species such as P. squarrosa, can provide useful data for national-scale biomonitoring programs, whereas soil acidification and soil C and N storage could be

  5. 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.

  6. Biogeochemical indicators of elevated nitrogen deposition in semiarid Mediterranean ecosystems.

    PubMed

    Ochoa-Hueso, Raúl; Arróniz-Crespo, María; Bowker, Matthew A; Maestre, Fernando T; Pérez-Corona, M Esther; Theobald, Mark R; Vivanco, Marta G; Manrique, Esteban

    2014-09-01

    Nitrogen (N) deposition has doubled the natural N inputs received by ecosystems through biological N fixation and is currently a global problem that is affecting the Mediterranean regions. We evaluated the existing relationships between increased atmospheric N deposition and biogeochemical indicators related to soil chemical factors and cryptogam species across semiarid central, southern, and eastern Spain. The cryptogam species studied were the biocrust-forming species Pleurochaete squarrosa (moss) and Cladonia foliacea (lichen). Sampling sites were chosen in Quercus coccifera (kermes oak) shrublands and Pinus halepensis (Aleppo pine) forests to cover a range of inorganic N deposition representative of the levels found in the Iberian Peninsula (between 4.4 and 8.1 kg N ha(-1) year(-1)). We extended the ambient N deposition gradient by including experimental plots to which N had been added for 3 years at rates of 10, 20, and 50 kg N ha(-1) year(-1). Overall, N deposition (extant plus simulated) increased soil inorganic N availability and caused soil acidification. Nitrogen deposition increased phosphomonoesterase (PME) enzyme activity and PME/nitrate reductase (NR) ratio in both species, whereas the NR activity was reduced only in the moss. Responses of PME and NR activities were attributed to an induced N to phosphorus imbalance and to N saturation, respectively. When only considering the ambient N deposition, soil organic C and N contents were positively related to N deposition, a response driven by pine forests. The PME/NR ratios of the moss were better predictors of N deposition rates than PME or NR activities alone in shrublands, whereas no correlation between N deposition and the lichen physiology was observed. We conclude that integrative physiological measurements, such as PME/NR ratios, measured on sensitive species such as P. squarrosa, can provide useful data for national-scale biomonitoring programs, whereas soil acidification and soil C and N storage

  7. Biogeochemical characterisation of a coal tar distillate plume.

    PubMed

    Williams, G M; Pickup, R W; Thornton, S F; Lerner, D N; Mallinson, H E; Moore, Y; White, C

    2001-12-15

    The distillation of acidified coal tars for up to 50 years has given rise to a phenol plume approximately 500 m long, 50 m deep and containing up to 15 g l(-1) dissolved organic carbon (DOC) in the Triassic Sandstones aquifer. A conceptual biogeochemical model based on chemical and microbiological analysis of groundwater samples has been developed as a preliminary to more detailed studies of the controls on natural attenuation. While the development of redox zones and the production of methane and carbon dioxide provide evidence of natural attenuation, it appears that degradation is slow. The existence of sulphate in the plume indicates that this electron acceptor has not been depleted and that consequently methanogenesis is probably limited. Based on a simple estimate of sulphate input concentration, a half-life of about 15 years has been estimated for sulphate reduction. Geochemical modelling predicts that increased alkalinity within the plume has not led to carbonate precipitation, and thus within the limits of accuracy of the measurement, alkalinity may reflect the degree of biodegradation. This implies a loss of around 18% of the DOC over a 30-year period. Despite limited degradation, microbial studies show that there are diverse microbial communities in the aquifer with the potential for both anaerobic and aerobic biodegradation. Microbial activity was found to be greatest at the leading edge of the plume where DOC concentrations are 60 mg l(-1) or less, but activity could still be observed in more contaminated samples even though cells could not be cultured. The study suggests that degradation may be limited by the high phenol concentrations within the core of the plume, but that once diluted by dispersion, natural attenuation may proceed. More detailed studies to confirm these initial findings are identified and form the basis of associated papers.

  8. Aquifer/aquitard interfaces: mixing zones that enhance biogeochemical reactions

    NASA Astrophysics Data System (ADS)

    McMahon, P. B.

    2001-01-01

    Several important biogeochemical reactions are known to occur near the interface between aquifer and aquitard sediments. These reactions include O2 reduction; denitrification; and Fe3+, SO42-, and CO2 (methanogenesis) reduction. In some settings, these reactions occur on the aquitard side of the interface as electron acceptors move from the aquifer into the electron-donor-enriched aquitard. In other settings, these reactions occur on the aquifer side of the interface as electron donors move from the aquitard into the electron-acceptor-enriched, or microorganism-enriched, aquifer. Thus, the aquifer/aquitard interface represents a mixing zone capable of supporting greater microbial activity than either hydrogeologic unit alone. The extent to which biogeochemical reactions proceed in the mixing zone and the width of the mixing zone depend on several factors, including the abundance and solubility of electron acceptors and donors on either side of the interface and the rate at which electron acceptors and donors react and move across the interface. Biogeochemical reactions near the aquifer/aquitard interface can have a substantial influence on the chemistry of water in aquifers and on the chemistry of sediments near the interface. Résumé. Il se produit au voisinage de l'interface entre les aquifères et les imperméables plusieurs réactions biogéochimiques importantes. Il s'agit des réactions de réduction de l'oxygène, de la dénitrification et de la réduction de Fe3+, SO42- et CO2 (méthanogenèse). Dans certaines situations, ces réactions se produisent du côté imperméable de l'interface, avec des accepteurs d'électrons qui vont de l'aquifère vers l'imperméable riche en donneurs d'électrons. Dans d'autres situations, ces réactions se produisent du côté aquifère de l'interface, avec des donneurs d'électrons qui se déplacent de l'imperméable vers l'aquifère riche en accepteurs d'électrons ou en microorganismes. Ainsi, l'interface aquif

  9. Influence of hydrological, biogeochemical and temperature transients on subsurface carbon fluxes in a flood plain environment

    SciTech Connect

    Arora, Bhavna; Spycher, Nicolas F.; Steefel, Carl I.; Molins, Sergi; Bill, Markus; Conrad, Mark E.; Dong, Wenming; Faybishenko, Boris; Tokunaga, Tetsu K.; Wan, Jiamin; Williams, Kenneth H.; Yabusaki, Steven B.

    2016-02-01

    Flood plains play a potentially important role in the global carbon cycle. The accumulation of organic matter in flood plains often induces the formation of chemically reduced groundwater and sediments along riverbanks. In this study, our objective is to evaluate the cumulative impact of such reduced zones, water table fluctuations, and temperature gradients on subsurface carbon fluxes in a flood plain at Rifle, Colorado located along the Colorado River. 2-D coupled variably-saturated, non-isothermal flow and biogeochemical reactive transport modeling was applied to improve our understanding of the abiotic and microbially mediated reactions controlling carbon dynamics at the Rifle site. Model simulations considering only abiotic reactions (thus ignoring microbial reactions) underestimated CO2 partial pressures observed in the unsaturated zone and severely underestimated inorganic (and overestimated organic) carbon fluxes to the river compared to simulations with biotic pathways. Both model simulations and field observations highlighted the need to include microbial contributions from chemolithoautotrophic processes (e.g., Fe?2 and S-2 oxidation) to match locally-observed high CO2 concentrations above reduced zones. Observed seasonal variations in CO2 concentrations in the unsaturated zone could not be reproduced without incorporating temperature gradients in the simulations. Incorporating temperature fluctuations resulted in an increase in the annual groundwater carbon fluxes to the river by 170 % to 3.3 g m-2 d-1, while including water table variations resulted in an overall decrease in the simulated fluxes. We conclude that spatial microbial and redox zonation as well as temporal fluctuations of temperature and water table depth contribute significantly to subsurface carbon fluxes in flood plains and need to be represented appropriately in model simulations.

  10. Iron isotopes constrain biogeochemical redox cycling of iron and manganese in a Palaeoproterozoic stratified basin

    NASA Astrophysics Data System (ADS)

    Tsikos, Harilaos; Matthews, Alan; Erel, Yigal; Moore, John M.

    2010-09-01

    The Hotazel Formation in the uppermost stratigraphic portion of the Neoarchaean-Palaeoproterozoic Transvaal Supergroup of southern Africa is an unusual sedimentary sequence of banded iron-formation (BIF) intercalated with three manganese-rich layers. As such, it is a succession that holds great potential to offer a unique view of one of the most dramatic transitions in early Earth history — the switch to a full oxidative cycle in shallow oceans at ca. 2.3 Ga. We present iron isotope results from BIF and Mn-rich samples collected across the entire Hotazel sequence, with a view to constraining processes of biogeochemical redox cycling for both metals close to the transition from a reducing to an oxidizing ocean-atmosphere system. The recorded de-coupling of Fe- and Mn reduction during anaerobic organic carbon cycling in the Hotazel strata, suggests that manganese became an important electron acceptor in stratified marine environments of the Palaeoproterozoic during periods of increased primary manganese precipitation relative to iron. Very low δ 57Fe values registered across the entire Hotazel sequence and especially in manganese-rich samples (-2.4 to -3.5‰) signify deposition of iron and manganese in a terminal, stratified aqueous reservoir that was depleted in the heavy iron isotopes. These isotopic signatures, in conjunction with the unusual endowment of the Hotazel sequence in manganese, are interpreted to have evolved by Rayleigh distillation processes during protracted deposition of Mn-poor BIFs as preserved in the lower stratigraphic portion of the Transvaal Supergroup (Kuruman and Griquatown BIFs). The unique end-member geochemical and isotopic characteristics of the Hotazel rocks may therefore constitute a potential link between the widespread deposition of BIF during the Neoarchaean and Palaeoproterozoic, and the postulated rise in atmospheric oxygen levels around 2.3 Ga ago.

  11. Genomic reconstruction of novel sediment phyla enlightens roles in sedimentary biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Baker, B.; Lazar, C.; Seitz, K.; Teske, A.; Hinrichs, K. U.; Dick, G.

    2015-12-01

    Estuaries are among the most productive habitats on the planet. Microbes in estuary sediments control the turnover of organic carbon, and the anaerobic cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments. We reconstructed 82 bacterial and 24 archaeal high-quality genomes from different redox regimes (sulfate-rich, sulfate-methane transition zone, and methane-rich zones) of estuary sediments. These bacteria belong to 23 distinct groups, including uncultured candidate phyla (eg. KSB1, TA06, and KD3-62), and three newly described phyla (WOR-1, and -2, and -3). The archaea encompass 8 widespread sediment lineages including MGB-D, RC-III and IV, Z7ME43, Parvarchaeota, Lokiarchoaeta (MBG-B), SAGMEG, Bathyarchaeota (groups MCG-1, -6, -7, and -15) and previously unrecognized deeply branched phylum "Thorarchaeota". The uncultured phyla mediate essential biogeochemical processes of the estuarine environment. Z7ME43 archaea have genes for S disproportionation (S0 reduction and thiosulfate reduction and oxidation). SAGMEG appear to be strict anaerobes capable of coupling CO/H2 oxidation to either S0 or nitrite reduction and have novel RubisCO genes for carbon fixation. Thorarchaeota contain pathways for acetate production from the degradation of detrital proteins and intermediate S cycling. Furthermore, the gene content of this group revealed links in the evolutionary histories of archaea and eukaryotes. This dataset extents our knowledge of the metabolic potential of several uncultured phyla. We were able to chart the flow of carbon and nutrients through the multiple layers of bacterial processing and reveal potential ecological interactions within the communities.

  12. Development of Arsenic and Iron Biogeochemical Gradients upon Anaerobiosis at Soil Aggregate Scale

    NASA Astrophysics Data System (ADS)

    Masue-Slowey, Y.; Pallud, C.; Bedore, P.; Tufano, K.; Fendorf, S.

    2008-12-01

    In aerated soils, As release is limited due to the strong interaction between As(V) and soil minerals. However, under anaerobic conditions, As desorption is stimulated by As(V) reduction to As(III) and reductive dissolution/transformation of Fe (hydr)oxides, common hosts of As. The effect of As(V) and Fe(III) reduction on As release has been extensively studied in laboratory batch and column systems; correlation of apparent Fe and As reduction, with concomitant release to pore water, has also been noted under field conditions. What remains unresolved is the coupling of biogeochemical and physical processes that ultimately control As transport within structured media such as soils. Soils are heterogeneous porous media that are comprised of individual aggregates having pores that are dominated by diffusive (aggregate interiors) or advective (aggregate exteriors) transport. As a consequence of physical and chemical differences in the interior and the exterior of aggregates, As(III,V) and Fe(II,III) chemical gradients develop. Here, we examine As release from constructed aggregates exposed to fluctuating redox conditions. Artificial aggregates were made with As(V) adsorbed ferrihydrite-coated sand homogeneously inoculated with Shewanella sp. ANA-3 (model As(V) and Fe(III) reducer) and then fused using an agarose binder into spheres. Aggregates were placed in a flow reactor and saturated flow of aerobic or anaerobic artificial groundwater media was initiated. Redox fluctuated in select systems to examine changes in chemical gradient under changing aeration status. Our results show that within aerated solutions, oxidized aggregate exteriors provide a "gprotective barrier"h against As release despite anoxia within diffusively constrained aggregate interiors. During a transition to anaerobic conditions in advective zones, however, As is released and transport is promoted. Our study illustrates the microscale variation in biogeoechemical processes within soils and the

  13. Consequences of ecological, evolutionary and biogeochemical uncertainty for coral reef responses to climatic stress.

    PubMed

    Mumby, Peter J; van Woesik, Robert

    2014-05-19

    Coral reefs are highly sensitive to the stress associated with greenhouse gas emissions, in particular ocean warming and acidification. While experiments show negative responses of most reef organisms to ocean warming, some autotrophs benefit from ocean acidification. Yet, we are uncertain of the response of coral reefs as systems. We begin by reviewing sources of uncertainty and complexity including the translation of physiological effects into demographic processes, indirect ecological interactions among species, the ability of coral reefs to modify their own chemistry, adaptation and trans-generational plasticity. We then incorporate these uncertainties into two simple qualitative models of a coral reef system under climate change. Some sources of uncertainty are far more problematic than others. Climate change is predicted to have an unambiguous negative effect on corals that is robust to several sources of uncertainty but sensitive to the degree of biogeochemical coupling between benthos and seawater. Macroalgal, zoanthid, and herbivorous fish populations are generally predicted to increase, but the ambiguity (confidence) of such predictions are sensitive to the source of uncertainty. For example, reversing the effect of climate-related stress on macroalgae from being positive to negative had no influence on system behaviour. By contrast, the system was highly sensitive to a change in the stress upon herbivorous fishes. Minor changes in competitive interactions had profound impacts on system behaviour, implying that the outcomes of mesocosm studies could be highly sensitive to the choice of taxa. We use our analysis to identify new hypotheses and suggest that the effects of climatic stress on coral reefs provide an exceptional opportunity to test emerging theories of ecological inheritance.

  14. Catchment Legacies and Trajectories: Understanding Time Lags in Catchment Response as a Function of Hydrologic and Biogeochemical Controls

    NASA Astrophysics Data System (ADS)

    Basu, N. B.; Van Meter, K. J.

    2012-12-01

    agriculture depletes organic N in surface soil, but leads to N accumulations deeper in the profile. Nitrogen accumulation estimates (approximately 2 million Mt/yr) based on the historical data are startlingly close to the deficit suggested by mass-balance studies of the MRB (3 million Mt/yr). Understanding the lag times associated with such biogeochemical legacies requires quantification of this accumulation as a function of landscape attributes, climate, and management controls, as well as the rate of mineralization of accumulated N after implementation of management practices. Understanding hydrologic legacy requires a partitioning of flow along various pathways (e.g., overland flow, tile flow, or groundwater pathways), and the distribution of travel times along the pathways. Based on this framework, we developed a coupled hydrologic and biogeochemical model to quantify these legacies and predict landscape recovery times as a function of natural and anthropogenic controls.

  15. 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

  16. Extracellular enzyme activity and biogeochemical cycling in restored prairies

    NASA Astrophysics Data System (ADS)

    Lynch, L.; Hernandez, D.; Schade, J. D.

    2011-12-01

    during the spring. Microbial biomass C:N ratios increased from October to March, and decreased through the summer, while production of CBH, LAP and PHOS all showed the opposite pattern, decreasing through March and increasing in the summer. Following snowmelt, enzyme production preceded a recovery in microbial biomass, possibly as a result of increased competition for available resources between plant and microbial communities, or a shift to organic sources of C, N, and P which required a higher investment in enzymes. Due to their rapid growth rates and turnover, microbes are a particularly reactive component of terrestrial ecosystems and significantly influence biogeochemical cycling. Because carbon degradation may be constrained by nutrient availability, understanding how extracellular enzyme production, decomposition rate, and nutrient flux change over time is essential if we are to anticipate ecosystem responses to environmental changes.

  17. Nanostructural and biogeochemical features of the crinoid stereom

    NASA Astrophysics Data System (ADS)

    Gorzelak, P.; Stolarski, J.; Mazur, M.; Marrocchi, Y.; Meibom, A.; Chalmin, E.

    2009-04-01

    Representatives of all echinoderm clades (e.g., echinoids, holothuroids, ophiuroids, asteroids, and crinoids) form elaborate calcitic (polymorph of calcium carbonate) skeletons composed of numerous plates. Each plate consists of a three-dimensional meshwork of mineral trabeculae (stereom) that results from precisely orchestrated biomineralization processes. Individual skeletal plates behave as single calcite crystals as shown by X-ray diffraction and polarizing microscopy, however, their physico-chemical properties differ significantly from the properties of geologic or synthetic calcites. For example, echinoderm bio-calcite does not show cleavage planes typical of calcite but reveals conchoidal fracture surfaces that reduce the brittleness of the material. The unique properties of echinoderm bio-calcite result from intimate involvement of organic molecules in the biomineralization process and their incorporation into the crystal structure. Remnants of echinoderm skeleton are among the most frequently found fossils in the Mesozoic and Palaeozoic rocks thus, in order to use them as environmental proxies, it is necessary to understand the degree of biological ("vital effect") and inorganic control over their formation. Here, we show first nanoscale structural and biogeochemical properties of the stereom of extant and fossil crinoids. Using FESEM and AFM imaging techniques we show that the skeleton has nanocomposite structure: individual grains have ca. 100 nm in diameter and occasionally form larger aggregates. Fine scale geobiochemical mappings of crinoid plates (NanoSIMS microprobe) show that Mg is distributed heterogeneously in the stereom with higher concentration in the middle part of the trabecular bars. Although organic components constitute only ca. 0.10-0.26 wt% of modern echinoderm bio-calcite, in situ synchrotron sulphur K-edge x-ray absorption near edge structure (XANES) spectra show that the central parts of stereom bars contain higher levels of SO4 that

  18. Biogeochemical features of aquatic plants in the Selenga River delta

    NASA Astrophysics Data System (ADS)

    Shinkareva, Galina; Lychagin, Mikhail

    2014-05-01

    The Selenga River system provides more than a half of the Lake Baikal total inflow. The river collects a significant amount of pollutants (e.g. heavy metals) from the whole basin. These substances are partially deposited within the Selenga delta, and partially are transported further to the lake. A generous amount of aquatic plants grow in the delta area according to its favorable conditions. This vegetation works as a specific biofilter. It accumulates suspended particles and sorbs some heavy metals from the water. The study aimed to reveal the species of macrophytes which could be mostly important for biomonitoring according to their chemical composition. The field campaign took place in the Selenga River delta in July-August of 2011 (high water period) and in June of 2012 (low water period). 14 species of aquatic plants were collected: water starwort Callitriche hermaphroditica, small yellow pond lily Nuphar pumila, pondweeds Potamogeton crispus, P. pectinatus, P. friesii, broadleaf cattail Typha latifolia, hornwort or coontail Ceratophyllum demersum, arrowhead Sagittaria natans, flowering rush (or grass rush) Butomus umbellatus, reed Phragmites australis, parrot's feather Myriophyllum spicatum, the common mare's tail Hippuris vulgaris, Batrachium trichophyllum, canadian waterweed Elodea canadensis. The samples were dried, grinded up and digested in a mixture of HNO3 and H2O2. The chemical composition of the plant material was defined using ICP-MS and ICP-AES methods. Concentrations of Fe, Mn, Cr, Ni, Cu, B, Zn, V, Co, As, Mo, Pb, and U were considered. The study revealed that Potamogeton pectinatus and Myriophyllum spicatum concentrate elements during both high and low water periods. Conversely the Butomus umbellatus and Phragmites australis contain small amount of heavy metals. The reed as true grasses usually accumulates fewer amounts of elements than other macrophytes. To compare biogeochemical specialization of different species we suggest to use

  19. Multifactorial biogeochemical monitoring of linden alley in Moscow

    NASA Astrophysics Data System (ADS)

    Ermakov, Vadim; Khushvakhtova, Sabsbakhor; Tyutikov, Sergey; Danilova, Valentina; Roca, Núria; Bech, Jaume

    2015-04-01

    The ecological and biogeochemical assessment of the linden alley within the Kosygin Street was conducted by means of an integrated comparative study of soils, their chemical composition and morphological parameters of leaf linden. For this purpose 5 points were tested within the linden alley and 5 other points outside the highway. In soils, water extract of soil, leaf linden the content of Cu, Pb, Mn, Fe, Cd, Zn, As, Ni, Co Mo, Cr and Se were determined by AAS and spectrofluorimetric method [1]. Macrocomponents (Ca, Mg, K, Na, P, sulphates, chlorides), pH and total mineralization of water soil extract were measured by generally accepted methods. Thio-containing compounds in the leaves were determined by HPLC-NAM spectrofluorometry [2]. On level content of trace elements the soils of "contaminated" points different from background more high concentrations of lead, manganese, iron, selenium, strontium and low level of zinc. Leaf of linden from contaminated sites characterized by an increase of lead, copper, iron, zinc, arsenic, chromium, and a sharp decrease in the level of manganese and strontium. Analysis of the aqueous extracts of the soil showed a slight decrease in the pH value in the "control" points and lower content of calcium, magnesium, potassium, sodium and total mineralization of the water soil extract. The phytochelatins test in the leaves of linden was weakly effective and the degree of asymmetry of leaf lamina too. The most differences between the variants were marked by the degree of pathology leaves (chlorosis and necrosis) and the content of pigments (chlorophyll and carotene). The data obtained reflect the impact of the application of de-icing salts and automobile emissions. References 1. Ermakov V.V., Danilova V.N., Khyshvakhtova S.D. Application of HPLC-NAM spectrofluorimtry to determination of sulfur-containing compounds in the environmental objects// Science of the biosphere: Innovation. Moscow State University by M.V. Lomonosov, 2014. P. 10

  20. Key biogeochemical factors affecting soil carbon storage in Posidonia meadows

    NASA Astrophysics Data System (ADS)

    Serrano, Oscar; Ricart, Aurora M.; Lavery, Paul S.; Mateo, Miguel Angel; Arias-Ortiz, Ariane; Masque, Pere; Rozaimi, Mohammad; Steven, Andy; Duarte, Carlos M.

    2016-08-01

    Biotic and abiotic factors influence the accumulation of organic carbon (Corg) in seagrass ecosystems. We surveyed Posidonia sinuosa meadows growing in different water depths to assess the variability in the sources, stocks and accumulation rates of Corg. We show that over the last 500 years, P. sinuosa meadows closer to the upper limit of distribution (at 2-4 m depth) accumulated 3- to 4-fold higher Corg stocks (averaging 6.3 kg Corg m-2) at 3- to 4-fold higher rates (12.8 g Corg m-2 yr-1) compared to meadows closer to the deep limits of distribution (at 6-8 m depth; 1.8 kg Corg m-2 and 3.6 g Corg m-2 yr-1). In shallower meadows, Corg stocks were mostly derived from seagrass detritus (88 % in average) compared to meadows closer to the deep limit of distribution (45 % on average). In addition, soil accumulation rates and fine-grained sediment content (< 0.125 mm) in shallower meadows (2.0 mm yr-1 and 9 %, respectively) were approximately 2-fold higher than in deeper meadows (1.2 mm yr-1 and 5 %, respectively). The Corg stocks and accumulation rates accumulated over the last 500 years in bare sediments (0.6 kg Corg m-2 and 1.2 g Corg m-2 yr-1) were 3- to 11-fold lower than in P. sinuosa meadows, while fine-grained sediment content (1 %) and seagrass detritus contribution to the Corg pool (20 %) were 8- and 3-fold lower than in Posidonia meadows, respectively. The patterns found support the hypothesis that Corg storage in seagrass soils is influenced by interactions of biological (e.g., meadow productivity, cover and density), chemical (e.g., recalcitrance of Corg stocks) and physical (e.g., hydrodynamic energy and soil accumulation rates) factors within the meadow. We conclude that there is a need to improve global estimates of seagrass carbon storage accounting for biogeochemical factors driving variability within habitats.

  1. Biogeochemical aspects of uranium mineralization, mining, milling, and remediation

    USGS Publications Warehouse

    Campbell, Kate M.; Gallegos, Tanya J.; Landa, Edward R.

    2015-01-01

    Natural uranium (U) occurs as a mixture of three radioactive isotopes: 238U, 235U, and 234U. Only 235U is fissionable and makes up about 0.7% of natural U, while 238U is overwhelmingly the most abundant at greater than 99% of the total mass of U. Prior to the 1940s, U was predominantly used as a coloring agent, and U-bearing ores were mined mainly for their radium (Ra) and/or vanadium (V) content; the bulk of the U was discarded with the tailings (Finch et al., 1972). Once nuclear fission was discovered, the economic importance of U increased greatly. The mining and milling of U-bearing ores is the first step in the nuclear fuel cycle, and the contact of residual waste with natural water is a potential source of contamination of U and associated elements to the environment. Uranium is mined by three basic methods: surface (open pit), underground, and solution mining (in situ leaching or in situ recovery), depending on the deposit grade, size, location, geology and economic considerations (Abdelouas, 2006). Solid wastes at U mill tailings (UMT) sites can include both standard tailings (i.e., leached ore rock residues) and solids generated on site by waste treatment processes. The latter can include sludge or “mud” from neutralization of acidic mine/mill effluents, containing Fe and a range of coprecipitated constituents, or barium sulfate precipitates that selectively remove Ra (e.g., Carvalho et al., 2007). In this chapter, we review the hydrometallurgical processes by which U is extracted from ore, the biogeochemical processes that can affect the fate and transport of U and associated elements in the environment, and possible remediation strategies for site closure and aquifer restoration.This paper represents the fourth in a series of review papers from the U.S. Geological Survey (USGS) on geochemical aspects of UMT management that span more than three decades. The first paper (Landa, 1980) in this series is a primer on the nature of tailings and radionuclide

  2. 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

    computed to occur in a period of about 1,000 years as a result of diffusion-reaction processes. Coupled biogeochemical mechanisms, such as respiration of dissolved organic matter and aerobic methane oxidation, accelerate the oxygen uptake to less than a month.

  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. How does global biogeochemical cycle become complicated by terrestrial-aquatic interactions ?

    NASA Astrophysics Data System (ADS)

    Nakayama, Tadanobu; Maksyutov, Shamil

    2015-04-01

    Inland water such as river and lake are now known to be important and active components of global carbon cycle though its contribution has remained uncertain due to data scarcity (Battin et al., 2009; Aufdenkampe et al., 2011). 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-global scales, and can simulate iteratively nonlinear feedback between hydrologic, geomorphic, and ecological processes. In this study, NICE was coupled with various biogeochemical models to incorporate biogeochemical cycle including reaction between inorganic and organic carbons (DOC, POC, DIC, pCO2, etc.) in terrestrial and aquatic ecosystems including surface water and groundwater. The coupled model simulated CO2 evasion from inland water in global scale, was relatively in good agreement in that estimated by empirical regression model (Raymond et al., 2013). In particular, the simulated result implied importance of connectivity between terrestrial and aquatic ecosystems in addition to surface and groundwater, and hillslopes and stream channels, etc. The model further improved the accuracy of CH4 flux in wetland which is sensitive to fluctuations of shallow groundwater because the original NICE incorporates 3-D groundwater sub-model and simulates lateral subsurface flow more reasonably. This simulation system would play important role in integration of greenhouse gas budget of the biosphere, quantification of hot spots in boundless biogeochemical cycle, and bridging gap between top-down and bottom-up approaches (Cole et al., 2007; Frei et al., 2012; Kiel and Cardenas, 2014). References; Aufdenkampe, A.K., et al

  5. 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

  6. The role of phytoplankton photosynthesis in global biogeochemical cycles.

    PubMed

    Falkowski, P G

    1994-03-01

    Phytoplankton biomass in the world's oceans amounts to only ∽1-2% of the total global plant carbon, yet these organisms fix between 30 and 50 billion metric tons of carbon annually, which is about 40% of the total. On geological time scales there is profound evidence of the importance of phytoplankton photosynthesis in biogeochemical cycles. It is generally assumed that present phytoplankton productivity is in a quasi steady-state (on the time scale of decades). However, in a global context, the stability of oceanic photosynthetic processes is dependent on the physical circulation of the upper ocean and is therefore strongly influenced by the atmosphere. The net flux of atmospheric radiation is critical to determining the depth of the upper mixed layer and the vertical fluxes of nutrients. These latter two parameters are keys to determining the intensity, and spatial and temporal distributions of phytoplankton blooms. Atmospheric radiation budgets are not in steady-state. Driven largely by anthropogenic activities in the 20th century, increased levels of IR- absorbing gases such as CO2, CH4 and CFC's and NOx will potentially increase atmospheric temperatures on a global scale. The atmospheric radiation budget can affect phytoplankton photosynthesis directly and indirectly. Increased temperature differences between the continents and oceans have been implicated in higher wind stresses at the ocean margins. Increased wind speeds can lead to higher nutrient fluxes. Throughout most of the central oceans, nitrate concentrations are sub-micromolar and there is strong evidence that the quantum efficiency of Photosystem II is impaired by nutrient stress. Higher nutrient fluxes would lead to both an increase in phytoplankton biomass and higher biomass-specific rates of carbon fixation. However, in the center of the ocean gyres, increased radiative heating could reduce the vertical flux of nutrients to the euphotic zone, and hence lead to a reduction in phytoplankton

  7. The Neoproterozoic oxygenation event: Environmental perturbations and biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Och, Lawrence M.; Shields-Zhou, Graham A.

    2012-01-01

    The oxygen content of the Earth's surface environment is thought to have increased in two broad steps: the Great Oxygenation Event (GOE) around the Archean-Proterozoic boundary and the Neoproterozoic Oxygenation Event (NOE), during which oxygen possibly accumulated to the levels required to support animal life and ventilate the deep oceans. Although the concept of the GOE is widely accepted, the NOE is less well constrained and its timing and extent remain the subjects of debate. We review available evidence for the NOE against the background of major climatic perturbations, tectonic upheaval related to the break-up of the supercontinent Rodinia and reassembly into Gondwana, and, most importantly, major biological innovations exemplified by the Ediacarian Biota and the Cambrian 'Explosion'. Geochemical lines of evidence for the NOE include perturbations to the biogeochemical cycling of carbon. Generally high δ 13C values are possibly indicative of increased organic carbon burial and the release of oxidative power to the Earth's surface environment after c. 800 Ma. A demonstrably global and primary record of extremely negative δ 13C values after about 580 Ma strongly suggests the oxidation of a large dissolved organic carbon pool (DOC), the culmination of which around c. 550 Ma coincided with an abrupt diversification of Ediacaran macrobiota. Increasing 87Sr/ 86Sr ratios toward the Neoproterozoic-Cambrian transition indicates enhanced continental weathering which may have fuelled higher organic production and burial during the later Neoproterozoic. Evidence for enhanced oxidative recycling is given by the increase in sulfur isotope fractionation between sulfide and sulfate, exceeding the range usually attained by sulfate reduction alone, reflecting an increasing importance of the oxidative part in the sulfur cycle. S/C ratios attained a maximum during the Precambrian-Cambrian transition, further indicating higher sulfate concentrations in the ocean and a

  8. Sulfur and Methylmercury in the Florida Everglades - the Biogeochemical Connection

    NASA Astrophysics Data System (ADS)

    Orem, W. H.; Gilmour, C. C.; Krabbenhoft, D. P.; Aiken, G.

    2011-12-01

    Methylmercury (MeHg) is a serious environmental problem in aquatic ecosystems worldwide because of its toxicity and tendency to bioaccumulate. The Everglades receives some of the highest levels of atmospheric mercury deposition and has some of the highest levels of MeHg in fish in the USA, posing a threat to pisciverous wildlife and people through fish consumption. USGS studies show that a combination of biogeochemical factors make the Everglades especially susceptible to MeHg production and bioaccumulation: (1) vast wetland area with anoxic soils supporting anaerobic microbial activity, (2) high rates of atmospheric mercury deposition, (3) high levels of dissolved organic carbon (DOC) that complexes and stabilizes mercury in solution for transport to sites of methylation, and (4) high sulfate loading in surface water that drives microbial sulfate reduction and mercury methylation. The high levels of sulfate in the Everglades represent an unnatural condition. Background sulfate levels are estimated to be <1 mg/L, but about 60% of the Everglades has surface water sulfate concentrations exceeding background. Highly sulfate-enriched marshes in the northern Everglades have average sulfate levels of 60 mg/L. Sulfate loading to the Everglades is principally a result of land and water management in south Florida. The highest concentrations of sulfate, averaging 60-70 mg/L, are in canal water in the Everglades Agricultural Area (EAA). Geochemical data and a preliminary sulfur mass balance for the EAA are consistent with sulfur currently used in agriculture, and sulfur released by oxidation of organic EAA soils (including legacy agricultural applications and natural sulfur) as the primary sources of sulfate enrichment to the canals and ecosystem. Sulfate loading increases microbial sulfate reduction and MeHg production in soils. The relationship between sulfate loading and MeHg production, however, is complex. Sulfate levels up to about 20-30 mg/L increase mercury

  9. Biogeochemical factors which regulate the formation and fate of sulfide in wetlands

    NASA Technical Reports Server (NTRS)

    Hines, Mark E.; Lyons, W. Berry; Gaudette, H. E.

    1992-01-01

    Coastal wetland areas occupy a small percentage of the terrestrial environment yet are extremely productive regions which support rapid rates of belowground bacterial activity. Wetlands appear to be significant as biogenic sources of gaseous sulfur, carbon, and nitrogen. These gases are important as tracers of man's activities, and they influence atmospheric chemistry. The interactions among wetland biogeochemical processes regulate the anaerobic production of reduced gases and influence the fate of these volatiles. Therefore, spatial and temporal variations in hydrology, salinity, temperature and specification, and growth of vegetation affect the type and magnitude of gas emissions thus hindering predictive estimates of gas flux. Our research is divided into two major components, the first is the biogeochemical characterization of a selected tidal wetland area in terms of factors likely to regulate sulfide flux; the second is a direct measurement of gaseous sulfur flux as related to changes in these biogeochemical conditions. Presently, we are near completion of phase one.

  10. 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

  11. MODELING COUPLED HYDROLOGICAL AND CHEMICAL PROCESSES: LONG-TERM URANIUM TRANSPORT FOLLOWING PHOSPHOROUS-FERTILIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Contaminants in the vadose zone are affected by the physical processes of water flow, heat movement and multicomponent transport, as well as generally by a range of interacting biogeochemical processes. Coupling these various processes within one integrated numerical simulator provides a process-ba...

  12. A 15-year global biogeochemical reanalysis with ocean colour data assimilation

    NASA Astrophysics Data System (ADS)

    Ford, David; Barciela, Rosa

    2013-04-01

    A continuous global time-series of remotely sensed ocean colour observations is available from 1997 to the present day. However coverage is incomplete, and limited to the sea surface. Models are therefore required to provide full spatial coverage, and to investigate the relationships between physical and biological variables and the carbon cycle. Data assimilation can then be used to constrain models to fit the observations, thereby combining the advantages of both sources of information. As part of the European Space Agency's Climate Change Initiative (ESA-CCI), we assimilate chlorophyll concentration derived from ocean colour observations into a coupled physical-biogeochemical model. The data assimilation scheme (Hemmings et al., 2008, J. Mar. Res.; Ford et al., 2012, Ocean Sci.) uses the information from the observations to update all biological and carbon cycle state variables within the model. Global daily reanalyses have been produced, with and without assimilation of merged ocean colour data provided by GlobColour, for the period September 1997 to August 2012. The assimilation has been shown to significantly improve the model's representation of chlorophyll concentration, at the surface and at depth. Furthermore, there is evidence of improvement to the representation of pCO2, nutrients and zooplankton concentration compared to in situ observations. We use the results to quantify recent seasonal and inter-annual variability in variables including chlorophyll concentration, air-sea CO2 flux and alkalinity. In particular, we explore the impact of physical drivers such as the El Niño Southern Oscillation (ENSO) on the model's representation of chlorophyll and the carbon cycle, and the pros and cons of the model reanalyses compared to observation-based climatologies. Furthermore, we perform a comparison between the GlobColour product and an initial version of a new merged product being developed as part of the ESA-CCI. Equivalent year-long hindcasts are

  13. Iron: A Biogeochemical Engine That Drives Carbon, Nitrogen, and Phosphorus Cycling in Humid Tropical Forest Soils

    NASA Astrophysics Data System (ADS)

    Silver, W. L.; Hall, S. J.; Thompson, A.; Yang, W. H.

    2014-12-01

    The abundance of redox active Fe minerals has the potential to alter the storage and loss of C, contribute to gaseous N emissions, and control P retention in upland tropical forest soils. High concentrations of short-range order Fe minerals led to Fe(II) production rates of 26-206 μg g d-1 under short-term low redox conditions (Chacón et al. 2006, Liptzin and Silver 2009, Dubinsky et al. 2010). Potential C mineralization from Fe(II) reduction was 34-263 g CO2-C m-2 y-1, C losses equivalent to approximately 10-60 % of annual litterfall production in this forest. Decreased acidity during Fe reduction can destabilize soil aggregates and lead to C losses. Iron is rapidly reoxidized during aerobic periods, which can subsequently lead to C stabilization via complexation reactions. Fe oxidation can also stimulate C losses via pH-driven dissolved organic C production and directly via Fenton reactions. In laboratory experiments, rates of CO2 production were strongly linearly correlated with Fe(II) loss under aerobic conditions, increasing by 0.51 ± 0.02 µg CO2-C g soil h-1 respired for each mg of Fe(II) g-1 soil oxidized or sorbed (Hall and Silver 2013). Iron oxidation has also been linked to dissimilatory NO3- reduction to NH4+ leading to N retention in ecosystems. Fe(III) reduction coupled with NH4+ oxidation (Feammox) can lead to N losses as dinitrogen gas (N2) or nitrous oxide (N2O), a potent greenhouse gas. Estimates suggest that Feammox resulted in gaseous N losses of 1-4 kg N ha-1 y-1 (Yang et al. 2012), rates equivalent to total denitrification in this forest. Oxidized Fe can strongly bind P decreasing it's availability to plant roots. While this is commonly cited as a potential limitation to net primary production in tropical forests, it also helps to retain P in ecosystems with high rainfall and potential leaching losses. Microbial biomass P availability increased significantly with Fe(II) production, suggesting the P mobilized during Fe(II) reduction was

  14. Long time series of deep water particle flux in three biogeochemical provinces of the northeast Atlantic

    NASA Astrophysics Data System (ADS)

    Waniek, Joanna J.; Schulz-Bull, Detlef E.; Kuss, Joachim; Blanz, Thomas

    2005-06-01

    Long-term observations of the deep ocean particle flux from three sites in the northeast Atlantic (33°N, 22°W; 47°N, 20°W; 54°N, 20°W) provide the basis for comparison and characterization of the biogeochemical provinces in terms of sedimentation pattern. Deep ocean particle flux data (2000 m) for fluxes of total mass and the flux composition are presented and compared to published sediment trap data from this area to consider regional-scale variations in the quantity and composition of settling material. The observations show that in the northeast Atlantic gradient of decreasing mass flux from North to South, exists consistent with known changes of biological productivity in surface waters. This gradient is associated with similar trends in opal and particulate organic carbon, whereas calcium carbonate shows trend in the opposite direction. The changes in the composition of the settling material found along the transect are indicating that the calcium carbonate flux is critical in removing organic matter from the upper ocean to the deeper sink. Its role declines from the subtropical ocean (60-80% of the particle flux) towards North (< 40%) reflecting the decreasing importance of coccolithophorid/foraminiferal blooms for particle flux from the subtropical to the subpolar North Atlantic. In contrast, the role of biogenic silica (opal) in regard to the ballasting effect increases towards North. The northern sites have much higher percentage of biogenic silica than the sites in the South, because of the deep winter mixing and the seasonality of phytoplankton dominated by diatom blooms during spring and summer. The comparison of the seasonal pattern of particle flux with the seasonal pattern of surface chlorophyll a concentrations from SeaWiFS together with the similarity of the pattern observed in calcium carbonate and opal leads to the conclusion that the particle flux at two positions (33°N, 22°W; 47°N, 20°W) is fast and directly coupled to the

  15. Implications of variance in biogeochemical proxy records spanning Mesozoic Oceanic Anoxic Events

    NASA Astrophysics Data System (ADS)

    Gomes, M. L.; Mills, J. V.; Hurtgen, M. T.; Sageman, B. B.

    2013-12-01

    The cycling of key elements through the ocean and atmosphere varied widely in the Mesozoic in response to changes in primary productivity and organic carbon burial, volcanism, weathering, and evaporite burial. Many of these processes have been proposed as triggers for the discreet periods of widespread organic carbon production and/or preservation termed Ocean Anoxic Events or OAE's. Thus, it might be expected that similar patterns of elemental cycling would characterize most major OAE intervals and could be used to help elucidate the controls on initiation and/or termination of these events. Yet this is not the case. In this study we compare the variability of a series of geochemical proxies, focusing on sulfur (S) isotopes of marine sulfate and sulfide minerals, through a series of Mesozoic OAE's. The data set includes our own results from OAE1a (ca. 125Ma) and OAE2 (ca. 94Ma), as well as published data from other events. The results indicate that S cycling varied significantly among the events, despite many similarities in the behavior of carbon isotopes and geochemical indicators of oxygen deficiency. Specifically, S isotope compositions of seawater sulfate and pyrite are quite variable during OAE2 suggesting that a short-term increase in sulfate levels upon a low background occurred at the onset due to enhanced volcanism and/or weathering. In contrast, S isotope compositions of seawater sulfate and pyrite decrease dramatically through the OAE1a and are completely decoupled from the carbon cycle. We evaluate these trends using coupled sulfur and carbon box models and show that patterns of S cycling during OAE1a were predominantly controlled by volcanism, whereas S cycling during OAE2 represents a stronger interplay between volcanic processes and linkage with the carbon cycle. An analysis of the differences in S cycling among events provides improved insight into the suite of processes that interacted to drive large-scale changes in environmental conditions

  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. Spatial distributions of polyunsaturated aldehydes and their biogeochemical implications in the Pearl River Estuary and the adjacent northern South China Sea

    NASA Astrophysics Data System (ADS)

    Wu, Zhengchao; Li, Qian P.

    2016-09-01

    This study reports the first comprehensive exploration of the spatial patterns of dissolved and particulate polyunsaturated aldehydes (PUAs), their physical and biological controlling factors, and their potential biogeochemical influences in the Pearl River Estuary (PRE) of the northern South China Sea (NSCS). High levels of total particulate PUAs (0-41 nM) and dissolved PUAs (0.10-0.37 nM) were observed with substantial spatial variation during an intense summer phytoplankton bloom outside the PRE mouth. We found the particulate PUAs strongly correlated with temperature within the high chlorophyll bloom, while showing a generally positive correlation with chlorophyll-a for the entire region. Additionally, the Si/N ratio significantly correlated with the particulate PUAs along the estuary suggesting the important role of silica on PUA production in this region. The dissolved PUAs counterparts exhibited a positive correlation with chlorophyll-a within the high chlorophyll bloom, but a negatively one with temperature outside, reflecting the essential bio-physical coupling effects on the dissolved PUAs distributions in the ocean. Biogeochemical implications of PUAs on the coastal ecosystem include not only the deleterious restriction of high PUAs-producing diatom bloom on copepod population, but also the profound influence of particulate PUAs on the microbial cycling of organic carbon in the NSCS.

  18. Contributions of physical and biogeochemical processes to phytoplankton biomass enhancement in the surface and subsurface layers during the passage of Typhoon Damrey

    NASA Astrophysics Data System (ADS)

    Pan, Shanshan; Shi, Jie; Gao, Huiwang; Guo, Xinyu; Yao, Xiaohong; Gong, Xiang

    2017-01-01

    In this study, a one-dimensional physical-biogeochemical coupled model was established to investigate the responses of the upper ocean to Typhoon Damrey in the basin area of the South China Sea. The surface chlorophyll a concentration (Chl a) increased rapidly from 0.07 to 0.17 mg m-3 when the typhoon arrived and then gradually reached a peak of 0.61 mg m-3 after the typhoon's passage. The subsurface Chl a decreased from 0.34 to 0.17 mg m-3 as the typhoon arrived and then increased gradually to 0.71 mg m-3. Analyses of model results indicated that the initial rapid increase in the surface Chl a and the decrease in the subsurface Chl a were caused mainly by physical process (vertical mixing), whereas the subsequent gradual increases in the Chl a in both the surface and subsurface layers were due mainly to biogeochemical processes (net growth of phytoplankton). The gradual increase in the Chl a lasted for longer in the subsurface layer than in the surface layer. Typhoon Damrey yielded an integrated primary production (IPP) of 6.5 × 103 mg C m-2 ( 14% of the annual IPP in this region).

  19. Performance and results of the high-resolution biogeochemical model PELAGOS025 v1.0 within NEMO v3.4

    NASA Astrophysics Data System (ADS)

    Epicoco, Italo; Mocavero, Silvia; Macchia, Francesca; Vichi, Marcello; Lovato, Tomas; Masina, Simona; Aloisio, Giovanni

    2016-06-01

    The present work aims at evaluating the scalability performance of a high-resolution global ocean biogeochemistry model (PELAGOS025) on massive parallel architectures and the benefits in terms of the time-to-solution reduction. PELAGOS025 is an on-line coupling between the Nucleus for the European Modelling of the Ocean (NEMO) physical ocean model and the Biogeochemical Flux Model (BFM) biogeochemical model. Both the models use a parallel domain decomposition along the horizontal dimension. The parallelisation is based on the message passing paradigm. The performance analysis has been done on two parallel architectures, an IBM BlueGene/Q at ALCF (Argonne Leadership Computing Facilities) and an IBM iDataPlex with Sandy Bridge processors at the CMCC (Euro Mediterranean Center on Climate Change). The outcome of the analysis demonstrated that the lack of scalability is due to several factors such as the I/O operations, the memory contention, the load unbalancing due to the memory structure of the BFM component and, for the BlueGene/Q, the absence of a hybrid parallelisation approach.

  20. Catchment hydro-biogeochemical response to forest harvest intensity and spatial pattern

    EPA Science Inventory

    We apply a new model, Visualizing Ecosystems for Land Management Assessment (VELMA), to Watershed 10 (WS10) in the H.J. Andrews Experimental Forest to simulate the effects of harvest intensity and spatial pattern on catchment hydrological and biogeochemical processes. Specificall...

  1. Biogeochemical research priorities for sustainable biofuel and bioenergy feedstock production in the Americas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rapid expansion in biomass production for biofuels and bioenergy in the Americas is increasing demands on the ecosystem resources required to sustain soil and site productivity. We review the current state of knowledge and highlight gaps in research on biogeochemical processes and ecosystem sustaina...

  2. INTERACTIVE EFFECTS OF OZONE DEPLETION AND CLIMATE CHANGE ON BIOGEOCHEMICAL CYCLES

    EPA Science Inventory

    The effects of ozone depletion on global biogeochemical cycles, via increased UV-B radiation at the Earth's surface, have continued to be documented over the past 4 years. In this report we also document various effects of UV-B that interact with global climate change because the...

  3. Investigation of In-situ Biogeochemical Reduction of Chlorinated Solvents in Groundwater by Reduced Iron Minerals

    EPA Science Inventory

    Biogeochemical transformation is a process in which chlorinated solvents are degraded abiotically by reactive minerals formed by, at least in part or indirectly from, anaerobic biological processes. Five mulch biowall and/or vegetable oil-based bioremediation applications for tr...

  4. A tubular-coring device for use in biogeochemical sampling of succulent and pulpy plants

    USGS Publications Warehouse

    Campbell, W.L.

    1986-01-01

    A hand-operated, tubular-coring device developed for use in biogeochemical sampling of succulent and pulpy plants is described. The sampler weighs about 500 g (1.1 lb); and if 25 ?? 175 mm (1 ?? 7 in) screw-top test tubes are used as sample containers, the complete sampling equipment kit is easily portable, having both moderate bulk and weight. ?? 1986.

  5. A Virtual Soil System to Study Macroscopic Manifestation of Pore-Scale Biogeochemical Processes

    NASA Astrophysics Data System (ADS)

    Liu, C.; Fang, Y.; Shang, J.; Bailey, V. L.

    2012-12-01

    Mechanistic soil biogeochemical processes occur at the pore-scale that fundamentally control the moisture and CO2 fluxes at the soil and atmosphere interface. This presentation will present an on-going research to investigate pore-scale moisture migration and biogeochemical processes of organic carbon degradation, and their macroscopic manifestation in soils. Soil cores collected from Rattlesnake Mountain in southeastern Washington, USA, where a field experiment was conducted to investigate dynamic response of soil biogeochemistry to changing climate conditions, were used as an example for this study. The cores were examined using computerized x-ray tomography (XCT) to determine soil pore structures. The XCT imaging, together with various measurements of soil properties such as porosity, moisture content, organic carbon, biochemistry, etc are used to establish a virtual soil core with a high spatial resolution (~20um). The virtual soil system is then used to simulate soil moisture migration and organic carbon degradation, to identify important physical and biogeochemical factors controlling macroscopic moisture and CO2 fluxes in response to changing climate conditions, and to develop and evaluate pragmatic biogeochemical process models for larger scale applications. Core-scale measurements of CO2 flux and moisture change are used for development and validation of the process models.

  6. Comparing the Biogeochemical Potential of Hyporheic Zones Driven by Different River Morphologies

    NASA Astrophysics Data System (ADS)

    Gomez, J. D.; Harvey, J. W.

    2013-12-01

    Channel morphology controls the hydrodynamics of hyporheic exchange and its residence times. As a result, it also constrains the hyporheic zone's biogeochemical processes that transform carbon, nutrients, metals, and contaminants and the hyporheic zone's net effect at the local, reach and watershed scales. Previous studies of different morphologies (e.g., meanders, bars, and smaller bedforms such as dunes) have mainly focused on the amount of exchange or, if biogeochemistry was involved, have been specific to a particular morphology. In this work, we present a quantitative intercomparison of the amount of exchange, residence time distributions (RTDs), and biogeochemical potential for four channel morphologies: ripples, dunes, bars, and meander bends. To this end, simple two-dimensional conceptualizations and semi-analytical solutions for the hyporheic zone's flow and transport are used. In general, all morphologies are characterized by heavy-tail RTDs, implying long-term memory to solute inputs. We hypothesize that even though meander bends induce larger hyporheic exchange per unit length of channel and longer residence times, substrate limitations result in less biogeochemical processing when compared with the cumulative effect of multiple bedforms. The models presented are a function of geometric and physical properties easily measured or constrained with field or remote sensing data. The simplicity of this approach allows for practical calculations of the hyporheic zone's exchange and biogeochemical potential over a broad range of scenarios and morphologies, making it a useful tool for experimental design, sampling, and watershed scale assessment.

  7. Switchgrass influences soil biogeochemical processes in dryland region of the Pacific Northwest

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Switchgrass and other perennial grasses have been promoted as biomass crops for production of renewable fuels. The objective of this study was to evaluate the effect of biomass removal on soil biogeochemical processes. A three year field study consisting of three levels of net primary productivity (...

  8. Effects of Solar UV Radiation and Climate Change on Biogeochemical Cycling: Interactions and Feedbacks

    EPA Science Inventory

    Solar UV radiation, climate and other drivers of global change are undergoing significant changes and models forecast that these changes will continue for the remainder of this century. Here we assess the effects of solar UV radiation on biogeochemical cycles and the interactions...

  9. INTERACTIONS OF CHANGING CLIMATE AND ULTRAVIOLET RADIATION IN AQUATIC AND TERRESTRIAL BIOGEOCHEMICAL CYCLES

    EPA Science Inventory

    During the past decade interest has developed in the interactive effects of climate change and UV radiation on aquatic and terrestrial biogeochemical cycles. This talk used selected case studies to illustrate approaches that are being used to investigate these intriguing processe...

  10. Catchment hydro-biogeochemical response to climate change and future land-use

    EPA Science Inventory

    The potential interacting effects of climate change and future land-use on hydrological and biogeochemical dynamics rarely have been described at the catchment level and are difficult or impossible to capture through experimentation or observation alone. We apply a new model, Vi...

  11. Helix coupling

    DOEpatents

    Ginell, William S.

    1989-04-25

    A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the "U" sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

  12. Helix coupling

    DOEpatents

    Ginell, W.S.

    1982-03-17

    A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the U sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

  13. Geomorphic and substrate controls on spatial variability in river solute transport and biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Blaen, Phillip; Kurz, Marie; Knapp, Julia; Mendoza-Lera, Clara; Lee-Cullin, Joe; Klaar, Megan; Drummond, Jen; Jaeger, Anna; Zarnetske, Jay; Lewandowski, Joerg; Marti, Eugenia; Ward, Adam; Fleckenstein, Jan; Datry, Thibault; Larned, Scott; Krause, Stefan

    2016-04-01

    Nutrient concentrations in surface waters and groundwaters are increasing in many agricultural catchments worldwide as a result of anthropogenic activities. Increasing geomorphological heterogeneity in river channels may help to attenuate nutrient pollution by facilitating water exchange fluxes with the hyporheic zone; a site of intense microbial activity where biogeochemical transformation rates (e.g. denitrification) can be high. However, the controls on spatial variability in biogeochemical cycling, particularly at scales relevant for river managers, are not well understood. Here, we aimed to assess: 1) how differences in geomorphological heterogeneity control river solute transport and rates of biogeochemical cycling at sub-reach scales (102 m); and 2) the relative magnitude of these differences versus those relating to reach scale substrate variability (103 m). We used the reactive 'smart' tracer resazurin (Raz), a weakly fluorescent dye that transforms to highly fluorescent resorufin (Rru) under mildly reducing conditions, as a proxy to assess rates of biogeochemical cycling in a lowland river in southern England. Solute tracer tests were conducted in two reaches with contrasting substrates: one sand-dominated and the other gravel-dominated. Each reach was divided into sub-reaches that varied in geomorphic complexity (e.g. by the presence of pool-riffle sequences or the abundance of large woody debris). Slug injections of Raz and the conservative tracer fluorescein were conducted in each reach during baseflow conditions (Q ≈ 80 L/s) and breakthrough curves monitored using in-situ fluorometers. Preliminary results indicate overall Raz:Rru transformation rates in the gravel-dominated reach were more than 50% higher than those in the sand-dominated reach. However, high sub-reach variability in Raz:Rru transformation rates and conservative solute transport parameters suggests small-scale targeted management interventions to alter geomorphic heterogeneity may be

  14. Multi-scale controls on spatial variability in river biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Blaen, Phillip; Kurz, Marie; Knapp, Julia; Mendoza-Lera, Clara; Lee-Cullin, Joe; Klaar, Megan; Drummond, Jennifer; Jaeger, Anna; Zarnetske, Jay; Lewandowski, Joerg; Marti, Eugenia; Ward, Adam; Fleckenstein, Jan; Datry, Thibault; Larned, Scott; Krause, Stefan

    2016-04-01

    Excessive nutrient concentrations are common in surface waters and groundwaters in agricultural catchments worldwide. Increasing geomorphological heterogeneity in river channels may help to attenuate nutrient pollution by facilitating water exchange fluxes with the hyporheic zone; a site of intense microbial activity where biogeochemical cycling rates can be high. However, the controls on spatial variability in biogeochemical cycling, particularly at scales relevant for river managers, are largely unknown. Here, we aimed to assess: 1) how differences in river geomorphological heterogeneity control solute transport and rates of biogeochemical cycling at sub-reach scales (102 m); and 2) the relative magnitude of these differences versus those relating to reach scale substrate variability (103 m). We used the reactive tracer resazurin (Raz), a weakly fluorescent dye that transforms to highly fluorescent resorufin (Rru) under mildly reducing conditions, as a proxy to assess rates of biogeochemical cycling in a lowland river in southern England. Solute tracer tests were conducted in two reaches with contrasting substrates: one sand-dominated and the other gravel-dominated. Each reach was divided into sub-reaches that varied in geomorphic complexity (e.g. by the presence of pool-riffle sequences or the abundance of large woody debris). Slug injections of Raz and the conservative tracer fluorescein were conducted in each reach during baseflow conditions (Q ≈ 80 L/s) and breakthrough curves monitored using in-situ fluorometers. Preliminary results indicate overall Raz:Rru transformation rates in the gravel-dominated reach were more than 50% higher than those in the sand-dominated reach. However, high sub-reach variability in Raz:Rru transformation rates and conservative solute transport parameters suggests small scale targeted management interventions to alter geomorphic heterogeneity may be effective in creating hotspots of river biogeochemical cycling and nutrient load

  15. Biogeochemical Cycling at Soil Interfaces in the Vadose Zone and its Impact on Hydraulic Conductivity

    NASA Astrophysics Data System (ADS)

    Hansen, D. J.; McGuire, J. T.; Mohanty, B. P.

    2007-12-01

    Much research has focused on understanding and predicting chemical fate and transport in subsurface systems to protect drinking water reserves and ecosystem health. However, chemical changes that occur in the unsaturated zone due to processes such as mineral-water interactions, desorption, or biogeochemical cycling have often been neglected. In particular, the effects of soil structure (i.e. layers, lenses, macropores, or fractures) on these processes remain poorly understood. This study focuses on characterizing the linkages between geochemical processes, hydrologic flow, and microbial activity in the vadose zone using packed soil columns. We constructed three laboratory soil columns: a homogenized medium-grained sand, homogenized organic-rich silty clay, and a sand-over-clay layered column. Both upward and downward infiltration of water was evaluated during experiments to simulate rising water table and rainfall events respectively. In situ collocated probes measured soil water content, matric potential, and Eh. Water samples extracted by lysimeter were analyzed for major cations and anions, ammonium, organic acids, alkalinity, Fe2+, and total sulfide. Enhanced biogeochemical cycling was observed in the layered column. For example, concentrations of the electron acceptor sulfate were two-fold greater in the layered column than in either of the homogeneous columns likely due to increased oxidation/reduction reactions. Rainfall events enhanced denitrification in the layered column through the addition of NO3- via enhanced ammonium oxidation. Biogeochemical cycling was directly linked to hydrologic flow and varied as a function of water infiltration direction (upward/downward). Enhanced biogeochemical activity produced mineral crusts and biofilms that decreased overall hydraulic conductivity. Preliminary results suggest that changes in the vadose zone occur too rapidly for the system to achieve redox equilibrium and suggest that a new conceptual framework to analyze

  16. Catchment Hydro-biogeochemical Responses to Forest Harvest Intensity and Spatial Pattern

    NASA Astrophysics Data System (ADS)

    Abdelnour, A.; Stieglitz, M.; Pan, F.; McKane, R.

    2009-12-01

    We apply a new model, Visualizing Ecosystems for Land Management Assessment (VELMA), to Watershed 10 (WS10) in the H.J. Andrews Experimental Forest to simulate the effects of harvest intensity and spatial pattern on catchment hydrological and biogeochemical processes. Specifically, we test for the occurrence of hydrological and biogeochemical threshold behavior in the catchment response. VELMA is a spatially-distributed eco-hydrology model that simulates the effects of climate, and land cover on daily changes in soil water storage, surface and subsurface runoff, vertical drainage, evapotranspiration, vegetation and soil C and N dynamics, and transport of nitrate, ammonium, DON, and DOC to streams. We simulate pre- and post-disturbance hydrological and biogeochemical responses of the WS10 catchment. Model parameters were initialized to simulate the post-fire build-up of ecosystem C and N stocks from 1725 to 1975. These parameters are then fixed and used to simulate the hydro-biogeochemical response after the 1975 clear-cut. Comparison of modeled and observed soil moisture, streamflow, DIN, DON and DOC losses for the post-clear-cut period (1975-2007) show that VELMA accurately captures spatial and temporal dynamics of hydrological and biogeochemical processes in WS10. We then examine the catchment response to alternative clear-cut scenarios for which the location and fraction of harvested area varied. These alternative clear-cut simulations suggest that the streamflow and harvest area relationship in this rain-dominated catchment is nearly linear, irrespective of clear-cut area and location. Simulations designed to identify threshold responses of DOC, DON and DIN export in relation to harvest area and location will be presented.

  17. Integrated Biogeochemical and Hydrologic Processes Driving Arsenic Release from Shallow Sediments to Groundwaters of the Mekong Delta

    SciTech Connect

    Kocar, Benjamin D.; Polizzotto, Matthew L.; Benner, Shawn G.; Ying, Samantha C.; Ung, Mengieng; Ouch, Kagna; Samreth, Sopheap; Suy, Bunseang; Phan, Kongkea; Sampson, Michael; Fendorf, Scott

    2008-11-01

    Arsenic is contaminating the groundwater of Holocene aquifers throughout South and Southeast Asia. To examine the biogeochemical and hydrological processes influencing dissolved concentrations and transport of As within soils/sediments in the Mekong River delta, a ~50 km₂ field site was established near Phnom Penh, Cambodia, where aqueous As concentrations are dangerously high and where groundwater retrieval for irrigation is minimal. Dissolved As concentrations vary spatially, ranging up to 1300 µg/L in aquifer groundwater and up to 600 µg/L in surficial clay pore water. Groundwaters with high As concentrations are reducing with negligible dissolved O₂ and high concentrations of Fe(II), NH⁺₄ , and dissolved organic C. Within near-surface environments, these conditions are most pronounced in sediments underlying permanent wetlands, often found within oxbow channels near the Mekong River. There, labile C, co-deposited with As-bearing Fe (hydr)oxides under reducing conditions, drives the reductive mobilization (inclusive of Fe and As reduction) of As. Here, conditions are described under which As is mobilized from these sediments, and near-surface As release is linked to aquifer contamination over long time periods (100s to 1000s of years). Site biogeochemistry is coupled with extensive hydrologic measurements, and, accordingly, a comprehensive interpretation of spatial As release and transport within a calibrated hydraulic flow-field is provided of an As-contaminated aquifer that is representative of those found throughout South and Southeast Asia.

  18. 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.

  19. Biogeochemical signatures and microbial activity of different cold-seep habitats along the Gulf of Mexico deep slope

    NASA Astrophysics Data System (ADS)

    Joye, Samantha B.; Bowles, Marshall W.; Samarkin, Vladimir A.; Hunter, Kimberley S.; Niemann, Helge

    2010-11-01

    Microorganisms and the processes they mediate serve as the metabolic foundation of cold seeps. We characterized a suite of biogeochemical constituents and quantified rates of two key microbial processes, Sulfate Reduction (SR) and Anaerobic Oxidation of Methane (AOM), to assess variability between habitats at water depths exceeding 1000 m in the northern Gulf of Mexico. Rates of SR were highest in sediments beneath microbial mats, lower in brine-influenced and oil-influenced sediments, and lowest in animal habitats. Sediments collected near tubeworms had the highest SR rates for animal habitats. Rates of AOM generally were low, but higher rates were associated with brine-influenced, oil-influenced, tubeworm- and urchin-inhabited sediments. Rates of both SR and AOM were orders of magnitude lower at deep-slope sites compared to upper-slope sites examined previously. As observed at upper-slope sites, SR and AOM rates were often loosely coupled. At one site, AOM rates exceeded SR rates, suggesting that an alternate electron acceptor for AOM is possible. Extremely depleted δ13C values in methane illustrated the broad significance of biogenic methane production at deep-slope sites. Brine-influenced habitats were characterized by extremely high concentrations of ammonium and dissolved organic carbon, serving as important focused sources of these chemicals to adjacent environments.

  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. 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.

  2. Periodic mid-Cretaceous oceanic anoxic events linked by oscillations of the phosphorus and oxygen biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Handoh, Itsuki C.; Lenton, Timothy M.

    2003-12-01

    A series of oceanic anoxic events (OAEs) occurred in the mid-Cretaceous warm period (120-80 Ma) that have been linked with high rates of organic carbon burial, warm high- and low- latitude temperatures, and sea-level changes. OAEs have been studied individually, but a causal mechanism that connects them has been lacking. We show that peaks in phosphorus accumulation in marine sediments broadly coincide with OAEs 1a, 1b, 1d, 2, and 3, and exhibit a 5-6 Myr periodicity, which for reactive-P is prominent over 100-80 Ma. Oxic-anoxic oscillations of this frequency are also found in a model of the coupled N, P, C, and O2 biogeochemical cycles. These oscillations are maintained by positive feedbacks between phosphate concentration, biological productivity, and anoxia in the global ocean and counteracting, but slower, negative feedbacks involving changes in atmospheric oxygen. An increase in phosphorus weathering rate above a critical threshold can shift the system into self-sustaining oscillation. This could have been caused by tectonic and volcanic forcing increasing atmospheric CO2 and global warmth 120-80 Ma, augmented by the rise of flowering plants around 100 Ma. With a plausible forcing scenario, we are able to reproduce the approximate timing of OAEs 1a, 1b, 1d, 2, and 3 in the model.

  3. Realistic primary and new productions in a 3D global biogeochemical model: biological complexity or physical forcing?

    NASA Astrophysics Data System (ADS)

    Popova, E. E.; Coward, A. C.

    2003-04-01

    A nitrogen-based, five compartment biological model has been coupled to a one degree OCCAM (Ocean Circulation and Climate Advanced Modelling Project) model with a KPP ("K profile parameterisation") of the vertical mixing. The biological model state variables are Phytoplankton, Zooplankton, Detritus, Nitrate, and Ammonium. A comparison of the solution with global satellite ocean colour shows that the model is capable of a realistic description of the main seasonal and regional patterns of the surface chlorophyll. Agreement is also good for satellite derived estimates of primary production. In situ data available from local study sites (such as BATS, NABE, India, Papa) are used for the detailed comparison of the model output with the observed ecosystem dynamics in different biological provinces. We discuss performance of the physical and biological model in contrasting areas of the World Ocean. In spite of the biological model being a very simple one, we are able to reproduce the major differences between ecosystem dynamics of these areas. We believe that the success of any global biogeochemical model is dependent first of all on the correct representation of the upper mixed layer (UML) dynamics. Without being able to reproduce contrasting UML regimes in different areas of the World Ocean (such as difference between the North Atlantic and Southern Ocean, or North Atlantic and North Pacific), increased complexity biological models are in danger of producing the right results by the wrong reason.

  4. Hydrological and biogeochemical constraints on terrestrial carbon cycle feedbacks

    NASA Astrophysics Data System (ADS)

    Mystakidis, Stefanos; Seneviratne, Sonia I.; Gruber, Nicolas; Davin, Edouard L.

    2017-01-01

    The feedbacks between climate, atmospheric CO2 concentration and the terrestrial carbon cycle are a major source of uncertainty in future climate projections with Earth systems models. Here, we use observation-based estimates of the interannual variations in evapotranspiration (ET), net biome productivity (NBP), as well as the present-day sensitivity of NBP to climate variations, to constrain globally the terrestrial carbon cycle feedbacks as simulated by models that participated in the fifth phase of the coupled model intercomparison project (CMIP5). The constraints result in a ca. 40% lower response of NBP to climate change and a ca. 30% reduction in the strength of the CO2 fertilization effect relative to the unconstrained multi-model mean. While the unconstrained CMIP5 models suggest an increase in the cumulative terrestrial carbon storage (477 PgC) in response to an idealized scenario of 1%/year atmospheric CO2 increase, the constraints imply a ca. 19% smaller change. Overall, the applied emerging constraint approach offers a possibility to reduce uncertainties in the projections of the terrestrial carbon cycle, which is a key determinant of the future trajectory of atmospheric CO2 concentration and resulting climate change.

  5. The Oceanic Biogeochemical Cycle of Zinc and Its Isotopes

    NASA Astrophysics Data System (ADS)

    Vance, D.; Little, S. H.; de Souza, G. F.; Cullen, J. T.; Lohan, M. C.

    2014-12-01

    Zinc (Zn) is the most abundant trace metal in the phytoplankton that dominate vertical carbon export in the ocean, the diatoms. But the strong relationship between the vertical distributions of Zn and the silicon (Si) that makes up the opal hard parts of diatoms represents a long-standing puzzle. Zn is overwhelmingly co-located with phosphate in the organic matter of diatom cells, not with Si in opal, and is regenerated with phosphate in the upper ocean, not with Si in the deep. The resolution of this apparent paradox is key both to an understanding of the global oceanic cycling of Zn, and to the rates and mechanisms by which biologically-assimilated trace metals are returned to the photic zone. Here, we show that oceanic dissolved Zn exhibits significant isotopic variation in the upper ocean that is consistent with vertical cycling. However, we suggest that the isotopically homogeneous global deep ocean Zn pool is largely sourced from the Southern Ocean. This leads to a new view of the global oceanic cycling of this important trace metal, one that is consistent with the unique physiology of Southern Ocean diatoms, the coupling of Zn and Si in the global deep ocean, and the emerging paradigm for global ocean nutrient dynamics. Our data and interpretation imply a small Zn pool that is biologically cycled in the upper ocean, but is to a great extent decoupled from the much larger Southern-Ocean-dominated deep ocean pool.

  6. Biogeochemical phosphorus mass balance for Lake Baikal, southeastern Siberia, Russia

    USGS Publications Warehouse

    Callender, E.; Granina, L.

    1997-01-01

    Extensive data for Lake Baikal have been synthesized into a geochemical mass balance for phosphorus (P). Some of the P budget and internal cycling terms for Baikal have been compared to similar terms for oligotrophic Lake Superior, mesotrophic Lake Michigan and the Baltic Sea, and the Ocean. Lake Baikal has a large external source of fluvial P compared to the Laurentian upper Great Lakes and the Ocean. The major tributary to Lake Baikal has experienced substantial increases in organic P loading during the past 25 years. This, coupled with potential P inputs from possible phosphorite mining, may threaten Baikal's oligotrophic status in the future. Water-column remineralization of particulate organic P is substantially greater in Lake Baikal than in the Laurentian Great Lakes. This is probably due to the great water depths of Lake Baikal. There is a gradient in P burial efficiency, with very high values (80%) for Lake Baikal and Lake Superior, lower values (50%) for Lake Michigan and the Baltic Sea, and a low value (13%) for the Ocean. The accumulation rate of P in Lake Baikal sediments is somewhat greater than that in the Laurentian upper Great Lakes and the Baltic Sea, and much greater than in the Ocean. Benthic regeneration rates are surprisingly similar for large lacustrine and marine environments and supply less than 10% of the P utilized for primary production in these aquatic environments.

  7. How important are biogeochemical hotspots at aquifer-river interfaces for surface water and groundwater quality?

    NASA Astrophysics Data System (ADS)

    Krause, S.; Blume, T.; Weatherill, J.; Munz, M.; Tecklenburg, C.; Angermann, L.; Cassidy, N. J.

    2012-04-01

    The mixing of groundwater (GW) and surface water (SW) can have substantial impact on the transformation of solutes transported between aquifer and river. The assessment of biogeochemical cycling at reactivity hotspots as the aquifer-river interface and its implications for GW and SW quality require detailed understanding of the complex patterns of GW-SW exchange fluxes and residence time distributions in particular under changing climatic and landuse conditions. This study presents combined experimental and model-based investigations of the physical drivers and chemical controls of nutrient transport and transformation at the aquifer-river interfaces of two upland and lowland UK rivers. It combines the application of in-stream geophysical exploration techniques, multi-level mini-piezometer networks, active and passive heat tracing methods (including fibre-optic distributed temperature sensing - FO-DTS) for identifying hyporheic exchange fluxes and residence time distributions with multi-scale approaches of hyporheic pore-water sampling and reactive tracers for analysing the patterns of streambed redox conditions and chemical transformation rates. The analysis of hyporheic pore water from nested multi-level mini piezometers and passive gel probe samplers revealed significant spatial variability in streambed redox conditions and concentration changes of nitrogen species, dissolved oxygen and bio-available organic carbon. Hot spots of increased nitrate attenuation were identified beneath semi-confining peat lenses in the streambed of the investigated lowland river. The intensity of concentration changes underneath the confining peat pockets correlated with the state of anoxia in the pore water as well as the supply of organic carbon and hyporheic residence times. In contrast, at locations where flow inhibiting peat layers were absent or disrupted - fast exchange between aquifer and river caused a break-through of nitrate without significant concentration changes along

  8. 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

  9. Vadose zone attenuation of organic compounds at a crude oil spill site - Interactions between biogeochemical reactions and multicomponent gas transport

    USGS Publications Warehouse

    Molins, S.; Mayer, K.U.; Amos, R.T.; Bekins, B.A.

    2010-01-01

    Contaminant attenuation processes in the vadose zone of a crude oil spill site near Bemidji, MN have been simulated with a reactive transport model that includes multicomponent gas transport, solute transport, and the most relevant biogeochemical reactions. Dissolution and volatilization of oil components, their aerobic and anaerobic degradation coupled with sequential electron acceptor consumption, ingress of atmospheric O2, and the release of CH4 and CO2 from the smear zone generated by the floating oil were considered. The focus of the simulations was to assess the dynamics between biodegradation and gas transport processes in the vadose zone, to evaluate the rates and contributions of different electron accepting processes towards vadose zone natural attenuation, and to provide an estimate of the historical mass loss. Concentration distributions of reactive (O2, CH4, and CO2) and non-reactive (Ar and N2) gases served as key constraints for the model calibration. Simulation results confirm that as of 2007, the main degradation pathway can be attributed to methanogenic degradation of organic compounds in the smear zone and the vadose zone resulting in a contaminant plume dominated by high CH4 concentrations. In accordance with field observations, zones of volatilization and CH4 generation are correlated to slightly elevated total gas pressures and low partial pressures of N2 and Ar, while zones of aerobic CH4 oxidation are characterized by slightly reduced gas pressures and elevated concentrations of N2 and Ar. Diffusion is the most significant transport mechanism for gases in the vadose zone; however, the simulations also indicate that, despite very small pressure gradients, advection contributes up to 15% towards the net flux of CH4, and to a more limited extent to O2 ingress. Model calibration strongly suggests that transfer of biogenically generated gases from the smear zone provides a major control on vadose zone gas distributions and vadose zone carbon

  10. 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

    In soils and sediments microorganisms perform essential ecosystem services through their roles in regulating the stability of carbon and the flux of nutrients, and the purification of water. But these are complex systems with the physical, chemical and biological components all intimately connected. Components of this complexity are gradually being uncovered and our understanding of the extent of microbial functional diversity in particular has been enhanced greatly with the development of cultivation independent approaches. However we have not moved far beyond a descriptive and correlative use of this powerful resource. As the ability to reconstruct thousands of genomes from microbial populations using metagenomic techniques gains momentum, the challenge will be to develop an understanding of how these metabolic blueprints serve to influence the fitness of organisms within these complex systems and how populations emerge and impact the physical and chemical properties of their environment. In the presentation we will discuss the development of a trait-based model of microbial activity that simulates coupled guilds of microorganisms that are parameterized including traits extracted from large-scale metagenomic data. Using a reactive transport framework we simulate the thermodynamics of coupled electron donor and acceptor reactions to predict the energy available for respiration, biomass development and exo-enzyme production. Each group within a functional guild is parameterized with a unique combination of traits governing organism fitness under dynamic environmental conditions. This presentation will address our latest developments in the estimation of trait values related to growth rate and the identification and linkage of key fitness traits associated with respiratory and fermentative pathways, macromolecule depolymerization enzymes and nitrogen fixation from metagenomic data. We are testing model sensitivity to initial microbial composition and intra

  11. Novel tracer method to measure isotopic labeled gas-phase nitrous acid (HO15NO) in biogeochemical studies.

    PubMed

    Wu, Dianming; Kampf, Christopher J; Pöschl, Ulrich; Oswald, Robert; Cui, Junfang; Ermel, Michael; Hu, Chunsheng; Trebs, Ivonne; Sörgel, Matthias

    2014-07-15

    Gaseous nitrous acid (HONO), the protonated form of nitrite, contributes up to ∼60% to the primary formation of hydroxyl radical (OH), which is a key oxidant in the degradation of most air pollutants. Field measurements and modeling studies indicate a large unknown source of HONO during daytime. Here, we developed a new tracer method based on gas-phase stripping-derivatization coupled to liquid chromatography-mass spectrometry (LC-MS) to measure the 15N relative exceedance, ψ(15N), of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye, purified by solid phase extraction (SPE), and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). In the optimal working range of ψ(15N)=0.2-0.5, the relative standard deviation of ψ(15N) is <4%. The optimum pH and solvents for extraction by SPE and potential interferences are discussed. The method was applied to measure HO15NO emissions from soil in a dynamic chamber with and without spiking 15) labeled urea. The identification of HO15NO from soil with 15N urea addition confirmed biogenic emissions of HONO from soil. The method enables a new approach of studying the formation pathways of HONO and its role for atmospheric chemistry (e.g., ozone formation) and environmental tracer studies on the formation and conversion of gaseous HONO or aqueous NO2- as part of the biogeochemical nitrogen cycle, e.g., in the investigation of fertilization effects on soil HONO emissions and microbiological conversion of NO2- in the hydrosphere.

  12. Hydrological and biogeochemical constraints on terrestrial carbon cycle projections

    NASA Astrophysics Data System (ADS)

    Mystakidis, Stefanos; Davin, Edouard L.; Gruber, Nicolas; Seneviratne, Sonia I.

    2016-04-01

    The terrestrial biosphere is currently acting as a sink for about a third of the total anthropogenic CO2 emissions. However, the future fate of this sink in the coming decades is very uncertain, as current Earth System Models (ESMs) simulate diverging responses of the terrestrial carbon cycle to upcoming climate change. Here, we use observation-based constraints of water and carbon fluxes to reduce uncertainties in the projected terrestrial carbon cycle response derived from simulations of ESMs conducted as part of the 5th phase of the Coupled Model Intercomparison Project (CMIP5). We find in the ESMs a clear linear relationship between present-day Evapotranspiration (ET) and Gross Primary Productivity (GPP), as well as between these present-day fluxes and projected changes in GPP, thus providing an emergent constraint on projected GPP. Constraining the ESMs based on their ability to simulate present-day ET and GPP leads to a substantial decrease of the projected GPP and to a ca. 50% reduction of the associated model spread in GPP by the end of the century. Given the strong correlation between projected changes in GPP and in NBP in the ESMs, applying the constraints on Net Biome Productivity (NBP) reduces the model spread in the projected land sink by more than 30% by 2100. Also, the projected decline in the land sink is at least doubled in the constrained ensembles and the probability that the terrestrial biosphere is turned into a net carbon source by the end of the century is strongly increased. Moreover, a similar strategy is used to provide constraints on the feedbacks involving the terrestrial carbon cycle and the climate system. The findings indicate that the decline in the future land carbon uptake might be stronger than previously thought, which would have important implications for the rate of increase of the atmospheric CO2 concentration and for future climate change.

  13. Nonadiabatic Coupling

    NASA Astrophysics Data System (ADS)

    Kryachko, Eugene S.

    The general features of the nonadiabatic coupling and its relation to molecular properties are surveyed. Some consequences of the [`]equation of motion', formally expressing a [`]smoothness' of a given molecular property within the diabatic basis, are demonstrated. A particular emphasis is made on the relation between a [`]smoothness' of the electronic dipole moment and the generalized Mulliken-Hush formula for the diabatic electronic coupling.

  14. 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.

  15. Biogeochemical evolution of sulfide ore mine tailings profiles under semi-arid climate

    NASA Astrophysics Data System (ADS)

    Chorover, J.

    2014-12-01

    Mining represents a principal form of earth surface disturbance in the anthropocene. Weathering reactions that ensue following tailings deposition are strongly affected by climatic forcing and tailings composition, and these also affect the weathering-induced transformations of the associated mineral assemblages and metal(loid) contaminants. The presence or absence of plants and associated microbiota can have a profound influence on these weathering trajectories. We employed field, laboratory and modeling approaches to resolve the impact of (bio)geochemical weathering reactions on the transformation of mine tailings parent materials into soil over the time following mining cessation. Using controlled experiments, we have evaluated the impacts of plants and associated rhizosphere microbiota on these reactions, hydrologic fluxes, and the molecular speciation of mining derived contaminants. Plant establishment is shown to alter site ecohydrology and biogeochemical weathering processes leading to distinctly different weathering products and patterns.

  16. Peatlands as Dynamic Biogeochemical Ecotones: Elemental Concentrations, Stoichiometries and Accumulation in Peatland Soils of Ontario, Canada

    NASA Astrophysics Data System (ADS)

    Moore, T. R.; Wang, M.; Talbot, J.; Riley, J. L.

    2015-12-01

    Peatlands act as biogeochemical interfaces between terrestrial and aquatic systems and are 'hotspots', particularly for carbon cycling and the accumulation of nutrients and other elements within the peat profile. This results in storage of substantial amounts of carbon, nutrients and metals, particularly in northern peatlands. Using a data base of over 400 peat profiles and 1700 individual peat samples from bog, fen and swamp sites in Ontario, Canada, we examine the profile concentrations of C, N, P, Ca, Mg, K, Hg, Pb, As, Cu, Mn, Zn, Fe and Al, and estimate the storage and accumulation of these elements. We show how these profiles, spatial patterns, stoichiometries and accumulation rates are controlled by biogeochemical processes and influenced by geochemical setting, hydrology, atmospheric input and pollution, and ecological and microbial transformations.

  17. 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.

  18. Biogeochemical controls of arsenic occurrence and mobility in the Indian Sundarban mangrove ecosystem.

    PubMed

    Mandal, S K; Dey, Mitali; Ganguly, D; Sen, S; Jana, T K

    2009-05-01

    This study aims to investigate the control of arsenic distribution by biogeochemical processes in the Indian Sundarban mangrove ecosystem and the importance of this ecosystem as an arsenic source for surrounding coastal water. The As(V)/As(III) ratio was found to be significantly lower in both surface and pore waters compared to sea water, which could be attributed to biogeochemical interconversion of these arsenic forms. The biological uptake of arsenic due to primary and benthic production occurs during the post-monsoon season, and is followed by the release of arsenic during the biochemical degradation and dissolution of plankton in the pre-monsoon season. These results suggest that arsenic is immobilized during incorporation into the arsenic-bearing initial phase, and unlikely to be released into pore water until the complete microbial degradation of arsenic-bearing organic compounds.

  19. Defining Mediterranean and Black Sea Biogeochemical Subprovinces and Synthetic Ocean Indicators Using Mesoscale Oceanographic Features

    PubMed Central

    Nieblas, Anne-Elise; Drushka, Kyla; Reygondeau, Gabriel; Rossi, Vincent; Demarcq, Hervé; Dubroca, Laurent; Bonhommeau, Sylvain

    2014-01-01

    The Mediterranean and Black Seas are semi-enclosed basins characterized by high environmental variability and growing anthropogenic pressure. This has led to an increasing need for a bioregionalization of the oceanic environment at local and regional scales that can be used for managerial applications as a geographical reference. We aim to identify biogeochemical subprovinces within this domain, and develop synthetic indices of the key oceanographic dynamics of each subprovince to quantify baselines from which to assess variability and change. To do this, we compile a data set of 101 months (2002–2010) of a variety of both “classical” (i.e., sea surface temperature, surface chlorophyll-a, and bathymetry) and “mesoscale” (i.e., eddy kinetic energy, finite-size Lyapunov exponents, and surface frontal gradients) ocean features that we use to characterize the surface ocean variability. We employ a k-means clustering algorithm to objectively define biogeochemical subprovinces based on classical features, and, for the first time, on mesoscale features, and on a combination of both classical and mesoscale features. Principal components analysis is then performed on the oceanographic variables to define integrative indices to monitor the environmental changes within each resultant subprovince at monthly resolutions. Using both the classical and mesoscale features, we find five biogeochemical subprovinces for the Mediterranean and Black Seas. Interestingly, the use of mesoscale variables contributes highly in the delineation of the open ocean. The first axis of the principal component analysis is explained primarily by classical ocean features and the second axis is explained by mesoscale features. Biogeochemical subprovinces identified by the present study can be useful within the European management framework as an objective geographical framework of the Mediterranean and Black Seas, and the synthetic ocean indicators developed here can be used to monitor

  20. Characterization of Biogeochemical Variability in a Tidal Estuary Using High Resolution Optical Measurements

    NASA Astrophysics Data System (ADS)

    Chang, G.; Jones, C.; Martin, T.

    2015-12-01

    The Berry's Creek Study Area (BCSA) is a tidal estuary located in New Jersey. Several chemicals of potential concern (COPCs) are present in the BCSA waterway and marshes, including mercury, methyl mercury, and polychlorinated biphenyls. Concentrations of COPCs and suspended solids in the BCSA vary temporally and spatially due to tidal variability, freshwater flow events, and interaction of marsh, waterway, and sediment bed materials. This system-wide variability confounds evaluation of COPC sources and transport mechanisms when using conventional laboratory-based analysis of discrete water column samples. Therefore, an optically-based biogeochemical monitoring program was conducted using near-continuous measurements of optical properties and an optical-biogeochemical partial least-squares regression model pioneered by B. Bergamaschi (USGS) and colleagues. The objective of the study was to characterize COPC concentration dynamics in the BCSA water column and relate the analysis to sediment bed processes. Optical-biogeochemical model results indicated that, in general, measured optical properties were sufficient for predicting COPC concentrations to within 10% of the accuracy of laboratory-based analytical measurements. The continuous, high temporal resolution time series of COPC concentrations determined by the optical-biogeochemical model enabled evaluation of the sediment bed dynamics and variability of COPCs in the surface water of the BCSA. Results indicate that tidally-induced resuspension of waterway sediment bed particulates is the primary mechanism for transport of COPCs to surface water. Waterway-marsh tidal exchange shows a net mass flux of particulate COPCs from waterway to marsh, indicating that particulate COPCs are retained and accumulate in the marshes with relatively little net export of dissolved COPCs from the marshes to the waterway.

  1. A state-space Bayesian framework for estimating biogeochemical transformations using time-lapse geophysical data

    SciTech Connect

    Chen, J.; Hubbard, S.; Williams, K.; Pride, S.; Li, L.; Steefel, C.; Slater, L.

    2009-04-15

    We develop a state-space Bayesian framework to combine time-lapse geophysical data with other types of information for quantitative estimation of biogeochemical parameters during bioremediation. We consider characteristics of end-products of biogeochemical transformations as state vectors, which evolve under constraints of local environments through evolution equations, and consider time-lapse geophysical data as available observations, which could be linked to the state vectors through petrophysical models. We estimate the state vectors and their associated unknown parameters over time using Markov chain Monte Carlo sampling methods. To demonstrate the use of the state-space approach, we apply it to complex resistivity data collected during laboratory column biostimulation experiments that were poised to precipitate iron and zinc sulfides during sulfate reduction. We develop a petrophysical model based on sphere-shaped cells to link the sulfide precipitate properties to the time-lapse geophysical attributes and estimate volume fraction of the sulfide precipitates, fraction of the dispersed, sulfide-encrusted cells, mean radius of the aggregated clusters, and permeability over the course of the experiments. Results of the case study suggest that the developed state-space approach permits the use of geophysical datasets for providing quantitative estimates of end-product characteristics and hydrological feedbacks associated with biogeochemical transformations. Although tested here on laboratory column experiment datasets, the developed framework provides the foundation needed for quantitative field-scale estimation of biogeochemical parameters over space and time using direct, but often sparse wellbore data with indirect, but more spatially extensive geophysical datasets.

  2. Investigation of Biogeochemical Functional Proxies in Headwater Streams Across a Range of Channel and Catchment Alterations

    NASA Astrophysics Data System (ADS)

    Berkowitz, Jacob F.; Summers, Elizabeth A.; Noble, Chris V.; White, John R.; DeLaune, Ronald D.

    2014-03-01

    Historically, headwater streams received limited protection and were subjected to extensive alteration from logging, farming, mining, and development activities. Despite these alterations, headwater streams provide essential ecological functions. This study examines proxy measures of biogeochemical function across a range of catchment alterations by tracking nutrient cycling (i.e., inputs, processing, and stream loading) with leaf litter fall, leaf litter decomposition, and water quality parameters. Nutrient input and processing remained highest in second growth forests (the least altered areas within the region), while recently altered locations transported higher loads of nutrients, sediments, and conductivity. Biogeochemical functional proxies of C and N input and processing significantly, positively correlated with rapid assessment results (Pearson coefficient = 0.67-0.81; P = 0.002-0.016). Additionally, stream loading equations demonstrate that N and P transport, sediment, and specific conductivity negatively correlated with rapid assessment scores (Pearson coefficient = 0.56-0.81; P = 0.002-0.048). The observed increase in stream loading with lower rapid assessment scores indicates that catchment alterations impact stream chemistry and that rapid assessments provide useful proxy measures of function in headwater ecosystems. Significant differences in nutrient processing, stream loading, water quality, and rapid assessment results were also observed between recently altered (e.g., mined) headwater streams and older forested catchments (Mann-Whitney U = 24; P = 0.01-0.024). Findings demonstrate that biogeochemical function is reduced in altered catchments, and rapid assessment scores respond to a combination of alteration type and recovery time. An analysis examining time and economic requirements of proxy measurements highlights the benefits of rapid assessment methods in evaluating biogeochemical functions.

  3. Cyclic biogeochemical processes and nitrogen fate beneath a subtropical stormwater infiltration basin.

    PubMed

    O'Reilly, Andrew M; Chang, Ni-Bin; Wanielista, Martin P

    2012-05-15

    A stormwater infiltration basin in north-central Florida, USA, was monitored from 2007 through 2008 to identify subsurface biogeochemical processes, with emphasis on N cycling, under the highly variable hydrologic conditions common in humid, subtropical climates. Cyclic variations in biogeochemical processes generally coincided with wet and dry hydrologic conditions. Oxidizing conditions in the subsurface persisted for about one month or less at the beginning of wet periods with dissolved O(2) and NO(3)(-) showing similar temporal patterns. Reducing conditions in the subsurface evolved during prolonged flooding of the basin. At about the same time O(2) and NO(3)(-) reduction concluded, Mn, Fe and SO(4)(2-) reduction began, with the onset of methanogenesis one month later. Reducing conditions persisted up to six months, continuing into subsequent dry periods until the next major oxidizing infiltration event. Evidence of denitrification in shallow groundwater at the site is supported by median NO(3)(-)-N less than 0.016 mg L(-1), excess N(2) up to 3 mg L(-1) progressively enriched in δ(15)N during prolonged basin flooding, and isotopically heavy δ(15)N and δ(18)O of NO(3)(-) (up to 25‰ and 15‰, respectively). Isotopic enrichment of newly infiltrated stormwater suggests denitrification was partially completed within two days. Soil and water chemistry data suggest that a biogeochemically active zone exists in the upper 1.4m of soil, where organic carbon was the likely electron donor supplied by organic matter in soil solids or dissolved in infiltrating stormwater. The cyclic nature of reducing conditions effectively controlled the N cycle, switching N fate beneath the basin from NO(3)(-) leaching to reduction in the shallow saturated zone. Results can inform design of functionalized soil amendments that could replace the native soil in a stormwater infiltration basin and mitigate potential NO(3)(-) leaching to groundwater by replicating the biogeochemical

  4. A state-space Bayesian framework for estimating biogeochemical transformations using time-lapse geophysical data

    NASA Astrophysics Data System (ADS)

    Chen, Jinsong; Hubbard, Susan S.; Williams, Kenneth H.; Pride, Steve; Li, Li; Steefel, Carl; Slater, Lee

    2009-08-01

    We develop a state-space Bayesian framework to combine time-lapse geophysical data with other types of information for quantitative estimation of biogeochemical parameters during bioremediation. We consider characteristics of end products of biogeochemical transformations as state vectors, which evolve under constraints of local environments through evolution equations, and consider time-lapse geophysical data as available observations, which could be linked to the state vectors through petrophysical models. We estimate the state vectors and their associated unknown parameters over time using Markov chain Monte Carlo sampling methods. To demonstrate the use of the state-space approach, we apply it to complex resistivity data collected during laboratory column biostimulation experiments that were poised to precipitate iron and zinc sulfides during sulfate reduction. We develop a petrophysical model based on sphere-shaped cells to link the sulfide precipitate properties to the time-lapse geophysical attributes and estimate volume fraction of the sulfide precipitates, fraction of the dispersed, sulfide-encrusted cells, mean radius of the aggregated clusters, and permeability over the course of the experiments. Results of the case study suggest that the developed state-space approach permits the use of geophysical data sets for providing quantitative estimates of end-product characteristics and hydrological feedbacks associated with biogeochemical transformations. Although tested here on laboratory column experiment data sets, the developed framework provides the foundation needed for quantitative field-scale estimation of biogeochemical parameters over space and time using direct, but often sparse wellbore data with indirect, but more spatially extensive geophysical data sets.

  5. Strong Seasonality of Biogeochemical Characteristics and Source Regions in Permafrost Watersheds

    NASA Astrophysics Data System (ADS)

    Douglas, T. A.

    2015-12-01

    High latitude watersheds experience a dramatic seasonality of up to nine months of cold, snow covered winter and a warm, bright, summer. Spring melt runoff is a dramatic two to three week period when up to 75% of the yearly precipitation runs off. Identifying sources and measuring fluxes of compounds out of Arctic rivers is difficult in large rivers because they represent the combined effect of innumerable plot-scale melt water sources, each coming from different soil and vegetation types, each experiencing a slightly different melt timing and evolution. Numerous studies have shown spring melt is characterized by an ionic pulse of solutes, dissolved organic carbon and other nutrients (ammonium, phosphate and nitrate) leached by snow melt water from surface vegetation and soils. Summer and fall flows are comprised largely of shallow to deepening sources from a downwardly expanding seasonally thawed ("active") layer. In late summer flowpaths deepen and the biogeochemical composition of surface waters may be sourced from an increasing mineral weathering zone representing landscape scale soil processes. The watershed biogeochemical response to precipitation may also yield insight into subsurface permafrost geomorphological characteristics and flowpaths through water tracks or other small depressions. Winter processes are the least studied or understood but overflow ice ("aufeis") provides access to deep, old waters. The deeper snow pack in depressions can provide protection against winter cold and feed back to deeper summer season thaw. This presentation will focus on using water stable isotopes, major ion concentrations, trace metals, nutrients, and permafrost delineation to identify biogeochemical sources in watersheds draining continuous and discontinuous permafrost in Alaska. Biogeochemical processes associated with scaling, meteorology, and climate warming will be discussed.

  6. Cyclic biogeochemical processes and nitrogen fate beneath a subtropical stormwater infiltration basin

    USGS Publications Warehouse

    O'Reilly, Andrew M.; Chang, Ni-Bin; Wanielista, Martin P.

    2012-01-01

    A stormwater infiltration basin in north–central Florida, USA, was monitored from 2007 through 2008 to identify subsurface biogeochemical processes, with emphasis on N cycling, under the highly variable hydrologic conditions common in humid, subtropical climates. Cyclic variations in biogeochemical processes generally coincided with wet and dry hydrologic conditions. Oxidizing conditions in the subsurface persisted for about one month or less at the beginning of wet periods with dissolved O2 and NO3- showing similar temporal patterns. Reducing conditions in the subsurface evolved during prolonged flooding of the basin. At about the same time O2 and NO3- reduction concluded, Mn, Fe and SO42- reduction began, with the onset of methanogenesis one month later. Reducing conditions persisted up to six months, continuing into subsequent dry periods until the next major oxidizing infiltration event. Evidence of denitrification in shallow groundwater at the site is supported by median NO3-–N less than 0.016 mg L-1, excess N2 up to 3 mg L-1 progressively enriched in δ15N during prolonged basin flooding, and isotopically heavy δ15N and δ18O of NO3- (up to 25‰ and 15‰, respectively). Isotopic enrichment of newly infiltrated stormwater suggests denitrification was partially completed within two days. Soil and water chemistry data suggest that a biogeochemically active zone exists in the upper 1.4 m of soil, where organic carbon was the likely electron donor supplied by organic matter in soil solids or dissolved in infiltrating stormwater. The cyclic nature of reducing conditions effectively controlled the N cycle, switching N fate beneath the basin from NO3- leaching to reduction in the shallow saturated zone. Results can inform design of functionalized soil amendments that could replace the native soil in a stormwater infiltration basin and mitigate potential NO3- leaching to groundwater by replicating the biogeochemical conditions under the observed basin.

  7. Global Biogeochemical Changes at Both Ends of the Proterozoic: Insights from Phosphorites

    NASA Astrophysics Data System (ADS)

    Papineau, Dominic

    2010-03-01

    The distribution of major phosphate deposits in the Precambrian sedimentary rock record is restricted to periods that witnessed global biogeochemical changes, but the cause of this distribution is unclear. The oldest known phosphogenic event occurred around 2.0 Ga and was followed, after more than 1.3 billion years, by an even larger phosphogenic event in the Neoproterozoic. Phosphorites (phosphate-rich sedimentary rocks that contain more than 15% P2O5) preserve a unique record of seawater chemistry, biological activity, and oceanographic changes. In an attempt to emphasize the potentially crucial significance of phosphorites in the evolution of Proterozoic biogeochemical cycles, this contribution provides a review of some important Paleoproterozoic phosphate deposits and of models proposed for their origin. A new model is then presented for the spatial and temporal modes of occurrence of phosphorites along with possible connections to global changes at both ends of the Proterozoic. Central to the new model is that periods of atmospheric oxygenation may have been caused by globally elevated rates of primary productivity stimulated by high fluxes of phosphorus delivery to seawater as a result of increased chemical weathering of continental crust over geological timescales. The striking similarities in biogeochemical evolution between the Paleo- and Neoproterozoic are discussed in light of the two oldest major phosphogenic events and their possible relation to the stepwise rise of atmospheric oxygen that ultimately resulted in significant leaps in biological evolution.

  8. Global biogeochemical changes at both ends of the proterozoic: insights from phosphorites.

    PubMed

    Papineau, Dominic

    2010-03-01

    The distribution of major phosphate deposits in the Precambrian sedimentary rock record is restricted to periods that witnessed global biogeochemical changes, but the cause of this distribution is unclear. The oldest known phosphogenic event occurred around 2.0 Ga and was followed, after more than 1.3 billion years, by an even larger phosphogenic event in the Neoproterozoic. Phosphorites (phosphate-rich sedimentary rocks that contain more than 15% P(2)O(5)) preserve a unique record of seawater chemistry, biological activity, and oceanographic changes. In an attempt to emphasize the potentially crucial significance of phosphorites in the evolution of Proterozoic biogeochemical cycles, this contribution provides a review of some important Paleoproterozoic phosphate deposits and of models proposed for their origin. A new model is then presented for the spatial and temporal modes of occurrence of phosphorites along with possible connections to global changes at both ends of the Proterozoic. Central to the new model is that periods of atmospheric oxygenation may have been caused by globally elevated rates of primary productivity stimulated by high fluxes of phosphorus delivery to seawater as a result of increased chemical weathering of continental crust over geological timescales. The striking similarities in biogeochemical evolution between the Paleo- and Neoproterozoic are discussed in light of the two oldest major phosphogenic events and their possible relation to the stepwise rise of atmospheric oxygen that ultimately resulted in significant leaps in biological evolution.

  9. 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).

  10. 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.

  11. Biogeochemical significance of pelagic ecosystem function: an end-Cretaceous case study.

    PubMed

    Henehan, Michael J; Hull, Pincelli M; Penman, Donald E; Rae, James W B; Schmidt, Daniela N

    2016-05-19

    Pelagic ecosystem function is integral to global biogeochemical cycling, and plays a major role in modulating atmospheric CO2 concentrations (pCO2). Uncertainty as to the effects of human activities on marine ecosystem function hinders projection of future atmospheric pCO2 To this end, events in the geological past can provide informative case studies in the response of ecosystem function to environmental and ecological changes. Around the Cretaceous-Palaeogene (K-Pg) boundary, two such events occurred: Deccan large igneous province (LIP) eruptions and massive bolide impact at the Yucatan Peninsula. Both perturbed the environment, but only the impact coincided with marine mass extinction. As such, we use these events to directly contrast the response of marine biogeochemical cycling to environmental perturbation with and without changes in global species richness. We measure this biogeochemical response using records of deep-sea carbonate preservation. We find that Late Cretaceous Deccan volcanism prompted transient deep-sea carbonate dissolution of a larger magnitude and timescale than predicted by geochemical models. Even so, the effect of volcanism on carbonate preservation was slight compared with bolide impact. Empirical records and geochemical models support a pronounced increase in carbonate saturation state for more than 500 000 years following the mass extinction of pelagic carbonate producers at the K-Pg boundary. These examples highlight the importance of pelagic ecosystems in moderating climate and ocean chemistry.

  12. Invasive Fishes Generate Biogeochemical Hotspots in a Nutrient-Limited System

    PubMed Central

    Capps, Krista A.; Flecker, Alexander S.

    2013-01-01

    Fishes can play important functional roles in the nutrient dynamics of freshwater systems. Aggregating fishes have the potential to generate areas of increased biogeochemical activity, or hotspots, in streams and rivers. Many of the studies documenting the functional role of fishes in nutrient dynamics have focused on native fish species; however, introduced fishes may restructure nutrient storage and cycling freshwater systems as they can attain high population densities in novel environments. The purpose of this study was to examine the impact of a non-native catfish (Loricariidae: Pterygoplichthys) on nitrogen and phosphorus remineralization and estimate whether large aggregations of these fish generate measurable biogeochemical hotspots within nutrient-limited ecosystems. Loricariids formed large aggregations during daylight hours and dispersed throughout the stream during evening hours to graze benthic habitats. Excretion rates of phosphorus were twice as great during nighttime hours when fishes were actively feeding; however, there was no diel pattern in nitrogen excretion rates. Our results indicate that spatially heterogeneous aggregations of loricariids can significantly elevate dissolved nutrient concentrations via excretion relative to ambient nitrogen and phosphorus concentrations during daylight hours, creating biogeochemical hotspots and potentially altering nutrient dynamics in invaded systems. PMID:23342083

  13. Invasive fishes generate biogeochemical hotspots in a nutrient-limited system.

    PubMed

    Capps, Krista A; Flecker, Alexander S

    2013-01-01

    Fishes can play important functional roles in the nutrient dynamics of freshwater systems. Aggregating fishes have the potential to generate areas of increased biogeochemical activity, or hotspots, in streams and rivers. Many of the studies documenting the functional role of fishes in nutrient dynamics have focused on native fish species; however, introduced fishes may restructure nutrient storage and cycling freshwater systems as they can attain high population densities in novel environments. The purpose of this study was to examine the impact of a non-native catfish (Loricariidae: Pterygoplichthys) on nitrogen and phosphorus remineralization and estimate whether large aggregations of these fish generate measurable biogeochemical hotspots within nutrient-limited ecosystems. Loricariids formed large aggregations during daylight hours and dispersed throughout the stream during evening hours to graze benthic habitats. Excretion rates of phosphorus were twice as great during nighttime hours when fishes were actively feeding; however, there was no diel pattern in nitrogen excretion rates. Our results indicate that spatially heterogeneous aggregations of loricariids can significantly elevate dissolved nutrient concentrations via excretion relative to ambient nitrogen and phosphorus concentrations during daylight hours, creating biogeochemical hotspots and potentially altering nutrient dynamics in invaded systems.

  14. Biogeochemical hotspots within forested landscapes: quantifying the functional role of vernal pools in ecosystem processes

    NASA Astrophysics Data System (ADS)

    Capps, K. A.; Rancatti, R.; Calhoun, A.; Hunter, M.

    2013-12-01

    Biogeochemical hotspots are characterized as small areas within a landscape matrix that show comparably high chemical reaction rates relative to surrounding areas. For small, natural features to generate biogeochemical hotspots within a landscape, their contribution to nutrient dynamics must be significant relative to nutrient demand of the surrounding landscape. In northeastern forests in the US, vernal pools are abundant, small features that typically fill in spring with snow melt and precipitation and dry by the end of the summer. Ephemeral flooding alters soil moisture and the depth of the oxic/anoxic boundary in the soil, which may affect leaf-litter decomposition rates and nutrient dynamics including denitrification. Additionally, pool-breeding organisms may influence nutrient dynamics via consumer-driven nutrient remineralization. We studied the effects of vernal pools on rates of leaf-litter decomposition and denitrification in forested habitats in Maine. Our results indicate leaf-litter decomposition and denitrification rates in submerged habitats of vernal pools were greater than in upland forest habitat. Our data also suggest pool-breeding organisms, such as wood frogs, may play an important role in nutrient dynamics within vernal pools. Together, the results suggest vernal pools may function as biogeochemical hotspots within forested landscapes.

  15. Biogeochemical processes on tree islands in the greater everglades: Initiating a new paradigm

    USGS Publications Warehouse

    Wetzel, P.R.; Sklar, Fred H.; Coronado, C.A.; Troxler, T.G.; Krupa, S.L.; Sullivan, P.L.; Ewe, S.; Price, R.M.; Newman, S.; Orem, W.H.

    2011-01-01

    Scientists' understanding of the role of tree islands in the Everglades has evolved from a plant community of minor biogeochemical importance to a plant community recognized as the driving force for localized phosphorus accumulation within the landscape. Results from this review suggest that tree transpiration, nutrient infiltration from the soil surface, and groundwater flow create a soil zone of confluence where nutrients and salts accumulate under the head of a tree island during dry periods. Results also suggest accumulated salts and nutrients are flushed downstream by regional water flows during wet periods. That trees modulate their environment to create biogeochemical hot spots and strong nutrient gradients is a significant ecological paradigm shift in the understanding of the biogeochemical processes in the Everglades. In terms of island sustainability, this new paradigm suggests the need for distinct dry-wet cycles as well as a hydrologic regime that supports tree survival. Restoration of historic tree islands needs further investigation but the creation of functional tree islands is promising. Copyright ?? 2011 Taylor & Francis Group, LLC.

  16. Biogeochemical regions of the Mediterranean Sea: An objective multidimensional and multivariate environmental approach

    NASA Astrophysics Data System (ADS)

    Reygondeau, Gabriel; Guieu, Cécile; Benedetti, Fabio; Irisson, Jean-Olivier; Ayata, Sakina-Dorothée; Gasparini, Stéphane; Koubbi, Philippe

    2017-02-01

    When dividing the ocean, the aim is generally to summarise a complex system into a representative number of units, each representing a specific environment, a biological community or a socio-economical specificity. Recently, several geographical partitions of the global ocean have been proposed using statistical approaches applied to remote sensing or observations gathered during oceanographic cruises. Such geographical frameworks defined at a macroscale appear hardly applicable to characterise the biogeochemical features of semi-enclosed seas that are driven by smaller-scale chemical and physical processes. Following the Longhurst's biogeochemical partitioning of the pelagic realm, this study investigates the environmental divisions of the Mediterranean Sea using a large set of environmental parameters. These parameters were informed in the horizontal and the vertical dimensions to provide a 3D spatial framework for environmental management (12 regions found for the epipelagic, 12 for the mesopelagic, 13 for the bathypelagic and 26 for the seafloor). We show that: (1) the contribution of the longitudinal environmental gradient to the biogeochemical partitions decreases with depth; (2) the partition of the surface layer cannot be extrapolated to other vertical layers as the partition is driven by a different set of environmental variables. This new partitioning of the Mediterranean Sea has strong implications for conservation as it highlights that management must account for the differences in zoning with depth at a regional scale.

  17. 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.

  18. Comparing soil biogeochemical processes in novel and natural boreal forest ecosystems

    NASA Astrophysics Data System (ADS)

    Quideau, S. A.; Swallow, M. J. B.; Prescott, C. E.; Grayston, S. J.; Oh, S.-W.

    2013-08-01

    Emulating the variability that exists in the natural landscape prior to disturbance should be a goal of soil reconstruction and land reclamation efforts following resource extraction. Long-term ecosystem sustainability within reclaimed landscapes can only be achieved with the re-establishment of biogeochemical processes between reconstructed soils and plants. In this study, we assessed key soil biogeochemical attributes (nutrient availability, organic matter composition, and microbial communities) in reconstructed, novel, anthropogenic ecosystems, covering different reclamation treatments following open-cast mining for oil extraction. We compared the attributes to those present in a range of natural soils representative of mature boreal forest ecosystems in the same area of Northern Alberta. Soil nutrient availability was determined in situ with resin probes, organic matter composition was described with 13C nuclear magnetic resonance spectroscopy and soil microbial community structure was characterized using phospholipid fatty acid analysis. Significant differences among natural ecosystems were apparent in nutrient availability and seemed more related to the dominant tree cover than to soil type. When analyzed together, all natural forests differed significantly from the novel ecosystems, in particular with respect to soil organic matter composition. However, there was some overlap between the reconstructed soils and some of the natural ecosystems in nutrient availability and microbial communities, but not in organic matter characteristics. Hence, our results illustrate the importance of considering the range of natural landscape variability and including several soil biogeochemical attributes when comparing novel, anthropogenic ecosystems to the mature ecosystems that constitute ecological targets.

  19. Comparing soil biogeochemical processes in novel and natural boreal forest ecosystems

    NASA Astrophysics Data System (ADS)

    Quideau, S. A.; Swallow, M. J. B.; Prescott, C. E.; Grayston, S. J.; Oh, S.-W.

    2013-04-01

    Emulating the variability that exists in the natural landscape prior to disturbance should be a goal of soil reconstruction and land reclamation efforts following resource extraction. Long-term ecosystem sustainability within reclaimed landscapes can only be achieved with the re-establishment of biogeochemical processes between reconstructed soils and plants. In this study, we assessed key soil biogeochemical attributes (nutrient availability, organic matter composition, and microbial communities) in reconstructed, novel, anthropogenic ecosystems covering different reclamation treatments following open-cast mining for oil extraction. We compared the attributes to those present in a range of natural soils representative of mature boreal forest ecosystems in the same area of northern Alberta. Soil nutrient availability was determined in situ with resin probes, organic matter composition was described with 13C nuclear magnetic resonance spectroscopy and soil microbial community structure was characterized using phospholipid fatty acid analysis. Significant differences among natural ecosystems were apparent in nutrient availability and seemed more related to the dominant tree cover than to soil type. When analyzed together, all natural forests differed significantly from the novel ecosystems, in particular with respect to soil organic matter composition. However, there was some overlap between the reconstructed soils and some of the natural ecosystems in nutrient availability and microbial communities, but not in organic matter characteristics. Hence, our results illustrate the importance of considering the range of natural landscape variability, and including several soil biogeochemical attributes when comparing novel, anthropogenic ecosystems to the mature ecosystems that constitute ecological targets.

  20. Biogeochemical factors which regulate the formation and fate of sulfide in wetlands

    NASA Technical Reports Server (NTRS)

    Hines, Mark E.; Lyons, W. Berry; Gaudette, H. E.

    1985-01-01

    Coastal wetland areas occupy a small percentage of the terrestrial environment yet are extremely productive regions which support rapid rates of below ground bacterial activity. Wetlands appear to be significant as biogenic sources of gaseous sulfur, carbon, and nitrogen. These gases are important as tracers of man's activities, and they influence atmospheric chemistry. The interactions among wetland biogeochemical processes regulate the anaerobic production of reduced gases and influence the fate of these volatiles. Therefore, spatial and temporal variations in hydrology, salinity, temperature, and speciation and growth of vegetation affect the type and magnitude of gas emissions thus hindering predictive estimates of gas flux. The research is divided into two major parts, the first is the biogeochemical characterization of a selected tidal wetland area in terms of factors likely to regulate sulfide flux; the second is a direct measurement of gaseous sulfur flux as related to changes in these biogeochemical conditions. Variant factors affecting sulfide flux include the wetlands' tidal range, seasonal salinity, and other hydrological conditions, grass species and plant growth, soil composition, and microbial activity.

  1. Biogeophysical and Biogeochemical Climate Impacts of Mountaintop Coal Mining in Southern Appalachia USA

    NASA Astrophysics Data System (ADS)

    Fox, J.; Campbell, J.; Snyder, M. A.; Cirbus-Sloan, L.

    2013-12-01

    Mountaintop coal mining (MCM) practices are a controversial energy extraction approach that is common in the southern Appalachian forest region (SAFR) producing approximately one third of coal in the United States. The biogeochemical consequences of MCM practices on existing terrestrial carbon stocks and future carbon sequestration rates have been the focus of our recent study. Using terrestrial carbon data and modeling, our findings suggest that removal of temperature forests and soils during mining and reclamation to grassland land use has resulted in emissions of 0.4 Pg CO2 from MCM lands over the past 40 years. In our on-going developments, we are combining these biogeochemical climate impacts with the unstudied biogeophysical climate impacts of this extreme and widespread MCM land-use change. Here we develop land-use change maps for MCM practices and consider the change in temperature and albedo that results using remote sensing data. These land-use change maps provide a starting point for regional climate simulations that can be used to further characterize the biogeophysical consequences of MCM. Our biogeochemical and biogeophysical results are being integrated into a life cycle assessment and scenario predictions for future mining rates and future reclamation practices, e.g., grassland reclamation versus reforestation, for the next 90 years.

  2. Biogeochemical Cycling at Natural System Interfaces at the Norman Landfill, Norman, OK: Living on the Edge

    NASA Astrophysics Data System (ADS)

    McGuire, J. T.; Baez-Cazull, S.; Cozzarelli, I. M.; Voytek, M. A.; Smith, E. W.; Kneeshaw, T. A.; Kirshstein, J. D.

    2006-05-01

    Steep biogeochemical gradients were observed at mixing interfaces in a wetland-aquifer system impacted by landfill leachate in Norman, Oklahoma. The system lies within the reworked alluvial plain of the Canadian River and is characterized by layered low hydraulic conductivity wetland sediments and interbedded sandy aquifer material. Using cm-scale passive diffusion samplers (peepers), water samples were collected to span the interfaces between surface water, wetland sediments, and sandy sediments. Geochemical indicators of terminal electron accepting processes, including low molecular weight fatty acids, were analyzed by capillary electrophoresis and field techniques to maximize low sample volumes. Iron reduction and sulfate reduction appear to coexist at the sediment-water interface. Maximum concentrations of other biogeochemical indicators (ex. acetate (1.80mM, 8.8mM) and ammonium (13mM, 36mM)) were observed at the sediment/water, and wetland sediment/sand interfaces. Findings support the hypothesis that increased biogeochemical cycling occurs at interfaces where limiting electron acceptors and donors mix. The linkages between geochemical gradients and microbiological cycling are being evaluated using in-situ experiments designed to collect microbiological and geochemical data at similar spatial and temporal scales within the aquifer-wetland system.

  3. A framework to assess biogeochemical response to ecosystem disturbance using nutrient partitioning ratios

    USGS Publications Warehouse

    Kranabetter, J. Marty; McLauchlan, Kendra K.; Enders, Sara K.; Fraterrigo, Jennifer M.; Higuera, Philip E.; Morris, Jesse L.; Rastetter, Edward B.; Barnes, Rebecca; Buma, Brian; Gavin, Daniel G.; Gerhart, Laci M.; Gillson, Lindsey; Hietz, Peter; Mack, Michelle C.; McNeil, Brenden; Perakis, Steven

    2016-01-01

    Disturbances affect almost all terrestrial ecosystems, but it has been difficult to identify general principles regarding these influences. To improve our understanding of the long-term consequences of disturbance on terrestrial ecosystems, we present a conceptual framework that analyzes disturbances by their biogeochemical impacts. We posit that the ratio of soil and plant nutrient stocks in mature ecosystems represents a characteristic site property. Focusing on nitrogen (N), we hypothesize that this partitioning ratio (soil N: plant N) will undergo a predictable trajectory after disturbance. We investigate the nature of this partitioning ratio with three approaches: (1) nutrient stock data from forested ecosystems in North America, (2) a process-based ecosystem model, and (3) conceptual shifts in site nutrient availability with altered disturbance frequency. Partitioning ratios could be applied to a variety of ecosystems and successional states, allowing for improved temporal scaling of disturbance events. The generally short-term empirical evidence for recovery trajectories of nutrient stocks and partitioning ratios suggests two areas for future research. First, we need to recognize and quantify how disturbance effects can be accreting or depleting, depending on whether their net effect is to increase or decrease ecosystem nutrient stocks. Second, we need to test how altered disturbance frequencies from the present state may be constructive or destructive in their effects on biogeochemical cycling and nutrient availability. Long-term studies, with repeated sampling of soils and vegetation, will be essential in further developing this framework of biogeochemical response to disturbance.

  4. Forms and lability of phosphorus in algae and aquatic macrophytes characterized by solution 31P NMR coupled with enzymatic hydrolysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increased information on forms and lability of phosphorus (P) in aquatic macrophytes and algae is crucial for better understanding of P biogeochemical cycling in eutrophic lakes. In this work, solution 31P nuclear magnetic resonance (NMR) spectroscopy coupled with enzymatic hydrolysis (EH) was used ...

  5. 239,240Pu/137Cs ratios in the water column of the North Pacific: a proxy of biogeochemical processes.

    PubMed

    Hirose, Katsumi; Aoyama, Michio; Povinec, Pavel P

    2009-03-01

    Anthropogenic radionuclides in seawater have been used as transient tracers of processes in the marine environment. Especially, plutonium in seawater is considered to be a valuable tracer of biogeochemical processes due to its particle-reactive properties. However, its behavior in the ocean is also affected by physical processes such as advection, mixing and diffusion. Here we introduce Pu/(137)Cs ratio as a proxy of biogeochemical processes and discuss its trends in the water column of the North Pacific Ocean. We observed that the (239,240)Pu/(137)Cs ratio in seawater exponentially increased with increasing depth (depth range: 100-1000 m). This finding suggests that the profiles of the (239,240)Pu/(137)Cs ratios in shallower waters directly reflect biogeochemical processes in the water column. A half-regeneration depth deduced from the curve fitting the observed data, showed latitudinal and longitudinal distributions, also related to biogeochemical processes in the water column.

  6. Effects of Stratospheric Ozone Depletion, Solar UV Radiation, and Climate Change on Biogeochemical Cycling: Interactions and Feedbacks

    EPA Science Inventory

    Climate change modulates the effects of solar UV radiation on biogeochemical cycles in terrestrial and aquatic ecosystems, particularly for carbon cycling, resulting in UV-mediated positive or negative feedbacks on climate. Possible positive feedbacks discussed in this assessment...

  7. EFFECT OF NUTRIENT LOADING ON BIOGEOCHEMICAL AND MICROBIAL PROCESSES IN A NEW ENGLAND HIGH SALT MARSH, SPARTINA PATNES, (AITON MUHL)

    EPA Science Inventory

    Coastal marshes represent an important transitional zone between uplands and estuaries and can assimilate nutrient inputs from uplands. We examined the effects of nitrogen (N) and phosphorus (P) fertilization on biogeochemical and microbial processes during the summer growing sea...

  8. A coupled geochemical and biogeochemical approach to characterize the bioreactivity of dissolved organic matter from a headwater stream

    NASA Astrophysics Data System (ADS)

    Sleighter, Rachel L.; Cory, Rose M.; Kaplan, Louis A.; Abdulla, Hussain A. N.; Hatcher, Patrick G.

    2014-08-01

    The bioreactivity or susceptibility of dissolved organic matter (DOM) to microbial degradation in streams and rivers is of critical importance to global change studies, but a comprehensive understanding of DOM bioreactivity has been elusive due, in part, to the stunningly diverse assemblages of organic molecules within DOM. We approach this problem by employing a range of techniques to characterize DOM as it flows through biofilm reactors: dissolved organic carbon (DOC) concentrations, excitation emission matrix spectroscopy (EEMs), and ultrahigh resolution mass spectrometry. The EEMs and mass spectral data were analyzed using a combination of multivariate statistical approaches. We found that 45% of stream water DOC was biodegraded by microorganisms, including 31-45% of the humic DOC. This bioreactive DOM separated into two different groups: (1) H/C centered at 1.5 with O/C 0.1-0.5 or (2) low H/C of 0.5-1.0 spanning O/C 0.2-0.7 that were positively correlated (Spearman ranking) with chromophoric and fluorescent DOM (CDOM and FDOM, respectively). DOM that was more recalcitrant and resistant to microbial degradation aligned tightly in the center of the van Krevelen space (H/C 1.0-1.5, O/C 0.25-0.6) and negatively correlated (Spearman ranking) with CDOM and FDOM. These findings were supported further by principal component analysis and 2-D correlation analysis of the relative magnitudes of the mass spectral peaks assigned to molecular formulas. This study demonstrates that our approach of processing stream water through bioreactors followed by EEMs and FTICR-MS analyses, in combination with multivariate statistical analysis, allows for precise, robust characterization of compound bioreactivity and associated molecular level composition.

  9. Novel imaging techniques, integrated with mineralogical, geochemical and microbiological characterizations to determine the biogeochemical controls on technetium mobility in FRC sediments

    SciTech Connect

    Jonathan R. Lloyd

    2009-02-03

    life 6 hours) and its mobility was monitored using a {gamma}-camera. Incorporation of low concentrations of the long-lived 99Tc gave a tracer that can be followed by scintillation counting, should the metastable form of the radionuclide decay to below detection limits before the end of the experiment (complete immobilization or loss of the Tc from the column). After the Tc was reduced and immobilized, or passed through the system, the columns were dismantled carefully in an anaerobic cabinet and the pore water geochemistry and mineralogy of the columns profiled. Microbial community analysis was determined, again using molecular and culture-dependent techniques. Experimental results were also modeled using an established coupled speciation and transport code, to develop a predictive tool for the mobility of Tc in FRC sediments. From this multidisciplinary approach, we hoped to obtain detailed information on the microorganisms that control the biogeochemical cycling of key elements at the FRC, and we would also be able to determine the key factors that control the mobility of Tc at environmentally relevant concentrations at this site.

  10. Projecting the long-term biogeochemical impacts of a diverse agroforestry system in the Midwest

    NASA Astrophysics Data System (ADS)

    Wolz, K. J.; DeLucia, E. H.; Paul, R. F.

    2014-12-01

    Annual, monoculture cropping systems have become the standard agricultural model in the Midwestern US. Unintended consequences of these systems include surface and groundwater pollution, greenhouse gas emissions, loss of biodiversity, and soil erosion. Diverse agroforestry (DA) systems dominated by fruit and nut trees/shrubs have been proposed as an agricultural model for the Midwestern US that can restore ecosystem services while simultaneously providing economically viable and industrially relevant staple food crops. A DA system including six species of fruit and nut crops was established on long-time conventional agricultural land at the University of Illinois at Urbana-Champaign in 2012, with the conventional corn-soybean rotation (CSR) as a control. Initial field measurements of the nitrogen and water cycles during the first two years of transition have indicated a significant decrease in N losses and modification of the seasonal evapotranspiration (ET) pattern. While these early results suggest that the land use transition from CSR to DA can have positive biogeochemical consequences, models must be utilized to make long-term biogeochemical projections in agroforestry systems. Initial field measurements of plant phenology, net N2O flux, nitrate leaching, soil respiration, and soil moisture were used to parameterize the DA system within the DayCENT biogeochemical model as the "savanna" ecosystem type. The model was validated with an independent subset of field measurements and then run to project biogeochemical cycling in the DA system for 25 years past establishment. Model results show that N losses via N2O emission or nitrate leaching reach a minimum within the first 5 years and then maintain this tight cycle into the future. While early ET field measurements revealed similar magnitudes between the DA and CSR systems, modeled ET continued to increase for the DA system throughout the projected time since the trees would continue to grow larger. These modeling

  11. Intra- versus inter-site macroscale variation in biogeochemical properties along a paddy soil chronosequence

    NASA Astrophysics Data System (ADS)

    Mueller-Niggemann, C.; Bannert, A.; Schloter, M.; Lehndorff, E.; Schwark, L.

    2012-03-01

    In order to assess the intrinsic heterogeneity of paddy soils, a set of biogeochemical soil parameters was investigated in five field replicates of seven paddy fields (50, 100, 300, 500, 700, 1000, and 2000 yr of wetland rice cultivation), one flooded paddy nursery, one tidal wetland (TW), and one freshwater site (FW) from a coastal area at Hangzhou Bay, Zhejiang Province, China. All soils evolved from a marine tidal flat substrate due to land reclamation. The biogeochemical parameters based on their properties were differentiated into (i) a group behaving conservatively (TC, TOC, TN, TS, magnetic susceptibility, soil lightness and colour parameters, δ13C, δ15N, lipids and n-alkanes) and (ii) one encompassing more labile properties or fast cycling components (Nmic, Cmic, nitrate, ammonium, DON and DOC). The macroscale heterogeneity in paddy soils was assessed by evaluating intra- versus inter-site spatial variability of biogeochemical properties using statistical data analysis (descriptive, explorative and non-parametric). Results show that the intrinsic heterogeneity of paddy soil organic and minerogenic components per field is smaller than between study sites. The coefficient of variation (CV) values of conservative parameters varied in a low range (10% to 20%), decreasing from younger towards older paddy soils. This indicates a declining variability of soil biogeochemical properties in longer used cropping sites according to progress in soil evolution. A generally higher variation of CV values (>20-40%) observed for labile parameters implies a need for substantially higher sampling frequency when investigating these as compared to more conservative parameters. Since the representativeness of the sampling strategy could be sufficiently demonstrated, an investigation of long-term carbon accumulation/sequestration trends in topsoils of the 2000 yr paddy chronosequence under wetland rice cultivation restricted was conducted. Observations cannot be extrapolated to

  12. FLEXIBLE COUPLING

    DOEpatents

    Babelay, E.F.

    1962-02-13

    A flexible shaft coupling for operation at speeds in excess of 14,000 rpm is designed which requires no lubrication. A driving sleeve member and a driven sleeve member are placed in concentric spaced relationship. A torque force is transmitted to the driven member from the driving member through a plurality of nylon balls symmetrically disposed between the spaced sleeves. The balls extend into races and recesses within the respective sleeve members. The sleeve members have a suitable clearance therebetween and the balls have a suitable radial clearance during operation of the coupling to provide a relatively loose coupling. These clearances accommodate for both parallel and/or angular misalignments and avoid metal-tometal contact between the sleeve members during operation. Thus, no lubrication is needed, and a minimum of vibrations is transmitted between the sleeve members. (AEC)

  13. Prosthesis coupling

    NASA Technical Reports Server (NTRS)

    Reswick, J. B.; Mooney, V.; Bright, C. W.; Owens, L. J. (Inventor)

    1979-01-01

    A coupling for use in an apparatus for connecting a prosthesis to the bone of a stump of an amputated limb is described which permits a bio-compatible carbon sleeve forming a part of the prosthesis connector to float so as to prevent disturbing the skin seal around the carbon sleeve. The coupling includes a flexible member interposed between a socket that is inserted within an intermedullary cavity of the bone and the sleeve. A lock pin is carried by the prosthesis and has a stem portion which is adapted to be coaxially disposed and slideably within the tubular female socket for securing the prosthesis to the stump. The skin around the percutaneous carbon sleeve is able to move as a result of the flexing coupling so as to reduce stresses caused by changes in the stump shape and/or movement between the bone and the flesh portion of the stump.

  14. 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).

  15. 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.

  16. New HYDRUS Modules for Simulating Preferential Flow, Colloid-Facilitated Contaminant Transport, and Various Biogeochemical Processes in Soils

    NASA Astrophysics Data System (ADS)

    Simunek, J.; Sejna, M.; Jacques, D.; Langergraber, G.; Bradford, S. A.; van Genuchten, M. Th.

    2012-04-01

    We have dramatically expanded the capabilities of the HYDRUS (2D/3D) software package by developing new modules to account for processes not available in the standard HYDRUS version. These new modules include the DualPerm, C-Hitch, HP2/3, Wetland, and Unsatchem modules. The dual-permeability modeling approach of Gerke and van Genuchten [1993] simulating preferential flow and transport is implemented into the DualPerm module. Colloid transport and colloid-facilitated solute transport, the latter often observed for many contaminants, such as heavy metals, radionuclides, pharmaceuticals, pesticides, and explosives [Šimůnek et al., 2006] are implemented into the C-Hitch module. HP2 and HP3 are the two and three-dimensional alternatives of the HP1 module, currently available with HYDRUS-1D [Jacques and Šimůnek, 2005], that couple HYDRUS flow and transport routines with the generic geochemical model PHREEQC of Parkhurst and Appelo [1999]. The Wetland module includes two alternative approaches (CW2D of Langergraber and Šimůnek [2005] and CWM1 of Langergraber et al. [2009]) for modeling aerobic, anaerobic, and anoxic biogeochemical processes in natural and constructed wetlands. Finally, the Unsatchem module simulates the transport and reactions of major ions in a soil profile. Brief descriptions and an application of each module will be presented. Except for HP3, all modules simulate flow and transport processes in two-dimensional transport domains. All modules are fully supported by the HYDRUS graphical user interface. Further development of these modules, as well as of several other new modules (such as Overland), is still envisioned. Continued feedback from the research community is encouraged.

  17. MEDUSA-2.0: an intermediate complexity biogeochemical model of the marine carbon cycle for climate change and ocean acidification studies

    NASA Astrophysics Data System (ADS)

    Yool, A.; Popova, E. E.; Anderson, T. R.

    2013-10-01

    MEDUSA-1.0 (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification) was developed as an "intermediate complexity" plankton ecosystem model to study the biogeochemical response, and especially that of the so-called "biological pump", to anthropogenically driven change in the World Ocean (Yool et al., 2011). The base currency in this model was nitrogen from which fluxes of organic carbon, including export to the deep ocean, were calculated by invoking fixed C:N ratios in phytoplankton, zooplankton and detritus. However, due to anthropogenic activity, the atmospheric concentration of carbon dioxide (CO2) has significantly increased above its natural, inter-glacial background. As such, simulating and predicting the carbon cycle in the ocean in its entirety, including ventilation of CO2 with the atmosphere and the resulting impact of ocean acidification on marine ecosystems, requires that both organic and inorganic carbon be afforded a more complete representation in the model specification. Here, we introduce MEDUSA-2.0, an expanded successor model which includes additional state variables for dissolved inorganic carbon, alkalinity, dissolved oxygen and detritus carbon (permitting variable C:N in exported organic matter), as well as a simple benthic formulation and extended parameterizations of phytoplankton growth, calcification and detritus remineralisation. A full description of MEDUSA-2.0, including its additional functionality, is provided and a multi-decadal spin-up simulation (1860-2005) is performed. The biogeochemical performance of the model is evaluated using a diverse range of observational data, and MEDUSA-2.0 is assessed relative to comparable models using output from the Coupled Model Intercomparison Project (CMIP5).

  18. Integrated Coupling of Surface and Subsurface Flow with HYDRUS-2D

    NASA Astrophysics Data System (ADS)

    Hartmann, Anne; Šimůnek, Jirka; Wöhling, Thomas; Schütze, Niels

    2016-04-01

    Describing interactions between surface and subsurface flow processes is important to adequately define water flow in natural systems. Since overland flow generation is highly influenced by rainfall and infiltration, both highly spatially heterogeneous processes, overland flow is unsteady and varies spatially. The prediction of overland flow needs to include an appropriate description of the interactions between the surface and subsurface flow. Coupling surface and subsurface water flow is a challenging task. Different approaches have been developed during the last few years, each having its own advantages and disadvantages. A new approach by Weill et al. (2009) to couple overland flow and subsurface flow based on a generalized Richards equation was implemented into the well-known subsurface flow model HYDRUS-2D (Šimůnek et al., 2011). This approach utilizes the one-dimensional diffusion wave equation to model overland flow. The diffusion wave model is integrated in HYDRUS-2D by replacing the terms of the Richards equation in a pre-defined runoff layer by terms defining the diffusion wave equation. Using this approach, pressure and flux continuity along the interface between both flow domains is provided. This direct coupling approach provides a strong coupling of both systems based on the definition of a single global system matrix to numerically solve the coupled flow problem. The advantage of the direct coupling approach, compared to the loosely coupled approach, is supposed to be a higher robustness, when many convergence problems can be avoided (Takizawa et al., 2014). The HYDRUS-2D implementation was verified using a) different test cases, including a direct comparison with the results of Weill et al. (2009), b) an analytical solution of the kinematic wave equation, and c) the results of a benchmark test of Maxwell et al. (2014), that included several known coupled surface subsurface flow models. Additionally, a sensitivity analysis evaluating the effects

  19. 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 ex