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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

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

    NASA Astrophysics Data System (ADS)

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

    2008-07-01

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

  3. 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

  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. Coupled Monitoring and Inverse Modeling to Investigate Surface - Subsurface Hydrological and Thermal Dynamics in the Arctic Tundra

    NASA Astrophysics Data System (ADS)

    Tran, A. P.; Dafflon, B.; Hubbard, S. S.; Bisht, G.; Peterson, J.; Ulrich, C.; Romanovsky, V. E.; Kneafsey, T. J.; Wu, Y.

    2015-12-01

    Quantitative characterization of the soil surface-subsurface hydrological and thermal processes is essential as they are primary factors that control the biogeochemical processes, ecological landscapes and greenhouse gas fluxes. In the Artic region, the surface-subsurface hydrological and thermal regimes co-interact and are both largely influenced by soil texture and soil organic content. In this study, we present a coupled inversion scheme that jointly inverts hydrological, thermal and geophysical data to estimate the vertical profiles of clay, sand and organic contents. Within this inversion scheme, the Community Land Model (CLM4.5) serves as a forward model to simulate the land-surface energy balance and subsurface hydrological-thermal processes. Soil electrical conductivity (from electrical resistivity tomography), temperature and water content are linked together via petrophysical and geophysical models. Particularly, the inversion scheme accounts for the influences of the soil organic and mineral content on both of the hydrological-thermal dynamics and the petrophysical relationship. We applied the inversion scheme to the Next Generation Ecosystem Experiments (NGEE) intensive site in Barrow, AK, which is characterized by polygonal-shaped arctic tundra. The monitoring system autonomously provides a suite of above-ground measurements (e.g., precipitation, air temperature, wind speed, short-long wave radiation, canopy greenness and eddy covariance) as well as below-ground measurements (soil moisture, soil temperature, thaw layer thickness, snow thickness and soil electrical conductivity), which complement other periodic, manually collected measurements. The preliminary results indicate that the model can well reproduce the spatiotemporal dynamics of the soil temperature, and therefore, accurately predict the active layer thickness. The hydrological and thermal dynamics are closely linked to the polygon types and polygon features. The results also enable the

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  8. 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.

  9. 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 ...

  10. 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

  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

  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. Isolating Effects of Terrain and Subsurface Heterogeneity on Land Surface Energy Fluxes using Coupled Surface-Subsurface Simulations

    NASA Astrophysics Data System (ADS)

    Rihani, J.; Maxwell, R. M.; Chow, F. K.

    2009-12-01

    Idealized simulations are used to study effects of terrain, subsurface formations, properties, land cover and climatology on the feedbacks between water table depth and energy fluxes at the land surface. Vertical and lateral water transport are taken into account in an interactive manner between overland and subsurface flow while having an explicit representation of the water table. This is done by using a three-dimensional variably saturated groundwater code (ParFlow) coupled to a land surface model (the Common Land Model). Results indicate a strong coupling between water table depth and land surface energy fluxes in certain transitional areas between very shallow and very deep water table locations along the hillsides of the simulation cases. Subsurface formations and properties are identified as having the strongest effect on the location, extent, and strength of coupling between water table depth and energy fluxes. These feedbacks are strongly affected by changing thickness of the top-most subsurface formation, and they become more complex as more layers are introduced in the system. Terrain has a more pronounced effect on the hydrology of the system than on the coupling between water table and energy fluxes. Vegetative land cover on the other hand has a small effect on hydrology and water table dynamics, but a large effect on the energy fluxes at the land surface. Two different climatologies are tested and similar trends are observed even with dramatically different atmospheric forcings. A drier climate however will produce narrower transition zones of coupling. This demonstrates that lateral surface and subsurface flows have a great effect on land surface fluxes even for very simplistic terrain and geologic settings. It is thus important that these results are extended to more realistic settings and applied to understand the more complicated coupling processes that occur in a real watershed.

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed Central

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

    2016-01-01

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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. A Coupled Model of Multiphase Flow, Reactive Biogeochemical Transport, Thermal Transport and Geo-Mechanics.

    NASA Astrophysics Data System (ADS)

    Tsai, C. H.; Yeh, G. T.

    2015-12-01

    In this investigation, a coupled model of multiphase flow, reactive biogeochemical transport, thermal transport and geo-mechanics in subsurface media is presented. It iteratively solves the mass conservation equation for fluid flow, thermal transport equation for temperature, reactive biogeochemical transport equations for concentration distributions, and solid momentum equation for displacement with successive linearization algorithm. With species-based equations of state, density of a phase in the system is obtained by summing up concentrations of all species. This circumvents the problem of having to use empirical functions. Moreover, reaction rates of all species are incorporated in mass conservation equation for fluid flow. Formation enthalpy of all species is included in the law of energy conservation as a source-sink term. Finite element methods are used to discretize the governing equations. Numerical experiments are presented to examine the accuracy and robustness of the proposed model. The results demonstrate the feasibility and capability of present model in subsurface media.

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

    NASA Astrophysics Data System (ADS)

    Arndt, Sandra

    2016-04-01

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. A coupled biogeochemical-Dynamic Energy Budget model as a tool for managing fish production ponds.

    PubMed

    Serpa, Dalila; Pousão-Ferreira, Pedro; Caetano, Miguel; Cancela da Fonseca, Luís; Dinis, Maria Teresa; Duarte, Pedro

    2013-10-01

    The sustainability of semi-intensive aquaculture relies on management practices that simultaneously improve production efficiency and minimize the environmental impacts of this activity. The purpose of the present work was to develop a mathematical model that reproduced the dynamics of a semi-intensive fish earth pond, to simulate different management scenarios for optimizing fish production. The modeling approach consisted of coupling a biogeochemical model that simulated the dynamics of the elements that are more likely to affect fish production and cause undesirable environmental impacts (nitrogen, phosphorus and oxygen) to a fish growth model based on the Dynamic Energy Budget approach. The biogeochemical sub-model successfully simulated most water column and sediment variables. A good model fit was also found between predicted and observed white seabream (Diplodus sargus) growth data over a production cycle. In order to optimize fish production, different management scenarios were analysed with the model (e.g. increase stocking densities, decrease/increase water exchange rates, decrease/increase feeding rates, decrease phosphorus content in fish feeds, increase food assimilation efficiency and decrease pellets sinking velocity) to test their effects on the pond environment as well as on fish yields and effluent nutrient discharges. Scenarios were quantitatively evaluated and compared using the Analytical Hierarchical Process (AHP) methodology. The best management options that allow the maximization of fish production while maintaining a good pond environment and minimum impacts on the adjacent coastal system were to double standard stocking densities and to improve food assimilation efficiency. PMID:23872182

  12. 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

  13. 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

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

    NASA Astrophysics Data System (ADS)

    Dale, Andy; Stolpovsky, Konstantin; Wallmann, Klaus

    2016-04-01

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. 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.

  19. 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

  20. Modeling Nitrogen Leaching With A Biogeochemical Model Coupled With Soil Hydrology Model

    NASA Astrophysics Data System (ADS)

    Barman, R.; Yang, X.; Jain, A.; Post, W. M.; Sivapalan, M.

    2008-12-01

    Land use changes for cropland, excessive application of fertilizers in agriculture, and increase in anthropogenic activities such as fossil fuel burning have lead to widespread increases in anthropogenic production of reactive N and NH3 emissions, and N deposition rates. An important consequence of these processes is intensification of soil nutrient leaching activities, leading to serious ground water contamination problems. The current study focuses on the issue of nitrogen (nitrate and ammonium) leaching due to land cover changes for cropland, excess N fertilizer application, and atmospheric nitrogen deposition on nitrogen leaching at a global scale. Simulations of nitrogen leaching require integration of processes involving soil hydrology and biogeochemical cycles. An existing terrestrial coupled carbon-nitrogen cycle model, Integrated Science Assessment Model (ISAM), was used to estimate nitrogen leaching. The N-cycle in ISAM includes the major processes associated with nitrogen (immobilization, mineralization, nitrification, denitrification, leaching, nitrogen fixation, and vegetation nitrogen uptake). ISAM also considers how carbon and nitrogen dynamics are influenced by the effects of human perturbations to the N cycle including atmospheric deposition and fertilizer application, and the fate of N in land use activities, i.e., deforestation and agricultural harvest. In this study, the ISAM soil hydrology was extended and improved with CLM 3.5 hydrology processes and algorithms, which extended the modeling capabilities to consider the prediction of nitrogen leaching. The model performance was evaluated with flow and nutrient data at several locations within the Upper Sangamon River Basin in Illinois, and flow data in contrasting watersheds in Oklahoma. This talk will focus on describing the results of a series of modeling experiments examining the influence of land management changes for cropland and nitrogen deposition on nitrogen leaching at a global scale

  1. 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

  2. Controllability of mixing errors in a coupled physical biogeochemical model of the North Atlantic: a nonlinear study using anamorphosis

    NASA Astrophysics Data System (ADS)

    Béal, D.; Brasseur, P.; Brankart, J.-M.; Ourmières, Y.; Verron, J.

    2009-06-01

    In biogeochemical models coupled to ocean circulation models, vertical mixing is an important physical process which governs the nutrient supply and the plankton residence in the euphotic layer. However, mixing is often poorly represented in numerical simulations because of approximate parameterizations of sub-grid scale turbulence, wind forcing errors and other mis-represented processes such as restratification by mesoscale eddies. Getting a sufficient knowledge of the nature and structure of these error sources is necessary to implement appropriate data assimilation methods and to evaluate their controllability by a given observation system. In this paper, Monte Carlo simulations are conducted to study mixing errors induced by approximate wind forcings in a three-dimensional coupled physical-biogeochemical model of the North Atlantic with a 1/4° horizontal resolution. An ensemble forecast involving 200 members is performed during the 1998 spring bloom, by prescribing realistic wind perturbations to generate mixing errors. It is shown that the biogeochemical response can be rather complex because of nonlinearities and threshold effects in the coupled model. In particular, the response of the surface phytoplankton depends on the region of interest and is particularly sensitive to the local stratification. We examine the robustness of the statistical relationships computed between the various physical and biogeochemical variables, and we show that significant information on the ecosystem can be obtained from observations of chlorophyll concentration or sea surface temperature. In order to improve the analysis step of sequential assimilation schemes, we propose to perform a simple nonlinear change of variables that operates separately on each state variable, by mapping their ensemble percentiles on the Gaussian percentiles. It is shown that this method is able to substantially reduce the estimation error with respect to the linear estimates computed by the Kalman

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. 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.

  16. Biogeochemical Transformation Pathways through the Land-water Geosphere

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  17. 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

  18. 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

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

    PubMed

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

    2015-05-01

    Carbon isotopic analysis and molecular-based methods were used in conjunction with geochemical data sets to assess the dechlorination of pentachlorophenol (PCP) when coupled to biogeochemical processes in a mangrove soil having no prior history of anthropogenic contamination. The PCP underwent 96% dechlorination in soil amended with acetate, compared to 21% dehalogenation in control soil. Carbon isotope analysis of residual PCP demonstrated an obvious enrichment of 13C (εC, -3.01±0.1%). Molecular and statistical analyses demonstrated that PCP dechlorination and Fe(III) reduction were synergistically combined electron-accepting processes. Microbial community analysis further suggested that enhanced dechlorination of PCP during Fe(III) reduction was mediated by members of the multifunctional family of Geobacteraceae. In contrast, PCP significantly suppressed the growth of SO4(2-) reducers, which, in turn, facilitated the production of CH4 by diversion of electrons from SO4(2-) reduction to methanogenesis. The integrated data regarding stoichiometric alterations in this study gives direct evidence showing PCP, Fe(III), and SO4(2-) reduction, and CH4 production are coupled microbial processes during changes in soil redox. PMID:25853431

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

    NASA Astrophysics Data System (ADS)

    Liu, X.

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  2. 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

  3. 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

  4. 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

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

    SciTech Connect

    Crawford, Ronald L; Paszczynski, Andrzej J

    2010-02-19

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

  6. 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.

  7. Characterization of mixing errors in a coupled physical biogeochemical model of the North Atlantic: implications for nonlinear estimation using Gaussian anamorphosis

    NASA Astrophysics Data System (ADS)

    Béal, D.; Brasseur, P.; Brankart, J.-M.; Ourmières, Y.; Verron, J.

    2010-02-01

    In biogeochemical models coupled to ocean circulation models, vertical mixing is an important physical process which governs the nutrient supply and the plankton residence in the euphotic layer. However, vertical mixing is often poorly represented in numerical simulations because of approximate parameterizations of sub-grid scale turbulence, wind forcing errors and other mis-represented processes such as restratification by mesoscale eddies. Getting a sufficient knowledge of the nature and structure of these errors is necessary to implement appropriate data assimilation methods and to evaluate if they can be controlled by a given observation system. In this paper, Monte Carlo simulations are conducted to study mixing errors induced by approximate wind forcings in a three-dimensional coupled physical-biogeochemical model of the North Atlantic with a 1/4° horizontal resolution. An ensemble forecast involving 200 members is performed during the 1998 spring bloom, by prescribing perturbations of the wind forcing to generate mixing errors. The biogeochemical response is shown to be rather complex because of nonlinearities and threshold effects in the coupled model. The response of the surface phytoplankton depends on the region of interest and is particularly sensitive to the local stratification. In addition, the statistical relationships computed between the various physical and biogeochemical variables reflect the signature of the non-Gaussian behaviour of the system. It is shown that significant information on the ecosystem can be retrieved from observations of chlorophyll concentration or sea surface temperature if a simple nonlinear change of variables (anamorphosis) is performed by mapping separately and locally the ensemble percentiles of the distributions of each state variable on the Gaussian percentiles. The results of idealized observational updates (performed with perfect observations and neglecting horizontal correlations) indicate that the implementation

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  9. 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

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    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.

  12. 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.

  13. 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

  14. A parallel computational framework for integrated surface-subsurface flow and transport simulations

    NASA Astrophysics Data System (ADS)

    Park, Y.; Hwang, H.; Sudicky, E. A.

    2010-12-01

    HydroGeoSphere is a 3D control-volume finite element hydrologic model describing fully-integrated surface and subsurface water flow and solute and thermal energy transport. Because the model solves tighly-coupled highly-nonlinear partial differential equations, often applied at regional and continental scales (for example, to analyze the impact of climate change on water resources), high performance computing (HPC) is essential. The target parallelization includes the composition of the Jacobian matrix for the iterative linearization method and the sparse-matrix solver, a preconditioned Bi-CGSTAB. The matrix assembly is parallelized by using a coarse-grained scheme in that the local matrix compositions can be performed independently. The preconditioned Bi-CGSTAB algorithm performs a number of LU substitutions, matrix-vector multiplications, and inner products, where the parallelization of the LU substitution is not trivial. The parallelization of the solver is achieved by partitioning the domain into equal-size subdomains, with an efficient reordering scheme. The computational flow of the Bi-CGSTAB solver is also modified to reduce the parallelization overhead and to be suitable for parallel architectures. The parallelized model is tested on several benchmark simulations which include linear and nonlinear flow problems involving various domain sizes and degrees of hydrologic complexities. The performance is evaluated in terms of computational robustness and efficiency, using standard scaling performance measures. The results of simulation profiling indicate that the efficiency becomes higher with an increasing number of nodes/elements in the mesh, for increasingly nonlinear transient simulations, and with domains of irregular geometry. These characteristics are promising for the large-scale analysis water resources problems involved integrated surface/subsurface flow regimes.

  15. 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.

  16. Quantifying the dynamic coupling of hydrologic and biogeochemical processes in stream ecosystems: examples from streams in the McMurdo Dry Valleys, Antarctica

    NASA Astrophysics Data System (ADS)

    McKnight, D. M.; Lyons, W. B.; Gooseff, M. N.; Koch, J. C.; Neupauer, R.; Cozzetto, K.; Bencala, K.; Cullis, J. D.

    2014-12-01

    While continuous monitoring of stream flow and stream temperature has been a widely used resource for some time, currently there is great potential to expand continuous monitoring to include important water quality parameters such as nutrients and dissolved organic material. In many systems distinguishing between watershed and stream ecosystem controls can be challenging, and the usefulness of such monitoring can be enhanced by application of quantitative models to interpret observed patterns. The glacial meltwater streams of the McMurdo Dry Valleys, Antarctica, are surrounded by large expanses of patterned ground devoid of plants. In contrast, many streams have thriving cyanobacterial mats that are freeze-dried through the winter and begin photosynthesis with the onset of flow. Thus, the daily signal in terms of biogeochemical processes controlling water quality is generated within the stream. 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 of major ions, microbial cycling of nitrogen species, and streams temperature regulation. We have also adapted modelling approaches from sediment transport to understand mobilization of stream biomass with increasing flows. These models are relevant to understanding the role of in-stream processes in diverse stream systems where watershed processes also contribute to observed patterns.

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Shokri, Ali; Bardsley, William Earl

    2016-06-01

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

  20. 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.

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

    NASA Technical Reports Server (NTRS)

    Watson, Gregg W.

    2000-01-01

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

  2. 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).

  3. A comparison of coupled biogeophysical and biogeochemical dynamics across a precipitation gradient in Oregon using data assimilation

    NASA Astrophysics Data System (ADS)

    Pettijohn, J. C.; Law, B. E.; Williams, M. D.; Stoekli, R.; Thornton, P. E.; Thomas, C. K.; Hudiburg, T. W.; Martin, J.

    2010-12-01

    We present results from our coupled biophysical - biochemical model data fusion (MDF) analysis across a climatic gradient in Oregon, USA, using data from a coast-range Douglas-fir (US-Fir; 2006-2008) and a semi-arid ponderosa pine (US-Me2; 2002-2008) AmeriFlux site. Our MDF scheme couples the Ensemble Kalman Filter (EnKF) with the National Center for Atmospheric Research (NCAR) Community Land Model with Carbon-Nitrogen coupling (CLM-CN, version 3.5). Assimilated data includes continuous eddy covariance measurements of forest-atmosphere CO2 (NEE, net ecosystem exchange) and water vapor fluxes (λE, latent heat flux), chamber-based soil respiratory flux, soil moisture and temperature, snow depth (US-Me2), MODIS-derived 8 day LAI, and carbon and nitrogen pools. We quantify the ecosystem carbon and nitrogen budgets, partition NEE and λE fluxes, and thus increase confidence in multi-scale controls on CO2 and water vapor exchange. The MDF did a better job predicting NEE than λE at both sites (r2 = 0.86 for NEE at both sites; λE r2 = 0.65 and 0.63 at the US-ME2 and US-Fir sites, respectively) partly due to a weighting scheme we prescribed for NEE. The distribution of carbon and nitrogen differed significantly between sites, with total ecosystem carbon (vegetation, detritus, soil) of the US-Fir site being about 1.4 times higher than the US-Me2 site (35 kg C m-2 vs. 25 kg C m-2). Mean NEE over overlapping water years ‘07-‘08 was -495 gC m-2 at the US-Me2 site as opposed to -809 gC m-2 at the US-Fir site, nearly a two-fold difference in C uptake across this precipitation gradient. Average GPP and ecosystem respiration (Re) over these two water years were both ~1.7x greater at the US-Fir site, with 1712 gC m^-2 and 1217 gC m-2, respectively, at the US-Me2 site vs. 2841 gC m-2 and 2032 gC m-2 at the US-Fir. Autotrophic respiration contributed 79% and 72% to the Re flux at the US-Me2 and US-Fir sites, respectively, with total soil respiration contributing 53% and 58% to

  4. HydroSphere: Fully-Integrated, Surface/Subsurface Numerical Model for Watershed Analysis of Hydrologic, Water Quality and Sedimentation Processes

    NASA Astrophysics Data System (ADS)

    Matanga, G. B.; Nelson, K. E.; Sudicky, E.; Therrien, R.; Panday, S.; McLaren, R.; Demarco, D.; Gessford, L.

    2004-12-01

    A distributed, physically based and fully-coupled surface/subsurface numerical model, HydroSphere, has recently been developed for watershed analysis of hydrologic and water quality processes. It accounts for flow and transport in lateral two-dimensional surface water, one-dimensional tile drains and three-dimensional variably-saturated subsurface water. One-, two- and three-dimensional forms of the advection-dispersion equation are used to describe solute transport in the tile drains, surface water and subsurface water, respectively. Full integration of the surface, tile-drain and subsurface water regimes is achieved by assembling and solving one system of discrete algebraic equations, such that surface flow rates and water depths, tile-drain flow rates and water depths, subsurface pressure heads, saturations and velocities, as well as water fluxes between continua, are determined simultaneously. Likewise, discrete advective-dispersive transport equations for the various continua are solved simultaneously to obtain the solute concentrations in the surface, tile-drain and subsurface systems. One of the major issues calling for capabilities of surface/subsurface water interactions, water quality and erosion/sedimentation is the optimal management of water supply for fish and agricultural irrigation. For example, the USGS has demonstrated that the massive September 2002 fish-kill in the Klamath River Basin was caused by low 2002 streamflows and the resulting high water temperatures. The streams in the Klamath River Basin are fed primarily by ground water. The 2002 streamflows were lower than the flows predicted by Bureau of Reclamation based on the snowpack data alone, neglecting subsurface water data. It is also well-known that erosion/sedimentation processes impair fish habitat by impacting spawning gravel areas and upstream migration to spawning areas. The models currently being applied in the Klamath River Basin and in all Bureau of Reclamation Regions completely

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

    DOE PAGESBeta

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

    2016-08-11

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

  6. 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.

  7. 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

  8. 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.

  9. High-resolution reactive transport: A coupled parallel hydrogeochemical model

    NASA Astrophysics Data System (ADS)

    Beisman, J. J.; Maxwell, R. M.; Steefel, C. I.; Sitchler, A.; Molins, S.

    2013-12-01

    Subsurface hydrogeochemical systems are an especially complex component of the terrestrial environment and play host to a multitude of interactions. Parameterizations of these interactions are perhaps the least understood component of terrestrial systems, presenting uncertainties in the predictive understanding of biogeochemical cycling and transport. Thorough knowledge of biogeochemical transport processes is critical to the quantification of carbon/nutrient fluxes in the subsurface, and to the development of effective contaminant remediation techniques. Here we present a coupled parallel hydrogeochemical model, ParCrunchFlow, as a tool to further our understanding of governing processes and interactions in natural hydrogeochemical systems. ParCrunchFlow is a coupling of the reactive transport simulator CrunchFlow with the hydrologic model ParFlow. CrunchFlow is a multicomponent reactive flow and transport code that can be used to simulate a range of important processes and environments, including reactive contaminant transport, chemical weathering, carbon sequestration, biogeochemical cycling, and water-rock interaction. ParFlow is a parallel, three-dimensional, variably-saturated, coupled surface-subsurface flow and transport code with the ability to simulate complex topography, geology, and heterogeneity. ParCrunchflow takes advantage of the efficient parallelism built into Parflow, allowing the numerical simulation of reactive transport processes in chemically and physically heterogeneous media at high spatial resolutions. This model provides an ability to further examine the interactions and feedbacks between biogeochemical systems and complex subsurface flow fields. In addition to the details of model construction, results will be presented that show floodplain nutrient cycling and the effects of heterogeneity on small-scale mixing reactions at the Department of Energy's Old Rifle Legacy site.

  10. 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.

  11. Analysis of mixing and biogeochemical effects induced by tides on the Atlantic Mediterranean flow in the Strait of Gibraltar through a physical biological coupled model

    NASA Astrophysics Data System (ADS)

    Macías, D.; Martin, A. P.; García-Lafuente, J.; García, C. M.; Yool, A.; Bruno, M.; Vázquez-Escobar, A.; Izquierdo, A.; Sein, D. V.; Echevarría, F.

    2007-08-01

    The output of a two-layer hydrodynamic model along a west-east section of the Gibraltar Strait is used to estimate tidal induced mixing between the Mediterranean and Atlantic water layers and to simulate the effects of mixing processes on biogeochemical fluxes and the pelagic community of the area. The hydrodynamic model is used to estimate interfacial mixing and water advection which drive the dynamics of the pelagic community. The model was run for 13 months, in order to analyse the effect of annual modulations in tidal amplitude on mixing. Incorporation of a third intermediate layer leads to a significant improvement in the model results, showing the necessity for a three layer circulation scheme when modelling biogeochemical processes in the Strait of Gibraltar. Pelagic processes are modelled using a simple Nutrient-Phytoplankton-Zooplankton (NPZ) model. The intense physical mixing and advection in the channel are the main influence on plankton dynamics in the area. It is found that residence times within the channel are so short that phytoplankton communities cannot grow appreciably during their transit. As a consequence, the use of a more sophisticated biogeochemical model does not lead to significant changes in the results obtained. According to the model, mixing over the Camarinal Sill causes an average of 16% of the out-flowing nutrients to be returned back to the Mediterranean. This fraction varies between 4% and 35% as a function of the tidal amplitude. The comparison of the model results with field data suggests that in order to obtain an accurate simulation of the plankton ecosystem dynamics in the strait, it is necessary to take into account the full horizontal flow, as recirculation and coast-channel interactions seems to be very important processes in explaining the biological patterns in the area.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  14. 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

  15. 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.

  16. A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 for UVic 2.9

    NASA Astrophysics Data System (ADS)

    Nickelsen, L.; Keller, D. P.; Oschlies, A.

    2015-05-01

    Marine biological production as well as the associated biotic uptake of carbon in many ocean regions depends on the availability of nutrients in the euphotic zone. While large areas are limited by nitrogen and/or phosphorus, the micronutrient iron is considered the main limiting nutrient in the North Pacific, equatorial Pacific and Southern Ocean. Changes in iron availability via changes in atmospheric dust input are discussed to play an important role in glacial-interglacial cycles via climate feedbacks caused by changes in biological ocean carbon sequestration. Although many aspects of the iron cycle remain unknown, its incorporation into marine biogeochemical models is needed to test our current understanding and better constrain its role in the Earth system. In the University of Victoria Earth System Climate Model (UVic) iron limitation in the ocean was, until now, simulated pragmatically with an iron concentration masking scheme that did not allow a consistent interactive response to perturbations of ocean biogeochemistry or iron cycling sensitivity studies. Here, we replace the iron masking scheme with a dynamic iron cycle and compare the results to available observations and the previous marine biogeochemical model. Sensitivity studies are also conducted with the new model to test the sensitivity of the model to parameterized iron ligand concentrations, the importance of considering the variable solubility of iron in dust deposition, the importance of considering high-resolution bathymetry for the sediment release of iron, the effect of scaling the sedimentary iron release with temperature and the sensitivity of the iron cycle to a climate change scenario.

  17. 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

  18. 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

  19. 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

  20. 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.

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

    SciTech Connect

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

    2013-08-14

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

  2. 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.

  3. 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.

  4. 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...

  5. 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.

  6. Modeling study on the surface morphology evolution during removing the optics surface/subsurface damage using atmospheric pressure plasma processing

    NASA Astrophysics Data System (ADS)

    Xin, Qiang; Su, Xing; Wang, Bo

    2016-09-01

    Plasma processing has been widely reported as an effective tool in relieving or removing surface/subsurface damage induced by previous mechanical machining process. However, the surface morphology evolution during removing the damage using plasma processing is rarely reported. In this research, this procedure is studied based on experiments and robust numerical models developed on the basis of Level Set Method (LSM). Even if some unique properties of plasma etching are observed, such as particle redistribution, the dominant role of isotropic etching of plasma processing is verified based on experiments and 2D LSM simulations. With 2D LSM models, the damage removal process under various damage characteristics is explored in detail. Corresponding peak-to-valley roughness evolution is investigated as well. Study on morphology evolution is also conducted through the comparison between experiments and 3D LSM computations. The modeling results and experiments show good agreement with each other. The trends of simulated roughness evolution agree with the experiments as well. It is revealed that the plasma processing may end up with a planar surface depending on the damage characteristics. The planarization procedure can be divided into four parts: crack opening and pit formation; pit coalescing and shallow pits subsumed by deep ones; morphology duplicate etching; and finally a planar and damage free surface.

  7. 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.

  8. 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

  9. 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."

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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).

  15. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  17. Biogeochemical modeling at mass extinction boundaries

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  18. 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.

  19. 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

  20. 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.

  1. 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)

  2. Eddy Permitting Simulations of Biogeochemical Cycles in the Global Ocean

    NASA Astrophysics Data System (ADS)

    Sumata, H.; Hashioka, T.; Suzuki, T.; Yamanaka, Y.

    2008-12-01

    A 3D ecosystem-biogeochemical model simulation for the global domain is performed in order to investigate variability of oceanic ecosystem on time scales of years to decades. The model has a horizontal resolution of 1/4 times 1/6 degrees and 51 vertical levels, covering the entire domain of the world ocean. The ecosystem- biogeochemical part of the model is based on NEMURO (North Pacific Ecosystem Model Used for Regional Oceanography), and is coupled with CCSR Ocean Component Model (COCO) version 4.3 by an offline technique. The physical part of the model is driven by the inter-annual forcing by common ocean-ice reference experiments (CORE) data from 1958 to 2004, and reasonably simulates inter-annual to decadal variabilities of ocean conditions related to biogeochemical cycles. These properties of the physical model with its eddying filed enable us to reproduce the realistic distributions of nutrients and plankton productions. Comparisons with historical station data show that the model also reasonably simulates the observed variabilities of ecosystem on time scales of years to decades. In particular, the model captures the transitions of biogeochemical cycles associated with regime shifts.

  3. Biogeochemical cycling and remote sensing

    NASA Technical Reports Server (NTRS)

    Peterson, D. L.

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Laurent, Arnaud; Fennel, Katja; Wilson, Robin; Lehrter, John; Devereux, Richard

    2014-05-01

    Sediment biogeochemical processes are important drivers of water column biogeochemistry in coastal areas. For example, sediment oxygen consumption can be an important driver of bottom water oxygen depletion in hypoxic systems, and sediment-water nutrient fluxes support primary productivity in the overlying water column. Yet, biogeochemical sediment-water fluxes are often parameterized crudely and only poorly constrained in coupled physical-biogeochemical models. Here, we present a method for parameterizing biogeochemical sediment-water fluxes realistically and efficiently, using in-situ measurements and a steady state diagenetic model. We apply this method to the Louisiana Shelf where high primary production induced by excess nutrient loads from the Mississippi-Atchafalaya River system promotes the development of hypoxic bottom waters in summer. The implementation of the parameterizations in a coupled circulation-biogeochemical model of the northern Gulf of Mexico results in realistic sediment-water fluxes that enable a sediment-water column feedback at low bottom oxygen concentrations.

  5. 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

  6. 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

  7. 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)

  8. 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

  9. 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.

  10. The global troposphere: Biogeochemical cycles, chemistry, and remote sensing.

    PubMed

    Levine, J S; Allario, F

    1982-09-01

    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, we review 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. We also consider future thrusts in remote sensing of the troposphere. PMID:24264018

  11. 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.

  12. Development of assimilative biogeochemical ocean models for operational and research applications

    NASA Astrophysics Data System (ADS)

    Brasseur, Pierre

    The Green-Mercator project (2007-2009, http://mercator-vert.ipsl.jussieu.fr/) aims at implementing the marine biogeochemical model PISCES at global scale into the MERCATOR operational monitoring and forecasting system. Besides the development of the model system itself, this project relies on two major research activities to improve biogeochemical simulations: (1) the refinement of process resolution to investigate the impact of the transition between eddy permitting to eddy resolving on biogeochemical simulations at global scale, and (2) the assimilation of physical and biogeochemical data (such as ocean color) into the model. The project also includes research activities to demonstrate the potential of an operational biogeochemical model for regional downscaling and extension towards marine resources. In this talk, we will focus on developments achieved in the framework of the E.U. MERSEA project (2004-2008) to assimilate satellite and in situ data into coupled models. Experiments using the SEEK filter in a North Atlantic prototype at 1/4° resolution illustrate the feasability of the approach. The results show that traditional methods such as the Kalman filter may lead to physical inconsistencies originating from the gaussian nature of the KF analysis scheme. A new scheme based on truncated gaussian pdfs is therefore developed (TGF) to integrate inequality constraints during the assimilation process. This new scheme represents a major step toward the assimilation of a variety of satellite data, such as sea-ice thickness and ocean colour data, into coupled models.

  13. 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.

  14. Cretaceous-Palaeogene experiments in Biogeochemical Resilience

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  20. PFLOTRAN: Recent Developments Facilitating Massively-Parallel Reactive Biogeochemical Transport

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.

    2015-12-01

    With the recent shift towards modeling carbon and nitrogen cycling in support of climate-related initiatives, emphasis has been placed on incorporating increasingly mechanistic biogeochemistry within Earth system models to more accurately predict the response of terrestrial processes to natural and anthropogenic climate cycles. PFLOTRAN is an open-source subsurface code that is specialized for simulating multiphase flow and multicomponent biogeochemical transport on supercomputers. The object-oriented code was designed with modularity in mind and has been coupled with several third-party simulators (e.g. CLM to simulate land surface processes and E4D for coupled hydrogeophysical inversion). Central to PFLOTRAN's capabilities is its ability to simulate tightly-coupled reactive transport processes. This presentation focuses on recent enhancements to the code that enable the solution of large parameterized biogeochemical reaction networks with numerous chemical species. PFLOTRAN's "reaction sandbox" is described, which facilitates the implementation of user-defined reaction networks without the need for a comprehensive understanding of PFLOTRAN software infrastructure. The reaction sandbox is written in modern Fortran (2003-2008) and leverages encapsulation, inheritance, and polymorphism to provide the researcher with a flexible workspace for prototyping reactions within a massively parallel flow and transport simulation framework. As these prototypical reactions mature into well-accepted implementations, they can be incorporated into PFLOTRAN as native biogeochemistry capability. Users of the reaction sandbox are encouraged to upload their source code to PFLOTRAN's main source code repository, including the addition of simple regression tests to better ensure the long-term code compatibility and validity of simulation results.

  1. 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.

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

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

    PubMed

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

    2012-01-01

    Substantially different biogeochemical processes affecting nitrogen fate and transport were observed beneath two stormwater infiltration basins in north-central Florida. Differences are related to soil textural properties that deeply link hydroclimatic conditions with soil moisture variations in a humid, subtropical climate. During 2008, shallow groundwater beneath the basin with predominantly clayey soils (median, 41% silt+clay) exhibited decreases in dissolved oxygen from 3.8 to 0.1 mg L and decreases in nitrate nitrogen (NO-N) from 2.7 mg L to <0.016 mg L, followed by manganese and iron reduction, sulfate reduction, and methanogenesis. In contrast, beneath the basin with predominantly sandy soils (median, 2% silt+clay), aerobic conditions persisted from 2007 through 2009 (dissolved oxygen, 5.0-7.8 mg L), resulting in NO-N of 1.3 to 3.3 mg L in shallow groundwater. Enrichment of δN and δO of NO combined with water chemistry data indicates denitrification beneath the clayey basin and relatively conservative NO transport beneath the sandy basin. Soil-extractable NO-N was significantly lower and the copper-containing nitrite reductase gene density was significantly higher beneath the clayey basin. Differences in moisture retention capacity between fine- and coarse-textured soils resulted in median volumetric gas-phase contents of 0.04 beneath the clayey basin and 0.19 beneath the sandy basin, inhibiting surface/subsurface oxygen exchange beneath the clayey basin. Results can inform development of soil amendments to maintain elevated moisture content in shallow soils of stormwater infiltration basins, which can be incorporated in improved best management practices to mitigate NO impacts. PMID:22370419

  11. 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.

  12. The interaction between biogeophysical and biogeochemical processes and their feedback on permafrost soil carbon stocks

    NASA Astrophysics Data System (ADS)

    ElMasri, B.; Barman, R.; Jain, A. K.

    2013-12-01

    Our current understanding of the full suite of processes and their responses to recent warming in terrestrial high-latitudes are far from complete. While continued research on development of more detailed Earth system models (ESMs) is essential to understand the interactions and feedbacks between vegetation, soils and climate change in the Northern high latitudes (NHL), one of the major challenges is the treatment of the biophysical and biogeochemical processes and feedback in the ESM and their impact on soil organic carbon. We used a land surface model, the Integrated Science Assessment Model (ISAM), which coupled carbon-nitrogen biogeochemical and energy and hydrology biogeophysical processes, to investigate the effects of feedbacks between the biogeochemical and biogeophysical processes on the model estimated soil organic carbon (SOC) for the NHL permafrost region. We not only focused on recent improvement in the ISAM biogeophysical processes that are deemed important for the high latitude soils/snow; such as deep soil column, modulation of soil thermal and hydrological properties, wind compaction of snow, and depth hoar formation; on permafrost SOC, but also biogeochemical processes; such as dynamic phenology and root distribution, litter carbon decomposition rates and nitrogen amount remaining; on soil biogeochemistry. We selected multiple sites representative of different high latitude biomes to calibrate and evaluate the model. We then carried out several ISAM model simulations to study the effects of feedbacks between biogeochemical and biogeophysical processes on SOC. Our model analysis shows that including the biogeophysical processes alone could increase modeled Northern high-latitude permafrost carbon by about 30% compared to measurements. Accounting for the biogeochmical processes further improve the NHL soil carbon. This study demonstrates that improvements in biogeophysical or biogeochemical processes alone does not help to improve the modeled SOC

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

    PubMed

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

    2012-08-15

    Soil beneath a stormwater infiltration basin receiving runoff from a 23 ha predominantly residential watershed in north-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 an innovative stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO(3)(-)/Cl(-)) ratios for the shallow groundwater indicates that prior to using BAM, NO(3)(-) concentrations were substantially influenced by nitrification or variations in NO(3)(-) input. In contrast, for the new basin utilizing BAM, NO(3)(-)/Cl(-) ratios indicate minor nitrification and NO(3)(-) 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 that NO(3)(-) 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 the 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 (PO(4)(3-)) 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 PO(4)(3-)/Cl(-) ratios for shallow

  14. Biogeochemical weathering under ice: Size matters

    NASA Astrophysics Data System (ADS)

    Wadham, J. L.; Tranter, M.; Skidmore, M.; Hodson, A. J.; Priscu, J.; Lyons, W. B.; Sharp, M.; Wynn, P.; Jackson, M.

    2010-09-01

    The basal regions of continental ice sheets are gaps in our current understanding of the Earth's biosphere and biogeochemical cycles. We draw on existing and new chemical data sets for subglacial meltwaters to provide the first comprehensive assessment of sub-ice sheet biogeochemical weathering. We show that size of the ice mass is a critical control on the balance of chemical weathering processes and that microbial activity is ubiquitous in driving dissolution. Carbonate dissolution fueled by sulfide oxidation and microbial CO2 dominate beneath small valley glaciers. Prolonged meltwater residence times and greater isolation characteristic of ice sheets lead to the development of anoxia and enhanced silicate dissolution due to calcite saturation. We show that sub-ice sheet environments are highly geochemically reactive and should be considered in regional and global solute budgets. For example, calculated solute fluxes from Antarctica (72-130 t yr-1) are the same order of magnitude as those from some of the world's largest rivers and rates of chemical weathering (10-17 t km-2 yr-1) are high for the annual specific discharge (2.3-4.1 × 10-3 m). Our model of chemical weathering dynamics provides important information on subglacial biodiversity and global biogeochemical cycles and may be used to design strategies for the first sampling of Antarctic Subglacial Lakes and other sub-ice sheet environments for the next decade.

  15. Catchment Legacies and Trajectories: Hydrologic and Biogeochemical Controls

    NASA Astrophysics Data System (ADS)

    Basu, N. B.; Loukinova, N. V.

    2012-04-01

    Increased nutrient loads delivered from watersheds due to agricultural intensification, industrialization, and urbanization have contributed to the persistence of large hypoxic zones in inland and coastal waters at a global scale. Watershed management practices to target these non-point source pollutants have reportedly resulted in 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. Conservation measures are often implemented without explicit consideration of the lag time and with the expectation that they will lead to immediate benefits; the resulting failure to meet such expectations then discourages vital restoration efforts. In order to address this problem, it is important to quantify the lag times associated with watershed management efforts a priori and to implement restoration strategies that are targeted specifically at minimizing lag times as well as maximizing restoration benefits. The focus of this research is to develop an analytical framework for understanding the time lags between land use changes and stream water quality benefits. Watershed lag times are a function of coupled hydrologic and biogeochemical factors that modify pollutant loads as these pollutants are transported through the landscape. Hydrologic factors include the pathways of delivery of the solute to streams (e.g., overland flow, tile flow, or groundwater pathways), and the distribution of travel times along the pathways. Biogeochemical factors include the reactivity of the pollutant, and whether there are internal sources of the pollutant within the landscape. Results of a data synthesis effort of the MARB and the Baltic Basin indicate that landscapes having been subject to fertilizer application for

  16. 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.

  17. 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.

  18. Eastern Mediterranean biogeochemical flux model - Simulations of the pelagic ecosystem

    NASA Astrophysics Data System (ADS)

    Petihakis, G.; Triantafyllou, G.; Tsiaras, K.; Korres, G.; Pollani, A.; Hoteit, I.

    2009-02-01

    During the second phase (2003-2006) of the Mediterranean ocean Forecasting System Project (MFS) named Toward Environmental Predictions (MFSTEP) one of the three major aims was the development of numerical forecasting systems. In this context a generic Biogeochemical Flux Model (BFM) was developed and coupled with hydrodynamic models already operating at basin scale as well as in regional areas. In the Eastern Mediterranean basin the BFM was coupled with the Aegean Levantine Eddy Resolving MOdel (ALERMO). The BFM is a generic highly complex model based on ERSEM and although a detailed description of the model and its components is beyond the scope of this work, a short overview of the main processes, laying emphasis on the parameter values used is presented. In addition the performance of the model is evaluated with some preliminary results being qualitatively compared against field observations. The model in its present form is rather promising and reproduces all important major features although there are some slight inefficiencies mostly related to primary and bacterial productivity rates.

  19. Solving the equation for the Iberian upwelling biogeochemical dynamics: an optimization experience

    NASA Astrophysics Data System (ADS)

    Reboreda, R.; Santaren, D.; Castro, C. G.; Alvarez-Salgado, X. A.; Nolasco, R.; Queiroga, H.; Dubert, J.

    2012-04-01

    Trying to find a set of parameters to properly reproduce the biogeochemical dynamics of the region of study is a major concern in biogeochemical ocean modelling. Model parameters are constant values introduced in the equations that calculate the time and space evolution of the state variables of the biogeochemical model. A good set of parameters allows for a better representation of the biological and chemical processes in the system, and thus to model results more approximated to reality. However, it is not a straightforward task, because many parameters are not well constrained in the literature, or they may be unknown or vary considerably between different regions. Usually, the approach to find the appropriate values is running several simulations, after some sensitivity test to individual parameters, until a satisfactory result is obtained. This may be very time consuming and quite subjective. A more systematic way to find this set of parameters has arisen over the last years by using mathematical optimization techniques. The basic principle under optimization is to minimize the difference between an observed and a simulated data series by using a cost function. We have applied an optimization technique to find an appropriate set of parameters for modelling the biogeochemical dynamics of the western Iberian shelf, off the Atlantic coast of Portugal and Galicia (NW Spain), which is characterized by a conspicuous seasonal upwelling. The ocean model is a high resolution 3D regional configuration of ROMS coupled to a N2PZD2 biogeochemical model. Results using the a priori parameters and the optimized parameters are compared and discussed. The study is the result of a multidisciplinary collaborative effort between the University of Aveiro ocean modelling group (Portugal), the ETHZ (Switzerland) and the IIM-CSIC Vigo oceanography group (Spain).

  20. Terrestrial biogeochemical feedbacks in the climate system

    NASA Astrophysics Data System (ADS)

    Arneth, A.; Harrison, S. P.; Zaehle, S.; Tsigaridis, K.; Menon, S.; Bartlein, P. J.; Feichter, J.; Korhola, A.; Kulmala, M.; O'Donnell, D.; Schurgers, G.; Sorvari, S.; Vesala, T.

    2010-08-01

    The terrestrial biosphere is a key regulator of atmospheric chemistry and climate. During past periods of climate change, vegetation cover and interactions between the terrestrial biosphere and atmosphere changed within decades. Modern observations show a similar responsiveness of terrestrial biogeochemistry to anthropogenically forced climate change and air pollution. Although interactions between the carbon cycle and climate have been a central focus, other biogeochemical feedbacks could be as important in modulating future climate change. Total positive radiative forcings resulting from feedbacks between the terrestrial biosphere and the atmosphere are estimated to reach up to 0.9 or 1.5 W m-2 K-1 towards the end of the twenty-first century, depending on the extent to which interactions with the nitrogen cycle stimulate or limit carbon sequestration. This substantially reduces and potentially even eliminates the cooling effect owing to carbon dioxide fertilization of the terrestrial biota. The overall magnitude of the biogeochemical feedbacks could potentially be similar to that of feedbacks in the physical climate system, but there are large uncertainties in the magnitude of individual estimates and in accounting for synergies between these effects.

  1. 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.

  2. 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

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  5. 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

  6. Diel biogeochemical processes in terrestrial waters

    USGS Publications Warehouse

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

    2011-01-01

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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  14. 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.

  15. 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.

  16. Towards an assessment of simple global marine biogeochemical models of different complexity

    NASA Astrophysics Data System (ADS)

    Kriest, I.; Khatiwala, S.; Oschlies, A.

    2010-09-01

    We present a suite of experiments with a hierarchy of biogeochemical models of increasing complexity coupled to an offline global ocean circulation model based on the “transport matrix method”. Biogeochemical model structures range from simple nutrient models to more complex nutrient-phytoplankton-zooplankton-detritus-DOP models. The models’ skill is assessed by various misfit functions with respect to observed phosphate and oxygen distributions. While there is generally good agreement between the different metrics employed, an exception is a cost function based on the relative model-data misfit. We show that alterations in parameters and/or structure of the models - especially those that change particle export or remineralization profile - affect subsurface and mesopelagic phosphate and oxygen, particularly in the upwelling regions. Visual inspection of simulated biogeochemical tracer distributions as well as the evaluation of different cost functions suggest that increasing complexity of untuned, unoptimized models, simulated with parameters commonly used in large-scale model studies does not necessarily improve performance. Instead, variations in individual model parameters may be of equal, if not greater, importance.

  17. Plant Nitrogen Uptake in Terrestrial Biogeochemical Models

    NASA Astrophysics Data System (ADS)

    Marti Donati, A.; Cox, P.; Smith, M. J.; Purves, D.; Sitch, S.; Jones, C. D.

    2013-12-01

    Most terrestrial biogeochemical models featured in the last Intergovernmental Panel on Climate Change (IPPC) Assessment Report highlight the importance of the terrestrial Carbon sequestration and feedbacks between the terrestrial Carbon cycle and the climate system. However, these models have been criticized for overestimating predicted Carbon sequestration and its potential climate feedback when calculating the rate of future climate change because they do not account for the Carbon sequestration constraints caused by nutrient limitation, particularly Nitrogen (N). This is particularly relevant considering the existence of a substantial deficit of Nitrogen for plants in most areas of the world. To date, most climate models assume that plants have access to as much Nitrogen as needed, but ignore the nutrient requirements for new vegetation growth. Determining the natural demand and acquisition for Nitrogen and its associated resource optimization is key when accounting for the Carbon sequestration constrains caused by nutrient limitation. The few climate models that include C-N dynamics have illustrated that the stimulation of plant growth over the coming century may be significantly smaller than previously predicted. However, models exhibit wide differences in their predictive accuracy and lead to widely diverging and inconsistent projections accounting for an uncertain Carbon sequestration decrease due to Nitrogen limitation ranging from 7 to 64%. This reduction in growth is partially offset by an increase in the availability of nutrients resulting from an accelerated rate of decomposition of dead plants and other organic matter that occurring with a rise in temperature. However, this offset does not counterbalance the reduced level of plant growth calculated by natural nutrient limitations. Additionally, Nitrogen limitation is also expected to become more pronounced in some ecosystems as atmospheric CO2 concentration increases; resulting in less new growth and

  18. 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

  19. 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.

  20. Quantifying biogeochemical responses to hydrological perturbations in terrestrial systems using geophysical monitoring and inversion schemes

    NASA Astrophysics Data System (ADS)

    Hubbard, S. S.; Dafflon, B.; Tran, A. P.; Chen, J.; Wainwright, H. M.

    2015-12-01

    Although recognized that terrestrial hydrological processes drive a variety of biogeochemical processes, quantifying interactions that occur across a range of scales and compartments is challenging. We describe recently developed approaches to quantify these interactions, and demonstrate the value of developed approaches in two different terrestrial systems. The first is a relatively flat Arctic tundra polygonal ground system, where snowmelt-dominated, surface water distribution significantly influences soil microbial activity and resulting production of greenhouse gasses. The second is a Colorado River floodplain-catchment, where a transient snowmelt pulse leads to hydrological and biogeochemical interactions between different compartents of the system. Three capabilties were developed to improve understanding of hydrology influences on biogeochemistry at these sites. The first is a networked sensing system that coincidently measures below-, at- and above-ground critical properties (such as soil moisture, soil temperature, canopy greenness, surface water inundation, active layer depth, and snow thickness). The approach takes advantage of autonomous data acquisition using unmanned aerial vehicles, tram-based sensors, and surface geophysical approaches. The dense datasets enable 'visualization' of interactions that occur across compartments in response to freeze-thaw and runoff processes. The second advance is the development of a coupled hydro-thermal-geophysical inversion scheme that takes advantage of spatially extensive geophysical data as well as direct but sparse measurements in the quantitative estimation of terrestrial responses to hydrological perturbations. The third is the development of stochastic 'zonation' approaches, which use multi-type, multi-scale datasets to identify regions in the landscape that have unique distributions of properties that influence biogeochemical cycling. Together, the sensing, modeling, and integrative functional zonation

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  2. 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.

  3. 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

  4. 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

  5. Redox chemistry in the phosphorus biogeochemical cycle

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  6. Understanding oceanic migrations with intrinsic biogeochemical markers.

    PubMed

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

    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

  7. 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

  8. 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...

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

    SciTech Connect

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

    1994-12-31

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

  10. 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.

  11. Terrestrial ecosystems and the global biogeochemical silica cycle

    NASA Astrophysics Data System (ADS)

    Conley, Daniel J.

    2002-12-01

    Most research on the global Si cycle has focused nearly exclusively on weathering or the oceanic Si cycle and has not explored the complexity of the terrestrial biogeochemical cycle. The global biogeochemical Si cycle is of great interest because of its impact on global CO2 concentrations through the combined processes of weathering of silicate minerals and transfer of CO2 from the atmosphere to the lithosphere. A sizable pool of Si is contained as accumulations of amorphous silica, or biogenic silica (BSi), in living tissues of growing plants, known as phytoliths, and, after decomposition of organic material, as remains in the soil. The annual fixation of phytolith silica ranges from 60-200 Tmol yr-1 and rivals that fixed in the oceanic biogeochemical cycle (240 Tmol yr-1). Internal recycling of the phytolith pool is intense with riverine fluxes of dissolved silicate to the oceans buffered by the terrestrial biogeochemical Si cycle, challenging the ability of weathering models to predict rates of weathering and consequently, changes in global climate. Consideration must be given to the influence of the terrestrial BSi pool on variations in the global biogeochemical Si cycle over geologic time and the influence man has had on modifying both the terrestrial and aquatic biogeochemical cycles.

  12. Biogeochemical tracers of the marine cyanobacterium Trichodesmium

    NASA Astrophysics Data System (ADS)

    Carpenter, Edward J.; Harvey, H. Rodger; Fry, Brian; Capone, Douglas G.

    1997-01-01

    We examined the utility of several biogeochemical tracers for following the fate of the planktonic diazotrophic cyanobacterium Trichodesmium in the sea. The presence of a (CIO) fatty acid previously reported was observed in a culture of Trichodesmium but was not found in natural samples. This cyanobacterium had high concentrations of C 14 and C 16 acids, with lesser amounts of several saturated and unsaturated C 18 fatty acids. This composition was similar to that of other marine cyanobacteria. The major hydrocarbon identified was the C 17n-alkane, which was present in all samples from the five stations examined. Sterols common to algae and copepods were observed in many samples along with hopanoids representative of bacteria, suggesting a varied community structure in colonies collected from different stations. We found no unique taxonomic marker of Trichodesmium among the sterols. Measurements of the σ 15N and σ 13C in Trichodesmium samples from the SW Sargasso and NW Caribbean Seas averaged -0.4960 (range from -0.7 to -0.25960) and -12.9%0 (range from -15.2 to -11.9960), respectively, thus confirming previous observations that this cyanobacterial diazotroph has both the lowest σ 15N and highest σ 13C of any marine phytoplankter observed to date. A culture of Trichodesmium grown under diazotrophic conditions had a σ 15N between -1.3 and -3.6960. Our results support the supposition that the relatively low σ 15N and high σ 13C values observed in suspended and sediment-trapped material from some tropical and subtropical seas result from substantial input of C and N by Trichodesmium.

  13. 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

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. Ecotoxicological, ecophysiological and biogeochemical fundamentals of risk assessment

    SciTech Connect

    Bashkin, V.; Evstafjeva, E.

    1995-12-31

    A quantitative risk assessment (RA) for complex influence of different factors in heavy polluted regions is possible to carry out only on a basis of determination of various links of biogeochemical trophical chains and analysis of the whole biogeochemical structure of the region under study. As an integrative assessment, the human adaptability should be chosen because the majority of trophical chains are closed by man. The given integrative criteria includes biogeochemical, ecophysiological and ecotoxicological assessment of risk factors. Consequently, ecological-biogeochemical regionalization, ecophysiological and ecotoxicological monitoring of human population health are the important approaches to RA. These criteria should be conjugated with LCA of various industrial and agricultural products. At the ultimate degree, the given approaches are needed for areas where traditional pollutants (heavy metals, POPS, pesticides, fertilizers) are enforced sharply by radioactive pollution. Due to the complex influence of pollutants, it is impossible to use individual guidelines. For RA of these complex pollutants, the methods of human adaptability assessment to a polluted environment have to be carried out. These methods include biogeochemical, ecotoxicological and ecophysiological analysis of risk factors as well as quantitative uncertainty analysis. Furthermore, the modern statistical methods such as correlative graphs etc., have to be used for quantitative assessment of human adaptability to complex influence of pollutants. The results obtained in the Chernobyl region have shown the acceptability of suggested methods.

  18. Ecosystem biogeochemical function and services in an urbanizing desert region

    NASA Astrophysics Data System (ADS)

    Grimm, N. B.; Cook, E. M.; Earl, S.; Hale, R. L.; Hall, S. J.; Hartnett, H. E.; Iwaniec, D.; Larson, E. K.; McHale, M.; Sponseller, R. A.

    2009-12-01

    Ecosystem services derive from underlying ecosystem processes but are distinguished by their benefits to society. Among ecosystem services, those associated with biogeochemical cycling and regulation of water, air, and soil quality are relatively unrecognized by the public, although concentrations of some materials are regulated by local, state and national laws. The disconnection between their importance and the degree to which these services are acknowledged means that biogeochemical ecosystem services have seldom been considered in urban planning and design. Drawing from research at multiple scales in the central Arizona region that includes over twenty cities and towns comprising metropolitan Phoenix, we illustrate the relationships between ecosystem functions and services in three areas. First, at household to whole-city scales, we show that the overriding influence of water and material inputs mediated by humans is changing biogeochemical patterns in soil and vegetation. Second, we show how human modification of aquatic ecosystems for water delivery, stormwater management, and wastewater removal give rise to important trade-offs among these services. And finally, we illustrate the limited capacity of surrounding unproductive desert ecosystems to assimilate the air pollutants generated by this region of >4 million inhabitants. We argue that urban planning and design that take into account the ecosystem functions underlying biogeochemical ecosystem services will be most effective in management of potential pollution problems associated with all of these cases. This paper thus highlights biogeochemical research conducted at the central Arizona-Phoenix LTER within a framework of ecosystem services.

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  1. 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

  2. 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

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

    USGS Publications Warehouse

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

    2008-01-01

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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

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

    NASA Astrophysics Data System (ADS)

    Morris, J. T.

    2015-12-01

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

  10. 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,...

  11. 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.

  12. 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...

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. 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

  16. 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

  17. 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.

  18. Thermodynamic stability analysis of the carbon biogeochemical cycle in aquatic shallow environments

    NASA Astrophysics Data System (ADS)

    Lvov, S. N.; Pastres, R.; Marcomini, A.

    1996-10-01

    We carry out the thermodynamic stability analysis of the carbon cycle in a lagoon. Our approach differs from linear stability analysis, and is based on the excess entropy production. The coupled biogeochemical processes in the lagoon include gas transfer, photosynthesis, respiration, decomposition, sedimentation, and oxidation of algae. The thermodynamic stability criterion derived from this analysis indicates that, in addition to known limiting factors of biomass production such as temperature, light, and nitrogen and phosphorous concentrations, the rate of carbon dioxide delivery from the air reservoir to the water can be also a limiting factor. For the Venice lagoon, the criterion obtained predicts that a doubling of the CO 2 partial pressure in the atmosphere can render the system unstable, driving it to dramatic biomass production and degradation.

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

    NASA Astrophysics Data System (ADS)

    Singhal, Naresh; Islam, Jahangir

    2008-02-01

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  2. 3D Modeling of influence of oxygenated inflows on biogeochemical structure of redox-layer of enclosed seas

    NASA Astrophysics Data System (ADS)

    Podymov, O.

    2009-04-01

    In this study we used a coupled hydrophysical-biogeochemical model. Biogeochemical processes were described with O-N-S-P-Mn-Fe ROLM model (Yakushev et al, 2007), designed to study processes of organic matter (OM) formation and decay, reduction and oxidation of species of nitrogen, sulphur, manganese and iron, transformation of phosphorus species. Phytoplankton, zooplankton and bacteria were also parameterized and divided into four groups according to their relation to particular energy source and to OM transformation. Hydrophysical processes where described with 3D General Estuarine Transport Model (Burchard et al, 2004). We modeled the influence of oxygenated intrusions on the vertical biogeochemical structure of the central Gotland Sea. The model simulations demonstrate that a complete ventilation of the Gotland Deep bottom water caused by massive inflows of oxygenated North Sea water led to substantial changes of the vertical biogeochemical structure within this basin. During the inflow events large amounts of iron and manganese precipitate and discharge from the water column. In this phase redox reactions are accelerated and growth of bacteria leads to an increase of particulate matter content and consecutive particle sedimentation. An unbalanced structure of water column exists during the period of reestablishment of anoxic conditions. Its appearance is related to the absence of Mn species that play the dominant role in the oxidation-reduction reactions at the pelagic redox interfaces. This unbalanced structure can serve as a biotope for a development of untypical microbial redox-cline reactions (i.e. anammox). According to the model simulations the duration of the reestablishment period for a steady state of biogeochemistry after a complete flushing is about 1.5 years.

  3. 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

  4. Marine viruses and their biogeochemical and ecological effects

    NASA Astrophysics Data System (ADS)

    Fuhrman, Jed A.

    1999-06-01

    Viruses are the most common biological agents in the sea, typically numbering ten billion per litre. They probably infect all organisms, can undergo rapid decay and replenishment, and influence many biogeochemical and ecological processes, including nutrient cycling, system respiration, particle size-distributions and sinking rates, bacterial and algal biodiversity and species distributions, algal bloom control, dimethyl sulphide formation and genetic transfer. Newly developed fluorescence and molecular techniques leave the field poised to make significant advances towards evaluating and quantifying such effects.

  5. Implementing high-latitude biogeochemical processes into Earth System Models

    NASA Astrophysics Data System (ADS)

    Brovkin, Victor; Kleinen, Thomas; Cresto-Aleina, Fabio; Kloster, Silvia; Ilyina, Tatiana

    2016-04-01

    Projections of future climate changes suggest that air temperatures in the Arctic could rise to the levels unprecedented in the last million years. Sensitivity of carbon storages on land and shelves to climate change of that scale is highly uncertain. Earth System models (ESMs), consisting of atmosphere, ocean, land, and cryosphere components are the main tools to understand interactions between carbon cycle and climate. However, ESM representation of ecological and biogeochemical processes in the Arctic is extremely simplistic. For example, all ESMs agree that tree cover in the future warming scenarios will move northwards to the Arctic coast, but they ignore interactions between vegetation, permafrost, and disturbances such as fires, which are critical for vegetation dynamics in this region. Improving modeling of interactions between model components and their evaluation against growing observational evidence is a promising research area. The first attempts to account for the permafrost carbon dynamics in the ESM framework suggest that CO2 and CH4 emissions from high-latitude regions in the 21st century are relatively small, but they become much more significant afterwards due to committed climate changes. Therefore, extension of ESM simulations beyond 2100 is essential to estimate a proper scale of frozen carbon pool response to human-induced climate change. Additionally, inclusion of sub-sea permafrost component into ESMs is an active research area that brings together terrestrial and marine biogeochemical communities, as well as geologists analyzing climate proxies on glacial timescales. Another challenging aspect of biogeochemical interactions in Arctic is an extreme land surface heterogeneity. A mixture of wetlands, lakes, and vegetation-covered surfaces on fine local scale is not properly reflected in the model structure. A promising approach of dealing with scaling gaps in modeling high-latitude biogeochemical processes in ESMs will be presented.

  6. 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.

  7. Can ocean color assimilation improve biogeochemical hindcasts in shelf seas?

    NASA Astrophysics Data System (ADS)

    Ciavatta, Stefano; Torres, Ricardo; Saux-Picart, Stephane; Allen, Julian Icarus

    2011-12-01

    The objective of this paper is to investigate if the assimilation of ocean color data into a complex marine ecosystem model can improve the hindcast of key biogeochemical variables in shelf seas. A localized Ensemble Kalman filter was used to make a yearlong assimilation of weekly satellite chlorophyll data into a three-dimensional ecosystem model of the western English Channel. The skill of assimilation was evaluated with respect to non assimilated in situ data using twelve time series of biogeochemical observations collected weekly at the monitoring station L4. It was found that the assimilation scheme reduced the root mean square error and increased the correlation with the spatial distributions of the assimilated chlorophyll data, with respect to the reference run. More significantly, the skill metrics for non assimilated variables indicate that the hindcast of the mean data values at L4 was improved; however improvements in the short term forecast were not discernable. On the basis of our application, we provide general recommendations for the successful application of ocean color assimilation to hindcast key biogeochemical variables in shelf seas.

  8. 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.

  9. Investigating the Impact of Pore Scale Microenvironments on Contaminant Biogeochemical Reactive Transport

    NASA Astrophysics Data System (ADS)

    Wilkins, M. J.; Pearce, C.; Zhang, C.; Heald, S.; Fredrickson, J. K.; Zachara, J. M.

    2011-12-01

    Microenvironments and transition zones dominate the subsurface biogeochemical cycling of key contaminants, with strong effects resulting from the coupling of chemical reactions, physical transport and microbiological processes. Understanding the impact of pore-scale environments (e.g. spatial heterogeneity, chemical gradients, and redox potential) is essential for modeling contaminant fate and transport in the subsurface. The driver for biogeochemical processes at the pore scale changes from macroscopic advection to microscale diffusion, and this has a significant effect on the retention of soluble, highly mobile contaminants such as U(VI). Here, etched-silicon microfluidic models with defined chemistry, mineralogy, microbiology, and flow regimes are used for the incremental development of complex microenvironments that approach real-world systems. We demonstrate the colonization of such pore spaces by an anaerobic Fe(III)-reducing bacterium, the enzymatic reduction of a bioavailable Fe(III) phase within this environment, and the subsequent effects of both oxidized and reduced Fe phases on uranium biogeochemistry under flow conditions using both X-ray Microprobe (XMP) and X-ray Absorption Spectroscopy (XAS). Precipitated Fe(III) phases within the microfluidic model were most effectively reduced in the presence of an electron shuttle (e.g. AQDS), with Fe(II) ions adsorbing onto mineral precipitates and surfaces. In the absence of Fe, U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated within biomass. In the presence of both oxidized and reduced Fe phases however, differing effects were observed with regards to U behavior; oxidized U(VI) was frequently adsorbed to poorly crystalline Fe(III), and reduced U(IV) associated with more reduced regions of the microscale flow cell. In the future, the flexibility in the design of the microfluidic models, in combination with advanced

  10. 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

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Reimer, Joscha; Piwonski, Jaroslaw; Slawig, Thomas

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  14. 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

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  17. 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.

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

    PubMed

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

    2011-02-01

    Solar UV radiation, climate and other drivers of global change are undergoing significant changes and models forecast that these changes will continue for the remainder of this century. Here we assess the effects of solar UV radiation on biogeochemical cycles and the interactions of these effects with climate change, including feedbacks on climate. Such interactions occur in both terrestrial and aquatic ecosystems. While there is significant uncertainty in the quantification of these effects, they could accelerate the rate of atmospheric CO(2) increase and subsequent climate change beyond current predictions. The effects of predicted changes in climate and solar UV radiation on carbon cycling in terrestrial and aquatic ecosystems are expected to vary significantly between regions. The balance of positive and negative effects on terrestrial carbon cycling remains uncertain, but the interactions between UV radiation and climate change are likely to contribute to decreasing sink strength in many oceanic regions. Interactions between climate and solar UV radiation will affect cycling of elements other than carbon, and so will influence the concentration of greenhouse and ozone-depleting gases. For example, increases in oxygen-deficient regions of the ocean caused by climate change are projected to enhance the emissions of nitrous oxide, an important greenhouse and ozone-depleting gas. Future changes in UV-induced transformations of aquatic and terrestrial contaminants could have both beneficial and adverse effects. Taken in total, it is clear that the future changes in UV radiation coupled with human-caused global change will have large impacts on biogeochemical cycles at local, regional and global scales. PMID:21253663

  19. 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.

  20. 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.

  1. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Krause, S.

    2015-12-01

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

  2. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  3. Biogeochemical effects and remote sensing characteristics of gold deposit

    NASA Astrophysics Data System (ADS)

    Ma, Yueliang; Xu, Ruisong

    1998-08-01

    In vegetation district, as a result of that the plant absorb Au and associated elements of locks and soils, the contents of Au and associated elements, pigment, water, surface temperature, and cells structure in leaves occur variations, even the plant cause abnormality of biogeochemical effect, thus it appear abnormality in the spectral information of TM image. This paper takes the Hetai gold deposit in Guangdong as researh target. The results proved that Au content of leaves in the gold deposit is as high as the background value, Au content in chlorophyll of leaves is 2 - 8 times higher than that, the contents of the chlorophyll a and b as well as the carotenoid are also higher than those of the control area, the water content and surface temperature of leaves are lower than the background value, the cells structure in leaves are deformed and broken, the spectral reflectance of the leave is 5% - 30% higher than that in the reference areas, the spectral wave shape is more shifted toward the short wavelength. According to these feature and difference, the remote sensing image processing technologies are utilized to extract the abnormal feature of biogeochemical effect, and enclose the remote sensing abnormal areas of mineral; Gold exploration was thus conducted in the surrounding areas of the Hetai bold deposits in Guangdong and two remote sensing abnormal areas of gold mineralization were rapidly evaluated in this way. The research proved that the remote sensing technology is a rapid, accurate and economical method of extracting abnormal information about the biogeochemical effect in vegetation and applying it to the mineral exploration practice, and this constitutes a new way in exploring hidden ore deposits in vegetation regions.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  5. 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.

  6. 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.

  7. Seasonal biogeochemical profiling of an unlined landfill in rural Victoria (Australia): implications for stream and groundwater contamination

    NASA Astrophysics Data System (ADS)

    Minard, A.; Moreau, J. W.

    2010-12-01

    Unlined landfills and waste transfer stations lack collection systems to prevent groundwater pollution. Unmonitored leakage into shallow groundwater can lead to eutrophication of freshwater ecosystems. Such sites are fairly common in rural Australia, and seven years of groundwater and leachate biogeochemical data taken near a rural landfill in Beaufort (Victoria) Australia, showed that interacting biogeochemical cycles (i.e. C, N, S, Fe) influenced contaminant transport into groundwaters seasonally. Reductive dissolution of iron oxyhydroxides coupled with alkalinity spikes was coupled to higher carbon turnover rates within a methanogenic landfill cell. This process appeared to occur mainly during summers and less during winters. Dissolved trace metal concentrations (Co, Cu, Ni, Zn) alternated with increases in dissolved iron, but with less frequency during the winter months. Nitrate and sulphate however seasonally alternated with high nitrate/low sulphate during the winter, and low nitrate/high sulphate during the summer, within the landfill cell. The seasonal variability of nitrate and sulphate in landfill leachate was also reflected in the down-flow groundwater chemistry.

  8. 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

  9. Biogeochemical distinction of methane releases from two Amazon hydroreservoirs.

    PubMed

    Lima, Ivan Bergier Tavares

    2005-06-01

    Biogeochemical distinction of methane emissions to the atmosphere may essentially rely on the surface area and morphometry of Amazon hydroreservoirs. Tucurui (deep) and Samuel (shallow) reservoirs released in average 13.82+/-22.94 and 71.19+/-107.4 mg CH4 m(-2)d(-1), respectively. delta13C-CH4 values from the sediments to the atmosphere indicate that the deep reservoir has extended methanotrophic layer, oxidizing large quantities of light isotope methane coming from the sediments, while sediment-generated methane can easily evade the shallow reservoir. PMID:15894055

  10. 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...