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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 to what extent sinking particles are further broken down in the underlying waters of the Twilight Zone.

  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 underlying waters of the Twilight Zone.

  3. A Coupled Land Surface-Subsurface Biogeochemical Model for Aqueous and Gaseous Nitrogen Losses

    NASA Astrophysics Data System (ADS)

    Gu, C.; Maggi, F.; Riley, W.; Pan, L.; Xu, T.; Oldenburg, C.; Miller, N.

    2008-12-01

    In recent years concern has grown over the contribution of nitrogen (N) fertilizers to nitrate (NOB3PB-P) water pollution and atmospheric pollution of nitrous oxide (NB2BO), nitric oxide (NO), and ammonia (NHB3B). Characterizing the amount and species of N losses is therefore essential in developing a strategy to estimate and mitigate N leaching and emission to the atmosphere. Indeed, transformations of nitrogen depend strongly on water content, soil temperature, and nitrogen concentration. Land surface processes therefore have to be taken into account to properly characterize N biogeochemical cycling. However, most current nitrogen biogeochemical models take the land surface as the upper boundary by lumping the complex processes above the surface as known boundary conditions. In this study, an extant subsurface mechanistic N cycle model (TOUGHREACT-N) was coupled with the community land model (CLM). The resulting coupled model extends the modeling capability of TOUGHREACT-N to include the important energy, momentum, and moisture dynamics provided by CLM. The coupled model showed a significant impact of land-surface diurnal forcing on soil temperature and moisture and on nitrogen fluxes. We also discuss field applications of the model and discuss how temporal dynamics of nitrogen fluxes are affected by land surface processes.

  4. A Coupled Surface/Subsurface Model for Hydrological Drought Investigations

    NASA Astrophysics Data System (ADS)

    Musuuza, J. L.; Kumar, R.; Samaniego, L. E.; Fischer, T.; Kolditz, O.; Attinger, S.

    2013-12-01

    Hydrological droughts occur when storage in the ground and surface-water bodies falls below statistical average. Due to the inclusion of regional groundwater, hydrological droughts evolve relatively slowly. The atmospheric and surface components of the hydrological cycle have been widely studied, are well understood, and their prognoses are fairly accurate. In large-scale land surface models on the other hand, subsurface (groundwater) flow processes are usually assumed unidirectional and limited to the vertically-downward percolation and the horizontal runoffs. The vertical feedback from groundwater to the unsaturated zone as well as the groundwater recharge from surface waters are usually misrepresented, resulting in poor model performance during low-flow periods. The feedback is important during meteorological droughts because it replenishes soil moisture from ground- and surface water, thereby delaying the onset of agricultural droughts. If sustained for long periods however, the depletion can significantly reduce surface and subsurface storage and lead to severe hydrological droughts. We hypothesise that an explicit incorporation of the groundwater component into an existing land surface model would lead to better representation of low flows, which is critical for drought analyses. It would also improve the model performance during low-flow periods. For this purpose, we coupled the process-based mHM surface model (Samaniego et al. 2010) with MODFLOW (Harbaugh 2005) to analyse droughts in the Unstrut catchment, one of the tributaries of the Elbe. The catchment is located in one of the most drought-prone areas of Germany. We present results for stand-alone and coupled mHM simulations for the period 1970-2000. References Arlen W. Harbaugh. MODFLOW-2005, The U.S. Geological Survey Modular Ground-water Model-the Ground-water Flow Process, chapter Modelling techniques, sec. A. Ground water, pages 1:1-9:62. USGS, 2005. Luis Samaniego, Rohini Kumar, and Sabine Attinger. Multiscale parameter regionalization of a grid-based hydrologic model at the mesoscale. Water Resour. Res., 46(W05523), 2010. doi: 10.1029/2008WR007327.

  5. An exploration of coupled surface-subsurface solute transport in a fully integrated catchment model

    NASA Astrophysics Data System (ADS)

    Liggett, Jessica E.; Partington, Daniel; Frei, Sven; Werner, Adrian D.; Simmons, Craig T.; Fleckenstein, Jan H.

    2015-10-01

    Coupling surface and subsurface water flow in fully integrated hydrological codes is becoming common in hydrological research; however, the coupling of surface-subsurface solute transport has received much less attention. Previous studies on fully integrated solute transport focus on small scales, simple geometric domains, and have not utilised many different field data sources. The objective of this study is to demonstrate the inclusion of both flow and solute transport in a 3D, fully integrated catchment model, utilising high resolution observations of dissolved organic carbon (DOC) export from a wetland complex during a rainfall event. A sensitivity analysis is performed to span a range of transport conditions for the surface-subsurface boundary (e.g. advective exchange only, advection plus diffusion, advection plus full mechanical dispersion) and subsurface dispersivities. The catchment model captures some aspects of observed catchment behaviour (e.g. solute discharge at the catchment outlet, increasing discharge from wetlands with increased stream discharge, and counter-clockwise concentration-discharge relationships), although other known behaviours are not well represented in the model (e.g. slope of concentration-discharge plots). Including surface-subsurface solute transport aids in evaluating internal model processes, however there are challenges related to the influence of dispersion across the surface-subsurface interface, and non-uniqueness of the solute transport solution. This highlights that obtaining solute field data is especially important for constraining integrated models of solute transport.

  6. Control of coupling mass balance error in a process-based numerical model of surface-subsurface flow interaction

    NASA Astrophysics Data System (ADS)

    Fiorentini, Marcello; Orlandini, Stefano; Paniconi, Claudio

    2015-07-01

    A process-based numerical model of integrated surface-subsurface flow is analyzed in order to identify, track, and reduce the mass balance errors affiliated with the model's coupling scheme. The sources of coupling error include a surface-subsurface grid interface that requires node-to-cell and cell-to-node interpolation of exchange fluxes and ponding heads, and a sequential iterative time matching procedure that includes a time lag in these same exchange terms. Based on numerical experiments carried out for two synthetic test cases and for a complex drainage basin in northern Italy, it is shown that the coupling mass balance error increases during the flood recession limb when the rate of change in the fluxes exchanged between the surface and subsurface is highest. A dimensionless index that quantifies the degree of coupling and a saturated area index are introduced to monitor the sensitivity of the model to coupling error. Error reduction is achieved through improvements to the heuristic procedure used to control and adapt the time step interval and to the interpolation algorithm used to pass exchange variables from nodes to cells. The analysis presented illustrates the trade-offs between a flexible description of surface and subsurface flow processes and the numerical errors inherent in sequential iterative coupling with staggered nodal points at the land surface interface, and it reveals mitigation strategies that are applicable to all integrated models sharing this coupling and discretization approach.

  7. External iterative coupling strategy for surface-subsurface flow calculations in surface irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Coupling the unsteady open-channel flow equations of surface irrigation with the equation of variably saturated porous media flow is a computationally complex problem, because of the dependence of infiltration on flow depths. Several models of this coupled process have been developed, all of which ...

  8. 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. PMID:23603354

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Insights into three-dimensional simulation of coastal flow dynamics using a fully coupled surface-subsurface approach

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Graf, Thomas

    2013-04-01

    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 subsurfacial 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 of the coastal catchment area of Unterweser, Northern Germany (ca. 2500 km2). To optimize the simulation and to reduce CPU cost, the actual simulation domain is only a part of the total catchment area: We selected a narrow strip of about 10 km width parallel to the coastline. The catchment area outside of that strip is not affected by saltwater intrusion and does therefore not need to be included in the numerical model. The seaside boundary condition of the reduced simulation domain is obtained from a 3D hydrodynamic-numerical flow model where changes in sea level are being simulated. The landside boundary condition is obtained from a 3D steady-state flow model of the total catchment area. The 3D model is calibrated using field data previously gathered at the study site. Results indicate that the fully coupled approach with a reduced simulation domain is effective in the simulation of 3D coastal flow dynamics.

  11. 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 in how the governing equations are solved, and we will compare different surface flow formulations as well as coupling strategies between the surface and subsurface domains. Additionally, for studies of hydrology in Arctic regions, we have added a three-phase ice model. We will present some demonstrations of this capability and discuss solver strategies for handling the strong nonlinearities that arise. To provide a unified treatment of the unsaturated and saturated zones and to enable lateral redistribution of soil moisture (and eventually surface water, heat, and nutrients) in regional climate models, we have developed an approach for coupling PFLOTRAN with CLM. CLM is the global land model component used within the Community Earth System Model (CESM) to simulate an extensive set of biogeophysical and biogeochemical processes occurring at or near the terrestrial surface. We will describe our approach for replacing the existing CLM hydrology using PFLOTRAN and present some preliminary simulations undertaken with the CLM-PFLOTRAN coupled model.

  12. Coupled surface-subsurface hydrologic measurements reveal infiltration, recharge, and discharge dynamics across the swash zone of a sandy beach

    NASA Astrophysics Data System (ADS)

    Heiss, James W.; Puleo, Jack A.; Ullman, William J.; Michael, Holly A.

    2015-11-01

    Swash-groundwater interactions affect the biogeochemistry of beach aquifers and the transport of solutes and sediment across the beachface. Improved understanding of the complex, coupled dynamics of surface and subsurface flow processes in the swash zone is required to better estimate chemical fluxes to the sea and predict the morphological evolution of beaches. Simultaneous high-frequency measurements of saturation, water table elevation, and the cross-shore locations of runup and the boundary between the saturated and unsaturated beachface (surface saturation boundary) were collected on a sandy beach to link groundwater flow dynamics with swash zone forcing. Saturation and lysimeter measurements showed the dynamic response of subsurface saturation to swash events and permitted estimation of infiltration rates. Surface and subsurface observations revealed a decoupling of the surface saturation boundary and the intersection between the water table and the beachface. Surface measurements alone were insufficient to delineate the infiltration and discharge zones, which moved independently of the surface saturation boundary. Results show for the first time the motion and areal extent of infiltration and recharge zones, and constrain the maximum size of the subaerial discharge zone over swash and tidal time scales. The width of the infiltration zone was controlled by swash processes, and subaerial discharge was controlled primarily by tidal processes. These dynamics reveal the tightly coupled nature of surface and subsurface processes over multiple time scales, with implications for sediment transport and fluid and solute fluxes through the hydrologically and biogeochemically active intertidal zone of sandy beaches.

  13. 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 allows to discuss some of the strengths and weaknesses, both physical and numerical, of EnKF and PF and to learn the implications related to the choice of the statistics used to build the ensemble of realizations.

  14. Measuring groundwater flow at the Sanford Laboratory with coupled surface/subsurface time-lapse gravity measurements

    NASA Astrophysics Data System (ADS)

    Kennedy, J.; Murdoch, L.; Long, A. J.; Koth, K.

    2011-12-01

    Limited options exist to measure groundwater processes, particularly at large depths. Coupled time-lapse gravity measurements at the surface and underground are one possibility, but despite recent advances in borehole instruments, no repeat underground gravity measurements of water-mass change have been reported. At the Sanford Laboratory-located at the Homestake Mine in Lead, South Dakota, and site of the proposed Deep Underground Science and Engineering Laboratory (DUSEL)-the U.S. Geological Survey has established a network of 19 surface and 5 underground gravity stations to monitor groundwater-storage change over the projected 20-year existence of the underground laboratory. Continuous pumping is planned to dewater the mine to a depth of 2,500 m; the current pumping regime began in 2007 and current water levels (2011) are at a depth of about 1,700 m. Measurements using a field-portable A-10 absolute gravimeter have been made approximately annually at surface stations since 2007. Underground stations forming a vertical profile along the Ross Shaft on the 300, 800, 2000, 4100, and 4850 levels (numbers indicate approximate depth in feet) were established in 2011, and it is expected all stations will be surveyed annually. To date, surface time-lapse measurements show gravity increases of 50 to 100 nm/s^2 (10 nm/s^2 = 1 microgal) at some stations and equivalent decreases at others, indicating little evidence of water-mass change from pumping. Preliminary modeling, in which the dewatered zone is represented by a series of horizontal prisms that undergo mass change equal to the porosity (assumed 0.005, an average of rock porosity and mined-out voids), indicates that this is the expected result. At pumping rates required to maintain drawdown to a depth of 2,500 m, however, the expected gravity change increases from about 50 nm/s^2 at the surface to 250 nm/s^2 at the 4850 level. Gravity stations in the subsurface are advantageous because they are both closer to the water-mass change from pumping and removed from water-mass change at the surface caused by inter-annual climate variability. Furthermore, the predicted gravity response varies along the vertical profile depending on the distribution of water-mass change in the deep subsurface, indicating the subsurface measurements will be useful for calibrating and validating a groundwater flow model. A tunnel on the 300 level that traverses beneath a forested hillslope and exits at the land surface is a significant future opportunity for monitoring hydrologic processes; concurrent surface and subsurface gravity profiles above and below this hillslope, combined with other measurements, would likely lead to new advances in hillslope-scale hydrology.

  15. Combined assimilation of soil moisture and streamflow data by an ensemble Kalman filter in a coupled model of surface-subsurface flow.

    NASA Astrophysics Data System (ADS)

    Camporese, M.; Paniconi, C.; Putti, M.; Salandin, P.

    2007-12-01

    Hydrologic models can largely benefit from the use of data assimilation algorithms, which allow to update the modeled system state incorporating in the solution of the model itself information coming from experimental measurements of various quantities, as soon as the data become available. In this context, data assimilation seems to be well fit for coupled surface--subsurface models, which, considering the watershed as the ensemble of surface and subsurface domains, allow a more accurate description of the hydrological processes at the catchment scale, where soil moisture largely influences the partitioning of rain between runoff and infiltration and thus controls the flow at the outlet. The need for a better determination of the variables of interest (streamflow at the outlet section, water table, soil water content, etc.) has led to a many efforts focused on the development of coupled numerical models, together with field and laboratory observations. Nevertheless, uncertainty in the schematic description of physical processes and inaccuracies on source data collection induce errors in the model predictions. The ensemble Kalman filter (EnKF) represents an extension to nonlinear problems of the classic Kalman filter by means of a Monte Carlo approach. A sequential assimilation procedure based on EnKF is developed and integrated in a process-based numerical model, which couples a three-dimensional finite element Richards equation solver for variably saturated porous media and a finite difference diffusion wave approximation based on a digital elevation data for surface water dynamics. A detailed analysis of the data assimilation algorithm behavior within the coupled model has been carried out on a synthetic 1D test case in order to verify the correct implementation and derive a series of fundamental parameters, such as the minimum ensemble size that can ensure a sufficient accuracy in the statistical estimates. The assimilation frequency, as well as the effects induced by assimilation on the surface and/or subsurface system state, was tested on a 3D synthetic test case represented by a 1.62 km2 tilted v-catchment, for which observations of pressure head and streamflow data are assimilated in order to retrieve the true watershed state in 2 scenarios: i) starting from a drier initial condition and ii) intentionally imposing a biased atmospheric forcing. In general, streamflow prediction is improved by assimilation of both pressure head and streamflow individually and by coupled assimilation. However, assimilation of streamflow data only does not improve the subsurface system state, leading to a deficit in soil moisture compared to both the true and the open loop simulations. Combined assimilation is therefore more adequate for the description of the entire surface--subsurface system state. The sensitivity analysis to the assimilation frequency yields contradictory results: as expected, a higher assimilation frequency improves the true state retrieval in the drier initial condition scenario, while for the biased atmospheric forcing scenario an analogous improvement is not manifest.

  16. Revisiting "nutrient trapping" in global coupled biogeochemical ocean circulation models

    NASA Astrophysics Data System (ADS)

    Dietze, H.; Loeptien, U.

    2013-04-01

    We analyze an extensive set of global coupled biogeochemical ocean circulation models. The focus is on the equatorial Pacific. In all simulations, which are consistent with observed standing stocks of relevant biogeochemical species at the surface, we find spuriously enhanced (reduced) macronutrient (oxygen) concentrations in the deep eastern equatorial Pacific. This modeling problem, apparently endemic to global coupled biogeochemical ocean circulation models, was coined "nutrient trapping" by Najjar et al. (1992). In contrast to Aumont et al. (1999), we argue that "nutrient trapping" is still a persistent problem, even in eddy-permitting models and, further, that the scale of the problem retards model projections of nitrogen cycling. In line with previous work, our results indicate that a deficient circulation is at the core of the problem rather than an admittedly poor quantitative understanding of biogeochemical cycles. More specifically, we present indications that "nutrient trapping" in models is a result of a spuriously damped Equatorial Intermediate (zonal) Current System and Equatorial Deep Jets—phenomenon which await a comprehensive understanding and have, to date, not been successfully simulated.

  17. 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.

  18. 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.

  19. 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. PMID:20182510

  20. 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.

  1. 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.

  2. Coupling of hydrodynamic and biogeochemical processes at aquatic interfaces

    NASA Astrophysics Data System (ADS)

    Lewandowski, Jrg; Krause, Stefan

    2015-04-01

    The overall aim of this contribution is a general conceptual framework for aquatic interfaces that is applicable to a wide range of systems, scales and processes. Aquatic interfaces are characterized by steep physical, chemical and biological gradients due to the contrast between the two adjacent environments. Investigating the spatially heterogeneous and temporally variable hydrodynamic and biogeochemical processes requires innovative monitoring technologies and sophisticated measurement techniques that can cope with different spatial scales. Although enhanced biogeochemical processing rates are inherent to aquatic interfaces due to their steep biogeochemical gradients and their intensive structural and compositional heterogeneity, the effective turnover depends strongly on the residence time distribution along the flow paths with their particular biogeochemical milieus and reaction kinetics. Thus, identification and characterization of the highly complex flow patterns in and across aquatic interfaces are crucial to understand biogeochemical processing along exchange flow paths and to quantify transport across aquatic interfaces; i.e. hydrodynamic and biogeochemical processes are closely interlinked. But interface processing rates are not only enhanced compared to the adjacent compartments that they connect; also completely different reactions might occur if certain thresholds are exceeded or the biogeochemical milieu differs significantly from the adjacent environments. Single events, temporal variability and spatial heterogeneity might increase overall processing rates of aquatic interfaces and thus, should not be neglected when studying aquatic interfaces. Aquatic interfaces are key zones relevant for the ecological state of the entire ecosystem and thus, understanding interface functioning and controls is paramount for ecosystem management.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    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.

  4. 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 climate models.

  5. 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

  6. Diffuse hydrological mass transport through catchments: scenario analysis of coupled physical and biogeochemical uncertainty effects

    NASA Astrophysics Data System (ADS)

    Persson, K.; Jarsjö, J.; Destouni, G.

    2011-10-01

    This paper quantifies and maps the effects of coupled physical and biogeochemical variability on diffuse hydrological mass transport through and from catchments. It further develops a scenario analysis approach and investigates its applicability for handling uncertainties about both physical and biogeochemical variability and their different possible cross-correlation. The approach enables identification of conservative assumptions, uncertainty ranges, as well as pollutant/nutrient release locations and situations for which further investigations are most needed in order to reduce the most important uncertainty effects. The present scenario results provide different statistical and geographic distributions of advective travel times for diffuse hydrological mass transport. The geographic mapping can be used to identify potential hotspot areas with large mass loading to downstream surface and coastal waters, as well as their opposite, potential lowest-impact areas within the catchment. Results for alternative travel time distributions show that neglect or underestimation of the physical advection variability, and in particular of those transport pathways with much shorter than average advective solute travel times, can lead to substantial underestimation of pollutant and nutrient loads to downstream surface and coastal waters. This is particularly true for relatively high catchment-characteristic product of average attenuation rate and average advective travel time, for which mass delivery would be near zero under assumed transport homogeneity but can be orders of magnitude higher for variable transport conditions. A scenario of high advection variability, with a significant fraction of relatively short travel times, combined with a relevant average biogeochemical mass attenuation rate, emerges consistently from the present results as a generally reasonable, conservative assumption for estimating maximum diffuse mass loading, when the prevailing physical and biogeochemical variability and cross-correlation are uncertain.

  7. 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.

  8. Effects of Coupled Biogeochemical and Transport Processes on Soil Aggregate-Scale Selenium Speciation

    NASA Astrophysics Data System (ADS)

    Pallud, C. E.; Kausch, M. F.

    2014-12-01

    Biogeochemical processes controlling elemental cycling in soil are heterogeneously distributed due to its complex physical structure. The aggregate scale (mm-cm) is of particular interest due to the sharp transition in pore size between the aggregates themselves and the macropores surrounding them, which can lead to mass-transfer limitations and to chemical gradients over short distances. The objective of this study is to investigate how the coupled transport and biogeochemical processes that occur at the soil-aggregate scale affect selenium speciation and immobilization within soils. We present a combined experimental and modelling study on artificial soil aggregates using a complex, but controlled, setting representative of natural systems. Circumventing byproduct accumulation and substrate exhaustion common in batchs and avoiding the poor physical analogy to soils of homogenously packed columns, our experiments mimic soils using constructed cm-scale aggregates in flow-through reactors, which results in diffusively and advectively controlled regions. A reactive transport model is used to delineate transport regimes, identify reaction zones, and estimate kinetic parameters and reaction rates at the aggregate scale. Model simulations showed extensive intra-aggregate, mm-scale radial variations in selenium distribution, reproducing the trends observed experimentally. Anoxic microzones developed over time within soil aggregates, both under oxic and anoxic conditions. We showed that those chemical gradients are mainly controlled by the coupling and respective importance of transport and microbial selenium reduction. Furthermore, we found that solid-phase concentrations of reduced selenium increased from the advection boundary (macropore) toward the aggregate cores, which would imply that more selenium can be sequestered in soils with larger aggregates. Simulations predict that selenium retention is positively correlated with aggregate size. Overall, this work highlights the importance of the spatial connection between reaction and transport fronts. It points out to the importance of obtaining information on transport-limited, intra-aggregate biogeochemical dynamics to better understand reactive transport of redox-sensitive species in structured soils.

  9. 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.

  10. Coupled Biogeochemical and Hydrologic Processes Governing Arsenic Mobility Within Sediments of Southeast Asia

    NASA Astrophysics Data System (ADS)

    Kocar, B. D.; Polizzotto, M. L.; Ying, S. C.; Benner, S. G.; Sampson, M.; Fendorf, S.

    2008-12-01

    Weathering of As-bearing rocks in the Himalayas has resulted in the transport of sediments down major river systems such as the Brahmaputra, Ganges, Red, Irrawaddy, and Mekong. Groundwater in these river basins commonly has As concentrations exceeding the World Health Organization's recommended drinking water limit (10 μg L-1) by more than an order of magnitude. Coupling of hydrology and biogeochemical processes underlies the elevated concentrations of As in these aquifers, necessitating studies that allow their deconvolution. Furthermore, to fully elucidate the biogeochemical mechanisms of sedimentary As release, the thermodynamic favorability of controlling biogeochemical reactions must be considered. We therefore used a combination of spectroscopic and wet chemical measurements to resolve the dominant processes controlling As release and transport in surficial soils/sediments within an As-afflicted field area of the Mekong delta. Based on these measurements, we assess the thermodynamic potential for As, Fe, and S reduction to transpire--major processes influencing As release and mobility. Our results illustrate that clay (0-12m deep) underlying oxbow and wetland environments are subjected to continuously reducing conditions due to ample carbon input and saturated conditions. Ensuing reductive mobilization of As from As-bearing Fe (hydr)oxides results in its migration to the underlying sandy aquifer (>12 m deep). Reactive transport modeling using PHREEQC and MIN3P, constrained with chemical and hydrologic field measurements, provides a calibrated illustration of As release and transport occurring within the clays underlying organic-rich, permanently inundated locations. These areas provide sufficient As to the aqueous phase for widespread contamination of the aquifer, and release is predicted to occur for several thousand years prior to depletion of As from the solid phase.

  11. PEATBOG: a biogeochemical model for analyzing coupled carbon and nitrogen dynamics in northern peatlands

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.

    2013-08-01

    Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.

  12. PEATBOG: a biogeochemical model for analyzing coupled carbon and nitrogen dynamics in northern peatlands

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.

    2013-03-01

    Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.

  13. 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 for organic matters and the nutrients. Second, we described for each basin the particularities with evoking the main dynamics and biogeochemical aspects affecting primary production and export of particulate carbon outside the photic zone.

  14. 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.

  15. 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 first three years of our project, led to several major new insights on the interaction between ocean biogeochemistry and circulation. This work, which is described in the following Section II on “Large scale fertilization,” has continued to appear in the literature over the past few years, including two high visibility papers in Nature. Early on in the first three years of our project, it became clear that small "patch-scale" fertilizations over limited regions of order 100 km diameter were much more likely than large scale fertilization, and we carried out a series of idealized patch fertilization simulations reported on in Gnanadesikan et al. (2003). Based on this paper and other results we had obtained by the end of our first three-year grant, we identified a number of important issues that needed to be addressed in the second three-year period of this grant. Section III on “patch fertilization” discusses the major findings of this phase of our research, which is described in two major manuscripts that will be submitted for publication in the near future. This research makes use of new more realistic ocean ecosystem and iron cycling models than our first paper on this topic. We have several major new insights into what controls the efficiency of iron fertilization in the ocean. Section IV on “model development” summarizes a set of papers describing the progress that we made on improving the ecosystem models we use for our iron fertilization simulations.

  16. Multi-scale Characterization and Prediction of Coupled Subsurface Biogeochemical-Hydrological Processes

    SciTech Connect

    Hubbard, Susan; Williams, Ken; Steefel, Carl; Banfield, Jill; Long, Phil; Slater, Lee; Pride, Steve; Jinsong Chen

    2006-06-01

    To advance solutions needed for remediation of DOE contaminated sites, approaches are needed that can elucidate and predict reactions associated with coupled biological, geochemical, and hydrological processes over a variety of spatial scales and in heterogeneous environments. Our previous laboratory experimental experiments, which were conducted under controlled and homogeneous conditions, suggest that geophysical methods have the potential for elucidating system transformations that often occur during remediation. Examples include tracking the onset and aggregation of precipitates associated with sulfate reduction using seismic and complex resistivity methods (Williams et al., 2005; Ntarlagiannis et al., 2005) as well as estimating the volume of evolved gas associated with denitrification using radar velocity. These exciting studies illustrated that geophysical responses correlated with biogeochemical changes, but also that multiple factors could impact the geophysical signature and thus a better understanding as well as integration tools were needed to advance the techniques to the point where they can be used to provide quantitative estimates of system transformations.

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

    TOXLINE Toxicology Bibliographic Information

    Lu C; Tian H

    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 -376.3146.4Tg CO2 eqyr(-1) (the standard deviation is interannual variability of GWP) during 2000-2008. The chemical N fertilizer uses were estimated to increase GWP by 45.634.3Tg CO2 eqyr(-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.

  18. Observations of physical-biogeochemical coupling in the tropical Northeast Atlantic using a fleet of gliders

    NASA Astrophysics Data System (ADS)

    Kanzow, T.; Krahmann, G.; Karstensen, J.

    2012-12-01

    To study the coupling between physical and biogeochemical parameters, high-spatial resolution, multi-parameter measurements are required. This poses a challenge to ocean observing systems. We present results from a study in the tropical Northeast Atlantic, employing simultaneous observations from 5 gliders. Each glider recorded temperature, salinity, chlorophyll, oxygen and turbidity for the duration of 50 days. A 45 by 45 km wide area was sampled using butterfly-shaped courses, to optimize the area coverage of the gliders. Our analysis focuses on the quantification of the spatial scales of variability in the recorded parameters and the demonstration of coupling between physical and biogeochemical parameters. The gliders observed strong variability in form of changes of thermohaline properties including pronounced submesoscale variability. The scale-dependence of the different parameters is presented. Below the mixed layer, changes in oxygen and salinity imply spatio-temporal variability of the ratio of North to South Atlantic waters. We report the passing of an open-ocean salinity front, associated with pronounced changes in both the vertical chlorophyll distribution and the possible communication between the mixed layer base and the sub-surface chlorophyll maximum. Our results imply, that these variations might pose challenges to estimating chlorophyll profiles by remote sensing.Salinity (upper panel) and chlorophyll fluorescence (lower panel), as observed from a glider north of the Cape Verde Islands. Also shown are the mixed laxer base (magenta line) and a potential density surface (black line). Note that the mixed layer base ceases to reach the subsurface chlorophyll maximum after passing through the salinity front.

  19. Marine biological feedback associated with Indian Ocean Dipole in a coupled ocean/biogeochemical model

    NASA Astrophysics Data System (ADS)

    Park, Jong-Yeon; Kug, Jong-Seong

    2014-01-01

    The impact of marine ecosystem on the tropical climate variability in the Indian Ocean is investigated by performing coupled ocean/biogeochemical model experiments, which are forced by realistic surface winds from 1951 to 2010. Results from a suite of chlorophyll perturbation experiments reveal that the presence of chlorophyll can have significant effects on the characteristics of the Indian Ocean Dipole (IOD), including its amplitude and skewness, as well as on the mean state. Specifically, chlorophyll increases mean sea surface temperature due to direct biological heating in regions where the mean mixed layer depth is generally shallow. It is also found that the presence of chlorophyll affects the IOD magnitude by two different processes: One is the amplifying effect by the mean chlorophyll, which leads to shoaling of mean thermocline depth, and the other is the damping effect by the interactively varying chlorophyll coupled with the physical model. There is also a biological impact on the skewness of the IOD, resulting in enhanced positive skewness. This skewness change is primarily caused by the phase dependency of the above two contradicting effects involving the asymmetric thermocline feedback and the nonlinear mixed layer heating.

  20. 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. PMID:23504794

  1. Evaluation of an operational ocean configuration at 1/12° on the Indonesian seas: Physical/Biogeochemical coupling

    NASA Astrophysics Data System (ADS)

    Gutknecht, Elodie; Reffray, Guillaume; Gehlen, Marion

    2015-04-01

    In the framework of the INDESO (Infrastructure Development of Space Oceanography) project, an operational ocean forecasting center has been developed to monitor the state of the Indonesian seas in terms of circulation, biogeochemistry and fisheries. The forecasting system combines a suite of numerical models connecting physical and biogeochemical parameters to population dynamics of large marine predators. Developed by Mercator Ocean and CLS, the physical/biogeochemical coupled component (INDO12BIO configuration) covers a large region extending from the western Pacific Ocean to the Eastern Indian Ocean at 1/12° resolution. The OPA/NEMO physical ocean model and the PISCES biogeochemical model are coupled in mode "on-line" without degradation in space and time. The operational global ocean forecasting system (1/4°) operated by Mercator Ocean provides the physical forcing while climatological open boundary conditions are prescribed for the biogeochemistry. This poster describes the performances of the INDO12BIO configuration. They are assessed by the evaluation of a reference hindcast simulation covering the last 8 years (2007-2014). Confrontations to satellite, in-situ and climatological observations are commented. Diagnostics are performed on chlorophyll-a, primary production, nutrients and oxygen. The model catches the main characteristics of the biogeochemical tracers in space and time. The seasonal cycle of chlorophyll-a and primary production is in phase with satellite-based products. The northern and southern parts of the archipelago present a distinct seasonal cycle, with higher chlorophyll biomass and production rates in the southern (northern) part during SE (NW) monsoon. Nutrient and oxygen concentrations are correctly reproduced in terms of horizontal and vertical distributions. The biogeochemical content of water masses entering in the archipelago as well as the water mass transformation across the archipelago conserves realistic vertical distribution in Banda sea and at the exit of the archipelago.

  2. 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.

  3. 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 with these variants will be presented and discussed. References Aumont O., 1998. Etude du cycle naturel du carbone dans un modèle 3D de l'océan mondial. Ph.D. thesis, Univ. Pierre et Marie Curie, Paris, 1998 Madec, G. Delecluse, P., Imbard M., Levy. C, 1998. OPA8.1 Ocean General Circulation Model Reference manual. Notes du pôle de modélisation, Tech. rep., Institut Pierre-Simon Laplace (IPSL). 91p. Pham D.T., Verron J. et Roubaud M.C., 1998:, Singular evolutive extended kalman filter with EOF initialization for data assimilation in oceanography, J. Mar. Systems., 16, 323-340. Testut, C-E., Brasseur, P., J-M., Brankart., Verron, J. 2003, Assimilation of sea-surface temperature and altimetric observations during 1992-1993 into an eddy-permiting primitive equation model of the North Atlantic Ocean. J. Mar. Systems., 40-41, 291-316

  4. 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 and denitrification with a direct impact on the stream nutrient removal and transport.

  5. 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.

  6. Modeling the Nd Oceanic Cycle Using a Fully Prognostic Dynamical/Biogeochemical Coupled Model

    NASA Astrophysics Data System (ADS)

    Arsouze, T.; Dutay, J.; Lacan, F.; Jeandel, C.

    2008-12-01

    The "Nd paradox" refers to the decoupling of Nd isotopic composition (hereafter refered as epsNd) and Nd concentration in the ocean. While epsNd is commonly used as a conservative water-mass tracer in the ocean interior far from any lithogenic inputs, Nd concentration increases with depth and along the thermohaline circulation, resembling typical non-conservative patterns of nutrients that are affected by vertical scavenging. Also, Nd oceanic budgets inferred from traditional sources (aeolian dusts and riverine discharge) cannot account for both epsNd and Nd concentration (Tachikawa et al., 2003). Recently, "Boundary Exchange" (BE, i.e. process of boundary scavenging compensated by inputs from the sediments along the continental margin) has been proposed as an important source/sink term of Nd that could solve the "Nd paradox". Here, we simulate the oceanic epsNd and Nd concentrations using the coupled dynamical/biogeochemical ocean general circulation model NEMO/PISCES. A reversible scavenging model has been parameterized to reproduce vertical cycling and dissolved/particulate interactions. Sources taken into consideration are partial dissolution of sediment (source of the BE process), atmospheric dust and dissolved riverine discharge. Some discrepancies in modeled particle fields create too pronounced vertical gradients in Nd concentrations and may lead to an overestimated role of the reversible scavenging. However, results show that: 1) the reversible scavenging is a necessary component to reproduce both epsNd and Nd concentration distributions and thus explain the "Nd paradox", and 2) BE is the predominant Nd source to the ocean (1.0E+10 g(Nd)/year) with fluxes as large as 25 times those of other sources (4.0E+8 g(Nd)/year). Hence it likely represents the missing flux necessary to reconcile Nd and Nd concentration budgets. Nevertheless, dust inputs are necessary to constrain epsNd values in surface waters. Tachikawa, K., Athias, V., and Jeandel, C.: Neodymium budget in the ocean and paleoceanographic implications, Journ. Geophys.Res., 108, 3254 doi:3210.1029/1999JC000285, 2003.

  7. Modeling the Nd Oceanic Cycle Using a Fully Prognostic Dynamical/Biogeochemical Coupled Model

    NASA Astrophysics Data System (ADS)

    Arsouze, T.; Dutay, J.-C.; Lacan, F.; Jeandel, C.

    2009-04-01

    The "Nd paradox" refers to the decoupling of Nd isotopic composition (hereafter refered as epsNd) and Nd concentration in the ocean. While epsNd is commonly used as a conservative water-mass tracer in the ocean interior far from any lithogenic inputs, Nd concentration increases with depth and along the thermohaline circulation, resembling typical non-conservative patterns of nutrients that are affected by vertical scavenging. Also, Nd oceanic budgets inferred from traditional sources (aeolian dusts and riverine discharge) cannot account for both epsNd and Nd concentration (Tachikawa et al., 2003). Recently, "Boundary Exchange" (BE, i.e. process of boundary scavenging compensated by inputs from the sediments along the continental margin) has been proposed as an important source/sink term of Nd that could solve the "Nd paradox". Here, we simulate the oceanic epsNd and Nd concentrations using the coupled dynamical/biogeochemical ocean general circulation model NEMO/PISCES. A reversible scavenging model has been parameterized to reproduce vertical cycling and dissolved/particulate interactions. Sources taken into consideration are partial dissolution of sediment (source of the BE process), atmospheric dust and dissolved riverine discharge. Some discrepancies in modeled particle fields create too pronounced vertical gradients in Nd concentrations and may lead to an overestimated role of the reversible scavenging. However, results show that: 1) the reversible scavenging is a necessary component to reproduce both epsNd and Nd concentration distributions and thus explain the "Nd paradox", and 2) BE is the predominant Nd source to the ocean (1.0E+10 g(Nd)/year) with fluxes as large as 25 times those of other sources (4.0E+8 g(Nd)/year). Hence it likely represents the missing flux necessary to reconcile Nd and Nd concentration budgets. Nevertheless, dust inputs are necessary to constrain epsNd values in surface waters. Tachikawa, K., Athias, V., and Jeandel, C.: Neodymium budget in the ocean and paleoceanographic implications, Journ. Geophys.Res., 108, 3254 doi:3210.1029/1999JC000285, 2003.

  8. 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 compounds and molecular hydrogen, the oxidation of which may be coupled to the reductive immobilization of aqueous uranium by a variety of indigenous microorganism (e.g. Geobacter sp.). The ability to utilize geophysical techniques to assess a site's prospects for natural attenuation thus constitutes an exciting new development in the emerging field of biogeophysics.

  9. 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.

  10. 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.

  11. 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, measurements show low salinity stratification (when compared to the January observations). During this month, stratification is mainly due to water temperature. In general, the correlation between water temperature from the model and satellite data, reveals values higher than 0.5 (significant values) for the whole simulation period, presenting high correlations (about 0.8) in January and February, when the plume propagation is mainly controlled by the estuarine discharge. The correlation between the model results of suspended sediments and the satellite data (suspended matter) presents significant values (higher than 0.5) for almost the whole simulation period. On the shelf, near the Tagus mouth, the export of estuarine waters forms a plume which is highly influenced by the geography of the coastline, inducing a plume trajectory very close to shore. Northern winds events cause a displacement of the coastally trapped plume, driving a new offshore plume. The relaxation of the northern wind regime pushes back the coastal jet toward the coast, propagating estuarine water to the north along the coastline. The model was also able to reproduce the effect of the estuary plume over the coastal surface chlorophyll patterns observed remotely and the in situ chlorophyll and nutrient profiles, especially in the periods of low wind intensity. In periods of persistent Northerly winds the effect of the Sintra Mountains Ridge over the wind field tend to be underestimated. This leads to a southerly transport by the model slightly more intense than the one observed remotely.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  14. 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.

  15. Surface micro-topography causes hot spots of biogeochemical activity in wetland systems: A virtual modeling experiment

    NASA Astrophysics Data System (ADS)

    Frei, S.; Knorr, K. H.; Peiffer, S.; Fleckenstein, J. H.

    2012-12-01

    Wetlands provide important ecohydrological services by regulating fluxes of nutrients and pollutants to receiving waters, which can in turn mitigate adverse effects on water quality. Turnover of redox-sensitive solutes in wetlands has been shown to take place in distinct spatial and temporal patterns, commonly referred to as hot spots and hot moments. Despite the importance of such patterns for solute fluxes the mechanistic understanding of their formation is still weak and their existence is often explained by variations in soil properties and diffusive transport only. Here we show that surface micro-topography in wetlands can cause the formation of biogeochemical hot spots solely by the advective redistribution of infiltrating water as a result of complex subsurface flow patterns. Surface and subsurface flows are simulated for an idealized section of a riparian wetland using a fully integrated numerical code for coupled surface-subsurface systems. Biogeochemical processes and transport along advective subsurface flow paths are simulated kinetically using the biogeochemical code PHREEQC. Distinct patterns of biogeochemical activity (expressed as reaction rates) develop in response to micro-topography induced subsurface flow patterns. Simulated vertical pore water profiles for various redox-sensitive species resemble profiles observed in the field. This mechanistic explanation of hot spot formation complements the more static explanations that relate hot spots solely to spatial variability in soil characteristics and can account for spatial as well as temporal variability of biogeochemical activity, which is needed to assess future changes in the biogeochemical turnover of wetland systems.

  16. Modeling distinct vertical biogeochemical structure of the Black Sea: Dynamical coupling of the oxic, suboxic, and anoxic layers

    NASA Astrophysics Data System (ADS)

    Oguz, Temel; Ducklow, Hugh W.; Malanotte-Rizzoli, Paola

    2000-12-01

    A one-dimensional, vertically resolved, physical-biogeochemical model is used to provide a unified representation of the dynamically coupled oxic-suboxic-anoxic system for the interior Black Sea. The model relates the annual cycle of plankton production in the form of a series of successive phytoplankton, mesozooplankton, and higher consumer blooms to organic matter generation and to the remineralization-ammonification-nitrification-denitrification chain of the nitrogen cycle as well as to anaerobic sulfide oxidation in the suboxic-anoxic interface zone. The simulations indicate that oxygen consumption during remineralization and nitrification, together with a lack of ventilation of subsurface waters due to the presence of strong stratification, are the two main factors limiting aerobic biogeochemical activity to the upper ˜75 m of the water column, which approximately corresponds to the level of nitrate maximum. The position of the upper boundary and thus the thickness of the suboxic layer are controlled by upper layer biological processes. The quasi-permanent character of this layer and the stability of the suboxic-anoxic interface within the last several decades are maintained by a constant rate of nitrate supply from the nitrate maximum zone. Nitrate is consumed to oxidize sinking particulate organic matter as well as hydrogen sulfide and ammonium transported upward from deeper levels.

  17. Evaluating sources of arsenic to groundwater in the Mekong Delta based on coupled hydrologic and biogeochemical analyses

    NASA Astrophysics Data System (ADS)

    Polizzotto, M.; Benner, S. G.; Kocar, B. D.; Sampson, M.; Ouch, K.; Phan, K.; Fendorf, S.

    2007-12-01

    Tens of millions of people living on the large river deltas of Southeast Asia routinely consume groundwater with unsafe arsenic levels. While there is general agreement that arsenic is naturally derived, the particular sources of arsenic, as well as the mechanisms promoting its release from the solid-phase, remain unresolved, thereby limiting our ability to predict arsenic concentrations in space (between wells) and time (future concentrations). This uncertainty is attributed, in part, to a poor understanding of groundwater flow paths due to extensive irrigation pumping in the Ganges-Brahmaputra River system, where most research has focused. In order to elucidate the most important arsenic sources and the processes controlling arsenic contamination in Southeast Asian groundwater, we have established a field area within the minimally disturbed Mekong River Delta in Cambodia. While the Mekong Delta system in Cambodia has similar depositional history, regional hydrology, and biogeochemical conditions to other arsenic-contaminated deltaic aquifers of Asia, land use alteration, inclusive of irrigation, is minimal. Thus, the hydrology of our system remains governed by natural rather than anthropogenic processes, allowing us to formulate a steady-state, coupled hydrologic and biogeochemical model of arsenic release and transport. Using robust principles of mass balance, we show that, while liberation mechanisms within the deeper aquifer sediments may contribute arsenic to the groundwater, the majority of the dissolved arsenic is derived from arsenic release at the near-surface and is transported through the aquifer, a finding that has important implications for management of the arsenic crisis.

  18. 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.

  19. Coupled physical/biogeochemical modeling including O2-dependent processes in the Eastern Boundary Upwelling Systems: application in the Benguela

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    The Eastern Boundary Upwelling Systems (EBUS) contribute to one fifth of the global catches in the ocean. Often associated with Oxygen Minimum Zones (OMZs), EBUS represent key regions for the oceanic nitrogen (N) cycle. Important bioavailable N loss due to denitrification and anammox processes as well as greenhouse gas emissions (e.g, N2O) occur also in these EBUS. However, their dynamics are currently crudely represented in global models. In the climate change context, improving our capability to properly represent these areas is crucial, due to anticipated changes in the winds, productivity, and oxygen content. We developed a biogeochemical model (BioEBUS) taking into account the main processes linked with EBUS and associated OMZs. We implemented this model in a 3-D realistic coupled physical/biogeochemical configuration in the Namibian upwelling system (Northern Benguela) using the high-resolution hydrodynamical model ROMS. We present here a validation using in situ and satellite data as well as diagnostic metrics, and sensitivity analyses of key parameters and N2O parameterizations. The impact of parameter values on the OMZ off Namibia, on N loss, and on N2O concentrations and emissions is detailed. The model realistically reproduces the vertical distribution and seasonal cycle of observed oxygen, nitrate and Chl a concentrations, and the rates of microbial processes (e.g. NH4+ and NO2- oxidation, NO3- reduction and anammox) as well. Based on our sensitivity analyses, biogeochemical parameter values associated with organic matter decomposition, vertical sinking and nitrification play a key role for the low-oxygen water content, N loss and N2O concentrations in the OMZ. Moreover, the importance of both steps of nitrification, ammonium oxidation to nitrate with nitrite as an explicit intermediate, is highlighted to improve the representation of microbial activity linked with OMZ. The simulated minimum oxygen concentrations are driven by the poleward meridional advection of oxygen-depleted waters offshore of 300 m isobath and by the biogeochemical activity inshore of this isobath, highlighting a spatial shift of dominant processes maintaining the minimum oxygen concentrations off Namibia. In the OMZ off Namibia, N2O emissions to the atmosphere are comparable with N loss. Anammox contributes to about 20% of total N loss, an estimate lower than currently assumed (up to 50%) for the global ocean.

  20. Coupled physical/biogeochemical modeling including O2-dependent processes in the Eastern Boundary Upwelling Systems: application in the Benguela

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    The Eastern Boundary Upwelling Systems (EBUS) contribute to one fifth of the global catches in the ocean. Often associated with Oxygen Minimum Zones (OMZs), EBUS represent key regions for the oceanic nitrogen (N) cycle. Important bioavailable N loss due to denitrification and anammox processes as well as greenhouse gas emissions (e.g, N2O) occur also in these EBUS. However, their dynamics are currently crudely represented in global models. In the climate change context, improving our capability to properly represent these areas is crucial due to anticipated changes in the winds, productivity, and oxygen content. We developed a biogeochemical model (BioEBUS) taking into account the main processes linked with EBUS and associated OMZs. We implemented this model in a 3-D realistic coupled physical/biogeochemical configuration in the Namibian upwelling system (northern Benguela) using the high-resolution hydrodynamic ROMS model. We present here a validation using in situ and satellite data as well as diagnostic metrics and sensitivity analyses of key parameters and N2O parameterizations. The impact of parameter values on the OMZ off Namibia, on N loss, and on N2O concentrations and emissions is detailed. The model realistically reproduces the vertical distribution and seasonal cycle of observed oxygen, nitrate, and chlorophyll a concentrations, and the rates of microbial processes (e.g, NH4+ and NO2- oxidation, NO3- reduction, and anammox) as well. Based on our sensitivity analyses, biogeochemical parameter values associated with organic matter decomposition, vertical sinking, and nitrification play a key role for the low-oxygen water content, N loss, and N2O concentrations in the OMZ. Moreover, the explicit parameterization of both steps of nitrification, ammonium oxidation to nitrate with nitrite as an explicit intermediate, is necessary to improve the representation of microbial activity linked with the OMZ. The simulated minimum oxygen concentrations are driven by the poleward meridional advection of oxygen-depleted waters offshore of a 300 m isobath and by the biogeochemical activity inshore of this isobath, highlighting a spatial shift of dominant processes maintaining the minimum oxygen concentrations off Namibia. In the OMZ off Namibia, the magnitude of N2O outgassing and of N loss is comparable. Anammox contributes to about 20% of total N loss, an estimate lower than currently assumed (up to 50%) for the global ocean.

  1. The CO2 system in the Mediterranean Sea inferred from a 3D coupled physical-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Ulses, Caroline; Kessouri, Fayçal; Estournel, Claude; Marsaleix, Patrick; Beuvier, Jonathan; Somot, Samuel; Touratier, Frank; Goyet, Catherine; Coppola, Laurent; Diamond, Emilie; Metzl, Nicolas

    2015-04-01

    The semi-enclosed Mediterranean Sea characterized by short residence times is considered as a region particularly sensitive to natural and anthropogenic forcing. Due to scarce CO2 measurements in the whole basin, the CO2 system, for instance the air-sea CO2 exchanges and the effects of the increase of atmospheric CO2, are poorly characterized. 3D physical-biogeochemical coupled models are unique tools that can provide integrated view and gain understanding in the temporal and spatial variation of the CO2 system variables (dissolved inorganic carbon, total alkalinity, partial pressure of CO2 and pH). An extended version of the biogeochemical model Eco3m-S (Auger et al., 2014), that describes the cycles of carbon, nitrogen, phosphorus and silica, was forced by a regional circulation model (Beuvier et al., 2012) to investigate the CO2 system in the Mediterranean Sea over a 13-years period (2001-2013). First, the quality of the modelling was evaluated through comparisons with satellite and in situ observations collected in the whole basin over the study period (Touratier and Goyet, 2009; 2011 ; Rivaro et al., 2010 ; Pujo-Pay et al., 2011 ; Alvarez et al, 2014). The model reasonably reproduced the various biological regimes (north-western phytoplanctonic bloom regime, oligotrophic eastern regime, etc.) as well as the recorded spatial distribution and temporal variations of the carbonate system variables. The coupled model was then used to estimate the air-sea pCO2 exchanges and the transport of DIC and TA towards the Atlantic Ocean at the Strait of Gibraltar.

  2. A Coupled Biogeochemical Reactive Transport Model in Bed Sediments and Water Column of Riverine Systems

    NASA Astrophysics Data System (ADS)

    Massoudieh, A.; Bombardelli, F. A.; Sengor, S. S.; Ginn, T. R.

    2007-12-01

    ABSTRACT: A multi-scale, quasi-two-dimensional, biogeochemical reactive theoretical and numerical model is presented, able to simulating sediment associated transport and transformations of contaminants in the water column and bed sediments of riverine systems as a result of sediment associated transport, as well as resuspension, deposition and burial. The model considers contaminant mass exchange between sediments and aqueous phase both in benthic sediments and water column as a kinetically controlled process. It also takes into account the effect of microbially-mediated redox reactions affecting the speciation of chemicals. Transport of species in the sediments is modeled using a set of vertical one-dimensional sub-models which take into account the reactive transport of chemicals, burial, sorption/desorption to/from the solid phase, and diffusive transport of aqueous species. An innovative multi-time step approach is used to model the fully kinetic nonlinear reaction terms using a non-iterative explicit method. This approach enables the model to handle fast and near- equilibrium reactions without a significant increase in computational burden. Ongoing and planned applications of this multiscale modeling strategy to two cases, multiple metal transport in Lake Coeur d'Alene, Idaho, and Mercury Cycling in Walker Creek, California, are discussed.

  3. 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 70% NCP occurred steadily throughout the main bloom, while respiration, rather than sinking, drove the rapid drop in POC at bloom termination. Sensor networks require proper intercalibration to support quantitative use of the measurements, but calibration efforts become increasingly difficult as the number of independent sensors grows. NAB08 offers a suitable model for modest networks, but alternative approaches will be required for larger arrays.

  4. 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, chemical, and radiative environments encountered in the global oceans.

  5. Surface-Subsurface Exchange and Transient Storage in Relation to Riparian Corridor Land Cover in an Urban Watershed

    NASA Astrophysics Data System (ADS)

    Ryan, R. J.; Welty, C.; Larson, P.; Runyan, C.; Poole, S.; Lapa-Lilly, P.; Miller, A.

    2008-12-01

    A suite of methods is being utilized by the Baltimore Waters Test Bed to develop an understanding of the interaction between groundwater and surface water at multiple space and time scales. As part of this effort, bromide tracer experiments were conducted over two 10-day periods in August 2007 and May 2008 along two 900-m reaches of Dead Run, a small urban stream located in Baltimore County, Maryland, to investigate the influence of distinct zones of riparian land cover on surface-subsurface exchange and transient storage under low- and high-baseflow conditions. Riparian land cover varied by reach along a gradient of land use spanning parkland, suburban/residential, and commercial, and included wooded, meadow, turf grass, and impervious cover. Reach-average surface-subsurface exchange was estimated using tracer-dilution and velocity-gaging stream flow measurements. Transient storage parameters (active storage area and storage exchange rate coefficient) were estimated using the USGS-code OTIS. Bed sediment grain size distribution was found to be unrelated to watershed position and riparian cover; however, a trend of finer bed sediment under low baseflow conditions was observed at most stations. In the lower section of Dead Run, gross inflow, gross outflow and surface-subsurface exchange (defined as the absolute value of net inflow) tended to be higher under high baseflow conditions (May 2008) compared to low baseflow conditions (August 2007). Surface-subsurface exchange was highest in reaches with greater riparian pervious cover while transient storage area and exchange rate were highest in reaches with greater impervious cover. Results from the tracer test are being incorporated into a coupled watershed model of the region. When working in urban watersheds, many complexities not typically encountered in more pristine areas must be addressed. Among these are high ambient salt concentrations (> 200 mg/L chloride), unexpected (and transient) stream discharges and withdrawals, and potential interactions with the public and police.

  6. 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 show direct and rapid effects on forest streams that may be widespread, although undocumented, throughout nitrogen-polluted temperate forests. In contrast to a week-long nitrate decline during peak autumn litterfall, base flow DON concentrations increased after leaf fall and remained high for 2 months. Dissolved organic nitrogen was hydrologically flushed to the stream from riparian soils during stormflow. In contrast to distinct seasonal changes in base flow nitrate and DON concentrations, ammonium concentrations were typically at or below the detection limit, similar to the rest of the year. Our findings reveal couplings among catchment flow paths, nutrient sources, and transformations that control seasonal extremes of stream nitrogen in forested landscapes.

  7. Bayesian inverse modeling at the hydrological surface-subsurface interface

    NASA Astrophysics Data System (ADS)

    Cucchi, K.; Rubin, Y.

    2014-12-01

    In systems where surface and subsurface hydrological domains are highly connected, modeling surface and subsurface flow jointly is essential to accurately represent the physical processes and come up with reliable predictions of flows in river systems or stream-aquifer exchange. The flow quantification at the interface merging the two hydrosystem components is a function of both surface and subsurface spatially distributed parameters. In the present study, we apply inverse modeling techniques to a synthetic catchment with connected surface and subsurface hydrosystems. The model is physically-based and implemented with the Gridded Surface Subsurface Hydrologic Analysis software. On the basis of hydrograph measurement at the catchment outlet, we estimate parameters such as saturated hydraulic conductivity, overland and channel roughness coefficients. We compare maximum likelihood estimates (ML) with the parameter distributions obtained using the Bayesian statistical framework for spatially random fields provided by the Method of Anchored Distributions (MAD). While ML estimates maximize the probability of observing the data and capture the global trend of the target variables, MAD focuses on obtaining a probability distribution for the random unknown parameters and the anchors are designed to capture local features. We check the consistency between the two approaches and evaluate the additional information provided by MAD on parameter distributions. We also assess the contribution of adding new types of measurements such as water table depth or soil conductivity to the reduction of parameter uncertainty.

  8. Global Biogeochemical Cycle of Si: Its Coupling to the Perturbed C-N-P cycles in Industrial Time

    NASA Astrophysics Data System (ADS)

    Lerman, A.; Li, D. D.; MacKenzie, F. T.

    2010-12-01

    The importance of silicon (Si) in global biogeochemical cycles is demonstrated by its abundance in the land and aquatic biomass, where Si/C is 0.02 in land plants and 0.15 in marine organisms. Estimates show that Si-bioproduction accounts for ~1.5% of terrestrial primary production, and ~4.5% in the coastal ocean. Human land-use activities have substantially changed regional patterns of vegetation distribution, soil conditions, and nutrient fluxes via runoff to the coastal ocean. Anthropogenic chemical fertilization of the land has caused a significant increase in fluvial nitrogen (N) and phosphorus (P) transport, whereas land-use and vegetation mass changes have caused variations in the riverine Si input, all eventually affecting the cycling of nutrients in the marine environment. We developed a global biogeochemical model of the Si cycle as coupled to the global C-N-P cycle model, TOTEM II (Terrestrial-Ocean-aTmosphere-Ecosystem-Model). In the model analysis from year 1700, taken as the start of the Anthropocene, to 2050, the bioproduction of Si on land and in the ocean is coupled to the bioproduction of C, perturbed by the atmospheric CO2 rise, land-use changes, and chemical fertilization. Also, temperature rise affects the Si cycling on land through bioproduction rates, terrestrial organic matter remineralization, and weathering, thereby affecting its delivery to the coastal zone. The results show that biouptake and subsequent release of Si on land strongly affect the Si river flux to the coastal ocean. During the 350-year period, Si river discharge has increased by ~10% until ~1940, decreasing since then to below its 1700 value and continuing to drop, under the current IPCC IS92 projections of CO2, temperature and other forcings. From 1700 to ~1950, land-use changes, associated with slash and burn of large areas of high-productivity land, caused a decrease of global land vegetation. Dissolution of Si in soil humus and weathering of silicate minerals are the main dissolved Si sources for rivers and groundwater. The decrease in Si uptake by land biomass made more Si available for river discharge, causing an increase in the Si river input until an increase in the land primary production reversed the process. Around 1950, the use of fertilizer on land, especially N and P, increased, driving the growth of coastal marine primary producers, including such Si organisms as diatoms, silicoflagellates, and sponge spicules, and thus causing a decrease of dissolved Si in the surface ocean. The percent decrease of coastal dissolved Si due to increased primary production is greater than that of surface open ocean due to the shorter residence time of Si in coastal water (~2.7 years) compared to that of surface open ocean (~10 years. The combination of the relatively small size and location of the coastal ocean at the junction of the land, atmosphere, and open ocean make it important to changes in water chemistry, in situ biological production, and sedimentary storage. Its buffer effect and fast response to perturbations are also shown in the results of this coupling study of the C-N-P-Si cycles.

  9. New Insights from Electrochemical Noise: A Coupled Biogeochemical and Electrochemical Investigation of an Anoxic Groundwater Seep

    NASA Astrophysics Data System (ADS)

    Enright, A. M.; Ferris, F. G.

    2013-12-01

    Understanding the electrochemical properties of microbial processes is a significant step towards developing physical and chemical signatures of biotic activity and the impact of microbes within Earth systems. Electrochemical noise techniques, borrowed from corrosion science, hold promise as a method of discerning contributions from chemical reactions occurring in a natural system. These techniques rely exclusively on measurements of fluctuation in potential or current to assess different chemical contributors. To this end, a coupled electrochemical and geochemical study of flocculent ocherous mats of bacteriogenic iron oxides in an anoxic, neutral pH groundwater seep near Deep River, Ontario, Canada, was undertaken. Hydrogeochemical properties, including redox potential, dissolved oxygen, and dissolved ferrous and total iron concentrations were measured in a series of three microcosms. (A), a chemical control of 0.22 μm filtered groundwater; (B) an abiotic control with 50 mL of autoclaved biogenic iron oxides (BIOS), and (C), a live microcosm with 50 mL of BIOS. All BIOS and groundwater samples were collected at a distance of 200 cm from the spring source using sterile syringes, and measurements were recorded every 30 minutes over a period of two hours from initial collection. Redox potential was measured using a Pt/Ag/Ag-Cl electrode and a National Instruments data-acquisition device (DAQ) at a frequency of 200 Hz for 60 seconds at 30 minute intervals, for the purpose of electrochemical noise analysis. After 120 minutes, for microcosm (A), 75% of the initial total dissolved iron remained in solution, as well as 32% of the initial dissolved ferrous iron. The pseudo-first order rate constant for Fe2+ oxidation was 0.007 min-1. Dissolved oxygen increased from 1.40 mg/L to 2.74 mg/L, and redox potential remained relatively constant at approximately 248 mV, relative to the standard hydrogen electrode (SHE), over this time interval. In microcosm (B), 16% of the total dissolved iron remained in after 120 minutes, and 16% of the initial dissolved ferrous iron with an Fe2+ oxidation rate constant of 0.021 min-1. Dissolved oxygen increased from 0.38 mg/L to 0.88 mg/L, while redox potential increased from 254.2 mV to 282.9 mV relative to SHE. In microcosm (C), 18% of the initial dissolved total iron remained in solution, and 17% of the initial dissolved ferrous iron with an Fe2+ oxidation rate constant of 0.036 min-1. Dissolved oxygen decreased from 0.31 mg/L to 0.5 mg/L, and redox potential increased from 301.9 mV to 328.8 mV. A slight (approximately 5.87-6.31) increase in pH was observed in all three microcosms. Preliminary analysis of electrochemical noise data indicates that each microcosm can be differentiated on this basis in the frequency domain; but relationships between rates of chemical reactions, such as iron oxidation, precipitation of iron from solution, and oxygen dissolution, are still being elucidated. This technique shows promise in providing evidence that the contributions to overall redox condition from various redox-active chemical species will be distinguished in the frequency domain.

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

    SciTech Connect

    Crawford, Ronald L; Paszczynski, Andrzej J

    2010-02-19

    Our goal within the overall project is to demonstrate the presence and abundance of methane monooxygenases (MMOs) enzymes and their genes within the microbial community of the Idaho National Laboratory (INL) Test Area North (TAN) site. MMOs are thought to be the primary catalysts of natural attenuation of trichloroethylene (TCE) in contaminated groundwater at this location. The actual presence of the proteins making up MMO complexes would provide direct evidence for its participation in TCE degradation. The quantitative estimation of MMO genes and their translation products (sMMO and pMMO proteins) and the knowledge about kinetics and substrate specificity of MMOs will be used to develop mathematical models of the natural attenuation process in the TAN aquifer. The model will be particularly useful in prediction of TCE degradation rate in TAN and possibly in the other DOE sites. Bacteria known as methanotrophs produce a set of proteins that assemble to form methane monooxygenase complexes (MMOs), enzymes that oxidize methane as their natural substrate, thereby providing a carbon and energy source for the organisms. MMOs are also capable of co-metabolically transforming chlorinated solvents like TCE into nontoxic end products such as carbon dioxide and chloride. There are two known forms of methane monooxygenase, a membrane-bound particulate form (pMMO) and a cytoplasmic soluble form (sMMO). pMMO consists of two components, pMMOH (a hydroxylase comprised of 47-, 27-, and 24-kDa subunits) and pMMOR (a reductase comprised of 63 and 8-kDa subunits). sMMO consists of three components: a hydroxylase (protein A-250 kDa), a dimer of three subunits (α2β2γ2), a regulatory protein (protein B-15.8 kDa), and a reductase (protein C-38.6 kDa). All methanotrophs will produce a methanol dehydrogenase to channel the product of methane oxidation (methanol) into the central metabolite formaldehyde. University of Idaho (UI) efforts focused on proteomic analyses using mass 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.

  11. Numerical modeling of coupled fluid flow and thermal and reactive biogeochemical transport in porous and fractured media

    SciTech Connect

    Yeh, Gour T.; Fang, Yilin; Zhang, Fan; Sun, Jiangtao; Li, Yuan; Li, Ming-Hsu; Siegel, Malcolm D.

    2010-01-01

    Subsurface contamination problems of metals and radionuclides are ubiquitous. Metals and radionuclides may exist in the solute phase or may be bound to soil particles and interstitial portions of the geologic matrix. Accurate tools to reliably predict the migration and transformation of these metals and radionuclides in the subsurface environment enhance the ability of environmental scientists, engineers, and decision makers to analyze their impact and to evaluate the efficacy of alternative remediation techniques prior to incurring expense in the field. A mechanistic-based numerical model could provide such a tool. This paper communicates the development and verification of a mechanistically coupled fluid-flow thermal-reactive biogeochemical-transport model where both fast and slow reactions occur in porous and fractured media. Theoretical bases, numerical implementations, and numerical experiments using the model are described. A definition of the "rates" of fast/equilibrium reactions is presented to come up with a consistent set of governing equations. Two example problems are presented. The first one is a reactive transport problem which elucidates the non-isothermal effects on heterogeneous reactions. It also demonstrates that the rates of fast/equilibrium reactions are not necessarily greater than that of slow/kinetic reactions in the context of reactive transport. The second example focuses on a complicated but realistic advective-dispersive-reactive transport problem. This example exemplifies the need for innovative numerical algorithms to solve problems involving stiff geochemical reactions. It also demonstrates that rates of all fast/equilibrium reactions are finite and definite. Furthermore, it is noted that a species-versus-time curve cannot be used to characterize the rate of homogeneous fast/equilibrium reaction in a reactive transport system even if one and only one such reaction is responsible for the production of this species.

  12. Emergent biological patterns and surface-subsurface interactions at landscape scales

    USGS Publications Warehouse

    Pringle, C.M.; Triska, F.J.

    2000-01-01

    In this chapter, we focus on emergent biological patterns in riverine ecosystems at landscape scales resulting from surface-subsurface water interaction. Our objectives are to examine (1) how the balance of physical and chemical factors on the "natural" geologic template affects biological patterns, (2) how natural hydrothermal systems can be used as a model for understanding surface-subsurface interactions and biological patterns in streams, and (3) how anthropogenic influences decouple the stream from the landscape by altering the nature of surface-subsurface water interactions and affecting biological patterns. We conclude with a synthesis and recommendations for further studies.

  13. 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.

  14. 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

    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 various virtual landscapes / catchment to demonstrate the capabilities of the modelling system. The modelling system was applied to simulate water and nutrient transport at the 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, 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.

  15. Biogeochemical Cycling

    NASA Technical Reports Server (NTRS)

    Bebout, Brad; Fonda, Mark (Technical Monitor)

    2002-01-01

    This lecture will introduce the concept of biogeochemical cycling. The roles of microbes in the cycling of nutrients, production and consumption of trace gases, and mineralization will be briefly introduced.

  16. Denitrification versus Anammox in the Eastern Tropical Pacific in a high-resolution coupled physical-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Montes, I.; Oschlies, A.; Gutknecht, E.; Dadou, I.; Garcon, V.

    2012-12-01

    The Eastern Tropical Pacific hosts one of the most productive eastern boundary upwelling of the world oceans, encompassing an extended Oxygen Minimum Zone (OMZ), which is maintained by sluggish oceanic circulation and high rates of organic matter decomposition consuming dissolved oxygen. This OMZ is also recognized as a major region of marine nitrogen loss, brought about by the two processes denitrification and anammox. The relative importance of these processes has, however, been subject to some debate. Here, we use a high-resolution physical-biogeochemical model (ROMS-BioBus) of the Peruvian upwelling system that has been calibrated to achieve good agreement with observed biogeochemical tracer distributions. By varying biogeochemical model parameters, we specifically construct different model configurations with either anammox or denitrification being the dominant nitrogen loss process. Biogeochemical and physical conditions governing the relative contributions of the two processes in our model are analysed and, by comparison with field data, used to make inferences about the relative contributions of anammox and denitrification in the OMZ off Peru.

  17. 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

  18. 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 production estimated for the South Atlantic subtropical gyre. Export production (16.9 ± 1.3 × 1010 mol N yr-1) helps to maintain an OMZ off Namibia in which coupled nitrification, denitrification and anammox processes lead to losses of fixed N and N2O production. However, neither N losses (0.04 ± 0.025 × 1010 mol N yr-1) nor N2O emissions (0.03 ± 0.002 × 1010 mol N yr-1) significantly impact the main N exports of the Walvis Bay area. The studied area does not significantly contribute to N2O emissions (0.5 to 2.7%) compared to the global coastal upwelling emissions. Locally produced N2O is mostly advected southward by the poleward undercurrent.

  19. 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.

  20. In situ response of bay productivity to nutrient loading from a small tributary: The Delaware Bay-Murderkill Estuary tidally-coupled biogeochemical reactor

    NASA Astrophysics Data System (ADS)

    Voynova, Yoana G.; Lebaron, Karine C.; Barnes, Rebecca T.; Ullman, William J.

    2015-07-01

    A small, turbid and nutrient-rich tributary, the Murderkill Estuary, and a large estuarine ecosystem, the Delaware Bay, are tightly linked and form an efficient, tidally-coupled biogeochemical reactor during the summer. Nitrate loading from the Murderkill Estuary generates an instantaneous increase in biological oxygen production in the adjacent Delaware Bay. We are able to capture this primary production response with continuous hourly measurements of dissolved oxygen, chlorophyll, and nitrate. The nitrate influxes from the Murderkill support primary production rates in the Delaware Bay margins that are twice as high as the average production rates measured in the central Bay regions. This elevates chlorophyll in the Bay margins in the summer and fuels metabolism. Tidal transport of the newly produced autochthonous chlorophyll particles from the Bay into the Estuary could also provide a source of labile material to the marshes surrounding the Murderkill, thus perhaps fueling marsh respiration. As a consequence of the tidal coupling between Delaware Bay and the Murderkill Estuary, ecosystem productivity and metabolism in the Bay and Estuary are linked, generating an ecosystem feedback mechanism. Storms modulate this tidally-coupled biogeochemical reactor, by generating significant nitrate and salinity changes. Depending on their magnitude and duration, storms induce large phytoplankton blooms in the Delaware Bay. Such large phytoplankton blooms may occur more often with climate change, since century-long discharge records document an increase in storm frequency.

  1. A Coupled Hydrological and Biogeochemical Process Model for Fate and Transport of Nitrate in Agricultural Areas of Texas

    NASA Astrophysics Data System (ADS)

    Mendoza Sanchez, I.; Mohanty, B. P.

    2010-12-01

    In agricultural areas the use of fertilizers to maintain high crop productivity contributes to high concentrations of nitrate in groundwater. The objective of the study is to accurately estimate historical and future nitrate concentration in domestic wells in agricultural areas in Texas. To date most transport models have focused on groundwater processes, neglecting critical biogeochemical processes that occur as contaminated water percolates through the soil profile. Transport, transformation, and distribution of nitrogen from the point of application through the soil profile to groundwater depend upon complex physical, biological, and chemical processes. We developed a mathematical model that accounts for key biogeochemical processes that occur as contaminated water is transported from the land surface to the groundwater. Key features of the model include: root growth, root uptake of nutrients, mineral precipitation-dissolution and biogeochemical cycles of carbon, nitrogen, iron and sulfur (C-N-Fe-S). The model also includes biological mediated secondary reactions. Depending on aquifer soils, crop type, irrigation technology and climate characteristics, secondary denitrification by ferrous iron may play an important role by inducing nitrate reduction at the interface between nitrate-rich percolating waters and highly-reduced waters. The improved model can be applied for: 1) estimate contaminant levels in a hindcast mode for conducting epidemiologic studies 2) evaluate physical, chemical or biological transformation rates of different contaminants for conducting mitigation studies; and 3) evaluate the effect of land-use change on contaminant concentrations in soil and groundwater aquifers for developing remediation strategies.

  2. On the key role of nutrient data to constrain a coupled physical-biogeochemical assimilative model of the North Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Ourmires, Yann; Brasseur, Pierre; Lvy, Marina; Brankart, Jean-Michel; Verron, Jacques

    2009-01-01

    A sequential assimilative system has been implemented into a coupled physical-biogeochemical model (CPBM) of the North Atlantic basin at eddy-permitting resolution (1/4), with the long-term goal of estimating the basin scale patterns of the oceanic primary production and their seasonal variability. The assimilation system, which is based on the SEEK filter [Brasseur, P., Verron, J., 2006. The SEEK filter method for data assimilation in oceanography: a synthesis. Ocean Dynamics. doi: 10.1007/s10236-006-0080-3], has been adapted to this CPBM in order to control the physical and biogeochemical components of the coupled model separately or in combination. The assimilated data are the satellite Topex/Poseidon and ERS altimetric data, the AVHRR Sea Surface Temperature observations, and the Levitus climatology for salinity, temperature and nitrate. In the present study, different assimilation experiments are conducted to assess the relative usefulness of the assimilated data to improve the representation of the primary production by the CPBM. Consistently with the results obtained by Berline et al. [Berline, L., Brankart, J-M., Brasseur, P., Ourmires, Y., Verron, J., 2007. Improving the physics of a coupled physical-biogeochemical model of the North Atlantic through data assimilation: impact on the ecosystem. J. Mar. Syst. 64 (1-4), 153-172] with a comparable assimilative model, it is shown that the assimilation of physical data alone can improve the representation of the mixed layer depth, but the impact on the ecosystem is rather weak. In some situations, the physical data assimilation can even worsen the ecosystem response for areas where the prior nutrient distribution is significantly incorrect. However, these experiments also show that the combined assimilation of physical and nutrient data has a positive impact on the phytoplankton patterns by comparison with SeaWiFS ocean colour data, demonstrating the good complementarity between SST, altimetry and in situ nutrient data. These results suggest that more intensive in situ measurements of biogeochemical nutrients are urgently needed at basin scale to initiate a permanent monitoring of oceanic ecosystems.

  3. 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 equally to seasonal and stream-size related variations in the percentage of the stream nitrate flux removed in each watershed. ?? 2008 The Author(s).

  4. Biogeochemical Considerations

    NASA Technical Reports Server (NTRS)

    Delwiche, C. C.

    1984-01-01

    Some questions relating to biogeochemical cycles and the nature of the biosphere driving them is best approached by means of remote (satellite) monitoring. Important among these are the distribution of various ecosystems and the boundaries between them, the extent and rate of modification of ecosystems by human or other factors, and various climatic and physical factors affecting ecosystem performance as influenced by human or natural processes.

  5. 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.

  6. Biogeochemical Coupling of Fe and Tc Speciation in Subsurface Sediments: Implications to Long-Term Tc Immobilization

    SciTech Connect

    Jim K. Fredrickson; C. I. Steefel; R. K. Kukkadapu; S. M. Heald

    2006-06-01

    The project has been focused on biochemical processes in subsurface sediments involving Fe that control the valence state, solubility, and effective mobility of 99Tc. Our goal has been to understand the Tc biogeochemistry as it may occur in suboxic and biostimulated subsurface environments. Two objectives have been pursued: (1) To determine the relative reaction rates of 99Tc(VII)O2(aq) with metal reducing bacteria and biogenic Fe(II); and to characterize the identity, structure, and molecular speciation of Tc(IV) products formed through reaction with both biotic and abiotic reductants. (2) To quantify the biogeochemical factors controlling the reaction rate of O2 with Tc(IV)O2?nH2O in sediment resulting from the direct enzymatic reduction of Tc(VII) by DIRB and/or the reaction of Tc(VII) with the various types of biogenic Fe(II) produced by DIRB.

  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. 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.

  9. A Multi-scale Coupled Physical-Biogeochemical FVCOM System for Massachusetts Bay: Application for Mechanism Studies of Seasonal Variability of Dissolved Oxygen

    NASA Astrophysics Data System (ADS)

    Xue, P.; Chen, C.; Qi, J.; Beardsley, R. C.; Tian, R.; Zhao, L.

    2011-12-01

    A long-term (1992-present) water quality monitoring program reveals that the dissolved oxygen (DO) in Massachusetts Bay (MB) exhibits a clear seasonal cycle with little interannual variability. A multi-domain nested coupled physical-biogeochemical FVCOM model system was developed with the aim at assessing water quality conditions and identifying the key mechanisms controlling the temporal/spatial variability of DO in MB. Built on good agreement in model-computed and observed DO, nitrogen and other water quality variables, results of a 14-year (1995-2008) simulation indicate that DO in MB is dominated by two modes: 1) seasonal cycle and 2) spatial variation. A well defined DO seasonal cycle, with highest DO in March-April and lowest in October, persists in all years. The magnitude and phase of the DO season cycle varies spatially, with less variation in the northern part of MB than to the south. . Horizontal advection plays an essential role in the DO variation in the northern MB, where it is connected to the western Gulf of Maine coastal processes and southwest mean circulation. The southern region, particularly within Cape Cod Bay, features a well-defined local retention mechanism with a longer residence time. In this region, DO variation is mainly driven by local processes associated with reaeration, oxidation, sediment oxygen demand (SOD) and photosynthesis-respiration. Although biogeochemical, advection and mixing processes vary year to year, the DO in MB is characterized by a "self-regulation" process, which keeps their net contributions to DO relatively constant each year, and thus leads to a persistent DO seasonal cycle.

  10. 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 SeaWiFS data as a decline in the spring/summer bloom in 1999 relative to 1998, resulted in the model from a more slowly shoaling mixed layer, allowing herbivore populations to keep pace with increasing phytoplankton populations. However, several aspects of the interannual cycle were not well-represented by the model. Explanations ranged from inherent model deficiencies, to monthly averaging of forcing fields, to biases in SeaWiFS atmospheric correction procedures.

  11. 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).

  12. 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.

  13. Quantifying the effects of nutrient loading on dissolved O2 cycling and hypoxia in Chesapeake Bay using a coupled hydrodynamic-biogeochemical model

    NASA Astrophysics Data System (ADS)

    Testa, Jeremy M.; Li, Yun; Lee, Younjoo J.; Li, Ming; Brady, Damian C.; Di Toro, Dominic M.; Kemp, W. Michael; Fitzpatrick, James J.

    2014-11-01

    The Regional Ocean Modeling System (ROMS) was coupled to a biogeochemical model (RCA) to understand the controls on dissolved oxygen (O2) depletion in Chesapeake Bay. The model was calibrated to observational data in the year 2000 and subsequent simulations were performed for a 10-year period, where water-column state variables were validated against observations using multiple error metrics and model-simulated rate processes were compared to available measurements. ROMS-RCA captured observed seasonal and regional dynamics of water-column chlorophyll-a, dissolved O2, and nutrient concentrations, as well as sediment-water nutrient and oxygen fluxes and community respiration rates, but for the year 2000, the model over-predicted surface-water chlorophyll-a and bottom-water O2 in some regions. A series of model experiments were made using the physical regime for the year 2000 to understand ecosystem responses to altered loads of nitrogen and phosphorus and to quantify the spatial and temporal response of Chesapeake Bay to altered nutrient loading. Nutrient loading experiments revealed a non-linear response of hypoxia to nitrogen load, where hypoxic-volume-days maximized at nitrogen loads twice of that observed in the year 2000. O2 levels were more sensitive to nitrogen loads than phosphorus loads, consistent with the preponderance of nitrogen limitation in Chesapeake Bay in late spring and summer months. Expanded hypoxic volumes under higher nitrogen loads were associated with increases in water-column production and respiration in seaward regions of Chesapeake Bay during summer (June to August) months. Analysis of the 10-year model run with realistic hydrodynamics and nutrient loading revealed a similar pattern, emphasizing phytoplankton growth during summer in more nitrogen-limited, lower-Bay regions as a mechanism supporting elevated summer hypoxic volumes. This analysis (1) presents ROMS-RCA as a tool for investigating linked biogeochemical processes in coastal ecosystems, (2) identifies phytoplankton growth in seaward Bay regions as a key link between nitrogen loading and hypoxic volume, and (3) suggests that given similar climatic conditions, nutrient load reductions will lead to reduced hypoxic volumes.

  14. Benthic phosphorus regeneration, net primary production, and ocean anoxia: A model of the coupled marine biogeochemical cycles of carbon and phosphorus

    NASA Astrophysics Data System (ADS)

    van Cappellen, Philippe; Ingall, Ellery D.

    1994-10-01

    We examine the relationships between ocean ventilation, primary production, water column anoxia, and benthic regeneration of phosphorus using a mass balance model of the coupled marine biogeochemical cycles of carbon (C) and phosphorus (P). The elemental cycles are coupled via the Redfield C/P ratio of marine phytoplankton and the C/P ratio of organic matter preserved in marine sediments. The model assumes that on geologic timescales, net primary production in the oceans is limited by the upwelling of dissolved phosphorus to the photic zone. The model incorporates the dependence on bottom water oxygenation of the regeneration of nutrient phosphorus from particulate matter deposited at the water-sediment interface. Evidence from marine and lacustrine settings, modern and ancient, demonstrates that sedimentary burial of phosphorus associated with organic matter and ferric oxyhydroxides decreases when bottom water anoxia-dysoxia expands. Steady state simulations show that a reduction in the rate of thermohaline circulation, or a decrease of the oxygen content of downwelling water masses, intensifies water column anoxia-dysoxia and at the same time increases surface water productivity. The first effect reflects the declining supply of oxygen to the deeper parts of the ocean. The second effect is caused by the enhanced benthic regeneration of phosphorus from organic matter and ferric oxyhydroxides. Sedimentary burial of organic carbon and authigenic calcium phosphate mineral (francolite), on the other hand, is promoted by reduced ocean ventilation. According to the model, global-scale anoxia-dysoxia leads to a more efficient recycling of reactive phosphorus within the ocean system. Consequently, higher rates of primary production and organic carbon burial can be achieved, even when the continental supply of reactive phosphorus to the oceans remains unchanged.

  15. Coupled effects of biogeochemical and hydrological processes on C, N, and P export during extreme rainfall events in a purple soil watershed in southwestern China

    NASA Astrophysics Data System (ADS)

    Gao, Yang; Zhu, Bo; Yu, Guirui; Chen, Weiliang; He, Nianpeng; Wang, Tao; Miao, Chiyuan

    2014-04-01

    As global warming and extreme weather events increase and intensify across the globe, it becomes ever more urgent to study and understand the effects of extreme rainfall events on carbon (C), nitrogen (N), and phosphorus (P) export from terrestrial to riverine ecosystems. There is still much to learn regarding C, N, and P non-point source discharge that results from extremely heavy rainfall as well as their effects on downstream ecosystems. This study aimed to shed light on C, N, and P biogeochemical and hydrological coupling processes. Long-term and short-term water composition monitoring research was carried out within a purple soil watershed in China's Sichuan Province. This study captured both base flow from long-term observations and dynamic runoff under extreme rainfall events that took place during the 2012 rainy season. Dissolved total nitrogen (DTN) was the largest percentage of total nitrogen (TN) in storm runoff. DTN exceeded particulate nitrogen (PN), which itself exceeded dissolved organic nitrogen (DON). Under site conditions, particulate phosphorus (PP) formed the largest constituent of total phosphorus (TP) followed by dissolved total phosphorus (DTP) and dissolved organic phosphorus (DOP). Furthermore, results showed that C, N, and P loads increased sharply in response to heavy rainfall. Although P abundance in purple soils is limited, it was nevertheless shown that C:N:P ratios measured during rainstorms corresponded much more closely to the Redfield ratio than to ratios measured in base flows. This adds to the evidence that suggests that increased storm runoff will increase eutrophication likelihood in ecosystems further downstream.

  16. Drainflow: a fully distributed integrated surface/subsurface flow model for drainage studies

    NASA Astrophysics Data System (ADS)

    Shokri, Ali; Bardsley, William Earl

    2015-04-01

    The scale of drainage studies may vary from high-resolution small scale investigations through to comprehensive catchment or regional-scale studies. This wide range of scales poses a significant challenge for the development of a suitable drainage model. To meet this demand, a fully distributed surface/subsurface interactive flow model named henceforth Drainflow has been developed. Drainflow includes both the Saint Venant equations for surface flow components and the Richards equation for saturated and unsaturated zones. To develop the model, surface and subsurface flow modules are formulated separately, then each component is connected to the other parts. All modules simultaneously interact to calculate water level and discharge in tile drains, channel networks, and overland flow. In the subsurface domain, the model also yields soil moisture and water table elevation. A smoothed Heaviside function is introduced to give a continuous transition of the model between Dirichlet and Neumann boundary conditions for tile drains and surface/subsurface flow interface boundaries. Compared to traditional drainage studies, Drainflow has the advantage of estimating the land surface recharge (LSR) directly from the partial differential Richards equation rather than via an analytical or empirical drainage method like the Green and Ampt equation. To test the model's accuracy, comparisons are made between Drainflow and a range of surface/subsurface flow models for five published integrated surface and subsurface problems. The comparison indicates Drainflow has a reasonably good agreement with the other integrated models. Furthermore, it is shown that the smoothed Heaviside functions technique is a very effective method to overcome the non-linearity problem created from switching between dry and wet boundary conditions. In addition, Drainflow was run for some drainage study examples and was found to be fairly flexible in terms of changing all or part of the model dimensions as required by problem complexity, scale, and data availability. Drainflow can be easily simplified dimensionally or methodologically to a less comprehensive and less complex model if required. This flexibility gives Drainflow the capacity to be modified to meet the specific requirements of the varying scale and boundary conditions often encountered in drainage studies.

  17. Topographic controls on scaling of hydrologic and thermal processes in polygonal ground features of an Arctic ecosystem: A case study using idealized non-isothermal surface-subsurface simulations

    NASA Astrophysics Data System (ADS)

    Bisht, G.; Riley, W. J.; Collier, N.; Kumar, J.

    2014-12-01

    Arctic and sub-Arctic soils currently contain approximately 1700 billion metric tones of frozen organic carbon, approximately 200 times current annual anthropogenic emissions. This carbon is vulnerable to release to the atmosphere as CO2 and CH4 as high-latitude temperatures warm. Microtopographic features, such as polygonal ground, are characteristic sources of landscape heterogeneity in the Alaskan Arctic coastal plain. In a future warmer climate, the spatial distribution of soil moisture and active layer depth are expected to be key factors controlling the fate of thawed permafrost carbon. Polygonal ground structures, with high or low centers, dominate the local hydrologic environment, thereby impacting the energy balance, biogeochemical dynamics, vegetation communities, and carbon releases from the subsurface. In spite of their importance to local hydrologic and thermal processes, the impact of these microtopographic features at larger spatial scales is not well understood. Our previous work from isothermal surface-subsurface simulations has indicated that statistical moments of soil moisture follow a non-linear scaling relationship. In this study, we perform surface-subsurface non-isothermal flow simulations using PFLOTRAN for four study sites located near Barrow, AK. Simulations are performed on domains at multiple horizontal resolutions for several years. We describe the statistical moments of simulated soil moisture and soil temperature fields across spatial resolutions.

  18. The application of a coupled hydrological and biogeochemical model (CHANGE) for modeling of energy, water, and CO2 exchanges over a larch forest in eastern Siberia

    NASA Astrophysics Data System (ADS)

    Park, Hotaek; Iijima, Yoshihiro; Yabuki, Hironori; Ohta, Takeshi; Walsh, John; Kodama, Yuji; Ohata, Tetsuo

    2011-08-01

    A coupled hydrological and biogeochemical model (CHANGE) that evaluates heat, water, and CO2 exchange between the biosphere and atmosphere across a spectrum of various time and space scales is described in this paper. The CHANGE model, which merges important components and functions in Arctic terrestrial ecosystems, is a process model with a self-constrained nature that is based on a complex and nonlinear interplay among hydrological, physiological, biochemical, ecological, and edaphic factors and meteorological conditions. This model was applied to a larch forest in eastern Siberia for the period of 1998-2006. A key objective was to assess the seasonal and interannual variability of the surface water, energy, and carbon fluxes over the larch forest in order to understand the responses of this ecosystem to climate change and to provide their controlling factors. Two types of simulations were performed with half-hourly and daily forcing data, and temporal correlation and other statistical measures supported the agreement between the simulations and observations. The simulated annual evapotranspiration (ET) ranged from 125 to 196 mm with a mean of 164 mm, 67% of which was contributed by transpiration. The simulated annual mean net ecosystem exchange (NEE) was -138.6 g C m-2 y-1 with a range of -79 to -195 g C m-2 y-1. The NEE variation was closely correlated with the net primary production (NPP). The simulation showed 23-43% interannual variability in heterotrophic respiration (Rh) for a mean of 273.1 g C m-2 y-1. Soil water was found to be a determinant that influences ET and CO2 fluxes in the larch forest. NEE was largely correlated to precipitation (PG). Thicker snow depth in the previous winter season contributed to higher NEE. The contribution of snow depth to NEE was significant in the dry years. The combination of summer PG and snow water resulted in higher NEE, which was found since 2004. In dry years, the access of roots to soil-thawed water alleviated soil water deficit and contributed to ecosystem net C uptake. The model sensitivity addressed the potential importance of the dynamic soil organic carbon on soil temperature.

  19. Influence of particle size and type on 231Pa and 230Th simulation with a global coupled biogeochemical-ocean general circulation model: A first approach

    NASA Astrophysics Data System (ADS)

    Dutay, J.-C.; Lacan, F.; Roy-Barman, M.; Bopp, L.

    2009-01-01

    The oceanic distributions of 231Pa and 230Th are simulated with the global coupled biogeochemical-ocean general circulation model NEMO-PISCES. These natural nonconservative tracers, which are removed from the water column by reversible scavenging processes onto particles, have been used to study modern and past ocean circulation. Our model includes three different types of particles: particulate organic matter (POM), calcium carbonate (CaCO3), and biogenic silica (BSi). It also considers two particle classes: small particles (POM) that sink slowly (3 m/d) and large particles (POM, CaCO3, BSi) that sink much more rapidly (50 m/d to 200 m/d) in the water column. 231Pa and 230Th are simulated with a reversible scavenging model that uses partition coefficients between dissolved and particulate phases that depend on particle type and size. Model results are then compared with 231Pa and 230Th observations in the water column and modern sediments. A preliminary evaluation of the particle fields simulated by the PISCES model has revealed that particle concentrations are reasonable at the surface but largely underestimated in the deep ocean. Largely to compensate for this, we find it necessary to use partition coefficients that vary as a function of particle size by significantly more that observed to obtain relatively realistic results. In the water column, 231Pa and 230Th fluxes are mainly controlled by the slowly sinking particles and partition coefficients need to be parameterized as a function of particle flux, as suggested by observations. Considering discrepancies between the modeling particle fields and those observed, we were forced to use exaggerated values for partition coefficients in order to get realistic tracer distributions. These 231Pa and 230Th simulations have provided an opportunity to propose some future developments of the PISCES model, in order to make progress in the simulation of trace elements. Assigning calcium carbonate, biogenic silica, and aluminosilicates to the small particle pool represents a credible approach to increase its concentration and subsequently simulate realistic tracer distributions in the water column using reasonable values for the partition coefficients, as well as a realistic fractionation in the sediments at all depths.

  20. Biogeochemical Considerations and Complexities

    SciTech Connect

    Ainsworth, Calvin C.; Brockman, Fred J.; Jardine, Phillip M.

    2000-12-29

    Chapter 6 Biogeochemical Considerations and Complexities INTRODUCTION-Geochemical and microbiological processes influence the transport of any contaminant in either unsaturated or saturated environments.

  1. Coupled in situ Ammonium and Nitrate analyses of a tidally dominated estuary: New developments from the Elkhorn Slough Land/Ocean Biogeochemical Observatory network

    NASA Astrophysics Data System (ADS)

    Gibson, P. J.; Plant, J.; Johnson, K. S.

    2012-12-01

    For nearly nine years the Elkhorn Slough Land/Ocean Biogeochemical Observatory (LOBO) network of moorings has been delivering freely available hourly data to the web in near real time. Each mooring hosts a suite of instruments including an ISUS nitrate sensor. In addition to providing valuable information on ecosystem scale processes, the moorings serve as ideal test platforms for novel in situ chemical sensors & analyzers developed by the Monterey Bay Aquarium Research Institute. The recent addition of a newly developed in situ NH4+ analyzer, the DigiScan-II, has provided additional insights into N cycling mechanisms within the slough. The analysis method estimates NH4+ concentration via base conversion to NH3 gas and diffusion across a membrane into an acid carrier stream with subsequent conductivity detection. Although this new NH4+ analyzer is reagent based, it was developed to be relatively cheap, robust, and configurable for a range of deployment options and requires minimal, infrequent maintenance that is ultimately governed by battery life. The fundamental DigiScan-II platform can also be used for other analyses of interest, such as PO4 or CT (total inorganic carbon), by swapping the necessary reagents and components and by making minor code modifications. For deployment in Elkhorn Slough, the NH4+ DigiScan-II was configured for mid-scale concentration detection with a linear calibration range of <0.2 to >30.0 μM NH4+. The flux of different forms of bioavailable DIN through the system is driven by runoff inputs, tidal exchange, and biological processing. Large inputs of NO3- are sourced from the agriculturally influenced Old Salinas River (OSR), which enters the Slough near the estuary mouth and confluence with Monterey Bay. Rising ocean tides force this eutrophied water mass up into the slough where it is accessed by various biological communities during the course of the tidal period. Mass balance estimates suggest there is an imbalance between the amount of NO3- received by the slough and the amount that is released, with a net NO3- influx to the ecosystem. However, the slough ecosystem releases more NH4+ than it receives, resulting in a net efflux of NH4+ due to remineralization of organic matter (and potentially DNRA) in the slough. Although there is high variability among day to day flux estimates, the sign of the net flux term for NO3- and NH4+ are constant on a monthly scale and seasonal trends in flux magnitude are apparent. Excess N inputs to the slough ecosystem calculated from the LOBO data can serve to estimate productivity when coupled with published estimates of sediment N flux. Published rates of denitrification in the system are few but generally very low. Using the LOBO nitrogen mass balance calculations and Redfield stoichiometry, we estimate that the nitrogen inputs from OSR and Monterey Bay support a net production of roughly 220 g C m-2 yr-1 in Elkhorn Slough, assuming no N is lost to denitrification. This estimate will be revised with detailed hydrological dynamics and available O2 data to provide more accurate estimates of net ecosystem metabolism and the relative influence of allochthonous inputs on ecosystem productivity.

  2. Colloid Transport and Surface-Subsurface Exchange in an Acid Mine Drainage-Impacted Stream

    NASA Astrophysics Data System (ADS)

    Norvell, A. S.; Ryan, J. N.; Ren, J.; McKnight, D. M.

    2010-12-01

    Colloidal particles may provide an important control on the mobility of contaminants of concern; e.g., metals introduced into a stream from an acid mine drainage. In order to examine colloidal transport and surface-subsurface exchange, we injected synthesized ferrihydrite colloids along with a conservative tracer, bromide, into Lefthand Creek, a stream contaminated by acid mine drainage in northwestern Boulder County, Colorado. The ferrihydrite colloids were co-precipitated with yttrium to form yttrium-labelled colloids so that we could differentiate them from environmental colloids. Yttrium was measured in samples collected from the surface water and the hyporheic zone. The hyporheic zone samples were collected from a series of mini-piezometers embedded up to 1 m in depth and over a 61 m reach of the stream. A one-dimensional transient storage model (OTIS-P) was used to quantify parameters describing the transport of the conservative tracer and the colloids. Approximately 20% of the colloidal mass was lost over the 61 m reach. The loss of colloids is attributed to deposition in the shallow hyporheic zone. Laboratory column experiments demonstrated that the stream bed sediments effectively remove colloids from suspension at the pH, ionic strength, and dissolved organic matter concentration conditions occurring in Lefthand Creek.

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

    SciTech Connect

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

    2009-01-01

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

  4. 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. PMID:21112074

  5. A simple iterative method for estimating evapotranspiration with integrated surface/subsurface flow models

    NASA Astrophysics Data System (ADS)

    Hwang, H.-T.; Park, Y.-J.; Frey, S. K.; Berg, S. J.; Sudicky, E. A.

    2015-12-01

    This work presents an iterative, water balance based approach to estimate actual evapotranspiration (ET) with integrated surface/subsurface flow models. Traditionally, groundwater level fluctuation methods have been widely accepted and used for estimating ET and net groundwater recharge; however, in watersheds where interactions between surface and subsurface flow regimes are highly dynamic, the traditional method may be overly simplistic. Here, an innovative methodology is derived and demonstrated for using the water balance equation in conjunction with a fully-integrated surface and subsurface hydrologic model (HydroGeoSphere) in order to estimate ET at watershed and sub-watershed scales. The method invokes a simple and robust iterative numerical solution. For the proof of concept demonstrations, the method is used to estimate ET for a simple synthetic watershed and then for a real, highly-characterized 7000 km2 watershed in Southern Ontario, Canada (Grand River Watershed). The results for the Grand River Watershed show that with three to five iterations, the solution converges to a result where there is less than 1% relative error in stream flow calibration at 16 stream gauging stations. The spatially-averaged ET estimated using the iterative method shows a high level of agreement (R2 = 0.99) with that from a benchmark case simulated with an ET model embedded directly in HydroGeoSphere. The new approach presented here is applicable to any watershed that is suited for integrated surface water/groundwater flow modelling and where spatially-averaged ET estimates are useful for calibrating modelled stream discharge.

  6. 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.

  7. 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.

  8. 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 data assimilation system. Results show that data assimilation effectively corrects model states and parameters of the integrated model towards the reference values. Scaling tests provide evidence that the data assimilation system for TerrSysMP can make efficient use of parallel computational resources for > 30 k processors. Simulations with a large problem size (20 million unknowns) for the forward model were also efficiently handled by the data assimilation system. The proposed data assimilation framework is useful in simulating and estimating uncertainties in predicted states and fluxes of the terrestrial system over large spatial scales at high resolution utilising integrated models.

  9. 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, W.; He, G.; Kollet, S.; Maxwell, R.; Vereecken, H.; Hendricks Franssen, H.-J.

    2015-11-01

    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 parameterization 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 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 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 Mio. unknowns) is used to demonstrate the effects of data assimilation in the integrated model TerrSysMP and to access the scaling behaviour of the data assimilation system. Results show that data assimilation effectively corrects model states and parameters of the integrated model towards the reference values. Scaling tests provide evidence that the data assimilation system for TerrSysMP can make efficient use of parallel computational resources for > 30 k processors. Simulations with a large problem size (20 Mio. unknows) for the forward model were also efficiently handled by the data assimilation system. The proposed data assimilation framework is useful in simulating and estimating uncertainties in predicted states and fluxes of the terrestrial system over large spatial scales at high resolution utilizing integrated models.

  10. 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 the first three years of our project, led to several major new insights on the interaction between ocean biogeochemistry and circulation. This work, which is described in 2 the following Section II on “Large scale fertilization,” has continued to appear in the literature over the past few years, including two high visibility papers in Nature. Early on in the first three years of our project, it became clear that small "patch-scale" fertilizations over limited regions of order 100 km diameter were much more likely than large scale fertilization, and we carried out a series of idealized patch fertilization simulations reported on in Gnanadesikan et al. (2003). Based on this paper and other results we had obtained by the end of our first three-year grant, we identified a number of important issues that needed to be addressed in the second three-year period of this grant. Section III on “patch fertilization” discusses the major findings of this phase of our research, which is described in two major manuscripts that will be submitted for publication in the near future. This research makes use of new more realistic ocean ecosystem and iron cycling models than our first paper on this topic. We have several major new insights into what controls the efficiency of iron fertilization in the ocean. Section IV on “model development” summarizes a set of papers describing the progress that we made on improving the ecosystem models we use for our iron fertilization simulations.

  11. Biogeochemical Processes in Microbial Ecosystems

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

    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 population, and their metabolic properties. 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 diel (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.

  12. 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

    Subsurface bacteria including sulfate reducing bacteria (SRB) reduce soluble U(VI) to insoluble U(IV) with subsequent precipitation of UO2. We have shown that SRB reduce U(VI) to nanometer-sized UO2 particles (1-5 nm) which are both intra- and extracellular, with UO2 inside the cell likely physically shielded from subsequent oxidation processes. We evaluated the UO2 nanoparticles produced by Desulfovibrio desulfuricans G20 under growth and non-growth conditions in the presence of lactate or pyruvate and sulfate, thiosulfate, or fumarate, using ultrafiltration and HR-TEM. Results showed that a significant mass fraction of bioreduced U (35-60%) existed as a mobile phase when the initial concentration of U(VI) was 160 µM. Further experiments with different initial U(VI) concentrations (25 - 900 M) in MTM with PIPES or bicarbonate buffers indicated that aggregation of uraninite depended on the initial concentrations of U(VI) and type of buffer. It is known that under some conditions SRB-mediated UO2 nanocrystals can be reoxidized (and thus remobilized) by Fe(III)-(hydr)oxides, common constituents of soils and sediments. To elucidate the mechanism of UO2 reoxidation by Fe(III) (hydr)oxides, we studied the impact of Fe and U chelating compounds (citrate, NTA, and EDTA) on reoxidation rates. Experiments were conducted in anaerobic batch systems in PIPES buffer. Results showed EDTA significantly accelerated UO2 reoxidation with an initial rate of 9.5M day-1 for ferrihydrite. In all cases, bicarbonate increased the rate and extent of UO2 reoxidation with ferrihydrite. The highest rate of UO2 reoxidation occurred when the chelator promoted UO2 and Fe(III) (hydr)oxide dissolution as demonstrated with EDTA. When UO2 dissolution did not occur, UO2 reoxidation likely proceeded through an aqueous Fe(III) intermediate as observed for both NTA and 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.

  13. Determination of the effect of ammonia on clathrate hydrates at Titan' surface-subsurface conditions

    NASA Astrophysics Data System (ADS)

    Munoz-Iglesias, V.; Vu, T. H.; Smythe, W.; Sotin, C.; Choukroun, M.

    2015-10-01

    The development and combination of two facilities, a cryogenic calorimeter and a cryostage coupled with a Raman spectrometer, allows for detailed studies of the chemical reactions/phase transformations that may take place in the upper layer of Titan's crust and the subsequent exchange processes with the atmosphere due to phase transitions related to the composition in icy materials and the thermal state of the upper few km.

  14. Polar Front around the Kerguelen Islands: An up-to-date determination and associated circulation of surface/subsurface waters

    NASA Astrophysics Data System (ADS)

    Park, Young-Hyang; Durand, Isabelle; Kestenare, Elodie; Rougier, Gilles; Zhou, Meng; d'Ovidio, Francesco; Cotté, Cédric; Lee, Jae-Hak

    2014-10-01

    The circulation of iron-rich shelf waters around the Kerguelen Islands plays a crucial role for a climatically important, annually recurrent phytoplankton spring bloom over the sluggish shelf region and its downstream plume area along the Antarctic circumpolar flow. However, there is a long-standing confusion about the Polar Front (PF) in the Kerguelen region due to diverse suggestions in the literature for its geographical location with an extreme difference over 10° of latitude. Based on abundant historical hydrographic data, the in situ hydrographic and current measurements during the 2011 KEOPS2 cruise, satellite chlorophyll images, and altimetry-derived surface velocity fields, we determine and validate an up-to-date location of the PF around the Kerguelen Islands. Artificial Lagrangian particle trajectories computed from altimetric velocity time series are analyzed for the possible pathways and sources of different surface/subsurface waters advected into the chlorophyll bloom area east off the islands studied during the KEOPS2 cruise. The PF location determined as the northernmost boundary of the Winter Water colder than 2°C, which is also associated with a band of strong currents, appears to be primarily controlled by topography. The PF rounds the Kerguelen Islands from the south to deflect northward along the eastern escarpment up to the northeastern corner of the Kerguelen Plateau before making its southward retroflection. It is shown that the major surface/subsurface waters found within the deep basin east of the Kerguelen Islands originate from the shelf around the Heard Island, rather than from the shallow shelf north of the Kerguelen Islands.

  15. 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.

  16. Incorporating atmospheric boundary layer processes in an integrated surface/subsurface flow and transport model

    NASA Astrophysics Data System (ADS)

    Davison, J. H.; Hwang, H.; Sudicky, E. A.; Lin, J. C.

    2012-12-01

    Traditional land surface-atmosphere models idealize variably-saturated subsurface flow by parameterizing the non-linear processes. Many previous models reduce the subsurface systems to either one-dimensional infiltration or constant-value boundary conditions. Consequently, the shortfalls of the currently available models constrain our ability to estimate the role of a spatially and temporally dynamic subsurface flow on atmospheric processes. In order to overcome these limitations, we developed a coupled atmospheric boundary layer model, which is a zero-dimensional energy balance model, with HydroGeoSphere, a three-dimensional integrated surface/variably-saturated subsurface flow and energy transport model. The atmospheric boundary layer model calculates the net radiation, air temperature, moisture content, and precipitation in the atmosphere and relays the information directly to HydroGeoSphere to compute the water flow, land surface and subsurface temperatures, and evapotranspiration. As an illustration, the coupled model is applied to land-use change in a Mediterranean climate transitioning from irrigated agriculture to urban communities to evaluate the variation in latent and sensible heat fluxes. Finally, our model's performance and results are compared to those of the traditional land surface models.

  17. Planetary Biogeochemical Stewardship (Invited)

    NASA Astrophysics Data System (ADS)

    Schlesinger, W. H.

    2010-12-01

    Many of today’s most pressing environmental problems have a basis in chemistry—that is human disruption of global biogeochemical cycles. Humans have enhanced the movement of C, N, P, and S in the global cycle of these elements, with widespread consequences such as climate change, hypoxia and acid rain. Recent attempts to calculate thresholds of global vulnerability ignore ample evidence that human impacts on the Earth’s chemical environment yield progressive degradation of the biosphere, especially its species diversity. Our collect global impact now exceeds natural processes of planetary remediation—clearly an unsustainable path. I will attempt to provide a framework to evaluate suggested attempts to mitigate current human impact on global biogeochemical cycles. Cap-and-trade systems are ideal for perturbations that involve a limited number of point sources that supplement a small background flux to the atmosphere, such as S. Better land management may be the most attractive way to mitigate human impacts to the Nitrogen cycle, where the potential for enhanced denitrification could respond to the order-of-magnitude of the current human perturbation. Impacts to the carbon cycle, seen through rising CO2 in Earth’s atmosphere, will require switching to energy that does not depend on fossil carbon.

  18. A Coupled Finite-Volume Model for 2-D Surface and 3-D Subsurface Flows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Surface-subsurface interactions are an intrinsic component of the hydrologic response within a watershed; therefore, hydrologic modeling tools should consider these interactions to provide reliable predictions, especially during rainfall-runoff processes. This paper presents a fully implicit coupled...

  19. Vegetation Influence on Regional Climate Change: A 3D Integrated Atmospheric-Surface-Subsurface Analysis

    NASA Astrophysics Data System (ADS)

    Davison, J. H.; Hwang, H.; Sudicky, E. A.; Lin, J. C.

    2013-12-01

    Human induced land-use change has been shown to be one of the major contributing factors to anthropogenic regional climate change. The transition from densely vegetated forests with deep root zones to shallow rooted agricultural ecosystems drastically limits the natural buffering capacity of deep groundwater during severe drought conditions. In order to quantify the magnitude of climate change from altered ecosystems, we employed the 3D model HydroGeoSphere, an integrated variably-saturated subsurface/surface flow and heat transport model, coupled with a simplified zero-dimensional atmospheric boundary layer model to simulate an extended seasonal drought period. It is found that during drought conditions, trees with deep root zones are capable of maintaining higher evapotranspiration rates, higher latent heat fluxes, and a damped atmospheric temperature response. In contrast, grasses with shallow root zones have minimal evapotranspiration rates, lower latent heat fluxes, and a rapid and sharp atmospheric temperature response. On the whole, converting a naturally wooded ecosystem to a farmland or pasture effectively decreases the available water in the subsurface for transpiration subsequently amplifying the atmospheric response to severe weather.

  20. Numerical Modeling of Surface-Subsurface Flow Interaction for Flood Routing in Ephemeral Channels

    NASA Astrophysics Data System (ADS)

    Balamurugan, M.; Murty, B. S.

    2013-12-01

    Arid climatic conditions may favor high intensity rainfalls for shorter duration which result in quick runoff response and flash floods in ephemeral streams. Flood flow movements in these channels are mainly influenced by transmission losses due to channel bed infiltration. This transmission loss is an important source of groundwater recharge in arid and semi arid region. Accurate estimation of water balance or any water management activity in this region requires numerical simulation of flood flow movement along with channel transmission losses simultaneously. Incomplete consideration of all these processes as well as inaccurate numerical solutions results in an inadequate understanding of water balance in these regions. In this study, an alternative model for routing floods in ephemeral channels is presented. The proposed flood routing model solves the governing one-dimensional Saint-Venant equations for surface flow along with one-dimensional Richards equation for unsaturated sub-surface flow. Surface and sub-surface flow components interact through the infiltration process at the ground surface. The predictor-corrector ENO (Essentially Non Oscillating) scheme is employed for solving the surface flow equation while a mass conservative finite volume scheme is used for subsurface component. The infiltration rate which is obtained as a result of the subsurface flow acts as a link between the surface and subsurface systems. An iterative procedure is used for coupling the surface and sub-surface components. Results obtained using the proposed 1-D surface and pseudo 3-D sub-surface model are compared with those obtained using 1-D surface and pseudo 2-D subsurface flow model, for studying the effect of varying infiltration rate at a cross section, on the flood wave movement. Further the developed model is validated with data available in the literature. *%K Groundwater/surface water interaction, Modeling, Infiltration, Floodplain dynamics

  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

    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. 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.

  3. 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, organic matter mineralisation, nitrification, denitrification, chemodenitrification and methanogenesis producing and consuming soil based greenhouse gases. The model application will present first validation 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.

  4. Arctic Ocean shelf biogeochemical cycling under climate change

    NASA Astrophysics Data System (ADS)

    Bellerby, Richard; Silyakova, Anna; Slagstad, Dag

    2014-05-01

    Changes to Arctic Ocean biogeochemistry will result from a complex array of climate and chemical perturbations over the next decades. Changes to freshwater and nutrient supply through ice melt and continental runoff; warming of the ocean and an increasing ocean acidification through partial equilibrium with a rising anthropogenic CO2 load will change the nature of Arctic Ocean ecological and biogeochemical coupling. This is no more apparent on the shelf regions where there is strong influence from land sources of freshwater and total alkalinity. This presentation will document our combined approach of studying Arctic biogeochemical change through coupled observational, experimental and modelling campaigns. We have identified large changes in recent anthropogenic carbon transport to the Arctic and have characterised the associated regional and water mass ocean acidification. We have determined, through targeted Arctic pelagic ecosystem perturbations experiments, changes to ecosystem structure, succession and biogeochemical cycling under high CO2. Observations have been incorporated into regional, coupled physical-ecosystem-carbon biogeochemical models (informed at the boundaries by downscaled global earth system models) to develop scenarios of change in biogeochemical pathways. We have identified large regional variability in ocean acidification that is shown to impact on shelf biogeochemistry, ecosystems and climate feedbacks in the Arctic Ocean.

  5. 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."

  6. 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.

  7. A Reactive Transport Simulator for Biogeochemical Processes in Subsurface System

    Energy Science and Technology Software Center (ESTSC)

    2003-04-01

    BIOGEOCHEM is a Fortran code that mumerically simulates the coupled processes of solute transport, microbial population dynamics, microbial metabolism, and geochemical reactions. The potential applications of the code include, but not limited to, (a) sensitivity and uncertainty analyses for assessing the impact of microbial activity on subsurface geochemical systems; (b) extraction of biogeochemical parameter values from field observations or laboratory measurements, (c) helping to design and optimize laboratory biogeochemical experiments, and (d) data integration. Methodmore » of Solution: A finite difference method and a Newton-Raphson technique are used to solve a set of coupled nonlinear partial differential equations and algebraic equations. Practical Application: Environmental analysis, bioremediation performance assessments of radioactive or non-radioactive wase disposal, and academic research.« less

  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. Topographic controls on soil moisture scaling properties in polygonal ground using idealized high-resolution surface-subsurface simulations

    NASA Astrophysics Data System (ADS)

    Bisht, G.; Riley, W. J.

    2014-11-01

    Microtopographic features, such as polygonal ground, are characteristic sources of landscape heterogeneity in the Alaskan Arctic coastal plain. Here, we analyze the hypothesis that microtopography is a dominant controller of soil moisture in polygonal landscapes. We perform multi-year surface-subsurface isothermal flow simulations using the PFLOTRAN model for summer months at six spatial resolutions (0.25-8 m, in increments of a factor of 2). Simulations are performed for four study sites near Barrow, Alaska that are part of the NGEE-Arctic project. Results indicate a non-linear scaling relationship for statistical moments of soil moisture. Mean soil moisture for all study sites is accurately captured in coarser resolution simulations, but soil moisture variance is significantly under-estimated in coarser resolution simulations. The decrease in soil moisture variance in coarser resolution simulations is greater than the decrease in soil moisture variance obtained by coarsening out the fine resolution simulations. We also develop relationships to estimate the fine-resolution soil moisture probability distribution function (PDF) using coarse resolution simulations and topography. Although the estimated soil moisture PDF is underestimated during very wet conditions, the moments computed from the inferred soil moisture PDF had good agreement with the full model solutions (bias < ± 4 % and correlation > 0.99) for all four sites. Lastly, we develop two spatially-explicit methods to downscale coarse-resolution simulations of soil moisture. The first downscaling method requires simulation of soil moisture at fine and coarse resolution, while the second downscaling approach uses only topographical information at the two resolutions. Both downscaling approaches are able to accurately estimate fine-resolution soil moisture spatial patterns when compared to fine-resolution simulations (mean error for all study sites are < ± 1 %), but the first downscaling method more accurately estimates soil moisture variance.

  11. 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).

  12. 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).

  13. 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. Theoretical constructs, such as the River Continuum Concept, that aim to elucidate general mechanistic underpinnings of freshwater ecosystem function via testable hypotheses about relative rates of photosynthesis and respiration, for example, may be readily examined using data collected at hourly time scales at the NEON facility once constructed. By taking advantage of NEON data and adding PI-driven research to the Observatory, we can further our understanding of the relative roles of water flow, nutrients, temperature, and light on freshwater ecosystem function and structure.

  14. 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.

  15. 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.

  16. 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 simulations reproduce the three major C-Q patterns observed in published data, offering valuable insight into coupled catchment processes. The findings have important implications for effective catchment management for water quality improvement, and stream monitoring strategies.

  17. 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 simulation results and find that the model simulations reproduce the three major C-Q patterns observed in published data, offering valuable insight into coupled catchment processes. The findings can be used to develop effective catchment management and stream monitoring strategies.

  18. Solute Transport and Surface-Subsurface Exchange in the Everglades Characterized by a Tracer Release in Surface Water

    NASA Astrophysics Data System (ADS)

    Harvey, J. W.; Saiers, J. E.; Newlin, J. T.

    2003-12-01

    Solute tracer injections into flowing surface water are useful to characterize water velocity, dispersive mixing, and biogeochemical reactions that result from processes such as solute exchange between surface water and sediment porewater. Presently, there are few data or guidelines to understand transport processes in the Everglades. Our tracer study was conducted in central Shark Slough, Everglades National Park (25° 38' 31.2'' N, 80° 43' 20.4'' W) at an experimental flume facility. The flume consists of 4 side-by-side channels enclosing wetland vegetation in open-ended flow-ways (3-m by 100-m) that are subject to ambient flow conditions. The injection was conducted in one channel that, at the time of the experiment, had 60-cm of surface water and a typical assemblage of Everglades' slough vegetation, including rooted macrophytes (mainly Eleocharis sp.), and a well-developed layer (15-cm) of periphyton-coated vegetation (mainly Utricularia sp.) below the water surface. A constant-rate injection of sodium bromide (NaBr) was conducted for 22 hours by dividing the flow between four horizontally oriented soaker hoses that were evenly spaced in the water column. At a distance of 6.8 m downstream of the injection, small-volume (10 to 20-ml) water samples were collected on regular intervals for 48 hrs by withdrawing them by suction from 1/8-inch tubes deployed throughout the water column and in the peat sediment to a depth of 30-cm. Transport was characterized by adjusting the parameters of the USGS model OTIS (One-dimensional Transport with Inflow and Storage). Mean velocity of surface water during the experiment was 0.63 cm/s, longitudinal dispersion was 5 x 10-5 m2/s, and fluid residence times in two storage zones, where local mixing but no appreciable downstream transport occurred, were 1 hr (in periphyton-dominated floating vegetation)and 24 hrs in peat porewater), respectively. We conclude that storage-exchange affects solute transport in the Everglades by decreasing the mean water velocity and increasing the time available for biogeochemical processing of non-conservative solutes.

  19. 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.

  20. COUPLING

    DOEpatents

    Hawke, B.C.

    1963-02-26

    This patent relates to a releasable coupling connecting a control rod to a control rod drive. This remotely operable coupling mechanism can connect two elements which are laterally and angviarly misaligned, and provides a means for sensing the locked condition of the elements. The coupling utilizes a spherical bayonet joint which is locked against rotation by a ball detent lock. (AEC)

  1. 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

  2. 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. PMID:25624488

  3. 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 effect of these phenomena on the biogeochemical patterns at longer time scales.

  4. 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)

  5. Simulating non-point source pollution with an integrated surface-subsurface hydrologic approach in an agricultural watershed

    NASA Astrophysics Data System (ADS)

    Xiang, L.; Chen, L.; Yu, Z.

    2009-12-01

    The non-point source pollution is a major threat for water security in agricultural watersheds. A physically-based integrated hydrological model system is implemented in Meilin watershed, a small agricultural watershed in the southwest part of Tai Lake drainage system, China to study surface and subsurface hydrologic processes and to evaluate the solute (N, P) transport along various pathways at a watershed scale. Based on past and ongoing field studies, the watershed is reasonably well characterized and has been monitored on a regular base. Field observed data were used to assess the overland flow and infiltration processes and evaluate how different factors (i.e., soil texture, land use-land cover, and micro-topography) would affect these hydrologic processes. The model is driven by the observed precipitation to simulate surface water, soil moisture, groundwater and solute transport. The model calibration was conducted by using a multi-objective approach and the objectives include streamflow, soil moisture, groundwater level, solute concentration, etc. Numerical experiments were designed to elucidate the dynamics of watershed hydrologic processes as well as the interactive relationship on variables in land surface, unsaturated zone, and groundwater. The results illustrate how soil texture, land use-land cover, and topography would affect different hydrologic processes and their inter-relationship. The work will help better understand physically-coupled flow and solute transport in the watershed and enhance the quality of watershed flow and solute simulation.

  6. Combining high resolution space- and air-borne data with borehole monitoring to investigate surface-subsurface water relations in landslide-prone slopes

    NASA Astrophysics Data System (ADS)

    Wasowski, Janusz; Lamanna, Caterina; Dipalma Lagreca, Marina; Pasquariello, Guido

    2013-04-01

    Water still seems to be a relatively little studied environmental factor in applications of multispectral space- and air-borne data to landslide investigations, even though stagnated drainage conditions have long been used as diagnostic elements for landslide recognition and mapping based on airphoto interpretation. Here we use both satellite imagery and airphotos, focusing on water as a critical factor of the recurrent instability of poorly drained slopes in a 15.6 km2 catchment area in the Apennine mountains (Italy) characterized by predominance of clay-rich flysch units and agricultural land use. We expand on our recent study (Wasowski et al., 2012) that exploited high resolution multispectral satellite imagery from early spring of 2006 for mapping active landslides, investigating their close association with seasonally wet zones (areas covered by free surface-water including ponds, migrating surface-water, seeps), and for inferring surface-subsurface relationships in unstable slopes. In particular, we use sub-meter resolution multispectral orthophotos acquired in late winter of 2011 to map the distributions of active landslides and wet zones. Considerable spatial-temporal recurrence of these features is indicated from a comparison of the 2011 and 2006 inventories. Furthermore, using the extensive subsurface dataset from piezometer boreholes (ongoing monitoring since 2009) we show that a number of remotely sensed wet zones are indicative of sites with seasonally persistent very high groundwater levels within landslide-prone slopes and on intermittently active landslides. Where such surface-subsurface water linkage can be established, the appearance of the wet zones (fully saturated ground/soil) resulting from groundwater discharge or seepage can be used as a forewarning signal of the increased susceptibility to landsliding, since the hillslopes with shallow groundwater tables are generally more prone to failure. However, the feasibility of retrieving reliable information about surface-water conditions from high resolution optical data, and the degree of its usefulness can be site-specific. This work suggests that useful results can be obtained in settings with similar topography (shallow slopes), lithology (clay-rich) and land use/land cover (agricultural soils with little woodland). A critical factor that will influence the results is the suitable timing of the imagery acquisition, in our case during wet season and early in vegetation period. Furthermore, acquisitions shortly after intense rainfall should be avoided if the focus is on wet zones indicative of shallow groundwater tables, that is those resulting from groundwater discharge and not just from accumulations of surface-water runoff. References Wasowski J., Lamanna C., Gigante G., Casarano D. 2012. High resolution satellite imagery analysis for inferring surface-subsurface water relationships in unstable slopes. Remote Sensing of Environment, 124, 135-148. doi: 10.1016/j.rse.2012.05.007

  7. 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 improve distributed watershed models.

  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. Linkages beyond boundaries between surface/subsurface and land /ocean for better management of groundwater under the changing climate and society in Asia

    NASA Astrophysics Data System (ADS)

    Taniguchi, Makoto

    2010-05-01

    Change in reliable water resources between groundwater and surface water occurred in many Asian cities depending on the development stage of urbanization and climate change. Although the subsurface water is connected with surface water in hydrological cycle, both waters were treated separately. Intensive field observations and data collections had been made in the basins including Tokyo, Osaka, Bangkok, Jakarta, Manila, Seoul, and Taipei, to evaluate the relationship between development stage of the city and various subsurface environments in Asia beyond the boundary between surface and subsurface environment under the condition of climate change. As a factor of separating water, energy and material at the earth surface into above and below the surface, land use/cover changes at three ages (1940's, 1970's and 2000's) in Asian 7 cities have been analyzed based on GIS with 0.5 km grid at seven targeted cities. Urbanization causes the decease in groundwater recharge rate and increase thermal energy transport into the subsurface. Global warming and heat island effects are also evaluated with in the cities and compared. Another boundary for water and material transports exists between land and ocean. Regarding material (contaminant) transports to the coast, direct groundwater discharge is recently recognized as a significant water and material pathway from land to ocean. Many Asian major cities are located in the coastal zone so material and contaminant transports by groundwater is a key to understanding the coastal water pollution and the effects on associated ecosystems. The exchanges of sea water and fresh water between the boundary were analyzed during the last 100 years in Asian coasts. In this paper, the importance of integrated treatments between surface/subsurface and land/ocean will be shown for better understanding and management of subsurface environment including groundwater under the condition of climate variation.

  11. Stepwise sensitivity analysis from qualitative to quantitative: Application to the terrestrial hydrological modeling of a Conjunctive Surface-Subsurface Process (CSSP) land surface model

    NASA Astrophysics Data System (ADS)

    Gan, Yanjun; Liang, Xin-Zhong; Duan, Qingyun; Choi, Hyun Il; Dai, Yongjiu; Wu, Huan

    2015-06-01

    An uncertainty quantification framework was employed to examine the sensitivities of 24 model parameters from a newly developed Conjunctive Surface-Subsurface Process (CSSP) land surface model (LSM). The sensitivity analysis (SA) was performed over 18 representative watersheds in the contiguous United States to examine the influence of model parameters in the simulation of terrestrial hydrological processes. Two normalized metrics, relative bias (RB) and Nash-Sutcliffe efficiency (NSE), were adopted to assess the fit between simulated and observed streamflow discharge (SD) and evapotranspiration (ET) for a 14 year period. SA was conducted using a multiobjective two-stage approach, in which the first stage was a qualitative SA using the Latin Hypercube-based One-At-a-Time (LH-OAT) screening, and the second stage was a quantitative SA using the Multivariate Adaptive Regression Splines (MARS)-based Sobol' sensitivity indices. This approach combines the merits of qualitative and quantitative global SA methods, and is effective and efficient for understanding and simplifying large, complex system models. Ten of the 24 parameters were identified as important across different watersheds. The contribution of each parameter to the total response variance was then quantified by Sobol' sensitivity indices. Generally, parameter interactions contribute the most to the response variance of the CSSP, and only 5 out of 24 parameters dominate model behavior. Four photosynthetic and respiratory parameters are shown to be influential to ET, whereas reference depth for saturated hydraulic conductivity is the most influential parameter for SD in most watersheds. Parameter sensitivity patterns mainly depend on hydroclimatic regime, as well as vegetation type and soil texture. This article was corrected on 26 JUN 2015. See the end of the full text for details.

  12. 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.

  13. Indian Ocean Biogeochemical Processes and Ecological Variability

    NASA Astrophysics Data System (ADS)

    Ofori, Leslie

    2010-11-01

    The Sustained Indian Ocean Biogeochemistry and Ecosystem Research (SIBER) conference was held in 2006 in Goa, India. The goals of the workshop were to assess the known facts about basin-wide biogeochemical and ecological dynamics of the Indian Ocean, to answer major questions, and to draw a road map for future research. The AGU monograph Indian Ocean Biogeochemical Processes and Ecological Variability, edited by Jerry D. Wiggert, Raleigh R. Hood, S. Wajih A. Naqvi, Kenneth H. Brink, and Sharon L. Smith, synthesizes the talks that were presented at this conference. In this interview, Eos talks with Jerry Wiggert, assistant professor of marine science at University of Southern Mississippi, Hattiesburg.

  14. Managing biogeochemical cycles to reduce greenhouse gases

    SciTech Connect

    Post, Wilfred M; Venterea, Rodney

    2012-01-01

    This special issue focuses on terrestrial biogeochemical cycles as they relate to North America-wide budgeting and future projection of biogenic greenhouse gases (GHGs). Understanding the current magnitude and providing guidance on the future trajectories of atmospheric concentrations of these gases requires investigation of their (i) biogeochemical origins, (ii) response to climate feedbacks and other environmental factors, and (iii) susceptibility to management practices. This special issue provides a group of articles that present the current state of continental scale sources and sinks of biogenic GHGs and the potential to better manage them in the future.

  15. Modelling Marine Biological and Biogeochemical Data

    NASA Astrophysics Data System (ADS)

    Soetaert, Karline; van Oevelen, Dick

    2011-09-01

    In the environmental sciences, mathematic models are commonly applied to analyze ecological and biogeochemical data. The technique where a model is used to interpret available measurements such as to retrieve unmeasured information on the system being observed is called "inverse modelling". In this paper we will discuss and give examples of two modeling techniques used to analyse ecological and biogeochemical data. On the one hand are mechanistic mathematical models that are written as a set of non-linear differential equations. On the other hand are so-called linear inverse models (LIMs) that consist of a set of linear equations that need to be solved for the unknowns.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. Towards bridging biogeochemical and fish-production models

    NASA Astrophysics Data System (ADS)

    Fennel, Wolfgang

    The paper presents a theoretical approach to formulate a model which comprises the full food web. The lower part of the food web is represented by a biogeochemical model which interacts explicitly with a fish-production model. The fish-production model component builds on existing theories but was substantially reformulated in order to facilitate the model coupling. The dynamics of the fish-production model is basically driven by the predator-prey interaction. We use the example of the Baltic Sea, which has a relatively simple foodweb structure. The fish biomass is dominated by three groups, sprat, herring and cod, which represent about 80% of fish biomass in the Baltic. The zooplanktivors sprat and herring are eaten by cod. In this paper we start the construction of the model as a simple box system, which can be considered as an isolated water column of 10 × 10 km 2 times the water depth in the central Bornholm basin of the Baltic Sea. The stepwise building up of the model is illustrated by example simulations, which allow to assess the consistence of the theoretical approach and the choices of parameters. As last step we introduce a simple biogeochemical model and link it with the fish model. The resulting model system is strictly mass conserving without unspecified sources of food or so. We conduct experiments with the model system and show that it can reproduce features such as interannual variation in fish catches and trophic cascades.

  1. Passive regulation of soil biogeochemical cycling by root water transport

    NASA Astrophysics Data System (ADS)

    Quijano, Juan C.; Kumar, Praveen; Drewry, Darren T.

    2013-06-01

    Surface and subsurface moisture dynamics are strongly influenced by the ability of vegetation to take up and redistribute soil moisture using hydraulic redistribution (HR). These dynamics in turn affect soil biogeochemical cycling through controls on decomposition and mineralization rates and ion transport. The goal of this study is to explore this coupling between HR and biogeochemistry using a numerical model. We examine decomposition and mineralization of organic matter and analyze whether differences in decomposition rates induced by HR influence the long-term storage of carbon in the soil and the movement of nitrate (NO 3-) and ammonium (NH 4+) in the rhizosphere. These dynamics are studied in a framework that incorporates the interaction between multiple plant species. The net effect of HR on decomposition is controlled by a trade-off between the resultant moisture and temperature states. This trade-off is conditioned by the availability of fine roots near the surface, and it impacts the long-term storage and vertical distribution of carbon in the soil. HR also impacts the transport and uptake of ions from the soil. It reduces the leaching of nitrate considerably, and, therefore facilitates the uptake of nitrate by vegetation roots. Furthermore, the magnitude and patterns of the feedbacks induced by HR are also influenced by the presence of different plant species that coexist. These results suggest that the alteration of soil moisture by plants through associated processes such as HR can have considerable impact on the below-ground biogeochemical cycling of carbon and nitrogen.

  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 the ocean. Future “organic geotraces” studies should focus on extracting and establishing new organic proxies which are suitable to characterize and, in particular, quantify organic matter sources and transformation processes in the ocean. Longhurst AR (2007) Ecological geography of the sea. Academic Press, San Diego, 542 pp.

  3. 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.

  4. 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 beneath meandering river banks mainly has importance only in large rivers. For solutes entering networks in proportion to water inputs it is the lower order streams that tend to dominate cumulative reaction progress.

  5. Long-term Simulations of Pluto's Atmosphere and Surface as a Coupled System

    NASA Astrophysics Data System (ADS)

    Zalucha, Angela M.

    2015-11-01

    Previous work has modeled either Pluto's atmosphere or surface/subsurface as separate entities. In reality, these two regions should be coupled energetically and physically because of the accumulation, sublimation, and transport of volatiles (here, N2). Simulation results over multi-Pluto years are presented from a general circulation model that has both detailed atmospheric and surface/subsurface modules. As the initial model conditions that will ultimately reproduce the observed surface pressures from New Horizons, stellar occultation data, and spectroscopic observations are not known, by trial and error the model is initialized with different surface pressures and amounts of surface ice (collectively known as the volatile inventory). This “brute force” method is now a viable strategy given the ongoing development of the Pluto general circulation model (based on the MIT general circulation model dynamical core; Zalucha & Michaels 2013) and modern supercomputing power. The coupled atmosphere and surface/subsurface model is run until a yearly repeatable frost cycle occurs (if at all). Surface coverage of volatiles and surface pressure will be presented from the various scenarios. Ancillary variables such temperature (of both the atmosphere and surface/subsurface) and wind direction and magnitude will also be shown for cases of particular interest.

  6. 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.

  7. Coastal-zone biogeochemical dynamics under global warming

    SciTech Connect

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

    2000-03-01

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

  8. 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.

  9. Indian Ocean Biogeochemical Processes and Ecological Variability

    NASA Astrophysics Data System (ADS)

    Wiggert, Jerry D.; Hood, Raleigh R.; Naqvi, S. Wajih A.; Brink, Kenneth H.; Smith, Sharon L.

    Indian Ocean Biogeochemical Processes and Ecological Variability provides a synthesis of current knowledge on Indian Ocean biogeochemistry and ecology and an introduction to new concepts and topical paradigm challenges. It also reports on the development of more extensive/frequent observational capacity being deployed in the Indian Ocean. This represents the first collection of syntheses that emphasize a basin-wide perspective, and the contributing authors include some of the most esteemed oceanographers and Indian Ocean experts in the world. The volume is derived from invited plenary talks that were presented at the initial Sustained Indian Ocean Biogeochemistry and Ecosystem Research (SIBER) workshop held at the National Institute of Oceanography (NIO) in Goa, India, in October 2006. The volume discusses • The overlying physical processes set by monsoonal forcing and how these control biological production and variability • Nutrient cycling and limitation • Pelagic carbon cycling and air-sea exchange • Benthic biogeochemistry and ecology • The impact of climate and human activities on biogeochemistry and ecosystems. The readership for this book will consist of academic and governmental researchers interested in exploring how oceanographic, atmospheric, and hydrological processes combine to establish the environmental setting that supports and drives the pelagic system and which are especially relevant to understanding the complex biogeochemical and ecological interactions in the Indian Ocean.

  10. 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.

  11. 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 has been applied to the Mediterranean Sea for the period 1999-2010 with weekly assimilation. The results of the multi-annual run show that the assimilation improves the model skill in terms of a better representation of the mean chlorophyll concentrations over the Mediterranean Sea sub-regions and also in terms of spatial and temporal definition of local bloom events. Furthermore, the comparison with nutrients climatology based on in situ measurements show that the non assimilated variables are consistent with observations. The application of the 3DVAR revealed that in specific cases the correction introduced by the assimilation is not maintained by the model dynamics. In these cases, the satellite observations are characterized by local patchy bloom events, which are not well captured by the model. It has been observed that, since the bloom events are strongly affected by the vertical mixing dynamics, which support nutrients to the surface layer, a possible source of error are the mixing conditions provided by the physical model. Oddo et al. 2009. Ocean Science, 5(4), 461-473, doi:10.5194/os-5-461-2009. Lazzari et al. 2012. Biogeosciences, 9(1), 217-233, doi:10.5194/bg-9-217-2012. Teruzzi et al. 2014. Journal of Geophysical Research, 119, 1-18, doi:10.1002/2013JC009277. Volpe et al. 2012. Ocean Science Discussions, 9(2), 1349-1385, doi:10.5194/osd-9-1349-2012.

  12. 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/sediment chemistry, aquatic organisms, geomorphology). The aquatic network will produce ~212 low-level data products for each site. NEON will produce several higher level data products such as measurements of whole-stream metabolism, gross primary productivity, ecosystem respiration, and fluxes of nitrogen, phosphorous and carbon that will enable users to analyze processes on a gross scale. These data may be integrated with NEON's terrestrial and airborne networks to bridge the gap between aquatic and terrestrial biogeochemical research. The NEON Aquatic Network is poised to greatly expand our ability to create more robust biogeochemical models. For example, hydrologic and stable isotope data will allow investigation of terrestrial-aquatic carbon flux. Constraints provided by NEON's terrestrial and atmospheric data concurrent with remotely sensed data will facilitate the scaling to regional and continental scales, potentially leading to greater accuracy in the global carbon budget. The NEON Aquatic Network represents a powerful tool that will give the scientific community access to standardized data over spatiotemporal scales that are needed to answer fundamental questions about natural ecological variability and responses to changes in the environment.

  13. 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.

  14. Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns.

    PubMed

    Helton, Ashley M; Ardón, Marcelo; Bernhardt, Emily S

    2015-10-01

    Carbon and nitrogen cycles are coupled through both stoichiometric requirements for microbial biomass and dissimilatory metabolic processes in which microbes catalyse reduction-oxidation reactions. Here, we integrate stoichiometric theory and thermodynamic principles to explain the commonly observed trade-off between high nitrate and high organic carbon concentrations, and the even stronger trade-off between high nitrate and high ammonium concentrations, across a wide range of aquatic ecosystems. Our results suggest these relationships are the emergent properties of both microbial biomass stoichiometry and the availability of terminal electron acceptors. Because elements with multiple oxidation states (i.e. nitrogen, manganese, iron and sulphur) serve as both nutrients and sources of chemical energy in reduced environments, both assimilative demand and dissimilatory uses determine their concentrations across broad spatial gradients. Conceptual and quantitative models that integrate rather than independently examine thermodynamic, stoichiometric and evolutionary controls on biogeochemical cycling are essential for understanding local to global biogeochemical patterns. PMID:26259672

  15. The biogeochemical footprint of agricultural soil erosion

    NASA Astrophysics Data System (ADS)

    Govers, Gerard; Van Oost, Kristof; Wang, Zhengang

    2015-04-01

    Global biogeochemical cycles are a key component of the functioning of the Earth System: these cycles are all, to a varying extent, disturbed by human activities which not only has dramatic consequences for the global climate but also for the acidity of the world's oceans. It is only relatively recently that the role of lateral fluxes related to surface water movement and soil erosion and deposition (and the way those fluxes are modified by human action) is explicitly considered by the scientific community. In this paper we present an overview of our present-day understanding of the role of agricultural soil erosion in the global cycles of carbon, nitrogen, phosphorous and silica. We discuss the major processes through which erosion affects these global cycles and pay particular attention to the knowledge gaps that prevent us from accurately assessing the impact of soil erosion on global biogeochemical cycling at different temporal scales. Furthering our understanding (and better constraining our estimates) will require progress both in terms of model development and process understanding. Research needs can be most clearly identified with respect to soil organic carbon: (i) at present, large-scale soil erosion (and deposition) models are poorly constrained so that the amount of carbon mobilised by erosion (and its fate) cannot be accurately estimated and (ii) the fate of soil organic carbon buried by deposition or delivered to river network is poorly understood. Uncertainties for N, P and Si are larger than those for C as we have less information on the amount of these elements stored in agricultural soils and/or do not fully understand how these elements cycle through the soil/plant system. Agricultural soil erosion does not affect soil functioning through its effect on biogeochemical cycling. Erosion directly affects soil hydrological functioning and is likely to affect weathering processes and soil production. Addressing all these issues requires the combination of a wide range of approaches, allowing not only to assess current processes, but also their cumulative effects over long time spans.

  16. 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 reduction capability will be later selected and used to facilitate biogeochemical reduction of iron under simulated temperature and pressure of Europa's ocean. The results of this work will enable us to ascertain whether Europa's cold, high-pressure ocean is capable of supporting life. In addition, the data from this study will help in generating a list of organic and inorganic target molecules for future remote sensing and in situ exploration missions.

  17. 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.

  18. Oceanographic and Biogeochemical Insights from Diatom Genomes

    NASA Astrophysics Data System (ADS)

    Bowler, Chris; Vardi, Assaf; Allen, Andrew E.

    2010-01-01

    Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes.

  19. Oceanographic and biogeochemical insights from diatom genomes.

    PubMed

    Bowler, Chris; Vardi, Assaf; Allen, Andrew E

    2010-01-01

    Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes. PMID:21141668

  20. Archiving numerical models of biogeochemical dynamics

    NASA Astrophysics Data System (ADS)

    Thornton, Peter E.; Cook, Robert B.; Braswell, Bobby H.; Law, Beverly E.; Corvallis, Wilfred M.; Shugart, Herman H.; Rhyne, B. Timothy; Hook, Leslie A.

    No adequate community-wide mechanism or set of standards currently exists to ensure the long-term reproducibility of results from numerical modeling in biogeochemical research. Various investigators maintain copies of code and supporting materials through ad hoc methods, and some models and modeling studies are not archived by any mechanism other than the published manuscripts describing specific research results. This state of affairs invites trouble.To illustrate this situation, one of the authors of this article was recently involved in producing a state-of-the-art review on the topic of the effects of climate change on forests. The literature on this topic contains a rich array of results from dynamic models of global or regional vegetation produced by forcing these models with climate change scenarios.

  1. River restoration: morphological, hydrological, biogeochemical and ecological changes and challenges

    NASA Astrophysics Data System (ADS)

    Schirmer, M.; Luster, J.; Linde, N.; Perona, P.; Mitchell, E. A. D.; Barry, D. A.; Cirpka, O. A.; Schneider, P.; Vogt, T.; Durisch-Kaiser, E.

    2013-08-01

    River restoration is essential as a means to enhance river dynamics, environmental heterogeneity and biodiversity. The underlying processes governing the dynamic changes need to be understood thoroughly to ensure that restoration projects meet their goals. In particular, we need to understand quantitatively how hydromorphological variability relates to ecosystem functioning and services, biodiversity and (ground)water quality in restored river corridors. Here, we provide a short overview on the literature and present a study of a restored river corridor in Switzerland combining physical, chemical, and biological observations with modeling. The results show complex spatial patterns of bank infiltration, habitat-type, biotic communities and biogeochemical processes. In particular, we found an increase in taxonomic and functional diversity for earthworms, testate amoebae and bacteria in the restored part of the river. This complexity is driven by river hydrology and morphodynamics, which are in turn actively coupled to riparian vegetation processes. Given this complexity and the multiple constraints on the uses and management of floodplains, a multi-disciplinary approach is needed to monitor the success of restoration measures and to make recommendations for future restoration projects.

  2. Biogeochemical impact of tropical instability waves in the equatorial Pacific

    NASA Astrophysics Data System (ADS)

    Gorgues, T.; Menkes, C.; Aumont, O.; Vialard, J.; Dandonneau, Y.; Bopp, L.

    2005-12-01

    Tropical Instability Waves (TIW) have been suggested to fertilize the equatorial Pacific in iron leading to enhanced ecosystem productivity. Using a coupled dynamical-biogeochemical model, we show that contrary to this suggestion, TIWs induce a decrease of iron concentration by 10% at the equator and by about 3% over the Wyrtki box [90W-180, 5N-5S]. Chlorophyll decreases by 10% at the equator and 1% over the Wyrtki box. This leads to a decrease of new production up to 10% at the equator (4% over the Wyrtki box). TIW-induced horizontal advection exports iron-rich equatorial water to the north, but also brings iron-depleted water to the equator leading to a net decrease in iron. Additional iron decrease is caused by TIW-induced iron vertical diffusion. These two mechanisms are partly counter balanced by a decrease of iron biological uptake, driven by lower phytoplankton concentrations, and to a lesser extent by TIW-induced iron vertical advection.

  3. Biogeochemical Heterogeneity in Mars Analog Soils from the Atacama Desert

    NASA Astrophysics Data System (ADS)

    Claire, M.; Shirey, B.; Brown, M.; Anderson, D.; Van Mourik, M.

    2014-12-01

    Water is ubiquitous on Earth and plays a fundamental role in all aspects of biogeochemical cycling. Our existence on an aqua planet hampers our ability to interpret a planet like Mars where it may not have rained for a billion years. Soils from the hyperarid core of Chile's Atacama Desert may represent the closest geochemical analog to Martian soils, as this region has the lowest precipitation on Earth. The extreme lack of rainfall (a few mm per decade) limits both weathering and biological activity to the point where soils are effectively sterile. Oxidized end products of atmospheric chemistry such as nitrate and perchlorate build up to values approaching those measured on Mars by NASA's Phoenix Lander. In June 2012, we collected soil samples from 8 locations along an aridity gradient from the hyperarid core of the Atacama (rainfall < 1 mm/yr) towards the arid (5-100 mm/yr) surrounding areas where microbial community activity is sufficient to support the hardiest of desert plant species. Field observations indicate that microbial activity and geochemical heterogeneity are anti-correlated. We will present our quantitative results coupling geochemical heterogeneity (salt concentrations, org C/N, trace metals) and microbial community activity (TRFLP, nitrogen cycling) along this transect, and argue that geochemical heterogeneity (which could be measured by a rover or lander on Mars) may be a proxy for lifeless soils.

  4. 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 decreases in PO43- with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had not undergone significant chemical changes. Observed nitrogen and phosphorus losses demonstrate the potential, as well as future research needs to improve performance, of the prototype stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  6. 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.

  7. 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.

  8. 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 persistence of volcanism on Mars may well have influenced the persistence of a martian biosphere. The geologic processing of the crust can affect the availability of nutrients and also control the deposition of minerals that could have served as a medium for the preservation of fossil information. Finally, the activity of liquid water is crucial to life. Was there ever an Earth-like hydrologic cycle with rainfall? Has aqueous activity instead been restricted principally to hydrothermal activity below the surface? To what extent did the inorganic chemistry driven by sunlight and hydrothermal activity influence organic chemistry (prebiotic chemical evolution)? This paper addresses these and other key questions.

  9. Hydrologic and biogeochemical functioning of intensively managed catchments: A synthesis of top-down analyses

    NASA Astrophysics Data System (ADS)

    Basu, Nandita B.; Thompson, Sally E.; Rao, P. Suresh C.

    2011-10-01

    This paper synthesizes a 3-year collaborative effort to characterize the biogeochemical and hydrological features of intensively managed agricultural catchments by combining data analysis, modeling, and preliminary hypothesis testing. The specific focus was on the Midwestern region of the United States. The results suggest that: (1) water management, specifically the homogenization of evapotranspiration losses driven by mono-cultural vegetation cover, and the homogenization of runoff generation driven by artificial drainage, has created engineered, predictable hydrologic systems; (2) nutrient and pesticide management, specifically their regular applications have created two kinds of biogeochemical export regimes: chemostatic (low variability in concentration as exhibited by nitrate) and episodic (high variability in concentration as exhibited by pesticides); (3) coupled mass-balance models for water and solutes reproduce these two regimes as a function of chemical rate constants. Phosphorus transport regimes were found to be episodic at smaller spatial scales, but chemostatic at larger scales. Chemostatic response dominates in transport-limited catchments that have internal sources of the solute to buffer the periodicity in episodic inputs, while episodic response dominates in source-limited catchments. The shift from episodic nitrate export in pristine catchments to chemostatic regimes in managed watersheds was attributed to legacy stores of nitrogen (built from continued fertilizer applications) that buffer interannual variations in biogeochemical processing. Fast degradation kinetics of pesticides prevents the build-up of legacy sources, and leads to episodic export. Analytical expressions were derived for the probability density functions of solute delivery ratio as a function of the stochastics of rainfall-runoff events and biogeochemical controls.

  10. 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.

  11. Geologic nitrogen in terrestrial biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Holloway, Joann M.; Dahlgren, Randy A.

    1999-06-01

    Recent research implicates geologic nitrogen as a large and reactive pool of nitrogen that can have significant ecological effects. This study was conducted to determine the landscape distribution of geologic nitrogen and the fate of this nitrogen during rock to soil transformation in the lower Mokelumne River watershed located in the western Sierra Nevada of California. Mineralogy and chemistry were determined for six major lithologies in the study area to examine the spatial distribution of nitrogen in bedrock. In addition, soil samples were collected from two watersheds having high stream-water nitrate concentrations to determine the fate of nitrogen during weathering and soil formation. With the exception of diorite, all bedrock contained detectable concentrations of nitrogen: 153 1801 and 98 739 mg N kg-1 for metasedimentary and metavolcanic lithologies, respectively. A significant amount of nitrogen was released during soil formation: 2350 and 2570 kg N ha-1 for soils formed on greenstone and slate, respectively. This amount of nitrogen represents from 30% to 50% of the current soil nitrogen pool. In these ecosystems, nitrogen released from bedrock contributes to an excess of available nitrogen relative to biotic demands, leading to nitrate leaching and elevated concentrations of nitrate in stream water. Given the widespread occurrence of geologic nitrogen and the large global inventory of nitrogen contained within bedrock, the role of geologic nitrogen as a source of nitrogen for terrestrial biogeochemical cycling must be considered.

  12. 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

  13. Redox chemistry in the phosphorus biogeochemical cycle.

    PubMed

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

    2014-10-28

    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

  14. 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

  15. [DNDC model, a model of biogeochemical processes: Research progress and applications].

    PubMed

    Guo, Jia-Wei; Zou, Yuan-Chun; Huo, Li-Li; L, Xian-Guo

    2013-02-01

    Denitrification-decomposition (DNDC) model can estimate the emission fluxes of soil trace gases such as carbon dioxide (CO2), methane (CH4) , and nitrous oxide (N2O) via the coupling of the denitrification and decomposition processes driven by soil environmental factors. At present, DNDC model is one of the most successful models in the world in simulating the terrestrial biogeochemical cycles. This paper mainly reviewed the development process of the DNDC model, its structure, model validation, and sensitive factor analysis, and summarized the hot fields in the applications of the model. PMID:23705407

  16. A Physically Based Surface/ Subsurface Flow Model to Assess the Impacts of Climate Change Extremes on the Hydrology of an Upper Midwest U.S. Watershed

    NASA Astrophysics Data System (ADS)

    Acar, O.; Franz, K.; Simpkins, W. W.

    2014-12-01

    Climate change is already affecting the Midwest U.S. Occurrence and intensity of extreme events such as heat waves, droughts and floods are expected to increase in the next few decades. It is the climate extremes, not averages, that have the greater impact on crop and livestock productivity which are vital for the State's economy. Accordingly, potential changes in the hydrologic cycle under prospective climate conditions need to be addressed at the watershed scale for the Midwestern agricultural region to develop better management and adaptation solutions. For this purpose, the 3-D finite element model, HydroGeoSphere has been applied to and calibrated for a representative watershed in north-central Iowa, Tipton Creek watershed. The conceptual model for the watershed consists of all the elements of the hydrologic cycle from the ground surface through the Quaternary aquitard and into the underlying Mississippian limestone aquifer. Extreme wet and dry conditions derived from statistically downscaled climate model scenarios have been used as input to the basin model to simulate the impacts on streamflow and groundwater flow. The model accomplishes integrated hydrologic analysis by the coupled solution of the diffusion wave equation governing 2-D (areal) surface water flow and the Richards' equation governing 3-D unsaturated/ saturated subsurface flow. Thus, actual evapotranspiration is calculated internally as a function of the soil moisture at each node of the defined evaporative zone at each time step and interdependent processes like recharge that are critical for climate change can be handled more accurately. Preliminary results for HadCM3 scenario combined with two SRES projections, A2 and A1fi predict more remarkable increases in stream levels in response to wet periods than the decreases in flows for dry periods in comparison to control (contemporary) period simulations. The impacts on the water table levels seem to be more prominent, in the range of ±4 m for dry and wet period simulations than for the potentiometric surface map changes that are 0-2.6 m of declines for the drought and up to 1.7 m of rise for the wet scenarios. The variations in the projected changes depend on the location throughout the model domain and the climate change scenario analyzed.

  17. Plankton Functional Types in a New Generation of Biogeochemical Models

    NASA Astrophysics Data System (ADS)

    Le Qur, Corinne; Pesant, Stphane

    2009-01-01

    Integration of Plankton Abundance Data for the Evaluation of Marine Biogeochemical Models; Cambridge, United Kingdom, 1-3 October 2008; It has long been recognized that biological activity has a large influence on biogeochemical cycles in the ocean. However, the recognition that the ecosystem composition may also be significant is more recent. The newest generation of biogeochemical models used to study climate-ocean interactions represents the diversity of planktonic ecosystems by grouping similar species into ``plankton functional types'' (PFTs). These models can thus include specific biogeochemical processes mediated by distinct PFTs, such as the ballasting effect of mineral shells, the aggregation effect of some organic material, and the packaging effect of grazing by large zooplankton.

  18. 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...

  19. Redox regime shifts in microbially mediated biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Bush, T.; Butler, I. B.; Free, A.; Allen, R. J.

    2015-06-01

    Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

  20. 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.

  1. 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 the procedure.

  2. Europa: Geological activity and surface - subsurface exchange

    NASA Astrophysics Data System (ADS)

    Phillips, C. B.; Cowell, W.

    2005-12-01

    Jupiter's moon Europa has a geologically young surface, allowing the possibility of current, ongoing geological activity. We are searching the Galileo database for overlapping images taken during the 5-year mission, and are comparing images using an iterative coregistration technique to look for changes due to geological activity. We will also discuss methods by which such activity could occur on Europa. We are particularly interested in the ability of geological processes to bring surface material down into the subsurface, and to bring subsurface material up to the surface. We are continuing a survey of such processes, including endogenic tectonic and cryovolcanic activity, and exogenic processes such as gardening and impact cratering.

  3. A Generic Biogeochemical Module for Earth System Models: Next Generation BioGeoChemical Module (NGBGC), Version 1.0

    SciTech Connect

    Fang, Yilin; Huang, Maoyi; Liu, Chongxuan; Li, Hongyi; Leung, Lai-Yung R.

    2013-11-13

    Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from atmosphere, influencing global climate changes. Integration of these processes into earth system models (e.g., community land models (CLM)), however, currently faces three major challenges: 1) extensive efforts are required to modify modeling structures and to rewrite computer programs to incorporate new or updated processes as new knowledge is being generated, 2) computational cost is prohibitively expensive to simulate biogeochemical processes in land models due to large variations in the rates of biogeochemical processes, and 3) various mathematical representations of biogeochemical processes exist to incorporate different aspects of fundamental mechanisms, but systematic evaluation of the different mathematical representations is difficult, if not possible. To address these challenges, we propose a new computational framework to easily incorporate physical and biogeochemical processes into land models. The new framework consists of a new biogeochemical module with a generic algorithm and reaction database so that new and updated processes can be incorporated into land models without the need to manually set up the ordinary differential equations to be solved numerically. The reaction database consists of processes of nutrient flow through the terrestrial ecosystems in plants, litter and soil. This framework facilitates effective comparison studies of biogeochemical cycles in an ecosystem using different conceptual models under the same land modeling framework. The approach was first implemented in CLM and benchmarked against simulations from the original CLM-CN code. A case study was then provided to demonstrate the advantages of using the new approach to incorporate a phosphorus cycle into the CLM model. To our knowledge, the phosphorus-incorporated CLM is a new model that can be used to simulate phosphorus limitation on the productivity of terrestrial ecosystems.

  4. Impact of resolved scales on global marine biogeochemical models

    NASA Astrophysics Data System (ADS)

    McKiver, William; Vichi, Marcello; Lovato, Tomas; Storto, Andrea; Masina, Simona

    2014-05-01

    Here we examine the impact of resolving mesoscale processes on the global marine biogeochemical system by performing simulations at two different resolutions, 2° (LO-res) and 1/4° resolution (HI-res) using the PELAGOS model. Both the LO-res and HI-res simulations are set up with the same forcings and biogeochemical parameterizations, while the initial conditions are provided by a spinup of the LO-res simulation. This allows us to perform a direct inter-comparison of the two cases with a view to understanding how the introduction of mesoscale features affects the biogeochemical system, specifically how differences in the resolved horizontal and vertical motions are reflected in the plankton biomass and the nutrient availability. While the global large-scale oceanographic features (fronts, gyres, etc) are captured in both the LO-res and HI-res simulations, differences in the mesoscale flow structures, and in particular the resolved vertical physics in the HI-res simulation generate very different behaviour in the biogeochemical system. These differences in the physics drives what is a spun-up biogeochemical system in the LO-res simulation into a new regime in the HI-res simulation with significant reduction of typical low resolution biases. Coastal features are well reproduced due to stronger Ekman upwelling at the continental margins and increased eddy kinetic energy in the Southern Ocean reduces the winter overestimation. These biases in the model are a result of inadequate vertical dynamics.

  5. 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.

  6. 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 investigate the estuarine biogeochemistry at the regional scale.

  7. 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. PMID:23744573

  8. A GIS-based Framework for Examining the Effects of Water-Driven Erosion on Soil Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Abban, B. K.; Papanicolaou, T.; Wacha, K.; Wilson, C. G.

    2014-12-01

    Soil erosion has long been identified as one of the key mechanisms affecting biogeochemical processes in the soil, through the transport and delivery of carbon and nutrients adsorbed to soil particles in the soil active layer. However, most biogeochemical models treat soil erosion contributions simplistically and lack the capacity to accurately account for the mechanisms that control soil erosion and deposition on the landscape. This stems from the fact that the majority of the biogeochemical models have traditionally been employed on landscapes where lateral and downslope fluxes due to soil erosion have been less significant compared to other vertical fluxes and processes occurring at a fixed location on the landscape. In intensely managed landscapes, however, this may not be the case since land management practices such as tillage and exposed land cover can lead to copious amounts of erosion on the landscape. Therefore, to better understand the role of soil erosion on soil biogeochemical cycling in IMLs, we present a framework for simulating the spatiotemporal effects of soil erosion and deposition on soil biogeochemical cycling. We focus specifically on tillage- and runoff-induced erosion since these are prevalent in IMLs. The framework employs a geospatial approach that loosely couples a GIS-based upland water erosion model, GeoWEPP, with a soil biogeochemistry model, Century, to predict downslope and lateral fluxes of soil erosion and the resultant impacts on soil biogeochemical cycling. The use of a geospatial approach allows us to better capture the effects of topography, soil type, land use/land cover, and climate on soil erosion fluxes as well as soil biogeochemical cycling. The spatiotemporal resolution of the framework makes it particularly beneficial for identifying hotspots in fields and hot moments at scales ranging from daily to annual time scales. We employ the framework to study the monthly redistribution of soil organic carbon over the course of a year in the South Amana Sub-Watershed, located in the headwaters of Clear Creek, Iowa, USA. Preliminary results indicate that the framework is able to capture observed erosional and depositional patterns in the watershed and can provide insight into soil carbon redistribution and sequestration.

  9. 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 are therefore difficult to study with standard mineralogical tools. Sequential extraction techniques are commonly used as proxies. We provide an example where Mössbauer spectroscopy can replace sequential extraction techniques where mineralogical information is sought. Where mineral separation is needed, for example in the investigation of Fe or S isotope fractionation, Mössbauer spectroscopy can help to optimize sequential extraction procedures. This can be employed in a large number of investigations of soils and sediments, potentially even for mineral separation to study Fe and S isotope fractionation in samples returned from Mars, which might reveal signatures of biological activity. When looking for the possibility of life outside Earth, Jupiter's icy moon Europa is one of the most exciting places. It may be just in reach for a Mössbauer spectrometer deployed by a future lander to study the red streak mineral deposits on its surface to look for clues about the composition of the ocean hidden under the moon's icy surface.

  10. 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 from low permeability clay lenses sustain biogeochemical cycling for a longer period of time than in homogeneous soil columns. Preliminary results indicate: i) certain variables (anion, cation concentrations, etc.) do not follow normal or lognormal distributions even at the column scale, ii) strong correlations exist between parameters related to redox geochemistry (pH with S2- concentrations), and iii) PCA can identify dominant processes (e.g. iron and sulfate reduction) occurring in the system by grouping together causative variables (e.g. dominant TEAPs).

  11. Scaling of Contaminant Loads in Fractal River Networks: Hydrologic, Geomorphic and Biogeochemical Controls (Invited)

    NASA Astrophysics Data System (ADS)

    Ye, S.; Zanardo, S.; Basu, N. B.; Sivapalan, M.; Rao, P. C.

    2009-12-01

    Nutrient loads delivered from the hillslopes to the river network during runoff events are moderated by biogeochemical transformations within the sediment, thus mitigating the likely impacts on downstream ecosystems. Modeling of the attenuation and aggregation of nutrient loads requires dynamic coupling of hydrology and biogeochemistry at the reach scale and propagation of reach-scale attenuation along the network. Most network models of nutrient transport use nonlinear empirical regression functions between removal rate constant and stream stage to simulate nutrient retention at daily or monthly time scales. In contrast, stream tracer experiments at the reach scale are usually analyzed in a more mechanistic way, using the 1-D transport model OTIS-P, based on the two-compartment, transient-storage model (TSM; Bencala et al. 1983). We integrated the reach-scale TSM for biogeochemistry with a dynamic network hydrologic model (THREW) for hydrology to explore spatio-temporal scaling in nutrient dynamics as a function of climate, biogeochemical and geomorphic controls in the system. Two representative watersheds (~ 500 km2), one in an arid and another in a humid environment, were selected for the analysis. The effect of climate was explored by varying the frequency and mean depth of the rainfall forcing function. Geomorphic effects were explored by varying channel dimensions and sinuosity, while chemical transformation rate constants were modified to investigate biogeochemical controls. The effect of network structure (e.g., Horton ratios) was evaluated by comparing responses from the two watersheds. Initial results indicate that climatic controls have a weaker effect on the nutrient removal effectiveness than geomorphologic characteristics, especially in the wet climate. The predictability of the scaling responses as a function of the different controls was explored using simple analytical approaches.

  12. Ocean biogeochemical response to phytoplankton-light feedback in a global model

    NASA Astrophysics Data System (ADS)

    Manizza, Manfredi; Le QuéRé, Corinne; Watson, Andrew J.; Buitenhuis, Erik T.

    2008-10-01

    Oceanic phytoplankton, absorbing solar radiation, can influence the bio-optical properties of seawater and hence upper ocean physics. We include this process in a global ocean general circulation model (OGCM) coupled to a dynamic green ocean model (DGOM) based on multiple plankton functional types (PFT). We not only study the impact of this process on ocean physics but we also explore the biogeochemical response due to this biophysical feedback. The phytoplankton-light feedback (PLF) impacts the dynamics of the upper tropical and subtropical oceans. The change in circulation enhances both the vertical supply in the tropics and the lateral supply of nutrients from the tropics to the subtropics boosting the subtropical productivity by up to 60 gC m-2 a-1. Physical changes, due to the PLF, impact on light and nutrient availability causing shifts in the ocean ecosystems. In the extratropics, increased stratification favors calcifiers (by up to ˜8%) at the expense of mixed phytoplankton. In the Southern Ocean, silicifiers increase their biomass (by up to ˜10%) because of the combined alleviation of iron and light limitation. The PLF has a small effect globally on air-sea fluxes of carbon dioxide (CO2, 72 TmolC a-1 outgassing) and oxygen (O2, 46 TmolO2 a-1 ingassing) because changes in biogeochemical processes (primary production, biogenic calcification, and export production) highly vary regionally and can also oppose each other. From our study it emerges that the main impact of the PLF is an amplification of the seasonal cycle of physical and biogeochemical properties of the high-latitude oceans mostly driven by the amplification of the SST seasonal cycle.

  13. Geophysical monitoring of hydrological and biogeochemical transformations associated with Cr(VI) bioremediation.

    PubMed

    Hubbard, Susan S; Williams, Ken; Conrad, Mark E; Faybishenko, Boris; Peterson, John; Chen, Jinsong; Long, Phil; Hazent, Terry

    2008-05-15

    Understanding how hydrological and biogeochemical properties change over space and time in response to remedial treatments is hindered by our ability to monitor these processes with sufficient resolution and over field relevant scales. Here, we explored the use of geophysical approaches for monitoring the spatiotemporal distribution of hydrological and biogeochemical transformations associated with a Cr(VI) bioremediation experiment performed at Hanford, WA. We first integrated hydrological wellbore and geophysical tomographic data sets to estimate hydrological zonation at the study site. Using results from laboratory biogeophysical experiments and constraints provided by field geochemical data sets, we then interpreted time-lapse seismic and radar tomographic data sets, collected during thirteen acquisition campaigns over a three year experimental period, in terms of hydrological and biogeochemical transformations. The geophysical monitoring data sets were used to infer: the spatial distribution of injected electron donor; the evolution of gas bubbles; variations in total dissolved solids (nitrate and sulfate) as a function of pumping activity; the formation of precipitates and dissolution of calcites; and concomitant changes in porosity. Although qualitative in nature, the integrated interpretation illustrates how geophysical techniques have the potential to provide a wealth of information about coupled hydrobiogeochemical responses to remedial treatments in high spatial resolution and in a minimally invasive manner. Particularly novel aspects of our study include the use of multiple lines of evidence to constrain the interpretation of a long-term, field-scale geophysical monitoring data set and the interpretation of the transformations as a function of hydrological heterogeneity and pumping activity. PMID:18546719

  14. Biogeochemical Process Comparison of the Five USGS Water, Energy, and Biogeochemical Budget (WEBB) Sites

    NASA Astrophysics Data System (ADS)

    Shanley, J. B.; Peters, N. E.; Aulenbach, B. T.; Blum, A. E.; Campbell, D. H.; Clow, D. W.; Larsen, M. C.; Mast, M. A.; Stallard, R. F.; Troester, J. W.; Walker, J. F.; Webb, R. M.; White, A. F.

    2001-12-01

    Input - output budgets (in wet deposition and streamwater) have been constructed for water and major solutes at the five USGS Water, Energy, and Biogeochemical Budget (WEBB) sites for the period 1992-97 (Peters et al., 2000). In this poster we interpret the net chemical fluxes to identify the controlling biogeochemical processes, as influenced by the strong physical and biological contrasts (climate, geology, physiography, and vegetation types) in the five diverse environments. The five sites are: Allequash Creek, Wisconsin (low-relief humid continental forest); Andrews Creek, Colorado (cold alpine, taiga/tundra, and subalpine boreal forest); Icacos River, Puerto Rico (lower montane, wet tropical forest); Panola Mountain, Georgia (humid subtropical piedmont forest); and Sleepers River, Vermont (humid northern hardwood forest). Base cations and Si produced by chemical weathering displayed a net export at each site. The magnitude and stoichiometry of export reflects mineralogy, climate (temperature and rainfall), and water residence time in the subsurface. The lowest and highest mass export generally was for Andrews Creek and Icacos River, respectively, consistent with their extreme mean annual temperatures (0/degC in Colorado to 21/degC in Puerto Rico) and the limited residence time of meltwater at Andrews Creek. Calcite in bedrock at the three coldest watersheds caused somewhat higher relative export of Ca, especially at Sleepers River where calcite weathering is a dominant control on stream chemistry. In contrast, the high Mg content of the volcaniclastic rocks at Icacos River and glacial deposits at Allequash Creek caused disproportionately high Mg export relative to the other sites. Relatively high Na export at Panola Mountain and K export at Sleepers River are probably caused by plagioclase and biotite weathering, respectively. SO4 is retained at the two warmest sites, Panola Mountain and Icacos River. SO4 adsorption is known to limit SO4- export in highly weathered subtropical and tropical soils. At Sleepers River, net SO4 export occurs as a result of weathering of sulfide minerals in the bedrock, and correspondingly limited soil SO4 adsorption capacity. A small net export of SO4 occurs at Allequash Creek and Andrews Creek, but the SO4 may be in balance if dry deposition were added to the inputs. All sites except Icacos River retain NO3. At Andrews Creek and Sleepers River, net export of NO3 occurs during the peak snowmelt months, as soils are flushed during a time of low biological uptake. Additional analysis will be performed to evaluate the relative importance of temperature (affecting weathering rates and biological uptake) and water yield (i.e., the amount of water flushing through a catchment) in controlling solute fluxes.

  15. Developing biogeochemical tracers of apatite weathering by ectomycorrhizal fungi

    NASA Astrophysics Data System (ADS)

    Vadeboncoeur, M. A.; Bryce, J. G.; Hobbie, E. A.; Meana-Prado, M. F.; Blichert-Toft, J.

    2012-12-01

    Chronic acid deposition has depleted calcium (Ca) from many New England forest soils, and intensive harvesting may reduce phosphorus (P) available to future rotations. Thin glacial till soils contain trace amounts of apatite, a primary calcium phosphate mineral, which may be an important long-term source of both P and Ca to ecosystems. The extent to which ECM fungi enhance the weathering rate of primary minerals in soil which contain growth-limiting nutrients remains poorly quantified, in part due to biogeochemical tracers which are subsequently masked by within-plant fractionation. Rare earth elements (REEs) and Pb isotope ratios show some potential for revealing differences in soil apatite weathering rates across forest stands and silvicultural treatments. To test the utility of these tracers, we grew birch seedlings semi-hydroponically under controlled P-limited conditions, supplemented with mesh bags containing granite chips. Our experimental design included nonmycorrhizal (NM) as well as ectomycorrhizal cultures (Cortinarius or Leccinum). Resulting mycorrhizal roots and leachates of granite chips were analyzed for these tracers. REE concentrations in roots were greatly elevated in treatments with granite relative to those without granite, demonstrating uptake of apatite weathering products. Roots with different mycorrhizal fungi accumulated similar concentrations of REEs and were generally elevated compared to the NM cultures. Ammonium chloride leaches of granite chips grown in contact with mycorrhizal hyphae show elevated REE concentrations and significantly radiogenic Pb isotope signatures relative to bulk rock, also supporting enhanced apatite dissolution. Our results in culture are consistent with data from field-collected sporocarps from hardwood stands in the Bartlett Experimental Forest in New Hampshire, in which Cortinarius sporocarp Pb isotope ratios were more radiogenic than those of other ectomycorrhizal sporocarps. Taken together, the experimental and field results imply that the coupled approach of REE and Pb isotopic values afford a means to quantify the degree to which primary mineral weathering inputs are contributing to ecosystem nutrient budgets and potentially the role of different types of ECM fungi in the weathering process.

  16. Past and present of sediment and carbon biogeochemical cycling models

    NASA Astrophysics Data System (ADS)

    MacKenzie, F. T.; Lerman, A.; Andersson, A. J.

    2004-05-01

    The global carbon cycle is part of the much more extensive sedimentary cycle that involves large masses of carbon in the Earth's inner and outer spheres. Studies of the carbon cycle generally followed a progression in knowledge of the natural biological, then chemical, and finally geological processes involved, culminating in a more or less integrated picture of the biogeochemical carbon cycle by the 1920s. However, knowledge of the ocean's carbon cycle behavior has only within the last few decades progressed to a stage where meaningful discussion of carbon processes on an annual to millennial time scale can take place. In geologically older and pre-industrial time, the ocean was generally a net source of CO2 emissions to the atmosphere owing to the mineralization of land-derived organic matter in addition to that produced in situ and to the process of CaCO3 precipitation. Due to rising atmospheric CO2concentrations because of fossil fuel combustion and land use changes, the direction of the air-sea CO2 flux has reversed, leading to the ocean as a whole being a net sink of anthropogenic CO2. The present thickness of the surface ocean layer, where part of the anthropogenic CO2 emissions are stored, is estimated as of the order of a few hundred meters. The oceanic coastal zone net air-sea CO2 exchange flux has also probably changed during industrial time. Model projections indicate that in pre-industrial times, the coastal zone may have been net heterotrophic, releasing CO2 to the atmosphere from the imbalance between gross photosynthesis and total respiration. This, coupled with extensive CaCO3 precipitation in coastal zone environments, led to a net flux of CO2 out of the system. During industrial time the coastal zone ocean has tended to reverse its trophic status toward a non-steady state situation of net autotrophy, resulting in net uptake of anthropogenic CO2 and storage of carbon in the coastal ocean, despite the significant calcification that still occurs in this region. Furthermore, evidence from the inorganic carbon cycle indicates that deposition and net storage of CaCO3 in sediments exceed inflow of inorganic carbon from land and produce CO2 emissions to the atmosphere. In the shallow-water coastal zone, increase in atmospheric CO2 during the last 300 years of industrial time may have reduced the rate of calcification, and continuation of this trend is an issue of serious environmental concern in the global carbon balance.

  17. Past and present of sediment and carbon biogeochemical cycling models

    NASA Astrophysics Data System (ADS)

    MacKenzie, F. T.; Lerman, A.; Andersson, A. J.

    The global carbon cycle is part of the much more extensive sedimentary cycle that involves large masses of carbon in the Earth's inner and outer spheres. Studies of the carbon cycle generally followed a progression in knowledge of the natural biological, then chemical, and finally geological processes involved, culminating in a more or less integrated picture of the biogeochemical carbon cycle by the 1920s. However, knowledge of the ocean's carbon cycle behavior has only within the last few decades progressed to a stage where meaningful discussion of carbon processes on an annual to millennial time scale can take place. In geologically older and pre-industrial time, the ocean was generally a net source of CO2 emissions to the atmosphere owing to the mineralization of land-derived organic matter in addition to that produced in situ and to the process of CaCO3 precipitation. Due to rising atmospheric CO2 concentrations because of fossil fuel combustion and land use changes, the direction of the air-sea CO2 flux has reversed, leading to the ocean as a whole being a net sink of anthropogenic CO2. The present thickness of the surface ocean layer, where part of the anthropogenic CO2 emissions are stored, is estimated as of the order of a few hundred meters. The oceanic coastal zone net air-sea CO2 exchange flux has also probably changed during industrial time. Model projections indicate that in pre-industrial times, the coastal zone may have been net heterotrophic, releasing CO2 to the atmosphere from the imbalance between gross photosynthesis and total respiration. This, coupled with extensive CaCO3 precipitation in coastal zone environments, led to a net flux of CO2 out of the system. During industrial time the coastal zone ocean has tended to reverse its trophic status toward a non-steady state situation of net autotrophy, resulting in net uptake of anthropogenic CO2 and storage of carbon in the coastal ocean, despite the significant calcification that still occurs in this region. Furthermore, evidence from the inorganic carbon cycle indicates that deposition and net storage of CaCO3 in sediments exceed inflow of inorganic carbon from land and produce CO2 emissions to the atmosphere. In the shallow-water coastal zone, increase in atmospheric CO2 during the last 300 years of industrial time may have reduced the rate of calcification, and continuation of this trend is an issue of serious environmental concern in the global carbon balance.

  18. Vesicomyid Clams Alter Biogeochemical Processes at Pacific Methane Seeps

    NASA Astrophysics Data System (ADS)

    Bertics, V. J.; Treude, T.; Ziebis, W.

    2007-12-01

    There exists a close relationship between fluid flow, biogeochemistry, and biota in seep sediments. Upwelling of methane and sulfide-rich fluids supports abundant macrofauna species harboring thiotrophic or methanotrophic symbionts. Variations in fluid flow, thus supply of methane and sulfide, are considered key factors controlling benthic communities. Vesicomyid clams harbor thiotrophic symbionts in their gills, which are supplied with oxygen from the surrounding water and hydrogen sulfide from the sediment. The clams are capable of extending their foot into the sediment to tap sulfide sources in deeper layers, consequently affecting water-sediment solute exchange. Because seep fluids are generally depleted in sulfate compared to seawater, this bioturbation activity may enhance the supply of sulfate to otherwise sulfate-limited sediments, thus boosting microbial activity of sulfate reduction (SR) coupled to anaerobic oxidation of methane (AOM). The goal of this study was to investigate the activity of three species of vesicomyid clams ( Calyptogena pacifica, C. kilmeri, C. gigas) from three methane seep habitats (Eel River Basin, Hydrate Ridge, Monterey Bay Canyon) and to evaluate its effect on biogeochemical processes. Sediment cores and clams were collected using the submersible Alvin or the ROV Jason, during three cruises with the R/V Atlantis in July and October 2006 and July 2007 (AT 15-7, AT 15-11, and AT 15-20). We performed high-resolution measurements of geochemical gradients in intact sediment cores using microsensors (O2, H2S, pH, redox potential). The cores were then sliced (1 cm intervals) for detailed chemical and microbiological analyses. Parallel cores were used to determine microbial activity (AOM, SR) with radioactive tracers. For detailed laboratory investigations, clams were kept in narrow aquaria (15 cm x 20 cm x 5 cm) in the ship's cold room. The front of the aquaria was perforated with holes at 1 cm resolution. These silicone-filled holes served as sampling ports or for direct microsensor measurements. Vertical and horizontal microprofiles were measured, pore water samples were extracted, and small sediment cores were taken along the length of the aquaria for microbial rate measurements and chemical and microbiological analyses. We documented different bioturbation activity for the three species of vesicomyid clam that related to distinct geochemical gradients and differences in microbial activity. Sulfate reduction, thus sulfide production, was significantly enhanced in the presence of clams compared to the control.

  19. 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 and weathering. Communities sustained by oxygenic photosynthesis apparently thrived wherever supplies of sunlight, moisture and nutrients were sufficient. Prior to the development of oxygenic photosynthesis, the net global effect of the ancient global biosphere was to facilitate chemical equilibrium between reduced species from thermal activity and weathering and more oxidized constituents in the surface environment. But even this ancient biosphere might have been globally pervasive. The global geothermal heat flow was substantially higher during Earth's first billion years, and thus reduced chemical species might have persisted in sunlit aquatic environments. Perhaps the substantial decline in thermal activity between 4000 and 3000 Ma created a driver for oxygenic photosynthesis to develop.

  20. 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...

  1. [Endemic and biogeochemical characteristics of the territory of Chuvash Republic].

    PubMed

    Amirov, N Kh; Khokhlova, E A

    2010-01-01

    The study of endemic and biogeochemical features of the territory of Chuvash Republic showed that dietary patterns of the local population reflect specific environmental factors including selenium, manganese, and iron deficiency. Calcium deficit is mainly due to poorly balanced nutrition. PMID:20922843

  2. Continental Drilling to Explore Earth's Sedimentary, Paleobiological, and Biogeochemical Record

    NASA Astrophysics Data System (ADS)

    Cohen, Andrew; Soreghan, Gerilyn

    2013-07-01

    A workshop to promote research using continental scientific drilling to explore the Earth's sedimentary, paleobiological, and biogeochemical record was held in Norman, Okla. The workshop, funded by the U.S. National Science Foundation (NSF), was intended to encourage U.S.-based scientists to take advantage of the exceptional capacity of unweathered, continuous sediment cores to serve as archives of the Earth's history.

  3. 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...

  4. EFFECTS OF INCREASED SOLAR ULTRAVIOLET RADIATION ON BIOGEOCHEMICAL CYCLES

    EPA Science Inventory

    Increases in solar UV radiation could affect terrestrial and aquatic biogeochemical cycles thus altering both sources and sinks of greenhouse and chemically important trace gases (e.g., carbon dioxide (CO2), carbon monoxide (CO), carbonyl sulfide (COS)). n terrestrial ecosystems,...

  5. 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.

  6. 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.

  7. 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.

  8. Modeling ocean circulation and biogeochemical variability in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Xue, Z.; He, R.; Fennel, K.; Cai, W.-J.; Lohrenz, S.; Hopkinson, C.

    2013-11-01

    A three-dimensional coupled physical-biogeochemical model is applied to simulate and examine temporal and spatial variability of circulation and biogeochemical cycling in the Gulf of Mexico (GoM). The model is driven by realistic atmospheric forcing, open boundary conditions from a data assimilative global ocean circulation model, and observed freshwater and terrestrial nitrogen input from major rivers. A 7 yr model hindcast (2004-2010) was performed, and validated against satellite observed sea surface height, surface chlorophyll, and in situ observations including coastal sea level, ocean temperature, salinity, and dissolved inorganic nitrogen (DIN) concentration. The model hindcast revealed clear seasonality in DIN, phytoplankton and zooplankton distributions in the GoM. An empirical orthogonal function analysis indicated a phase-locked pattern among DIN, phytoplankton and zooplankton concentrations. The GoM shelf nitrogen budget was also quantified, revealing that on an annual basis the DIN input is largely balanced by the removal through denitrification (an equivalent of ~ 80% of DIN input) and offshore exports to the deep ocean (an equivalent of ~ 17% of DIN input).

  9. Modeling ocean circulation and biogeochemical variability in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Xue, Z.; He, R.; Fennel, K.; Cai, W.-J.; Lohrenz, S.; Hopkinson, C.

    2013-05-01

    A three-dimensional coupled physical-biogeochemical model is applied to simulate and examine temporal and spatial variability of circulation and biogeochemical cycling in the Gulf of Mexico (GoM). The model is driven by realistic atmospheric forcing, open boundary conditions from a data assimilative global ocean circulation model, and observed freshwater and terrestrial nutrient input from major rivers. A 7 yr model hindcast (2004-2010) was performed, and validated against satellite observed sea surface height, surface chlorophyll, and in-situ observations including coastal sea-level, ocean temperature, salinity, and nutrient concentration. The model hindcast revealed clear seasonality in nutrient, phytoplankton and zooplankton distributions in the GoM. An Empirical Orthogonal Function analysis indicated a phase-locked pattern among nutrient, phytoplankton and zooplankton concentrations. The GoM shelf nutrient budget was also quantified, revealing that on an annual basis ~80% of nutrient input was denitrified on the shelf and ~17% was exported to the deep ocean.

  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 biogeochemical fluxes will be possible at regional scales using relatively easily obtained vegetation structural and functional information.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  13. 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 and understanding reach-scale in-stream biogeochemical processes. In this paper we discuss the advantages and limitations of the in-situ high-frequency nutrient monitoring, the challenges related to data analysis and process inference and the integration of the short-term biogeochemical behaviour with the long-term trends. Finally the potential for integration of the long-term high-temporal resolution datasets with the predictions of reach- and catchment-scale biogeochemical models and observations from coarse-sampling monitoring strategies has been discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter are identified as important in sustaining this productivity. Microbial production in young soils is supported by labile organic matter, whereas carbon stocks in older soils are more refractory. Nitrogen fixing bacteria are responsible for the initial accumulation of available nitrates in the soil. Biogeochemical rates are highly seasonal, as observed in experimental data. The development and application of SHIMMER not only provides important new insights into forefield dynamics, but also highlights aspects of these systems that require further field and laboratory research. The most pressing advances need to come in quantifying nutrient budgets and biogeochemical rates, in exploring seasonality, the fate of allochthonous deposition in relation to autochthonous production, and empirical studies of microbial growth and cell death, to increase understanding of how glacier forefield development contributes to the global biogeochemical cycling and climate in the future.

  15. Estimating biogeochemical fluxes across sagebrush-steppe landscapes with Thematic Mapper imagery

    NASA Technical Reports Server (NTRS)

    Reiners, W. A.; Strong, L. L.; Matson, P. A.; Burke, I. C.; Ojima, D. S.

    1989-01-01

    Thematic Mapper (TM) satellite data were coupled to an ecosystem simulation model to simulate variation in nitrogen mineralization over time and space in a sagebrush steppe. This system of data inputs and calculations provides estimates of ecosystem properties including rates of biogeochemical processes over extensive and complex landscapes, and under changing management and climatic conditions. The landscape surface was divided into three sagebrush ecosystem types plus one other class consisting of nonsagebrush vegetation. This classification presented a complex mosaic of ecosystem types that shifted markedly in composition from one end of the 933-sq km study area to the other. Annual N-mineralization rates ranged from 5 to 25 kg N/ha among the three sagebrush types. The most active type comprised 42 percent of the entire area but contributed 60 percent to the nitrogen mineralization throughout the landscape.

  16. 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.

  17. 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 conditions on the stability/solubility of Fe(II) and Tc(IV), found 80 % resolubilization of the Tc. Column experiments exploring this behavior are being planned. HYPOTHESIS 4 The mobility of 99mTc in the sediment columns can be modeled using a coupled speciation and transport code. Microbiological and geochemical characterization of the column experiments is ongoing and transport and geochemical modeling experiments are being planned.

  18. Microbial activity and biogeochemical cycling in first-order Russian Arctic streams

    NASA Astrophysics Data System (ADS)

    Rhoades, R. E.; Lynch, L. M.; Ortega, J. C.; Holmes, R. M.; Mann, P. J.; Vonk, J. E.; Schade, J. D.

    2011-12-01

    Global climate change is strongly impacting Arctic ecosystems and is predicted to lead to thawing of permafrost soils. These soils are rich in organic matter and other nutrients and influence biogeochemical cycling in terrestrial and aquatic ecosystems. Small arctic streams are likely to be the first aquatic ecosystems to receive materials exported as soils warm. These first-order streams are characterized by strong interactions between the water column and stream bottom and have the potential to affect nutrient flux. Previous studies suggest that phosphorous availability limits biological productivity in many first-order arctic streams, however, they remain understudied, particularly in the Russian Arctic. Our objective was to assess microbial activity and biogeochemical cycling among arctic streams. We used three approaches to meet our objectives, including a survey of 9 streams, intensive longitudinal sampling in 5 streams, and nutrient pulse addition experiments in 4 streams, designed to assess the potential for limitation by N or P. We measured pH, temperature, dissolved oxygen, NH4, SRP, DOC, and TDN at all sampling sites. We also conducted biological oxygen demand (BOD) incubations designed to assess DOC lability, and correlated these measurements with background nutrient concentrations. We found a strong positive linear correlation between BOD and phosphate concentration, suggesting P limitation of production and/or consumption of labile DOC. To complement ambient stream measurements, we conducted whole stream nutrient addition experiments to calculate N and P uptake lengths, which we then used to infer whether N or P is more likely to limit biological processes, and the degree of coupling between N and P cycling. Results from the nutrient addition experiments suggest both N and P limitation among streams depending on stream location and characteristics. In addition, these experiments suggest a significant, but complex interaction between N and P cycles, with evidence that co-addition of N and P reduced P uptake rates over measurements made with addition of P alone. Because carbon degradation may be constrained by nutrient availability, we need a better understanding of the degree of coupling between element cycles, and the influence of small streams on biogeochemical cycling. Our findings show that first order streams have diverse impacts on nutrient flux and should be considered when modeling Arctic ecosystem response to climate change.

  19. Biogeochemical and Ecological Research in the Indian Ocean

    NASA Astrophysics Data System (ADS)

    Hood, Raleigh R.; Wajih, S.; Naqvi, A.; Wiggert, Jerry D.; Subramaniam, Ajit

    2007-03-01

    Sustained Indian Ocean Biogeochemical and Ecological Research Workshop, Goa, India, 3-6 October 2006 The Indian Ocean has many unique characteristics that give rise to a variety of physical, biogeochemical, and ecological responses that are not observed in other ocean basins. For instance, atmospheric circulation over the ocean is seasonally influenced by the presence of the Asian landmass. The monsoonal forcing results in seasonally reversing surface oceanic circulations throughout the northern Indian Ocean, which are particularly energetic in the Arabian Sea. Unlike the Pacific and Atlantic oceans, there is no strong equatorial upwelling or biological response in the east. Furthermore, the Indian Ocean contains one of the most intense oxygen minimum zones (OMZs) in the world oceans, but unlike the Atlantic and Pacific, its OMZ is located in the north rather than along the eastern boundary.

  20. The Microbial Engines That Drive Earth’s Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

    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.

  1. 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. PMID:18497287

  2. 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.

  3. 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.

  4. Aquifer/aquitard interfaces: Mixing zones that enhance biogeochemical reactions

    USGS Publications Warehouse

    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.

  5. Inorganic Carbon Cycling and the Biogeochemical Processes in Hudson Bay

    NASA Astrophysics Data System (ADS)

    Pengelly, Leah; Thomas, Helmuth; Burt, William; Papakyriakou, Tim; Miller, Lisa

    2014-05-01

    Coastal seas, like Hudson Bay, are biogeochemically active areas with high primary productivity. High productivity can be expected to lead to fractionation of 13C/12C creating depletion of 12C isotope of Dissolved Inorganic Carbon (12CDIC) in the surface and enrichment of 12CDIC in deeper waters. The increase of anthropogenic CO2 concentration can have drastic impacts on the biogeochemical properties of the ocean. Since the Arctic and coastal seas are primarily sensitive to these changes, assessing the carbon cycle of this area is very important for future studies. We present the carbon cycle and related data from the Arctic Net 2010 Cruise. We investigate and assess the processes governing the carbon cycle over the entire water column of Hudson Bay. We find that the deep waters of Hudson Bay are Pacifically derived and do not interact with Atlantic waters beyond the mouth of the Bay. River input greatly affect the waters of Hudson Bay. Also, the longer residence time of the deep Hudson Bay waters allows the accumulation of products due to various biogeochemical and physical processes. These include respiration of organic matter, which causes greater DIC and lower del13C values at depth, and brine formation, which increases salinity, DIC and alkalinity. The eastern side of Hudson is observed to have greater DIC concentrations and is isotopically lighter in del13C than the western side.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

    Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted in higher concentrations of TEAP reaction products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions with localized effects of the fine lithofacies having the largest impact on U(VI) surface complexation. The ability to model the comprehensive biogeochemical reaction network, and spatially and temporally variable processes, properties, and conditions controlling uranium behavior during engineered bioremediation in the naturally complex Rifle IFRC subsurface system required a subsurface simulator that could use the large memory and computational performance of a massively parallel computer. In this case, the eSTOMP simulator, operating on 128 processor cores for 12 h, was used to simulate the 110-day field experiment and 50 days of post-biostimulation behavior.

  8. 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 entire mass balance of nutrients and of the mineralization rates (denitrification and aerobic benthic mineralization) calculated from the model fitted well to the field measurements. Furthermore, this analysis indicates that the benthic mineralizations are the dominant processes involved in the nutrients release. This is the first implementation of a biogeochemical model applied to a highly productive reservoir in the TMVB in order to estimate nutrients release from sediments. It could be used for scenarios of reduction of eutrophication in the reservoir. This study provides a good example of the behavior of a small tropical reservoir under intense human pressure and it will help stakeholders to adopt appropriate strategies for the management of turbid tropical reservoirs.

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

    PubMed

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

    2011-11-01

    Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted in higher concentrations of TEAP reaction products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions with localized effects of the fine lithofacies having the largest impact on U(VI) surface complexation. The ability to model the comprehensive biogeochemical reaction network, and spatially and temporally variable processes, properties, and conditions controlling uranium behavior during engineered bioremediation in the naturally complex Rifle IFRC subsurface system required a subsurface simulator that could use the large memory and computational performance of a massively parallel computer. In this case, the eSTOMP simulator, operating on 128 processor cores for 12h, was used to simulate the 110-day field experiment and 50 days of post-biostimulation behavior. PMID:22115092

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  11. IBIRYS: a Regional High Resolution Reanalysis (physical and biogeochemical) over the European North East Shelf

    NASA Astrophysics Data System (ADS)

    Levier, Bruno; Benkiran, Mounir; Reffray, Guillaume; García Sottilo, Marcos

    2014-05-01

    Mercator-Ocean has developed a regional forecasting system at 1/12° resolution over the North East Atlantic (IBI: Iberia, Biscay and Irish), taking advantage of the recent developments in NEMO. A reanalysis, called IBIRYS, was performed with the IBI system on the 2002-2012 period. The physical model was coupled on-line with the biogeochemical component of NEMO based on the PISCES model. The model was forced by ERA-interim products (every 3 hours) including the atmospheric pressure. In addition to atmospheric forcing, the model included astronomical tidal forcing. This regional forecasting system used boundary conditions from the Mercator-Ocean global reanalysis (GLORYS: GLobal Ocean ReanalYses and Simulations).The assimilation component SAM2 (Mercator Ocean assimilation system), was based on a reduced-order Kalman filter (the SEEK or Singular Extended Evolutive Kalman filter). An IAU method (Incremental Analysis Updates) was used to apply the increments in the system. The error statistics were represented in a sub-space spanned by a small number of dominant 3D error directions. A 3D-Var scheme corrected for the slowly evolving large-scale biases in temperature and salinity. The data assimilation system allowed to constrain the model in a multivariate way with Sea Surface Temperature (AVHRR + Multi-satellite High resolution), together with all available satellite Sea Level Anomalies, and with in situ observations from the CORA-03 data base, including ARGO floats temperature and salinity measurements. In this presentation, the results obtained with IBIRYS are compared to GLORYS results. The consistency of the IBIRYS and GLORYS results at large scales is demonstrated. The capacity of IBIRYS to provide useful information at high frequencies in the North East Atlantic is shown. The biogeochemical results of IBIRYS are evaluated.

  12. Pre-treatments, characteristics, and biogeochemical dynamics of dissolved organic matter in sediments: A review.

    PubMed

    Chen, Meilian; Hur, Jin

    2015-08-01

    Dissolved organic matter (DOM) in sediments, termed here sediment DOM, plays a variety of important roles in global biogeochemical cycling of carbon and nutrients as well as in the fate and transport of xenobiotics. Here we reviewed sediment DOM, including pore waters and water extractable organic matter from inland and coastal sediments, based on recent literature (from 1996 to 2014). Sampling, pre-treatment, and characterization methods for sediment DOM were summarized. The characteristics of sediment DOM have been compared along an inland to coastal ecosystems gradient and also with the overlying DOM in water column to distinguish the unique nature of it. Dissolved organic carbon (DOC) from inland sediment DOM was generally higher than coastal areas, while no notable differences were found for their aromaticity and apparent molecular weight. Fluorescence index (FI) revealed that mixed sources are dominant for inland sediment DOM, but marine end-member prevails for coastal sediment DOM. Many reports showed that sediments operate as a net source of DOC and chromophoric DOM (CDOM) to the water column. Sediment DOM has shown more enrichment of nitrogen- and sulfur-containing compounds in the elemental signature than the overlying DOM. Fluorescent fingerprint investigated by excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) further demonstrated the characteristics of sediment DOM lacking in the photo-oxidized and the intermediate components, which are typically present in the overlying surface water. In addition, the biogeochemical changes in sediment DOM and the subsequent environmental implications were discussed with the focus on the binding and the complexation properties with pollutants. PMID:25965884

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  15. The significance of GW-SW interactions for biogeochemical processes in sandy streambeds

    NASA Astrophysics Data System (ADS)

    Arnon, Shai; De Falco, Natalie; Fox, Aryeh; Laube, Gerrit; Schmidt, Christian; Fleckenstein, Jan; Boano, Fulvio

    2015-04-01

    Stream-groundwater interactions have a major impact on hyporheic exchange fluxes in sandy streambeds. However, the physical complexity of natural streams has limited our ability to study these types of interactions systematically, and to evaluate their importance to biogeochemical processes and nutrient cycling. In this work we were able to quantify the effect of losing and gaining fluxes on hyporheic exchange and nutrient cycling in homogeneous and heterogeneous streambeds by combining experiments in laboratory flumes and modeling. Tracer experiments for measuring hyporheic exchange were done using dyes and NaCl under various combinations of overlying water velocity and losing or gaining fluxes. Nutrient cycling experiments were conducted after growing a benthic biofilm by spiking with Sodium Benzoate (as a source of labile dissolved organic carbon, DOC) and measuring DOC and oxygen dynamics. The combination of experimental observations and modeling revealed that interfacial transport increases with the streambed hydraulic conductivity and proportional to the square of the overlying water velocity. Hyporheic exchange fluxes under losing and gaining flow conditions were similar, and became smaller when the losing or gaining flux increases. Increasing in streambed hydraulic conductivity led to higher hyporheic fluxes and reduction in the effects of losing and gaining flow conditions to constrain exchange. Despite the evident effect of flow conditions on hyporheic exchange, labile DOC uptake was positively linked to increasing overlying water velocity but was not affected by losing and gaining fluxes. This is because microbial aerobic activity was taking place at the upper few millimeters of the streambed as shown by local oxygen consumption rates, which was measured using microelectrodes. Based on modeling work, it is expected that GW-SW interaction will be more significant for less labile DOC and anaerobic processes. Our results enable us to study systematically the coupling between flow conditions and biogeochemical processes under highly controlled physical and chemical conditions and are expected to improve our understanding of nutrient cycling in streams.

  16. Hyporheic transport and biogeochemical reactions in pool-riffle systems under varying ambient groundwater flow conditions

    NASA Astrophysics Data System (ADS)

    Trauth, Nico; Schmidt, Christian; Vieweg, Michael; Maier, Uli; Fleckenstein, Jan H.

    2014-05-01

    At the interface between stream water, groundwater, and the hyporheic zone (HZ), important biogeochemical processes that play a crucial role in fluvial ecology occur. Solutes that infiltrate into the HZ can react with each other and possibly also with upwelling solutes from the groundwater. In this study, we systematically evaluate how variations of gaining and losing conditions, stream discharge, and pool-riffle morphology affect aerobic respiration (AR) and denitrification (DN) in the HZ. For this purpose, a computational fluid dynamics model of stream water flow is coupled to a reactive transport model. Scenarios of variations of the solute concentration in the upwelling groundwater were conducted. Our results show that solute influx, residence time, and the size of reactive zones strongly depend on presence, magnitude, and direction of ambient groundwater flow. High magnitudes of ambient groundwater flow lower AR efficiency by up to 4 times and DN by up to 3 orders of magnitude, compared to neutral conditions. The influence of stream discharge and morphology on the efficiency of AR and DN are minor, in comparison to that of ambient groundwater flow. Different scenarios of O2 and NO3 concentrations in the upwelling groundwater reveal that DN efficiency of the HZ is highest under low upwelling magnitudes accompanied with low concentrations of O2 and NO3. Our results demonstrate how ambient groundwater flow influences solute transport, AR, and DN in the HZ. Neglecting groundwater flow in stream-groundwater interactions would lead to a significant overestimation of the efficiency of biogeochemical reactions in fluvial systems.

  17. 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. PMID:25066365

  18. 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

  19. 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.

  20. 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.

  1. Mangrove forests: a potent nexus of coastal biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Barr, J. G.; Fuentes, J. D.; Shoemaker, B.; O'Halloran, T. L.; Lin, G., Sr.; Engel, V. C.

    2014-12-01

    Mangrove forests cover just 0.1% of the Earth's terrestrial surface, yet they provide a disproportionate source (~10 % globally) of terrestrially derived, refractory dissolved organic carbon to the oceans. Mangrove forests are biogeochemical reactors that convert biomass into dissolved organic and inorganic carbon at unusually high rates, and many studies recognize the value of mangrove ecosystems for the substantial amounts of soil carbon storage they produce. However, questions remain as to how mangrove forest ecosystem services should be valuated and quantified. Therefore, this study addresses several objectives. First, we demonstrate that seasonal and annual net ecosystem carbon exchange in three selected mangrove forests, derived from long-term eddy covariance measurements, represent key quantities in defining the magnitude of biogeochemical cycling and together with other information on carbon cycle parameters serves as a proxy to estimate ecosystem services. Second, we model ecosystem productivity across the mangrove forests of Everglades National Park and southern China by relating net ecosystem exchange values to remote sensing data. Finally, we develop a carbon budget for the mangrove forests in the Everglades National Park for the purposes of demonstrating that these forests and adjacent estuaries are sites of intense biogeochemical cycling. One conclusion from this study is that much of the carbon entering from the atmosphere as net ecosystem exchange (~1000 g C m-2 yr-1) is not retained in the net ecosystem carbon balance. Instead, a substantial fraction of the carbon entering the system as net ecosystem exchange is ultimately exported to the oceans or outgassed as reaction products within the adjacent estuary.

  2. 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.

  3. Ocean and Climate Studies: Linking Physical, Biogeochemical, and Ecosystems Research

    NASA Astrophysics Data System (ADS)

    Hazeleger, Wilco

    2008-06-01

    Climate Driving of Marine Ecosystem Changes (CLIMECO): Training for Young Marine Scientists; Brest, France, 21-24 April 2008; Earth system science has inherent interdisciplinary aspects. In the marine environment, biogeochemical, ecological, and physical climate science processes interact strongly. Examples of these interactions are feedbacks between variations in the marine carbon cycle and radiative forcing in the atmosphere, variations in the distribution of tuna related to El Niño-Southern Oscillation, and the distribution of nutrients in ventilated water masses that are subject to climate variability.

  4. 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 as TCE, PAH, PCB as well as riverine microbiological considerations. Such expansions meet the challenge of measuring much smaller concentrations compared to groundwater contaminant plumes. Further combinations of stable N, H, O, and S isotope systems would also help to resolve overlapping trends when only carbon isotopes are measured. Apart from combining traditional light stable isotope systems, addition of newly accessible isotope groups by multicollector ICP-MS (i.e. Fe, Cr, Zn) and radioisotope techniques can provide innovative tools for resolving gradients and their biogeochemical cycling within rivers.

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

    PubMed

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

    2013-10-15

    South Florida's watersheds have endured a century of urban and agricultural development and disruption of their hydrology. Spatial characterization of South Florida's estuarine and coastal waters is important to Everglades' restoration programs. We applied Factor Analysis and Hierarchical Clustering of water quality data in tandem to characterize and spatially subdivide South Florida's coastal and estuarine waters. Segmentation rendered forty-four biogeochemically distinct water bodies whose spatial distribution is closely linked to geomorphology, circulation, benthic community pattern, and to water management. This segmentation has been adopted with minor changes by federal and state environmental agencies to derive numeric nutrient criteria. PMID:23968989

  6. 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

  7. Operator-splitting errors in coupled reactive transport codes for flow and transport under atmospheric boundary conditions or layered soil profiles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One possible way of integrating subsurface flow and transport processes with (bio)geochemical reactions is to couple by means of an operator-splitting approach two completely separate codes, one for variably-saturated flow and solute transport and one for equilibrium and kinetic biogeochemical react...

  8. 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.

  9. Isotopes and Isoscapes: Tools for Testing Hydrological and Biogeochemical Models

    NASA Astrophysics Data System (ADS)

    Kendall, C.

    2014-12-01

    In the 21st century, the importance of high quality water resources cannot be overstated. New approaches are needed to pinpoint sources and ages of multiple contaminants, and to better understand critical hydrologic systems. Stable isotopic compositions of materials often show strong spatial and temporal distributions related to combinations of sources and processes. Isoscapes (spatial and/or temporal maps) of riverine and atmospheric data are increasingly being found to be effective means for assessing the effects of different land uses and biogeochemical processes on water resources. Hence, isotopes and isoscapes are a potentially powerful component of monitoring and assessment programs that are aimed at quantifying and mitigating alterations to environments from human activities (anthropogenic disturbances). Locations exhibiting unusually high rates of biogeochemical cycling or elevated pollution levels usually have distinctive isotopic compositions that are suggestive or diagnostic of specific reactions and pollution sources. Isotopes can be more effective at identifying hot spots and hot moments than concentrations alone because isotopic ratios may change even when concentrations do not. Hence, isotopes provide valuable additions to standard chemical and hydrological mass balance methods. This presentation will examine how the field of isotope hydrology has evolved over my 40+ year career as an isotope geochemist, highlight several exciting recent research thrusts, and share some thoughts on future research directions.

  10. The Impacts of Climate-Induced Drought on Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Peng, C.

    2014-12-01

    Terrestrial ecosystems and, in particular, forests exert strong controls on the global biogeochemical cycles and influence regional hydrology and climatology directly through water and surface energy budgets. Recent studies indicated that forest mortality caused by rising temperature and drought from around the world have unexpectedly increased in the past decade and they collectively illustrate the vulnerability of many forested ecosystems to rapid increases in tree mortality due to warmer temperatures and more severe drought. Persistent changes in tree mortality rates can alter forest structure, composition, and ecosystem services (such as albedo and carbon sequestration). Quantifying potential impacts of tree mortality on ecosystem processes requires research into mortality effects on carbon, energy, and water budgets at both site and regional levels. Despite recent progress, the uncertainty around mortality responses still limits our ability to predict the likelihood and anticipate the impacts of tree die-off. Studies are needed that explore tree death physiology for a wide variety of functional types, connect patterns of mortality with climate events, and quantify the impacts on carbon, energy, and water flux. In this presentation, I will highlight recent research progress, and identify key research needs and future challenges to predict the consequence and impacts of drought-induced large-scale forest mortality on biogeochemical cycles. I will focus on three main forest ecosystems (tropic rainforest in Amazon, temperate forest in Western USA, and boreal forest in Canada) as detailed case studies.

  11. 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).

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Atmospheric-induced variability of hydrological and biogeochemical signatures in the NW Alboran Sea. Consequences for the spawning and nursery habitats of European anchovy

    NASA Astrophysics Data System (ADS)

    Macías, D.; Catalán, I. A.; Solé, J.; Morales-Nin, B.; Ruiz, J.

    2011-12-01

    The north-western Alboran Sea is a highly dynamic region in which the hydrological processes are mainly controlled by the entrance of the Atlantic Jet (AJ) through the Strait of Gibraltar. The biological patterns of the area are also related to this variability in which atmospheric pressure distributions and wind intensity and direction play major roles. In this work, we studied how changes in atmospheric forcing (from high atmospheric pressure over the Mediterranean to low atmospheric pressure) induced alterations in the physical and biogeochemical environment by re-activating coastal upwelling on the Spanish shore. The nursery area of European anchovy ( Engraulis encrasicolus) in the NW Alboran Sea, confirmed to be the very coastal band around Malaga Bay, did not show any drastic change in its biogeochemical characteristics, indicating that this coastal region is somewhat isolated from the rest of the basin. Our data also suggests that anchovy distribution is tightly coupled to the presence of microzooplankton rather than mesozooplankton. Finally, we use detailed physical and biological information to evaluate a hydrological-biogeochemical coupled model with a specific hydrological configuration to represent the Alboran basin. This model is able to reproduce the general circulation patterns in the region forced by the AJ movements only including two variable external forcings; atmospheric pressure over the western Mediterranean and realistic wind fields.

  17. 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

  18. 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, the projected atmospheric CO{sub 2} concentrations range from about 550 ppmv (TOTEM, based on IPCC projected emissions) to 510 ppmv (IPCC projection) and to 460 ppmv (TOTEM, based on the Kyoto Protocol reduced emissions).

  19. 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 pollutants, and the flexibility of the model allows the user to apply current and future theories when analyzing the dynamics of pollutants in shallow surface flow through dense vegetation. The ultimate goal of the model's flexibility is to help researchers and decision-makers estimate optimal vegetation buffer characteristics (length, slope, vegetation) to achieve targeted runoff pollutant removal efficiency, while still considering the complex processes involved.

  20. 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, 4, 239

  1. 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, i.e. nutrient or C content, with regards to their mobility within local, regional and global biogeochemical cycles, including past, current and future rates of transfer. In this presentation, an initial framework illustrating a concept for linking soil properties and the mobility (lateral and vertical) of nutrients and organic matter critical for environmental conditions and services is developed.

  2. 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, i.e. nutrient or C content, with regards to their mobility within local, regional and global biogeochemical cycles, including past, current and future rates of transfer. In this presentation, an initial framework illustrating a concept for linking soil properties and the mobility (lateral and vertical) of nutrients and organic matter critical for environmental conditions and services is developed.

  3. Investigating Plot and Watershed Scale Hydrologic and Biogeochemical Responses

    NASA Astrophysics Data System (ADS)

    Easton, Z. M.; Walter, M. T.; Steenhuis, T. S.

    2010-12-01

    While there are numerous water quality studies at either the plot-, field- or watershed-scale, there are very few studies that integrate the hydrologic and biogeochemical responses across scales. A review of the literature reveals seemingly contradictory responses at the plot and watershed scales, e.g., in some cases pollutant concentrations decrease with increasing discharge at plot scales but increase with discharge at watershed scales. We investigate the biogeochemical responses of several plots and at a watershed outlet in a small mixed-use watershed in New York State. Runoff plots established along a gradient in topographic position and land use types distributed throughout the watershed were monitored for a seven year period and runoff, dissolved and particulate phosphorus (DP and PP, respectively) and sediment (TSS) were collected from storm 213 events. Flow, sediment, and phosphorus (P) were also measured at the watershed outlet for the same period and events. The watershed outlet response for DP, PP and sediment were characterized by a linear increases in concentration [mg/L] with increasing runoff [mm] (DP = 0.002(runoff) + 0.019, PP = 0.006(runoff) +0.006, and TSS = 1.055(runoff) + 2.389) while plot scale responses for DP, PP and TSS showed decreasing concentrations with increasing runoff losses. The specific runoff-concentration relationships varied but were generally characterized by a negative power-function-type decline with increasing runoff, although some landcover types (fertilized lawns) and constituents (esp. DP) exhibited more linear declines with increasing runoff, presumably a result of greater easily transported P at the soil surface. These plot scale results show the classical first flush response typical of bound pollutants (DP, PP, TSS), while the watershed clearly exhibits a concentrating effect with higher flows. However, these seemingly contradictory responses can be explained by considering the hydrologic spatio-temporal variability in the watershed. Plots located in hydrologically active areas, which produce more frequent and greater quantities of runoff with generally smaller average concentrations, explain the small runoff events with smaller concentrations at the watershed scale; areas with few runoff events and smaller runoff volumes with generally greater average concentrations were associated with large runoff events and correspond to higher concentrations at the watershed scale. These results show that the hydrologic and biogeochemical response can vary substantially at various scales, but are in fact related. This points towards a more parsimonious, accurate means of initializing watershed models and increasing their applicability by combining field monitoring with modeling in non-traditional ways.

  4. 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...

  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 incorporated into the modeling. In this case, an initially small population of slow growing sulfate reducers is active from the initiation of biostimulation. Three-dimensional, variably saturated flow modeling was used to address impacts of a falling water table during acetate injection. These impacts included a significant reduction in aquifer saturated thickness and isolation of residual reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted in higher concentrations of TEAP products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions; however, the ranges were sufficiently small to preserve general trends. Large computer memory and high computational performance were required to simulate the detailed coupled process models for multiple biogeochemical components in highly resolved heterogeneous materials for the 110-day field experiment and 50 days of post-biostimulation behavior. In this case, a highly-scalable subsurface simulator operating on 128 processor cores for 12 hours was used to simulate each realization. An equivalent simulation without parallel processing would have taken 60 days, assuming sufficient memory was available.

  7. 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.

  8. Comparative study of infrared techniques for fast biogeochemical sediment analyses

    NASA Astrophysics Data System (ADS)

    Hahn, A.; RosN, P.; Kliem, P.; Ohlendorf, C.; Zolitschka, B.

    2011-10-01

    Analysis of sediment samples in the visible to mid infrared (IR) region requires small amounts of sample material and enables rapid and cost efficient geochemical analysis of mineral and organic sediment components. Here we use geochemical properties (total organic and inorganic carbon, biogenic silica, total nitrogen) from the ICDP deep drilling project PASADO to compare three different IR spectroscopy techniques: Diffuse Reflectance Fourier Transform IR Spectrometry (DRIFTS), Attenuated Total Reflectance Fourier Transform IR Spectroscopy (ATR-FTIRS) and Visible Near IR Spectroscopy (VNIRS). ATR-FTIRS and VNIRS are more rapid techniques compared to DRIFTS. Results show that calibration models developed using DRIFTS are most robust (correlation coefficient: R = 0.92 for TIC, R = 0.84 for BSi, R = 0.97 for TOC, R = 0.95 for TN). However, good statistical performance was also obtained by using ATR-FTIRS and VNIRS. When time and costs are limiting factors, these tools may be given preference for rapid biogeochemical screening.

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

    PubMed Central

    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. PMID:25083171

  10. 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. PMID:25083171

  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. Research highlights: elucidation of biogeochemical factors influencing methylmercury production.

    PubMed

    Erickson, Paul R; Lin, Vivian S

    2015-10-01

    Coal combustion and other human activities release inorganic mercury into the atmosphere at levels far greater than emissions from natural sources, significantly perturbing the global mercury cycle. Subsequent biogeochemical transformation of inorganic mercury to highly toxic methylmercury allows this heavy metal pollutant to enter the food web, where it bioaccumulates and can have severe impacts on animal and human populations. This Highlight features recent articles that examine in detail the effects of nutrient availability on the methylation-demethylation activity of microorganisms living in sediment with mercury contamination. By investigating differences in levels of sulfate, iron, organic matter, and other environmental factors, this research provides insight into the conditions that may favor methylmercury formation and thereby better inform remediation efforts in the future. PMID:26376357

  13. Sensitivity analysis of global terrestrial biogeochemical cycling model

    SciTech Connect

    Chambers, J.Q.; Kercher, J.R. Lawrence Livermore National Lab., CA )

    1993-06-01

    We are developing a global model of terrestrial productivity and biogeochemical cycling (TERRA) designed to be a component of an Earth System Model being developed at LLNL. An initial version of TERRA incorporating five state variables has been calibrated to 17 vegetation types. During sensitivity analysis, model parameters were individually varied by 10% and the model was run to steady-state. Total system response was found to be most sensitive to parameters affecting soil moisture which, in turn, affects soil respiration rate. Parameters describing optimum soil moisture for soil respiration rate, field capacity, pore volume, root depth and soil organic matter (SOM) decomposition rate, all exhibited significant sensitivity. These findings underscore the importance of the soil system in descriptions of ecosystems dynamics. Future versions of TERRA will divide the soil profile into a series of horizontal layers and include more detailed descriptions of SOM.

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  16. 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.

  17. COUPLED REACTIVE TRANSPORT MODELING BASED ON THE NEW BIOGEOCHEMICAL CODE HP1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The migration of many naturally occurring elements and contaminants in the subsurface is affected by a multitude of complex, interactive physical, chemical, mineralogical, geological, and biological processes. Recently, a new comprehensive simulation tool HP1 (HYDRUS1D-PHREEQC) was developed by cou...

  18. 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...

  19. Scaling analysis of biogeochemical parameters in coastal waters

    NASA Astrophysics Data System (ADS)

    Zongo, Sylvie; Schmitt, Franois

    2010-05-01

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

  20. Biogeochemical consequences of an oxygenated intrusion into an anoxic fjord

    PubMed Central

    2014-01-01

    Background This paper is based on the studies of the biogeochemical structure of the water column in the anoxic Fjord Hunnbunn (south-eastern Norway) performed in 2009, 2011 and 2012. This Fjord is an enclosed basin of brackish water separated by a narrow and shallow outlet to the sea with a permanently anoxic layer. We show how an oxygenated intrusion could lead to both positive and negative effects on the ecosystem state in Hunnbunn due to a change in the biogeochemical structure. Results During the stratified periods in 2009 and 2012 the anoxic layer amounted to approximately 10% of the total water volume in the Fjord, while dissolved oxygen (DO) was present in 80-90% of the water. In the autumn of 2011 the water chemistry structure observed in Fjord Hunnbunn was clearly affected by a recent oxygenated intrusion defined by abnormal salinity patterns. This led to a shift of the DO boundary position to shallower depths, resulting in a thicker anoxic layer comprising approximately 40% of the total water volume, with DO present only in approximately 60% of the water. The oxygenated water intrusions led to a twofold decrease of the concentrations of hydrogen sulphide, ammonia, phosphate and silicate in the deep layers with a simultaneous increase of these nutrients and a decrease of the pH level in the surface layers. The concentrations of manganese, iron, and mercury species changed dramatically and in particular revealed a significant supply of iron and methylmercury to the water column. Conclusions Oxic water intrusions into anoxic fjords could lead not only to the flushing of the bottom anoxia, but to a dispersal of sulphidic and low oxygen conditions to the larger bottom area. The elevation of the hydrogen sulphide to the shallower layers (that can be rapidly oxidized) is accompanied by the appearance in the subsurface water of methylmercury, which is easily accumulated by organisms and can be transported to the surrounding waters, affecting the ecosystem over a larger area. PMID:24872727

  1. 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.

  2. 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.

  3. Trimethylbenzoic acids as metabolite signatures in the biogeochemical evolution of an aquifer contaminated with jet fuel hydrocarbons

    NASA Astrophysics Data System (ADS)

    Namocatcat, J. A.; Fang, J.; Barcelona, M. J.; Quibuyen, A. T. O.; Abrajano, T. A.

    2003-12-01

    Evolution of trimethylbenzoic acids in the KC-135 aquifer at the former Wurtsmith Air Force Base (WAFB), Oscoda, MI was examined to determine the functionality of trimethylbenzoic acids as key metabolite signatures in the biogeochemical evolution of an aquifer contaminated with JP-4 fuel hydrocarbons. Changes in the composition of trimethylbenzoic acids and the distribution and concentration profiles exhibited by 2,4,6- and 2,3,5-trimethylbenzoic acids temporally and between multilevel wells reflect processes indicative of an actively evolving contaminant plume. The concentration levels of trimethylbenzoic acids were 3-10 orders higher than their tetramethylbenzene precursors, a condition attributed to slow metabolite turnover under sulfidogenic conditions. The observed degradation of tetramethylbenzenes into trimethylbenzoic acids obviates the use of these alkylbenzenes as non-labile tracers for other degradable aromatic hydrocarbons, but provides rare field evidence on the range of high molecular weight alkylbenzenes and isomeric assemblages amenable to anaerobic degradation in situ. The coupling of actual tetramethylbenzene loss with trimethylbenzoic acid production and the general decline in the concentrations of these compounds demonstrate the role of microbially mediated processes in the natural attenuation of hydrocarbons and may be a key indicator in the overall rate of hydrocarbon degradation and the biogeochemical evolution of the KC-135 aquifer.

  4. Trimethylbenzoic acids as metabolite signatures in the biogeochemical evolution of an aquifer contaminated with jet fuel hydrocarbons.

    PubMed

    Namocatcat, J A; Fang, J; Barcelona, M J; Quibuyen, A T O; Abrajano, T A

    2003-12-01

    Evolution of trimethylbenzoic acids in the KC-135 aquifer at the former Wurtsmith Air Force Base (WAFB), Oscoda, MI was examined to determine the functionality of trimethylbenzoic acids as key metabolite signatures in the biogeochemical evolution of an aquifer contaminated with JP-4 fuel hydrocarbons. Changes in the composition of trimethylbenzoic acids and the distribution and concentration profiles exhibited by 2,4,6- and 2,3,5-trimethylbenzoic acids temporally and between multilevel wells reflect processes indicative of an actively evolving contaminant plume. The concentration levels of trimethylbenzoic acids were 3-10 orders higher than their tetramethylbenzene precursors, a condition attributed to slow metabolite turnover under sulfidogenic conditions. The observed degradation of tetramethylbenzenes into trimethylbenzoic acids obviates the use of these alkylbenzenes as non-labile tracers for other degradable aromatic hydrocarbons, but provides rare field evidence on the range of high molecular weight alkylbenzenes and isomeric assemblages amenable to anaerobic degradation in situ. The coupling of actual tetramethylbenzene loss with trimethylbenzoic acid production and the general decline in the concentrations of these compounds demonstrate the role of microbially mediated processes in the natural attenuation of hydrocarbons and may be a key indicator in the overall rate of hydrocarbon degradation and the biogeochemical evolution of the KC-135 aquifer. PMID:14607476

  5. 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.

  6. 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. PMID:15134877

  7. Winners and losers: Ecological and biogeochemical changes in a warming ocean

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, S.; Scott, J. R.; Follows, M. J.

    2013-04-01

    We employ a marine ecosystem model, with diverse and flexible phytoplankton communities, coupled to an Earth system model of intermediate complexity to explore mechanisms that will alter the biogeography and productivity of phytoplankton populations in a warming world. Simple theoretical frameworks and sensitivity experiments reveal that ecological and biogeochemical changes are driven by a balance between two impacts of a warming climate: higher metabolic rates (the "direct" effect), and changes in the supply of limiting nutrients and altered light environments (the "indirect" effect). On globally integrated productivity, the two effects compensate to a large degree. Regionally, the competition between effects is more complicated; patterns of productivity changes are different between high and low latitudes and are also regulated by how the supply of the limiting nutrient changes. These complex regional patterns are also found in the changes to broad phytoplankton functional groups. On the finer ecological scale of diversity within functional groups, we find that ranges of some phytoplankton types are reduced, while those of others (potentially minor players in the present ocean) expand. Combined change in areal extent of range and in regionally available nutrients leads to global "winners and losers." The model suggests that the strongest and most robust signal of the warming ocean is likely to be the large turnover in local phytoplankton community composition.

  8. Skill assessment of a high-resolution global marine biogeochemical model

    NASA Astrophysics Data System (ADS)

    Lovato, Tomas; Storto, Andrea; Vichi, Marcello; Masina, Simona; Santoleri, Rosalia; Sathyendranath, Shubha

    2015-04-01

    Here we present the skill assessment of the PELAgic biogeochemistry for Global Ocean Simulations (PELAGOS) model against different observational products, encompassing gridded climatological fields, satellite and in-situ datasets. PELAGOS is a coupling between the NEMO general circulation model and the Biogeochemical Flux Model (BFM). In particular, BFM is based on a biomass continuum description of the marine ecosystem and it solves the fluxes of multi-nutrients among selected biological functional groups representing the major components of the lower trophic levels. We illustrate the model validation for major inorganic nutrients (nitrate, phosphate, silica), oxygen, and chlorophyll utilizing a multi-decade (1980-2013) hindcast experiment realized at 1/4° horizontal resolution in the framework of MyOcean project. Model-data residuals were analysed to asses the reliability of time-mean spatial patterns and seasonal cycles at both global and regional scales and, where in-situ data from sustained observations are available, long-term dynamics were also addressed. Overall performances of the model were satisfactory, especially for inorganic nutrients and oxygen spatial distributions. Although the timing of the phytoplankton dynamics is well reproduced in some oceanic regions, a systematic bias affected the simulated amplitude of chlorophyll in comparison to the ESA-CCI satellite observations.

  9. The Biogeochemical Role of Baleen Whales and Krill in Southern Ocean Nutrient Cycling

    PubMed Central

    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. PMID:25469984

  10. Reservoir and contaminated sediments impacts in high-Andean environments: Morphodynamic interactions with biogeochemical processes

    NASA Astrophysics Data System (ADS)

    Escauriaza, C. R.; Contreras, M. T.; Müllendorff, D. A.; Pasten, P.; Pizarro, G. E.

    2014-12-01

    Rapid changes due to anthropic interventions in high-altitude environments, such as the Altiplano region in South America, require new approaches to understand the connections between physical and biogeochemical processes. Alterations of the water quality linked to the river morphology can affect the ecosystems and human development in the long-term. The future construction of a reservoir in the Lluta river, located in northern Chile, will change the spatial distribution of arsenic-rich sediments, which can have significant effects on the lower parts of the watershed. In this investigation we develop a coupled numerical model to predict and evaluate the interactions between morphodynamic changes in the Lluta reservoir, and conditions that can potentially desorb arsenic from the sediments. Assuming that contaminants are mobilized under anaerobic conditions, we calculate the oxygen concentration within the sediments to study the interactions of the delta progradation with the potential arsenic release. This work provides a framework for future studies aimed to analyze the complex connections between morphodynamics and water quality, when contaminant-rich sediments accumulate in a reservoir. The tool can also help to design effective risk management and remediation strategies in these extreme environments. Research has been supported by Fondecyt grant 1130940 and CONICYT/FONDAP Grant 15110017

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  12. Performance and results of the high-resolution biogeochemical model PELAGOS025 within NEMO

    NASA Astrophysics Data System (ADS)

    Epicoco, I.; Mocavero, S.; Macchia, F.; Vichi, M.; Lovato, T.; Masina, S.; Aloisio, G.

    2015-12-01

    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 physical ocean model NEMO and the 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 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.

  13. 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...

  14. 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 of the Mistelbach, a second order stream running through agricultural land near the city of Bayreuth. Radon was measured at 1-3 locations on two occasions and at 5 different depths (-5 to-25 cm). Geochemical parameters NO3-, NO2-, SO4-, Fe2+, CO2 and CH4 was measured in peepers with a vertical resolution of 1-2 cm to a depth of 50 cm as well as in the same samples as the Rn. Groundwater activities were measured in incubation experiments and by the deepest sampling point in the hyporheic zone. The results showed that there was a clear dependence of biogeochemical processes on the residence time. Nitrate was reduced within 2 days, while sulfate reduction began after 5 days while Fe2+ was produced after 10 days. CH4 production occurred at >20 days, which is above the upper limit of residence time detection using Rn. Obviously, biogeochemical processes are controlled by the balance between reaction rates and advection rates in the hyporheic zone, and that the ratio of these rates (i.e. the Damköhler number) will control the efficiency of material processing. The uncertainty in the method increases towards longer residence times, as secular equilibrium activities and measured activities converge. It is also influenced by the heterogeneity of emanation in the sediments. However, research within the hyporheic zone is usually focused on residence times shorter than two weeks, and emanation can be quantified in the laboratory. Thus Rn appears well suited to the study of time scales over which biogeochemical processes occur in the hyporheic zone.

  15. Major outputs of the recent multidisciplinary biogeochemical researches undertaken in the Aegean Sea

    NASA Astrophysics Data System (ADS)

    Lykousis, V.; Chronis, G.; Tselepides, A.; Price, N. B.; Theocharis, A.; Siokou-Frangou, I.; Van Wambeke, F.; Danovaro, R.; Stavrakakis, S.; Duineveld, G.; Georgopoulos, D.; Ignatiades, L.; Souvermezoglou, A.; Voutsinou-Taliadouri, F.

    2002-06-01

    The main outputs of a multidisciplinary and integrated studies are summarised. The results incorporate the latest biogeochemical researches, at basin scale, in the Aegean Sea (including thermohaline circulation studies, SPM dynamics, mass and energy fluxes, acknowledge biochemical processes in the euphotic and the benthic layer and benthic response to downward fluxes). The data were acquired within five (seasonal) research cruises, during 1997-1998. Data analysis and evaluation hence provided important new information on the functional processes of the Aegean ecosystem. In terms of water circulation, no new deep water formation in the Aegean Sea was observed, during 1997-1998, but rather intermediate water, due mainly to the mild winter conditions. All the biochemical parameters of the euphotic zone (nutrients, Particulate Organic Carbon (POC), chlorophyll- a, phytoplankton, primary and bacterial production), although high in the N. Aegean Sea reflect clearly the highly oligotrophic character of the Aegean Sea. In the N. Aegean, microbial food web was the main pathway of carbon, whereas in the S. Aegean, the food web could be classified as multivorous. An important Black Sea Water (BSW) signal was observed in the dissolved phase; this was especially pronounced in the Dissolved Organic Carbon (DOC), Mn and to a lesser degree to Cd, Cu and Ni concentrations. The downward material fluxes are higher in the N. Aegean, relative to the S. Aegean. Substantially higher values of near-bottom mass fluxes were measured in the deep basins of the N. Aegean, implying significant deep lateral fluxes of POM. The N. Aegean could be classified as a "continental margin" ecosystem, whilst the S. Aegean is a typical "oceanic margin" environment. There is a close relationship and, consequently, coupling between the near-bottom mass fluxes and the accumulation rates of organic matter (OM), with the near-bottom mineralisation, bioturbation, redox potential, oxygen consumption rates, the sediment microbiological and enzymatic activity and the meio-macro- and mega fauna abundances in the Aegean Sea. The N. Aegean is characterised by higher fluxes of labile POC and higher rates of benthic mineralisation and displays much higher benthic productivity and diversity relatively to the S. Aegean. The deep isolated N. Aegean basins should be regarded as "hot spots" of organic matter accumulation, benthic abundances and diversity. There is a general N-S gradient in the biogeochemical and benthic processes in the Aegean that is especially pronounced during winter-early spring, implied mainly by the of Black Sea Water (BSW) inflow (through the dissolved phase) and the lateral marginal inputs.

  16. Do We Need to Account for Variable Microbial Nitrogen-Use Efficiency in Biogeochemical Models?

    NASA Astrophysics Data System (ADS)

    Mooshammer, M.; Wanek, W.; Wild, B.; Hofhansl, F.; Richter, A.

    2012-12-01

    The carbon-use efficiency (CUE; or growth yield) of heterotrophic microbial communities is one of the key factors determining microbial growth and ultimately carbon sequestration. Microbial CUE is known to be controlled by resource stoichiometry, i.e. CUE increases with nutrient availability (at low C:N ratio) and decreases when nutrients become limiting (at high C:N ratio). In contrast, very little is known about microbial nitrogen-use efficiency (NUE), i.e. the ratio of N used for growth over N uptake. Specifically, empirical data on NUE of terrestrial decomposers is lacking and NUE has rarely been explored in biogeochemical models. Microbial NUE is at the core of N cycling by reflecting the partitioning of N taken up between N incorporated into biomass and N recycled to the environment. It is therefore likely that NUE ultimately determines N sequestration. Furthermore, NUE is tightly coupled to the C cycle because C and N are processed together through the uptake of organic N compounds. Here we report a novel experimental approach to investigate the role of NUE in heterotrophic microbial communities and study how NUE is controlled during organic matter decomposition. Experiments with plant litter and soil demonstrated that microbial communities were remarkably efficient in assimilating organic N in litter (NUE 80-98%) and some soils (30-95%). Microbial NUE was strongly controlled by resource C:N ratio, i.e. it increased with increasing C:N of organic matter. This clearly demonstrates that NUE is not constant but varies with microbial N demand and N availability. Given that microbial communities are homeostatic regarding resource C:N, variations in microbial CUE and NUE with resource stoichiometry determine the mineralization of organic C and organic N. We therefore suggest that accounting for variable NUE and CUE in response to resource stoichiometry could improve current biogeochemical models. We provide here empirical data showing a statistical relationship between resource C:N and NUE and a theoretical framework for the implementation of microbial NUE in numerical models.

  17. 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. PMID:22926879

  18. Element distribution over the surface of fish scales and its connection to the geochemical environment of habitats: a potential biogeochemical tag.

    PubMed

    Wang, TsingHai; Lai, Yan-Chen; Chiang, Chia-Che; Cheng, Yu-Rong; Hsieh, Yi-Kong; Wang, Chu-Fang

    2016-03-01

    The elemental content of fish scales is known to be a reliable biogeochemical tag for tracing the origin of fishes. In this study, this correlation is further confirmed to exist on the surface of fish scales using a novel environmental analytical method, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), which bypasses several complicated sample preparation procedures such as acid digestion and pre-concentration. The results suggest that the elemental ratios of Sr/Ca, Ba/Ca, and Mn/Ca on the surface of fish scales are strongly correlated with the geochemical environment of their original habitat. This correlation is further demonstrated to be sensitive to variation of water in the habitat due to the adsorbed inorganic ions. In this sense, the limitation of fish scales as a biogeochemical tag is the sensitivity of LA-ICP-MS toward the studied elements. Graphical abstract Illustration of the connection between element distribution pattern over the surface of fish scales and biogeochemical environment of its habitat. PMID:26899028

  19. 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 bacteria uptake of ammonia is obtained by, UB=UB∗, bacteria uptake of DOM, FB=U+UB, bacteria respiration, SB=RBFB{r_b}/{1-r_b}, remineralization by bacteria, EB=-UB. CDOM photolysis (Bissett et al., 1999a): UVLDOC=a(410)×RtUVLDOC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, UVSDOC=a(410)×RtUVSDOC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, UVLDIC=a(410)×RtUVLDIC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, UVSDIC=a(410)×RtUVSDIC×{PAR(0)}/{410}×exp∫z0Kd(300)dz, a(410)=acdoc∗×CLDOC, a(410)=acdoc∗×CSDOC, Kd(300)=[a(410)+a(410)]×exp[0.0145×(410-300)]+0.154. The dissolution rate for biogenic silica (Jiang et al., 2003): D=(0.19T/25+0.01)×exp(0.069(T-25)). The air-sea flux of CO2 is calculated using the transfer velocity-wind speed relationships from Wanninkhof (1992): air-sea CO flux=0.31U2(660S{()sea-()air}, where U is the wind speed at sea surface and Sc is the Schmidt number for CO2 that can be calculated as: Sc=2073.1-125.62T+3.6276T2-0.043219T3, S is the solubility of CO2 and (pCO2)air is the partial pressure of CO2 in the air. In the model, we set a spatially uniform distribution of (pCO2)air observed at the Mauna Loa Observatory (Keeling et al., 1976).Dissolved oxygen (DO) is modeled using constant oxygen-to-nitrate and oxygen-to-ammonium ratios. At the surface, air-sea exchange of O2 is calculated as: O flux=0.31U2(660(DOsat-DO), where DOsat is the saturation concentration of DO calculated from temperature and salinity. So2 is the Schmidt number for O2 that can be calculated as follows: So2=1638.0-81.83T+1.483T2-0.008004T3.

  20. 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

    On April 20, 2010, the drilling rig Deepwater Horizon exploded in the Gulf of Mexico, resulting in the release of approximately 5 million barrels of crude oil into the environment. Oil and its associated trace metals have been demonstrated to have a detrimental effect on coastal wetland ecosystems. Wetlands are particularly susceptible to oil contamination because they are composed largely of fine-grained sediments, which have a high capacity to adsorb organic matter and metals. The biogeochemical cycling of trace metals can be strongly influenced by microbial activity, specifically those of sulfate- and iron-reducing bacteria. Microbial activity may be enhanced by an increase in amounts of organic matter such as oil. This research incorporates an assessment of levels of trace metals and associated biogeochemical changes from ten coastal marshes in Alabama, Mississippi, and Louisiana. These sampling sites range in their pollution levels from pristine to highly contaminated. A total digestion analysis of wetland sediments shows higher concentrations of certain trace metals (e.g., Ni, Cu, Pb, Zn, Sr, Co, V, Ba, Hg, As) in heavily-oiled areas compared to less-affected and pristine sites. Due to chemical complexation among organic compounds and metals, crude oils often contain elevated levels (up to hundreds of mg/kg) of trace metals At the heavily-oiled Louisiana sites (e.g., Bay Jimmy, Bayou Dulac, Bay Batiste), elevated levels of metals and total organic carbon have been found in sediments down to depths of 30 cm. Clearly the contamination is not limited to shallow sediments and oil, along with various associated metals, may be invading into deeper (pre-industrial) portions of the marsh sediments. Pore-waters extracted from contaminated sediments are characterized by very high levels of reduced sulfur (up to 80 mg/kg), in contrast to fairly low ferrous iron concentrations (<0.02 mg/kg). The influx of oil into the wetlands might provide the initial substrate and 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.

  1. 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.

  2. 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.

  3. 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 biogeochemical properties. The variability in main thermocline temperature and nitrate in this synoptic spatial survey spans the range observed in these quantities in the 10-year time series available at BATS to date (1988-1998).

  4. 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 biogeochemical properties. The variability in main thermocline temperature and nitrate in this synoptic spatial survey spans the range observed in these quantities in the 10-year time series available at BATS to date (1988-1998).

  5. Biogeochemical value of managed realignment, Humber estuary, UK.

    PubMed

    Andrews, J E; Burgess, D; Cave, R R; Coombes, E G; Jickells, T D; Parkes, D J; Turner, R K

    2006-12-01

    We outline a plausible, albeit extreme, managed realignment scenario ('Extended Deep Green' scenario) for a large UK estuary to demonstrate the maximum possible biogeochemical effects and economic outcomes of estuarine management decisions. Our interdisciplinary approach aims to better inform the policy process, by combining biogeochemical and socioeconomic components of managed realignment schemes. Adding 7494 ha of new intertidal area to the UK Humber estuary through managed realignment leads to the annual accumulation of a 1.2 x 10(5) t of 'new' sediment and increases the current annual sink of organic C and N, and particle reactive P in the estuary by 150%, 83% and 50%, respectively. The increase in intertidal area should also increase denitrification. However, this positive outcome is offset by the negative effect of enhanced greenhouse gas emissions in new marshes in the low salinity region of the estuary. Short-term microbial reactions decrease the potential benefits of CO(2) sequestration through gross organic carbon burial by at least 50%. Net carbon storage is thus most effective where oxidation and denitrification reactions are reduced. In the Humber this translates to wet, saline marshes at the seaward end of estuaries. Cost-benefit analysis (CBA) was used to determine the economic efficiency of the Extended Deep Green managed realignment. When compared to a 'Hold-the-Line' future scenario, i.e. the present state/extent of sea defences in the estuary, the CBA shows that managed realignment is cost effective when viewed on >25 year timescales. This is because capital costs are incurred in the first years, whereas the benefits from habitat creation, carbon sequestration and reduced maintenance costs build up over time. Over 50- and 100-year timescales, the Extended Deep Green managed realignment scenario is superior in efficiency terms. The increased sediment accumulation is also likely to enhance storage of contaminant metals. In the case of Cu, a metal that currently causes significant water quality issues, Cu removal due to burial of suspended sediment in realigned areas translates to a value of approximately pounds sterling 1000 a(-1) (avoided clean up costs). Although this is not formally included in the CBA it illustrates another likely positive economic outcome of managed realignment. Although we focus on the Humber, the history of reclamation and its biogeochemistry is common to many estuaries in northern Europe. PMID:16996577

  6. Spatial heterogeneity in biogeochemical transport on Arctic hill slopes

    NASA Astrophysics Data System (ADS)

    Risser, R.; Harms, T.; Jones, J.

    2013-12-01

    Water tracks, saturated regions of the hill slope in permafrosted Arctic catchments, likely deliver the majority of water entering streams in these regions, and may play a central role in delivery of nutrients. Fate of dissolved nutrients and carbon as they are transported in water tracks has a substantial effect on stream ecosystems, as water tracks may cover up to 35% of the catchment land area. Water tracks are distinguished from adjacent areas of the hillslope by higher rates of hydrologic transport, greater woody biomass, and increased pools of nutrients. Substantial spatial heterogeneity within and between water tracks may influence their role in transfer of materials between the terrestrial and aquatic landscape. We examined spatial variability of hydrologic and chemical characteristics within and between water tracks in the Kuparuk Basin of northern Alaska to increase understanding of the factors influencing nutrient export from arctic catchments. We studied a sedge-dominated water track with perennial surface water flow with shrub-dominated water tracks containing intermittent surface flow. Nominal transit times of water in the perennial site was 5 hours, compared to 15.5 h in an ephemeral track over a 50 meter reach, indicating substantial variation in water residence time and opportunity for biogeochemical reaction across sites. We evaluated spatial heterogeneity in biogeochemical characteristics within 25-m reaches at each site with a grain size of 10 m. Dissolved CH4 concentration was elevated above atmospheric equilibrium only at the perennial water track, where CH4 concentration varied by more than 15-fold within the water track, indicating hot spots of anaerobic microbial activity. Dissolved CO2 concentration was 9 times greater on average at the perennial water track, compared to the ephemeral site, suggesting that continuous water flow supports more rapid microbial activity. CO2 concentration was also more variable in the perennial water track, with a CV of 64% compared to 11% in an ephemeral water track. Despite spatial heterogeneity in dissolved gas concentrations within the perennial site, NH4+ concentration in surface and soil water was less variable, with a CV of 38%. In contrast, NH4+ concentration was more variable (CV=41%) than dissolved gases within the ephemeral site, and mean concentration was 2 times greater than at the perennial site, suggesting less active biological retention of nitrogen at the ephemeral site. These differences in dissolved gases and nutrient concentrations among water tracks indicate that nutrient processing during hydrologic transport on hill slopes varies across the catchment, which will likely result in spatially heterogeneous responses of elemental cycles in response to permafrost loss.

  7. 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. Community building through social activities and scientific forums is a priority in both the undergraduate and graduate programs. In addition, entering Ph.D. students build cohort identity by taking a course that introduces them to BRIE faculty and research facilities through hands-on laboratory and field-based research activities. The BRIE undergraduate summer internship program has provided interdisciplinary research opportunities for a total of 35 students over the past five summers. This program aims to recruit students to the Ph.D. program, and at present, two Ph.D. students have entered this way. Our efforts have focused on attracting students from under-represented groups. Diversity in this program has been above national norms: and summer students have include 10 (29 %) African-American or Hispanic-American students, and 25 (over 70 %) females. The Ph.D. students and graduates are 50% female, with three students from minority populations.

  8. Suspended Particles: Their Role in Estuarine Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Turner, A.; Millward, G. E.

    2002-12-01

    Suspended particles are instrumental in controlling the reactivity, transport and biological impacts of substances in aquatic environments, and provide a crucial link for chemical constituents between the water column, bed sediment and food chain. This article reviews the role of suspended particles in the chemical and biological cycling of trace constituents (trace metals, organo-metallic compounds and hydrophobic organic micropollutants; HOMs) in estuaries, with particular emphasis on the effects of and changes to particle reactivity and composition. The partitioning (or distribution coefficient, KD ) and bioavailability of chemical constituents, and assimilation efficiency (AE) of such by bivalve suspension feeders, are identified as key parameters requiring definition for accurate biogeochemical modelling, and the discussion centres around the determination of and controls on these parameters. Particle-water interactions encompass a variety of physical, biological, electrostatic and hydrophobic effects, and are largely dependent on the character and concentration of suspended particles and salinity. The salinity-dependence results from the competing and complexing effects of seawater ions for trace metals, and the compression of water in the presence of dissolved seawater ions and consequent salting out of neutral solute (HOMs, organo-metallic compounds and some trace metal complexes). The extent of biological solubilization of chemical constituents from suspended particles is dependent on the nature of chemical components of the gastro-intestinal environment and their interactions with ingested particles, and the physiological (e.g. gut passage time) and chemical (e.g. redox conditions and pH) constraints imposed on these interactions. Generally, chemicals that associate with fine, organic-rich particles (or, for some HOMs, fine inorganic particles), and desorb at pH 5-6 and/or complex with digestive enzymes or surfactants are most readily solubilized in the gut. The extent of assimilation of solubilized chemical is then determined by its ability to pass the gut lining and partition into cytosolic material. In practice, KD and AE are determined experimentally by means of radiotracers added to contained suspensions or mesocosms, while operational measurement of bioavailability relies on in vitro chemical or biological (enzymatic) extraction of particles. What is lacking, however, and is identified as an ultimate goal of future research, is the ability to predict these parameters from theoretical principles and thermodynamic constants. Since many of the inherent interactions and mechanisms are controlled by particle composition and reactivity, a more immediate objective would be better characterization of the biogeochemical properties of suspended particles themselves. This includes chemical resolution of the bulk organic matter, definition of the abundance and synergistic effects of component sorbent phases, and determination of the effects of particle-seawater ion interactions on the reactivity of the particle surface.

  9. 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 cycle models. Nevertheless, more research is needed to develop tools to decompose NPP and transient dynamics of the modeled carbon cycle into traceable components for structural analysis of land models. PMID:23505019

  10. 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.

  11. Applications of Geostatistics to Data Assimilation in Biogeochemical Models

    NASA Astrophysics Data System (ADS)

    Michalak, A. M.; Mueller, K. L.; Yadav, V.; Alkhaled, A. A.; Zhou, Y.; Gourdji, S. M.; Huntzinger, D. N.; Hirsch, A. I.; Andrews, A. E.; Wofsy, S. C.

    2008-12-01

    The field of geostatistics offers a rich set of tools for analyzing parameters that display spatial and/or temporal autocorrelation. Historically, these methods have been used primarily for interpolating sparse measurements of in situ data. More recently, however, methods based on geostatistical framework have used in an increasing numbers of areas of earth science. This presentation will discuss a number of recent developments in geostatistics relevant to data assimilation in biogeochemical models. The overall goal of the presentation is to emphasize the need to explicitly account for spatial and temporal covariance in sampled data, and the need to translate available data between relevant spatial and temporal scales. The emphasis will be on presenting a common framework that can be used to develop problem-specific approaches. The presented examples will include (i) the identification of environmental parameters controlling observed variability in eddy covariance flux measurements, (ii) downscaling and upscaling observed spatial variability across spatial scales, (iii) geostatistical inverse modeling for constraining carbon fluxes at fine spatial resolutions, and (iv) merging of flux data and atmospheric concentration measurements for constraining parameters in biospheric models.

  12. Biogeochemical Approaches to Assess PAH Pollution in an Urban Waterway.

    PubMed

    Cheng, Xianhao; Forsythe, Jennifer; Peterkin, Earl

    2015-12-01

    Biogeochemical approaches were applied to enhance the study on polycyclic aromatic hydrocarbon (PAH) pollution in an urban waterway. Chemical characterizations of PAHs in the studied area were identified, geochemical factors were revealed, and related mechanisms were discussed. It was found that, during summer, an early diagenetic process in the sediment could play a major role for the existence of high PAH concentrations, especially high molecular weight PAHs (≥ 4 rings), in the water column and sediment porewater. This effect could vary with tidal cycling, and higher PAH concentration in the water column would be expected during low tide. Other potential pollution sources were also evaluated in the studied creek. Results showed that pyrogenic sources dominated in the creek, generally. Nevertheless, petroleum products from a metal recycling plant could be an important point source to the waterway during wet weather. Comparing with previous studies in other waterways of the same watershed and published literature suggested that the limited toxicity to the ecosystem was only detected in sediments. More information needs to be collected during low tide for a more objective evaluation of PAH toxicity in the creek. PMID:26579786

  13. Biogeochemical Processes Controlling Microbial Reductive Precipitation of Radionuclides

    SciTech Connect

    Fredrickson, James K.; Brooks, Scott C.

    2004-03-17

    This project is focused on elucidating the principal biogeochemical reactions that govern the concentrations, chemical speciation, and distribution of the redox sensitive contaminants uranium (U) and technetium (Tc) between the aqueous and solid phases. The research is designed to provide new insights into the under-explored areas of competing geochemical and microbiological oxidation-reduction reactions that govern the fate and transport of redox sensitive contaminants and to generate fundamental scientific understanding of the identity and stoichiometry of competing microbial reduction and geochemical oxidation reactions. These goals and objectives are met through a series of hypothesis-driven tasks that focus on (1) the use of well-characterized microorganisms and synthetic and natural mineral oxidants, (2) advanced spectroscopic and microscopic techniques to monitor redox transformations of U and Tc, and (3) the use of flow-through experiments to more closely approximate groundwater environments. The results are providing an improved understanding and predictive capability of the mechanisms that govern the redox dynamics of radionuclides in subsurface environments. For purposes of this poster, the results are divided into three sections: (1) influence of Ca on U(VI) bioreduction; (2) localization of biogenic UO{sub 2} and TcO{sub 2}; and (3) reactivity of Mn(III/IV) oxides.

  14. Controls on Biogeochemical Cycling in a Turfgrass Ecosystem

    NASA Astrophysics Data System (ADS)

    Bijoor, N.; Pataki, D.; Trumbore, S.; Billings, S.; Czimczik, C.

    2006-12-01

    Turfgrass is the single largest irrigated crop in the U.S., yet turfgrass land cover has been largely neglected in ecological studies. The purpose of this study was to quantify biogeochemical cycling of a turfgrass lawn in southern California in response to varying fertilization and temperature in a controlled experiment. Replicated plots of mixed fescue/bermudagrass were subjected to an average of 4°C nighttime warming with infrared lamps and were fertilized with two levels of N (48 and 196 kg ha-1yr-1 in a factorial experiment. The fertilization events cause pulses of nitrous oxide emissions. Thus far, emissions ranged from 0.27 mg N m-2d- 1 in unheated and unfertilized plots to 0.54 mg N mg N m-2d-1 in plots treated with both high N and high temperature, and are comparable to emissions from fertilized agricultural soil. Observed nitrous oxide emissions suggest that urban soils likely play an important role in local greenhouse gas budgets, and that more intensive management may be required at elevated temperatures to sustain high turfgrass productivity.

  15. Tracking evolution of urban biogeochemical cycles: salinization of fresh water

    NASA Astrophysics Data System (ADS)

    Kaushal, S.; McDowell, W. H.; Wollheim, W. M.; Duan, S.; Gorman, J. K.; Haq, S.; Hohman, S.; Smith, R. M.; Mayer, P. M.

    2014-12-01

    The built environment often changes quickly in response to human activities, thus contributing to an evolution of stream chemistry over time. Depending upon development and management strategies, these changes can result in pulses and/or long-term trends. Here, we explore patterns of evolving salinization of fresh water over time, and we evaluate the potential water quality implications of fresh water salinization. We show that there has been global salinization of freshwater across urbanizing landscapes over a century. We also show that human-accelerated weathering in watersheds and river alkalinization can further influence regional rates of salinization (in addition to anthropogenic sources such as road salts, sewage leaks, etc.). Finally, we investigate how salinization of fresh water can impact stream sediment fluxes of carbon, nutrients, and sulfate in watersheds across a land use gradient at the Baltimore Long-Term Ecological Research (LTER) site. The impacts of salinization on mobilization and uptake of carbon, nutrients, and sulfate in streams warrant further consideration in water quality management strategies. Overall, we propose that salinization can be a "universal tracer" of watershed urbanization globally with major regional consequences for drinking water and evolution of biogeochemical cycles in freshwater ecosystems.

  16. 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.

  17. 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.

  18. Nitrate attenuation in groundwater: a review of biogeochemical controlling processes.

    PubMed

    Rivett, Michael O; Buss, Stephen R; Morgan, Philip; Smith, Jonathan W N; Bemment, Chrystina D

    2008-10-01

    Biogeochemical processes controlling nitrate attenuation in aquifers are critically reviewed. An understanding of the fate of nitrate in groundwater is vital for managing risks associated with nitrate pollution, and to safeguard groundwater supplies and groundwater-dependent surface waters. Denitrification is focused upon as the dominant nitrate attenuation process in groundwater. As denitrifying bacteria are essentially ubiquitous in the subsurface, the critical limiting factors are oxygen and electron donor concentration and availability. Variability in other environmental conditions such as nitrate concentration, nutrient availability, pH, temperature, presence of toxins and microbial acclimation appears to be less important, exerting only secondary influences on denitrification rates. Other nitrate depletion mechanisms such as dissimilatory nitrate reduction to ammonium and assimilation of nitrate into microbial biomass are unlikely to be important in most subsurface settings relative to denitrification. Further research is recommended to improve current understanding on the influence of organic carbon, sulphur and iron electron donors, physical restrictions on microbial activity in dual porosity aquifers, influences of environmental condition (e.g. pH in poorly buffered environments and salinity in coastal or salinized soil settings), co-contaminant influences (particularly the contrasting inhibitory and electron donor influences of pesticides) and improved quantification of denitrification rates in the laboratory and field. PMID:18721996

  19. 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.

  20. Biovolatilisation: a poorly studied pathway of the arsenic biogeochemical cycle.

    PubMed

    Mestrot, Adrien; Planer-Friedrich, Britta; Feldmann, Jrg

    2013-09-01

    It has been known for over a hundred years that microorganisms can produce volatile arsenic (As) species, termed "arsines". However, this topic has received relatively little attention compared to As behaviour in soils and biotransformation through the trophic level in the marine and terrestrial environment. We believe this is due to long-standing misconceptions regarding volatile As stability and transport as well as an absence, until recently, of appropriate sampling methods. First and foremost, an attempt is made to unify arsines' designations, notations and formulas, taking into account all the different terms used in the literature. Then, the stability of As volatile species is discussed and new analytical developments are explored. Further, the special cases of diffuse low-level emissions (e.g. soil and sediment biovolatilisation), and point sources with high-level emissions (geothermal environments, landfills, and natural gas) are comprehensively reviewed. In each case, future possible areas of research and unknown mechanisms are identified and their importance towards the global As biogeochemical cycle is explored. This review gathers new information regarding mechanisms, stability, transport and sampling of the very elusive arsines and shows that more research should be conducted on this important process. PMID:23824266

  1. 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.

  2. 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...

  3. 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...

  4. 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.

  5. 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...

  6. Quantifying the effects of mountain pine beetle infestation on water and biogeochemical cycles at multiple spatial and temporal scales

    NASA Astrophysics Data System (ADS)

    Brooks, P. D.; Harpold, A. A.; Somor, A. J.; Troch, P. A.; Gochis, D. J.; Ewers, B. E.; Pendall, E.; Biederman, J. A.; Reed, D.; Barnard, H. R.; Whitehouse, F.; Aston, T.; Borkhuu, B.

    2010-12-01

    Unprecedented levels of bark beetle infestation over the last decade have radically altered forest structure across millions of hectares of Western U.S. montane environments. The widespread extent of this disturbance presents a major challenge for governments and resource managers who lack a predictive understanding of how water and biogeochemical cycles will respond to this disturbance over various temporal and spatial scales. There is a widespread perception, largely based on hydrological responses to fire or logging, that a reduction in both transpiration and interception following tree death will increase soil water availability and catchment water yield. However, few studies have directly addressed the effects of insect-induced forest decline on water and biogeochemical cycling. We address this knowledge gap using observations and modeling at scales from 100 to 109 m2 across study sites in CO and WY that vary in the intensity and timing of beetle infestation and tree death. Our focus on multiple sites with different levels of impact allows us to address two broad, organizing questions: How do changes in vegetation structure associated with MPB alter the partitioning of energy and water? And How do these changes in energy and water availability affect local to regional scale water and biogeochemical cycles? This presentation will focus primarily on energy balance and water partitioning, providing context for ongoing biogeochemical work. During the growing season, stand-scale transpiration declines rapidly and soil moisture increases following infestation, consistent with streamflow data from regional catchments that shows an increase in baseflow following widespread attack. During the winter and spring, stand scale snow surveys and continuous snow depth sensors suggested that the variability in snow cover decreased as the severity of beetle impact increases, but there were no significant stand-scale differences in snow depth among levels of impact. This is due both to an increase in snow under the canopies of dead trees and a decrease in snow cover in canopy gaps. For example, mean snow depth under the canopy was 86cm (CV 0.02) in unimpacted sites and 95cm (CV 0.05) in heavily impacted sites. In canopy gaps however, mean snow depth was 117cm (CV 0.11) in unimpacted sites but only 93cm (CV 0.07) in heavily impacted sites. At the watershed scale, bark beetle infestation was more likely to decrease the amount of both snowmelt and annual runoff, suggesting that the opening of the canopy increases sublimation and evaporation of the snow cover. These data suggest that the disturbance due to bark beetle infestation is both quantitatively and qualitatively different than either fire or logging. Using these observations, we develop a conceptual model for evaluating how biotic and abiotic processes couple water and biogeochemical cycles in forest ecosystems.

  7. Effect of Vertical Flow Exchange on Biogeochemical Processes in Hyporheic Zones

    NASA Astrophysics Data System (ADS)

    Kim, H.; Lee, S.; Shin, D.; Hyun, Y.; Lee, K.

    2008-12-01

    Biogeochemical processes in hyporheic zones are of great interest because they make the hyporheic zones highly productive and complex environments. When contaminants or polluted water pass through hyporheic zones, in particular, biogeochemical processes play an important role in removing contaminants or attenuating contamination under certain conditions. The study site, a reach of Munsan stream (Paju-si, South Korea), exhibits severe contamination of surface water by nitrate released from Water Treatment Plant (WTP) nearby. The objectives of this study are to investigate the hydrologic and biogeochemical processes at the riparian area of the site which may contribute to natural attenuation of surface water driven nitrate, and analyze the effect of vertical (hyporheic) flow exchange on the biogeochemical processes in the area. To examine hydraulic mixing or dilution processes, vertical hydraulic gradients were measured at several depth levels using minipiezometers, and then soil temperatures were measured by using i-buttons installed inside the minipiezometers. The microbial analyses by means of polymerase chain reaction (PCR)-cloning methods were also done in order to identify the denitrification process in soil samples. In addition, correlation between vertical flow exchange, temperature data, and denitrifying bacteria activity was also investigated so as to examine the effects on one another. The results showed that there were significant effects of vertical flow exchange and hyporheic soil temperature on the biogeochemical processes of the site. This study found strong support for the idea that the biogeochemical function of hyporheic zone is a predictable outcome of the interaction between microbial activity and flow exchange.

  8. Expanding the Role of Reactive Transport Modeling in Biogeochemical Sciences

    NASA Astrophysics Data System (ADS)

    Li, Li; Maher, Katherine M.; Navarre-Sitchler, Alexis

    2014-09-01

    Earth systems are complex due to the intimate coupling of physical, chemical, and biological processes in the subsurface. Field observation and data analysis have provided significant insights into the coupling of these processes. However, mechanistic understanding often requires advanced modeling tools to quantify the role of individual processes while maintaining the process coupling that determines the overall system behavior. As a result, reactive transport modeling (RTM) has been used extensively to interrogate complex subsurface processes relevant to energy and the environment. Existing work has shown the significant research and educational advantages of RTM in elucidating mechanisms, integrating large data sets, testing hypotheses, and guiding the stewardship and management of water and energy resources.

  9. South Florida wetlands ecosystem; biogeochemical processes in peat

    USGS Publications Warehouse

    Orem, William; U.S. Geological Survey

    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 effects on water quality of (1) constructing buffer wetlands to alleviate nutrient contamination and (2) replumbing the ecosystem to restore natural water flow. The results may also suggest new approaches for solving problems of contamination and water quality in these wetlands. A second focus of this project will be on the geochemical history of the South Florida ecosystem. Peat is a repository of the history of past environmental conditions in the wetland. Before effective action can be taken to correct many of the problems facing these wetlands, we must first study the biogeochemistry of the peat at depth in order to understand whether current problems are the result of recent human activity or are part of a long-term natural cycle. Coordination with other (USGS) projects for South Florida is ongoing. These projects are studying the biological history of the ecosystem by using pollen and shells buried in the peat, together with procedures for dating the peat at various depths, to develop an overall ecosystem history model, with emphasis on the last 100 years.

  10. 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 cycles). To determine how fluxes of sulfur, carbon, and oxygen define oxygen levels before, during, and after the NOE, we add a sulfur cycle to the biogeochemical model of Claire et al. (2006). Understanding processes that impact the evolution of atmospheric oxygen on Earth is key to diagnosing the habitability of other planets because it is possible that other planets undergo a similar evolution. If a sulfidic deep ocean was instrumental in driving oxygen levels to modern values, then it would be valuable to remotely detect a sulfide-rich ocean on another planet. One such remotely-detectable signature could be the color of a sulfide-rich ocean. For example, Gallardo and Espinoza (2008) have hypothesized that a sulfidic ocean may be have been blacker in color. Even if a sulfidic ocean is not key to oxygenation, detecting a planet in transition--that is, a planet with intermediate levels of oxygen co-existing with higher levels of reduced gases - would be important for diagnosing habitability.

  11. Biogeochemical characterisation of a coal tar distillate plume

    NASA Astrophysics Data System (ADS)

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

    2001-12-01

    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.

  12. Microbial Reduction of Ferrous Arsenate: Biogeochemical Implications for Arsenic Mobilization

    SciTech Connect

    Babechuk, M.; Weisener, C.G.; Fryer, B.; Paktunc, D.; Maunders, C.

    2010-11-12

    In reduced aqueous environments, the presence of As in solution is a function of both biotic and abiotic mechanisms. Recent studies have demonstrated a significant release of As(III) through the microbial reduction of dissolved and mineral-bound As(V), which raises health concerns when the greater comparative mobility and toxicity of As(III) is considered. These release mechanisms do not operate in isolation but occur in concert with a number of removal processes, including secondary mineralization and sorption to other natural substrates. Thermodynamic and applied experimental studies have shown that ferrous arsenates, such as symplesite [Fe(II){sub 3}(As(V)O{sub 4}){sub 2} {center_dot} 8H{sub 2}O], may provide a significant sink for Fe(II) and As(V). In this study, the stability of a representative ferrous arsenate phase in the presence of the arsenate-reducing bacterium Shewanella sp. strain ANA-3 is examined. The reduction of ferrous arsenate by ANA-3 results in the release of aqueous As(III) and, subsequently, the progressive nucleation of a biogenic ferrous arsenite phase proximal to the microbial cells. The valence states of secondary solid-phase products were verified using X-ray absorption spectroscopy (XAS). Electron microscopy reveals that nucleation occurs on cellular exudates which may imply a role of extracellular reduction through c-type cytochromes as investigated in recent literature. These observations provide new insights into the reduction mechanisms of ANA-3 and the biogeochemical cycling of As(III) in natural systems.

  13. Subglacial (bio)geochemical weathering and the unexplored Antarctic system

    NASA Astrophysics Data System (ADS)

    Mitchell, A. C.; Christner, B. C.; Mikucki, J.; Priscu, J. C.

    2009-12-01

    Water exported from Alpine and polar glaciers is often concentrated in a range of major ions, and minor and trace elements, derived from the dissolution of subglacial rocks and minerals. The export of these species from subglacial environments to the oceans via subglacial hydrological systems appears to constitute an important global flux of biochemically essential species, such as Fe, potentially impacting upon plankton activity in the oceans and the associated consumption of CO2 on glacial-interglacial timescales. Recent studies have demonstrated the presence and activity of microorganisms in a range of subglacial environments, from Alpine glaciers, Arctic glaciers, and most recently in sub-Antarctic systems. Equally, isotopic studies at Alpine and Arctic glaciers provide evidence that microbe-mineral associations occur in subglacial environments, and account for the release and transformation of dissolved nutrients. However, the link between microbiological presence & activity, mineral weathering, ionic species transformations, and the configuration of the subglacial hydrological system, remains poorly understood. We will report on Whillans Ice Stream Subglacial Access Research Drilling (WISSARD), an NSF funded integrative study of ice sheet stability and life habitats in sub Antarctic aquatic environments. Direct sterile sampling from a subglacial Antarctic lake and grounding zone, will allow us for the first time to address these gaps in our knowledge, to determine the role of microbes on the weathering of rocks and the release and transport of nutrients in and from the unexplored sub-Antarctic environment. These data will yield seminal information on these systems and test the overarching hypothesis that active hydrological systems connect various subglacial environments and exert major control on geochemistry, metabolic and phylogenetic diversity, and biogeochemical transformations, as well as ice sheet dynamics. This will provide a basis for understanding the importance of subglacial hydrological-geochemical-microbiological interactions in the past, and in the future, at glacial-interglacial timescales.

  14. Stoichiometric vs hydroclimatic controls on soil biogeochemical processes

    NASA Astrophysics Data System (ADS)

    Manzoni, Stefano; Porporato, Amilcare

    2010-05-01

    Soil nutrient cycles are controlled by both stoichiometric constraints (e.g., carbon to nutrient ratios) and hydroclimatic conditions (e.g., soil moisture and temperature). Both controls tend to act in a nonlinear manner and give rise to complex dynamics in soil biogeochemistry at different space-time scales. We first review the theoretical basis of soil biogeochemical models, looking for the general principles underlying these models across space-time scales and scientific disciplines. By comparing more than 250 models, we show that similar kinetic and stoichiometric laws, formulated to mechanistically represent the complex biochemical constraints to decomposition, are common to most models, providing a basis for their classification. Moreover, a historic analysis reveals that the complexity (e.g., phase space dimension, model architecture) and degree and number of nonlinearities generally increased with date, while they decreased with increasing spatial and temporal scale of interest. Soil biogeochmical dynamics may be suitable conceptualized using a number of compartments (e.g., decomposers, organic substrates, inorganic ions) interacting among each other at rates that depend (nonlinearly) on climatic drivers. As a consequence, hydroclimatic-induced fluctuations at the daily scale propagate through the various soil compartments leading to cascading effects ranging from short-term fluctuations in the smaller pools to long-lasting changes in the larger ones. Such cascading effects are known to occur in dryland ecosystems, and are increasingly being recongnized to control the long-term carbon and nutrient balances in more mesic ecosystems. We also show that separating biochemical from climatic impacts on organic matter decomposition results in universal curves describing data of plant residue decomposition and nutrient mineralization across the globe. Future extensions to larger spatial scales and managed ecosystems are also briefly outlined. It is critical that future modeling efforts carefully account for the scale-dependence of their mathematical formulations, especially when applied to a wide range of scales.

  15. 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 could be useful as additional corroborating ecosystem indicators of chronic N pollution. PMID:24894911

  16. 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 useful as additional corroborating ecosystem indicators of chronic N pollution. PMID:24894911

  17. 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. PMID:11820470

  18. Terrestrial biogeochemical cycles - Global interactions with the atmosphere and hydrology

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    A review is presented of developments in ecosystem theory, remote sensing, and geographic information systems that support new endeavors in spatial modeling. A paradigm has emerged to predict ecosystem behavior based on understanding responses to multiple resources. Ecosystem models couple primary production to decomposition and nutrient availability utilizing this paradigm. It is indicated that coupling of transport and ecosystem processes alters the behavior of earth system components (terrestrial ecosystems, hydrology, and the atmosphere) from that of an uncoupled model.

  19. 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 aquifère/imperméable constitue une zone de mélange capable de supporter une plus grande activité microbienne que chacune des deux unités hydrogéologiques seules. L'extension des réactions biogéochimiques dans la zone de mélange et la largeur de cette zone dépendent de plusieurs facteurs, dont l'abondance et la solubilité des accepteurs et des donneurs d'électrons de chaque côté de l'interface, et le taux de réaction et de déplacement des accepteurs et des donneurs d'électrons au travers de cette interface. Les réactions biogéochimiques au voisinage de l'interface aquifère/imperméable peuvent avoir une influence appréciable sur le chimisme de l'eau des aquifères et sur celui des sédiments au niveau de l'interface. Resúmen. Es conocido que varias reacciones biogeoquímicas de importancia pueden tener lugar cerca de la interfaz entre los sedimentos de un acuífero y de un acuitardo. Entre ellas, destaca la reducción del O2, la denitrificación, y la reducción del Fe+3, SO4-2 y CO2 (metanogénesis). En algunos casos, estas reacciones se producen en la región cercana al acuitardo, ya que los dadores de electrones se mueven desde éste hacia el acuífero, el cual está enriquecido en aceptores de electrones o en microorganismos. Así, la interfaz acuífero/acuitardo constituye una zona de mezcla que es capaz de sustentar una actividad microbiana mayor que cualquier unidad hidrogeológica por sí misma. El alcance de las reacciones biogeoquímicas en la zona de mezcla y el ancho de esta zona de mezcla depende de varios factores, como la abundancia y la solubilidad de los aceptores y dadores de electrones en ambas caras de la interfaz y la velocidad a la que los aceptores y dadores de electrones reaccionan y se mueven a través de la interfaz. Las reacciones biogeoquímicas cerca de la interfaz acuífero/acuitardo pueden tener una influencia substancial en la hidroquímica de los acuíferos y en la química de los sedimentos cerca de la superficie.

  20. The role of estuarine discharges on the biogeochemical characteristics of the nearby continental shelf ecosystem. The Guadalquivir-Gulf of Cadiz case study

    NASA Astrophysics Data System (ADS)

    Guerreiro, Catarina; Macías, Diego; Peliz, Alvaro; Prieto, Laura; Ruiz, Javier

    2013-04-01

    The hydrodynamics and biogeochemical conditions of the Gulf of Cadiz (SW Iberian peninsula) is strongly influenced by the input of fresh, warm and nutrient-rich water from the main estuary in the region, the Guadalquivir River. This sea-river interaction favors the generation of surface retention structures that encompasses highly productive waters throughout the year constituting and ideal place for fish spawning and nursery. The biological productivity of the Gulf and its high fisheries yields are, thus, heavily forced by the Guadalquivir River discharges which are conditioned by the freshwater inputs from the upstream sections of the river and by the tidal mixing dynamics in the lower reaches of the estuary. In this work we use a coupled hydrological-biogeochemical 3D model of the Gulf of Cadiz, Strait of Gibraltar and Alboran Sea (a regional application of the Regional Ocean Model System) connected to a virtual estuary representing the Guadalquivir River. With this coupled model we quantify the relative importance of each process (freshwater discharges and tidal mixing) for creating the special conditions of the nearby continental shelf. We found that freshwater input is only relevant during fall and winter when precipitation are important in the river catchment area. Tidal mixing, on the other hand, is more constant throughout the entire year and provides a nutrient input to the marine ecosystem of the same order of magnitude as the freshwater runoff. We also run the model with and without the river input and quantify, for the first time, the exact role of this external forcing on the biogeochemical conditions of the continental shelf ecosystem.

  1. Carbon Cycle Model Linkage Project (CCMLP): Evaluating Biogeochemical Process Models with Atmospheric Measurements and Field Experiments

    NASA Astrophysics Data System (ADS)

    Heimann, M.; Prentice, I. C.; Foley, J.; Hickler, T.; Kicklighter, D. W.; McGuire, A. D.; Melillo, J. M.; Ramankutty, N.; Sitch, S.

    2001-12-01

    Models of biophysical and biogeochemical proceses are being used -either offline or in coupled climate-carbon cycle (C4) models-to assess climate- and CO2-induced feedbacks on atmospheric CO2. Observations of atmospheric CO2 concentration, and supplementary tracers including O2 concentrations and isotopes, offer unique opportunities to evaluate the large-scale behaviour of models. Global patterns, temporal trends, and interannual variability of the atmospheric CO2 concentration and its seasonal cycle provide crucial benchmarks for simulations of regionally-integrated net ecosystem exchange; flux measurements by eddy correlation allow a far more demanding model test at the ecosystem scale than conventional indicators, such as measurements of annual net primary production; and large-scale manipulations, such as the Duke Forest Free Air Carbon Enrichment (FACE) experiment, give a standard to evaluate modelled phenomena such as ecosystem-level CO2 fertilization. Model runs including historical changes of CO2, climate and land use allow comparison with regional-scale monthly CO2 balances as inferred from atmospheric measurements. Such comparisons are providing grounds for some confidence in current models, while pointing to processes that may still be inadequately treated. Current plans focus on (1) continued benchmarking of land process models against flux measurements across ecosystems and experimental findings on the ecosystem-level effects of enhanced CO2, reactive N inputs and temperature; (2) improved representation of land use, forest management and crop metabolism in models; and (3) a strategy for the evaluation of C4 models in a historical observational context.

  2. Anthropogenic forcing of estuarine hypoxic events in sub-tropical catchments: landscape drivers and biogeochemical processes.

    PubMed

    Wong, Vanessa N L; Johnston, Scott G; Burton, Edward D; Bush, Richard T; Sullivan, Leigh A; Slavich, Peter G

    2011-11-15

    Episodic hypoxic events can occur following summer floods in sub-tropical estuaries of eastern Australia. These events can cause deoxygenation of waterways and extensive fish mortality. Here, we present a conceptual model that links key landscape drivers and biogeochemical processes which contribute to post-flood hypoxic events. The model provides a framework for examining the nature of anthropogenic forcing. Modification of estuarine floodplain surface hydrology through the construction of extensive drainage networks emerges as a major contributing factor to increasing the frequency, magnitude and duration of hypoxic events. Forcing occurs in two main ways. Firstly, artificial drainage of backswamp wetlands initiates drier conditions which cause a shift in vegetation assemblages from wetland-dominant species to dryland-dominant species. These species, which currently dominate the floodplain, are largely intolerant of inundation and provide abundant labile substrate for decomposition following flood events. Decomposition of this labile carbon pool consumes oxygen in the overlying floodwaters, and results in anoxic conditions and waters with excess deoxygenation potential (DOP). Carbon metabolism can be strongly coupled with microbially-mediated reduction of accumulated Fe and Mn oxides, phases which are common on these coastal floodplain landscapes. Secondly, artificial drainage enhances discharge rates during the flood recession phase. Drains transport deoxygenated high DOP floodwaters rapidly from backswamp wetlands to the main river channel to further consume oxygen. This process effectively displaces the natural carbon metabolism processes from floodplain wetlands to the main channel. Management options to reduce the impacts of post-flood hypoxia include i) remodifying drainage on the floodplain to promote wetter conditions, thereby shifting vegetation assemblages towards inundation-tolerant species, and ii) strategic retention of floodwaters in the backswamp wetlands to reduce the volume and rate during the critical post-flood recession phase. PMID:21937090

  3. Large and mesoscale meteo-oceanographic patterns in local responses of biogeochemical concentrations.

    PubMed

    de Oliveira, Marilia Mitidieri F; Pereira, Gilberto C; de Oliveira, Jorge Luiz F; Ebecken, Nelson Francisco F

    2012-11-01

    Investigations surrounding the variability of productivity in upwelling regions are necessary for a better understanding the physical-biological coupling in these regions by monitoring systems of environmental impacts according to the needs of the regional coastal management. Using a spatial and temporal database from National Centers for Environmental Prediction (NCEP) and National Center for Atmospheric (NCAR) Research reanalysis, Quick Scatterometer vector wind, and surface stations from the Southeast coast of Brazil, we investigate the meteorological influences due to the large-scale systems in the variability of the nutrient and larvae concentration, and chlorophyll a, describing statistically relationships between them in upwelling regions. In addition, we used multivariate analysis, such as PCA and clustering to verify spatial and temporal variances and describe more clear the structure and composition of the ecosystem. Correlation matrix analyses were applied for different water masses present in the study area to identify the relations between physical and biogeochemical parameters in a region, where frequently upwelling occur. Statistical approaches and seasonal variability show that the period of November to March is more sensitive to nutrients (1.20 mg/m(3) for chlorophyll a, 2.20 ?mol/l for total nitrogen and 5.5 ml/l for DO) and larvae concentrations (120 org/m(3) for most of the larvae, except for cirripedia that presented values around 370 org/m(3)) relating to the influence of large and mesoescale meteorological patterns. The spatial and temporal variables analyzed with multivariate approach show meaningful seasonality variance of the physical and biological samples, characterizing the principal components responsible for this variance in spring and summer (upwelling period), emphasizing the monitoring of species as crustaceans and mussels that are present in the local economy. Then, the spring and summer season are characterized by high productivity due to the occurrence of upwelling in this period. PMID:22173788

  4. Large and mesoscale meteo-oceanographic patterns in local responses of biogeochemical concentrations.

    TOXLINE Toxicology Bibliographic Information

    de Oliveira MM; Pereira GC; de Oliveira JL; Ebecken NF

    2012-11-01

    Investigations surrounding the variability of productivity in upwelling regions are necessary for a better understanding the physical-biological coupling in these regions by monitoring systems of environmental impacts according to the needs of the regional coastal management. Using a spatial and temporal database from National Centers for Environmental Prediction (NCEP) and National Center for Atmospheric (NCAR) Research reanalysis, Quick Scatterometer vector wind, and surface stations from the Southeast coast of Brazil, we investigate the meteorological influences due to the large-scale systems in the variability of the nutrient and larvae concentration, and chlorophyll a, describing statistically relationships between them in upwelling regions. In addition, we used multivariate analysis, such as PCA and clustering to verify spatial and temporal variances and describe more clear the structure and composition of the ecosystem. Correlation matrix analyses were applied for different water masses present in the study area to identify the relations between physical and biogeochemical parameters in a region, where frequently upwelling occur. Statistical approaches and seasonal variability show that the period of November to March is more sensitive to nutrients (1.20 mg/m(3) for chlorophyll a, 2.20 ?mol/l for total nitrogen and 5.5 ml/l for DO) and larvae concentrations (120 org/m(3) for most of the larvae, except for cirripedia that presented values around 370 org/m(3)) relating to the influence of large and mesoescale meteorological patterns. The spatial and temporal variables analyzed with multivariate approach show meaningful seasonality variance of the physical and biological samples, characterizing the principal components responsible for this variance in spring and summer (upwelling period), emphasizing the monitoring of species as crustaceans and mussels that are present in the local economy. Then, the spring and summer season are characterized by high productivity due to the occurrence of upwelling in this period.

  5. 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. PMID:24845674

  6. The effect of tidal forcing on biogeochemical processes in intertidal salt marsh sediments

    PubMed Central

    Taillefert, Martial; Neuhuber, Stephanie; Bristow, Gwendolyn

    2007-01-01

    Background Early diagenetic processes involved in natural organic matter (NOM) oxidation in marine sediments have been for the most part characterized after collecting sediment cores and extracting porewaters. These techniques have proven useful for deep-sea sediments where biogeochemical processes are limited to aerobic respiration, denitrification, and manganese reduction and span over several centimeters. In coastal marine sediments, however, the concentration of NOM is so high that the spatial resolution needed to characterize these processes cannot be achieved with conventional sampling techniques. In addition, coastal sediments are influenced by tidal forcing that likely affects the processes involved in carbon oxidation. Results In this study, we used in situ voltammetry to determine the role of tidal forcing on early diagenetic processes in intertidal salt marsh sediments. We compare ex situ measurements collected seasonally, in situ profiling measurements, and in situ time series collected at several depths in the sediment during tidal cycles at two distinct stations, a small perennial creek and a mud flat. Our results indicate that the tides coupled to the salt marsh topography drastically influence the distribution of redox geochemical species and may be responsible for local differences noted year-round in the same sediments. Monitoring wells deployed to observe the effects of the tides on the vertical component of porewater transport reveal that creek sediments, because of their confinements, are exposed to much higher hydrostatic pressure gradients than mud flats. Conclusion Our study indicates that iron reduction can be sustained in intertidal creek sediments by a combination of physical forcing and chemical oxidation, while intertidal mud flat sediments are mainly subject to sulfate reduction. These processes likely allow microbial iron reduction to be an important terminal electron accepting process in intertidal coastal sediments. PMID:17567893

  7. 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

    Increased nutrient loads delivered from watersheds due to agricultural intensification, industrialization, and urbanization have contributed globally to the persistence of large hypoxic zones in inland and coastal waters. Watershed management practices targeting these non-point source pollutants often lead to little or no improvement in water quality, even after extensive implementation of conservation measures or Best Management Practices (BMPs). The lag time between implementation of a conservation measure and resultant water quality benefits has recently been recognized as an important factor in the "apparent" failure of these BMPs. When conservation measures are implemented without explicit consideration of the lag time and with expectations that they will lead to immediate benefits, the resulting failure to meet such expectations can discourage vital restoration efforts. It is therefore important to quantify the lag times associated with watershed management efforts a priori and to implement restoration strategies targeted specifically at minimizing lag times and maximizing restoration benefits. The focus of this research is to develop a framework for understanding the time lags between land-use changes and stream water quality benefits. We hypothesize that such time lags arise from nutrient legacies building over decades of fertilizer application. For nitrogen (N), one can conceptualize this as either hydrologic legacy, in the form of dissolved nitrate that is delayed due to slow groundwater transport, or as biogeochemical legacy, in the form of organic N, possibly in dissolved or readily mineralizable forms. Indeed, mass-balance studies across the Mississippi and Thames river basins indicate the possibility of missing N mass in these landscapes, with inputs being consistently greater than the outputs even when accounting for all possible pathways of nitrogen transformation. Historical soil data within the upper Mississippi River Basin (MRB) indicate that 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.

  8. Assessing Feedbacks between Remediation-Induced Biogeochemical Transformations and Flow Characteristics using Multi-Scale Geophysical Approaches (Invited)

    NASA Astrophysics Data System (ADS)

    Hubbard, S. S.; Wu, Y.; Chen, J.; Ajo Franklin, J. B.; Li, L.; Tuglus, C.; Williams, K. H.

    2009-12-01

    Although in situ strategies are frequently considered for environmental remediation, the impact of feedbacks between induced biogeochemical transformations and hydrological characteristics on remediation efficacy is not well understood. In situ remediation approaches that strongly perturb subsurface systems (such as chemical oxidation, pH manipulation, redox manipulation or biostimulation) typically lead to biogeochemical end-products, which form at grain-fluid boundaries, within pore spaces, and across pore throats. Our recent research has suggested that the evolution of these remediation-induced microscale end-products is significant enough to impact flow characteristics at the field scale. This feedback between biogeochemical transformations and flow characteristics may render it challenging to introduce additional amendments into the subsurface or may alter the hydrobiogeochemical conditions favorable for sustained treatment. Our research focuses on exploring how geophysical signatures change as a function of remediation-induced biotic and abiotic transformations, including the evolution of electrically conductive (e.g., FeS) and non-conductive (e.g., calcite) precipitates, gases, biofilms, TDS, and electroactive ions. Using numerical, theoretical, and experimental approaches, our nested investigations span from several microns to the field scale. Our research is aligned with biostimulation experiments that are ongoing at the Uranium-contaminated Rifle, Colorado DOE Site, where stimulation of iron- and sulfate-reducing microorganisms accompanying acetate injection has been shown to promote uranium removal, presumably as insoluble mineral precipitates. To explore these transformations and their impact on flow characteristics, we are performing research along five different fronts: 1) dynamic synchrotron tomography studies to explore the evolution in pore geometry and precipitate morphology due to remediation treatments; (2) laboratory column experiments to develop an understanding about geophysical (complex resistivity, seismic, and radar) attributes to remediation-induced end-products and to develop petrophysical relationships; (3) stochastic approaches that permit integration of the disparate geophysical, geochemical, and petrophysical datasets to quantify end-product attributes (i.e., volume fraction, mean radius, and distribution of evolved precipitates) as well as their impact on permeability; (4) Coupled imaging/inversion studies to explore the ability and resolution of geophysical methods for quantifying remediation-induced transformations at the field scale; and (5) iteration with reactive transport modeling to improve understanding of geophysical signatures as well as field-scale phenomena. This presentation will review advances in all of these research fronts and will discuss existing challenges for exploring complex system feedbacks using geophysical methods.

  9. 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 aftermath of the LJE. A mass balance calculation of Mo also demonstrates that the period is marked by an expansion of euxinia to ca. 9-40% of the whole seafloor. Under such conditions Mo levels would decrease to as low as ca. 2.0-6.5 nM where nitrogen fixation by Fe-Mo nitrogenase is very sensitive to Mo concentration. We propose that a pervasive euxinia was established in the wake of the LJE as a direct consequence of a substantial drop in atmospheric oxygen level and that such waxing and waning of the atmospheric oxygenation state in the Paleoproterozoic could have caused biological upheavals through dynamic oceanic euxinia, followed by long-term stability of anoxic/non-sulphidic conditions during the mid-Proterozoic.

  10. Ocean state estimation from hydrography and velocity observations during EIFEX with a regional biogeochemical ocean circulation model

    NASA Astrophysics Data System (ADS)

    Losch, Martin; Strass, Volker; Cisewski, Boris; Klaas, Christine; Bellerby, Richard G. J.

    2014-01-01

    In the European Iron Fertilization Experiment (EIFEX), the iron hypothesis was tested by an open ocean perturbation experiment. The success of EIFEX owes to the applied experimental strategy; namely to use the closed core of a mesoscale eddy for the iron injection. This strategy not only allowed tracking the phytoplankton bloom within the fertilized patch of mixed-layer water, but also allowed the export of biologically fixed carbon to the deep ocean to be quantified. In this present study, least-squares techniques are used to fit a regional numerical ocean circulation model with four open boundaries to temperature, salinity, and velocity observations collected during EIFEX. By adjusting the open boundary values of temperature, salinity and velocity, an optimized model is obtained that clearly improves the simulated eddy and its mixed layer compared to a first guess representation of the cyclonic eddy. A biogeochemical model, coupled to the optimized circulation model, simulates the evolution of variables such as chlorophyll a and particular organic carbon in close agreement with the observations. The estimated carbon export, however, is lower than the estimates obtained from observations without numerical modeling support. Tuning the sinking parameterization in the model increases the carbon export at the cost of unrealistically high sinking velocities. Repeating the model experiment without adding iron allows more insight into the effects of the iron fertilization. In the model this effect is about 40% lower than in previous estimates in the context of EIFEX. The likely causes for these discrepancies are potentially too high remineralization, inaccurate representation of the bloom-termination in the model, and ambiguity in budget computations and averaging. The discrepancies are discussed and improvements are suggested for the parameterization used in the biogeochemical model components.

  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. A Bay/Estuary Model to Simulated Hydrodynamics and Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Yeh, G.

    2010-12-01

    This talk presents the development of a numerical model to simulate integrated hydrodynamics and biogeochemical cycles in /bays/estuaries/coastal waters. The hydrodynamic module solves three-dimensional, density-dependent Navier-Stokes and thermal, salinity, and sediment transport equations. The moving free surface is explicitly handled by solving the kinematic boundary condition equation using a node-repositioning algorithm. The biogeochemical module considers the interaction of carbon, nitrogen, phosphorus, and oxygen cycles and biota kinetics. The interacting biogeochemical cycles and biota kinetics were transformed into a reaction network, from which the transport equations of all biogeochemical species and biota were set up automatically. These transport equations were then transformed into three subsets to decouple fast equilibrium reactions from slow kinetic reactions using a general paradigm of diagonalization. The first subset constitutes of transport equations of equilibrium variables. The second subset is made of transport equations of kinetic variables. Finally, the third subset composes transport equations of components for reaction invariance. The model was applied to the Loxahatchee Estuary river system. The computational domain includes the Loxahatchee estuary, Intracoastal Waterways, and three major tributaries of the river - the South Fork, North Fork, and Northwest Fork. The comparison between model simulations and field data is excellent for tides and adequate for salinities. To demonstrate the flexibility and generality of the biogeochemical transport module, three widely used water quality models, WASP5, QUAL2E, and CE-QUAL-ICM, were recast in the mode of reaction networks of biogeochemical processes. Simulations of QUAL2E and WASP5 using the model illustrated that they were treated simply as two examples in light of the general paradigm of modeling reactive biogeochemical transport.

  13. Calibration and validation of a one-dimensional complex marine biogeochemical flux model in different areas of the northern Adriatic shelf

    NASA Astrophysics Data System (ADS)

    Vichi, M.; Oddo, P.; Zavatarelli, M.; Coluccelli, A.; Coppini, G.; Celio, M.; Fonda Umani, S.; Pinardi, N.

    2003-01-01

    In this paper we show results from numerical simulations carried out with a complex biogeochemical fluxes model coupled with a one-dimensional high-resolution hydrodynamical model and implemented at three different locations of the northern Adriatic shelf. One location is directly affected by the Po River influence, one has more open-sea characteristics and one is located in the Gulf of Trieste with an intermediate behavior; emphasis is put on the comparison with observations and on the functioning of the northern Adriatic ecosystem in the three areas. The work has been performed in a climatological context and has to be considered as preliminary to the development of three-dimensional numerical simulations. Biogeochemical model parameterizations have been ameliorated with a detailed description of bacterial substrate utilization associated with the quality of the dissolved organic matter (DOM), in order to improve the models capability in capturing the observed DOM dynamics in the basin. The coupled model has been calibrated and validated at the three locations by means of climatological data sets. Results show satisfactory model behavior in simulating local seasonal dynamics in the limit of the available boundary conditions and the one-dimensional implementation. Comparisons with available measurements of primary and bacterial production and bacterial abundances have been performed in all locations. Model simulated rates and bacterial dynamics are in the same order of magnitude of observations and show a qualitatively correct time evolution. The importance of temperature as a factor controlling bacteria efficiency is investigated with sensitivity experiments on the model parameterizations.

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

    NASA Astrophysics Data System (ADS)

    Serrano, O.; Ricart, A. M.; Lavery, P. S.; Mateo, M. A.; Arias-Ortiz, A.; Masque, P.; Steven, A.; Duarte, C. M.

    2015-11-01

    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 stores were mostly derived from seagrass detritus (88 % in average) compared to meadows closer to the deep limit of distribution (45 % on average). Also, sediment 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 hypotheses 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 sediment 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.

  15. 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 concentration ratio relatively Phragmites australis as a background content. This factor showed that Nuphar pumila and Ceratophyllum demersum are acting like concentrators in comparison with the reed. According to this ratio, the mostly accumulated elements in aquatic plants in 2011 were V, Co, As, U, and in 2012 - Cu, As, Bi. Differences in chemical composition are due to different water periods. During the high water period in 2011 a large amount of soil particles after the heavy rains were taken into the flow from the river banks and then deposited within the delta. The transportation of suspended particles during the low water period of 2012 was significantly less.

  16. Proterozoic to recent tectonic tuning of biogeochemical cycles

    NASA Astrophysics Data System (ADS)

    Worsley, T. R.; Moody, J. B.; Nance, R. D.

    An approximately 0.5-Ga plate tectonic cycle (Worsley et al., 1984) of continental dispersion and accretion has been correlated with tectonic and platform sediment trends, climate, evolution of life forms, and stable isotope distributions for the last 3.0 Ga. Orogenic peaks center on 2.6, 2.1, 1.8-1.6, 1.1, 0.6, and 0.25 Ga, with the beginnings of the peaks marking the onset of supercontinent-producing collisions and the ends of the peaks corresponding to the thermal elevation that ultimately results in continental breakup. Continental rifting is also related to episodes of mafic-dike swarm production and subsequent rapid seafloor spreading. The major effect of the plate tectonic megacycle on platform sedimentation is to foster marine platform sedimentation during fragmentation-induced submergence and to inhibit sedimentation during assembly-produced emergence. Episodes of platform biogeochemical precipitation (magnetite, hematite, chert, bitumens, dolomite, calcite, phosphorite) and organic and inorganic lag deposits (detrital pyrite and uranitite, redbeds, coal) can be integrated with this plate tectonic cycle of continental fragmentation and assembly. Carbon dioxide and water vapor have controlled the earth's climate throughout its geologic history. The first strong suggestion for a drop in CO2 levels occurs at the onset of Proterozoic glaciation at 2.1 Ga because orogenic quiescence between 2.5 and 2.2 Ga would suggest drowned fragmented continents that would be difficult to glaciate. Continental assembly and emergence favor but do not mandate glacial intervals. The appearance of minute traces of oxygen in the atmosphere is related to the appearance of oxyphobic procaryotic photosynthesizers present in the late Archean ocean. O2 levels elevated dramatically as O2- tolerant eucaryotes first evolved and then achieved aerobic metabolism. The continued evolution of life is related not only to oxygen levels in the atmosphere/ocean system but also to marine transgressions caused by rifting and formation of passive-margined oceans. The carbon, sulfur, and strontium isotopic record can be correlated to platform sedimentation and the Phanerozoic freeboard record. The above correlations suggest that a ˜0.5-Ga plate tectonic episodicity is a driving variable responsible for orogenic, eustatic, stable isotope, platform-sediment, biogenetic, and carbon reservoir megacycles that can be recognized at least as far back as 2.5 Ga.

  17. Extracellular enzyme activity and biogeochemical cycling in restored prairies

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    Winter microbial activity in mid-latitude prairie ecosystems is thermally sensitive and significantly influenced by snow depth. Snow insulates the soil column facilitating microbial processing of complex organic substrates. Previous studies in forests and tundra ecosystems suggest patterns of substrate utilization and limitation are seasonal; above freezing, soil microbes access fresh litter inputs and sugar exudates from plant roots, while under frozen condition they recycle nutrients incorporated in microbial biomass. In order to liberate nutrients required for carbon degradation, soil microbes invest energy in the production of extracellular enzymes that cleave monomers from polymer bonds. The inverse relationship between relative enzyme abundance and substrate availability makes enzyme assays a useful proxy to assess changes in resources over time. Our objective in this study was to assess patterns in microbial biomass, nutrient availability, and extracellular enzyme activity in four snow exclosure sites over a seven-month period. Over the past three years, we have maintained a snow removal experiment on two restored prairies in central Minnesota. In each prairie, snow was continuously removed annually from two 4 x 4 m plots by shoveling after each snow event. Extractable C, N and P, and microbial C, N and P in soil samples were measured in samples collected from these snow removal plots, as well as in adjacent unmanipulated prairie control plots. Pools of C, N, and P were estimated using standard extraction protocols, and microbial pools were estimated using chloroform fumigation direct extraction (CFDE). We conducted fluorometric extracellular enzyme assays (EEA) to assess how the degradation potential of cellulose (cellobiohydrolase, CBH), protein (leucine aminopeptidase, LAP), and phosphate esters (phosphatase, PHOS) changed seasonally. Microbial C and N declined between October and June, while microbial P declined during the fall and winter, but increased 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.

  18. The changing role of dust in biogeochemical cycling

    NASA Astrophysics Data System (ADS)

    Neff, J. C.; Reynolds, R. L.; Farmer, G. L.; Reheis, M.

    2007-12-01

    Dust emission and deposition have the potential to deplete and enrich ecosystems of mineral resources essential to life. In many parts of the world, and particularly in semi-arid settings, wind erosion of soils and the subsequent long-distance transport and deposition of mineral aerosols play a basic role in soil composition and processes, including the production of essential plant nutrients through weathering. Although the long-term role of dust in the development of soils is reasonably well understood, the effects of recent dust emission and deposition on ecosystems are not. Recent work on ecosystems around the world has highlighted the fundamental importance of contemporary wind erosion and dust deposition in biogeochemical cycling. In the western U.S., studies of Sr and Nd isotopes, elemental concentrations, and magnetic properties elucidate the role of dust in recent soil development and soil loss by wind erosion related to land-use change. In the arid landscapes in and around Canyonlands National Park (Utah), these techniques provide insight into the development of soils in stable settings where human activities have been minimal but the loss of soil in areas affected by grazing and recreational activities. In stable settings of the central Colorado Plateau (Utah), dust deposition is responsible for a large proportion (as much as 20 percent) of surface soil mass and elemental content. In contrast, wind erosion is responsible for large losses of nutrients and surface soil of nearby, closely similar geomorphic settings disturbed by human activity. In the San Juan Mountains (Colorado) downwind of the Colorado Plateau, Nd and Sr isotopes in dust and lake sediments provide evidence for large increases in dust deposition during the 19th and 20th century compared to records from the middle to late Holocene. The recent enhancement in dust deposition is also responsible for increased loading of many elements, including essential nutrients that may influence ecological processes. In settings of continued dust accumulation over the past ca. 150 years, geochemical results point to changes in dust composition, particularly in some trace metals and P. The apparent, human-driven change in the amount and composition of emitted dusts has implications for both our understanding and prediction of mineralization processes across a range of landscapes.

  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. 10-12. 2. Ermakov V.V., Tyutikov S.F., Khushvakhtova S.D., Danilova V.N., Boev V.N., Barabanschikova R.N., Chudinova E.A. Peculiarities of quantitative determination of selenium in biological materials// Bulletin of the Tyumen State University Press, 2010, 3, 206-214. Supported by the Russian Foundation for Basic Research, grant number 15-05-00279a

  20. Significant differences in biogeochemical processes between a glaciated and a permafrost dominated catchment

    NASA Astrophysics Data System (ADS)

    Hindshaw, Ruth; Heaton, Tim; Boyd, Eric; Lang, Susan; Tipper, Ed

    2014-05-01

    It is increasingly recognised that microbially mediated processes have a significant impact on chemical fluxes from glaciated catchments. One important reaction is the oxidation of pyrite since the production of sulphuric acid facilitates the dissolution of minerals without the need for acidity generated by dissolved atmospheric CO2. Thus weathering processes can still continue even when isolated from the atmosphere, as is thought to occur under large ice masses. However, as a glacier melts, it is expected that the microbial community will change with knock-on effects on the stream water chemistry. Understanding the difference in solute generation processes between glaciated and un-glaciated terrain is key to understanding how glacial-interglacial cycles affect atmospheric CO2 consumption by chemical weathering. In order to investigate whether biogeochemical processes differ between glaciated and un-glaciated terrain we collected stream water samples from two small catchments (each approximately 3 km2) in Svalbard. One catchment is glaciated and the other catchment is un-glaciated but is affected by permafrost and a seasonal snow-pack. The two catchments are situated next to each other with identical bedrock (shale with minor siltstone and sandstone). The proximity of the catchments to each other ensures that meteorological variables such as temperature and precipitation are very similar. Sampling was conducted early in the melt-season when there was still significant snow-cover and in mid-summer when most of the seasonal snow-pack had melted. The water samples were analysed for δ34S-SO4, δ18O-SO4, δ18O-H2O, δ13C-DIC and δ13C-DOC, together with major anions and cations. Despite the nominally identical lithology, there were significant differences in the stream water chemistry between the two catchments. For example, sulphate was the dominant anion in the un-glaciated catchment whereas bicarbonate was the dominant anion in the glaciated catchment. Pyrite oxidation under anoxic conditions and microbially mediated sulphate reduction occur in both catchments. However, in the glaciated catchment pyrite oxidation is mainly coupled to carbonate dissolution and in the un-glaciated catchment it is mainly coupled to silicate dissolution. These significant differences in weathering processes will be discussed with reference to the microbial communities found in the two catchments.

  1. 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., Front. Ecol. Environ., doi:10.1890/100014, 2011. Battin, T.J., et al., Nat. Geosci., 2, 598-600, 2009. Cole, J.J. et al., Ecosystems, doi:10.1007/s10021-006-9013-8, 2007. Frei, S., et al., J. Geophys. Res., doi:10.1029/2012JG002012, 2012. Kiel, B.A. & Cardenas, M.B., Nat. Geosci., doi:10.1038/ngeo02157, 2014. Nakayama, T., Ecol. Model., doi:10.1016/j.ecolmodel.2008.02.017, 2008a. Nakayama, T. , Forest Ecol. Manag., doi:10.1016/j.foreco.2008.07.017, 2008b. Nakayama, T., River Res. Applic., doi:10.1002/rra.1253, 2010. Nakayama, T., Hydrol. Process., doi:10.1002/hyp.8009, 2011a. Nakayama, T., Agr. Forest Meteorol., doi:10.1016/j.agrformet.2010.11.006, 2011b. Nakayama, T., Water Sci. Technol., doi:10.2166/wst.2012.205, 2012a. Nakayama, T., Hydrol. Process., doi:10.1002/hyp.9347, 2012b. Nakayama, T., Ecohydrol. Hydrobiol., doi:10.1016/j.ecohyd.2013.03.004, 2013. Nakayama, T., Proc. Environ. Sci., doi:10.1016/j.proenv.2012.01.008, 2012c. Nakayama, T. & Fujita, T., Landscape Urban Plan., doi:10.1016/j.landurbplan.2010.02.003, 2010. Nakayama, T. & Hashimoto, S., Environ. Pollut., doi:10.1016/j.envpol.2010.11.016, 2011. Nakayama, T. & Shankman, D., Global Planet. Change, doi:10.1016/j.gloplacha.2012.10.004, 2013a. Nakayama, T. & Shankman, D., Hydrol. Process., doi:10.1002/hyp.9835, 2013b. Nakayama, T. & Watanabe, M., Water Resour. Res., doi:10.1029/2004WR003174, 2004. Nakayama, T. & Watanabe, M., Hydrol. Earth Syst. Sci. Discuss., 3, 2101-2144, 2006. Nakayama, T. & Watanabe, M., Hydrol. Process., doi:10.1002/hyp.6684, 2008a. Nakayama, T. & Watanabe, M., Global Planet. Change, doi:10.1016/j.gloplacha.2008.04.002, 2008b. Nakayama, T., et al., Hydrol. Process., doi:10.1002/hyp.6142, 2006. Nakayama, T., et al., Sci. Total Environ., doi:10.1016/j.scitotenv.2006.11.033, 2007. Nakayama, T., et al., Global Planet. Change, doi:10.1016/j.gloplacha.2010.06.001, 2010. Nakayama, T., et al., Hydrol. Process., doi:10.1002/hyp.9290, 2012. Raymond, P.A., et al., Nature, doi:10.1038/nature12760, 2013.

  2. Biogeochemical consequences of vertical and lateral transport of particulate organic matter in the southern North Sea: A multiproxy approach

    NASA Astrophysics Data System (ADS)

    Le Guitton, M.; Soetaert, K.; Damsté, J. S. Sinninghe; Middelburg, J. J.

    2015-11-01

    Vertical and lateral transports are of importance in continental shelf systems such as the North Sea and play a major role in the processing of organic matter. We investigated the biogeochemical consequences of these transports on particulate organic matter at the molecular level in the southern North Sea. We analysed suspended particulate matter and surface sediments for organic carbon, pigments and phospholipid derived fatty acids at 10 stations sampled in September 2011 along the particle transport route. The particulate organic matter in both suspended particulate matter and surface sediment was mainly from marine phytoplankton origin but of fresher quality in the water column. Particulate organic matter quality did not change from south to north in the suspended particulate matter, whereas it clearly decreased towards the north in the surface sediments, reflecting a decreased intensity of benthic-pelagic coupling. However, we also observed strong deposition of fresh organic matter in the northern station denoting that occasionally, intense benthic-pelagic coupling can occur. Finally, our study highlights the necessity to use a multiproxy approach covering multiple characteristic time scales, when investigating both suspended particulate matter and surface sediments.

  3. 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/kinetic reaction. An equilibrium reaction is modeled with an infinite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. Programmed kinetic reaction rates include multiple Monod kinetics, nth order empirical, and elementary formulations. In addition, user-specified rate formulations can be programmed into the model. No existing models to our knowledge offer these simultaneous features. Furthermore, most available reaction-based models assume chemical components a priori so that reactions can be written in basic (canonical) forms and implicitly assume that fast equilibrium reactions occur only for homogeneous reactions. The decoupling of fast reactions from slow reactions lessens the stiffness typical of these systems. The explicit enforcement of mass conservation overcomes the mass conservation error due to numerical integration errors. The removal of redundant fast reactions alleviates the problem of singularity. The exclusion of irrelevant slow reactions eliminates the issue of exporting their problematic rate formulations/parameter estimations to different environment conditions. Taking the advantage of the nonuniqueness of components, a dynamic basis-species switching strategy is employed to make the model numerically robust. Backward basis switching allows components to freely change in the simulation of the chemistry module, while being recovered for transport simulation. Three example problems were selected to demonstrate the versatility and robustness of the model.

  4. Biogeochemical dynamics of pollutants in Insitu groundwater remediation systems

    NASA Astrophysics Data System (ADS)

    Kumar, N.; Millot, R.; Rose, J.; Négrel, P.; Battaglia-Brunnet, F.; Diels, L.

    2010-12-01

    Insitu (bio) remediation of groundwater contaminants has been area of potential research interest in last few decades as the nature of contaminant encountered has also changed drastically. This gives tough challenge to researchers in finding a common solution for all contaminants together in one plume. Redox processes play significant role in pollutant dynamics and mobility in such systems. Arsenic particularly in reduced environments can get transformed into its reduced form (As3+), which is apparently more mobile and highly toxic. Also parallel sulfate reduction can lead to sulfide production and formation of thioarsenic species. On the other hand heavy metals (Zn, Fe, and Cd) in similar conditions will favour more stable metal sulfide precipitation. In the present work, we tested Zero Valent Iron (ZVI) in handling such issues and found promising results. Although it has been well known for contaminants like arsenic and chlorinated compounds but not much explored for heavy metals. Its high available surface area supports precipitation and co -precipitation of contaminants and its highly oxidizing nature and water born hydrogen production helps in stimulation of microbial activities in sediment and groundwater. These sulfate and Iron reducing bacteria can further fix heavy metals as stable metal sulfides by using hydrogen as potential electron donor. In the present study flow through columns (biotic and control) were set up in laboratory to understand the behaviour of contaminants in subsurface environments, also the impact of microbiology on performance of ZVI was studied. These glass columns (30 x 4cm) with intermediate sampling points were monitored over constant temperature (20°C) and continuous groundwater (up)flow at ~1ml/hr throughout the experiment. Simulated groundwater was prepared in laboratory containing sulfate, metals (Zn,Cd) and arsenic (AsV). While chemical and microbial parameters were followed regularly over time, solid phase has been characterized at the end of experiment using synchrotron and other microscopic techniques (SEM, µXRF). Stable isotope signatures have been proved as a critical tool in understanding the redox and microbial processes. We monitored ∂34S, ∂66Zn and ∂56Fe isotope evolution with time to understand the relationship between biogeochemical process and isotope fractionation. We observed Δ34S biotic - abiotic ~6‰ and ∂56Fe variation up to 1.5‰ in our study. ZVI was very efficient in metal removal and also in enhancing sulfate reduction in column sediment. Arsenic reduction and thiarsenic species were also detected in biotic columns showing a positive correlation with sulfide production and Fe speciation. Latest results will be presented with integration of different processes. This multidisciplinary approach will help in deep understanding of contaminants behaviour and also to constrain the efficiency and longitivity of treatment system for different contaminants. “This is contribution of the AquaTrain MRTN (Contract No. MRTN-CT-2006-035420) funded under the European Commission sixth framework programme (2002-2006) Marie Curie Actions, Human Resources & Mobility Activity Area- Research Training Networks”

  5. 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 methylation, but buildup of sulfide from microbial sulfate reduction begins to inhibit mercury methylation above this range. Sulfate from the EAA canals has primarily impacted the northern Everglades nearest the EAA, but recent evidence shows sulfate loading extending about 80 km further south into Everglades National Park. Current restoration plans to restore to deliver more water south to Everglades National Park may increase overall sulfur loads to the southern part of the ecosystem. A comprehensive Everglades restoration strategy should include reduction of sulfur loads as a goal because of the many detrimental impacts of sulfate on the ecosystem. Monitoring data show that the ecosystem response to changes in sulfate levels is rapid, and strategies for reducing sulfate loading may be effective in the near-term. A multifaceted approach employing best management practices for sulfur in agriculture, agricultural practices that minimize soil oxidation, and changes to stormwater treatment areas that increase sulfate retention, could help reduce sulfate loads to the Everglades, with resulting benefits.

  6. 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 transition from dominantly pyrite burial to sulfate burial after the Neoproterozoic. Strong evidence for the oxygenation of the deep marine environment has emerged through elemental approaches over the past few years which were able to show significant increases in redox-sensitive trace-metal (notably Mo) enrichment in marine sediments not only during the GOE but even more pronounced during the inferred NOE. In addition to past studies involving Mo enrichment, which has been extended and further substantiated in the current review, we present new compilations of V and U concentrations in black shales throughout Earth history that confirm such a rise and further support the NOE. With regard to ocean ventilation, we also review other sedimentary redox indicators, such as iron speciation, molybdenum isotopes and the more ambiguous REE patterns. Although the timing and extent of the NOE remain the subjects of debate and speculation, we consider the record of redox-sensitive trace-metals and C and S contents in black shales to indicate delayed ocean ventilation later in the Cambrian on a global scale with regard to rising oxygen levels in the atmosphere which likely rose during the Late Neoproterozoic.

  7. 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 biogeochemical state variables and was used to test short-term wind-driven dynamics that could influence dissolved oxygen concentrations in Hood Canal.

  8. Radionuclide release from simulated waste material after biogeochemical leaching of uraniferous mineral samples.

    PubMed

    Williamson, Aimee Lynn; Caron, François; Spiers, Graeme

    2014-12-01

    Biogeochemical mineral dissolution is a promising method for the released of metals in low-grade host mineralization that contain sulphidic minerals. The application of biogeochemical mineral dissolution to engineered leach heap piles in the Elliot Lake region may be considered as a promising passive technology for the economic recovery of low grade Uranium-bearing ores. In the current investigation, the decrease of radiological activity of uraniferous mineral material after biogeochemical mineral dissolution is quantified by gamma spectroscopy and compared to the results from digestion/ICP-MS analysis of the ore materials to determine if gamma spectroscopy is a simple, viable alternative quantification method for heavy nuclides. The potential release of Uranium (U) and Radium-226 ((226)Ra) to the aqueous environment from samples that have been treated to represent various stages of leaching and passive closure processes are assessed. Dissolution of U from the solid phase has occurred during biogeochemical mineral dissolution in the presence of Acidithiobacillus ferrooxidans, with gamma spectroscopy indicating an 84% decrease in Uranium-235 ((235)U) content, a value in accordance with the data obtained by dissolution chemistry. Gamma spectroscopy data indicate that only 30% of the (226)Ra was removed during the biogeochemical mineral dissolution. Chemical inhibition and passivation treatments of waste materials following the biogeochemical mineral dissolution offer greater protection against residual U and (226)Ra leaching. Pacified samples resist the release of (226)Ra contained in the mineral phase and may offer more protection to the aqueous environment for the long term, compared to untreated or inhibited residues, and should be taken into account for future decommissioning. PMID:24726552

  9. Surface-subsurface flow linkage in a snowmelt environment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In much of the western USA streamflow and water resources are driven by snowmelt. Hydrologic objectives for addressing water issues have generally revolved around predicting the timing and amount of snowmelt input and assessing the impact on streamflow. Groundwater is generally overlooked. We provid...

  10. Surface-subsurface flow linkage in a snowmelt environment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In much of the inter-mountain western USA streamflow and water resources are driven by snowmelt. Hydrologic objectives for addressing water issues have generally revolved around predicting the timing and amount of snowmelt input and assessing the impact on streamflow. Groundwater is generally overlo...

  11. Mechanisms of Physical-Biological-Biogeochemical Interaction at the Oceanic Mesoscale

    NASA Astrophysics Data System (ADS)

    McGillicuddy, Dennis J.

    2016-01-01

    Mesoscale phenomena are ubiquitous and highly energetic features of ocean circulation. Their influence on biological and biogeochemical processes varies widely, stemming not only from advective transport but also from the generation of variations in the environment that affect biological and chemical rates. The ephemeral nature of mesoscale features in the ocean makes it difficult to elucidate the attendant mechanisms of physical-biological-biogeochemical interaction, necessitating the use of multidisciplinary approaches involving in situ observations, remote sensing, and modeling. All three aspects are woven through this review in an attempt to synthesize current understanding of the topic, with particular emphasis on novel developments in recent years.

  12. Mechanisms of Physical-Biological-Biogeochemical Interaction at the Oceanic Mesoscale.

    PubMed

    McGillicuddy, Dennis J

    2016-01-01

    Mesoscale phenomena are ubiquitous and highly energetic features of ocean circulation. Their influence on biological and biogeochemical processes varies widely, stemming not only from advective transport but also from the generation of variations in the environment that affect biological and chemical rates. The ephemeral nature of mesoscale features in the ocean makes it difficult to elucidate the attendant mechanisms of physical-biological-biogeochemical interaction, necessitating the use of multidisciplinary approaches involving in situ observations, remote sensing, and modeling. All three aspects are woven through this review in an attempt to synthesize current understanding of the topic, with particular emphasis on novel developments in recent years. PMID:26359818

  13. Use of the Water, Energy, and Biogeochemical Model (WEBMOD) to Simulate Water Quality at Five U.S. Geological Survey Research Watersheds

    NASA Astrophysics Data System (ADS)

    Webb, R. M.; Leavesley, G. H.; Shanley, J. B.; Peters, N. E.; Aulenbach, B. T.; Blum, A. E.; Campbell, D. H.; Clow, D. W.; Mast, M. A.; Stallard, R. F.; Larsen, M. C.; Troester, J. W.; Walker, J. F.; White, A. F.

    2003-12-01

    The Water, Energy, and Biogeochemical Model (WEBMOD) was developed as an aid to compare and contrast basic hydrologic and biogeochemical processes active in the diverse hydroclimatic regions represented by the five U.S. Geological Survey (USGS) Water, Energy, and Biogeochemical Budget (WEBB) sites: Loch Vale, Colorado; Trout Lake, Wisconsin; Sleepers River, Vermont; Panola Mountain, Georgia; and Luquillo Experimental Forest, Puerto Rico. WEBMOD simulates solute concentrations for vegetation canopy, snow pack, impermeable ground, leaf litter, unsaturated and saturated soil zones, riparian zones and streams using selected process modules coupled within the USGS Modular Modeling System (MMS). Source codes for the MMS hydrologic modules include the USGS Precipitation Runoff Modeling System, the National Weather Service Hydro-17 snow model, and TOPMODEL. The hydrologic modules distribute precipitation and temperature to predict evapotranspiration, snow accumulation, snow melt, and streamflow. Streamflow generation mechanisms include infiltration excess, saturated overland flow, preferential lateral flow, and base flow. Input precipitation chemistry, and fluxes and residence times predicted by the hydrologic modules are input into the geochemical module where solute concentrations are computed for a series of discrete well-mixed reservoirs using calls to the geochemical engine PHREEQC. WEBMOD was used to better understand variations in water quality observed at the WEBB sites from October 1991 through September 1997. Initial calibrations were completed by fitting the simulated hydrographs with those measured at the watershed outlets. Model performance was then refined by comparing the predicted export of conservative chemical tracers such as chloride, with those measured at the watershed outlets. The model succeeded in duplicating the temporal variability of net exports of major ions from the watersheds.

  14. High-resolution physical and biogeochemical variability from a shallow back reef on Ofu, American Samoa: an end-member perspective

    NASA Astrophysics Data System (ADS)

    Koweek, David A.; Dunbar, Robert B.; Monismith, Stephen G.; Mucciarone, David A.; Woodson, C. Brock; Samuel, Lianna

    2015-09-01

    Shallow back reefs commonly experience greater thermal and biogeochemical variability owing to a combination of coral community metabolism, environmental forcing, flow regime, and water depth. We present results from a high-resolution (sub-hourly to sub-daily) hydrodynamic and biogeochemical study, along with a coupled long-term (several months) hydrodynamic study, conducted on the back reefs of Ofu, American Samoa. During the high-resolution study, mean temperature was 29.0 °C with maximum temperatures near 32 °C. Dissolved oxygen concentrations spanned 32-178 % saturation, and pHT spanned the range from 7.80 to 8.39 with diel ranges reaching 0.58 units. Empirical cumulative distribution functions reveal that pHT was between 8.0 and 8.2 during only 30 % of the observational period, with approximately even distribution of the remaining 70 % of the time between pHT values less than 8.0 and greater than 8.2. Thermal and biogeochemical variability in the back reefs is partially controlled by tidal modulation of wave-driven flow, which isolates the back reefs at low tide and brings offshore water into the back reefs at high tide. The ratio of net community calcification to net community production was 0.15 ± 0.01, indicating that metabolism on the back reef was dominated by primary production and respiration. Similar to other back reef systems, the back reefs of Ofu are carbon sinks during the daytime. Shallow back reefs like those in Ofu may provide insights for how coral communities respond to extreme temperatures and acidification and are deserving of continued attention.

  15. 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...

  16. Hydrologic flowpaths and biogeochemical cycles in the subalpine Como Creek catchment, Colorado Front Range, USA

    NASA Astrophysics Data System (ADS)

    Cowie, R. M.; Williams, M. W.; Zeliff, M. M.; Parman, J.

    2011-12-01

    An outstanding question for snowmelt-dominated watersheds of the western US are the responses of biogeochemical processes to two major drivers of environmental change: directional changes in climate and increasing dissolved inorganic nitrogen (DIN) deposition in wetfall. In the Colorado Front Range, atmospheric deposition of DIN has increased several-fold in the last 25 years. In response, nitrate concentrations at the alpine Green Lakes 4 (GL4) catchment have increased from 1985 to 2009 by 0.27 μeq L-1 yr-1. In contrast, we see no directional change in either nitrate concentrations or fluxes in the subalpine Como Creek catchment. We hypothesize that differences in surface/groundwater interactions result in the differing behavior of stream nitrate between the alpine and subalpine catchments that are receiving similar amounts of DIN from atmospheric deposition. For both basins we sampled precipitation, snowpack, snowmelt, surface water, and subsurface waters. All water samples are analyzed for geochemical, nutrient and isotopic (δ18O, δD) composition. Stream chemistry data from the last ten years at Como Creek show increases in nitrate concentration during baseflow conditions and then a sharp decline during snowmelt. In contrast, in the alpine basin there is sharp increase in surface water nitrate during snowmelt. Hydrograph separation at the alpine GL4 using end member mixing analysis (EMMA) shows that stream flow is a mixture of three components, groundwater, talus, and new snowmelt that each contribute to roughly a third of discharge, with talus flow supplying the majority of nitrate. In contrast, and somewhat surprisingly, EMMA shows that for the subalpine Como Creek basin, annual streamflow is a mixture of only two components, groundwater and new snowmelt. During snowmelt the groundwater and snow contributions are nearly equal and subsurface flows dominate the remainder of the year. Newly installed piezometers at Como Creek provide evidence that the basin is largely a losing reach during snowmelt, with water levels in the piezometers increasing 5-7 m. After peak snowmelt however, Como Creek becomes a gaining stream, with piezometer levels dropping. Thus, both EMMA and piezometers show that surface-groundwater interactions are tightly coupled during snowmelt, with snowmelt at Como first replenishing the subsurface water deficit and increasing groundwater levels before contributing to discharge. Thus, in contrast to the alpine GL4 basin, DIN released in snowmelt is assimilated belowground as snowmelt infiltrates the subsurface in the subalpine basin. Interestingly, at the subalpine Como Creek basin, isotopic and geochemical solute concentrations undergo shifts during periods of winter baseflow prior to snowmelt. In winter much of the stream is frozen and we hypothesize that cryo-concentration of solutes and fractionation of isotopes may influence the concentrations of winter stream samples.

  17. 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 rapidly immobilized into biological pools (Liptzin and Silver 2009). Data suggest that Fe-redox cycling may decrease P limitation to NPP, and help maintain forest nutrient stocks. In summary, our results highlight the biogeochemical significance of Fe cycling in upland soils environments and its important role in the dynamics of humid tropical forests.

  18. 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 performed with assimilation of each data set, and compared to a control run. Differences in the products are discussed, along with their impact on model accuracy compared to in situ observations, and the representation of the carbon cycle in each hindcast.

  19. 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 (1.10.3 pM) generally agree with the observed present-day total Hg concentration profiles (1.40.9 pM). In the surface ocean, observations show average total Hg concentrations of 1.00.6 pM, while our natural ocean model shows an average concentration of 0.170.1 pM, indicating enrichment between present-day and natural condition by a factor of 5-6. The results show that Hg accumulates in the tropical ocean basins at depth due to the stronger particle sinking flux. Higher levels of surface concentration are also modeled in the upwelling regions in the subarctic North Pacific, subpolar North Atlantic and in the Southern Ocean. The modeled HgIIaq concentration in the deep North Pacific is approximately twice of that of the deep North Atlantic because of the accumulated source from particles removing Hg from the surface waters. The Hg0aq concentrations are highest in the Pacific equatorial intermediate ocean (1000 - 2000 m), where the remineralization rate is largest and oxygen concentrations are low. We will present preliminary results from a 560 year (1450 - 2008) coupled atmosphere-ocean Hg simulation with increasing anthropogenic input.

  20. Gene-centric approach to integrating environmental genomics and biogeochemical models

    PubMed Central

    Reed, Daniel C.; Algar, Christopher K.; Huber, Julie A.; Dick, Gregory J.

    2014-01-01

    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 by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving 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. PMID:24449851

  1. 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 (...

  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. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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.

  11. Gene-centric approach to integrating environmental genomics and biogeochemical models.

    PubMed

    Reed, Daniel C; Algar, Christopher K; Huber, Julie A; Dick, Gregory J

    2014-02-01

    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 by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving 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. PMID:24449851

  12. Hydrogen and carbon isotope geochemistry of freshwater aquifers at the Mizunami Underground Research Laboratory: Implications for ongoing biogeochemical processes in deep granitic rocks

    NASA Astrophysics Data System (ADS)

    Konno, U.; Fukuda, A.; Kouduka, M.; Komatsu, D. D.; Tsunogai, U.; Aosai, D.; Mizuno, T.; Suzuki, Y.

    2010-12-01

    Granite is one of major plutonic rocks and widely distributed in the terrestrial deep subsurface. Although many studies of biogeochemical processes have been carried out for granitic aquifers associated with seawater in Scandinavian countries, there is not much knowledge of biogeochemical processes mediated in those associated with freshwater. The Mizunami Underground Research Laboratory (MIU), which is located in Central Japan, provides us opportunities to investigate freshwater aquifers in granitic rocks. We collected groundwater samples from 200-m to 1150-m depths below ground level. We measured the concentration of methane, ethane, total inorganic carbon (TIC), molecular hydrogen, acetate, sulfate and ammonium, and the carbon and hydrogen isotopic compositions of methane and TIC. The concentration of methane increased with depth from 127 to 1164 μM, and TIC decreased from 1300 to 50 μM, respectively. The C1/C2+C3 ratios of >~800 indicated that methane might be biogenic. In contrast, the carbon and hydrogen isotopic composition of methane ranged from -42.6 to -26.9 ‰ and from -157 to -111 ‰, respectively, and the carbon isotopic composition of TIC ranged from -2.5 to -14.7 ‰. As the higher isotopic composition of methane and the difference in carbon isotopic composition between methane and TIC were around 30 ‰, the origin of main methane pool could be abiogenic. The concentration of hydrogen is the most sensitive indicator of ongoing biogeochemical processes. The higher level of hydrogen was consistent with acetogenesis at a depth of 300-m (~100 nM), while the lower level was indicative of sulfate reduction at a depth of 200-m (~1.5 nM). The depletion of sulfate and the enrichment of acetate in the 300-m deep groundwater agreed with the hydrogen profile. Interestingly, this redox shift was associated with an increase in ammonia concentration. The depth profiles of sulfate and methane in which sulfate reduction is coupled to methane oxidation have been obtained from the seawater granitic aquifers in Olkiluoto, Finland. Apparent lack of the profiles characterized by anaerobic methane oxidation in Mizunami groundwater might be attributed to the low level of sulfate. From our results, it is suggested that dominant biogeochemical processes mediated in the deep granitic rocks differ significantly between freshwater and seawater aquifer systems. This study was supported by grants from the Nuclear and Industrial Safety Agency (NISA).

  13. Hybrid Numerical Methods for Multiscale Simulations of Subsurface Biogeochemical Processes

    SciTech Connect

    Scheibe, Timothy D.; Tartakovsky, Alexandre M.; Tartakovsky, Daniel M.; Redden, George D.; Meakin, Paul

    2007-08-01

    Many subsurface flow and transport problems of importance today involve coupled non-linear flow, transport, and reaction in media exhibiting complex heterogeneity. In particular, problems involving biological mediation of reactions fall into this class of problems. Recent experimental research has revealed important details about the physical, chemical, and biological mechanisms involved in these processes at a variety of scales ranging from molecular to laboratory scales. However, it has not been practical or possible to translate detailed knowledge at small scales into reliable predictions of field-scale phenomena important for environmental management applications. A large assortment of numerical simulation tools have been developed, each with its own characteristic scale including molecular (e.g., molecular dynamics), microbial (e.g., cellular automata or particle individual-based models), pore (e.g., lattice-Boltzmann, pore network models, and discrete particle methods such as smoothed particle hydrodynamics) and continuum scales (e.g., traditional partial differential equations solved by finite difference or finite element methods). While many problems can be effectively addressed by one of these models at a single scale, some problems may require explicit integration of models across multiple scales. We are developing a hybrid multi-scale subsurface reactive transport modeling framework that integrates models with diverse representations of physics, chemistry and biology at different scales (sub-pore, pore and continuum). The modeling framework is being designed to take advantage of advanced computational technologies including parallel code components using the Common Component Architecture, parallel solvers, gridding, data and workflow management, and visualization. This paper describes the specific methods/codes being used at each scale, techniques used to directly and adaptively couple across model scales, and preliminary results of application to a multi-scale model of mineral precipitation at a solute mixing interface.

  14. Do antibiotics have environmental side-effects? Impact of synthetic antibiotics on biogeochemical processes.

    PubMed

    Roose-Amsaleg, Céline; Laverman, Anniet M

    2016-03-01

    Antibiotic use in the early 1900 vastly improved human health but at the same time started an arms race of antibiotic resistance. The widespread use of antibiotics has resulted in ubiquitous trace concentrations of many antibiotics in most environments. Little is known about the impact of these antibiotics on microbial processes or "non-target" organisms. This mini-review summarizes our knowledge of the effect of synthetically produced antibiotics on microorganisms involved in biogeochemical cycling. We found only 31 articles that dealt with the effects of antibiotics on such processes in soil, sediment, or freshwater. We compare the processes, antibiotics, concentration range, source, environment, and experimental approach of these studies. Examining the effects of ant