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1

Exploring Dynamics of Land surface-Subsurface Coupling Under Change  

NASA Astrophysics Data System (ADS)

The degree of land surface-subsurface coupling is controlled by complex interactions between the atmosphere, land surface condition and subsurface hydrologic characteristics. Global climate models project increases in temperature and changes in precipitation rates and patterns which in turn alter terrestrial water and energy budgets impacting water resources. However, the degree of land surface-subsurface coupling under scenarios of land cover and climate change has not been fully explored. In this study, we used an integrated groundwater-surface water-land surface model (ParFlow.CLM) across a semi-arid catchment located in the central west New South Wales, Australia to assess variability in water and energy fluxes under historic condition and scenarios of climate and land cover change. The Baldry hydrological observatory situated in a topographically flat terrain has the area of 2 km2 and contains two distinct land cover types of pasture and a regenerated Eucalyptus forest. High resolution groundwater level measurements in the site reveal differences in groundwater connectivity in wet versus dry periods in pasture and Eucalyptus forest for the historic condition. Using downscaled climate forcing obtained from a regional climate model for eastern Australia, the degree of land surface-subsurface coupling within the catchment was examined under various scenarios of climate and changes in land cover types. It is expected that a fully integrated hydrologic model like ParFlow.CLM improve predictions in land-atmospheric feedback processes under changes in hydrologic conditions.

Ajami, Hoori; McCabe, Matthew F.; Evans, Jason P.

2013-04-01

2

Coupled surface—subsurface hydrologic model of a nuclear subsidence crater at the Nevada test site  

Microsoft Academic Search

A series of computer models describing overland flow, ponding and infiltration was dynamically linked to simulate the movement of water during seepage beneath a nuclear subsidence feature. The coupled surface-subsurface hydrologic model contains a terrain analysis module, an overland flow simulator using the kinematic wave equation and a numerical Richards' equation solver to simulate moisture migration within the vadose zone.

G. M. Pohll; J. J. Warwick; S. W. Tyler

1996-01-01

3

A Coupled Surface/Subsurface Model for Hydrological Drought Investigations  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

4

Coupling water flow and solute transport into a physically-based surface–subsurface hydrological model  

Microsoft Academic Search

A distributed-parameter physically-based solute transport model using a novel approach to describe surface–subsurface interactions is coupled to an existing flow model. In the integrated model the same surface routing and mass transport equations are used for both hillslope and channel processes, but with different parametrizations for these two cases. For the subsurface an advanced time-splitting procedure is used to solve

S. Weill; A. Mazzia; M. Putti; C. Paniconi

2011-01-01

5

Coupling water flow and solute transport into a physically-based surface-subsurface hydrological model  

NASA Astrophysics Data System (ADS)

A distributed-parameter physically-based solute transport model using a novel approach to describe surface-subsurface interactions is coupled to an existing flow model. In the integrated model the same surface routing and mass transport equations are used for both hillslope and channel processes, but with different parametrizations for these two cases. For the subsurface an advanced time-splitting procedure is used to solve the advection-dispersion equation for transport and a standard finite element scheme is used to solve Richards equation for flow. The surface-subsurface interactions are resolved using a mass balance-based surface boundary condition switching algorithm that partitions water and solute into actual fluxes across the land surface and changes in water and mass storage. The time stepping strategy allows the different time scales that characterize surface and subsurface water and solute dynamics to be efficiently and accurately captured. The model features and performance are demonstrated in a series of numerical experiments of hillslope drainage and runoff generation.

Weill, S.; Mazzia, A.; Putti, M.; Paniconi, C.

2011-01-01

6

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

Microsoft Academic Search

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

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

2008-01-01

7

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)

Accurately simulating regional water cycle dynamics is challenging because of strong soil moisture-rainfall feedbacks and large uncertainties associated with vegetation and energy interactions. Earth system models of today cannot accurately capture such interactions, because current-generation land surface models (LSMs) 1) do not explicitly represent the fine-scale spatial variability of topography, soils, and vegetation that play a significant role in determining the response of hydrologic states (soil moisture) and fluxes (interception, infiltration, runoff, evapotranspiration) and 2) over-simplify or completely omit some key physical processes, such as lateral flow of water and heat, surface-subsurface interactions, realistic groundwater-vadose zone interactions, and freeze-thaw dynamics. Capturing such processes is critically important for predicting regional precipitation, vegetation productivity, and the disposition of carbon stored in potentially vulnerable permafrost under scenarios of climate change. Towards this end, we have added coupled surface water-groundwater interactions to the the open-source, massively parallel flow and reactive transport model PFLOTRAN, and have been developing a framework for coupling PFLOTRAN with the Community Land Model (CLM). PFLOTRAN is an open-source (LGPL-licensed) code -- with a growing community of users -- developed for simulation of multiscale, multiphase, multicomponent subsurface flow and reactive transport problems on machines ranging from laptops to leadership-class supercomputers. It has been applied in studies of contaminant fate and transport, geologic CO2 sequestration, and geothermal energy production, among others, and has been run using up to 262,144 processor cores on Jaguar, the Cray XK6 supercomputer at Oak Ridge National Laboratory. We have recently added a surface flow component in PFLOTRAN that is integrated with the subsurface. The underlying solver framework employed allows significant flexibility in how the governing equations are solved, and we will compare different surface flow formulations as well as coupling strategies between the surface and subsurface domains. Additionally, for studies of hydrology in Arctic regions, we have added a three-phase ice model. We will present some demonstrations of this capability and discuss solver strategies for handling the strong nonlinearities that arise. To provide a unified treatment of the unsaturated and saturated zones and to enable lateral redistribution of soil moisture (and eventually surface water, heat, and nutrients) in regional climate models, we have developed an approach for coupling PFLOTRAN with CLM. CLM is the global land model component used within the Community Earth System Model (CESM) to simulate an extensive set of biogeophysical and biogeochemical processes occurring at or near the terrestrial surface. We will describe our approach for replacing the existing CLM hydrology using PFLOTRAN and present some preliminary simulations undertaken with the CLM-PFLOTRAN coupled model.

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

8

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

NASA Astrophysics Data System (ADS)

Coastal aquifers are complex hydrologic systems because many physical processes interact: (i) variably saturated flow, (ii) spatial-temporal fluid density variations, (iii) tidal fluctuations, (iv) storm surges overtopping dykes, and (v) surface runoff of storm water. The HydroGeoSphere model is used to numerically simulate coastal flow dynamics, assuming a fully coupled surface-subsurface approach, accounting for all processes listed above. The diffusive wave approximation of the St. Venant equation is used to describe surface flow. Surface flow and salt transport are fully coupled with subsurfacial variably saturated, variable-density flow and salt transport through mathematical terms that represent exchange of fluid mass and solute mass, respectively. Tides and storm surges induce a time-variant head that is applied to nodes of the surface domain. The approach is applied to real cases of tide and storm surge events of the coastal catchment area of Unterweser, Northern Germany (ca. 2500 km2). To optimize the simulation and to reduce CPU cost, the actual simulation domain is only a part of the total catchment area: We selected a narrow strip of about 10 km width parallel to the coastline. The catchment area outside of that strip is not affected by saltwater intrusion and does therefore not need to be included in the numerical model. The seaside boundary condition of the reduced simulation domain is obtained from a 3D hydrodynamic-numerical flow model where changes in sea level are being simulated. The landside boundary condition is obtained from a 3D steady-state flow model of the total catchment area. The 3D model is calibrated using field data previously gathered at the study site. Results indicate that the fully coupled approach with a reduced simulation domain is effective in the simulation of 3D coastal flow dynamics.

Yang, Jie; Graf, Thomas

2013-04-01

9

On the coupling of benthic and pelagic biogeochemical models  

Microsoft Academic Search

Mutual interaction of water column and sediment processes is either neglected or only crudely approximated in many biogeochemical models.We have reviewed the approaches to couple benthic and pelagic biogeochemical models. It is concluded that they can be classified into a hierarchical set consisting of five levels, differing in the amount of detail given to the sediment processes. The most complex

Karline Soetaert; Jack J. Middelburg; Peter M. J. Herman; Kerst Buis

2000-01-01

10

Electric currents couple spatially separated biogeochemical processes in marine sediment  

Microsoft Academic Search

Some bacteria are capable of extracellular electron transfer, thereby enabling them to use electron acceptors and donors without direct cell contact. Beyond the micrometre scale, however, no firm evidence has previously existed that spatially segregated biogeochemical processes can be coupled by electric currents in nature. Here we provide evidence that electric currents running through defaunated sediment couple oxygen consumption at

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

2010-01-01

11

Surface-subsurface flow modeling with path-based runoff routing, boundary condition-based coupling, and assimilation of multisource observation data  

Microsoft Academic Search

A distributed physically based model incorporating novel approaches for the representation of surface-subsurface processes and interactions is presented. A path-based description of surface flow across the drainage basin is used, with several options for identifying flow directions, for separating channel cells from hillslope cells, and for representing stream channel hydraulic geometry. Lakes and other topographic depressions are identified and specially

M. Camporese; C. Paniconi; M. Putti; S. Orlandini

2010-01-01

12

Coupling a terrestrial biogeochemical model to the common land model  

SciTech Connect

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.

Shi, Xiaoying [ORNL; Mao, Jiafu [ORNL; Wang, Yingping [ORNL; Dai, Yongjiu [Beijing Normal University; Tang, Xuli [Chinese Academy of Sciences

2011-01-01

13

Plant impact on the coupled terrestrial biogeochemical cycles of silicon and carbon: Implications for biogeochemical carbon sequestration  

NASA Astrophysics Data System (ADS)

The coupled terrestrial biogeochemical cycles of silicon (Si) and carbon (C) that are driven by plant action play a crucial role in the regulation of atmospheric CO2. Generally, the processes involved in the coupled cycles of Si and C include plant-enhanced silicate weathering, phytolith formation and solubilization, secondary aluminosilicate accumulation, phytolith occlusion of C as well as physico-chemical protection of organic C in soils. There is increasing evidence of biological pumping of Si in terrestrial ecosystems, suggesting that complex feedbacks exist amongst the processes within the coupled Si and C cycles. Recent advances in the coupled Si and C cycles offer promising new possibilities for enhancing atmospheric CO2 sequestration. Organic mulching, rock powder amendment, cultivating Si-accumulating plants and partial plant harvesting are potential measures that may allow for long-term manipulation and biogeochemical sequestration of atmospheric CO2 in soil-plant systems.

Song, Zhaoliang; Wang, Hailong; Strong, P. James; Li, Zimin; Jiang, Peikun

2012-12-01

14

Electric currents couple spatially separated biogeochemical processes in marine sediment.  

PubMed

Some bacteria are capable of extracellular electron transfer, thereby enabling them to use electron acceptors and donors without direct cell contact. Beyond the micrometre scale, however, no firm evidence has previously existed that spatially segregated biogeochemical processes can be coupled by electric currents in nature. Here we provide evidence that electric currents running through defaunated sediment couple oxygen consumption at the sediment surface to oxidation of hydrogen sulphide and organic carbon deep within the sediment. Altering the oxygen concentration in the sea water overlying the sediment resulted in a rapid (<1-h) change in the hydrogen sulphide concentration within the sediment more than 12 mm below the oxic zone, a change explicable by transmission of electrons but not by diffusion of molecules. Mass balances indicated that more than 40% of total oxygen consumption in the sediment was driven by electrons conducted from the anoxic zone. A distinct pH peak in the oxic zone could be explained by electrochemical oxygen reduction, but not by any conventional sets of aerobic sediment processes. We suggest that the electric current was conducted by bacterial nanowires combined with pyrite, soluble electron shuttles and outer-membrane cytochromes. Electrical communication between distant chemical and biological processes in nature adds a new dimension to our understanding of biogeochemistry and microbial ecology. PMID:20182510

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

2010-02-25

15

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

National Technical Information Service (NTIS)

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 ...

W. W. Gregg

2000-01-01

16

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

NASA Astrophysics Data System (ADS)

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.

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

2014-01-01

17

Effect of Alternative Rainfall Temporal Averaging Scales on Predicting Water and Solute Exchange Fluxes Near Streams: Application of a Three-Dimensional Coupled Surface-Subsurface Model  

Microsoft Academic Search

The Integrated Hydrology Model (InHM) is a fully-coupled 3D control-volume finite element model which can simulate water flow and advective-dispersive solute transport on the 2D land surface and in the 3D subsurface under variably-saturated conditions. Full coupling of the surface and subsurface flow regimes is accomplished by simultaneously solving one system of non-linear discrete equations for overland flow rates and

T. A. Di Iorio; E. A. Sudicky; J. Jones; R. G. McLaren

2002-01-01

18

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

National Technical Information Service (NTIS)

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 ...

W. W. Gregg

1999-01-01

19

Significant Findings: Seasonal Distributions of Global Ocean Chlorophyll and Nutrients With a Coupled Ocean General Circulation, Biogeochemical, and Radiative Model, 2.  

National Technical Information Service (NTIS)

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...

W. W. Gregg

2000-01-01

20

Surface-subsurface model intercomparison: A first set of benchmark results to diagnose integrated hydrology and feedbacks  

NASA Astrophysics Data System (ADS)

are a growing number of large-scale, complex hydrologic models that are capable of simulating integrated surface and subsurface flow. Many are coupled to land-surface energy balance models, biogeochemical and ecological process models, and atmospheric models. Although they are being increasingly applied for hydrologic prediction and environmental understanding, very little formal verification and/or benchmarking of these models has been performed. Here we present the results of an intercomparison study of seven coupled surface-subsurface models based on a series of benchmark problems. All the models simultaneously solve adapted forms of the Richards and shallow water equations, based on fully 3-D or mixed (1-D vadose zone and 2-D groundwater) formulations for subsurface flow and 1-D (rill flow) or 2-D (sheet flow) conceptualizations for surface routing. A range of approaches is used for the solution of the coupled equations, including global implicit, sequential iterative, and asynchronous linking, and various strategies are used to enforce flux and pressure continuity at the surface-subsurface interface. The simulation results show good agreement for the simpler test cases, while the more complicated test cases bring out some of the differences in physical process representations and numerical solution approaches between the models. Benchmarks with more traditional runoff generating mechanisms, such as excess infiltration and saturation, demonstrate more agreement between models, while benchmarks with heterogeneity and complex water table dynamics highlight differences in model formulation. In general, all the models demonstrate the same qualitative behavior, thus building confidence in their use for hydrologic applications.

Maxwell, Reed M.; Putti, Mario; Meyerhoff, Steven; Delfs, Jens-Olaf; Ferguson, Ian M.; Ivanov, Valeriy; Kim, Jongho; Kolditz, Olaf; Kollet, Stefan J.; Kumar, Mukesh; Lopez, Sonya; Niu, Jie; Paniconi, Claudio; Park, Young-Jin; Phanikumar, Mantha S.; Shen, Chaopeng; Sudicky, Edward A.; Sulis, Mauro

2014-02-01

21

Physical/biogeochemical coupled model : impact of an offline vs online strategy  

NASA Astrophysics Data System (ADS)

Mercator-Ocean, the French ocean forecasting center, has been developing several operational forecasting systems and reanalysis of the physical and biogeochemical 3D-Ocean. Here we study the impact of an offline vs online strategy to couple the physical (OPA) and biogeochemical (PISCES) modules included in the NEMO platform. For this purpose, we perform global one-year long simulations at 1° resolution. The model was initialized with global climatologies. The spin-up involved 10 years of biogeochemical off-line simulation forced by a climatology of ocean physics. The online mode consists in running physical and biogeochemical models simultaneously whereas in the offline mode, the biogeochemical model is launched alone, forced by averaged physical forcing (1 day, 7 days,… ). The Mercator operational biogeochemical system is currently using the offline mode with a weekly physical forcing. A special treatment is applied to the vertical diffusivity coefficient (Kz): as it varies of several orders of magnitude, we compute the mean of the LOG10 of Kz. Moreover, a threshold value is applied to remove the highest values corresponding to enhanced convection. To improve this system, 2 directions are explored. First, 3 physical forcing frequencies are compared to quantify errors due to the offline mode: 1 hour (online mode), 1 day and 1 week (offline modes). Secondly, sensitivity tests to the threshold value applied to Kz are performed. The simulations are evaluated by systematically comparing model fields to observations (Globcolour product and World Ocean Atlas 2005) at global and regional scales. We show first that offline simulations are in good agreement with online simulation. As expected, the lower the physical forcing frequency is, the closer to the online solution is the offline simulation. The threshold value on the vertical diffusivity coefficient manages the mixing strength within the mixed layer. A value of 1 m2.s-1 appears to be a good compromise to approach the online solution. Our sensitivity tests show that increasing the temporal resolution of the forcing induces a temporal shift in the surface chlorophyll seasonal cycle: less chlorophyll in winter and a stronger spring bloom in offline mode. We attribute this behavior to the entrainment/detrainment process of chlorophyll and nutrients at the bottom of the mixed layer during winter.

Hameau, Angélique; Perruche, Coralie; Bricaud, Clément; Gutknecht, Elodie; Reffray, Guillaume

2014-05-01

22

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

PubMed

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

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

2013-10-01

23

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

NASA Astrophysics Data System (ADS)

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.

Wu, Y.; Blodau, C.

2013-08-01

24

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

SciTech Connect

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.

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

2006-06-01

25

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

PubMed

Increasing reactive nitrogen (N) input has been recognized as one of the important factors influencing climate system through affecting the uptake and emission of greenhouse gases (GHG). However, the magnitude and spatiotemporal variations of N-induced GHG fluxes at regional and global scales remain far from certain. Here we selected China as an example, and used a coupled biogeochemical model in conjunction with spatially explicit data sets (including climate, atmospheric CO2 , O3 , N deposition, land use, and land cover changes, and N fertilizer application) to simulate the concurrent impacts of increasing atmospheric and fertilized N inputs on balance of three major GHGs (CO2 , CH4 , and N2 O). Our simulations showed that these two N enrichment sources in China decreased global warming potential (GWP) through stimulating CO2 sink and suppressing CH4 emission. However, direct N2 O emission was estimated to offset 39% of N-induced carbon (C) benefit, with a net GWP of three GHGs averaging -376.3 ± 146.4 Tg CO2  eq yr(-1) (the standard deviation is interannual variability of GWP) during 2000-2008. The chemical N fertilizer uses were estimated to increase GWP by 45.6 ± 34.3 Tg CO2  eq yr(-1) in the same period, and C sink was offset by 136%. The largest C sink offset ratio due to increasing N input was found in Southeast and Central mainland of China, where rapid industrial development and intensively managed crop system are located. Although exposed to the rapidly increasing N deposition, most of the natural vegetation covers were still showing decreasing GWP. However, due to extensive overuse of N fertilizer, China's cropland was found to show the least negative GWP, or even positive GWP in recent decade. From both scientific and policy perspectives, it is essential to incorporate multiple GHGs into a coupled biogeochemical framework for fully assessing N impacts on climate changes. PMID:23504794

Lu, Chaoqun; Tian, Hanqin

2013-02-01

26

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

NASA Astrophysics Data System (ADS)

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.

Park, Jong-Yeon; Kug, Jong-Seong

2014-01-01

27

Carbon, nitrogen, oxygen and sulfide budgets in the Black Sea: A biogeochemical model of the whole water column coupling the oxic and anoxic parts  

Microsoft Academic Search

Carbon, nitrogen, oxygen and sulfide budgets are derived for the Black Sea water column from a coupled physical–biogeochemical model. The model is applied in the deep part of the sea and simulates processes over the whole water column including the anoxic layer that extends from ?115m to the bottom (?2000m). The biogeochemical model involves a refined representation of the Black

M. Grégoire; K. E. R. Soetaert

2010-01-01

28

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

National Technical Information Service (NTIS)

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), ...

N. L. Miller I. T. Foster

1994-01-01

29

Modeling Nitrogen Cycle at the Surface-Subsurface Water Interface  

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

30

A spatial and temporal continuous surface-subsurface hydrologic model  

Microsoft Academic Search

A hydrologic model integrating surface-subsurface processes was developed based on spatial and temporal continuity theory. The raster-based mass balance hydrologic model consists of several submodels which determine spatial and temporal patterns in precipitation, surface flow, infiltration, subsurface flow, and the linkages between these submodels. Model parameters and variables are derived directly or indirectly from satellite remote sensing data, topographic maps,

Qing-Fu Xiao; Susan L. Ustin; Wesley W. Wallender

1996-01-01

31

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

NASA Astrophysics Data System (ADS)

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.

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

2012-12-01

32

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

33

Coupling transport and biodegradation of VOCs in surface subsurface soils  

SciTech Connect

Volatile organic chemicals present at Superfund sites preferentially partition into the soil gas and may be available for microbial degradation. A simple mass transfer model for biodegradation for volatile substrates has been developed for the aerobic decomposition of aromatic and aliphatic hydrocarbons. The mass transfer analysis calculates diffusive fluxes from soil gas through water and membrane films and into the cell. This model predicts an extreme sensitivity of potential biodegradation rates to the air-water partition coefficients of the compounds. Aromatic hydrocarbons are removed rapidly while the aliphatic hydrocarbons are much slower by orders of magnitude. Furthermore, oxygen transfer is likely to limit aromatic hydrocarbon degradation rates. The model presents results that cast doubt on the practicality of using methane or propane for the co-metabolic destruction of trichloroethylene in a gas phase bioreactor. Toluene as a primary substrate has better mass transfer characteristics to achieve more efficient trichloroethylene degradation. Hence, in sites where these contaminants coexist, bioremediation could be improved. 12 refs., 3 figs., 1 tab.

Hunt, J.R.; Holden, P.A.; Firestone, M.K. [Univ. of California, Berkeley, CA (United States)

1995-06-01

34

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

SciTech Connect

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.

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

1994-04-01

35

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)

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.

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

2000-01-01

36

Conjunctive surface-subsurface modeling of overland flow  

Microsoft Academic Search

In this paper, details of a conjunctive surface-subsurface numerical model for the simulation of overland flow are presented. In this model, the complete one-dimensional Saint-Venant equations for the surface flow are solved by a simple, explicit, essentially non-oscillating (ENO) scheme. The two-dimensional Richards equation in the mixed form for the subsurface flow is solved using an efficient strongly implicit finite-difference

Vivekanand Singh; S. Murty Bhallamudi

1998-01-01

37

Evaluating CaCO3-cycle modules in coupled global biogeochemical ocean models  

NASA Astrophysics Data System (ADS)

The marine CaCO3 cycle is an important component of the oceanic carbon system and directly affects the cycling of natural and the uptake of anthropogenic carbon. In numerical models of the marine carbon cycle, the CaCO3 cycle component is often evaluated against the observed distribution of alkalinity. Alkalinity varies in response to the formation and remineralisation of CaCO3 and organic matter. However, it also has a large conservative component, which may strongly be affected by a deficient representation of ocean physics (circulation, evaporation, and precipitation) in models. Here we apply a global ocean biogeochemical model run into preindustrial steady state featuring a number of idealized tracers, explicitly capturing the model's CaCO3 dissolution, organic matter remineralisation, and various preformed properties (alkalinity, oxygen, phosphate). We compare the suitability of a variety of measures related to the CaCO3 cycle, including alkalinity (TA), potential alkalinity and TA*, the latter being a measure of the time-integrated imprint of CaCO3 dissolution in the ocean. It can be diagnosed from any data set of TA, temperature, salinity, oxygen and phosphate. We demonstrate the sensitivity of total and potential alkalinity to the differences in model and ocean physics, which disqualifies them as accurate measures of biogeochemical processes. We show that an explicit treatment of preformed alkalinity (TA0) is necessary and possible. In our model simulations we implement explicit model tracers of TA0 and TA*. We find that the difference between modeled true TA* and diagnosed TA* was below 10% (25%) in 73% (81%) of the ocean's volume. In the Pacific (and Indian) Oceans the RMS error of TA* is below 3 (4) mmol TA m-3, even when using a global rather than regional algorithms to estimate preformed alkalinity. Errors in the Atlantic Ocean are significantly larger and potential improvements of TA0 estimation are discussed. Applying the TA* approach to the output of three state-of-the-art ocean carbon cycle models we demonstrate the advantage of explicitly taking preformed alkalinity into account for separating the effects of biogeochemical processes and circulation on the distribution of alkalinity. In particular, we suggest to use the TA* approach for CaCO3-cycle model evaluation.

Koeve, W.; Duteil, O.; Oschlies, A.; Kähler, P.; Segschneider, J.

2013-11-01

38

Finite volume integrated surface-subsurface flow modeling on nonorthogonal grids  

NASA Astrophysics Data System (ADS)

this paper, we present an innovative finite volume surface-subsurface integrated flow model on nonorthogonal grids. The shallow water equation with diffusion wave approximation is used to formulate the surface flow system, while the Richards' equation is used to formulate the saturated-unsaturated subsurface flow system. These two flow systems are discretized using a finite volume method and are then coupled by enforcing the continuity of pressure and flux at the surface-subsurface interface, which does not require unphysical parameters such as the interface permeability and thickness. The numerical instability caused by enforcing the continuity of pressure and flux at the interface is resolved using a cell-centered finite volume discretization. The coupled systems are solved simultaneously by the Newton iterative method. A battery of benchmark analyses and laboratory experiments verify the proposed model's superior performance relative to existing models. Two numerical experiments over irregular terrain show that the nonorthogonal grids and diffusive wave approximation used in the proposed model accurately represent the interaction between surface and subsurface flows for irregular topographies. In particular, they capture the significant topographical effects on runoff discharges, especially where gentle slopes are involved.

An, Hyunuk; Yu, Soonyoung

2014-03-01

39

Seasonal variation of primary productivity in the East China Sea: A numerical study based on coupled physical-biogeochemical model  

NASA Astrophysics Data System (ADS)

The seasonal variation of phytoplankton growth in the East China Sea (ECS) is simulated with a three-dimensional coupled physical-biogeochemical model, which includes discharges from Changjiang (Yangtze River). The purpose is to determine the main control on the seasonality of primary productivity in the ECS shelf, which nurtures rich biological resources. The model has a horizontal resolution of 1/6° in the domain from 23°N to 41°N and from 116°E to 134°E, excluding the Japan/East Sea, and 33 layers in the vertical. The nitrogen-based biogeochemical model has four compartments: dissolved inorganic nitrogen (DIN), phytoplankton, zooplankton and detritus. The chlorophyll to phytoplankton ratio depends on light and DIN availability. The model is driven by monthly climatological winds with the sea-surface temperature, salinity and DIN relaxed towards the climatological mean values. It successfully reproduces the observed seasonal variation of primary productivity over the ECS shelf with a strong peak in later spring and summer. The modeled annual mean primary production (PP) over the entire ECS shelf is 441 mg C m -2 d -1, which falls within the reported range of 390-529 mg C m -2 d -1. It also reproduces the marked seaward gradient of DIN that decreases away from the Changjiang plume. Strong dependency on the amount of photosynthetically active radiation (PAR) is demonstrated for primary production. For 1% change in PAR 0.7% change in PP is effected. Numerical experiments show that the strong summer peak of DIN load from Changjiang cannot generate the seasonality of PP without the seasonal cycle of PAR. On the other hand, the model can still produces the seasonal pattern with Changjiang nutrient load set to zero, indicating light availability as the major control. Yet the Changjiang DIN load induces a PP increase of 77 mg C m -2 d -1, which represents 13-20% of the observation based estimates of PP. It is noted that the increase in nitrogen uptake associated with PP is 2.7 times the DIN provided by the Changjiang discharge, implying efficient recycling of the riverine nutrients in the shelf water. The model needs improvement on the sluggish dispersion of the Changjiang plume and insufficient vertical mixing. It also needs a more complicated biogeochemical model with more size classes of organisms, multiple-nutrient schemes and additional geochemical processes.

Liu, Kon-Kee; Chao, Shenn-Yu; Lee, Hung-Jen; Gong, Gwo-Ching; Teng, Yi-Cheng

2010-10-01

40

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

NASA Technical Reports Server (NTRS)

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

Gregg, Watson W.

1999-01-01

41

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

NASA Astrophysics Data System (ADS)

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 redox condition, while relatively higher P concentration in surface water suggests that surface runoff may be more responsible for the transport of P. Therefore, the value of this study is that it confirmed the connection of HGM and transport and fate of some contaminants, and also revealed that land use manner plays an important role in aquatic ecosystem sustainability and it should be considered in water resource management.

Liu, X.

2012-12-01

42

Estimating Stream Chemistry During the Snowmelt Pulse Using Remotely Sensed Snow Observations and a Coupled Snowmelt and Biogeochemical Modeling Approach  

Microsoft Academic Search

The use of robust physically based models should improve the predictions made by biogeochemical models across a range of ecosystems. While a widely held belief this statement has not been supported by that many integrated modeling studies. In this paper we will present our efforts to integrate a physically robust snowmelt model with a detailed biogeochemical model of alpine ecosystems.

J. Sickman; N. P. Molotch; T. Meixner; M. Williams

2006-01-01

43

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

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

44

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

Microsoft Academic Search

The overall objective of this presentation is to demonstrate a conceptual multiscale, multidomain model of coupling of biogeochemical and hydrogeological processes during bioremediation of Cr(VI) contaminated groundwater at Hanford 100H site. A slow release polylactate, Hydrogen Release Compound (HRCTM), was injected in Hanford sediments to stimulate immobilization of Cr(VI). The HRC injection induced a 2-order-of- magnitude increase in biomass and

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

2007-01-01

45

Biogeochemical Cycling  

NASA Technical Reports Server (NTRS)

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

Bebout, Brad; Fonda, Mark (Technical Monitor)

2002-01-01

46

Kinetic Modeling of Biogeochemical Processes in Subsurface Environments: Coupling Transport, Microbial Metabolism and Geochemistry  

NASA Astrophysics Data System (ADS)

Microbial reactions play an important role in regulating pore water chemistry (e.g., pH and Eh) as well as secondary mineral distribution in many subsurface systems and therefore directly control trace metal migration and recycling in those systems. In this paper, we present a multicomponent kinetic model that explicitly accounts for the coupling of microbial metabolism, microbial population dynamics, advective/dispersive transport of chemical species, aqueous speciation, and mineral precipitation/dissolution in porous geologic media. A modification to the traditional microbial growth kinetic equation is proposed, to account for the likely achievement of quasi-steady state biomass accumulations in natural environments. A scale dependence of microbial reaction rates is derived based on both field observations and the scaling analysis of reactive transport equations. As an example, we use the model to simulate a subsurface contaminant migration scenario, in which a water flow containing both uranium and a complexing organic ligand is recharged into an oxic carbonate aquifer. The model simulation shows that Mn and Fe oxyhydroxides may vary significantly along a flow path. The simulation also shows that uranium (VI) can be reduced and therefore immobilized in the anoxic zone created by microbial degradation. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy (US DOE) under Contract DE-AC04-94AL85000.

Wang, Y.

2002-12-01

47

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

SciTech Connect

Our goal within the overall project is to demonstrate the presence and abundance of methane monooxygenases (MMOs) enzymes and their genes within the microbial community of the Idaho National Laboratory (INL) Test Area North (TAN) site. MMOs are thought to be the primary catalysts of natural attenuation of trichloroethylene (TCE) in contaminated groundwater at this location. The actual presence of the proteins making up MMO complexes would provide direct evidence for its participation in TCE degradation. The quantitative estimation of MMO genes and their translation products (sMMO and pMMO proteins) and the knowledge about kinetics and substrate specificity of MMOs will be used to develop mathematical models of the natural attenuation process in the TAN aquifer. The model will be particularly useful in prediction of TCE degradation rate in TAN and possibly in the other DOE sites. Bacteria known as methanotrophs produce a set of proteins that assemble to form methane monooxygenase complexes (MMOs), enzymes that oxidize methane as their natural substrate, thereby providing a carbon and energy source for the organisms. MMOs are also capable of co-metabolically transforming chlorinated solvents like TCE into nontoxic end products such as carbon dioxide and chloride. There are two known forms of methane monooxygenase, a membrane-bound particulate form (pMMO) and a cytoplasmic soluble form (sMMO). pMMO consists of two components, pMMOH (a hydroxylase comprised of 47-, 27-, and 24-kDa subunits) and pMMOR (a reductase comprised of 63 and 8-kDa subunits). sMMO consists of three components: a hydroxylase (protein A-250 kDa), a dimer of three subunits (?2?2?2), a regulatory protein (protein B-15.8 kDa), and a reductase (protein C-38.6 kDa). All methanotrophs will produce a methanol dehydrogenase to channel the product of methane oxidation (methanol) into the central metabolite formaldehyde. University of Idaho (UI) efforts focused on proteomic analyses using mass spectrometry and genomic analyses using RT-PCR to characterize these enzyme systems. UI’s specific objectives were to develop the proteomics and genomic tools to assess the presence of the methane monooxygenase (MMO) proteins in the aquifers under study and relate this to the enumeration of methanotrophic microorganisms. We targeted the identification of both sMMO and pMMO. We believe that the copper level in the TAN aquifer is most likely suppressing the expression of sMMO and mediates the higher levels of pMMO expression. Hence our investigations included the identification of both forms of MMOs, and we expected a higher concentration of pMMO proteins in TAN samples. The amounts of these proteins present were correlated with numbers of methanotrophs determined by us and other members of the research team using PCR-based methods. In summary, to accomplish our objectives we applied environmental proteomics techniques to monitor proteins that are involved in the co-metabolic degradation of trichloroethylene (TCE) in groundwater of the INL TAN site on Department of Energy ands of near Idaho Falls, ID USA. To acquire peptides sequences information we used an ultra performance chromatography (UPLC) system coupled with QToF Premiere nano-electrospray tandem quadropole-time of flight mass spectrometer. Our goal was to identify signature peptides of methane monooxygenases (MMOs) within methanotrophic bacteria that are active in cometabolic degradation of TCE. We developed a new method for extracting total proteins from environmental planktonic and/or biofilm samples that involve a new time course cell lysis and protein extraction method in combination with chromatographic separation of peptide and tandem mass spectrometry sequencing. The techniques resulted in successful extraction and identification of MMO-based peptides from both pure cultures and TAN site samples. The work confirmed the importance of mathonotrophs in the co-metabolic removal of TCE from the TAN site aquifer.

Crawford, Ronald L; Paszczynski, Andrzej J.

2010-02-19

48

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

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.

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

2013-01-01

49

Emergent biological patterns and surface-subsurface interactions at landscape scales  

USGS Publications Warehouse

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

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

2000-01-01

50

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

51

Arithmetic Architecture for Surface/Subsurface Bearing - Only Radar Tracking by Microcomputer.  

National Technical Information Service (NTIS)

Passive localization and tracking techniques are of interest in a variety of microcomputer based surface/subsurface radar applications. Because a significant portion of the cost of building or maintaining a warship is the electronics in its sensor and wea...

F. Erdogdu

1979-01-01

52

Control of mass balance error in a detailed model of surface-subsurface flow interaction  

NASA Astrophysics Data System (ADS)

Several process-based catchment-scale hydrologic models have been developed in recent years to describe the interactions and feedbacks between different components of the water cycle, but few studies have considered the sources of coupling error in these models. In this work we analyze the sequential iterative coupling scheme of the distributed model CATHY (CATchment HYdrology) in order to identify the different sources of mass balance error and to examine how these are influenced by topography, hydraulic properties, and atmospheric forcing. A pair of adimensional indices that quantify the degree of coupling and of flux partitioning is presented. Our analysis shows that mass balance errors increase during the flood recession limb because of the exchange of information between surface and subsurface water flow. Surface water propagation is cell centered, while the subsurface flow equation is solved on the vertices of surface cells. Evaluation of surface pressure heads and exchange fluxes is critical on this staggered surface-subsurface mesh, especially during transitions from unsaturated to saturated conditions and vice versa. A modified version of the flux exchange algorithm is introduced that considers the effective availability of water on surface cells. The performance of the model is also improved by introducing a heuristic procedure to control and adapt the time step interval. Starting from numerical stability and convergence constraints, this procedure varies the computational interval as a function of the rate of change of surface saturation via the coupling degree index. A final improvement made to the sequential coupling scheme in CATHY is to solve the surface routing equation after rather than before the subsurface module. We find that the modified version improves the water balance by more than 50% in most of the tests considered for a simple v-shaped catchment. The results so far obtained for the synthetic v-catchment indicate the need for a more comprehensive analysis including real catchments.

Fiorentini, Marcello; Orlandini, Stefano; Paniconi, Claudio; Putti, Mario

2014-05-01

53

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

USGS Publications Warehouse

The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal in the river networks of two watersheds having widely differing levels of nitrate enrichment but nearly identical discharges. Stream denitrification is estimated by regression as a nonlinear function of nitrate concentration, streamflow, and temperature, using more than 300 published measurements from a variety of US streams. These relations are used in the stream transport model to characterize nitrate dynamics related to denitrification at a monthly time scale in the stream reaches of the two watersheds. Results indicate that the nitrate removal efficiency of streams, as measured by the percentage of the stream nitrate flux removed via denitrification per unit length of channel, is appreciably reduced during months with high discharge and nitrate flux and increases during months of low-discharge and flux. Biogeochemical factors, including land use, nitrate inputs, and stream concentrations, are a major control on reach-scale denitrification, evidenced by the disproportionately lower nitrate removal efficiency in streams of the highly nitrate-enriched watershed as compared with that in similarly sized streams in the less nitrate-enriched watershed. Sensitivity analyses reveal that these important biogeochemical factors and physical hydrological factors contribute nearly equally to seasonal and stream-size related variations in the percentage of the stream nitrate flux removed in each watershed. ?? 2008 The Author(s).

Alexander, R. B.; Bohlke, 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

54

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)

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.

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

2000-01-01

55

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

SciTech Connect

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.

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

2006-06-01

56

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

NASA Astrophysics Data System (ADS)

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.

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

2010-12-01

57

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

NASA Technical Reports Server (NTRS)

The Sea-Viewing Wide Field-of-view Sensor (SeaWiFS) has observed 2.5 years of routine global chlorophyll observations from space. The mission was launched into a record El Nino event, which eventually gave way to one of the most intensive and longest-lasting La Nina events ever recorded. The SeaWiFS chlorophyll record captured the response of ocean phytoplankton to these significant events in the tropical Indo-Pacific basins, but also indicated significant interannual variability unrelated to the El Nino/La Nina events. This included large variability in the North Atlantic and Pacific basins, in the North Central and equatorial Atlantic, and milder patterns in the North Central Pacific. This SeaWiFS record was tracked with a coupled physical/biogeochemical/radiative model of the global oceans using near-real-time forcing data such as wind stresses, sea surface temperatures, and sea ice. This provided an opportunity to offer physically and biogeochemically meaningful explanations of the variability observed in the SeaWiFS data set, since the causal mechanisms and interrelationships of the model are completely understood. The coupled model was able to represent the seasonal distributions of chlorophyll during the SeaWiFS era, and was capable of differentiating among the widely different processes and dynamics occurring in the global oceans. The model was also reasonably successful in representing the interannual signal, especially when it was large, such as, the El Nino and La Nina events in the tropical Pacific and Indian Oceans. The model provided different phytoplankton group responses for the different events in these regions: diatoms were predominant in the tropical Pacific during the La Nina but other groups were predominant during El Nino. The opposite condition occurred in the tropical Indian Ocean. Both situations were due to the different responses of the basins to El Nino. The interannual variability in the North Atlantic, which was exhibited in SeaWiFS data as a decline in the spring/summer bloom in 1999 relative to 1998, resulted in the model from a more slowly shoaling mixed layer, allowing herbivore populations to keep pace with increasing phytoplankton populations. However, several aspects of the interannual cycle were not well-represented by the model. Explanations ranged from inherent model deficiencies, to monthly averaging of forcing fields, to biases in SeaWiFS atmospheric correction procedures.

Watson, Gregg W.

2000-01-01

58

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

NASA Technical Reports Server (NTRS)

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).

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

2000-01-01

59

Simulating complex flow and transport dynamics in an integrated surface-subsurface modeling framework  

Microsoft Academic Search

A fully-integrated surface-subsurface flow and transport model is applied to a 17 km2 subcatchment of the Laurel Creek Watershed within the Grand River basin in Southern Ontario, Canada. Through past and ongoing\\u000a field studies, the subcatchment is reasonably well characterized and is being monitored on an ongoing basis. In addition to\\u000a diverse land-usage and surface cover and more than 65

Edward A. Sudicky; Jon P. Jones; Young-Jin Park; Andrea E. Brookfield; Dennis Colautti

2008-01-01

60

Integrated Surface–Subsurface Modeling of Fuxianhu Lake Catchment, Southwest China  

Microsoft Academic Search

This paper describes an integrated surface–subsurface modeling study of the Fuxianhu Lake catchment (southwest China). Pollution\\u000a threats to this important water resource have led to the need to evaluate transport pathways and the overall water balance\\u000a of the catchment. Catchment inputs to the lake include river inflows, direct overland flow and groundwater discharge, which\\u000a are incorporated into a mathematical model

Qi Zhang; Adrian D. Werner

2009-01-01

61

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)

The effects of extreme weather events on C, N, and P transport from inland watersheds.Discovering how C, N, P export would be affected by the size of the watershed.Changes in biogeochemical processes in storm runoff in contrast to those in base flow.

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

2014-04-01

62

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

NASA Astrophysics Data System (ADS)

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

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

2011-08-01

63

Global Biogeochemical Cycles and the Physical Climate System  

NSDL National Science Digital Library

This module focuses on the biogeochemical cycles of five of the major elements important to life - carbon, nitrogen, phosphorus, sulfur, and oxygen - and their role in climatic change. The chapters include: Biogeochemical Processes, Biogeochemical Cycles and Climate, The Modern Coupled C-N-P-S-O System, Carbon Cycles, The Important Nutrient Nitrogen, Phosphorus and Sulfur, and The Water Cycle. Study questions and answers are also available.

Mackenzie, Fred

1999-01-01

64

High-resolution reactive transport: A coupled parallel hydrogeochemical model  

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

65

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

Microsoft Academic Search

A coupled physical-biogeochemical model of the tropical Pacific Ocean with simultaneous iron and nitrogen limitation was developed to study questions of iron biogeochemistry, its e4ects on upper ocean production, and ultimately the biogeochemical cycles of the other elements. The model results suggest that iron limitation is ubiquitous in the equatorial Pacific, and extends further west than is generally believed unless

J. R. Christian; M. A. Verschell; R. Murtugudde; A. J. Busalacchi

2002-01-01

66

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

Microsoft Academic Search

A coupled physical–biogeochemical model of the tropical Pacific Ocean with simultaneous iron and nitrogen limitation was developed to study questions of iron biogeochemistry, its effects on upper ocean production, and ultimately the biogeochemical cycles of the other elements. The model results suggest that iron limitation is ubiquitous in the equatorial Pacific, and extends further west than is generally believed unless

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

2001-01-01

67

Effect of in-stream turbulent coherent structures on surface-subsurface exchange  

NASA Astrophysics Data System (ADS)

The penetration of turbulent eddies in stream sediments represents one of the most recognized interaction processes between surface and subsurface water in rivers, and it provides dissolved oxygen and nutrients that are vital for the life of hyporheic macroinvertebrates and salmonid embryos. Turbulence penetration is known to be rapidly dampened by the granulometry of the porous medium, which limits the depth of this exchange process to a thin sediment layer of a few grain diameters. Because of this small depth, it is commonly assumed that turbulence contributes to hyporheic exchange only in streams flowing on highly permeable gravel sediments. However, another effect of stream turbulence is to determine unsteady spatial variations of pressure over the streambed. These pressure variations are caused by the interaction between the streambed surface and the large turbulent coherent structures in the surface flow, and they result in hydraulic gradients and water seepage velocities deep within the sediments. In order to examine the significance of this exchange process, the present work presents a numerical analysis of the hyporheic flow induced by an idealized turbulent pressure profile on a streambed. The combined action of pressure-induced advection, underflow, and hydrodynamic dispersion is considered, and penetration depths and residence times of exchange water are evaluated. The simulation results show that stream turbulence has the potential to drive surface-subsurface exchange even if the penetration of eddies is prevented by the filtering action of the sediments.

Boano, Fulvio; Revelli, Roberto; Ridolfi, Luca

2010-05-01

68

Biogeochemical Processes in Microbial Ecosystems  

NASA Technical Reports Server (NTRS)

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.

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

2001-01-01

69

Cave Formation: Biogeochemical Cycles  

NSDL National Science Digital Library

This video explores the role of biogeochemical cycles in the formation of caves. It discusses a radical new theory that identifies sulfuric acid as a cave-forming agent. The video, adapted from a NOVA broadcast, identifies the source of the sulfuric acid, which, unlike carbonic acid, the typical cave-forming agent, does not readily form in nature. The segment is 5 minutes and forty seconds in length.

2011-07-28

70

Cave Formation: Biogeochemical Cycles  

NSDL National Science Digital Library

This video explores the role of biogeochemical cycles in the formation of caves. It discusses a radical new theory that identifies sulfuric acid as a cave-forming agent. The video, adapted from a NOVA broadcast, identifies the source of the sulfuric acid, which, unlike carbonic acid, the typical cave-forming agent, does not readily form in nature. The segment is 5 minutes and forty seconds in length.

71

Primer: Using Watershed Modeling System (WMS) for Gridded Surface Subsurface Hydrologic Analysis (GSSHA) Data Development - WMS 6.1 and GSSHA 1. 43C.  

National Technical Information Service (NTIS)

This document is a primer for use of the Watershed Modeling System (WMS) interface with the physically based, distributed-parameter hydrologic model Gridded Surface Subsurface Hydrologic Analysis (GSSHA). The primary purpose of this primer is to describe ...

C. W. Downer E. J. Nelson A. Byrd

2003-01-01

72

Effects of the Tide on the Marine Ecosystem in the Northwestern Pacific Marginal Seas using a 3-dimensional Coupled Physico-Biogeochemical Model  

NASA Astrophysics Data System (ADS)

Tide is a crucial factor for the proper simulation of the ocean circulation in the Northwestern Pacific Marginal Seas, especially in the Yellow Sea. The different physical status due to the inclusion (or exclusion) of tide in the coupled ocean physics and biogeochemistry system also produces a different ecosystem. In this study, we have applied 3-dimensional coupled ocean system model based on POLCOMS (Proudman Oceanographic Laboratory Coastal Ocean Modelling System) and ERSEM (European Regional Seas Ecosystem Model) to the Northwestern Pacific Marginal Seas and have investigated the influences of the tide in the marine system model on the ecosystem. The model covers the Yellow and the East China Seas (YES), the East/Japan Sea (EJS) and the Okhotsk Sea (OS) as well as the major western boundary currents, the Kuroshio and the Oyashio currents. The effects of tide in the physical system, as expected, are prominent in the YES circulation pattern change in terms of the Changiang Diluted Water (CDW) dispersion path, the Yellow Sea Warm Current (YSWC), the Yellow Sea Bottom Cold Water (YSBCW) distribution as well as local influences driven by tidal mixing. These changes of physical status control the changes of nutrients as well as plankton distributions in the YES. It is noteworthy that the ecosystem in the southern EJS is also highly affected by the lateral transport of different nutrients conditions and changed ecosystem from the YES. The changes of the OS ecosystem and physical status due to the tide are not notable compared to the YES but there are local changes especially in the northern shelf region. It is concluded that the tide is very important not only for the local ecosystem but also for the remote ecosystem, though the local tide seems not so much crucial, if it is linked with the strong tidal regime inflow region.

Kang, Hyoun-Woo; Kim, Hanna; Kwi So, Jae; Butenschon, Momme; Allen, Icarus

2014-05-01

73

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)

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.

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

2013-05-01

74

Simulation of Marine Nitrogen Cycling as Function of Atmospheric Oxygen: Results of a Coupled C,N,P,O,S Biogeochemical Model Including d15N  

NASA Astrophysics Data System (ADS)

Bioavailable nitrogen is a critical limiting nutrient in the modern marine biosphere. We expect that the rate of denitrification may have been higher in the geologic past due to decreased atmospheric O2 and expanded ocean anoxia. To examine the consequences of this idea, we present numerical simulations of coupled carbon, nitrogen, phosphorus, oxygen, and sulfur cycling as a function of atmospheric oxygen in an ocean with circulation similar to modern conditions. The model has been specifically developed to function over a wide range of ocean redox conditions and has been successfully tested in simulations of both the modern global ocean and Black Sea. Global rates of nitrogen fixation and pelagic denitrification, which are strongly coupled in our default model, reach maximum rates between 25% and 50% of the present atmospheric level of O2 (PAL O2). At 40% PAL O2, the simulated steady-state pelagic denitrification rate is 82.1 Tmol/yr, and the N- fixation rate is 85.7 Tmol/yr. These rates are 8-15× greater than modern estimates. The maximum simulated rate of N-fixation is determined by the N flux required to entirely support export production. At mid- levels of atmospheric oxygen, large areas of the oceans are characterized by a suboxic to anoxic "oxygen minimum zone" between 100m and 1000m depth which is over- and underlain by oxic water. Under these conditions, denitrification in the upper water column is nearly complete, suppressing the ?15N isotopic signal for this process. To test the impact of limitation of N-fixation (e.g. by trace metals, light, temperature) we imposed a cap on the global N-fixation rate. In these simulations, limitation of N-fixation below 50% PAL O2 results in severe N limitation of primary production and low mean oceanic N:P. Our results imply that N limitation may have been chronic at intermediate levels of atmospheric O2. At the same time, low N:P conditions would create evolutionary pressure for efficient N-fixation pathways and high N use efficiency in non-fixing marine phytoplankton, testing the limits of plasticity in the Redfield ratio. If N-fixation were unable to keep up with high rates of denitrification at intermediate levels of atmospheric O2, intense N limitation of Proterozoic marine primary production may have strongly inhibited any further rise of atmospheric O2, thus stabilizing atmospheric O2 at <25% PAL.

Romaniello, S. J.; Derry, L. A.

2008-12-01

75

Arctic Ocean shelf biogeochemical cycling under climate change  

NASA Astrophysics Data System (ADS)

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

Bellerby, Richard; Silyakova, Anna; Slagstad, Dag

2014-05-01

76

About the importance of small scale spatial variability in coupled surface-subsurface simulations and how it can be characterized.  

NASA Astrophysics Data System (ADS)

Small scale spatial variability of soil and aquifer hydraulic properties exerts an important influence on flow and transport processes. Connected structures as present in fluvial aquifers, or macropores in soil, provide preferential flow paths for water and contaminants. Their characterization is therefore also important for management purposes. The importance of small scale spatial variability of riverbed hydraulic properties for exchange fluxes of water and solutes between a stream and the underlying subsurface is not so well studied. A few studies were dedicated to this topic and found that riverbed hydraulic properties might vary over many orders of magnitude and that most of the exchange fluxes might be centered at only a few spots. Next question is whether this spatial variability can be represented well with effective, uniform properties. In earlier work we found that effective, uniform parameters result in a biased estimation of stream-aquifer exchange fluxes, especially if the flow regime is very different from the flow regime in the calibration period. Given these results, the role of small-scale variability of riverbed hydraulic conductivity (K) (and its parameterization in a model) was investigated further by studying a 6km river section in the city of Zurich (Switzerland) in a transient finite elements model for variably saturated flow. It was also assessed whether the small-scale spatial variability can be characterized with stochastic realizations in combination with parameter estimation. Although the simulation example mimics the real-world case (Zurich) as much as possible and uses transient model forcings obtained from real data, synthetic experiments were conducted in order to verify the procedure in detail. Parameter estimation was done with help of the Ensemble Kalman Filter (EnKF), on the basis of an augmented state vector approach for estimating the unknown parameters. We used three different setups to generate synthetic realities, and for each setup 10 different synthetic realities were generated. For each synthetic reality 100 different stochastic realizations were generated and updated with EnKF. The set-ups had a moderately heterogeneous K of the riverbed, a strongly heterogeneous riverbed K with strong K contrasts between five different river sections, and a strongly heterogeneous riverbed K without a clear zonation. In all cases, EnKF was used to assimilate either zero (open loop), 10 or 100 time series of hydraulic head data to update either the riverbed K of all nodes (stochastic field approach) or only effective riverbed K for five, three or two zones. The results showed that the stochastic field approach outperforms the approaches where only a limited number of effective parameters is updated. This is especially the case for strongly heterogeneous realities and many measurement data. A zonation approach systematically underestimates net stream-aquifer exchange fluxes, but in case the position of the zones is well-known, also the zonation approach gives good results.

Hendricks Franssen, H.; Kurtz, W.; Brunner, P.; Vereecken, H.

2012-12-01

77

National Wetlands Biogeochemical Database (NWBD)  

NSDL National Science Digital Library

The National Wetland Biogeochemical Database (NWBD) is "an effort to locate, collect and compile existing biogeochemical information on wetlands of the United States including Hawaii and Alaska." Funded in part by the Environmental Protection Agency (EPA), the database will be used to develop a Nutrient Criteria Technical Guidance Manual for US Wetlands -- for use in assessing potential nutrient-related trophic state impairment and pollution problems. Presently focused on water column and soil biogeochemical parameters (e.g., N, P, C, Metals, temp., DO, pH, etc.), the completed NWBD will act as a reference data set for biogeochemical parameters at different regional, community, and temporal scales. Data contributors are invited to participate using NWBD's on-site contact information.

78

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)

The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in a small catchment at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the evapotranspiration is based on Penman-Monteith. Biogeochemical processes are modelled by LandscapeDNDC, including soil microclimate, plant growth and biomass allocation, organic matter mineralisation, nitrification, denitrification, chemodenitrification and methanogenesis producing and consuming soil based greenhouse gases. The model application will present first validation results of the coupled model to simulate soil based greenhouse gas emissions as well as nitrate discharge from the Yanting catchment. The model application will also present the effects of different management practices (fertilization rates and timings, tilling, residues management) on the redistribution of N surplus within the catchment causing biomass productivity gradients and different levels of indirect N2O emissions along topographical gradients.

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

79

Field Testing of an Integrated Surface\\/Subsurface Modeling Technique for Planetary Exploration  

Microsoft Academic Search

While there has been much interest in developing ground-penetrating radar (GPR) technology for rover-based planetary exploration, relatively little work has been done on the data collection process. Starting from the manual method, we fully automate GPR data collection using only sensors typically found on a rover. Further, we produce two novel data products: (1) a three-dimensional, photorealistic surface model coupled

Paul Timothy Furgale; Timothy D. Barfoot; Nadeem Ghafoor; Kevin Williams; Gordon Osinski

2010-01-01

80

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

81

Multi-constraint calibration of a surface-subsurface-atmosphere model at the catchment scale  

NASA Astrophysics Data System (ADS)

A complex distributed numerical modelling framework including both groundwater- surface-water flow and heat flux exchange with the atmosphere, combined with a unique observational data set from the HOBE hydrological observatory in Western Denmark, enables a comprehensive application of multiple independent constraints to the model parameter optimization at the catchment scale (1050 km2). Five independent observational data sets consisting of stream discharge (8 stations), groundwater head (361 stations), latent heat flux (2 stations), soil moisture (28 stations) and remotely sensed land surface temperature (full spatial coverage on 28 days) are the basis for formulating 11 objective functions focussing on bias and RMSE of time series from multiple stations. In contrast to many multiple objective studies, where objective functions essentially originate from the same observational dataset (typically discharge time series), the dataset used in this study enables a truly multi-constraint evaluation of the states and fluxes simulated by the model. A preliminary sensitivity analysis of 35 model parameters reveals that even surface fluxes and states such as soil moisture, heat fluxes and land surface temperatures are highly sensitive to parameters that are typically associated with the groundwater components of the model. This indicates the importance of using fully coupled modelling approaches also in detailed studies of the near surface-atmosphere exchanges. The model parameter optimization, conducted using the gradient based search algorithm in PEST, has been carried out for three separate assumptions of available evaluation data. The first calibration uses only traditional observations of stream discharge and groundwater head, the second uses observations associated mainly with the land surface component, specifically latent heat flux, soil moisture and remotely sensed surface temperature. As a third scenario the model is calibrated using all available observational data sets, and finally each of the calibrated models are evaluated against the observations that were not used during calibration and for all observations for a validation period. The results illustrate the importance of multiple constraints to complex coupled models and the potential consequences of using model predictions of output that the model has not been constrained against. The study also highlights the need to develop spatial model calibration through new spatial performance metrics and new parameterisation and optimization frameworks that explicitly allow the models to improve their spatial pattern predictions while maintaining a reasonable number of free calibration parameters.

Stisen, Simon; Obel Sonnenborg, Torben; Refsgaard, Jens Christian; Koch, Julian; Bircher, Simone; Høgh Jensen, Karsten

2014-05-01

82

Biogeochemical modeling at mass extinction boundaries  

NASA Technical Reports Server (NTRS)

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.

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

1991-01-01

83

Root Distribution, Production, and Turnover in Riparian Subsurface Soils: Implications for Surface-Subsurface Connections  

NASA Astrophysics Data System (ADS)

Root-derived carbon (C) drives a large proportion of microbial activity in surface soils, and decomposing roots act as denitrification hot spots at 60-100 cm depth in riparian zones. However, root biomass and turnover has been measured rarely in saturated subsurface soils of riparian zones, where denitrification influences landscape-scale N fluxes. I here report data on root biomass (from soil cores), production (using ingrowth cores), and age (estimated with radiocarbon dating) from as deep as 150 cm in riparian zones on 1st - 3^{rd} order streams in Rhode Island, USA. I collected soil samples at three sites with sandy loam soils, vegetation dominated by 80 year old Acer rubrum, and <3% slopes. Water tables ranged from 50 cm in the growing season, to above the surface in the dormant season. Root biomass declined with depth from 0-50 cm but not between 50-100 cm. At site 1 (outwash), mean root biomass in surface soils 0-30 cm was 5,040 g m-2, and mean subsurface root biomass was 192 mp 81 g m-2 (95% CI), with a maximum value of 834 g m-2. Total root biomass did not differ among the three sites. The ingrowth cores yielded annual belowground production estimates of 331-680 g m-2 yr-1, almost all of which occurred in the top 30 cm. Root turnover in the surface is likely between 6 and 40%. After 30 months, very few roots had penetrated ingrowth cores below 40 cm despite substantial standing stocks of roots at depth. Radiocarbon analysis yielded further insights about root dynamics in the subsurface. In the shallow subsurface (40 - 75 cm), delta 14C values of fine roots ranged from 9.8 to 388 ‰, with corresponding ages between 14 and 47 years before present (ybp). With one exception, roots from the deep subsurface (below 80 cm) had 14C signatures < 0 ‰, and usually less than -100 ‰, corresponding to ages of 100-8,400 ybp. Fine root turnover appears to occur on decadal time scales at depths from ~45-75 cm, much more slowly than turnover in surface soils of upland forests. Samples from below 80 cm, with ages hundreds of years old, raise the possibility that episodic events (e.g., extreme droughts) lead to periods of deeper root growth and subsequent death. Coupling between the surface and subsurface in riparian zones appears to be strong in surface soils, moderately weak at depths of ~40-75 cm and very weak below 80 cm depth.

Gurwick, N. P.

2006-12-01

84

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

SciTech Connect

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).

Miller, N.L.

1993-01-01

85

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

SciTech Connect

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).

Miller, N.L.

1993-12-31

86

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

SciTech Connect

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.

Ling, Hao [The University of Texas at Austin] [The University of Texas at Austin; Hamilton, Mark F. [The University of Texas at Austin Applied Research Laboratories] [The University of Texas at Austin Applied Research Laboratories; Bhalla, Rajan [Science Applications International Corporation] [Science Applications International Corporation; Brown, Walter E. [The University of Texas at Austin Applied Research Laboratories] [The University of Texas at Austin Applied Research Laboratories; Hay, Todd A. [The University of Texas at Austin Applied Research Laboratories] [The University of Texas at Austin Applied Research Laboratories; Whitelonis, Nicholas J. [The University of Texas at Austin] [The University of Texas at Austin; Yang, Shang-Te [The University of Texas at Austin] [The University of Texas at Austin; Naqvi, Aale R. [The University of Texas at Austin] [The University of Texas at Austin

2013-09-30

87

Interpreting streamflow generation mechanisms from integrated surface-subsurface flow models of a riparian wetland and catchment  

NASA Astrophysics Data System (ADS)

The understanding of streamflow generation processes is vitally important in the management of water resources. In the absence of the data required to achieve this, Integrated Surface-Subsurface Hydrological Models (ISSHM) can be used to assist with the development of this understanding. However, the standard outputs from these models only enable elicitation of information about hydrological drivers and hydrological responses that occur at the same time. This generally limits the applicability of ISSHMs for the purposes of obtaining an improved understanding of streamflow generation processes to catchment areas that do not exhibit significant storage, travel times or flow depletion mechanisms. In order to overcome this limitation, a previously published Hydraulic Mixing-Cell (HMC) method is improved so that it can be used to follow surface water derived from direct rainfall and groundwater discharge to the stream and adjacent overland flow areas. The developed approach was applied to virtual experiments (based on the Lehstenbach catchment in southeastern Germany), which are composed of two ISSHMs of contrasting scales: (1) a riparian wetland of area 210 m2 and (2) a catchment of area 4.2 km2. For the two models, analysis of modeling results for a large storm event showed complex spatiotemporal variability in streamflow generation and surface water-groundwater interaction. Further analysis with the HMC method elucidated in-stream and overland flow generation mechanisms. This study showed within a modeling framework that identification and quantification of in-stream and overland flow generation better informed understanding of catchment functioning through decomposition of streamflow hydrographs, and analysis of spatiotemporal variability of flow generation mechanisms.

Partington, D.; Brunner, P.; Frei, S.; Simmons, C. T.; Werner, A. D.; Therrien, R.; Maier, H. R.; Dandy, G. C.; Fleckenstein, J. H.

2013-09-01

88

Impact of In-Channel Geomorphic Structures on Surface-Subsurface Exchange of Water and Heat in Streams  

NASA Astrophysics Data System (ADS)

In-channel geomorphic structures such as debris dams and steps are common in undisturbed streams, are often installed as part of stream restoration projects, and can significantly enhance exchange of water across the streambed. Surface-subsurface exchange is also an important cooling mechanism in summer for streams suffering elevated temperatures due to climate change or loss of riparian shade. However, the effects of many basic geomorphic structure characteristics (e.g., size and type) and hydro-geologic boundary conditions on water and heat exchange are poorly known but critical to understanding the impact of channel morphology on stream ecology. We combined surface and groundwater numerical hydraulic and heat flow models with field hydraulic and temperature measurements using a three-dimensional sensor network to quantify these relationships and their implications for stream functioning and restoration design. Results show that while water exchange with the subsurface generally increases linearly with geomorphic structure height, the residence time and size of the induced subsurface flow cell respond nonlinearly. Such hydrologic aspects of exchange also respond nonlinearly to various hydrologic and geologic controls, such as depth to bedrock, groundwater recharge, and channel slope. Finally, thermal effects, such as the degree of heat exchange via hydrodynamic mixing and heat conduction within the induced subsurface flow cell, and the corresponding temperature moderation of water as it returns to the surface, also appear to respond nonlinearly to basic descriptive parameters of in-channel geomorphic structures. These nonlinear trends have significant implications for understanding natural stream function as well as optimizing stream restoration design to maximize functions such as reactive time in the subsurface or reduction of maximum summer stream temperatures.

Hester, E. T.; Doyle, M. W.

2006-12-01

89

A comparison of recharge estimates to a fractured sedimentary aquifer in South Africa from a chloride mass balance and an integrated surface-subsurface model  

Microsoft Academic Search

The paper describes the use of an integrated surface-subsurface modelling approach to estimate recharge to a semi-arid Karoo aquifer and a comparison of the results with a chloride mass balance on a sub-area scale. Parameters were not calibrated, to test the success with which the model can be applied in regions of scarce data. The chloride balance suggests a mean

K. Sami; D. A. Hughes

1996-01-01

90

Biogeochemical Processes in Microbial Ecosystems  

NASA Technical Reports Server (NTRS)

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.

DesMarais, David J.

2001-01-01

91

The Global Biogeochemical Silicon Cycle  

Microsoft Academic Search

Silicon is one of the most important elements in the current age of the anthropocene. It has numerous industrial applications,\\u000a and supports a high-tech multi-billion Euro industry. Silicon has a fascinating biological and geological cycle, interacting\\u000a with other globally important biogeochemical cycles. In this review, we bring together both biological and geological aspects\\u000a of the silicon cycle to provide a

Eric Struyf; Adriaan Smis; Stefan Van Damme; Patrick Meire; Daniel J. Conley

2009-01-01

92

Benthic exchange and biogeochemical cycling in permeable sediments.  

PubMed

The sandy sediments that blanket the inner shelf are situated in a zone where nutrient input from land and strong mixing produce maximum primary production and tight coupling between water column and sedimentary processes. The high permeability of the shelf sands renders them susceptible to pressure gradients generated by hydrodynamic and biological forces that modulate spatial and temporal patterns of water circulation through these sediments. The resulting dynamic three-dimensional patterns of particle and solute distribution generate a broad spectrum of biogeochemical reaction zones that facilitate effective decomposition of the pelagic and benthic primary production products. The intricate coupling between the water column and sediment makes it challenging to quantify the production and decomposition processes and the resultant fluxes in permeable shelf sands. Recent technical developments have led to insights into the high biogeochemical and biological activity of these permeable sediments and their role in the global cycles of matter. PMID:23987916

Huettel, Markus; Berg, Peter; Kostka, Joel E

2014-01-01

93

Benthic Exchange and Biogeochemical Cycling in Permeable Sediments  

NASA Astrophysics Data System (ADS)

The sandy sediments that blanket the inner shelf are situated in a zone where nutrient input from land and strong mixing produce maximum primary production and tight coupling between water column and sedimentary processes. The high permeability of the shelf sands renders them susceptible to pressure gradients generated by hydrodynamic and biological forces that modulate spatial and temporal patterns of water circulation through these sediments. The resulting dynamic three-dimensional patterns of particle and solute distribution generate a broad spectrum of biogeochemical reaction zones that facilitate effective decomposition of the pelagic and benthic primary production products. The intricate coupling between the water column and sediment makes it challenging to quantify the production and decomposition processes and the resultant fluxes in permeable shelf sands. Recent technical developments have led to insights into the high biogeochemical and biological activity of these permeable sediments and their role in the global cycles of matter.

Huettel, Markus; Berg, Peter; Kostka, Joel E.

2014-01-01

94

The Role of Coastal Zones in Global Biogeochemical Cycles  

NASA Astrophysics Data System (ADS)

The unique and dynamic coastal ocean is a significant source and sink of a multitude of atmospheric species of importance to global biogeochemical cycles and climate. The transition zone between land and ocean, including the atmosphere as a medium for the exchange of matter and energy, is characterized by a strong physical-biogeochemical coupling, resulting in an inherently complex system. Important biogeochemical exchanges occurring in the coastal zone involve water, nutrients (e.g., nitrogen, phosphorous, iron, and silica), salts (e.g., chlorine, bromine, and iodine), carbon (e.g., dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), particulate organic carbon (POC), carbon dioxide (CO2)), reactive organic trace gases (e.g., nitrogenous, halogenated, and sulfurous hydrocarbons), and inorganic trace gases (e.g., nitrous oxide, N2O). Coastal zones are of particular importance to humans, as they are characterized by high per area productivity and are responsible for the majority of the world's fish catch. In addition, coastal ecosystems play an important role in the global carbon cycle as large fluxes of carbon and carbon-related tracers move between the land, ocean, and atmosphere in these regions. Most of the world's population lives near coastal zones, and anthropogenic changes and related climate change in these regions can pose serious consequences not only for fisheries but also for global biogeochemical cycles.

Siefert, Ronald; Plattner, Gian-Kasper

2004-11-01

95

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

96

Proterozoic ocean redox and biogeochemical stasis  

PubMed Central

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

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

2013-01-01

97

Characterization of terrestrial ecosystems for biogeochemical studies using remote sensing  

NASA Technical Reports Server (NTRS)

Work is in progress to estimate leaf area index (LAI) of temperate closed canopy coniferous forests using transects in Oregon and California. This variable will be measured using remote sensing techniques including correlations of ground dimensional analysis with linear waveband combinations. LAI will be related to important biological variables such as net primary productivity, biomass, and biogenic gas emission fluxes. The spatial variation in LAI, when coupled with species composition, will be used in part to describe the spatial variation and temporal dynamics of biogeochemical cycling.

Peterson, D. L.; Mouat, D. A.; Running, S.

1983-01-01

98

A GEOCLIM simulation of climatic and biogeochemical consequences of Pangea breakup  

Microsoft Academic Search

Large fluctuations in continental configuration occur throughout the Mesozoic. While it has long been recognized that paleogeography may potentially influence atmospheric CO2 via the continental silicate weathering feedback, no numerical simulations have been done, because of the lack of a spatially resolved climate-carbon model. GEOCLIM, a coupled numerical model of the climate and global biogeochemical cycles, is used to investigate

Y. Donnadieu; Y. Goddéris; R. Pierrehumbert; G. Dromart; F. Fluteau; R. Jacob

2006-01-01

99

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

Microsoft Academic Search

A literature survey shows how biogeochemical (coupled organic and inorganic reaction processes) transport models are based on considering the complete biodegradation process as either a single- or as a two-step process. It is demonstrated that some two-step process models rely on the Partial Equilibrium Approach (PEA). The PEA assumes the organic degradation step, and not the electron acceptor consumption step,

Adam Brun; Peter Engesgaard

2002-01-01

100

Sensitivity of the marine biospheric Si cycle for biogeochemical parameter variations  

Microsoft Academic Search

A systematic quantitative assessment of the marine silicon cycle is presented, based on a prognostic coupled water column-sediment global biogeochemical ocean general circulation model (HAMOCC). The resulting tracer distributions are compared with a comprehensive marine Si database of measurements. The model parameters which govern the Si cycle within the model world are optimized through a linear response model. The functional

C. Heinze; A. Hupe; E. Maier-Reimer; N. Dittert; O. Ragueneau

2003-01-01

101

Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment (INBOX): Biogeochemical impact of mesoscale disturbance  

NASA Astrophysics Data System (ADS)

Combination of autonomous float and biogeochemical sensor technologies has enabled concurrent measurements of physical and biogeochemical parameters for wide spatial and temporal ranges, which could open a new world of synergistic use of those data to advance not only each discipline but also a holistic understanding of the ocean. Study of mesoscale processes is one of those areas greatly benefitted from the synergistic use of physical and biogeochemical data acquired by autonomous platforms, because our understanding of those processes is still limited mainly due to the difficulty in measuring them despite their importance widely recognized. To acquire physical-biogeochemical data which could resolve mesoscale phenomena in the western North Pacific, JAMSTEC launched an interdisciplinary project "Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment (INBOX)" in 2010. INBOX aims to quantify impacts of physical processes on biogeochemical phenomena, so that we could also ultimately utilize biogeochemical information for understanding physical processes. Through a series of field experiments, we also hope that INBOX could contribute to designing effectively sustained biogeochemical observing system. As the first phase of INBOX, profiling floats with oxygen sensors were intensively deployed around the biogeochemical mooring station S1 maintained since spring 2010 at 30N, 145E, further south of the Kuroshio Extension. We have deployed 5 floats in fall 2010 and 25 floats in summer 2011 with profiling cycles of 2-3 days in the 150 km-square area centered at the S1. In this presentation, following the overall description of INBOX, we will highlight cyclonic eddies captured by the INBOX float array and impacts of their passage on primary production. In order to fully utilize data from the float array with a nominal resolution of "30 km x 2 days" for describing mesoscale physical-biogeochemical fields, oxygen sensors should be calibrated appropriately. The calibration procedure will be also presented briefly.

Suga, T.; Hosoda, S.; Sato, K.; Kita, T.; Inoue, R.; Kouketsu, S.; Kobayashi, T.; Kobashi, F.; Toyama, K.; Honda, M. C.; Kawano, T.; Saino, T.

2012-12-01

102

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

103

Indian Ocean Biogeochemical Processes and Ecological Variability  

NASA Astrophysics Data System (ADS)

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

Ofori, Leslie

2010-11-01

104

Managing biogeochemical cycles to reduce greenhouse gases  

SciTech Connect

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.

Post, Wilfred M [ORNL; Venterea, Rodney [United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Soil and Water

2012-01-01

105

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

106

Global Change: A Biogeochemical Perspective  

NASA Technical Reports Server (NTRS)

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.

Mcelroy, M.

1983-01-01

107

Molecular biogeochemical provinces in the Atlantic Surface Ocean  

NASA Astrophysics Data System (ADS)

One of the most important aspects to understand marine organic carbon fluxes is to resolve the molecular mechanisms which convert fresh, labile biomolecules into semi-labile and refractory dissolved and particulate organic compounds in the ocean. In this interdisciplinary project, which was performed on a cruise with RV Polarstern, we carried out a detailed molecular characterisation of dissolved organic matter (DOM) on a North-South transect in the Atlantic surface ocean in order to relate the data to different biological, climatic, oceanographic, and meteorological regimes as well as to terrestrial input from riverine and atmospheric sources. Our goal was to achieve a high resolution data set for the biogeochemical characterisation of the sources and reactivity of DOM. We applied ultrahigh resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS), nutrient, trace element, amino acid, and lipid analyses and other biogeochemical measurements for 220 samples from the upper water column (0-200m) and eight deep profiles. Various spectroscopic techniques were applied continuously in a constant sample water flow supplied by a fish system and the moon pool. Radiocarbon dating enabled assessing DOC residence time. Bacterial abundance and production provided a metabolic context for the DOM characterization work and pCO2 concentrations. Combining molecular organic techniques and inductively coupled plasma mass spectrometry (ICP-MS) established an important link between organic and inorganic biogeochemical studies. Multivariate statistics, primarily based on FT-ICR-MS data for 220 samples, allowed identifying geographical clusters which matched ecological provinces proposed previously by Longhurst (2007). Our study demonstrated that marine DOM carries molecular information reflecting the “history” of ocean water masses. This information can be used to define molecular biogeochemical provinces and to improve our understanding of element fluxes in the ocean. Future “organic geotraces” studies should focus on extracting and establishing new organic proxies which are suitable to characterize and, in particular, quantify organic matter sources and transformation processes in the ocean. Longhurst AR (2007) Ecological geography of the sea. Academic Press, San Diego, 542 pp.

Koch, B. P.; Flerus, R.; Schmitt-Kopplin, P.; Lechtenfeld, O. J.; Bracher, A.; Cooper, W.; Frka, S.; Gašparovi?, 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

108

Isotopic, petrologic and biogeochemical investigations of banded iron-formations  

NASA Technical Reports Server (NTRS)

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.

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

1986-01-01

109

Passive regulation of soil biogeochemical cycling by root water transport  

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

110

Biogeochemical tracers of the marine cyanobacterium Trichodesmium  

Microsoft Academic Search

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 C14 and C16 acids, with lesser amounts of several saturated

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

1997-01-01

111

Temporal dynamics of biogeochemical processes at the Norman Landfill site  

NASA Astrophysics Data System (ADS)

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, ?2H, 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.

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

2013-10-01

112

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

NASA Astrophysics Data System (ADS)

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

Duteil, Olaf; Boening, Claus; Oschlies, Andreas

2014-05-01

113

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

NASA Astrophysics Data System (ADS)

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, instead we emphasis on the importance of biogeophysical and biophysical processes and feedbacks between them in modeling permafrost carbon stocks.

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

2013-12-01

114

BIOGEOCHEMICAL STUDIES OF PHOTOSYNTHETIC MICROBIAL MATS AND THEIR BIOTA  

NASA Technical Reports Server (NTRS)

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.

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

2005-01-01

115

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

USGS Publications Warehouse

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.

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

2012-01-01

116

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

PubMed

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 groundwater indicate predominantly minor increases and decreases in PO(4)(3-) with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had undergone little biogeochemical transformation. Observed nitrogen and phosphorus losses demonstrate the potential, as well as the future research needs to improve performance, of the innovative stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure. PMID:22742948

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

2012-08-15

117

Description of a flexible and extendable physical biogeochemical model system for the water column  

NASA Astrophysics Data System (ADS)

A modelling system for coupled physical-biogeochemical simulations in the water column is presented here. The physical model component allows for a number of different statistical turbulence closure schemes, ranging from simple algebraic closures to two-equation turbulence models with algebraic second-moment closures. The biogeochemical module consists of models which are based on a number of state variables represented by their ensemble averaged concentrations. Specific biogeochemical models may range from simple NPZ (nutrient-phytoplankton-zooplankton) to complex ecosystem models. Recently developed modified Patankar solvers for ordinary differential equations allow for stable discretisations of the production and destruction terms guaranteeing conservative and non-negative solutions. The increased stability of these new solvers over explicit solvers is demonstrated for a plankton spring bloom simulation. The model system is applied to marine ecosystem dynamics the Northern North Sea and the Central Gotland Sea. Two different biogeochemical models are applied, a conservative nitrogen-based model to the North Sea, and a more complex model including an oxygen equation to the Baltic Sea, allowing for the reproduction of chemical processes under anoxic conditions. For both applications, earlier model results obtained with slightly different model setups could be basically reproduced. It became however clear that the choice for ecosystem model parameters such as maximum phytoplankton growth rates does strongly depend on the physical model parameters (such as turbulence closure models or external forcing).

Burchard, Hans; Bolding, Karsten; Kühn, Wilfried; Meister, Andreas; Neumann, Thomas; Umlauf, Lars

2006-07-01

118

Catchment Legacies and Trajectories: Hydrologic and Biogeochemical Controls  

NASA Astrophysics Data System (ADS)

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 decades have accumulated legacy nutrient stores that will sustain stream nitrate concentrations decades after the cessation of fertilizer application. Here, we have used a travel time-based approach to evaluate the hydrologic legacy and a stochastic carbon nitrogen cycling model to evaluate the biogeochemical legacy. Preliminary results indicate a strong dependence of the spatial allocation of the management practice on the benefits realized, both in terms of reductions in concentrations as well as lag times. A random correlation between implementation of management practices and watershed travel times has been found to result in an interesting linear relationship between the concentration reduction and the percent watershed undergoing land use changes, while power function relationships have emerged for cases of positive and negative correlations.

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

2012-04-01

119

Coastal-zone biogeochemical dynamics under global warming  

SciTech Connect

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.

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

2000-03-01

120

Apparatus for Cold, Pressurized Biogeochemical Experiments  

NASA Technical Reports Server (NTRS)

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.

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

2010-01-01

121

Monterey Bay Time Series Biogeochemical Data  

NSDL National Science Digital Library

This dataset includes a broad suite of biogeochemical measurements, particularly dissolvable iron. The measurements span the time period from August 1998 to December 2004 and were taken at the most inshore station of a set of three which are maintained by the Monterey Bay Aquarium Research Institute (MBARI). The data show a large pulse of dissolvable iron consistently occurring during the first spring upwelling event of each year that is derived from resuspended sediment. Iron concentrations then drop rapidly at all three stations. During the summer months, only the most inshore station (C1) maintains iron concentrations in excess of nitrate.

122

New challenges in biogeochemical gradient research  

NASA Astrophysics Data System (ADS)

At a recent workshop focusing on biogeochemical gradients predominantly in groundwater and sediments, 32 North American and German scientists discussed research needs in three areas including (1) redox and microbes; (2) contaminants, isotopes, and fluxes; and (3) instruments, monitoring, and modeling.The presentation topics at the workshop at the Eberhard Karls University of Tübingen in Germany ranged from new concepts for monitoring contaminant attenuation, microgradients, microbial and abiotic recycling of iron and arsenic, porous media characterization, modeling in marine and groundwater environments, and stable isotope as well as radioisotope techniques.

Barth, Johannes A. C.; Kappler, Andreas; Piepenbrink, Matthias; Werth, Charles; Regenspurg, Simona; Semprini, Lewis; Slater, Gregory F.; Schüth, Christoph; Grathwohl, Peter

123

Reanalysis of biogeochemical properties in the Mediterranean Sea  

NASA Astrophysics Data System (ADS)

In the 3D variational (3DVAR) assimilation approach the error covariance matrix can be decomposed in a series of operators. The decomposition makes the 3DVAR particularly suitable for marine biogeochemistry data assimilation, because of the reduced computational costs of the method and its modularity, which allows to define the covariance among the biogeochemical variables in a specific operator. In the present work, the results of 3DVAR assimilation of surface chlorophyll concentration in a multi-annual simulation of the Mediterranean Sea biogeochemistry are presented. The assimilated chlorophyll concentrations are obtained from satellite observations (Volpe et al. 2012). The multi-annual simulation is carried out using the OPATM-BFM model (Lazzari et al. 2012), which describes the low trophic web dynamics and is offline coupled with the MFS physical model (Oddo et al. 2009). In the OPATM-BFM four types of phytoplankton are simulated in terms of their content in carbon, nitrogen, phosphorous, silicon and chlorophyll. In the 3DVAR the error covariance matrix has been decomposed in three different operators, which account for the vertical, the horizontal and the biogeochemical covariance (Teruzzi et al. 2014). The biogeochemical operator propagates the result of the assimilation to the OPATM-BFM variables, providing innovation for the components of the four phytoplankton types. The biogeochemical covariance has been designed supposing that the assimilation preserves the physiological status and the relative abundances of phytoplankton types. Practically, the assimilation preserves the internal quotas of the components for each phytoplankton as long as the optimal growth rate condition are maintained. The quotas preservation is not applied when the phytoplankton is in severe declining growth phase, and the correction provided by the assimilation is set equal to zero. Moreover, the relative abundances among the phytoplankton functional types are preserved. The 3DVAR has been applied to the Mediterranean Sea for the period 1999-2010 with weekly assimilation. The results of the multi-annual run show that the assimilation improves the model skill in terms of a better representation of the mean chlorophyll concentrations over the Mediterranean Sea sub-regions and also in terms of spatial and temporal definition of local bloom events. Furthermore, the comparison with nutrients climatology based on in situ measurements show that the non assimilated variables are consistent with observations. The application of the 3DVAR revealed that in specific cases the correction introduced by the assimilation is not maintained by the model dynamics. In these cases, the satellite observations are characterized by local patchy bloom events, which are not well captured by the model. It has been observed that, since the bloom events are strongly affected by the vertical mixing dynamics, which support nutrients to the surface layer, a possible source of error are the mixing conditions provided by the physical model. Oddo et al. 2009. Ocean Science, 5(4), 461-473, doi:10.5194/os-5-461-2009. Lazzari et al. 2012. Biogeosciences, 9(1), 217-233, doi:10.5194/bg-9-217-2012. Teruzzi et al. 2014. Journal of Geophysical Research, 119, 1-18, doi:10.1002/2013JC009277. Volpe et al. 2012. Ocean Science Discussions, 9(2), 1349-1385, doi:10.5194/osd-9-1349-2012.

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

2014-05-01

124

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

125

Biogeochemical feedbacks on ocean carbon uptake and sensitivity to climate change in an earth system model  

NASA Astrophysics Data System (ADS)

Global models of the future anthropogenic carbon uptake by the world's oceans have shown a strong dependence on the degree of warming through solubility, enhancement of stratification through ventilation, and variability of the strength in the biological pump. In order to assess future sensitivity of the ocean's ability to take up anthropogenic carbon in the fully coupled biogeochemical context, we conducted a set of model sensitivity studies with GFDL's prototype earth system model (ESM2.1) independently varying the representation of atmospheric CO2 on both the atmospheric radiation scheme and the surface ocean boundary condition using various IPCC Special Report on Emissions Scenarios. We find a moderate decrease in ocean uptake of anthropogenic CO2 under warming conditions relative to conditions without warming, consistent with previous work. We also find almost no degassing of natural CO2 under climate warming, indicating a high degree of compensation between the independent biogeochemical feedbacks of solubility, ventilation and biological utilization efficiency. These modes of biogeochemical compensation are found to be quite variable from basin to basin, however. In the North Atlantic, climate change has opposing effects on the natural and anthropogenic carbon inventories. For natural carbon, we find climate change alone to drive an overall increase in uptake. For anthropogenic carbon, however, solubility decreases due to warming diminish anthropogenic uptake such that the overall effect of warming is a decrease in carbon uptake. In the Eastern Pacific, we find the opposite scenario under climate warming as natural carbon content decreases, but the anthropogenic uptake increases in compensation. The causality behind these changes is assessed in the context of the combined mechanisms of solubility, ventilation, and biological change. Implications for the long term ability of the ocean to take up anthropogenic CO2 in the coupled biogeochemical context are discussed.

Dunne, J. P.; John, J. G.

2010-12-01

126

Global Biology Research Program: Biogeochemical Processes in Wetlands  

NASA Technical Reports Server (NTRS)

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.

Bartlett, D. S. (editor)

1984-01-01

127

Oceanographic and Biogeochemical Insights from Diatom Genomes  

NASA Astrophysics Data System (ADS)

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.

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

2010-01-01

128

Oceanographic and biogeochemical insights from diatom genomes.  

PubMed

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

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

2010-01-01

129

Carbohydrates as indicators of biogeochemical processes  

NASA Astrophysics Data System (ADS)

A method is presented to study the carbohydrate composition of marine objects involved into sedimento- and diagenesis (plankton, particulate matter, benthos, and bottom sediments). The analysis of the carbohydrates is based upon the consecutive separation of their fractions with different solvents (water, alkali, and acid). The ratio of the carbohydrate fractions allows one to evaluate the lability of the carbohydrate complex. It is also usable as an indicator of the biogeochemical processes in the ocean, as well of the genesis and the degree of conversion of organic matter in the bottom sediments and nodules. The similarity in the monosaccharide composition is shown for dissolved organic matter and aqueous and alkaline fractions of seston and particulate matter.

Lazareva, E. V.; Romankevich, E. A.

2012-05-01

130

Biogeochemical cycling in the Strait of Georgia.  

PubMed

The papers in this special issue present the results of a five-year project to study sedimentary biogeochemical processes in the Strait of Georgia, with special emphasis on the near-field of a large municipal outfall. Included in this special issue are overviews of the sedimentology, benthic biology, status of siliceous sponge reefs and distribution of organic carbon in the water column. Other papers address the cycling of contaminants (PCBs, PBDEs) and redox metals in the sediment, a method to map the extent of the influence of municipal effluent from staining on benthic bivalves, and the relationships among geochemical conditions and benthic abundance and diversity. The latter set of papers addresses the role of municipal effluent as a pathway of organic carbon and other contaminants into the Strait of Georgia and the effect of the effluent on benthic geochemistry and biology. PMID:19022498

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

2008-12-01

131

Biogeochemical Filtering of Solute Signals Explored as a Function of Transport and Reaction Time Scales  

NASA Astrophysics Data System (ADS)

Catchment biogeochemical responses are the result of superposition of diverse dynamic components, which can be related to climate forcing, water flow, and biogeochemical reactions. The interactions among these components are highly non-linear and contribute to the generation of emergent patterns at multiple spatial and temporal scales. The aim of this work is to explore the following biogeochemical signatures arising from such interactions: (1) the relationship between contaminant loads (L) and discharge (Q) at the annual timescale, leading to an apparent chemostatic relationship (i.e., linear L-Q plots) for different contaminants and at different spatial scales; (2) spatial patterns in the slope and the scatter of the L-Q relationships; and (3) correlation between the intra-annual flow duration curves (FDC) and the load duration curves (LDC). Exploring this relationship necessitates the use of a parsimonious model, with few spatially uniform time constants, that can generate synthetic time series of load and flow at the outlet of river basins. The Mass Response Functions (MRF) approach (Rinaldo et al., 2006), lends itself suitable for the purpose since it relies on the assumption that the evolution of solute concentration in the water pulses depends only on the residence time, and not on its trajectory - thus space is replaced by time. The model simulates the episodic delivery of water and contaminant pulses from the hillslopes to the stream network in response to temporally random but spatially uniform effective rainfall patterns. The domain is described by an immobile source zone in which first order biogeochemical reactions (degradation rate constant ke) alter the solute mass, while multiple mobile rainfall pulses exchange mass with the source zone following linear kinetics (mass transfer rate constant ?). The biogeochemical module of MRF, that was originally written to simulate non-reactive tracer and nitrate transport, was modified to include the more complex biogeochemistry of pesticides. We calibrated and validated the model against nitrate and atrazine data collected in the Little Vermillion River basin (~400 km2; Illinois, IN). Comparison with data showed an excellent agreement of the model outputs with the observed hydrographs and chemographs. The model was then used to explore the effect of time constants on biogeochemical signatures. Four time constants were used to characterize the coupling of hydrologic and biogeochemical processes considered in the model: 1) mean rainfall frequency; 2) mean residence time; 3) mass-transfer rate constant; 4) degradation rate constant. The effect of the four temporal constants on the hillslope biogeochemical response was explored through a sesnsitivity analyses. We hypothesize that a single dimensionless number, a combination of all four temporal constants, could explain the observed patterns. Because this dimensionless number embeds all of the relevant time scales, relative significance of the hydrologic and biogeochemical processes can be examined.

Zanardo, S.; Basu, N. B.; Rao, P. C.

2009-12-01

132

An Integrated Biogeochemical and Biophysical Analysis of Bioenergy Crops  

NASA Astrophysics Data System (ADS)

Bioenergy crops are becoming increasingly important with growing concerns about the energy demand and climate change and the need to replace fossil fuels with carbon-neutral renewable sources of energy. The transition to a biofuel-based energy supply raises many questions such as: how and where to grow energy crops, what will be the impacts of growing large scale biofuel crops on climate system, the hydrological cycle and soil biogeochemistry. We are developing and applying an integrated system modeling framework to investigate the biophysical, physiological, and biogeochemical systems governing important processes that regulate crop growth such as water, energy and nutrient cycles. The framework has a two-big-leaf canopy scheme for photosynthesis, stomatal conductance, leaf temperature and energy fluxes. The soil/snow hydrology consists of 10 layers for soil and up to 5 layers for snow. The biogeochemistry component explicitly accounts for coupled carbon and nitrogen dynamics. The feedstocks currently considered include corn stover, Miscanthus and switchgrass. The parameters used for simulation of each crop have been calibrated using field experimental data from the US. The use of this modeling capability will be demonstrated through its applications to study the environmental effects (through changes in albedo and evapotranspiration) of biofuel production as well as the effective management practice in the United States.

Liang, M.; Song, Y.; Barman, R.; Jain, A. K.

2010-12-01

133

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

NASA Astrophysics Data System (ADS)

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.

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

134

Use of a coastal biogeochemical model to select environmental monitoring sites  

NASA Astrophysics Data System (ADS)

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.

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

2011-10-01

135

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

USGS Publications Warehouse

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.

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

2007-01-01

136

Biogeochemical cycling during Late Cretcaeous OAE2 - the modelling perspective  

NASA Astrophysics Data System (ADS)

Cretaceous anoxic events may have been triggered by massive volcanic CO2 degassing as large igneous provinces (LIPs) were emplaced on the seafloor. Here, we present a comprehensive modeling study to decipher the marine biogeochemical consequences of enhanced volcanic CO2 emissions. A biogeochemical box model has been developed for transient model runs with time-dependent volcanic CO2 forcing. The box model considers continental weathering processes, marine export production, degradation processes in the water column, the rain of particles to the seafloor, benthic fluxes of dissolved species across the seabed, and burial of particulates in marine sediments. The ocean is represented by twenty-seven boxes. To estimate horizontal and vertical fluxes between boxes, a coupled ocean-atmosphere general circulation model (AOGCM) is run to derive the circulation patterns of the global ocean under Late Cretaceous boundary conditions. The AOGCM modeling predicts a strong thermohaline circulation and intense ventilation in the Late Cretaceous oceans under high pCO2 values. With an appropriate choice of parameter values such as the continental input of phosphorus, the model produces ocean anoxia at low to mid latitudes and changes in marine ?13C that are consistent with geological data such as the well established ?13C curve. The spread of anoxia is supported by an increase in riverine phosphorus fluxes under high pCO2 and a decrease in phosphorus burial efficiency in marine sediments under low oxygen conditions in ambient bottom waters. Here, we suggest that an additional mechanism might contribute to anoxia, an increase in the C:P ratio of marine plankton which is induced by high pCO2 values. According to our AOGCM model results, an intensively ventilated Cretaceous ocean turns anoxic only if the C:P ratio of marine organic particles exported into the deep ocean is allowed to increase under high pCO2 conditions. Being aware of the uncertainties such as diagenesis, this modeling study implies that potential changes in Redfield ratios might be a strong feedback mechanism to attain ocean anoxia via enhanced CO2 emissions. The formation of C-enriched marine organic matter may also explain the frequent occurrence of global anoxia during other geological periods characterized by high pCO2 values.

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

2012-12-01

137

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

USGS Publications Warehouse

Soil beneath a stormwater infiltration basin receiving runoff from a 22.7 ha predominantly residential watershed in central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop a prototype stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO3-/Cl-) ratios for the shallow groundwater indicate that prior to using BAM, NO3- concentrations were substantially influenced by nitrification or variations in NO3- input. In contrast, for the prototype basin utilizing BAM, NO3-/Cl- ratios indicate minor nitrification and NO3- losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest NO3- losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO43-) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO43-/Cl- ratios for shallow groundwater indicate predominantly minor increases and decreases in PO43- with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had not undergone significant chemical changes. Observed nitrogen and phosphorus losses demonstrate the potential, as well as future research needs to improve performance, of the prototype stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure.

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

2012-01-01

138

A generic biogeochemical module for Earth system models: Next Generation BioGeoChemical Module (NGBGC), version 1.0  

NASA Astrophysics Data System (ADS)

Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from the atmosphere, influencing global climate changes. Integration of these processes into Earth system models (e.g., community land models (CLMs)), 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 impossible. 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, Next Generation BioGeoChemical Module (NGBGC), version 1.0, 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 CLM. 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. The method presented here could in theory be applied to simulate biogeochemical cycles in other Earth system models.

Fang, Y.; Huang, M.; Liu, C.; Li, H.; Leung, L. R.

2013-11-01

139

Plant Nitrogen Uptake in Terrestrial Biogeochemical Models  

NASA Astrophysics Data System (ADS)

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 two to three times smaller than previously predicted. 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 higher atmospheric CO2 concentrations than originally expected. This study compares alternative models of plant N uptake as found in different terrestrial biogeochemical models against field measurements, and introduces a new N-uptake model to the Joint UK Land Environment Simulator (JULES).. Acknowledgements This work has been funded by the European Commission FP7-PEOPLE-ITN-2008 Marie Curie Action: "Greencycles II: FP7-PEOPLE-ITN-2008 Marie Curie Action: "Networks for Initial Training"

Marti, Alejandro; Cox, Peter; Sitch, Stephen; Jones, Chris; Liddicoat, spencer

2013-04-01

140

Biotic and Biogeochemical Feedbacks to Climate Change  

NASA Astrophysics Data System (ADS)

Feedbacks to paleoclimate change are evident in ice core records showing correlations of temperature with carbon dioxide, nitrous oxide, and methane. Such feedbacks may be explained by plant and microbial responses to climate change, and are likely to occur under impending climate warming, as evidenced by results of ecosystem climate manipulation experiments and biometeorological observations along ecological and climate gradients. Ecosystems exert considerable influence on climate, by controlling the energy and water balance of the land surface as well as being sinks and sources of greenhouse gases. This presentation will focus on biotic and biogeochemical climate feedbacks on decadal to century time scales, emphasizing carbon storage and energy exchange. In addition to the direct effects of climate on decomposition rates and of climate and CO2 on plant productivity, climate change can alter species composition; because plant species differ in their surface properties, productivity, phenology, and chemistry, climate-induced changes in plant species composition can exert a large influence on the magnitude and sign of climate feedbacks. We discuss the effects of plant species on ecosystem carbon storage that result from characteristic differences in plant biomass and lifetime, allocation to roots vs. leaves, litter quality, microclimate for decomposition and the ultimate stabilization of soil organic matter. We compare the effect of species transitions on transpiration, albedo, and other surface properties, with the effect of elevated CO2 and warming on single species' surface exchange. Global change models and experiments that investigate the effect of climate only on existing vegetation may miss the biggest impacts of climate change on biogeochemical cycling and feedbacks. Quantification of feedbacks will require understanding how species composition and long-term soil processes will change under global warming. Although no single approach, be it experimental, observational, or modeling, can adequately capture the complex factors that govern species distributions over relevant spatial and temporal scales, careful integration of these methods can yield needed insights. The potential for large, rapid, or unexpected feedbacks of biogeochemistry and energy balance to climate change make this a worthwhile challenge.

Torn, M. S.; Harte, J.

2002-12-01

141

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...

142

Dynamic biogeochemical provinces in the global ocean  

NASA Astrophysics Data System (ADS)

In recent decades, it has been found useful to partition the pelagic environment using the concept of biogeochemical provinces, or BGCPs, within each of which it is assumed that environmental conditions are distinguishable and unique at global scale. The boundaries between provinces respond to features of physical oceanography and, ideally, should follow seasonal and interannual changes in ocean dynamics. But this ideal has not been fulfilled except for small regions of the oceans. Moreover, BGCPs have been used only as static entities having boundaries that were originally established to compute global primary production. In the present study, a new statistical methodology based on non-parametric procedures is implemented to capture the environmental characteristics within 56 BGCPs. Four main environmental parameters (bathymetry, chlorophyll a concentration, surface temperature, and salinity) are used to infer the spatial distribution of each BGCP over 1997-2007. The resulting dynamic partition allows us to integrate changes in the distribution of BGCPs at seasonal and interannual timescales, and so introduces the possibility of detecting spatial shifts in environmental conditions.

Reygondeau, Gabriel; Longhurst, Alan; Martinez, Elodie; Beaugrand, Gregory; Antoine, David; Maury, Olivier

2013-12-01

143

Biogeochemical Characterization of Constructed Wetland Functions  

NASA Astrophysics Data System (ADS)

Agricultural productions areas of the Midwestern United States are recognized as significant contributors of nonpoint source pollution and influence many aspects of water quality at both local and regional scales. In addition, ambitious land "improvement" programs stemming back to the mid-1800s have resulted in widespread loss of wetlands throughout the U.S., including heavy losses in agricultural production areas of the Mississippi River Basin. The combination of these two factors has been directly implicated as a contributing factor to high-profile environmental problems such as exacerbation of the zone of hypoxia in the Gulf of Mexico. Constructed wetlands are recognized for their potential to help mitigate the effects of agricultural nonpoint source pollution and previous loss of wetlands. The vast majority of previous studies of constructed wetlands have focused on the bulk movement of water quality constituents such as nitrogen, phosphorus, total carbon and sediment. While insightful, these studies do not address more detailed aspects of wetland function as it pertains to carbon flux and storage. In this study, we present results from biogeochemical analyses of influent and effluent of an experimental wetland constructed near row crop and animal production facilities in North-central Indiana. Cross flow utrafiltration and chemolytic techniques were used to collect and characterize organic components of wetland influent and effluent. Biomarker molecules were used to describe functions of the constructed wetland.

Dalzell, B. J.; Parker, G. R.; Filley, T. R.

2001-12-01

144

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

Microsoft Academic Search

A three-dimensional primitive equation model, the Regional Ocean Modeling Systems (ROMS), coupled to two biogeochemical configurations (NPZD and N2P2Z2D2) was used to study the dynamics of the first trophic levels of the pelagic food web in the southern Benguela upwelling system. The domain extends from the Agulhas Bank bordered by the Agulhas Current to 27°S on the west coast of

V. Koné; E. Machu; P. Penven; V. Andersen; V. Garçon; P. Fréon; H. Demarcq

2005-01-01

145

The emergence of ocean biogeochemical provinces: A quantitative assessment and a diagnostic for model evaluation  

NASA Astrophysics Data System (ADS)

The concept of ocean biogeochemical provinces is based on the observation that large ocean regions are characterized by coherent physical forcing and environmental conditions, which are eventually representative of macroscale ocean ecosystems. Biogeochemical models of the global ocean focus on simulating the coupling between prevalent physical conditions and the biogeochemical processes with the assumption that biological properties respond coherently to physics and therefore should produce such provinces as an emergent property. In this paper, we quantitatively assess the emergence of a reference set of predefined biogeochemical provinces in the available global data sets and propose a province-based approach to the evaluation of one of the most comprehensive models of ocean biogeochemistry. Multivariate statistical tools were applied to model and observation data, verifying the existence, distinctiveness and reliability of the predefined provinces and quantifying the correlation of model results with observations at the global scale. The analysis of similarity between provinces shows that they are statistically separable in data and model output and therefore can be used as reliable metrics. The analyses indicate that provinces can be more easily distinguished in terms of their environmental features rather than using chlorophyll concentration. The characterization of provinces by means of chlorophyll values shows a significant overlap in both the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) data and the model. It is likely this is related to the choice of province boundaries based on coarse-resolution mapped data, which are not necessarily the same as those derivable from high-resolution satellite data. We also demonstrated through cluster analysis that the long-term time series data collected at Joint Global Ocean Flux Study (JGOFS) stations are representative of environmental conditions of the respective province and can thus be used to evaluate model results extracted from that province. The method shows promise for helping to overcome problems with model verification due to under sampling of most ocean biogeochemical variables but also gives indications that unsupervised clustering may be required when more spatially resolved data and models are available.

Vichi, Marcello; Allen, J. Icarus; Masina, Simona; Hardman-Mountford, Nicholas J.

2011-06-01

146

Restoration of biogeochemical function in mangrove forests  

USGS Publications Warehouse

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

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

2000-01-01

147

A generic biogeochemical module for earth system models  

NASA Astrophysics Data System (ADS)

Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from the 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 impossible. 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.

Fang, Y.; Huang, M.; Liu, C.; Li, H.-Y.; Leung, L. R.

2013-06-01

148

A general simulator for reaction-based biogeochemical processes  

NASA Astrophysics Data System (ADS)

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 equilibria and kinetic rates (i.e., they are not defined in the format of the standardized database) are interpreted by the Maple V (Waterloo 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 governing equations, user-specified equilibrium expressions and rate laws. Matrix diagonalization eliminates the need to conceptualize the system of reactions as a tableau, which comprises a list of components, species, the stoichiometric matrix, and the formation equilibrium constant vector that forms the species from components ( Morel and Hering, 1993), while identifying a minimum rank set of basis species with enhanced numerical convergence properties. The newly generated code, which is designed to operate in the BIOGEOCHEM biogeochemical simulator, is then compiled and linked into the BIOGEOCHEM executable. With these features, users can avoid recoding the simulator to accept new equilibrium expressions or kinetic rate laws, while still taking full advantage of the stoichiometry and thermodynamics provided by an existing chemical database. Thus, the approach introduces efficiencies in the specification of biogeochemical reaction networks and eliminates opportunities for mistakes in preparing input files and coding errors. Test problems are used to demonstrate the features of the procedure.

Fang, Yilin; Yabusaki, Steven B.; Yeh, Gour-Tsyh

2006-02-01

149

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

SciTech Connect

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.

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

2013-11-13

150

Impact of resolved scales on global marine biogeochemical models  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

151

Aerosol indirect effect on biogeochemical cycles and climate.  

PubMed

The net effect of anthropogenic aerosols on climate is usually considered the sum of the direct radiative effect of anthropogenic aerosols, plus the indirect effect of these aerosols through aerosol-cloud interactions. However, an additional impact of aerosols on a longer time scale is their indirect effect on climate through biogeochemical feedbacks, largely due to changes in the atmospheric concentration of CO(2). Aerosols can affect land and ocean biogeochemical cycles by physical forcing or by adding nutrients and pollutants to ecosystems. The net biogeochemical effect of aerosols is estimated to be equivalent to a radiative forcing of -0.5 ± 0.4 watts per square meter, which suggests that reaching lower carbon targets will be even costlier than previously estimated. PMID:22076375

Mahowald, Natalie

2011-11-11

152

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

NASA Astrophysics Data System (ADS)

Fate and transport of contaminants in saturated and unsaturated zones in the subsurface is controlled by complex biogeochemical processes such as precipitation, sorption-desorption, ion-exchange, redox, etc. In dynamic systems such as wetlands and anaerobic aquifers, these processes are coupled and can interact non-linearly with each other. Variability in measured hydrological, geochemical and microbiological parameters thus corresponds to multiple processes simultaneously. To infer the contributing processes, it is important to eliminate correlations and to identify inter-linkages between factors. The objective of this study is to develop quantitative relationships between hydrological (initial and boundary conditions, hydraulic conductivity ratio, and soil layering), geochemical (mineralogy, surface area, redox potential, and organic matter) and microbiological factors (MPN) that alter the biogeochemical processes at the column scale. Data used in this study were collected from controlled flow experiments in: i) two homogeneous soil columns, ii) a layered soil column, iii) a soil column with embedded clay lenses, and iv) a soil column with embedded clay lenses and one central macropore. The soil columns represent increasing level of soil structural heterogeneity to better mimic the Norman Landfill research site. The Norman Landfill is a closed municipal facility with prevalent organic contamination. The sources of variation in the dataset were explored using multivariate statistical techniques and dominant biogeochemical processes were obtained using principal component analysis (PCA). Furthermore, artificial neural networks (ANN) coupled with HP1 was used to develop mathematical rules identifying different combinations of factors that trigger, sustain, accelerate/decelerate, or discontinue the biogeochemical processes. Experimental observations show that infiltrating water triggers biogeochemical processes in all soil columns. Similarly, slow release of water from low permeability clay lenses sustain biogeochemical cycling for a longer period of time than in homogeneous soil columns. Preliminary results indicate: i) certain variables (anion, cation concentrations, etc.) do not follow normal or lognormal distributions even at the column scale, ii) strong correlations exist between parameters related to redox geochemistry (pH with S2- concentrations), and iii) PCA can identify dominant processes (e.g. iron and sulfate reduction) occurring in the system by grouping together causative variables (e.g. dominant TEAPs).

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

2009-12-01

153

Urban metal sinks or biogeochemical hot spots?: potential for interactions  

NASA Astrophysics Data System (ADS)

Hotspots of biogeochemical activity allow balancing of otherwise puzzling material budgets in urban systems. Therefore, these hotspots are of great interest as they might be strategically used to manage persistent urban nutrient loadings. However, the landscape position of these hotspots leads to the predictable accumulation of urban contaminants, particularly metals. For example, in Baltimore, riparian soil calcium concentrations are greater than upland soil concentrations , though both increase with urbanization. Despite the spatial coherence, the implications of metal enrichment for ecological and biogeochemical function remains under characterized. Here, we synthesize results from Baltimore with available literature to explore potential interactions and the implications for urban landscape biogeochemistry.

Bain, D. J.; Yesilonis, I. D.; Pouyat, R.

2012-12-01

154

A Model-based estimate of Biogeophysical and Biogeochemical effect of deforestation (Invited)  

NASA Astrophysics Data System (ADS)

Since 1750, changes in land cover change have contributed almost a third of anthropogenic carbon emissions (~180 PgC out of 550 PgC) and hence altered both the global climate and carbon cycle. The change in atmospheric CO2 concentration from land cover change and the consequent climate change from the 'greenhouse' effect of CO2 is called the biogeochemical effect. Changes in land cover could also have biophysical climatic consequences: changes in roughness length, surface albedo and turbulent heat fluxes. Latent and sensible heat fluxes changes could alter evapotranspiration, water vapour content, cloud and precipitation. Surface albedo changes could potentially warm or cool the surface depending on the changes in solar absorption after land cover change. Therefore, when considering the effects of land cover and land use changes, it is also important to account for biophysical effects on climate in addition to the biogeochemical effects of CO2 emissions. Modelling studies in recent years have shown that deforestation in seasonally snow covered boreal and temperate regions is likely to increase the land surface albedo and have a net (biophysical plus biogeochemical) cooling effect, whereas deforestation in tropics is likely to decrease latent heat flux from evapotranspiration and consequently have a net warming effect in association with decreased cloudiness and precipitation. Consequently, the location of afforestation (opposite of deforestation) needs to be considered carefully when evaluating the net effects on climate. A useful quantitative metric for assessing the effectiveness of afforestation would be the net climate change per unit afforested area. A recent modelling study estimates that the warming reductions per unit afforested area as three times higher in the tropics than in the boreal and northern temperate regions, suggesting that afforestation in the tropics are effective forest management strategies from a climate perspective. In our present work, we use an atmospheric general circulation model coupled to a mixed layer ocean to estimate the individual contributions (climate change per unit area of deforestation) of biogeophysical and biogeochemical effects to net climate change from deforestation in the tropics, mid-latitudes and high latitudes.

Bala, G.; Narayanappa, D.

2013-12-01

155

Modelling biogeochemical tracer transport in sea ice due to gravity drainage  

NASA Astrophysics Data System (ADS)

Sea ice is a porous material, formed of an evolving array of solid ice crystals bathed in liquid brine. The liquid-filled pore space provides a habitat for life within the ice, and, when the ice is permeable, provides a pathway for exchange of gases and other chemicals between the ice, ocean, and atmosphere. This coupling between the physical, chemical, and biological evolution of sea ice has poorly constrained implications for biogeochemical processes, such as the impact of sea ice on the carbon cycle. During winter ice growth, so-called gravity drainage drives a convective exchange of brine between the ocean and the porous interior of sea ice. Here, we use two-dimensional mushy-layer simulations of convective flow to provide insight into the resulting transport of passive biogeochemical tracers through the ice. We quantify the chemical concentration in the liquid during periods of quasi-steady growth rate, and determine a scaling law for the total chemical tracer fluxes through the region of active convection inside the ice. Chemical concentrations show spatial heterogeneity, and our results predict enhanced chemical concentrations in the pore space near to brine channels. These results may provide useful insight for interpreting studies of sea-ice biogeochemistry, and offer a framework to develop models of physical, chemical, and biological interactions.

Hitchen, Joseph; Wells, Andrew

2014-05-01

156

Modeling Biogeochemical Cycling of Heavy Metals in Lake Coeur d'Alene Sediments  

NASA Astrophysics Data System (ADS)

Mining of precious metals since the late 1800's have left Lake Coeur d'Alene (LCdA) sediments heavily enriched with toxic metals, including Cd, Cu, Pb, and Zn. Indigenous microbes however are capable of catalyzing reactions that detoxify the benthic and aqueous lake environments, and thus constitute an important driving component in the biogeochemical cycles of these metals. Here we report on the development of a quantitative model of transport, fate, exposure and effects of toxic compounds on benthic microbial communities at LCdA. First, chemical data from the LCdA area have been compiled from multiple sources to investigate trends in chemical occurrence, as well as to define model boundary conditions. The model is structured as 1-D diffusive reactive transport model to simulate spatial and temporal distribution of metals through the benthic sediments. Inorganic reaction processes included in the model are aqueous speciation, surface complexation, mineral precipitation/dissolution and abiotic redox reactions. Simulations with and without surface complexation are carried out to evaluate the effect of sorption and the conservative behaviour of metals within the benthic sediments under abiotic and purely diffusive transport. The 1-D inorganic diffusive transport model is then coupled to a biotic reaction network including consortium biodegradation kinetics with multiple electron acceptors, product toxicity, and energy partitioning. Multiyear simulations are performed, with water column chemistry established as a boundary condition from extant data, to explore the role of biogeochemical dynamics on benthic fluxes of metals in the long term.

Sengor, S. S.; Spycher, N.; Belding, E.; Curthoys, K.; Ginn, T. R.

2005-12-01

157

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

158

Modeling ocean circulation and biogeochemical variability in the Gulf of Mexico  

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

159

Biogeochemical Changes Accompanying Woody Plant Encroachment in a Subtropical Savanna  

Microsoft Academic Search

Ecosystem properties of surficial (0-10 cm) soils in remnant herbaceous patches were compared to those of contrasting woody plant patch types (upland discrete cluster, upland grove, and lowland woodland) where shifting land cover is known to have occurred over the past 50-77 yr. The purpose of this study was to evaluate and quantify the biogeochemical consequences and subsequent developmental rates

K. A. Hibbard; S. Archer; D. S. Schimel; D. W. Valentine

2001-01-01

160

A biogeochemical paradigm for reconstruction of past shelf sea regimes  

Microsoft Academic Search

A new paradigm is proposed for reconstruction of past continental shelf regimes that were driven by tides. It is argued that the combined impact of dynamics, nutrients, and suspended matter produces strong spatial gradients in biogeochemical fluxes to the seabed. These gradients produce diagnostic signatures in seabed sediments so that mixed, frontal, and stratified regions of past shelf regimes can

C. F. Jago; S. E. Jones

2003-01-01

161

Physical Ecosystem Engineers as Agents of Biogeochemical Heterogeneity  

NSDL National Science Digital Library

This peer-reviewed article form BioScience is about organisms that act as agents of biogeochemical heterogeneity. Physical ecosystem engineers are organisms that physically modify the abiotic environment. They can affect biogeochemical processing by changing the availability of resources for microbes (e.g., carbon, nutrients) or by changing abiotic conditions affecting microbial process rates (e.g., soil moisture or temperature). Physical ecosystem engineers can therefore create biogeochemical heterogeneity in soils and sediments. They do so via general mechanisms influencing the flows of materials (i.e., modification of fluid dynamic properties, fluid pumping, and material transport) or the transfer of heat (i.e., modification of heat transfer properties, direct heat transfer, and convective forcing). The consequences of physical ecosystem engineering for biogeochemical processes can be predicted by considering the resources or abiotic conditions that limit or promote a reaction, and the effect of physical ecosystem engineering on these resources or abiotic conditions via the control they exert on material flows and heat transfer.

JORGE L. GUTIÃÂÃÂRREZ and CLIVE G. JONES (;)

2006-03-01

162

Developing biogeochemical tracers of apatite weathering by ectomycorrhizal fungi  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

163

Earth's Early Biosphere and the Biogeochemical Carbon Cycle  

NASA Technical Reports Server (NTRS)

Our biosphere has altered the global environment principally by influencing the chemistry of those elements most important for life, e g., C, N, S, O, P and transition metals (e.g., Fe and Mn). The coupling of oxygenic photosynthesis with the burial in sediments of photosynthetic organic matter, and with the escape of H2 to space, has increased the state of oxidation of the Oceans and atmosphere. It has also created highly reduced conditions within sedimentary rocks that have also extensively affected the geochemistry of several elements. The decline of volcanism during Earth's history reduced the flow of reduced chemical species that reacted with photosynthetically produced O2. The long-term net accumulation of photosynthetic O2 via biogeochemical processes has profoundly influenced our atmosphere and biosphere, as evidenced by the O2 levels required for algae, multicellular life and certain modem aerobic bacteria to exist. When our biosphere developed photosynthesis, it tapped into an energy resource that was much larger than the energy available from oxidation-reduction reactions associated with weathering and hydrothermal activity. Today, hydrothermal sources deliver globally (0.13-1.1)x10(exp l2) mol yr(sup -1) of reduced S, Fe(2+), Mn(2+), H2 and CH4; this is estimated to sustain at most about (0.2-2)xl0(exp 12)mol C yr(sup -1) of organic carbon production by chemautotrophic microorganisms. In contrast, global photosynthetic productivity is estimated to be 9000x10(exp 12) mol C yr(sup -1). Thus, even though global thermal fluxes were greater in the distant geologic past than today, the onset of oxygenic photosynthesis probably increased global organic productivity by some two or more orders of magnitude. This enormous productivity materialized principally because oxygenic photosynthesizers unleashed a virtually unlimited supply of reduced H that forever freed life from its sole dependence upon abiotic sources of reducing power such as hydrothermal emanations and weathering. Communities sustained by oxygenic photosynthesis apparently thrived wherever supplies of sunlight, moisture and nutrients were sufficient. Prior to the development of oxygenic photosynthesis, the net global effect of the ancient global biosphere was to facilitate chemical equilibrium between reduced species from thermal activity and weathering and more oxidized constituents in the surface environment. But even this ancient biosphere might have been globally pervasive. The global geothermal heat flow was substantially higher during Earth's first billion years, and thus reduced chemical species might have persisted in sunlit aquatic environments. Perhaps the substantial decline in thermal activity between 4000 and 3000 Ma created a driver for oxygenic photosynthesis to develop.

DesMarais, David

2004-01-01

164

Adapting to life: ocean biogeochemical modelling and adaptive remeshing  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

165

Spatial Organization of Lake Size-Distributions and Biogeochemical Patterns  

NASA Astrophysics Data System (ADS)

Lakes cover a small portion of Earth's surface, but emit substantial amounts of greenhouse gases to the atmosphere. Contributions of lakes to the global carbon cycle are estimated by up-scaling techniques because most lakes are too small to be captured by atmospheric carbon flux approaches that use inverse modeling. Typically lake size-distributions and biogeochemical driver-response relationships used in up scaling are considered constant over space, but this assumption might mask regional variability in relationships and cause substantial errors in bottom-up estimates. We use data from a high-resolution lake census and lake chemistry surveys to show that statistical driver-response relationships for biogeochemical patterns in Swedish lakes are non-stationary over space, but organize into relatively homogenous regions. These regions are associated with theoretically distinct lake size-distributions. This regional variability in lake size-abundance and biogeochemical relationships creates large uncertainties in estimates of carbon fluxes and stores. In Sweden, the contribution of small lakes to carbon fluxes depends on the shape of lake size-distributions, which is related to landscape morphometry. When accounting for regional differences, we find that the partial pressure of carbon dioxide in Swedish lake water is underestimated by a previously published size-distribution fit to global lake data. However, the relative importance of small lakes versus large lakes is overstated when estimates are based on the global lake size-distribution. This is mostly because larger lakes, not small lakes, dominate the total surface area of lakes. We conclude that lakes fall into physiographic regions characterized by common biogeochemical and abundance-size scaling relationships. Using biogeochemical-physiographic regions for global up-scaling analyses stands to substantially improve the accuracy of carbon flux estimates from lakes.

Seekell, D. A.; Pace, M. L.; Gudasz, C.; Sobek, S.; Tranvik, L.; Verpoorter, C.

2013-05-01

166

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

167

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

NASA Astrophysics Data System (ADS)

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

Bieroza, Magdalena; Heathwaite, Louise

2013-04-01

168

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

NASA Astrophysics Data System (ADS)

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.

Podymov, O.

2009-04-01

169

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

PubMed

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. PMID:17996980

Singhal, Naresh; Islam, Jahangir

2008-02-19

170

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

SciTech Connect

Tc(VII) will be reduced and precipitated in FRC sediments under anaerobic conditions in batch experiments (progressive microcosms). The complementary microcosm experiments using low pH/nigh nitrate sediments from 3 (near FW 009) are imminent, with the sediment cores already shipped to Manchester. HYPOTHESIS 2. Tc(VII) reduction and precipitation can be visualized in discrete biogeochemical zones in sediment columns using 99mTc and a gamma-camera. Preliminary experiments testing the use of 99mTc as a radiotracer to address hypotheses 2 and 3 have suggested that the 99mTc associates with Fe(II)-bearing sediments in microcosms and stratified columns containing FRC sediments. Initial proof of concept microcosms containing Fe(II)-bearing, microbially-reduced FRC sediments were spiked with 99mTc and imaged using a gamma-camera. In comparison with oxic controls, 99mTc was significantly partitioned in the solid phase in Fe(III)-reducing sediments in batch experiments. Column experiments using FRC background area soil with stratified biogeochemical zones after stimulation of anaerobic processes through nutrient supplementation, suggested that 99mTc transport was retarded through areas of Fe(III) reduction. HYPOTHESIS 3. Sediment-bound reduced 99mTc can be solubilized by perturbations including oxidation coupled to biological nitrate reduction, and mobilization visualized in real-time using a gamma-camera. Significant progress has been made focusing on the impact of nitrate on the biogeochemical behavior of technetium. Additions of 100 mM nitrate to FRC sediment microcosms, which could potentially compete for electrons during metal reduction, inhibited the reduction of both Fe(III) and Tc(VII) completely. Experiments have also addressed the impact of high nitrate concentrations on Fe(II) and Tc(IV) in pre-reduced sediments, showing no significant resolubilization of Tc with the addition of 25 mM nitrate. A parallel set of experiments addressing the impact of aerobic conditions on the stability/solubility of Fe(II) and Tc(IV), found 80 % resolubilization of the Tc. Column experiments exploring this behavior are being planned. HYPOTHESIS 4 The mobility of 99mTc in the sediment columns can be modeled using a coupled speciation and transport code. Microbiological and geochemical characterization of the column experiments is ongoing and transport and geochemical modeling experiments are being planned.

Lloyd, Jonathan R.

2005-06-01

171

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

172

Biogeochemical reduction processes in a hyperalkaline affected leachate soil profile  

Microsoft Academic Search

Hyperalkaline surface environments can occur naturally or because of contamination by hydroxide-rich wastes. The high pH produced in these areas has the potential to lead to highly specialised microbial communities and unusual biogeochemical processes. This paper reports an investigation into the geochemical processes that are occurring in a buried, saturated, organic–rich soil layer at pH 12.3. The soil has been

Ian T. Burke; Robert J. G. Mortimer; Shanmugam Palani; Robert A. Whittleston; Cindy L. Lockwood; David J. Ashley; Douglas I. Stewart

2012-01-01

173

Biogeochemical characteristics of nitrogen and phosphorus in Jiaozhou Bay sediments  

Microsoft Academic Search

Sediment samples were cored from 3 locations representing the inner bay, the outer bay and the bay mouth of Jiaozhou Bay in\\u000a September 2003 to study the source and biogeochemical characteristics of nitrogen and phosphorus in the bay. The content and\\u000a vertical distributions of total nitrogen (TN), total phosphorus (TP), organic nitrogen (ON), organic phosphorus (OP), inorganic\\u000a nitrogen (IN), inorganic

Xuegang Li; Jinming Song; Huamao Yuan; Jicui Dai; Ning Li

2007-01-01

174

Aquifer\\/aquitard interfaces: mixing zones that enhance biogeochemical reactions  

Microsoft Academic Search

.   Several important biogeochemical reactions are known to occur near the interface between aquifer and aquitard sediments.\\u000a These reactions include O2 reduction; denitrification; and Fe3+, SO4\\u000a 2–, and CO2 (methanogenesis) reduction. In some settings, these reactions occur on the aquitard side of the interface as electron acceptors\\u000a move from the aquifer into the electron-donor-enriched aquitard. In other settings, these reactions

P. B. McMahon

2001-01-01

175

Biogeochemical Processes in a Tropical Indian Mangrove (Pichavaram) Environment  

NASA Astrophysics Data System (ADS)

The Study area is a very sensitive marine ecosystem with high productivity and therefore has both biogeochemical and socio-economical significance. The study area undergoes changes by removal and addition of organic and inorganic materials brought by the rivers. The overall health of mangrove ecosystems and their impact on coastal zones is directly related to the biogeochemical processes taking place in the particular environment. In order to understand these processes, we have conducted several experiment, sulphate reduction, Fe-Mn reduction and aerobic respiration. Sulphate reduction was the dominant microbial process than the other two mechanisms. However, the sulphate reduction was dominant at the top few centimeters, leading to little (up to 5% of total C input) carbon burial in the mangrove ecosystem. The microbial mineralization reactions were spatially variable. Sulphate reduction was the dominant process in the disturbed forest zone than the pristine. The microbial mechanism was more rapid than the other world mangroves, reflecting higher phytoplankton production and organic matter retention in this mangrove ecosystem. Sharp variation in the sediment characters, water content, salinity, nutrient variability etc., was the direct result of the human disturbances which ultimately cause changes in the biogeochemical cycling of the nutrients. Thus, concrete steps are needed to control the human interference on the highly vulnerable mangrove wetlands for sustainable development.

Mathukumalli, B.

2006-05-01

176

Inorganic Carbon Cycling and the Biogeochemical Processes in Hudson Bay  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

177

Estimating impacts of lichens and bryophytes on global biogeochemical cycles  

NASA Astrophysics Data System (ADS)

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.

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

2014-02-01

178

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

179

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

180

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

PubMed

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

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

181

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

182

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

NASA Astrophysics Data System (ADS)

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 characterization techniques, will allow us to further probe a range of pore-structures with distinctive physical, chemical and biological properties to provide a better understanding of biogeochemical redox processes occurring at the pore scale and their impact on contaminant transport.

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

2011-12-01

183

Effects of Physical and Chemical Heterogeneities on Biogeochemical Processes Associated With Uranium Bioremediation at Rifle, Colorado  

NASA Astrophysics Data System (ADS)

Natural porous media are inherently heterogeneous at multiple spatial scales, which can have profound impacts on biogeochemical reactions in the subsurface. In this work, we aim to understand the effects of physical and chemical heterogeneities on various biogeochemical reaction processes associated with a field- scale uranium bioremediation experiment at Rifle, Colorado. Numerical experiments were designed to mimic the field biostimulation experiment: acetate was injected into the subsurface as the electron donor to stimulate the growth of bacteria and the microbially-mediated reduction of uranium, iron, and sulfate. The field measurements were used to estimate the initial physical property distribution and to infer a relationship between physical and chemical properties. The reactive transport model CrunchFlow couples the geochemical, transport, and microbial processes, and explicitly keeps track of the evolution of microbial community structures and their impact on reaction rates. The simulation results, which were validated using field monitoring well datasets, suggested that the physical heterogeneity, essentially the spatial variation in permeability, determines how the injected acetate is distributed, while the chemical heterogeneity, including the spatial distribution of iron hydroxide, determines where and how much iron reduction occurs. Because uranium is reduced by iron reducers, the chemical heterogeneities also determine where and how much uranium reduction occurs. The physical and chemical heterogeneities together determine the level of accessibility of acetate to iron hydroxide in the field. As a result, with different levels of spatial variation in Fe-hydroxide content, the efficacy of uranium bioremediation can differ by a factor of more than two. In contrast, for sulfate reduction, the effects of heterogeneities are much less significant because sulfate is uniformly distributed in the groundwater and is continuously replenished by upgradient groundwater flow. As a result, sulfate is mostly consumed close to the injection wells, leading to the accumulation of large amounts of sulfate reducers in these locations that can be order of magnitude larger than elsewhere. Because of the large spatial variations in the biomass, the rates of biogeochemical reactions vary significantly over time and space. As a result, the rate laws that do not take such spatial and temporal evolution of biomass into account cannot match the breakthrough curves of chemical species in the field. In addition, because of the possibility of pore clogging and the associated flow path changes due to precipitates and biomass accumulation, the characteristics of physical and chemical heterogeneities can also evolve with time, which can have profound impacts on the efficacy and sustainability of in situ bioremediation strategies.

Li, L.; Steefel, C. I.; Kowalsky, M. B.; Englert, A. L.; Hubbard, S. S.

2008-12-01

184

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

SciTech Connect

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.

Erickson III, David J [ORNL

2011-01-01

185

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

186

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

NASA Astrophysics Data System (ADS)

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.

Minard, A.; Moreau, J. W.

2010-12-01

187

Ghosts of vegetation past: Biogeochemical legacy effects in changing drylands  

NASA Astrophysics Data System (ADS)

Woody encroachment, the proliferation of woody plants into grasslands and savannas, is a major land cover change that has affected drylands worldwide over the past century. This vegetation change has fundamentally altered biogeochemical processes in drylands, with evidence that woody plant cover accounts for a significant, albeit highly uncertain, fraction of the Northern Hemisphere carbon (C) sink. Elevated under-canopy soil organic carbon (SOC) pools have been widely reported following woody encroachment. Although generalizing rates of SOC accumulation among encroached drylands remains challenging, integrating information on factors such as land management, soil properties, and spatio-temporal patterns of encroachment is improving estimates of these patterns. Recent work suggests that changes in SOC may occur fairly rapidly following shrub encroachment into southwestern drylands, but that these inputs are primarily in relatively labile, light fraction SOC. Isotopic analyses indicate that woody plant inputs are incorporated into heavy fraction C pools as well, suggesting that these pools may reflect relatively dynamic inputs and outputs. However, understanding the biogeochemical consequences of woody encroachment are complicated by land management practices. In the western US, landscapes are often a mosaic of sites undergoing woody encroachment and sites recovering from 'brush management' practices imposed to reduce woody plant cover. In contrast to the rapid changes in SOC following encroachment, biogeochemical legacies of removed shrubs may persist for decades following brush management. These legacy effects may be a function of slow degradation of stable SOC compounds. In addition, lag effects on surface litter decomposition may remain for many years following brush management, the result of persistent high grass density in the vicinity of "ghosts" shrubs. Results from the CENTURY model suggest that SOC losses would continue for ca. 105 years after shrub removal, although the degree of soil disturbance strongly affected SOC loss dynamics, with more rapid initial loss rates following management techniques that disturb the soil and coarse root material.

Throop, H. L.

2012-12-01

188

Biogeochemical C and N cycles in urban soils.  

PubMed

The percentage of urban population is projected to increase drastically. In 2030, 50.7 to 86.7% of the total population in Africa and Northern America may live in urban areas, respectively. The effects of the attendant increases in urban land uses on biogeochemical C and N cycles are, however, largely unknown. Biogeochemical cycles in urban ecosystems are altered directly and indirectly by human activities. Direct effects include changes in the biological, chemical and physical soil properties and processes in urban soils. Indirect effects of urban environments on biogeochemical cycles may be attributed to the introductions of exotic plant and animal species and atmospheric deposition of pollutants. Urbanization may also affect the regional and global atmospheric climate by the urban heat island and pollution island effect. On the other hand, urban soils have the potential to store large amounts of soil organic carbon (SOC) and, thus, contribute to mitigating increases in atmospheric CO(2) concentrations. However, the amount of SOC stored in urban soils is highly variable in space and time, and depends among others on soil parent material and land use. The SOC pool in 0.3-m depth may range between 16 and 232 Mg ha(-1), and between 15 and 285 Mg ha(-1) in 1-m depth. Thus, depending on the soil replaced or disturbed, urban soils may have higher or lower SOC pools, but very little is known. This review provides an overview of the biogeochemical cycling of C and N in urban soils, with a focus on the effects of urban land use and management on soil organic matter (SOM). In view of the increase in atmospheric CO(2) and reactive N concentrations as a result of urbanization, urban land use planning must also include strategies to sequester C in soil, and also enhance the N sink in urban soils and vegetation. This will strengthen soil ecological functions such as retention of nutrients, hazardous compounds and water, and also improve urban ecosystem services by promoting soil fertility. PMID:18597848

Lorenz, Klaus; Lal, Rattan

2009-01-01

189

Remote analysis of biological invasion and biogeochemical change  

PubMed Central

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

Asner, Gregory P.; Vitousek, Peter M.

2005-01-01

190

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

PubMed

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

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

2013-10-15

191

Rivers and Stable Isotopes as Indicators of Biogeochemical Gradients  

NASA Astrophysics Data System (ADS)

Consideration of processes on very small (microbe) to large (catchment) scales become increasingly important in biogeochemical gradient work. In this context, rivers are ideal indicators of biogeochemical gradients for large continental scales when geochemical- and discharge data are combined for flux evaluations. If these are further combined with isotope measurements, sources and turnover of water and dissolved constituents can be quantified. An example study is the combination of GIS-, discharge- and water stable isotope data on the in Clyde River basin in Scotland. Here we determined transpiration with an annual average of 0.489 km3 a-1. When combining this rate with the water use efficiency, the CO2 uptake of the entire basin yielded an annual net primary production (NPP) of 185.2 g C m-2. Compared to other temperate areas this is about half the NPP than expected, which is most likely caused by the predominant cover of grasslands. Therefore, agricultural and forest vegetation schemes could influence continental water balances on time scales of years to decades. In another study on the Lagan River in N. Ireland, stable isotope methods were applied to evaluate the role of carbonate versus silicate dissolution. Of these two types of weathering only silicate dissolution withdraws atmospheric CO2 to be stored in the continental crust over long time periods. A downstream evolution with increasing pH- and ?13CDIC values revealed carbonate dissolution despite their minor abundance in the catchment of less than 5 %. This dominant carbonate signal on the riverine carbon cycle outlines the capacity of buffering anthropogenic influences and CO2 turnover. It should be even more pronounced in other rivers where carbonates usually occupy a larger proportion of the basin geology. Future biogeochemical gradient work on rivers should apply particulate and dissolved organic constituent fluxes. This includes more refined compound specific isotope work on selected pollutants such as TCE, PAH, PCB as well as riverine microbiological considerations. Such expansions meet the challenge of measuring much smaller concentrations compared to groundwater contaminant plumes. Further combinations of stable N, H, O, and S isotope systems would also help to resolve overlapping trends when only carbon isotopes are measured. Apart from combining traditional light stable isotope systems, addition of newly accessible isotope groups by multicollector ICP-MS (i.e. Fe, Cr, Zn) and radioisotope techniques can provide innovative tools for resolving gradients and their biogeochemical cycling within rivers.

Barth, J. A.

2005-12-01

192

A biogeochemical paradigm for reconstruction of past shelf sea regimes  

NASA Astrophysics Data System (ADS)

A new paradigm is proposed for reconstruction of past continental shelf regimes that were driven by tides. It is argued that the combined impact of dynamics, nutrients, and suspended matter produces strong spatial gradients in biogeochemical fluxes to the seabed. These gradients produce diagnostic signatures in seabed sediments so that mixed, frontal, and stratified regions of past shelf regimes can be reconstructed using appropriate microbiological and isotopic proxies in the sediments. Much of the algal production in summer takes place in the thermocline and at tidal mixing fronts. The themocline stimulates plankton growth due to availability of light and nutrients and optimal conditions occur at fronts due to enhanced lateral mixing. Organic matter generated by algae is incorporated in suspended particulate matter (SPM) with most of the mass in large aggregates which settle to the seabed. Aggregation is facilitated by carbohydrates produced by the algae. Aggregates deposit on the seabed as benthic fluff. The potential for pelagic remineralisation of SPM is reduced in frontal regions due to rapid settling and limited resuspension. Combination of enhanced supply and rapid export means that benthic fluff deposition per unit area of seabed is greatest in frontal regions. Subsequent resuspension combined with cross-frontal mixing in summer and storms in winter should disperse fluff away from fronts. Net deposition of this material is most likely on the stratified side of the frontal regions. The end result is that there are differences in benthic fluff deposition in mixed, frontal and stratified regions. These differences impact on seabed exchanges. Fluff controls benthic oxygen demand (BOD) and determines whether biogeochemical exchanges are oxic or anoxic. Diagnostic indicators of water column and seabed regimes are preserved in the sediment record. For example, gradients in BOD and temperature are reflected in benthic foraminifera assemblages and stable isotope signatures in the sediments across the Celtic Sea front. In addition, there are gradients in dinoflagellate cyst assemblages which reflect the overlying water column structure. Such proxies, when suitably calibrated, can be used to interpret biogeochemical regimes of the past. Linked to biogeochemical and ecosystem models, they provide the potential for reconstruction of ecologically important parameters of past shelf regimes.

Jago, C. F.; Jones, S. E.

2003-04-01

193

A hybrid continuum-scale model with pore-scale refinements for biogeochemical processes  

NASA Astrophysics Data System (ADS)

Fate and transport of contaminants in aquifers are influenced by geochemical reactions (precipitation/dissolution) and biological activities (biofilm development). If simulations and observations of contaminant behavior are at a large-scale (continuum-scale), processes leading to their degradation occur at a small-scale (pore-scale). In terms of modeling, the complexity of these last processes requires to represent them at their natural scale and to consider computational limitations for large domain simulations. As classical methods for transferring information between scales are not relevant for strongly coupled processes, we aim at creating a new modeling approach combining different representation concepts over different sub-domains. The different models run simultaneously over the different sub-domains and are coupled at the sub-domains interfaces by defining boundary fluxes for each model. Where biogeochemical processes are determinant, a pore-scale representation will be used to describe the involved processes. For the rest of the domain, a continuum representation will be preferred with a level of complexity adapted to the processes characteristics. By optimizing the balance between computational efficiency and representation accuracy, this new approach for modeling contaminant behavior at their trajectory-scale promises the possibility of large domain simulations with an adequate representation of degradation processes.

Roubinet, D.; Tartakovsky, D. M.

2011-12-01

194

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

195

Hydro-biogeochemical Controls on Geophysical Signatures (Invited)  

NASA Astrophysics Data System (ADS)

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

Atekwana, E. A.

2013-12-01

196

Biogeochemical and ecological feedbacks in grassland responses to warming  

NASA Astrophysics Data System (ADS)

Plant growth often responds rapidly to experimentally simulated climate change. Feedbacks can modulate the initial responses, but these feedbacks are difficult to detect when they operate on long timescales. We transplanted intact plant-soil mesocosms down an elevation gradient to expose them to a warmer climate and used collectors and interceptors to simulate changes in precipitation. Here, we show that warming initially increased aboveground net primary productivity in four grassland ecosystems, but the response diminished progressively over nine years. Warming altered the plant community, causing encroachment by species typical of warmer environments and loss of species from the native environment--trends associated with the declining response of plant productivity. Warming stimulated soil nitrogen turnover, which dampened but did not reverse the temporal decline in the productivity response. Warming also enhanced N losses, which may have weakened the expected biogeochemical feedback where warming stimulates N mineralization and plant growth. Our results, describing the responses of four ecosystems to nearly a decade of simulated climate change, indicate that short-term experiments are insufficient to capture the temporal variability and trend of ecosystem responses to environmental change and their modulation through biogeochemical and ecological feedbacks.

Wu, Zhuoting; Dijkstra, Paul; Koch, George W.; Hungate, Bruce A.

2012-06-01

197

Different mechanisms of silicic acid leakage and their biogeochemical consequences  

NASA Astrophysics Data System (ADS)

the modern ocean, silicic acid is effectively trapped in the Southern Ocean. According to the silicic acid leakage hypothesis, a loosening of this trapping may have contributed to low atmospheric CO2 during glacial times. Using a model with dynamical feedbacks in ocean physics and biology, we explore three distinct mechanisms to loosen the trapping and trigger silicic acid leakage from the Southern Ocean: sea ice expansion, weaker winds, and iron addition. The basic idea of the iron addition mechanism was previously explored using a simple box model. Here we confirm the main results of the earlier work and demonstrate further that sea ice expansion and weaker southern westerlies can also trigger silicic acid leakage. The three mechanisms are not mutually exclusive, and their biogeochemical consequences are dissimilar in terms of the spatial patterns of Si:N uptake and the relative changes in opal and particulate organic carbon fluxes both in and outside the Southern Ocean. While it is not entirely clear how sea ice, winds, and iron deposition were different during the last glacial period compared to today, we examine the synergistic effects of these three triggers in one simulation. In this simulation, the combination of sea ice and iron reproduces the north-south dipole of productivity recorded in export production proxies, but effects of the iron perturbation seem to dominate the overall biogeochemical response.

Matsumoto, Katsumi; Chase, Zanna; Kohfeld, Karen

2014-03-01

198

Long-term biogeochemical impacts of liming the ocean  

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

199

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

PubMed Central

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

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

2013-01-01

200

Biogeochemical tracers and fluxes in the Western Mediterranean Sea, spring 2005  

Microsoft Academic Search

Only few studies about biogeochemical properties' distributions in wide areas of the Mediterranean Sea are available. We present a new biogeochemical dataset for the Western Mediterranean, collected in spring 2005. The paper presents a general description of the vertical and horizontal variability of dissolved inorganic nutrients and of the anomalous stoichiometric ratios. Nutrients are subsequently used as water mass tracers,

K. Schroeder; G. P. Gasparini; M. Borghini; G. Cerrati; R. Delfanti

2010-01-01

201

A New Biogeochemical Computational Framework Integrated within the Community Land Model  

NASA Astrophysics Data System (ADS)

Terrestrial biogeochemical processes, particularly carbon cycle dynamics, have been shown to significantly influence regional and global climate changes. Modeling terrestrial biogeochemical processes within the land component of Earth System Models such as the Community Land model (CLM), however, faces three major challenges: 1) extensive efforts in modifying modeling structures and rewriting computer programs to incorporate biogeochemical processes with increasing complexity, 2) expensive computational cost to solve the governing equations due to numerical stiffness inherited from large variations in the rates of biogeochemical processes, and 3) lack of an efficient framework to systematically evaluate various mathematical representations of biogeochemical processes. To address these challenges, we introduce a new computational framework to incorporate biogeochemical processes into CLM, which consists of a new biogeochemical module with a generic algorithm and reaction database. New and updated biogeochemical processes can be incorporated into CLM without significant code modification. To address the stiffness issue, algorithms and criteria will be developed to identify fast processes, which will be replaced with algebraic equations and decoupled from slow processes. This framework can serve as a generic and user-friendly platform to test out different mechanistic process representations and datasets and gain new insight on the behavior of the terrestrial ecosystems in response to climate change in a systematic way.

Fang, Y.; Li, H.; Liu, C.; Huang, M.; Leung, L.

2012-12-01

202

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

EPA Science Inventory

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

203

Linking soil and sediment properties for research on biogeochemical cycles  

NASA Astrophysics Data System (ADS)

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

Kuhn, Nikolaus J.

2013-04-01

204

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

SciTech Connect

Field experiments at a former uranium mill tailings site have identified the potential for stimulating indigenous bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. This effectively removes uranium from solution resulting in groundwater concentrations below actionable standards. Three-dimensional, coupled variably-saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport rates and biogeochemical reaction rates that determine the location and magnitude of key reaction products. A comprehensive reaction network, developed largely through previous 1-D modeling studies, was used to simulate the impacts on uranium behavior of pulsed acetate amendment, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. A principal challenge is the mechanistic representation of biologically-mediated terminal electron acceptor process (TEAP) reactions whose products significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. In general, these simulations of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado confirmed previously identified behaviors including (1) initial dominance by iron reducing bacteria that concomitantly reduce aqueous U(VI), (2) sulfate reducing bacteria that become dominant after {approx}30 days and outcompete iron reducers for the acetate electron donor, (3) continuing iron-reducer activity and U(VI) bioreduction during dominantly sulfate reducing conditions, and (4) lower apparent U(VI) removal from groundwater during dominantly sulfate reducing conditions. New knowledge on simultaneously active metal and sulfate reducers has been incorporated into the modeling. In this case, an initially small population of slow growing sulfate reducers is active from the initiation of biostimulation. Three-dimensional, variably saturated flow modeling was used to address impacts of a falling water table during acetate injection. These impacts included a significant reduction in aquifer saturated thickness and isolation of residual reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted in higher concentrations of TEAP products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions; however, the ranges were sufficiently small to preserve general trends. Large computer memory and high computational performance were required to simulate the detailed coupled process models for multiple biogeochemical components in highly resolved heterogeneous materials for the 110-day field experiment and 50 days of post-biostimulation behavior. In this case, a highly-scalable subsurface simulator operating on 128 processor cores for 12 hours was used to simulate each realization. An equivalent simulation without parallel processing would have taken 60 days, assuming sufficient memory was available.

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

2011-11-01

205

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

NASA Technical Reports Server (NTRS)

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

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

1985-01-01

206

Reconstructing disturbances and their biogeochemical consequences over multiple timescales  

USGS Publications Warehouse

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

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

2014-01-01

207

Sensitivity analysis of global terrestrial biogeochemical cycling model  

SciTech Connect

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

Chambers, J.Q.; Kercher, J.R. (Univ. of California, Santa Barbara (United States) Lawrence Livermore National Lab., CA (United States))

1993-06-01

208

Watershed Management and Mercury Biogeochemical Cycling in Lake Zapotlan, Mexico  

NASA Astrophysics Data System (ADS)

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

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

2009-05-01

209

Biogeochemical consequences of an oxygenated intrusion into an anoxic fjord  

PubMed Central

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

2014-01-01

210

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

PubMed

Leachate from municipal landfills can create groundwater contaminant plumes that may last for decades to centuries. The fate of reactive contaminants in leachate-affected aquifers depends on the sustainability of biogeochemical processes affecting contaminant transport. Temporal variations in the configuration of redox zones downgradient from the Norman Landfill were studied for more than a decade. The leachate plume contained elevated concentrations of nonvolatile dissolved organic carbon (NVDOC) (up to 300 mg/L), methane (16 mg/L), ammonium (650 mg/L as N), iron (23 mg/L), chloride (1030 mg/L), and bicarbonate (4270 mg/L). Chemical and isotopic investigations along a 2D plume transect revealed consumption of solid and aqueous electron acceptors in the aquifer, depleting the natural attenuation capacity. Despite the relative recalcitrance of NVDOC to biodegradation, the center of the plume was depleted in sulfate, which reduces the long-term oxidation capacity of the leachate-affected aquifer. Ammonium and methane were attenuated in the aquifer relative to chloride by different processes: ammonium transport was retarded mainly by physical interaction with aquifer solids, whereas the methane plume was truncated largely by oxidation. Studies near plume boundaries revealed temporal variability in constituent concentrations related in part to hydrologic changes at various time scales. The upper boundary of the plume was a particularly active location where redox reactions responded to recharge events and seasonal water-table fluctuations. Accurately describing the biogeochemical processes that affect the transport of contaminants in this landfill-leachate-affected aquifer required understanding the aquifer's geologic and hydrodynamic framework. PMID:21314684

Cozzarelli, I M; Böhlke, J K; Masoner, J; Breit, G N; Lorah, M M; Tuttle, M L W; Jaeschke, J B

2011-01-01

211

Biogeochemical evolution of a landfill leachate plume, Norman, Oklahoma  

USGS Publications Warehouse

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

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

2011-01-01

212

Can biogeochemical fluxes be recovered from nitrate and chlorophyll data? A case study assimilating data in the Northwestern Mediterranean Sea at the JGOFS-DYFAMED station  

NASA Astrophysics Data System (ADS)

One of the principal objectives of studying biogeochemical cycles is to obtain precise estimates of the main fluxes, such as total, new and export oceanic productions. Since models can incorporate the a priori knowledge of the most important processes, they are increasingly used for this purpose. However, biogeochemical models are characterized by a large number of poorly known parameters. Moreover, the available data are rather sparse in both time and space, and represent concentrations, not fluxes. Therefore, the major challenge is to constrain the relevant fluxes using information from a limited number of observations and from models incorporating poorly known internal parameters. The present study attempts to meet this challenge. In a 1D framework at the DYFAMED station (NW Mediterranean Sea), near-monthly nitrate and chlorophyll profiles and daily surface chlorophyll concentrations are assimilated in a coupled dynamical-biological model using the tangent linear and adjoint models. Following sensitivity analyses that show that some parameters cannot be recovered from the data set used, assimilation of observed 1997 data is performed. The first inversion considered clearly shows that, in agreement with previous studies, (1) the data impose a C/Chl ratio that varies with depth (i.e. light) and (2) the "initial" conditions (e.g. winter nitrate profile) strongly constrain the annual biogeochemical fluxes. After assimilation of the 1997 data, the agreement between the data and the model is quantitatively improved in 1995 and 1996, which can be considered a good validation of the methodology. However, the order of magnitude of the biogeochemical fluxes, and especially of the particulate export and regenerated production, are not correctly recovered. An analysis of the simulations shows that this result is associated with a strong decrease in zooplankton concentrations. An additional constraint of maintaining acceptable levels of zooplankton is therefore added. The results are improved, but remain unsatisfactory. A final inversion, which takes into account the a priori estimates of the major annual fluxes, is then performed. This shows that there is no inconsistency between the NO 3 and chlorophyll data, the order of magnitude of the fluxes and the model. The work therefore demonstrates that recovering biogeochemical fluxes from available data of concentrations and stocks is not a straightforward exercise: the coverage and type of observations, and the nonlinearities of the biogeochemical model all contribute to this difficulty.

Faugeras, Blaise; Lévy, Marina; Mémery, Laurent; Verron, Jacques; Blum, Jacques; Charpentier, Isabelle

2003-04-01

213

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

214

Pore-scale modeling of biogeochemical alteration of the transport properties of sediment  

NASA Astrophysics Data System (ADS)

In an in-situ environmental remediation project, the evolution of the contaminant plume and the efficient delivery of biological or chemical agents to the contaminated zone depend on the hydraulic properties that control flow and transport in the subsurface. At the same time, biogeochemical transformations induced by the remediation treatment, such as mineral precipitation and dissolution, and growth of bacterial colonies may alter the geometry of the pore space. Even though a contaminant plume develops at the field scale, the degree of alteration of the permeability of the sediment is determined at the pore level. Changes in sediment permeability due to dissolution and precipitation in individual pores may affect the remediation process. In this study, we use pore-scale modeling to simulate flow, transport and reactions in experimental columns. The model describes the dynamic coupling between flow and reactive transport. The flow field is computed by solving Navier-Stokes equations in the pore space. Then, the computed velocities are supplied to a multicomponent reactive transport code that computes dissolution and precipitation rates. The changes in the domain geometry caused by the reactive processes are tracked based on mass balance considerations. The updated flow field is supplied back to the reactive transport module. High-resolution images of the sediment pore space acquired at the Advanced Light Source Facility at Lawrence Berkeley National Laboratory provide the input data for computations. Simulations of the fluid flow estimate the trends of the absolute permeability modification over the duration of the experiments.

Molins, S.; Silin, D.

2009-12-01

215

Nitrate reduction in streambed sediments: Effects of flow and biogeochemical kinetics  

NASA Astrophysics Data System (ADS)

The effect of retention time on redox sequences along the hydrological flow path of groundwater discharging through low-relief coastal stream sediments and the subsequent impact on the fate of NO3- carried in the groundwater was examined in two intact cores. Rates of denitrification were determined for the organic-rich streambed sediments, and a macroscopic, multispecies, reactive transport model based on multiple Monod kinetics was developed to interpret and extend the experimental results. Regionalized sensitivity analysis and parameter estimation were used to determine a set of parameters that best describe the experimental data for one column. The calibrated model successfully replicated the spatial profiles of nitrate under both steady and transient conditions in the second column operated under different conditions. A dimensionless form of the model was used to examine how coupled biogeochemical reactions and hydrological transport processes operate within the stream sediments could be understood in terms of Peclet (ratio of advection to dispersion) and Damkohler numbers (the ratio of the characteristic time of transport to the characteristic time for reaction). At the study site, the Peclet number and the Damkohler numbers for both oxygen and nitrate are high (Pe = 25, DaN = 47.5, and DaO = 40). When Pe > 5, Damkohler numbers explain observed variations in nitrate removal rates; as the flow rate increases, the solute residence time in the reactive zone is shortened resulting in a lesser extent of reaction, such that more NO3- is delivered to the stream water.

Gu, Chuanhui; Hornberger, George M.; Mills, Aaron L.; Herman, Janet S.; Flewelling, Samuel A.

2007-12-01

216

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

NASA Astrophysics Data System (ADS)

The hyporheic zone is at the interface between groundwater and surface water systems. It is also often a geochemical and redox boundary between typically reduced groundwater and oxic surface water. It experiences dynamic physical and chemical conditions as both groundwater fluxes and surface water levels vary in time and space. This can be particularly important for processes such as biogeochemical processing of nutrients and carbon. There has recently been an increasing focus on coupling residence times of surface water in the hyporheic zone with biogeochemical reactions. While geochemical profiles can be readily measured using established geochemical sampling techniques (e.g. peepers), quantifying surface water residence times and flow paths within the hyporheic zone is more elusive. The nobel gas radon offers a method for quantification of surface water residence times in the hyporheic zone. Radon activities are typically low in surface waters due to degassing to the atmosphere and decay. However once the surface water flows into the hyporheic zone radon accumulates along the flow path due to emanation from the sediments. Using simple analytical equations the water residence time can be calculated based on the difference between measured 222Rn activities and 222Rn activities at secular equilibrium, with a maximum limit of about 20 days (depending on measurement precision). Rn is particularly suited to residence time measurements in the hyporheic zone since it does not require addition of tracers to the stream nor does it require complex simulations and assumptions (such as 1D vertical flow) as for temperature measurements. As part of the biogeochemistry course at the University of Bayreuth, we have investigated the coupling of redox processes and water residence times in the hyporheic zone using 222Rn as a tracer for residence time. Of particular interest were nitrate and sulfate reduction and methane and CO2 production. Measurements were made in a sandy section of the Mistelbach, a second order stream running through agricultural land near the city of Bayreuth. Radon was measured at 1-3 locations on two occasions and at 5 different depths (-5 to-25 cm). Geochemical parameters NO3-, NO2-, SO4-, Fe2+, CO2 and CH4 was measured in peepers with a vertical resolution of 1-2 cm to a depth of 50 cm as well as in the same samples as the Rn. Groundwater activities were measured in incubation experiments and by the deepest sampling point in the hyporheic zone. The results showed that there was a clear dependence of biogeochemical processes on the residence time. Nitrate was reduced within 2 days, while sulfate reduction began after 5 days while Fe2+ was produced after 10 days. CH4 production occurred at >20 days, which is above the upper limit of residence time detection using Rn. Obviously, biogeochemical processes are controlled by the balance between reaction rates and advection rates in the hyporheic zone, and that the ratio of these rates (i.e. the Damköhler number) will control the efficiency of material processing. The uncertainty in the method increases towards longer residence times, as secular equilibrium activities and measured activities converge. It is also influenced by the heterogeneity of emanation in the sediments. However, research within the hyporheic zone is usually focused on residence times shorter than two weeks, and emanation can be quantified in the laboratory. Thus Rn appears well suited to the study of time scales over which biogeochemical processes occur in the hyporheic zone.

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

2014-05-01

217

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

SciTech Connect

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

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

2006-06-01

218

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

SciTech Connect

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

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

2006-06-01

219

Biogeochemical Reaction Kinetics Associated With Uranium Bioremediation at Multiple Scales  

NASA Astrophysics Data System (ADS)

Effective bioremediation requires understanding and quantification of biogeochemical reaction kinetics in natural porous media. Although the intrinsic rates of biogeochemical reactions have been measured in well-mixed laboratory systems, extrapolation of those rates to natural porous media remains challenging, partly due to the fact that natural systems are rarely well-mixed. In this work, we examine the reaction kinetics of iron and sulfate reductions involved in a bioremediation field experiment at the Old Rifle UMTRA site in Western Colorado where acetate as an electron donor was injected into the subsurface to reduce mobile U(VI) to relatively immobile U(IV). We examine at multiple spatial scales how the biogeochemical reaction rates are affected by the extent of mixing and how this in turn affects the efficiency of bioremediation and the evolution of physical and chemical properties of bioremediation sites over the long term. The rates of iron and sulfate reduction were examined at the pore scale and the field scale. At the pore scale (tens to thousands of microns), numerical experiments show that transport processes are fast enough to homogenize the concentration and that the intrinsic rate measured under well-mixed conditions can be directly used. However, at the field scale (tens of meters), dispersion/diffusion processes are not fast enough to homogenize the concentration and the local reaction rates depend on local, spatially variable concentrations. As such, the overall reaction rates at the field scale depend largely on the extent of mixing, which is controlled in large part by the physical and chemical heterogeneities present in the subsurface. Focusing on dissimilatory Fe reduction and assuming the same average flow velocity and the same average total solid iron content, we compare three different cases: 1) a homogeneous permeability distribution with a homogeneous Fe distribution; 2) a heterogeneous permeability distribution, determined from the inverse modeling of field-scale tracer breakthrough data, with a homogeneous Fe distribution; and 3) the same heterogeneous permeability distribution as in the second case, but with a heterogeneous Fe distribution based on an assumed negative correlation between permeability and iron content. Reactive transport modeling results were compared to field data to determine the overall volume-averaged reaction rates. The first case represents the largest extent of mixing and therefore leads to the largest overall Fe reduction rates, while the second and third cases, respectively, represent progressively lower extents of mixing and therefore lead to slower reduction rates. Differences in the overall Fe reduction rates result in different amounts and spatial patterns of precipitated secondary minerals. In the homogeneous case, secondary minerals precipitate evenly across the transverse distance, while in the heterogeneous cases, secondary minerals precipitate primarily where the contact between the electron donor acetate and solid iron is greatest. As such, both physical and chemical heterogeneity may dramatically affect reductions in permeability over the long term.

Li, L.; Steefel, C. I.; Kowalsky, M. B.

2007-12-01

220

Mesoscale Variations of Biogeochemical Properties in the Sargasso Sea  

NASA Technical Reports Server (NTRS)

A mesoscale resolution biogeochemical survey was carried out in the vicinity of the US Joint Global Ocean Flux Study Bermuda Atlantic Time-Series Study (BATS) site during the summer of 1996. Real-time nowcasting and forecasting of the flow field facilitated adaptive sampling of several eddy features in the area. Variations in upper ocean nutrient and pigment distributions were largely controlled by vertical isopycnal displacements associated with the mesoscale field. Shoaling density surfaces tended to introduce cold, nutrient-rich water into the euphotic zone, while deepening isopycnals displaced nutrient-depleted water downward. Chlorophyll concentration was generally enhanced in the former case and reduced in the latter. Eddy-induced upwelling at the base of the euphotic zone was affected by features of two different types captured in this survey: (1) a typical mid-ocean cyclone in which doming of the main thermocline raised the near-surface stratification upward; and (2) a mode water eddy composed of a thick lens of 18 C water, which pushed up the seasonal thermocline and depressed the main thermocline. Model hindcasts using all available data provide a four-dimensional context in which to interpret temporal trends at the BATS site and two other locations during the two weeks subsequent to the survey. Observed changes in near-surface structure at the BATS site included shoaling iscpycnals, increased nutrient availability at the base of the euphotic zone, and enhanced chlorophyll concentration within the euphotic zone. These trends are explicable in terms of a newly formed cyclone that impinged upon the site during this time period. These observations reveal that eddy upwelling has a demonstrable impact on the way in which the nitrate-density relationship changes with depth from the aphotic zone into the euphotic zone. A similar transition is present in the BATS record, suggesting that eddy-driven upwelling events are present in the time series of upper ocean biogeochemical properties. The variability in main thermocline temperature and nitrate in this synoptic spatial survey spans the range observed in these quantities in the 10-year time series available at BATS to date (1988-1998).

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

1999-01-01

221

Mesoscale Variations of Biogeochemical Properties in the Sargasso Sea  

NASA Technical Reports Server (NTRS)

A mesoscale resolution biogeochemical survey was carried out in the vicinity of the U.S. Joint Global Ocean Flux Study Bermuda Atlantic Time-series Study (BATS) site during the summer of 1996. Real-time nowcasting and forecasting of the flow field facilitated adaptive sampling of several eddy features in the area. Variations in upper ocean nutrient and pigment distributions were largely controlled by vertical isopycnal displacements associated with the mesoscale field. Shoaling density surfaces tended to introduce cold, nutrient-rich water into the euphotic zone, while deepening isopycnals displaced nutrient-depleted water downward. Chlorophyll concentration was generally enhanced in the former case and reduced in the latter. Eddy-induced upwelling at the base of the euphotic zone was affected by features of two different types captured in this survey-, (1) a typical mid-ocean cyclone in which doming of the main thermocline raised the near-surface stratification upward and (2) a mode water eddy composed of a thick lens of 18C water, which pushed up the seasonal thermocline and depressed the main thermocline. Model hindcasts using all available data provide a four-dimensional context in which to interpret temporal trends at the BATS site and two other locations during the 2 weeks subsequent to the survey. Observed changes in near-surface structure at the BATS site included shoaling isopycnals, increased nutrient availability at the base of the euphotic zone, and enhanced chlorophyll concentration within the cuphotic zone. These trends are explicable in terms of a newly formed cyclone that impinged upon the site during this time period. These observations reveal that eddy upwelling has a demonstrable impact on the way in which the nitrate-density relationship changes with depth from the aphotic zone into the euphotic zone. A similar transition is present in the BATS record, suggesting that eddy-driven upwelling events are present in the time series of upper ocean biogeochemical properties. The variability in main thermocline temperature and nitrate in this synoptic spatial survey spans the range observed in these quantities in the 10-year time series available at BATS to date (1988-1998).

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

1999-01-01

222

Traceable components of terrestrial carbon storage capacity in biogeochemical models.  

PubMed

Biogeochemical models have been developed to account for more and more processes, making their complex structures difficult to be understood and evaluated. Here, we introduce a framework to decompose a complex land model into traceable components based on mutually independent properties of modeled biogeochemical processes. The framework traces modeled ecosystem carbon storage capacity (Xss ) to (i) a product of net primary productivity (NPP) and ecosystem residence time (?E ). The latter ?E can be further traced to (ii) baseline carbon residence times (?'E ), which are usually preset in a model according to vegetation characteristics and soil types, (iii) environmental scalars (?), including temperature and water scalars, and (iv) environmental forcings. We applied the framework to the Australian Community Atmosphere Biosphere Land Exchange (CABLE) model to help understand differences in modeled carbon processes among biomes and as influenced by nitrogen processes. With the climate forcings of 1990, modeled evergreen broadleaf forest had the highest NPP among the nine biomes and moderate residence times, leading to a relatively high carbon storage capacity (31.5 kg cm(-2) ). Deciduous needle leaf forest had the longest residence time (163.3 years) and low NPP, leading to moderate carbon storage (18.3 kg cm(-2) ). The longest ?E in deciduous needle leaf forest was ascribed to its longest ?'E (43.6 years) and small ? (0.14 on litter/soil carbon decay rates). Incorporation of nitrogen processes into the CABLE model decreased Xss in all biomes via reduced NPP (e.g., -12.1% in shrub land) or decreased ?E or both. The decreases in ?E resulted from nitrogen-induced changes in ?'E (e.g., -26.7% in C3 grassland) through carbon allocation among plant pools and transfers from plant to litter and soil pools. Our framework can be used to facilitate data model comparisons and model intercomparisons via tracking a few traceable components for all terrestrial carbon cycle models. Nevertheless, more research is needed to develop tools to decompose NPP and transient dynamics of the modeled carbon cycle into traceable components for structural analysis of land models. PMID:23505019

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

2013-07-01

223

Biogeochemical responses following coral mass spawning on the Great Barrier Reef: pelagic–benthic coupling  

Microsoft Academic Search

This study quantified how the pulse of organic matter from the release of coral gametes triggered a chain of pelagic and benthic\\u000a processes during an annual mass spawning event on the Australian Great Barrier Reef. Particulate organic matter (POM) concentrations\\u000a in reef waters increased by threefold to 11-fold the day after spawning and resulted in a stimulation of pelagic oxygen

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

2008-01-01

224

A coupled hydrologic and biogeochemical model for assessing watershed responses to climate and land use  

EPA Science Inventory

This seminar for Oregon State University’s Water Resources Graduate Program will describe the use of a spatially-distributed ecohydrological model, VELMA, for quantifying how alternative land use and climate scenarios affect tradeoffs among important ecosystem services. Sp...

225

Criteria to demonstrate that microbial community composition is important for biogeochemical function  

NASA Astrophysics Data System (ADS)

Will models of biogeochemical processes really be improved by considering microbial community composition? Given the importance of microbes for biogeochemical transformations, and the tremendous breadth of microbial diversity that continues to be cataloged, it is easy to assert or assume that differences in microbial community composition affect the way that ecosystems function. While reviews to date have argued whether this might be true for some processes but not others, there has not yet appeared a scientific framework describing the types of data needed to demonstrate that composition matters for function. In this talk, I present four criteria that, when met, demonstrate that improved prediction of biogeochemical transformations will come from knowledge of microbial community composition. In establishing these criteria, studies must reject a series of null hypotheses that microbial community composition does not matter. In rejecting these null hypotheses, studies will also collect information that improves our ability to predict biogeochemical processes.

von Fischer, J. C.

2009-12-01

226

Community Composition and Biogeochemical Element Cycling in Two Different Volcanic Soil Weathering Regimes  

NASA Astrophysics Data System (ADS)

Investigations of mineral weathering patterns and microbial community composition as a function of depth in two volcanic soil regimes can elucidate biogeochemical cycles useful in interpreting biosignatures in extraterrestrial systems.

Liermann, L. J.; Hausrath, E. M.; Buss, H. L.; Brantley, S. L.

2010-04-01

227

Biogeochemical conditions determine virulence of black band disease in corals  

PubMed Central

The microenvironmental dynamics of the microbial mat of black band disease (BBD) and its less virulent precursor, cyanobacterial patch (CP), were extensively profiled using microsensors under different light intensities with respect to O2, pH and H2S. BBD mats exhibited vertical stratification into an upper phototrophic and lower anoxic and sulphidic zone. At the progression front of BBD lesions, high sulphide levels up to 4977??M were measured in darkness along with lower than ambient levels of pH (7.43±0.20). At the base of the coral–BBD microbial mat, conditions were hypoxic or anoxic depending on light intensity exposure. In contrast, CP mats did not exhibit strong microchemical stratification with mostly supersaturated oxygen conditions throughout the mats at all light intensities and with levels of pH generally higher than in BBD. Two of three replicate CP mats were devoid of sulphide, while the third replicate showed only low levels of sulphide (up to 42??M) present in darkness and at intermediate light levels. The level of oxygenation and sulphide correlated well with lesion migration rates, that is virulence of the mats, which were greater in BBD than in CP. The results suggest that biogeochemical microgradients of BBD shaped by the complex microbial community, rather than a defined pathogen, are the major trigger for high virulence and the associated derived coral mortality of this disease.

Glas, Martin S; Sato, Yui; Ulstrup, Karin E; Bourne, David G

2012-01-01

228

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

PubMed

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

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

2013-09-01

229

Controls on Biogeochemical Cycling in a Turfgrass Ecosystem  

NASA Astrophysics Data System (ADS)

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

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

2006-12-01

230

Biogeochemical controls on nitrogen fixers in the global ocean  

NASA Astrophysics Data System (ADS)

We explore the biogeochemical controls on the nitrogen fixers (or diazotrophs) in a global ocean model. Diazotrophs are essential organisms in the ocean, as they provide most of the new nitrogen to the global ocean. We employ a three-dimensional global ocean model with a self-organizing phytoplanktonic community, which successfully accounts for diverse marine autotrophic diazotrophs (Trichodesmium, unicellular cyanobacteria and diatom-diazotroph associations). We examine in the model how temperature, nitrogen, iron and phosphate limitations influence the global distribution of marine diazotrophs. In the observations and model, total diazotroph population is distributed over most of the oligotrophic warm sub-and-tropical waters. We find that this global diazotroph distribution is restricted to the low fixed-nitrogen regions which have sufficient supplies in dissolved iron and phosphate. We use resource competition theory to illustrate the intertwined response of marine nutrients, dust input and ecosystem, and map out regions of iron and phosphate regulations of marine diazotroph distribution. The theory suggests that diazotroph distribution is largely regulated by iron availability, in particular in the South Atlantic, Pacific and Indian Oceans. This result demonstrates how important it is to understand the iron dust sources to the marine biological community in relation to the oceanic nitrogen cycle.

Monteiro, Fanny; Dutkiewicz, Stephanie; Follows, Michael

2010-05-01

231

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

USGS Publications Warehouse

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

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

2011-01-01

232

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

233

Biogeochemical controls on hexavalent chromium formation in estuarine sediments.  

PubMed

Predicting the aquatic and human health impacts of chromium (Cr) necessitates one to determine its speciation as either relatively nontoxic Cr(III) or toxic Cr(VI) and elucidate the influence of biogeochemical changes on its behavior and fate. In the Baltimore Harbor, Cr predominantly exists as Cr(III) associated with sediments. While reduction of Cr(VI) to Cr(III) is dominant in these anoxic sediments, the potential of Cr(III) oxidation and Cr(VI) reoccurrence during sediment resuspension and oxygenation resulting from dredging, bioturbation, and flood events poses a serious concern. In batch experiments, aqueous Cr(VI) spiked into continuously mixed anoxic suspensions was reduced to product Cr(III) under anaerobic conditions. No Cr(VI) reoccurrence was observed when conditions remained anaerobic. Aeration caused Cr(VI) reoccurrence from the abiotic oxidation of product Cr(III). Rates of aeration-driven Cr(VI) reoccurrence increased with pH, and Cr(VI) reoccurrence positively correlated with dissolved manganese (Mn) decline at pH ? 7. Aeration-driven oxidation of Mn(II) to Mn(III,IV)(hydr)oxides was the underlying mechanism causing product Cr(III) oxidation. Cr(VI) reoccurrence decreased with sediment loading and negatively correlated with the acid volatile sulfide (AVS) concentration. Although sediment resuspension and oxygenation may create temporary conditions conducive to Cr(VI) formation, long-term Cr(VI) persistence is unlikely in the presence of sediment reductants. While such natural attenuation in reducing environments mitigates the risk associated with Cr toxicity, this risk may still persist in Mn-rich and reductant-deficient environments. PMID:23802856

Wadhawan, Amar R; Stone, Alan T; Bouwer, Edward J

2013-08-01

234

Biogeochemical characteristics of nitrogen and phosphorus in Jiaozhou Bay sediments  

NASA Astrophysics Data System (ADS)

Sediment samples were cored from 3 locations representing the inner bay, the outer bay and the bay mouth of Jiaozhou Bay in September 2003 to study the source and biogeochemical characteristics of nitrogen and phosphorus in the bay. The content and vertical distributions of total nitrogen (TN), total phosphorus (TP), organic nitrogen (ON), organic phosphorus (OP), inorganic nitrogen (IN), inorganic phosphorus (IP), the ratio of organic carbon and total nitrogen (OC/TN), and the ratio of total nitrogen and total phosphorus (TN/TP) in the sediments were analyzed. The results show that both TN and TP in surface sediments decrease from the inner bay to the outer bay. In general, ON occupies 50%-70% of TN and IP accounts for more than 60% of TP. In ratio of OC:TN, the nitrogen accumulated in the sediments from the inner bay and the bay mouth came mainly from terrestrial sources, and the portion of autogenetic nitrogen was 28.9% and 13.1%, respectively. However, in the outer bay, nitrogen was mainly autogenetic, accounting for 62.1% of TN, whereas phosphorus was mainly land-derived. The sedimentation fluxes of nitrogen and phosphorus varied spatially. The overall diagenesis rate of nitrogen was higher than that of phosphorus. Specifically, the diagenesis rate of OP was higher than that of IP. However, the diagenesis rate of ON was not always higher than that of IN. In species, the diagenesis rate of IN is sometimes much higher than that of the OC. In various environments, the diagenesis rate is, to some degree, affected by OC, pH, Eh, and Es.

Li, Xuegang; Song, Jinming; Yuan, Huamao; Dai, Jicui; Li, Ning

2007-04-01

235

Quantification of Biogeochemical Mineral Dissolution Rates in the Vadose Zone  

NASA Astrophysics Data System (ADS)

Most mineral dissolution experiments are typically carried out in batch or flow-through reactors with very high ratios of solution to mineral, or continuous flow. These conditions are unlikely to support growth of most microorganisms typical of the soil environment and do not simulate realistic soil water compositions. To address these issues, we conducted mineral dissolution experiments in flow-through reactors modified to more closely reproduce conditions in the vadose zone. Within these reactors, crushed mineral samples sit on a polypropylene mesh surface. Periodically, solution is sprinkled over the sample, collecting in pore spaces between mineral grains and flushing out pore waters from the last application. In our initial experiments, apatite was dissolved in pH 5 solution containing 1 mM oxalate, with flushing events involving 7 mls of solution occurring every 8 hours. Ca and P were released from dissolving apatite in approximately equal molar amounts, with a rate of 2.0 +/- 0.15 * 10-10 mol/m2/sec for Ca, and 2.3 +/- 0.20 *10-10 mol/m2/sec for P. The measured rates are significantly slower than those measured for apatite dissolution at pH 5 in batch reactors (1.1*10-7, Valsami-Jones et al., 1998; 2*10-9 mol/m2/sec for a solution containing 1mM oxalate; Welch et al, 2002). We infer that dissolution rates are suppressed between flushing events by the presence of water films with higher saturation indices. These results provide a benchmark for comparison to measured rates of biogeochemical dissolution of apatite in the presence of cultures of Acidobacteria, a common soil microorganism.

Green, E.; Banfield, J. F.

2005-12-01

236

Biogeochemical characterisation of a coal tar distillate plume  

NASA Astrophysics Data System (ADS)

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

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

2001-12-01

237

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

NASA Astrophysics Data System (ADS)

Increased nutrient loads delivered from watersheds due to agricultural intensification, industrialization, and urbanization have contributed globally to the persistence of large hypoxic zones in inland and coastal waters. Watershed management practices targeting these non-point source pollutants often lead to little or no improvement in water quality, even after extensive implementation of conservation measures or Best Management Practices (BMPs). The lag time between implementation of a conservation measure and resultant water quality benefits has recently been recognized as an important factor in the "apparent" failure of these BMPs. When conservation measures are implemented without explicit consideration of the lag time and with expectations that they will lead to immediate benefits, the resulting failure to meet such expectations can discourage vital restoration efforts. It is therefore important to quantify the lag times associated with watershed management efforts a priori and to implement restoration strategies targeted specifically at minimizing lag times and maximizing restoration benefits. The focus of this research is to develop a framework for understanding the time lags between land-use changes and stream water quality benefits. We hypothesize that such time lags arise from nutrient legacies building over decades of fertilizer application. For nitrogen (N), one can conceptualize this as either hydrologic legacy, in the form of dissolved nitrate that is delayed due to slow groundwater transport, or as biogeochemical legacy, in the form of organic N, possibly in dissolved or readily mineralizable forms. Indeed, mass-balance studies across the Mississippi and Thames river basins indicate the possibility of missing N mass in these landscapes, with inputs being consistently greater than the outputs even when accounting for all possible pathways of nitrogen transformation. Historical soil data within the upper Mississippi River Basin (MRB) indicate that agriculture depletes organic N in surface soil, but leads to N accumulations deeper in the profile. Nitrogen accumulation estimates (approximately 2 million Mt/yr) based on the historical data are startlingly close to the deficit suggested by mass-balance studies of the MRB (3 million Mt/yr). Understanding the lag times associated with such biogeochemical legacies requires quantification of this accumulation as a function of landscape attributes, climate, and management controls, as well as the rate of mineralization of accumulated N after implementation of management practices. Understanding hydrologic legacy requires a partitioning of flow along various pathways (e.g., overland flow, tile flow, or groundwater pathways), and the distribution of travel times along the pathways. Based on this framework, we developed a coupled hydrologic and biogeochemical model to quantify these legacies and predict landscape recovery times as a function of natural and anthropogenic controls.

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

2012-12-01

238

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

SciTech Connect

High-Resolution Mineralogical Characterization and Biogeochemical Modeling of Uranium Reduction Pathways at the Oak Ridge Field-Research Center (FRC) Chen Zhu, Indiana University, David R. Veblen, Johns Hopkins University We have successfully completed a proof-of-concept, one-year grant on a three-year proposal from the former NABIR program, and here we seek additional two-year funding to complete and publish the research. Using a state-of-the-art 300-kV, atomic resolution, Field Emission Gun Transmission Electron Microscope (TEM), we have successfully identified three categories of mineral hosts for uranium in contaminated soils: (1) iron oxides; (2) mixed manganese-iron oxides; and (3) uranium phosphates. Method development using parallel electron energy loss spectroscopy (EELS) associated with the TEM shows great promise for characterizing the valence states of immobilized U during bioremediation. We have also collected 27 groundwater samples from two push-pull field biostimulation tests, which form two time series from zero to approximately 600 hours. The temporal evolution in major cations, anions, trace elements, and the stable isotopes 34S, 18O in sulfate, 15N in nitrate, and 13C in dissolved inorganic carbon (DIC) clearly show that biostimulation resulted in reduction of nitrate, Mn(IV), Fe(III), U(VI), sulfate, and Tc(VII), and these reduction reactions were intimately coupled with a complex network of inorganic reactions evident from alkalinity, pH, Na, K, Mg, and Ca concentrations. From these temporal trends, apparent zero order rates were regressed. However, our extensive suite of chemical and isotopic data sets, perhaps the first and only comprehensive data set available at the FRC, show that the derived rates from these field biostimulation experiments are composite and lump-sum rates. There were several reactions that were occurring at the same time but were masked by these pseudo-zero order rates. A reaction-path model comprising a total of nine redox couples (NO3–/NH4+, MnO2(s)/Mn2+, Fe(OH)3(s) /Fe2+, TcO4–/TcO2(s), UO22+/UO2(s), SO42–/HS–, CO2/CH4, ethanol/acetate, and H+/H2.) is used to simulate the temporal biogeochemical evolution observed in the field tests. Preliminary results show that the models based on thermodynamics and more complex rate laws can generate the apparent zero order rates when several concurrent or competing reactions occur. Professor Alex Halliday of Oxford University, UK, and his postdoctoral associates are measuring the uranium isotopes in our groundwater samples. Newly developed state-of-the-art analytical techniques in measuring variability in 235U/238U offer the potential to distinguish biotic and abiotic uranium reductive mechanisms.

Chen Zhu

2006-06-15

239

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

PubMed Central

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

Taillefert, Martial; Neuhuber, Stephanie; Bristow, Gwendolyn

2007-01-01

240

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

PubMed

Coral reefs are highly sensitive to the stress associated with greenhouse gas emissions, in particular ocean warming and acidification. While experiments show negative responses of most reef organisms to ocean warming, some autotrophs benefit from ocean acidification. Yet, we are uncertain of the response of coral reefs as systems. We begin by reviewing sources of uncertainty and complexity including the translation of physiological effects into demographic processes, indirect ecological interactions among species, the ability of coral reefs to modify their own chemistry, adaptation and trans-generational plasticity. We then incorporate these uncertainties into two simple qualitative models of a coral reef system under climate change. Some sources of uncertainty are far more problematic than others. Climate change is predicted to have an unambiguous negative effect on corals that is robust to several sources of uncertainty but sensitive to the degree of biogeochemical coupling between benthos and seawater. Macroalgal, zoanthid, and herbivorous fish populations are generally predicted to increase, but the ambiguity (confidence) of such predictions are sensitive to the source of uncertainty. For example, reversing the effect of climate-related stress on macroalgae from being positive to negative had no influence on system behaviour. By contrast, the system was highly sensitive to a change in the stress upon herbivorous fishes. Minor changes in competitive interactions had profound impacts on system behaviour, implying that the outcomes of mesocosm studies could be highly sensitive to the choice of taxa. We use our analysis to identify new hypotheses and suggest that the effects of climatic stress on coral reefs provide an exceptional opportunity to test emerging theories of ecological inheritance. PMID:24845674

Mumby, Peter J; van Woesik, Robert

2014-05-19

241

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

242

Hotspots and hot moments of aquifer river exchange and biogeochemical cyclinbg in the streambed of lowland rivers  

NASA Astrophysics Data System (ADS)

Exchange fluxes across aquifer-river interfaces can have a major impact on the biogeochemical cycling in streambed environments. This paper presents integrated experimental and model-based investigations of physical drivers and chemical controls on streambed biogeochemcial cycling at two UK lowland rivers. It combines in-stream geophysical surveys, multi-level mini-piezometer networks and active and passive heat tracing methods for identifying spatial patterns and temporal dynamics of aquifer-river exchange fluxes with multi-scale hyporheic pore-water sampling and applications of reactive "smart-tracers". Hyporheic pore water analysis from nested multi-level piezometers and passive gel probe samplers revealed significant spatial variability in streambed nitrogen cycling in dependence of redox-conditions, dissolved oxygen and bio-available organic carbon concentrations. Hot spots of increased nitrate attenuation and anaerobic respiration were associated with semi-confining streambed peat lenses. The intensity of concentration changes underneath the confining peat layers correlated with the state of anoxia in the pore water as well as the supply of organic carbon and hyporheic residence times. In contrast, at locations where flow inhibiting peat layers were absent or disrupted - fast exchange between aquifer and river caused a break-through of nitrate without significant concentration changes along the hyporheic flow path. Fibre-optic Distributed Temperature Sensing was applied for identifying groundwater - surface water exchange flow patterns in dependency of streambed structural heterogeneity and support the identification of the location and extend of flow inhibiting structures as indicators of streambed reactivity hot spots. Coupled groundwater-surface water model simulations supported the experimental results, indicating that hotspots of exchange fluxes and biogeochemical activity were predominantly controlled by the spatial heterogeneous impact of streambed conductivity patterns on groundwater up-welling while surface driven processes as advective pumping had only marginal impacts.

Krause, Stefan; Munz, Mathias; Tecklenburg, Christina; Blume, Theresa; Binley, Andrew

2013-04-01

243

Nanostructural and biogeochemical features of the crinoid stereom  

NASA Astrophysics Data System (ADS)

Representatives of all echinoderm clades (e.g., echinoids, holothuroids, ophiuroids, asteroids, and crinoids) form elaborate calcitic (polymorph of calcium carbonate) skeletons composed of numerous plates. Each plate consists of a three-dimensional meshwork of mineral trabeculae (stereom) that results from precisely orchestrated biomineralization processes. Individual skeletal plates behave as single calcite crystals as shown by X-ray diffraction and polarizing microscopy, however, their physico-chemical properties differ significantly from the properties of geologic or synthetic calcites. For example, echinoderm bio-calcite does not show cleavage planes typical of calcite but reveals conchoidal fracture surfaces that reduce the brittleness of the material. The unique properties of echinoderm bio-calcite result from intimate involvement of organic molecules in the biomineralization process and their incorporation into the crystal structure. Remnants of echinoderm skeleton are among the most frequently found fossils in the Mesozoic and Palaeozoic rocks thus, in order to use them as environmental proxies, it is necessary to understand the degree of biological ("vital effect") and inorganic control over their formation. Here, we show first nanoscale structural and biogeochemical properties of the stereom of extant and fossil crinoids. Using FESEM and AFM imaging techniques we show that the skeleton has nanocomposite structure: individual grains have ca. 100 nm in diameter and occasionally form larger aggregates. Fine scale geobiochemical mappings of crinoid plates (NanoSIMS microprobe) show that Mg is distributed heterogeneously in the stereom with higher concentration in the middle part of the trabecular bars. Although organic components constitute only ca. 0.10-0.26 wt% of modern echinoderm bio-calcite, in situ synchrotron sulphur K-edge x-ray absorption near edge structure (XANES) spectra show that the central parts of stereom bars contain higher levels of SO4 that in various carbonate biominerals are associated with sulphated polysaccharides. These data are consistent with modern models of biomineralization suggesting involvement of magnesium ions and sulphated polysaccharides in early phases of biomineral formation. Financial support: Polish Ministry of Science and Higher Education, projects N307-015733, 155/ESR/2006/03(EC-370), BW-120000-501/68-179210, and Museum National d'Histoire Naturelle and the Agence National de la Recherche.

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

2009-04-01

244

Biogeochemical features of aquatic plants in the Selenga River delta  

NASA Astrophysics Data System (ADS)

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

Shinkareva, Galina; Lychagin, Mikhail

2014-05-01

245

A marine biogeochemical perspective on black shale deposition  

NASA Astrophysics Data System (ADS)

Deposition of marine black shales has commonly been interpreted as having involved a high level of marine phytoplankton production that promoted high settling rates of organic matter through the water column and high burial fluxes on the seafloor or anoxic (sulfidic) water-column conditions that led to high levels of preservation of deposited organic matter, or a combination of the two processes. Here we review the hydrography and the budgets of trace metals and phytoplankton nutrients in two modern marine basins that have permanently anoxic bottom waters. This information is then used to hindcast the hydrography and biogeochemical conditions of deposition of a black shale of Late Jurassic age (the Kimmeridge Clay Formation, Yorkshire, England) from its trace metal and organic carbon content. Comparison of the modern and Jurassic sediment compositions reveals that the rate of photic zone primary productivity in the Kimmeridge Sea, based on the accumulation rate of the marine fraction of Ni, was as high as 840 g organic carbon m - 2 yr -1. This high level was possibly tied to the maximum rise of sea level during the Late Jurassic that flooded this and other continents sufficiently to allow major open-ocean boundary currents to penetrate into epeiric seas. Sites of intense upwelling of nutrient-enriched seawater would have been transferred from the continental margins, their present location, onto the continents. This global flooding event was likely responsible for deposition of organic matter-enriched sediments in other marine basins of this age, several of which today host major petroleum source rocks. Bottom-water redox conditions in the Kimmeridge Sea, deduced from the V:Mo ratio in the marine fraction of the Kimmeridge Clay Formation, varied from oxic to anoxic, but were predominantly suboxic, or denitrifying. A high settling flux of organic matter, a result of the high primary productivity, supported a high rate of bacterial respiration that led to the depletion of O 2 in the bottom water. A high rate of burial of labile organic matter, albeit a low percentage of primary productivity, in turn promoted anoxic conditions in the sediment pore waters that enhanced retention of trace metals deposited from the water column.

Piper, D. Z.; Calvert, S. E.

2009-06-01

246

Proterozoic to recent tectonic tuning of biogeochemical cycles  

NASA Astrophysics Data System (ADS)

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

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

247

Extracellular enzyme activity and biogeochemical cycling in restored prairies  

NASA Astrophysics Data System (ADS)

Winter microbial activity in mid-latitude prairie ecosystems is thermally sensitive and significantly influenced by snow depth. Snow insulates the soil column facilitating microbial processing of complex organic substrates. Previous studies in forests and tundra ecosystems suggest patterns of substrate utilization and limitation are seasonal; above freezing, soil microbes access fresh litter inputs and sugar exudates from plant roots, while under frozen condition they recycle nutrients incorporated in microbial biomass. In order to liberate nutrients required for carbon degradation, soil microbes invest energy in the production of extracellular enzymes that cleave monomers from polymer bonds. The inverse relationship between relative enzyme abundance and substrate availability makes enzyme assays a useful proxy to assess changes in resources over time. Our objective in this study was to assess patterns in microbial biomass, nutrient availability, and extracellular enzyme activity in four snow exclosure sites over a seven-month period. Over the past three years, we have maintained a snow removal experiment on two restored prairies in central Minnesota. In each prairie, snow was continuously removed annually from two 4 x 4 m plots by shoveling after each snow event. Extractable C, N and P, and microbial C, N and P in soil samples were measured in samples collected from these snow removal plots, as well as in adjacent unmanipulated prairie control plots. Pools of C, N, and P were estimated using standard extraction protocols, and microbial pools were estimated using chloroform fumigation direct extraction (CFDE). We conducted fluorometric extracellular enzyme assays (EEA) to assess how the degradation potential of cellulose (cellobiohydrolase, CBH), protein (leucine aminopeptidase, LAP), and phosphate esters (phosphatase, PHOS) changed seasonally. Microbial C and N declined between October and June, while microbial P declined during the fall and winter, but increased during the spring. Microbial biomass C:N ratios increased from October to March, and decreased through the summer, while production of CBH, LAP and PHOS all showed the opposite pattern, decreasing through March and increasing in the summer. Following snowmelt, enzyme production preceded a recovery in microbial biomass, possibly as a result of increased competition for available resources between plant and microbial communities, or a shift to organic sources of C, N, and P which required a higher investment in enzymes. Due to their rapid growth rates and turnover, microbes are a particularly reactive component of terrestrial ecosystems and significantly influence biogeochemical cycling. Because carbon degradation may be constrained by nutrient availability, understanding how extracellular enzyme production, decomposition rate, and nutrient flux change over time is essential if we are to anticipate ecosystem responses to environmental changes.

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

2011-12-01

248

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

NASA Astrophysics Data System (ADS)

Several countries around the world are considering deep repositories in fractured granitic formations for the final disposal of high-level radioactive waste. Evaluating the long term safety of such repositories requires sound conceptual and numerical models which are being developed from data and knowledge gained from in situ experiments carried out at deep underground laboratories such as that of Žsp” in Sweden. One of the key aspects for performance assessment concerns to groundwater redox conditions because: (a) the presence of oxygen will affect to the corrosion of canisters, (b) possible production of hydrogen sulphide from sulphate reduction will also have a negative effect on these metallic containers, and (c) several long-lived radionuclides are much more soluble and mobile under oxidizing conditions. Several projects have been performed at Žsp” to investigate different aspects of the groundwater redox evolution. The vast amount of in situ-generated information has been used in this work to set up coupled hydrobiogeochemical models. Numerical models account for saturated groundwater flow, solute transport by advection, dispersion and molecular diffusion, geochemical reactions involving both the liquid and solid phases, and microbially-catallyzed processes. For the Žsp” site, modelling results provide quantitative support for the following conclusions. (A) At the operational phase of the repository, shallow fresh groundwater could reach the depth of the underground facility. Shallow groundwaters loose dissolved oxygen during the infiltration through soil layers and then, respiration of dissolved organic matter is induced along the flow paths through the reduction of Fe(III)-bearing minerals of the fracture zones. Microbial anaerobic respiration of DOC provides additional reducing capacity at the depth of the tunnel. (B) After repository closure, atmospheric oxygen will remain trapped within the tunnel. Abiotic consumption of this oxygen has been computed to occur in a period of about 1,000 years as a result of diffusion-reaction processes. Coupled biogeochemical mechanisms, such as respiration of dissolved organic matter and aerobic methane oxidation, accelerate the oxygen uptake to less than a month.

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

2003-12-01

249

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

NASA Astrophysics Data System (ADS)

It is increasingly recognised that microbially mediated processes have a significant impact on chemical fluxes from glaciated catchments. One important reaction is the oxidation of pyrite since the production of sulphuric acid facilitates the dissolution of minerals without the need for acidity generated by dissolved atmospheric CO2. Thus weathering processes can still continue even when isolated from the atmosphere, as is thought to occur under large ice masses. However, as a glacier melts, it is expected that the microbial community will change with knock-on effects on the stream water chemistry. Understanding the difference in solute generation processes between glaciated and un-glaciated terrain is key to understanding how glacial-interglacial cycles affect atmospheric CO2 consumption by chemical weathering. In order to investigate whether biogeochemical processes differ between glaciated and un-glaciated terrain we collected stream water samples from two small catchments (each approximately 3 km2) in Svalbard. One catchment is glaciated and the other catchment is un-glaciated but is affected by permafrost and a seasonal snow-pack. The two catchments are situated next to each other with identical bedrock (shale with minor siltstone and sandstone). The proximity of the catchments to each other ensures that meteorological variables such as temperature and precipitation are very similar. Sampling was conducted early in the melt-season when there was still significant snow-cover and in mid-summer when most of the seasonal snow-pack had melted. The water samples were analysed for ?34S-SO4, ?18O-SO4, ?18O-H2O, ?13C-DIC and ?13C-DOC, together with major anions and cations. Despite the nominally identical lithology, there were significant differences in the stream water chemistry between the two catchments. For example, sulphate was the dominant anion in the un-glaciated catchment whereas bicarbonate was the dominant anion in the glaciated catchment. Pyrite oxidation under anoxic conditions and microbially mediated sulphate reduction occur in both catchments. However, in the glaciated catchment pyrite oxidation is mainly coupled to carbonate dissolution and in the un-glaciated catchment it is mainly coupled to silicate dissolution. These significant differences in weathering processes will be discussed with reference to the microbial communities found in the two catchments.

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

2014-05-01

250

An evaluation of selected ecological benefits of forest stands under acid stress based on biogeochemical processes in a catchment in Southwestern China  

NASA Astrophysics Data System (ADS)

Based on nutrient biogeochemical cycles between soil, plants and the atmosphere, four ecological functions and values of forest stands under acid stress in a small catchment in Southwestern China are evaluated in this work: nutrient retaining, carbon sequestration, erosion control and water conservation. Integrated remote sensing Landsat-5 TM spectral data and field measurements of acid deposition are applied to simulate the temporal and spatial distributions of soil acidification and nutrient cycling for a small catchment with various types of vegetations in Southwestern China, using the Model of Acidification of Groundwater in Catchments (MAGIC) coupled with a soil water balance module and a vegetation growth model. The major cations in the soil solution, the net primary productivity, the soil conservation and the rainfall intercept are considered in the evaluation of the four selected ecological benefits of forest stands in the study area. Biogeochemical processes including deposition, nitrification, weathering, mineralization, uptake, allocation and litterfall are considered in the simulation. The simulation results show that the average amounts of nutrient retaining, carbon sequestration, and soil and water conservation were 1.67 t/hm2, 2.96 t/hm2, 913 t/hm2 and 10000 t/hm2 respectively for the catchment during the period from April 2007 to April 2008. The ecological functions also vary with the vegetation types. The nutrient retaining amount is the highest in grassland and the mixed forest came next. The mixed forest has higher carbon sequestration amount than coniferous forest, shrubs and the grass. The coniferous forest and the shrubs have the highest soil conservation and water conservation amounts respectively. The forest ecological values for the selected four functions are also estimated by the prices of substitutes and found to be 20 times that of timber economic benefit. The forest ecological functions will change under different scenarios of acid deposition due to nutrient biogeochemical cycles and it is found that the mixed forest is about 10 times more resistant to increased acid stress.

Zhang, J.

2011-12-01

251

Sulfur and Methylmercury in the Florida Everglades - the Biogeochemical Connection  

NASA Astrophysics Data System (ADS)

Methylmercury (MeHg) is a serious environmental problem in aquatic ecosystems worldwide because of its toxicity and tendency to bioaccumulate. The Everglades receives some of the highest levels of atmospheric mercury deposition and has some of the highest levels of MeHg in fish in the USA, posing a threat to pisciverous wildlife and people through fish consumption. USGS studies show that a combination of biogeochemical factors make the Everglades especially susceptible to MeHg production and bioaccumulation: (1) vast wetland area with anoxic soils supporting anaerobic microbial activity, (2) high rates of atmospheric mercury deposition, (3) high levels of dissolved organic carbon (DOC) that complexes and stabilizes mercury in solution for transport to sites of methylation, and (4) high sulfate loading in surface water that drives microbial sulfate reduction and mercury methylation. The high levels of sulfate in the Everglades represent an unnatural condition. Background sulfate levels are estimated to be <1 mg/L, but about 60% of the Everglades has surface water sulfate concentrations exceeding background. Highly sulfate-enriched marshes in the northern Everglades have average sulfate levels of 60 mg/L. Sulfate loading to the Everglades is principally a result of land and water management in south Florida. The highest concentrations of sulfate, averaging 60-70 mg/L, are in canal water in the Everglades Agricultural Area (EAA). Geochemical data and a preliminary sulfur mass balance for the EAA are consistent with sulfur currently used in agriculture, and sulfur released by oxidation of organic EAA soils (including legacy agricultural applications and natural sulfur) as the primary sources of sulfate enrichment to the canals and ecosystem. Sulfate loading increases microbial sulfate reduction and MeHg production in soils. The relationship between sulfate loading and MeHg production, however, is complex. Sulfate levels up to about 20-30 mg/L increase mercury methylation, but buildup of sulfide from microbial sulfate reduction begins to inhibit mercury methylation above this range. Sulfate from the EAA canals has primarily impacted the northern Everglades nearest the EAA, but recent evidence shows sulfate loading extending about 80 km further south into Everglades National Park. Current restoration plans to restore to deliver more water south to Everglades National Park may increase overall sulfur loads to the southern part of the ecosystem. A comprehensive Everglades restoration strategy should include reduction of sulfur loads as a goal because of the many detrimental impacts of sulfate on the ecosystem. Monitoring data show that the ecosystem response to changes in sulfate levels is rapid, and strategies for reducing sulfate loading may be effective in the near-term. A multifaceted approach employing best management practices for sulfur in agriculture, agricultural practices that minimize soil oxidation, and changes to stormwater treatment areas that increase sulfate retention, could help reduce sulfate loads to the Everglades, with resulting benefits.

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

2011-12-01

252

Biogeochemical dynamics of pollutants in Insitu groundwater remediation systems  

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

253

The evolution of saline lake waters: gradual and rapid biogeochemical pathways in the Basotu Lake District, Tanzania  

Microsoft Academic Search

The biogeochemical evolution of solutes markedly alters the chemistry in the closed-basin maar lakes that comprise the Basotu Lake District (Tanzania, East Africa). Examination of 11 (out of 13) lakes in the Basotu Lake District identified two distinct evolutionary pathways: a gradual path and a rapid path. During the course of biogeochemical evolution these waters follow either the gradual path

Peter Kilham; Paul L. Cloke

1990-01-01

254

Biogeochemical interactions between iron and sulphate in freshwater wetlands and their implications for interspecific competition between aquatic macrophytes  

Microsoft Academic Search

SUMMARY 1. Wetlands are threatened by desiccation, eutrophication and changing water quality, generally leading to greatly altered biogeochemical processes. Sulphate pollution can lead to severe eutrophication and sulphide toxicity, but may also interact with the availability of iron and other metals. 2. In the present study, we examined the biogeochemical interactions between sulphate and iron availability, and their effects on

MARLIES E. W. V AN; W ELLE; J. P. S MOLDERS; HUUB J. M. O P D EN C AMP

2007-01-01

255

Modeling the physical and biogeochemical response of a marine shelf system to a tropical cyclone  

Microsoft Academic Search

We describe the first use of a fully integrated biogeochemical model to explore the response of a marine shelf system to a tropical cyclone. Ocean currents, nutrients, sediments and plankton dynamics were simulated under conditions representative of Tropical Cyclone Bobby, which traversed the Australian North West Shelf in February 1995. Results show strong upwelling of nutrients and a phytoplankton bloom.

S. A. Condie; M. Herzfeld; N. Margvelashvili; J. R. Andrewartha

2009-01-01

256

Biogeochemical characteristics of dissolved and particulate organic matter in Russian rivers entering the Arctic Ocean  

Microsoft Academic Search

The biogeochemical signature of riverine matter in the Russian Arctic was investigated to establish a background for tracing terrestrial organic material in the Arctic Ocean. Elemental and lignin compositions of particulate and dissolved organic matter (POM, DOM), stable carbon isotope ratios of POM and nutrient concentrations are reported for 12 Russian rivers along 4000 km of coastline. The 12 rivers

Jörg M Lobbes; Hans Peter Fitznar; Gerhard Kattner

2000-01-01

257

Biogeochemical Functioning of The Seine River and Its Sensitivity To Climate Change  

Microsoft Academic Search

A model was developed to study the influence of climate on riverine hydrology and ecology, which both control nutrient load and water quality. It includes a biogeochem- ical model, describing the transformations and fluxes of C, N, P and Si between the main microbiological populations, the water column and the sediment. Recognizing the continuity of the river system, it uses

A. Ducharne; G. Billen; J. Garnier; D. Brunstein

2002-01-01

258

Organic Carbon Degradation in Anoxic Organic-Rich Shelf Sediments: Biogeochemical Rates and Microbial Abundance  

Microsoft Academic Search

Identifying and explaining bottlenecks in organic carbon mineralization and the persistence of organic matter in marine sediments remain challenging. This study aims to illuminate the process of carbon flow between microorganisms involved in the sedimentary microbial food chain in anoxic, organic-rich sediments of the central Namibian upwelling system, using biogeochemical rate measurements and abundances of Bacteroidetes, Gammaproteobacteria, and sulfate-reducing bacteria

Elsabé M. Julies; Bernhard M. Fuchs; Carol Arnosti; Volker Brüchert

2010-01-01

259

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

EPA Science Inventory

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

260

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

USGS Publications Warehouse

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

Campbell, W. L.

1986-01-01

261

Let the data propose the model: Biogeochemical and hydrological processes at Plynlimon  

Microsoft Academic Search

Biogeochemical and hydrological processes are often intimately intertwined, especially in shallow soil catchments. As a consequence, a sound understanding of the former is not possible without consideration of the latter. Inversely hydrochemical data can reveal substantial information about hydrological processes. At Plynlimon, Wales, stream water and groundwater have been monitored since 1984 with many replicates. A tremendous amount of literature

F. Köck; G. Lischeid; C. Neal; M. Neal

2009-01-01

262

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

263

Biogeochemical responses of two forest streams to a 2-month calcium addition  

Microsoft Academic Search

SUMMARY 1. Calcium (Ca) has been lost from forest soils at the Hubbard Brook Experimental Forest (HBEF) because of decreased atmospheric input of Ca and high input of acid anions. Through time, this Ca loss has led to low streamwater Ca concentration and this change may affect stream ecosystem processes. 2. To test both the biogeochemical response of streams to

K ATE H. M ACNEALE; EMILY S. B ERNHARDT; MIANDRA F IELD

2001-01-01

264

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

EPA Science Inventory

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

265

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

266

Biogeochemical modelling in the Bay of Seine (France): an improvement by introducing phosphorus in nutrient cycles  

Microsoft Academic Search

As part of the French National Programme for Coastal Oceanography, this paper focuses on improvement of biogeochemical modelling in the Bay of Seine (Eastern Channel), by introducing phosphorus in nutrient cycles. The Bay of Seine receives the Seine river, which exhibits very high nutrient concentrations, and this coastal zone constitutes a typical case of eutrophication in a river plume area.

Jean-François Guillaud; Françoise Andrieux; Alain Menesguen

2000-01-01

267

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

NASA Astrophysics Data System (ADS)

An outstanding question for snowmelt-dominated watersheds of the western US are the responses of biogeochemical processes to two major drivers of environmental change: directional changes in climate and increasing dissolved inorganic nitrogen (DIN) deposition in wetfall. In the Colorado Front Range, atmospheric deposition of DIN has increased several-fold in the last 25 years. In response, nitrate concentrations at the alpine Green Lakes 4 (GL4) catchment have increased from 1985 to 2009 by 0.27 ?eq L-1 yr-1. In contrast, we see no directional change in either nitrate concentrations or fluxes in the subalpine Como Creek catchment. We hypothesize that differences in surface/groundwater interactions result in the differing behavior of stream nitrate between the alpine and subalpine catchments that are receiving similar amounts of DIN from atmospheric deposition. For both basins we sampled precipitation, snowpack, snowmelt, surface water, and subsurface waters. All water samples are analyzed for geochemical, nutrient and isotopic (?18O, ?D) composition. Stream chemistry data from the last ten years at Como Creek show increases in nitrate concentration during baseflow conditions and then a sharp decline during snowmelt. In contrast, in the alpine basin there is sharp increase in surface water nitrate during snowmelt. Hydrograph separation at the alpine GL4 using end member mixing analysis (EMMA) shows that stream flow is a mixture of three components, groundwater, talus, and new snowmelt that each contribute to roughly a third of discharge, with talus flow supplying the majority of nitrate. In contrast, and somewhat surprisingly, EMMA shows that for the subalpine Como Creek basin, annual streamflow is a mixture of only two components, groundwater and new snowmelt. During snowmelt the groundwater and snow contributions are nearly equal and subsurface flows dominate the remainder of the year. Newly installed piezometers at Como Creek provide evidence that the basin is largely a losing reach during snowmelt, with water levels in the piezometers increasing 5-7 m. After peak snowmelt however, Como Creek becomes a gaining stream, with piezometer levels dropping. Thus, both EMMA and piezometers show that surface-groundwater interactions are tightly coupled during snowmelt, with snowmelt at Como first replenishing the subsurface water deficit and increasing groundwater levels before contributing to discharge. Thus, in contrast to the alpine GL4 basin, DIN released in snowmelt is assimilated belowground as snowmelt infiltrates the subsurface in the subalpine basin. Interestingly, at the subalpine Como Creek basin, isotopic and geochemical solute concentrations undergo shifts during periods of winter baseflow prior to snowmelt. In winter much of the stream is frozen and we hypothesize that cryo-concentration of solutes and fractionation of isotopes may influence the concentrations of winter stream samples.

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

2011-12-01

268

Hybrid Multiscale Simulation of Mixing-Controlled Biogeochemical Reactions  

NASA Astrophysics Data System (ADS)

Most in situ remediation methods rely strongly on mixing of contaminants and other chemical species to promote targeted reactions that degrade or immobilize contaminants. It is now well known that the conventional approach to Darcy-scale solute transport simulation tends to overestimate in situ reaction rates because the dispersion process conceptualization combines advective spreading (due to heterogeneity) and diffusive mixing in a single lumped representation. Hybrid multiscale simulation methods, which combine microscale (pore-scale) and macroscale (Darcy-scale) simulations within a single unified framework, offers the potential to address this problem by explicitly resolving local diffusive mixing as impacted by large-scale advective spreading in a computationally tractable manner. In this talk we present methods and results of a multiscale hybrid simulation approach applied to a mixing-controlled reaction at the laboratory scale. Our approach couples a Smoothed Particle Hydrodynamics (SPH) pore-scale simulator with the STOMP Darcy-scale simulator using a custom workflow management system that adaptively selects SPH sub-domains and provides the coupling between SPH and STOMP simulations seamlessly on a scalable parallel computational platform.

Scheibe, T. D.; Schuchardt, K.; Agarwal, K.; Chase, J.; Palmer, B. J.; Tartakovsky, A. M.; Elsethagen, T.; Redden, G. D.

2012-12-01

269

Fundamental influence of carbon-nitrogen cycle coupling on climate-carbon cycle feedbacks  

Microsoft Academic Search

A long history of ecological and biogeochemical research demonstrates the critical role of nutrients in general, and nitrogen in particular, in the dynamics of the terrestrial carbon cycle. The current generation of global coupled climate-carbon cycle models has not included an explicit (prognostic) representation of the nitrogen cycle over land. Recent development of the NCAR Community Climate System Model (CCSM)

P. Thornton; K. Lindsay; S. Doney; J. K. Moore; N. Mahowald

2007-01-01

270

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

NASA Astrophysics Data System (ADS)

Microorganisms and the processes they mediate serve as the metabolic foundation of cold seeps. We characterized a suite of biogeochemical constituents and quantified rates of two key microbial processes, Sulfate Reduction (SR) and Anaerobic Oxidation of Methane (AOM), to assess variability between habitats at water depths exceeding 1000 m in the northern Gulf of Mexico. Rates of SR were highest in sediments beneath microbial mats, lower in brine-influenced and oil-influenced sediments, and lowest in animal habitats. Sediments collected near tubeworms had the highest SR rates for animal habitats. Rates of AOM generally were low, but higher rates were associated with brine-influenced, oil-influenced, tubeworm- and urchin-inhabited sediments. Rates of both SR and AOM were orders of magnitude lower at deep-slope sites compared to upper-slope sites examined previously. As observed at upper-slope sites, SR and AOM rates were often loosely coupled. At one site, AOM rates exceeded SR rates, suggesting that an alternate electron acceptor for AOM is possible. Extremely depleted ?13C values in methane illustrated the broad significance of biogenic methane production at deep-slope sites. Brine-influenced habitats were characterized by extremely high concentrations of ammonium and dissolved organic carbon, serving as important focused sources of these chemicals to adjacent environments.

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

2010-11-01

271

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

SciTech Connect

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

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

2008-11-01

272

Long-term simulation of main biogeochemical events in a coastal lagoon: Sacca Di Goro (Northern Adriatic Coast, Italy)  

NASA Astrophysics Data System (ADS)

A biogeochemical model for the Sacca di Goro Lagoon has been developed and partially validated with field data from 1989 to 1998. The model considers the nutrient cycles in the water column as well as in the sediments. Furthermore, phytoplankton, zooplankton, and Ulva sp. dynamics, as well as shellfish farming, are taken into account. Due to the recent anoxic crises in the lagoon, the dynamic of oxygen has also been simulated. The actual version of the model is a 0D with input fluxes from the watershed and exchange with the Northern Adriatic Sea. Nutrients from the watershed, wet and dry deposition, temperature, light intensity, wind speed and shellfish production are considered as forcing functions. The results show that the model is able to capture the essential dynamics of the lagoon, with values in the same order of magnitude with the measurements from experimental campaigns. The coupling with a 3D hydrodynamical model of the Sacca di Goro, as well as with the watershed model is presently under development.

Zaldívar, J. M.; Cattaneo, E.; Plus, M.; Murray, C. N.; Giordani, G.; Viaroli, P.

2003-11-01

273

Modeling soil moisture and oxygen effects on soil biogeochemical cycles including dissimilatory nitrate reduction to ammonium (DNRA)  

NASA Astrophysics Data System (ADS)

The emission of greenhouse gasses (GHG) from soils is controlled by biogeochemical reactions and the physical constraints on gas diffusion to the soil surface. Here we present and discuss a mathematical model that couples oxygen and soil water dynamics to biochemical reactions and gas transport to explore the major drivers of trace gas emission at daily time scale in unsaturated soils. The model accounts for trace gas emissions (CO2, and N2O from nitrification and denitrification), as well as for the competition for nitrate by denitrification and dissimilatory reduction of nitrate to ammonium (DNRA). Our results indicate that explicit modeling of oxygen dynamics is important when re-aeration is limited, such as under wet conditions, in particular for fine-textured soils. The balance of labile substrate, oxygen, and water availabilities explain the observed peaks in GHG emissions at moisture values around the soil field capacity. The timing of these peaks during a dry-down is delayed in fine-textured soils, due to the slower drying and limited gas exchange rates. In addition, N2O emissions may be limited by DNRA at high soil moisture.

Rubol, Simonetta; Manzoni, Stefano; Bellin, Alberto; Porporato, Amilcare

2013-12-01

274

Hybrid Numerical Methods for Multiscale Simulations of Subsurface Biogeochemical Processes  

SciTech Connect

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

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

2007-08-01

275

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

USGS Publications Warehouse

Contaminant attenuation processes in the vadose zone of a crude oil spill site near Bemidji, MN have been simulated with a reactive transport model that includes multicomponent gas transport, solute transport, and the most relevant biogeochemical reactions. Dissolution and volatilization of oil components, their aerobic and anaerobic degradation coupled with sequential electron acceptor consumption, ingress of atmospheric O2, and the release of CH4 and CO2 from the smear zone generated by the floating oil were considered. The focus of the simulations was to assess the dynamics between biodegradation and gas transport processes in the vadose zone, to evaluate the rates and contributions of different electron accepting processes towards vadose zone natural attenuation, and to provide an estimate of the historical mass loss. Concentration distributions of reactive (O2, CH4, and CO2) and non-reactive (Ar and N2) gases served as key constraints for the model calibration. Simulation results confirm that as of 2007, the main degradation pathway can be attributed to methanogenic degradation of organic compounds in the smear zone and the vadose zone resulting in a contaminant plume dominated by high CH4 concentrations. In accordance with field observations, zones of volatilization and CH4 generation are correlated to slightly elevated total gas pressures and low partial pressures of N2 and Ar, while zones of aerobic CH4 oxidation are characterized by slightly reduced gas pressures and elevated concentrations of N2 and Ar. Diffusion is the most significant transport mechanism for gases in the vadose zone; however, the simulations also indicate that, despite very small pressure gradients, advection contributes up to 15% towards the net flux of CH4, and to a more limited extent to O2 ingress. Model calibration strongly suggests that transfer of biogenically generated gases from the smear zone provides a major control on vadose zone gas distributions and vadose zone carbon balance. Overall, the model was successful in capturing the complex interactions between biogeochemical reactions and multicomponent gas transport processes. However, despite employing a process-based modeling approach, honoring observed parameter ranges, and generally obtaining good agreement between field observations and model simulations, accurate quantification of natural attenuation rates remains difficult. The modeling results are affected by uncertainties regarding gas phase saturations, tortuosities, and the magnitude of CH4 and CO2 flux from the smear zone. These findings highlight the need to better delineate gas fluxes at the model boundaries, which will help constrain contaminant degradation rates, and ultimately source zone longevity. ?? 2009 Elsevier B.V.

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

2010-01-01

276

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

NASA Astrophysics Data System (ADS)

Contaminant attenuation processes in the vadose zone of a crude oil spill site near Bemidji, MN have been simulated with a reactive transport model that includes multicomponent gas transport, solute transport, and the most relevant biogeochemical reactions. Dissolution and volatilization of oil components, their aerobic and anaerobic degradation coupled with sequential electron acceptor consumption, ingress of atmospheric O 2, and the release of CH 4 and CO 2 from the smear zone generated by the floating oil were considered. The focus of the simulations was to assess the dynamics between biodegradation and gas transport processes in the vadose zone, to evaluate the rates and contributions of different electron accepting processes towards vadose zone natural attenuation, and to provide an estimate of the historical mass loss. Concentration distributions of reactive (O 2, CH 4, and CO 2) and non-reactive (Ar and N 2) gases served as key constraints for the model calibration. Simulation results confirm that as of 2007, the main degradation pathway can be attributed to methanogenic degradation of organic compounds in the smear zone and the vadose zone resulting in a contaminant plume dominated by high CH 4 concentrations. In accordance with field observations, zones of volatilization and CH 4 generation are correlated to slightly elevated total gas pressures and low partial pressures of N 2 and Ar, while zones of aerobic CH 4 oxidation are characterized by slightly reduced gas pressures and elevated concentrations of N 2 and Ar. Diffusion is the most significant transport mechanism for gases in the vadose zone; however, the simulations also indicate that, despite very small pressure gradients, advection contributes up to 15% towards the net flux of CH 4, and to a more limited extent to O 2 ingress. Model calibration strongly suggests that transfer of biogenically generated gases from the smear zone provides a major control on vadose zone gas distributions and vadose zone carbon balance. Overall, the model was successful in capturing the complex interactions between biogeochemical reactions and multicomponent gas transport processes. However, despite employing a process-based modeling approach, honoring observed parameter ranges, and generally obtaining good agreement between field observations and model simulations, accurate quantification of natural attenuation rates remains difficult. The modeling results are affected by uncertainties regarding gas phase saturations, tortuosities, and the magnitude of CH 4 and CO 2 flux from the smear zone. These findings highlight the need to better delineate gas fluxes at the model boundaries, which will help constrain contaminant degradation rates, and ultimately source zone longevity.

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

2010-03-01

277

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

PubMed

Contaminant attenuation processes in the vadose zone of a crude oil spill site near Bemidji, MN have been simulated with a reactive transport model that includes multicomponent gas transport, solute transport, and the most relevant biogeochemical reactions. Dissolution and volatilization of oil components, their aerobic and anaerobic degradation coupled with sequential electron acceptor consumption, ingress of atmospheric O(2), and the release of CH(4) and CO(2) from the smear zone generated by the floating oil were considered. The focus of the simulations was to assess the dynamics between biodegradation and gas transport processes in the vadose zone, to evaluate the rates and contributions of different electron accepting processes towards vadose zone natural attenuation, and to provide an estimate of the historical mass loss. Concentration distributions of reactive (O(2), CH(4), and CO(2)) and non-reactive (Ar and N(2)) gases served as key constraints for the model calibration. Simulation results confirm that as of 2007, the main degradation pathway can be attributed to methanogenic degradation of organic compounds in the smear zone and the vadose zone resulting in a contaminant plume dominated by high CH(4) concentrations. In accordance with field observations, zones of volatilization and CH(4) generation are correlated to slightly elevated total gas pressures and low partial pressures of N(2) and Ar, while zones of aerobic CH(4) oxidation are characterized by slightly reduced gas pressures and elevated concentrations of N(2) and Ar. Diffusion is the most significant transport mechanism for gases in the vadose zone; however, the simulations also indicate that, despite very small pressure gradients, advection contributes up to 15% towards the net flux of CH(4), and to a more limited extent to O(2) ingress. Model calibration strongly suggests that transfer of biogenically generated gases from the smear zone provides a major control on vadose zone gas distributions and vadose zone carbon balance. Overall, the model was successful in capturing the complex interactions between biogeochemical reactions and multicomponent gas transport processes. However, despite employing a process-based modeling approach, honoring observed parameter ranges, and generally obtaining good agreement between field observations and model simulations, accurate quantification of natural attenuation rates remains difficult. The modeling results are affected by uncertainties regarding gas phase saturations, tortuosities, and the magnitude of CH(4) and CO(2) flux from the smear zone. These findings highlight the need to better delineate gas fluxes at the model boundaries, which will help constrain contaminant degradation rates, and ultimately source zone longevity. PMID:19853961

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

2010-03-01

278

Investigation of CO2 induced biogeochemical reactions and active microorganisms of two German gas fields  

NASA Astrophysics Data System (ADS)

The BMBF-Geotechnologien project "RECOBIO 2" continues the investigation of the long-term biogeochemical transformation of stored CO2. In addition to the Upper Carboniferous gas reservoir Schneeren (Westphalian C) the almost depleted Altmark gas field (Permian - Upper Rotliegend) is also investigated. Both sandstone reservoirs belong to the North German Basin and are operated by the GDF SUEZ E&P Germany (GDF SUEZ). The reservoirs differ in depth, initial and current fluid pressure as well as reservoir temperature, which is a biogeochemical important parameter. While the uplifted horst structure of Schneeren (approx. depth 2700 m) has a temperature level of 80 - 90 °C, the Altmark gas field (approx. depth 3300 m) shows temperatures around 120 °C. The Altmark site is known to be favourable for underground CO2-storage by enhanced gas recovery (EGR). This EGR process is operated by GDF SUEZ at the small and hydraulic isolated reservoir block "Altensalzwedel". This pilot test is accompanied by the scientific large-scale project CLEAN. In addition the RECOBIO2 project characterises the biogeochemical situation of the both large reservoir blocks of the Altmark gas field - „Salzwedel/ Peckensen" and „Heidberg/ Mellin". The produced formation waters of these reservoir blocks were sampled on different wellheads. The redox potentials are partly very low (Eh up to -300 mV) with slightly acidic pH-values (5,5 to 6). The high saline and (nearly) sulphate free formation waters of Na/Ca-Cl type have very high loads of Zn, Pb, Hg and As. In combination to the analysed DOC levels the talk discusses the importance of metal organic complexes. Also results of fluid geochemical calculations will be presented. Furthermore the diversity of bacteria and archaea of the formation waters as well as the potentials of CH4-, CO2-formation and sulphate reduction will be shown. Therefore the cultivation experiments were carried out with different substrates (H2/CO2, acetate, methanol). It can be summarised, that mainly the differences between wells treated with chemical foams (to enhance the gas lift) and such without this treatment have to take into account. The autoclave experiments for the Schneeren site show the importance of biogeochemical reactions for the long-term pressure behaviour of the storage unit. During autotrophic (CO2 consuming) metabolic activities a CO2 turnover into the liquid and solid phase takes place (DOC increase, carbonate phase formation). Without the knowledge of these biogeochemical induced processes the accompanied decreasing pressure can be interpreted wrongly as a leaky storage unit. That's why a well-founded biogeochemical process understanding is important.

Hoth, N.; Kassahun, A.; Seifert, J.; Krüger, M.; Bretschneider, H.; Gniese, C.; Frerichs, J.; Simon, A.; Simon, E.; Muschalle, T.

2009-04-01

279

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

NASA Astrophysics Data System (ADS)

The mixing of groundwater (GW) and surface water (SW) can have substantial impact on the transformation of solutes transported between aquifer and river. The assessment of biogeochemical cycling at reactivity hotspots as the aquifer-river interface and its implications for GW and SW quality require detailed understanding of the complex patterns of GW-SW exchange fluxes and residence time distributions in particular under changing climatic and landuse conditions. This study presents combined experimental and model-based investigations of the physical drivers and chemical controls of nutrient transport and transformation at the aquifer-river interfaces of two upland and lowland UK rivers. It combines the application of in-stream geophysical exploration techniques, multi-level mini-piezometer networks, active and passive heat tracing methods (including fibre-optic distributed temperature sensing - FO-DTS) for identifying hyporheic exchange fluxes and residence time distributions with multi-scale approaches of hyporheic pore-water sampling and reactive tracers for analysing the patterns of streambed redox conditions and chemical transformation rates. The analysis of hyporheic pore water from nested multi-level mini piezometers and passive gel probe samplers revealed significant spatial variability in streambed redox conditions and concentration changes of nitrogen species, dissolved oxygen and bio-available organic carbon. Hot spots of increased nitrate attenuation were identified beneath semi-confining peat lenses in the streambed of the investigated lowland river. The intensity of concentration changes underneath the confining peat pockets correlated with the state of anoxia in the pore water as well as the supply of organic carbon and hyporheic residence times. In contrast, at locations where flow inhibiting peat layers were absent or disrupted - fast exchange between aquifer and river caused a break-through of nitrate without significant concentration changes along the hyporheic flow path. Fibre-optic distributed temperature sensor networks and streambed electric resistivity tomography were applied for identifying exchange flow patterns between groundwater and surface water in dependency of streambed structural heterogeneity and for delineating the location and extend of flow inhibiting structures as indicators of streambed reactivity hot spots. Results of these surveys indicate that during summer, patterns of cold spots in the investigated streambed sediments can be attributed to fast groundwater up-welling in sandy and gravely sediments resulting in low hyporheic residence times. Contrasting conditions were found at warmer areas at the streambed surface where groundwater - surface water exchange was inhibited by the existence of peat or clay lenses within the streambed. Model simulations of coupled groundwater and surface water flow indicated that ignoring the increased reactivity in hyporheic streambed hotspots would lead to substantial under- or over-prediction of nitrate fluxes between aquifer and stream with potentially critical implications for river management and restoration. The investigations supported the development of a conceptual model of aquifer-river exchange and hyporheic reactivity in lowland rivers including temperature traceable hyporheic exchange fluxes at multiple scales and highlighted the necessity to adequately reflect hyporheic hotspot reactivity in coupled groundwater-surface water models for adequate water quality predictions.

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

2012-04-01

280

A multi-decadal hindcast of a physical-biogeochemical model and derived oceanographic indices in the Bay of Biscay  

NASA Astrophysics Data System (ADS)

Multiple year oceanographic simulations (hindcast) are identified as a priority oceanography product for fisheries and environment studies since they provide a unique continuous long-term dataset allowing integrated assessment of the ocean state and evolution. We performed a 37 year (1972-2008) hindcast run with a coupled physical-biogeochemical model in the Bay of Biscay. The coupled model and the hindcast configuration are described. A model skill assessment is performed with a large set of in-situ data. Average seasonal currents show major circulation patterns over the shelf. Among tracers, temperature and salinity have the best agreement, ahead of nitrates and silicates, chlorophyll, and finally phosphates and ammonium. For chlorophyll, improved pattern statistics are found when compared to monthly composites of satellite-derived chlorophyll data. From the hindcast, we derived indices related to mesoscale activity (eddies, plumes, fronts, stratification) and production (chlorophyll and primary production). They help characterise the evolution of the environment in a functional way, on both the seasonal and multi-decadal scales. From these indices, first, a multivariate analysis reveals an increasing number of years that deviate from the mean seasonal pattern. Second, we propose interpretations of the simulated increasing trends detected in several of them (temperature, thermocline depth and primary production). We also recommend further developments to confirm these simulated evolutions, from addition of open boundary forcing with a global circulation model, to the improvement of the dynamics of nutrient regeneration and of the seasonal variability of secondary production. As a perspective, we review the different applications made from our hindcast in relation to anchovy life cycle, a species of major interest in the Bay of Biscay.

Huret, Martin; Sourisseau, Marc; Petitgas, Pierre; Struski, Caroline; Léger, Fabien; Lazure, Pascal

2013-01-01

281

Novel Tracer Method To Measure Isotopic Labeled Gas-Phase Nitrous Acid (HO(15)NO) in Biogeochemical Studies.  

PubMed

Gaseous nitrous acid (HONO), the protonated form of nitrite, contributes up to ?60% to the primary formation of hydroxyl radical (OH), which is a key oxidant in the degradation of most air pollutants. Field measurements and modeling studies indicate a large unknown source of HONO during daytime. Here, we developed a new tracer method based on gas-phase stripping-derivatization coupled to liquid chromatography-mass spectrometry (LC-MS) to measure the (15)N relative exceedance, ?((15)N), of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye, purified by solid phase extraction (SPE), and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). In the optimal working range of ?((15)N) = 0.2-0.5, the relative standard deviation of ?((15)N) is <4%. The optimum pH and solvents for extraction by SPE and potential interferences are discussed. The method was applied to measure HO(15)NO emissions from soil in a dynamic chamber with and without spiking (15)N labeled urea. The identification of HO(15)NO from soil with (15)N urea addition confirmed biogenic emissions of HONO from soil. The method enables a new approach of studying the formation pathways of HONO and its role for atmospheric chemistry (e.g., ozone formation) and environmental tracer studies on the formation and conversion of gaseous HONO or aqueous NO2(-) as part of the biogeochemical nitrogen cycle, e.g., in the investigation of fertilization effects on soil HONO emissions and microbiological conversion of NO2(-) in the hydrosphere. PMID:24954648

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

2014-07-15

282

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

USGS Publications Warehouse

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

Callender, E.; Granina, L.

1997-01-01

283

The biogeochemical cycling of elemental mercury: Anthropogenic influences  

NASA Astrophysics Data System (ADS)

A review of the available information on global Hg cycling shows that the atmosphere and surface ocean are in rapid equilibrium; the evasion of Hg 0 from the oceans is balanced by the total oceanic deposition of Hg(II) from the atmosphere. The mechanisms whereby reactive Hg species are reduced to volatile Hg 0 in the oceans are poorly known, but reduction appears to be chiefly biological. The rapid equilibrium of the surface oceans and the atmosphere, coupled with the small Hg sedimentation in the oceans makes deposition on land the dominant sink for atmospheric Hg. About half of the anthropogenic emissions appear to enter the global atmospheric cycle while the other half is deposited locally, presumably due to the presence of reactive Hg in flue gases. We estimate that over the last century anthropogenic emissions have tripled the concentrations of Hg in the atmosphere and in the surface ocean. Thus, two-thirds of the present Hg fluxes (such are deposition on land and on the ocean) are directly or indirectly of anthropogenic origin. Elimination of the anthropogenic load in the ocean and atmosphere would take fifteen to twenty years after termination of all anthropogenic emissions.

Mason, R. P.; Fitzgerald, W. F.; Morel, F. M. M.

1994-08-01

284

Oceanic mesoscale turbulence drives large biogeochemical interannual variability at middle and high latitudes  

NASA Astrophysics Data System (ADS)

Observed phytoplankton interannual variability has been commonly related to atmospheric variables and climate indices. Here we showed that such relation is highly hampered by internal variability associated with oceanic mesoscale turbulence at middle and high latitudes. We used a 1/54° idealized biogeochemical model with a seasonally repeating atmospheric forcing such that there was no external source of interannual variability. At the scale of moorings, our experiment suggested that internal variability was responsible for interannual fluctuations of the subpolar phytoplankton bloom reaching 80% in amplitude and 2 weeks in timing. Over broader scales, the largest impact occurred in the subtropics with interannual variations of 20% in new production. The full strength of this variability could not be captured with the same model run at coarser resolution, suggesting that submesoscale resolving models are needed to fully disentangle the major drivers of biogeochemical variability at interannual time scales.

Lévy, Marina; Resplandy, Laure; Lengaigne, Matthieu

2014-04-01

285

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

USGS Publications Warehouse

A stormwater infiltration basin in north–central Florida, USA, was monitored from 2007 through 2008 to identify subsurface biogeochemical processes, with emphasis on N cycling, under the highly variable hydrologic conditions common in humid, subtropical climates. Cyclic variations in biogeochemical processes generally coincided with wet and dry hydrologic conditions. Oxidizing conditions in the subsurface persisted for about one month or less at the beginning of wet periods with dissolved O2 and NO3- showing similar temporal patterns. Reducing conditions in the subsurface evolved during prolonged flooding of the basin. At about the same time O2 and NO3- reduction concluded, Mn, Fe and SO42- reduction began, with the onset of methanogenesis one month later. Reducing conditions persisted up to six months, continuing into subsequent dry periods until the next major oxidizing infiltration event. Evidence of denitrification in shallow groundwater at the site is supported by median NO3-–N less than 0.016 mg L-1, excess N2 up to 3 mg L-1 progressively enriched in ?15N during prolonged basin flooding, and isotopically heavy ?15N and ?18O of NO3- (up to 25‰ and 15‰, respectively). Isotopic enrichment of newly infiltrated stormwater suggests denitrification was partially completed within two days. Soil and water chemistry data suggest that a biogeochemically active zone exists in the upper 1.4 m of soil, where organic carbon was the likely electron donor supplied by organic matter in soil solids or dissolved in infiltrating stormwater. The cyclic nature of reducing conditions effectively controlled the N cycle, switching N fate beneath the basin from NO3- leaching to reduction in the shallow saturated zone. Results can inform design of functionalized soil amendments that could replace the native soil in a stormwater infiltration basin and mitigate potential NO3- leaching to groundwater by replicating the biogeochemical conditions under the observed basin.

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

2012-01-01

286

Biogeochemical Reduction Processes in a HyperAlkaline Leachate Affected Soil Profile  

Microsoft Academic Search

Hyperalkaline surface environments can occur naturally or because of contamination by hydroxide-rich wastes. The high pH produced in these areas has the potential to lead to highly specialized microbial communities and unusual biogeochemical processes. This article reports an investigation into the geochemical processes that are occurring in a buried, saturated, organic-rich soil layer at pH 12.3. The soil has been

Ian T. Burke; Robert J. G. Mortimer; Shanmugam Palaniyandi; Robert A. Whittleston; Cindy L. Lockwood; David J. Ashley; Douglas I. Stewart

2012-01-01

287

Fast spin up of Ocean biogeochemical models using matrix-free Newton–Krylov  

Microsoft Academic Search

A novel computational approach is introduced for the efficient computation of equilibrium solutions of seasonally forced ocean biogeochemical models. The essential idea is to formulate the problem as a large system of nonlinear algebraic equations to be solved with a class of methods known as matrix-free Newton–Krylov (MFNK). MFNK is a combination of Newton-type methods for superlinearly convergent solution of

Samar Khatiwala

2008-01-01

288

Elucidating Geochemical and Biogeochemical U(VI) Reduction Via Soil Sterilization at Oak Ridge, Tennessee  

Microsoft Academic Search

The adsorption and reduction of U(VI) onto sterilized and nonsterilized soil from the Oak Ridge Reservation was studied to distinguish biogeochemical versus geochemical effects on metal reduction. The Oak Ridge soil under investigation is a saprolite sequence of interbedded weathered shale and limestone obtained at the capillary fringe with a pH near 7.6. Experiments were conducted on unaltered soils as

T. L. Bank; P. M. Jardine; T. J. Phelps; M. A. Ginder-Vogel; S. E. Fendorf; M. E. Baldwin

2005-01-01

289

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

SciTech Connect

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

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

2009-04-15

290

The influence of mesoscale and submesoscale heterogeneity on ocean biogeochemical reactions  

NASA Astrophysics Data System (ADS)

The oceanic circulation in the meso to submesoscale regime generates heterogeneity in the concentrations of biogeochemical components over these scales, horizontally between 1 and 100 km. Due to nonlinearities in the biogeochemical reactions, such as phytoplankton primary production and zooplankton grazing, this small-scale heterogeneity can lead to departure from the mean field approximation, whereby plankton reactions are evaluated from mean distributions at coarser scale. Here we explore the magnitude of these eddy reactions and compare their strength to those of the more widely studied eddy transports. We use the term eddy to denote effects arising from scales smaller than ˜ 100 km. This is done using a submesoscale permitting biogeochemical model, representative of the seasonally varying subtropical and subpolar gyres. We found that the eddy reactions associated with primary production and grazing account for ±5-30% of productivity and grazing, respectively, depending on location and time of year, and are scale dependent: two thirds are due to heterogeneities at scales 30-100 km and one third to those at scales below 30 km. Moreover, eddy productivities are systematically negative, implying that production tends to be reduced by nonlinear interactions at the mesoscale and smaller. The opposite result is found for eddy grazing, which is generally positive. The contrasting effects result from vertical advection, which negatively correlates phytoplankton and nutrients and positively correlates phytoplankton and zooplankton in the meso to submesoscale range. Moreover, our results highlight the central role played by eddy reactions for ecological aspects and the distribution of organisms and by eddy transport for biogeochemical aspects and nutrient budgets.

Levy, M.; Martin, A. P.

2013-12-01

291

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

Microsoft Academic Search

Laboratory and field studies have revealed that iron has multiple roles in phytoplankton physiology, with particular importance for light-harvesting cellular machinery. However, although iron-limitation is explicitly included in numerous biogeochemical\\/ecosystem models, its implementation varies, and its effect on the efficiency of light harvesting is often ignored. Given the complexity of the ocean environment, it is difficult to predict the consequences

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

2010-01-01

292

The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean  

Microsoft Academic Search

Seven years of time-series observations of biogeochemical processes in the subtropical North Pacific Ocean gyre have revealed dramatic changes in the microbial community structure and in the mechanisms of nutrient cycling in response to large-scale ocean-atmosphere interactions. Several independent lines of evidence show that the fixation of atmospheric nitrogen by cyanobacteria can fuel up to half of the new production.

D. Karl; R. Letelier; L. Tupas; J. Dore; J. Christian; D. Hebel

1997-01-01

293

Biogeochemical simulation of nitrous oxide cycle based on the major nitrogen processes  

Microsoft Academic Search

We modeled the biogeochemical nitrogen cycle with specific emphasis on N2O behavior to describe the global N2O cycle system quantitatively. Here all the major nitrogen cycle processes are included plus the processes directly related to N2O. The model includes 24 nitrogen reservoirs: 3 in the stratosphere (N2O, N2, and NOx), 4 in the troposphere (N2O, N2, NH3, and NOx), 7

Masao Sorai; Naohiro Yoshida; Masamichi Ishikawa

2007-01-01

294

Effect of nutrient loading on biogeochemical processes in tropical tidal creeks  

Microsoft Academic Search

The effect of increased nutrient loads on biogeochemical processes in macrotidal, mangrove-lined creeks was studied in tropical\\u000a Darwin Harbour, Australia. This study uses an integrative approach involving multiple benthic and pelagic processes as measures\\u000a of ecosystem function, and provides a comparison of these processes in three tidal creeks receiving different loads of treated\\u000a sewage effluent. There were significant differences in

Jodie SmithMichele; Michele A. Burford; Andrew T. Revill; Ralf R. Haese; Julia Fortune

295

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

NASA Astrophysics Data System (ADS)

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

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

2009-08-01

296

Precipitation of Barite by Myxococcus xanthus: Possible Implications for the Biogeochemical Cycle of Barium  

PubMed Central

Bacterial precipitation of barite (BaSO4) under laboratory conditions is reported for the first time. The bacterium Myxococcus xanthus was cultivated in a solid medium with a diluted solution of barium chloride. Crystallization occurred as a result of the presence of live bacteria and the bacterial metabolic activity. A phosphorous-rich amorphous phase preceded the more crystalline barite formation. These experiments may indicate the involvement of bacteria in the barium biogeochemical cycle, which is closely related to the carbon cycle.

Gonzalez-Munoz, Maria Teresa; Fernandez-Luque, Belen; Martinez-Ruiz, Francisca; Ben Chekroun, Kaoutar; Arias, Jose Maria; Rodriguez-Gallego, Manuel; Martinez-Canamero, Magdalena; de Linares, Concepcion; Paytan, Adina

2003-01-01

297

Biogeochemical dynamics in zero-valent iron columns: Implications for permeable reactive barriers  

Microsoft Academic Search

The impact of microbiological and geochemical processes has been a major concern for the long-term performance of permeable reactive barriers containing zero-valent iron (Fe°). To evaluate potential biogeochemical impacts, laboratory studies were performed over a 5-month period using columns containing a diverse microbial community. The conditions chosen for these experiments were designed to simulate high concentrations of bicarbonate and sulfate

B. Gu; T. J. Phelps; L. Liang; A. V. Palumbo; G. K. Jacobs; M. J. Dickey; Y. Roh; B. L. Kinsall

1999-01-01

298

A biogeochemical model for metabolism and nutrient cycling in a Southeastern Piedmont impoundment  

Microsoft Academic Search

While non-point nutrient loads are important determinants of biological productivity in Southeastern Piedmont impoundments, productivity can be attenuated by concomitant sediment loads that reduce the biological availability of these nutrients. A biogeochemical model is proposed that explicitly accounts for the effects of sediment–nutrient interactions on multiple components of phytoplankton metabolism dynamics, including algal photosynthesis and respiration, pH, carbonate speciation, dissolved

Xiaoqing Zeng; Todd C. Rasmussen; M. Bruce Beck; Amanda K. Parker; Zhulu Lin

2006-01-01

299

How to read elemental soil profiles to investigate the biogeochemical processes in Critical Zone?  

NSDL National Science Digital Library

In this exercise, students use elemental chemistry data in a soil profile to explore major biogeochemical processes that dominate in critical zone. Data will be provided, and students calculate and graph the mass transfer coefficients as a function of depth using Excel. Based on these plots, student make generalized statements about how different elements behave in this soil profile and what processes dominate, e.g., depletion by rock-water interaction, addition by dust inputs or elemental loading by human activities etc.

Jin, Lixin

300

Nucleic acid analysis of subsurface microbial communities: pitfalls, possibilities, and biogeochemical implications  

SciTech Connect

The objectives of this chapter are to (a) briefly introduce general strategies for culture-independent analysis of community nucleic acids, (b) elucidate some of the challenges, limitations and pitfalls of culture-independent techniques and data interpretation, (c) introduce some possible technological solutions for overcoming these pitfalls, and (d) discuss the potential implications of technology developments for a more comprehensive understanding of biogeochemical processes in (in situ and ex situ) subsurface materials.

Chandler, Darrell P.; Brockman, Fred J.

2001-01-17

301

Biogeochemical dynamics in zero-valent iron columns: Implications for permeable reactive barriers  

SciTech Connect

The impact of microbiological and geochemical processes has been a major concern for the long-term performance of permeable reactive barriers containing zero-valent iron (Fe{sup 0}). To evaluate potential biogeochemical impacts, laboratory studies were performed over a 5-month period using columns containing a diverse microbial community. The conditions chosen for these experiments were designed to simulate high concentrations of bicarbonate and sulfate containing groundwater regimes. Groundwater chemistry was found to significantly affect corrosion rates of Fe{sup 0} filings and resulted in the formation of a suite of mineral precipitates. HCO{sub 3}{sup {minus}} ions in SO{sub 4}{sup 2{minus}}-containing water were particularly corrosive to Fe{sup 0}, resulting in the formation of ferrous carbonate and enhanced H{sub 2} gas generation that stimulated the growth of microbial populations and increased SO{sub 4}{sup 2{minus}} reduction. Major mineral precipitates identified included lepidocrocite, akaganeite, mackinawite, magnetite/maghemite, goethite, siderite, and amorphous ferrous sulfide. Sulfide was formed as a result of microbial reduction of SO{sub 4}{sup 2{minus}} that became significant after about 2 months of column operations. This study demonstrates that biogeochemical influences on the performance and reaction of Fe{sup 0} may be minimal in the short term, necessitating longer-term operations to observe the effects of biogeochemical reactions on the performance of Fe{sup 0} barriers. Although major failures of in-ground treatment barriers have not been problematic to date, the accumulation of iron oxyhydroxides, carbonates, and sulfides from biogeochemical processes could reduce the reactivity and permeability of Fe{sup 0} beds, thereby decreasing treatment efficiency.

Gu, B.; Phelps, T.J.; Liang, L.; Palumbo, A.V.; Jacobs, G.K. [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.] [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.; Dickey, M.J.; Roh, Y.; Kinsall, B.L. [Oak Ridge Inst. for Science and Education, TN (United States)] [Oak Ridge Inst. for Science and Education, TN (United States)

1999-07-01

302

Anthropogenic Signatures in Nutrient Loads Exported from Managed Catchments: Emergence of Effective Biogeochemical Stationarity  

Microsoft Academic Search

Examining the impacts of large-scale human modifications of watersheds (e.g., land-use intensification for food production; hydrologic modification though extensive tile-drainage, etc.) on the hydrologic and biogeochemical responses, and ecological impacts at various scales has been the focus of monitoring and modeling studies over the past two decades. Complex interactions between hydrology and biogeochemistry and the need to predict responses across

N. B. Basu; G. Destouni; J. W. Jawitz; S. E. Thompson; A. Rinaldo; M. Sivapalan; P. C. Rao

2010-01-01

303

Geological and biogeochemical prerequisites for high Fe and Mn contents in the Amur River water  

Microsoft Academic Search

The role of natural and anthropogenic factors in the seasonal dynamics of the Fe and Mn ion migration in the Amur River water\\u000a is examined. The contribution of the biogeochemical processes in the migration of the Fe and Mn ions at the water-river bed\\u000a and groundwater-surface water contact zone is substantiated. The causes of the anomalously high Mn content in

V. V. Kulakov; L. M. Kondratyeva; Ye. M. Golubeva

2010-01-01

304

Integrating Microbial Community Composition With Biogeochemical Carbon and Nitrogen Dynamics: Examples From Lignin and Polyphenol Decomposition  

NASA Astrophysics Data System (ADS)

Biogeochemical models conceptually utilize box and arrow diagrams to explain the rates of carbon cycling in soil. Within these models, labile, intermediate, and recalcitrant pools of carbon are linked to each other, to respiration, and dissolved organic carbon (DOC) flux using parameterized rate functions. These models have often been successful at predicting carbon cycling rates, but they often have to be parameterized to new environmental conditions. This may occur in part because biogeochemical models do not explicitly include the underlying biological mechanisms controlling decomposition. Biogeochemical models may be improved by advances in our understanding the distribution, biomass, and activity of decomposer functional groups. It is especially useful to understand the dynamics of decomposer functional groups and enzyme systems that breakdown recalcitrant soil carbon such as lignin and condensed polyphenolics. Quantitative PCR (QPCR) is an advance in molecular biology that can target decomposer functional groups and functional genes that holds promise for understanding the landscape-level variability in microbial communities controlling the flow and fate of carbon. Here we provide examples of how the abundance and distribution of soil fungi in grassland, temperate and boreal forests predicts the enzymatic capacity of the soil community to decompose recalcitrant soil C. Moreover, the abundance of soil fungi has important implications for the response of decomposers to soil N availability.

Waldrop, M.; Zak, D. R.; Blackwood, C.; Harden, J.

2005-12-01

305

Swept under the carpet: the effect of organic matter burial in global biogeochemical ocean models  

NASA Astrophysics Data System (ADS)

Although of substantial importance for marine tracer distributions and eventually global carbon, oxygen, and nitrogen fluxes, the interaction between sinking and remineralization of organic matter, benthic fluxes and burial is not always represented consistently in global biogeochemical models. We here aim to investigate the relationships between these processes with a suite of global biogeochemical models, each simulated over millennia, and compared against observed distributions of pelagic tracers and benthic and pelagic fluxes. We concentrate on the representation of sediment-water interactions in common numerical models, and investigate their potential impact on simulated global sediment-water fluxes and nutrient and oxygen distributions. We find that model configurations with benthic burial simulate global oxygen well over a wide range of possible sinking flux parameterizations, making the model more robust with regard to uncertainties about the remineralization length scale. On a global scale, burial mostly affects oxygen in the meso- to bathypelagic zone. While all model types show an almost identical fit to observed pelagic particle flux, and the same sensitivity to particle sinking speed, comparison to observational estimates of benthic fluxes reveals a more complex pattern and may be influenced by the data distribution and methodology. Still, evaluating model results against observed pelagic and benthic fluxes of organic matter can complement model assessments based on more traditional tracers such as nutrients or oxygen. Based on a combined metric of dissolved tracers and biogeochemical fluxes, we here identify two model descriptions of burial as suitable candidates for further experiments and eventual model refinements.

Kriest, I.; Oschlies, A.

2013-07-01

306

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

307

Spatial variability in mercury cycling and relevant biogeochemical controls in the Florida Everglades.  

PubMed

Spatial patterns in mercury cycling and bioaccumulation at the landscape level in the Everglades were investigated by collecting and analyzing multimedia samples for mercury species and biogeochemical characteristics from 228 randomly located stations. Higher total mercury (THg) in environmental compartments (surface water, soil, flocculent detrital material (floc), and periphyton) generally occurred in the northern and central Everglades, but higher THg in water and periphyton in the Everglades National Park was an exception. Multiple biogeochemical characteristics, such as surface water dissolved organic matter (DOC(sw)), pH, chloride, and compositional properties of solid compartments (soil and floc), were identified to be important factors controlling THg distribution. Methylmercury (MeHg) was also higher in the northern Everglades for water, soil, and floc, but not for periphyton. Higher mosquitofish THg and bioaccumulation factor were observed in the central and southern Everglades, partially in accordance with periphyton MeHg distribution, but not in the "hot spot" areas of water, soil, or floc MeHg. The discrepancy in mercury bioaccumulation and mercury distribution in environmental compartments suggests that in addition to MeHg production, biogeochemical controls that make MeHg available to aquatic organisms, such as DOC(sw) and compositional properties of soil and floc, are important in mercury bioaccumulation. PMID:19603647

Liu, Guangliang; Cai, Yong; Mao, Yuxiang; Scheidt, Daniel; Kalla, Peter; Richards, Jennifer; Scinto, Leonard J; Tachiev, Georgio; Roelant, David; Appleby, Charlie

2009-06-15

308

Hydrologic and Biogeochemical Controls on Solute Export across Human Impact Gradients  

NASA Astrophysics Data System (ADS)

Intensively managed catchments are characterized by a dominance of human impacts and shifts in natural hydrological and biogeochemical functioning. Concentration discharge relationships of geogenic (weathering derived) solutes and nutrients (nitrogen and phosphorus species) from pristine and agricultural basins were compared to explore anthropogenic impacts on biogeochemical functioning. The results suggest that the export of nutrients shifts from episodic (highly variable concentration with minimal correlation between concentration and discharge) in pristine catchments to chemostatic (i.e. lower variability in concentration and strong correlation between concentration and discharge) in agricultural catchments. Chemostatic response was also characteristic of geogenic solutes in both pristine and managed systems. We hypothesized that 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. These sources buffer interannual variations in biogeochemical processing, and make predictions of nitrate loads easier than in pristine systems.

Basu, N. B.; Rao, S.; Thompson, S. E.

2011-12-01

309

Technical Note: Simple formulations and solutions of the dual-phase diffusive transport for biogeochemical modeling  

NASA Astrophysics Data System (ADS)

Representation of gaseous diffusion in variably saturated near-surface soils is becoming more common in land biogeochemical models, yet the formulations and numerical solution algorithms applied vary widely. We present three different but equivalent formulations of the dual-phase (gaseous and aqueous) tracer diffusion transport problem that is relevant to a wide class of volatile tracers in land biogeochemical models. Of these three formulations (i.e., the gas-primary, aqueous-primary, and bulk tracer based formulations), we contend the gas-primary formulation is the most convenient for modeling tracer dynamics in biogeochemical models. We then provide finite volume approximation to the gas-primary equation and evaluate its accuracy against three analytical models: one for steady-state soil CO2 dynamics, one for steady-state soil CO2 dynamics, and one for transient tracer diffusion from a constant point source into two different sequentially aligned medias. All evaluations demonstrated good accuracy of the numerical approximation. We expect our result will standardize an efficient mechanistic numerical method for solving relatively simple, multi-phase, one-dimensional diffusion problems in land models.

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

2014-01-01

310

Microbial biogeochemical dynamics in contrasting cold seep ecosystems in the Gulf of Mexico  

NASA Astrophysics Data System (ADS)

Seepage of gas, oil, brine, and/or fluidized mud is a critical driver that regulates microbial distributions, activity, and biogeochemical dynamics in sediments along the continental shelf and slope in the Gulf of Mexico. We examined microbial populations, activities, and environmental geochemical signatures at several cold seeps in the Gulf of Mexico over repeated samplings beginning in 2002. Fluid seepage generates a number of unique habitat features that are characterized by distinct microbial populations with specific biogeochemical functions. This presentation will contrast microbial biogeochemical dynamics in sediments impacted by advective gas and oil seepage or by brine seepage with dynamics observed in stable, diffusively-driven brine basins. The variability in microbial populations and activities in these different habitats was surprising. Qualitatively, fluid flow at brine-influenced sites tends to be more focused and/or intense than fluid flow at gas and oil seeps, the exception being brine basins, which are extremely stable, diffusively-driven systems. Differences in fluid flow - even among distinct types of advective brine seeps - drives unexpected and substantial differences in microbial community composition and activity. Microbial community compositions and activities reflect organic carbon inputs and a suite of environmental factors that seem to imprint and regulate biological communities.

Joye, S. B.; Teske, A. P.

2012-12-01

311

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

NASA Astrophysics Data System (ADS)

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

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

2006-05-01

312

Nitrogen biogeochemical cycling in the northwestern Indian Ocean  

NASA Astrophysics Data System (ADS)

The vertical distribution and fine scale structure of nitrate (NO 3), nitrite (NO 2), nitrous Oxide (N 2O), phosphate (PO 4), oxygen (O 2) and chlorophyll ? (chl ?) were determined in the North Western Indian Ocean (NWIO) along a meridional section (67°E) from the Equator to the Gulf of Oman using an Autoanalyser for micromolar levels of nutrients, and chemiluminescence and gas chromatographic methods for nanomolar levels of NO 3 and NO 2 and N 2O respectively. Three biogeochimically contrasting regimes were investigated: (1) the highly oligotrophic nutrient-depleted subtropical gyre; (2) the nonsoonal upwelling of nutrient-rich intermediate waters of the southeastern Arabian Coast; and (3) the denitrifying O 2-depleted zone (ODZ; ca 150-1200 m depth) in the Arabian Sea. Concentrations of NO 3 and NO 2 were severely depleted in surface oligotrophic waters from the equator (average 43 and 3.6 nM respectively) to the subtropical gyre (12-15°N; average 13.3 and 2.0 nM respectively) with similar levels in the more stratified Gulf of Oman. Upwelling waters off Southern Arabia had three orders of magnitude higher NO 3 levels, and throughout the NWIO, the calculated NO 3-fuelled primary production appeared to be regulated by NO 3 concentration. Existing Redfield ?O 2/?NO 3 regeneration ratios (=9.1) previously derived for the deep Indian Ocean were confirmed (= 9.35) within the oxic upper layers of the NWIO. The "NO"-potential temperature relationship ( BROECKER, 1974 Earth and Planetary Science Letters, 23, 100-107) needed for the derivation of expected NO 3 and NO 3-deficits within the denitrifying ODZ were refined using an isopycnal, binary mixing model along the ?? = 26.6%, density layer to take into account the inflowing contribution of NO 3-depleted Persian Gulf Water. Vertically integrated NO 3-deficits increased northwards from 0.8 mol NO 3-N m -2 at Sta. 2 (04°N), up to 6.49 mol NO 3-N m -2 at Sta. 9, at the mouth of the Gulf of Oman, then decreased to 4.10 moles NO 3-N m -2 toward Sta. 11, near the Straits of Hormuz. When averaged for the denitrification area of the Arabian Sea, this corresponds to a deficit of 118 Tg NO 3-N. Adopting a recent Freon-11 based estimate of water residence time of 10 years ( OLSONet al., 1993, Deep-Sea Research II, 40, 673-685) for the O 2-depleted layer, we calculate an annual net denitrification flux of 11.9 Tg N to the atmosphere or approximately 10% of the global water column denitrification rates. Supersaturated N 2O concentrations were found in both surface oxic and upwelling waters (up to 246%) and peaked at the base of the ODZ (up to 1264%) in the northern Arabian Sea. Both nitrification in oxic waters and denitrification in hypoxic layers can be invoked as sources of N 2O. The inventory of excess N 2O amounted to 2.55 ± 1.3 Tg N 2O-N, corresponding to annual production of 0.26 ± 0.13 Tg from denitrification. This is comparable to earlier ( LAW AND OWENS, 1990, Nature, 346, 826-828) estimates of the ventilation flux of N 2O (0.22-0.39 Tg yr -1) from the upwelling region of the Arabian Sea. The decadal response times for circulation, deoxygenation, denitrification and ventilation of the ODZ-derived N 2O and CO 2 greenhouse gases and their monsoonal coupling implies the Arabian Sea is a sensitive oceanic recorder of global climate change.

Fauzi, R.; Mantoura, C.; Law, Clifford S.; Owens, Nicholas J. P.; Burkill, Peter H.; Woodward, E. Malcolm S.; Howland, Robin J. M.; Llewellyn, Carole A.

313

Characterization of eco-hydraulic habitats for examining biogeochemical processes in rivers  

NASA Astrophysics Data System (ADS)

Spatial variability in biogeochemical reaction rates in streams is often attributed to sediment characteristics such as particle size, organic material content, and biota attached to or embedded within the sediments. Also important in controlling biogeochemical reaction rates are hydraulic conditions, which influence mass transfer of reactants from the stream to the bed, as well as hyporheic exchange within near-surface sediments. This combination of physical and ecological variables has the potential to create habitats that are unique not only in sediment texture but also in their biogeochemical processes and metabolism rates. In this study, we examine the two-dimensional (2D) variability of these habitats in an agricultural river in central Iowa. The streambed substratum was assessed using a grid-based survey identifying dominant particle size classes, as well as aerial coverage of green algae, benthic organic material, and coarse woody debris. Hydraulic conditions were quantified using a calibrated 2D model, and hyporheic exchange was assessed using a scaling relationship based on sediment and hydraulic characteristics. Point-metabolism rates were inferred from measured sediment dissolved oxygen profiles using an effective diffusion model and compared to traditional whole-stream measurements of metabolism. The 185 m study reach had contrasting geomorphologic and hydraulic characteristics in the upstream and downstream portions of an otherwise relatively straight run of a meandering river. The upstream portion contained a large central gravel bar (50 m in length) flanked by riffle-run segments and the downstream portion contained a deeper, fairly uniform channel cross-section. While relatively high flow velocities and gravel sediments were characteristic of the study river, the upstream island bar separated channels that differed with sandy gravels on one side and cobbley gravels on the other. Additionally, green algae was almost exclusively found in riffle portions of the cobbley gravel channel sediments while fine benthic organic material was concentrated at channel margins, regardless of the underlying sediments. A high degree of spatial variability in hyporheic exchange potential was the result of the complex 2D nature of topography and hydraulics. However, sediment texture classifications did a reasonable job in characterizing variability in hyporheic exchange potential because sediment texture mapping incorporates qualitative aspects of bed shear stress and hydraulic conductivity that control hyporheic exchange. Together these variables greatly influenced point-metabolism measurements in different sediment texture habitats separated by only 1 to 2 m. Results from this study suggest that spatial variability and complex interactions between geomorphology, hydraulics, and biological communities generate eco-hydraulic habitats that control variability in biogeochemical processes. The processes controlling variability are highly two-dimensional in nature and are not often accounted for in traditional one-dimensional analysis approaches of biogeochemical processes.

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

2009-12-01

314

Simulating the early Holocene eastern Mediterranean sapropel formation using an ocean biogeochemical model  

NASA Astrophysics Data System (ADS)

The early Holocene sapropel S1 is an organic-rich sediment layer deposited under oxygen depleted conditions below 1800 m between 10 to 6.5 kyr BP in the eastern Mediterranean Sea. Whereas this silled ocean basin is well-ventilated and has a low biological productivity today, the S1 formation indicates drastic changes in the deep water circulation and/or productivity. Commonly, both of these processes are attributed to an enhanced humidity over the broader Mediterranean area. In particular, an increase in the strength of the African monsoon during the African humid period (AHP) is thought to have provided enhanced Nile runoff and nutrient load. However, the exact mechanisms leading to S1 formation are still being debated. Here we apply a regional ocean general circulation model coupled to a marine biogeochemical model covering the entire Mediterranean Sea to explore some of the many published hypotheses on sapropel formation. With a set of simulations we show that S1 formation cannot be explained by either enhanced biological productivity fueled by increased riverine nutrient input, or by an AHP climatic induced stagnating deep water circulation combined with enhanced biological productivity. The main reasons are: (i) Enhanced biological productivity cannot overcome the effect of a continuous deep ventilation, so that a stagnating deep water circulation is a prerequisite for S1 formation. (ii) The pre-sapropel period is characterized by low particulate organic carbon (POC) sediment burial fluxes, implying that river induced eutrophication is not a viable scenario. (iii) The time span required for complete oxygen depletion within the stagnating deep water circulation exceeds the time span between the beginning of the AHP and the onset of the S1 oxygen deficiency, so that the enhanced Nile runoff fueled by the AHP climate is an unlikely trigger for deep water isolation that caused S1 formation. Available data suggest substantial freshening and warming of the Mediterranean upper ocean during the last glacial-interglacial transition that stabilized stratification and prevented deep water ventilation. Imposing the climatic signals of the last glacial-interglacial transition triggers a persistent (> 4 kyr) deep water stagnation in this simulation. The productivity regime in this simulation was assumed similar to the present-day oligotrophic regime, and the simulated POC burial fluxes agree with observed pre-sapropel burial fluxes in sediments. No deep water anoxia evolves in the short time frame of this simulation (4 kyr) relative to the temporal extent of the deglaciation period, which started at ~17.5 kyr BP. The trend of the modeled oxygen consumption suggests that it takes at least 6.5 kyr until deep water anoxia is established. The simulation also suggests that addition of freshwater is required to maintain the stratification in order to meet the reconstructed spatial extent and duration of the S1 deposition. An examination of records of epibenthic deep-sea foraminifera ?18O supports our findings, and indicates that the stagnation of the deep circulation started ~6 kyr before the onset of the S1 deposition.

Grimm, Rosina; Maier-Reimer, Ernst; Mikolajewicz, Uwe; Schmiedl, Gerhard; Adloff, Fanny; Emeis, Kay

2013-04-01

315

Minireview: The importance of benthic-pelagic coupling and the forgotten role of life cycles in coastal aquatic systems  

Microsoft Academic Search

The classical models of production and plankton community dynamics in coastal waters include an important role for benthic-pelagic coupling in the form of biogcochemical cycling (the turnover of nutrients in the form of either living matter or its decomposed constituents). We think, however, that biogeochemical explanations of eco- system functioning underrepresent the actual complexity of the studied phenomena. We suggest

Nancy H. Marcus; Ferdinando Boero

1998-01-01

316

A New Time-Dependent Inventory of Methane Emissions From Global Wetlands Based on Remote Sensing and Biogeochemical Modeling  

NASA Astrophysics Data System (ADS)

The dynamics of natural methane sources contribute to both seasonal and interannual variability in atmospheric methane concentrations. Wetlands are the largest natural source of methane and among the most variable in space and time. We compiled a new map of global wetlands using passive and active remote sensing based land cover information, and used these data to drive the LPJ-TG vegetation model to simulate wetland hydrology, biogeochemical cycling, and methane emissions over the period 1991-2004. Surface flux fields of wetland methane emissions were then coupled to the TM5 transport-chemistry model to simulate methane concentrations at a suite of tropospheric measuring stations. The new wetland map highlights the importance of seasonal wetlands in tropical floodplains and rainforests, while reducing estimates of boreal wetland area compared to previous work, especially in Europe. Our analysis further indicates that the tropics are likely to be a larger source of natural methane emissions than previously thought, and that interannual variability in methane emissions are driven by tropical wetlands, with year-on-year differences of up to 10% in the global wetland source. The seasonal cycle in wetland methane emissions is driven by northern hemisphere high-latitude peatlands, which have an annual amplitude of ca. 5 Tg. Sensitivity studies and comparison with observation networks of atmospheric methane concentrations demonstrate that this new inventory is a significant improvement over previous estimates in reproducing observed seasonal and interannual variability at several in-situ and aircraft-based measuring stations. The inventory will be an important component for evaluation of new remote sensing-based products of atmospheric methane concentrations.

Kaplan, J. O.; Bergamaschi, P.; Dentener, F.

2005-12-01

317

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

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

318

Bio-optical profiling floats as new observational tools for biogeochemical and ecosystem studies: Potential synergies with ocean color remote sensing  

Microsoft Academic Search

Profiling floats now represent a mature technology. In parallel with their emergence, the field of miniature, low power bio-optical and biogeochemical sensors is rapidly evolving. Over recent years, the bio-geochemical and bio-optical community has begun to benefit from the increase in observational capacities by developing profiling floats that allow the measurement of key biooptical variables and subsequent products of biogeochemical

Hervé Claustre; Jim Bishop; Emmanuel Boss; Stewart Bernard; Jean-François Berthon; Christine Coatanoan; Ken Johnson; A. Lotiker; O. Ulloa; M. J. Perry; F. DOrtenzio; O. H. F. Dandon; J. Uitz

2009-01-01

319

Biogeochemical characterization of a lithified paleosol: Implications for the interpretation of ancient Critical Zones  

NASA Astrophysics Data System (ADS)

Modern soils are characterized by an array of physical, chemical, mineralogical, and biological laboratory analyses of samples taken from horizons of pedogenic profiles. In contrast, fossil soils (paleosols) are typically characterized from assays of whole-rock molecular oxides because of sample lithification where element sources are unconstrained. Here we for the first time subject a lithified paleosol to an array of modern soil analytical techniques and new pedotransfer functions, providing a glimpse into the colloidal world of an ancient Critical Zone as an analog to research conducted on a network of modern Critical Zones. This methodology provides a framework for decoding a previously unknown archive of terrestrial biogeochemical information at multiple temporal and spatial scales. Application to a paleosol within an early Paleocene Critical Zone reveals that many biogeochemical properties have been preserved since burial that are similar to modern clay-rich, Vertisols. The measured and calculated physical properties of this paleosol include clay content and mineralogy, bulk density and water retention, available water capacity, and coefficient of linear extensibility (shrink-swell potential). The chemical properties include cation exchange capacity, exchangeable cations, base saturation, and exchangeable sodium percentage. The solution properties electrical conductivity and pH seem reasonable, but are interpreted with less confidence because of their greater vulnerability to alteration from fluid flow. New pedotransfer functions to reconstruct pre-burial organic carbon and nitrogen contents provide invaluable information of organically-derived nutrient content. The sum of the measured properties of the early Paleocene paleosol in context of reconstructed regional environmental conditions indicate the presence of a mid-successional hardwood forest in a humid climate with high water holding capacity, high nutrient retention, and rapid flux of elements through biogeochemical cycling.

Nordt, Lee C.; Hallmark, Charles T.; Driese, Steven G.; Dworkin, Steven I.; Atchley, Stacy C.

2012-06-01

320

Marine geochemical data assimilation in an efficient Earth System Model of global biogeochemical cycling  

NASA Astrophysics Data System (ADS)

We have extended the 3-D ocean based "Grid ENabled Integrated Earth system model'' (GENIE-1) to help understand the role of ocean biogeochemistry and marine sediments in the "long-term'' (~100 to 100 000 year) regulation of atmospheric CO2, and the importance of feedbacks between CO2 and climate. Here we describe the ocean carbon cycle, which is based around a simple single nutrient (phosphate) control on biological productivity. The addition of ocean-sediment interactions is presented elsewhere (Ridgwell and Hargreaves, 2006). We have calibrated the model parameters controlling ocean carbon cycling in GENIE-1 by assimilating 3-D observational datasets of phosphate and alkalinity using an ensemble Kalman filter method. The calibrated (mean) model predicts a global export production of particulate organic carbon (POC) of 8.9 PgC yr-1, and reproduces the main features of dissolved oxygen distributions in the ocean. For estimating biogenic calcium carbonate (CaCO3 production, we have devised a parameterization in which the CaCO3:POC export ratio is related directly to ambient saturation state. Calibrated global CaCO3 export production (1.2 PgC yr-1 is close to recent marine carbonate budget estimates. The GENIE-1 Earth system model is capable of simulating a wide variety of dissolved and isotopic species of relevance to the study of modern global biogeochemical cycles as well as past global environmental changes recorded in paleoceanographic proxies. Importantly, even with 12 active biogeochemical tracers in the ocean and including the calculation of feedbacks between atmospheric CO2 and climate, we achieve better than 1000 years per (2.4 GHz) CPU hour on a desktop PC. The GENIE-1 model thus provides a viable alternative to box and zonally-averaged models for studying global biogeochemical cycling over all but the very longest (>1 000 000 years) time-scales.

Ridgwell, A.; Hargreaves, J. C.; Edwards, N. R.; Annan, J. D.; Lenton, T. M.; Marsh, R.; Yool, A.; Watson, A.

2006-08-01

321

Marine geochemical data assimilation in an efficient Earth System Model of global biogeochemical cycling  

NASA Astrophysics Data System (ADS)

We have extended the 3-D ocean based "Grid ENabled Integrated Earth system model" (GENIE-1) to help understand the role of ocean biogeochemistry and marine sediments in the long-term (~100 to 100 000 year) regulation of atmospheric CO2, and the importance of feedbacks between CO2 and climate. Here we describe the ocean carbon cycle, which in its first incarnation is based around a simple single nutrient (phosphate) control on biological productivity. The addition of calcium carbonate preservation in deep-sea sediments and its role in regulating atmospheric CO2 is presented elsewhere (Ridgwell and Hargreaves, 2007). We have calibrated the model parameters controlling ocean carbon cycling in GENIE-1 by assimilating 3-D observational datasets of phosphate and alkalinity using an ensemble Kalman filter method. The calibrated (mean) model predicts a global export production of particulate organic carbon (POC) of 8.9 PgC yr-1, and reproduces the main features of dissolved oxygen distributions in the ocean. For estimating biogenic calcium carbonate (CaCO3) production, we have devised a parameterization in which the CaCO3:POC export ratio is related directly to ambient saturation state. Calibrated global CaCO3 export production (1.2 PgC yr-1) is close to recent marine carbonate budget estimates. The GENIE-1 Earth system model is capable of simulating a wide variety of dissolved and isotopic species of relevance to the study of modern global biogeochemical cycles as well as past global environmental changes recorded in paleoceanographic proxies. Importantly, even with 12 active biogeochemical tracers in the ocean and including the calculation of feedbacks between atmospheric CO2 and climate, we achieve better than 1000 years per (2.4 GHz) CPU hour on a desktop PC. The GENIE-1 model thus provides a viable alternative to box and zonally-averaged models for studying global biogeochemical cycling over all but the very longest (>1 000 000 year) time-scales.

Ridgwell, A.; Hargreaves, J. C.; Edwards, N. R.; Annan, J. D.; Lenton, T. M.; Marsh, R.; Yool, A.; Watson, A.

2007-01-01

322

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

PubMed

Projections of future changes in land carbon (C) storage using biogeochemical models depend on accurately modeling the interactions between the C and nitrogen (N) cycles. Here, we present a framework for analyzing N limitation in global biogeochemical models to explore how C-N interactions of current models compare to field observations, identify the processes causing model divergence, and identify future observation and experiment needs. We used a set of N-fertilization simulations from two global biogeochemical models (CLM-CN and O-CN) that use different approaches to modeling C-N interactions. On the global scale, net primary productivity (NPP) in the CLM-CN model was substantially more responsive to N fertilization than in the O-CN model. The most striking difference between the two models occurred for humid tropical forests, where the CLM-CN simulated a 62% increase in NPP at high N addition levels (30 g N m(-2) yr(-1)), while the O-CN predicted a 2% decrease in NPP due to N fertilization increasing plant respiration more than photosynthesis. Across 35 temperate and boreal forest sites with field N-fertilization experiments, we show that the CLM-CN simulated a 46% increase in aboveground NPP in response to N, which exceeded the observed increase of 25%. In contrast, the O-CN only simulated a 6% increase in aboveground NPP at the N-fertilization sites. Despite the small response of NPP to N fertilization, the O-CN model accurately simulated ecosystem retention of N and the fate of added N to vegetation when compared to empirical (15) N tracer application studies. In contrast, the CLM-CN predicted lower total ecosystem N retention and partitioned more losses to volatilization than estimated from observed N budgets of small catchments. These results point to the need for model improvements in both models in order to enhance the accuracy with which global C-N cycle feedbacks are simulated. PMID:23744637

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

2013-10-01

323

Seasonal ITCZ migration dynamically controls the location of the (sub)tropical Atlantic biogeochemical divide  

PubMed Central

Inorganic nitrogen depletion restricts productivity in much of the low-latitude oceans, generating a selective advantage for diazotrophic organisms capable of fixing atmospheric dinitrogen (N2). However, the abundance and activity of diazotrophs can in turn be controlled by the availability of other potentially limiting nutrients, including phosphorus (P) and iron (Fe). Here we present high-resolution data (?0.3°) for dissolved iron, aluminum, and inorganic phosphorus that confirm the existence of a sharp north–south biogeochemical boundary in the surface nutrient concentrations of the (sub)tropical Atlantic Ocean. Combining satellite-based precipitation data with results from a previous study, we here demonstrate that wet deposition in the region of the intertropical convergence zone acts as the major dissolved iron source to surface waters. Moreover, corresponding observations of N2 fixation and the distribution of diazotrophic Trichodesmium spp. indicate that movement in the region of elevated dissolved iron as a result of the seasonal migration of the intertropical convergence zone drives a shift in the latitudinal distribution of diazotrophy and corresponding dissolved inorganic phosphorus depletion. These conclusions are consistent with the results of an idealized numerical model of the system. The boundary between the distinct biogeochemical systems of the (sub)tropical Atlantic thus appears to be defined by the diazotrophic response to spatial–temporal variability in external Fe inputs. Consequently, in addition to demonstrating a unique seasonal cycle forced by atmospheric nutrient inputs, we suggest that the underlying biogeochemical mechanisms would likely characterize the response of oligotrophic systems to altered environmental forcing over longer timescales.

Schlosser, Christian; Klar, Jessica K.; Wake, Bronwyn D.; Snow, Joseph T.; Honey, David J.; Woodward, E. Malcolm S.; Lohan, Maeve C.; Achterberg, Eric P.; Moore, C. Mark

2014-01-01

324

Estimating the Effects of Mountain Pine Beetle Outbreaks on Biophysical and Biogeochemical Variables Using MODIS Products  

NASA Astrophysics Data System (ADS)

Insects such as mountain pine beetle (Dendroctonus ponderosae Hopkins) are major disturbances in forested ecosystems, affecting forest structure and function. In recent decades, mountain pine beetles have affected large forested areas in the United States and Canada. Insect disturbances impact biophysical variables important for atmosphere/ecosystem exchanges of mass, energy, and momentum as well as biogeochemical processes, notably carbon cycling. Our goal was to estimate the effects of insect disturbance, in particular mountain pine beetle infestations, on carbon cycling in Colorado by using MODIS biophysical and biogeochemical data products in conjunction with fine-resolution aerial imagery that identified the infestation locations. We classified a fine-resolution aerial image, acquired on August 13 2008 in Colorado, into five classes: (1) undisturbed forests, (2) red-attack (when needles are red and still on trees), (3) gray-attack (when trees have lost most of their needles), (4) herbaceous vegetation, and (5) non-vegetation. The classified aerial image was evaluated using field observations, and high accuracies were achieved. The classified aerial image was then aggregated to the MODIS resolution to investigate different levels of insect-caused tree mortality (i.e., the percentage of fine-resolution red-attack and gray-attack pixels in the aggregated pixels). MODIS-derived biophysical and biogeochemical products, including gross and net primary production, leaf area index (LAI), and surface albedo were overlaid on locations with the different levels of outbreak severity. Trajectories of these variables across time were extracted and pre- and post-outbreak values were compared. The outcomes of the effects of MPB on biophysical parameters can be used to increase understanding of impacts of insects to forest functioning and carbon cycling in the western United States.

Meddens, A. J.; Hicke, J. A.

2009-12-01

325

Seasonal ITCZ migration dynamically controls the location of the (sub)tropical Atlantic biogeochemical divide.  

PubMed

Inorganic nitrogen depletion restricts productivity in much of the low-latitude oceans, generating a selective advantage for diazotrophic organisms capable of fixing atmospheric dinitrogen (N2). However, the abundance and activity of diazotrophs can in turn be controlled by the availability of other potentially limiting nutrients, including phosphorus (P) and iron (Fe). Here we present high-resolution data (?0.3°) for dissolved iron, aluminum, and inorganic phosphorus that confirm the existence of a sharp north-south biogeochemical boundary in the surface nutrient concentrations of the (sub)tropical Atlantic Ocean. Combining satellite-based precipitation data with results from a previous study, we here demonstrate that wet deposition in the region of the intertropical convergence zone acts as the major dissolved iron source to surface waters. Moreover, corresponding observations of N2 fixation and the distribution of diazotrophic Trichodesmium spp. indicate that movement in the region of elevated dissolved iron as a result of the seasonal migration of the intertropical convergence zone drives a shift in the latitudinal distribution of diazotrophy and corresponding dissolved inorganic phosphorus depletion. These conclusions are consistent with the results of an idealized numerical model of the system. The boundary between the distinct biogeochemical systems of the (sub)tropical Atlantic thus appears to be defined by the diazotrophic response to spatial-temporal variability in external Fe inputs. Consequently, in addition to demonstrating a unique seasonal cycle forced by atmospheric nutrient inputs, we suggest that the underlying biogeochemical mechanisms would likely characterize the response of oligotrophic systems to altered environmental forcing over longer timescales. PMID:24367112

Schlosser, Christian; Klar, Jessica K; Wake, Bronwyn D; Snow, Joseph T; Honey, David J; Woodward, E Malcolm S; Lohan, Maeve C; Achterberg, Eric P; Moore, C Mark

2014-01-28

326

Validating a Biogeochemical Watershed Disturbance and Climate Change Proxy: Tampa Bay. FL  

NASA Astrophysics Data System (ADS)

The Tampa Bay estuary and watershed have been impacted in the past century by residential and industrial development activities that have resulted in pollutant release via runoff and wastewater discharges. Mangrove forest loss, mining activities, accidental spills and nutrient loading have also decreased water quality in this aquatic environment. The primary goal of this project is to provide historical water quality and climate information by determining biogeochemical properties of oyster shells and sediments collected from various locations throughout the Tampa Bay region including ancient Native American shell mounds. Biogeochemical properties of shells collected from these middens will provide insight regarding historical water quality of Tampa Bay. It is expected that a pristine, pre-Columbian baseline may be revealed from the midden shells, and changes in the biogeochemical record may be demonstrated over the recent past from the industrial age to modern day on a seasonal and yearly scale. In order to achieve the goal of this project, midden shells and sediments will be collected and compared from three stations in Tampa Bay that range from undisturbed to severely impacted; Emerson Point, Weedon Island, and Bayboro Harbor, respectively. Water and sediment samples have also been examined to provide additional information regarding radiogeochemical properties of the three study sites. Sediments will be dated using gamma spectrometry techniques (U/Th series). Standard ICP-OES methods are being utilized to determine concentrations of trace, minor and major elements in the oyster and sediment samples. This project is part of a larger on-going investigation. If successful, this investigation will ultimately yield a high-resolution tool for establishing the history of terrestrial land use and climate change.

Schwing, P. T.; Martinez, E.; Pyrtle, A. J.; Haynes, S.

2007-12-01

327

The biogeochemical cycle of the adsorbed template. I - formation of the template  

NASA Technical Reports Server (NTRS)

Experimental results are presented for the verification of the first adsorption step of the 'adsorbed template' biogeochemical cycle, a simple model for a primitive prebiotic replication system. The adsorption of Poly-C, Poly-U, Poly-A, Poly-G, and 5'-AMP, 5'-GMP, 5'-CMP and 5'-UMP onto gypsum was studied. It was found that under the conditions of the experiment, the polymers have a very high affinity for the mineral surface, while the monomers adsorb much less efficiently.

Lazard, Daniel; Lahav, Noam; Orenberg, J. B.

1987-01-01

328

The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean  

NASA Astrophysics Data System (ADS)

Seven years of time-series observations of biogeochemical processes in the subtropical North Pacific Ocean gyre have revealed dramatic changes in the microbial community structure and in the mechanisms of nutrient cycling in response to large-scale ocean-atmosphere interactions. Several independent lines of evidence show that the fixation of atmospheric nitrogen by cyanobacteria can fuel up to half of the new production. These and other observations demand a reassessment of present views of nutrient and carbon cycling in one of the Earth's largest biomes.

Karl, D.; Letelier, R.; Tupas, L.; Dore, J.; Christian, J.; Hebel, D.

1997-08-01

329

Trees actively and directly influence biogeochemical processes in boreal forested watersheds  

NASA Astrophysics Data System (ADS)

Trees actively and directly influence biogeochemical processes in boreal forested watersheds Peter Högberg, Dept. of Forest Ecology and Management, SLU, SE-901 83 Umeå, Sweden It is increasingly realized that trees are directly influencing soil processes, and thereby significantly also biogeochemical processes at the scale of watersheds. For example, it is now well established that recent photosynthesis supports on average around 50% of the soil respiratory activity. It takes only a few days from tree canopy photosynthesis to the use of that C by plant roots and soil microbes. Importantly, not only does this represent a significant and rapid return flux of CO2 back to the atmosphere, but it also relates to a range of important biogeochemical processes. These occur not only in the soil, but also in streams and lakes, e.g., in nutrient-poor boreal forests areas labile C compounds produced by tree roots and their associated microorganisms constitute an important C source for lake biota. Furthermore, the tree belowground C allocation is under strong physiological control and responds to the supply of nutrients, especially to the supply of nitrogen. When this is low, as in most boreal forests, the belowground C allocation to roots and mycorrhizal fungi is large. This explains the very large N retention capacity of these forests. However, after large additions of N, this belowground C flux is reduced and consequently also the N retention capacity of mycorrhizal fungi. When this occurs, bacteria, organisms with a much lower C/N ratio, become dominant; but as these are C-limited, their capacity to sequester N is much lower than that of fungi. As a consequence, the N cycle opens up, and N is lost through leaching of nitrate and denitrification. However, if the N-load is removed, the trees start to allocate more C belowground to their mycorrhizal fungi again, and this important N-trap is restored. Thus, there are many examples of how trees actively and directly (with short time lags) involve biogeochemical processes in boreal forested watersheds.

Högberg, Peter

2010-05-01

330

Tracing biogeochemical processes in stream water and groundwater using non-linear statistics  

NASA Astrophysics Data System (ADS)

SummaryStream water and groundwater solute concentration are subject to a multitude of biogeochemical processes that act at different scales and are often characterized by non-linear relationships and feedback loops. Different multivariate statistical methods were applied to investigate the interplay of different processes. The data set from the Lehstenbach catchment in South Germany comprised 2641 stream water and groundwater samples from 38 different sites in the catchment, where 13 different solutes had been determined. According to the correlation dimension analysis, the number of dominant processes was four. The first four components determined via principal component analysis comprised 88% of the total variance, whereas the non-linear isometric feature mapping explained 92% with the first four components. These components were ascribed to prevailing biogeochemical processes and were used to investigate spatial and temporal patterns. Redox processes and contamination by road salt explained 35% of the variance each. Another 13% were ascribed to near-surface runoff in the acidified topsoil, and 9% to the impact of contaminated filter gravel in some of the groundwater wells. The redox component exhibited clear seasonal patterns at most stream water and groundwater sampling sites, with the most reduced conditions in late summer, immediately before the onset of re-wetting. There was clear evidence that redox processes, especially denitrification, play an important role even in the oxic aquifer. During discharge peaks, stream water exhibited higher values of the near-surface runoff component. However, the associated lower values of the redox component pointed to near-surface runoff in the riparian wetlands as the predominating runoff generation process rather than to a contribution of upslope soil water. A series of major rain storms in fall 1998 altered groundwater and stream water solute concentration for months: stream water and groundwater became more oxic and more acidified, and showed a higher impact of road salt contamination at some sites. Overall, the spatial and temporal patterns of the predominating components gave a consistent picture and helped considerably to better understand the interplay between biogeochemical and hydrological processes. The chosen approach is a promising tool for investigating apparently complex hydrological and biogeochemical systems.

Lischeid, Gunnar; Bittersohl, Jochen

2008-07-01

331

Biogeochemical study of areas of sulphide mineralisation in eastern Thrace, Greece.  

PubMed

The uptake of copper, lead and zinc by plants in several areas of sulphide mineralisation in eastern Thrace, Greece, has been studied. Two indicator plants for sulphide deposits in central Macedonia,Rumex acetosella L. andMinuartia verna (L.) Hiern, have not been found on Thracian soils high in sulphides. However, the widespread speciesHypericum perforatum L. andScleranthus perennis L. are tolerant of the elevated metal levels in these soils. AlthoughH. perforatum is not useful as a biogeochemical indicator, the levels of Cu, Pb and Zn inS. perennis were found to be strongly correlated with the corresponding concentrations in the soil. PMID:24202203

Kelepertsis, A E; Reeves, R D

1989-03-01

332

The biogeochemical cycle of the adsorbed template. II - Selective adsorption of mononucleotides on adsorbed polynucleotide templates  

NASA Technical Reports Server (NTRS)

Experimental results are presented for the verification of the specific interaction step of the 'adsorbed template' biogeochemical cycle, a simple model for a primitive prebiotic replication system. The experimental system consisted of gypsum as the mineral to which an oligonucleotide template attaches (Poly-C or Poly-U) and (5-prime)-AMP, (5-prime)-GMP, (5-prime)-CMP and (5-prime)-UMP as the interacting biomonomers. When Poly-C or Poly-U were used as adsorbed templates, (5-prime)-GMP and (5-prime)-AMP, respectively, were observed to be the most strongly adsorbed species.

Lazard, Daniel; Lahav, Noam; Orenberg, James B.

1988-01-01

333

The contribution of plant-soil interactions to biogeochemical cycles in a changing world  

NASA Astrophysics Data System (ADS)

In terrestrial ecosystems, plants are the transducers that provide the energy for microbial metabolism through root exudation, cell sloughing, and the turnover of leaves and roots. Changes in the Earth's atmosphere such as increasing concentrations of atmospheric carbon dioxide, tropospheric ozone, and the atmospheric deposition of nitrogen, will modify plant net primary productivity (NPP) and plant carbon (C) allocation. These changes will, in turn, initiate a series of biochemical alterations in dead leaves and fine roots, responses which move through the soil to structure food webs and control rates of biogeochemical cycling. In our conceptual framework, plant physiology, plant tissue biochemistry, and the production and mortality of plant modules (leaves and roots) are pivotal control points in the soil for the regulation of ecosystem biogeochemistry. In other words, understanding how plant form and function as well as the associated microbial dynamics respond to changes in the Earth's atmosphere is important to understanding the biogeochemical feedbacks which may ultimately constrain long-term ecosystem responses. We will review examples of how changes in the Earth's atmosphere directly modify plant growth and C allocation, which initiates a series of physiological and biochemical changes in live and dead leaves and fine roots. We will then examine how these plant responses structure rhizosphere food webs and control rates of microbial metabolism. Microbial enzyme activity regulates many of the transformation and weathering processes in the soil, thus changes in the microbial community can strongly alter ecosystem biogeochemistry. For example, we will explore how plants and microbes are linked to ecosystem-level feedbacks between soil respiration, dissolved inorganic carbon (DIC), and dissolved organic carbon (DOC) leaching. The basic premise of our conceptual model is that altered atmospheric chemistry directly impacts plant form and function. Theses human-induced changes to the Earth's atmosphere will cascade through plants into the soil, where microbial communities mediate the ecosystem functions that regulate biogeochemical cycles. There are several key research opportunities as we attempt to understand how changes in the Earth's atmosphere cascade through terrestrial ecosystems to alter biogeochemical cycles. For example, far too little attention has been given to how the interactions between changes in atmospheric chemistry (e.g. carbon dioxide and nitrogen, or carbon dioxide and ozone) will impact C transformations in the soil. If we deliberately set out to understand how variable plant and microbial physiology are to interactive changes in atmospheric chemistry, it should be possible to build a deeper understanding of the fundamental processes controlling ecosystem response to global change.

Pregitzer, K.

2005-12-01

334

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

SciTech Connect

The overall project has been investigating the reactivity of pertechnetate [Tc(VII)] with Fe(II) forms in model mineral and mineral-microbe systems, and with sediments from the Oak Ridge FRC and the Hanford site. Past project results with Hanford and Oak Ridge sediments have been published in Fredrickson et al., (2004) and Kukkadapu et al., (2006). This poster summarizes a series of model system experiments that investigates whether microbes or biogenic Fe(II) were more important in the reduction of Tc(VII) in an anoxic suspension of ferrihydrite, Shewanella oneidensis MR-1, Tc(VII), and electron donor. Ferrihydrite is used to represent a bioavailable Fe(III) oxide present in small amounts in Oak Ridge and Hanford sediments. In order to address this overall goal, Tc(VII) reduction rates and redox products were studied in less complex systems where individual abiotic and biotic reactions were isolated for rigorous characterization. The specific objectives of the individual experiments in the series were as follows: (1) Identify the rates and products of the reaction of Tc(VII) with aqueous Fe(II) at circumneutral pH values (homogeneous reduction). (2) Identify the rates and products of the reaction of Tc(VII) with surface complexed Fe(II) on goethite and hematite in the circumneutral pH range (heterogeneous reduction). (3) Identify the rates and products of the reaction of Tc(VII) with MR-1 under anoxic conditions individually with hydrogen and lactate as electron donors (biologic reduction). (4) Use insights from the above experiments to determine which of the three above, potentially parallel reactions determine the final speciation of Tc in a mixture of ferrihydrite, respiring MR-1, and Tc(VII).

Zachara, John M.; Kukkadapu, Ravi K.; Heald, Steve M.; McKinley, James P.; Dohnalkova, Alice C.; Fredrickson, James K.; Byong-Hun Jeon

2006-04-05

335

Coupling between pore water fluxes, structural heterogeneity, and biogeochemical processes controls contaminant mobility, bioavailability, and toxicity in sediments  

NASA Astrophysics Data System (ADS)

Sediments can serve as both sinks and sources of contaminants in aquatic systems. Contaminants are typically not sequestered permanently in sediments, and instead release slowly to the water column, posing an ongoing threat to aquatic ecosystems and human health. Many processes, including hydrodynamic transport, sediment diagenesis, and bioturbation regulate the behavior and effects of contaminants in sediments. While many of these processes have been studied individually, it is extremely important to understand how they interact to control the form, flux and toxicity of metals in sediments. We used well-defined experimental mesocosms to investigate the effects of hydrodynamic and biological processes on the redistribution of metals between sediments, pore water and overlying water, associated changes in metals speciation, and resulting bioavailability and toxicity to benthic organisms. Metals speciation was evaluated in deposited and resuspended particles using x-ray absorption spectroscopy. We also used time-lapse photography and oxygen optode imaging to evaluate how bioturbation and bioirrigation control sediment structure, sediment mixing process, and oxygen delivery to sediments. In the extremely fine sediments used here, local contaminant fluxes are mainly dominated by diffusion, but episodic bioturbation and resuspension cause extreme variability in contaminant flux and increases oxidation of reduced sediments. Metals contamination substantially reduced bioturbation by indwelling organisms. Sediment resuspension decreased survival and increased tissue burden of epi-benthic organisms. Bioturbation mixed sediments as deep as several centimeters, while associated bioirrigation through worm burrows delivered oxygen over an order of magnitude deeper than local diffusion. These results show that it is important to understand how local transport processes, sediment chemistry, and biological activity interact to control rates and patterns of metals speciation and efflux from contaminated sediments.

Xie, M.; Fetters, K.; Jarrett, B.; Yuen, J.; Cadoux, C.; EI-Natour, M.; Packman, A. I.; Gaillard, J.; Burton, G.

2012-12-01

336

Reconstructing paleo-ocean silicon chemistry and ecology during Last Glacial Maximum, a biogeochemical cycle modeling approach  

NASA Astrophysics Data System (ADS)

It has been established by a number of investigators that opal content and Si-C isotope studies in the marine sediments reveal information about paleooceanography and the impact on silicic acid utilization by marine autotrophes (diatoms, silicoflagellates) and heterotrophes (radiolarians) during the Last Glacial Maximum (LGM). Opal, as an amorphous form of SiO2, formed by marine Si-secreting organisms, has been used as a proxy to indicate chemical ocean evolution, paleoproductivity and temperature variations in the paleoenvironment and regional ocean water biogeochemical studies, both on million- and thousand-year scales. Here, we are using a model of the global silicon biogeochemical cycle to understand and reconstruct evolutionary history of the paleobiogeochemical cycle and paleoenvironment since LGM. The model is process-driven, temperature-driven, and land-ocean-sediment coupled with specific marine Si-secreting organisms that represent different trophic levels and physiological mechanisms. Specifically, Si utilization by marine silicoflagellates and radiolarians are each about 5% of that of ubiquitous marine diatoms. Available marine reactive Si is controlled by variation of diatom bioproduction that represents 5% of the total marine primary productivity (Si/C Redfield ratio in the marine organic matter is ~0.13, which is an order of magnitude higher than ratio in land organic matter). River input of Si is controlled by chemical weathering of silicate rocks and biocyling of land plant phytoliths. Decreasing dissolved and particulate Si input from land and less favorable climatic condition into LGM diminished the primary production of marine diatoms. However, because radiolarians favor deep-water habitat, where a higher level of DSi is found and that is less affected by temperature changes, a peak of relative abundance is usually observed in sedimentary record during LGM. Given that opal formation fractionated seawater ?30Si (1‰) and enriched seawater with heavier 30Si, the sediment isotope records of ?30Si variations have been found to support the suppressed diatom Si biological bump. Since the LGM, the temperature increased about 5°C and contributed to almost 50% of land bio-productivity rise. On the other hand, warming climate and enhanced hydrological cycle drove the chemical weathering of continental silicate rocks and soil phytoliths remineralization that increased riverine input of dissolved Si, that promoted the Si utilization of diatom in the surface waters. We present a history of species-specific Si utilization due to the environmental and hydrological changes on land and in the ocean. We also use and compare available data of opal sedimentation, Si and C isotope records, as well as temperature history to better quantify the biogeochemistry of the Si cycle during LGM and in later time. The results provide insight into paleoproductivity of Si-C cycles in the ocean and assist the Si model in its projections of future environmental changes.

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

2012-12-01

337

Biophysical and Biogeochemical Responses to Climate Change Depend on Dispersal and Migration  

NSDL National Science Digital Library

This peer- reviewed article from BioScience looks at the effects of dispersal and migration on biophysical and biogeochemical responses to climate change. Different species, populations, and individuals disperse and migrate at different rates. The rate of movement that occurs in response to changes in climate, whether fast or slow, will shape the distribution of natural ecosystems in the decades to come. Moreover, land-use patterns associated with urban, suburban, rural, and agricultural development will complicate ecosystem adaptation to climate change by hindering migration. Here we examine how vegetation's capacity to disperse and migrate may affect the biophysical and biogeochemical characteristics of the land surface under anthropogenic climate change. We demonstrate that the effectiveness of plant migration strongly influences carbon storage, evapotranspiration, and the absorption of solar radiation by the land surface. As a result, plant migration affects the magnitude, and in some cases the sign, of feedbacks from the land surface to the climate system. We conclude that future climate projections depend on much better understanding of and accounting for dispersal and migration.

PAUL A. T. HIGGINS and JOHN HARTE (;)

2006-05-01

338

Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species.  

PubMed

The Marinobacter genus comprises widespread marine bacteria, found in localities as diverse as the deep ocean, coastal seawater and sediment, hydrothermal settings, oceanic basalt, sea-ice, sand, solar salterns, and oil fields. Terrestrial sources include saline soil and wine-barrel-decalcification wastewater. The genus was designated in 1992 for the Gram-negative, hydrocarbon-degrading bacterium Marinobacter hydrocarbonoclasticus. Since then, a further 31 type strains have been designated. Nonetheless, the metabolic range of many Marinobacter species remains largely unexplored. Most species have been classified as aerobic heterotrophs, and assessed for limited anaerobic pathways (fermentation or nitrate reduction), whereas studies of low-temperature hydrothermal sediments, basalt at oceanic spreading centers, and phytoplankton have identified species that possess a respiratory repertoire with significant biogeochemical implications. Notable physiological traits include nitrate-dependent Fe(II)-oxidation, arsenic and fumarate redox cycling, and Mn(II) oxidation. There is also evidence for Fe(III) reduction, and metal(loid) detoxification. Considering the ubiquity and metabolic capabilities of the genus, Marinobacter species may perform an important and underestimated role in the biogeochemical cycling of organics and metals in varied marine habitats, and spanning aerobic-to-anoxic redox gradients. PMID:23734151

Handley, Kim M; Lloyd, Jonathan R

2013-01-01

339

Contrasting biogeochemical characteristics of the Oubangui River and tributaries (Congo River basin)  

PubMed Central

The Oubangui is a major tributary of the Congo River. We describe the biogeochemistry of contrasting tributaries within its central catchment, with watershed vegetation ranging from wooded savannahs to humid rainforest. Compared to a 2-year monitoring record on the mainstem Oubangui, these tributaries show a wide range of biogeochemical signatures, from highly diluted blackwaters (low turbidity, pH, conductivity, and total alkalinity) in rainforests to those more typical for savannah systems. Spectral analyses of chromophoric dissolved organic matter showed wide temporal variations in the Oubangui compared to spatio-temporal variations in the tributaries, and confirm that different pools of dissolved organic carbon are mobilized during different hydrological stages. ?13C of dissolved inorganic carbon ranged between ?28.1‰ and ?5.8‰, and was strongly correlated to both partial pressure of CO2 and to the estimated contribution of carbonate weathering to total alkalinity, suggesting an important control of the weathering regime on CO2 fluxes. All tributaries were oversaturated in dissolved greenhouse gases (CH4, N2O, CO2), with highest levels in rivers draining rainforest. The high diversity observed underscores the importance of sampling that covers the variability in subcatchment characteristics, to improve our understanding of biogeochemical cycling in the Congo Basin.

Bouillon, Steven; Yambele, Athanase; Gillikin, David P.; Teodoru, Cristian; Darchambeau, Francois; Lambert, Thibault; Borges, Alberto V.

2014-01-01

340

The role of airborne volcanic ash for the surface ocean biogeochemical iron-cycle: a review  

NASA Astrophysics Data System (ADS)

Iron is a key micronutrient for phytoplankton growth in the surface ocean. Yet the significance of volcanism for the marine biogeochemical iron-cycle is poorly constrained. Recent studies, however, suggest that offshore deposition of airborne ash from volcanic eruptions is a way to inject significant amounts of bio-available iron into the surface ocean. Volcanic ash may be transported up to several tens of kilometres high into the atmosphere during large-scale eruptions and fine ash may encircle the globe for years, thereby reaching even the remotest and most iron-starved oceanic areas. Scientific ocean drilling demonstrates that volcanic ash layers and dispersed ash particles are frequently found in marine sediments and that therefore volcanic ash deposition and iron-injection into the oceans took place throughout much of the Earth's history. The data from geochemical and biological experiments, natural evidence and satellite techniques now available suggest that volcanic ash is a so far underestimated source for iron in the surface ocean, possibly of similar importance as aeolian dust. Here we summarise the development of and the knowledge in this fairly young research field. The paper covers a wide range of chemical and biological issues and we make recommendations for future directions in these areas. The review paper may thus be helpful to improve our understanding of the role of volcanic ash for the marine biogeochemical iron-cycle, marine primary productivity and the ocean-atmosphere exchange of CO2 and other gases relevant for climate throughout the Earth's history.

Duggen, S.; Olgun, N.; Croot, P.; Hoffmann, L.; Dietze, H.; Teschner, C.

2009-07-01

341

Molecular organic tracers of biogeochemical processes in a saline meromictic lake (Ace Lake)  

NASA Astrophysics Data System (ADS)

The chemical structures, distribution and stable carbon isotopic compositions of lipids in a sediment core taken in meromictic Ace Lake (Antarctica) were analyzed to trace past biogeochemical cycling. Biomarkers from methanogenic archaea, methanotrophic bacteria and photosynthetic green sulfur bacteria were unambiguously assigned using organic geochemical understanding and by reference to what is known about the lake's present-day ecosystem. For instance, saturated and unsaturated 2,6,10,15,19-pentamethylicosane, archaeol and sn2-hydroxyarchaeol were derived from methanogenic archaea. Carotenoid analysis revealed chlorobactene and isorenieratene derived from the green-colored and brown-colored strains of the green sulfur bacteria (Chlorobiaceae); isotopic analyses showed that they were 13C-enriched. Phytenes appear to be derived from photoautotrophs that use the Calvin-Benson cycle, while phytane has a different source, possibly within the archaea. The most 13C-depleted compounds (ca. -55‰) identified were 4-methyl-5?-cholest-8(14)-en-3?-ol, identified using an authentic standard, and co-occurring 4-methylsteradienes: these originate from the aerobic methanotrophic bacterium Methylosphaera hansonii. Lipids of photoautotrophic origin, steranes and alkenones, are relatively depleted (ca. -28 to -36‰) whilst archaeal biomarkers are relatively enriched in 13C (ca. -17 to -25‰). The structural and carbon isotope details of sedimentary lipids thus revealed aspects of in situ biogeochemical processes such as methane generation and oxidation and phototrophic sulfide oxidation.

Schouten, S.; Rijpstra, W. I. C.; Kok, M.; Hopmans, E. C.; Summons, R. E.; Volkman, J. K.; Sinninghe Damsté, J. S.

2001-05-01

342

Terrestrial biogeochemical feedbacks in the climate system: from past to future  

SciTech Connect

The terrestrial biosphere plays a major role in the regulation of atmospheric composition, and hence climate, through multiple interlinked biogeochemical cycles (BGC). Ice-core and other palaeoenvironmental records show a fast response of vegetation cover and exchanges with the atmosphere to past climate change, although the phasing of these responses reflects spatial patterning and complex interactions between individual biospheric feedbacks. Modern observations show a similar responsiveness of terrestrial biogeochemical cycles to anthropogenically-forced climate changes and air pollution, with equally complex feedbacks. For future conditions, although carbon cycle-climate interactions have been a major focus, other BGC feedbacks could be as important in modulating climate changes. The additional radiative forcing from terrestrial BGC feedbacks other than those conventionally attributed to the carbon cycle is in the range of 0.6 to 1.6 Wm{sup -2}; all taken together we estimate a possible maximum of around 3 Wm{sup -2} towards the end of the 21st century. There are large uncertainties associated with these estimates but, given that the majority of BGC feedbacks result in a positive forcing because of the fundamental link between metabolic stimulation and increasing temperature, improved quantification of these feedbacks and their incorporation in earth system models is necessary in order to develop coherent plans to manage ecosystems for climate mitigation.

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

2010-01-05

343

Contrasting biogeochemical characteristics of the Oubangui River and tributaries (Congo River basin).  

PubMed

The Oubangui is a major tributary of the Congo River. We describe the biogeochemistry of contrasting tributaries within its central catchment, with watershed vegetation ranging from wooded savannahs to humid rainforest. Compared to a 2-year monitoring record on the mainstem Oubangui, these tributaries show a wide range of biogeochemical signatures, from highly diluted blackwaters (low turbidity, pH, conductivity, and total alkalinity) in rainforests to those more typical for savannah systems. Spectral analyses of chromophoric dissolved organic matter showed wide temporal variations in the Oubangui compared to spatio-temporal variations in the tributaries, and confirm that different pools of dissolved organic carbon are mobilized during different hydrological stages. ?(13)C of dissolved inorganic carbon ranged between -28.1‰ and -5.8‰, and was strongly correlated to both partial pressure of CO2 and to the estimated contribution of carbonate weathering to total alkalinity, suggesting an important control of the weathering regime on CO2 fluxes. All tributaries were oversaturated in dissolved greenhouse gases (CH4, N2O, CO2), with highest levels in rivers draining rainforest. The high diversity observed underscores the importance of sampling that covers the variability in subcatchment characteristics, to improve our understanding of biogeochemical cycling in the Congo Basin. PMID:24954525

Bouillon, Steven; Yambélé, Athanase; Gillikin, David P; Teodoru, Cristian; Darchambeau, François; Lambert, Thibault; Borges, Alberto V

2014-01-01

344

Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed.  

PubMed

Wildfires can significantly alter forest carbon (C) storage and nitrogen (N) availability, but the long-term biogeochemical legacy of wildfires is poorly understood. We obtained a lake-sediment record of fire and biogeochemistry from a subalpine forest in Colorado, USA, to examine the nature, magnitude, and duration of decadal-scale, fire-induced ecosystem change over the past c. 4250 yr. The high-resolution record contained 34 fires, including 13 high-severity events within the watershed. High-severity fires were followed by increased sedimentary N stable isotope ratios (?(15) N) and bulk density, and decreased C and N concentrations - reflecting forest floor destruction, terrestrial C and N losses, and erosion. Sustained low sediment C : N c. 20-50 yr post-fire indicates reduced terrestrial organic matter subsidies to the lake. Low sedimentary ?(15) N c. 50-70 yr post-fire, coincident with C and N recovery, suggests diminishing terrestrial N availability during stand development. The magnitude of post-fire changes generally scaled directly with inferred fire severity. Our results support modern studies of forest successional C and N accumulation and indicate pronounced, long-lasting biogeochemical impacts of wildfires in subalpine forests. However, even repeated high-severity fires over millennia probably did not deplete C or N stocks, because centuries between high-severity fires allowed for sufficient biomass recovery. PMID:24803372

Dunnette, Paul V; Higuera, Philip E; McLauchlan, Kendra K; Derr, Kelly M; Briles, Christy E; Keefe, Margaret H

2014-08-01

345

Biogeochemical processes governing exposure and uptake of organic pollutant compounds in aquatic organisms.  

PubMed Central

This paper reviews current knowledge of biogeochemical cycles of pollutant organic chemicals in aquatic ecosystems with a focus on coastal ecosystems. There is a bias toward discussing chemical and geochemical aspects of biogeochemical cycles and an emphasis on hydrophobic organic compounds such as polynuclear aromatic hydrocarbons, polychlorinated biphenyls, and chlorinated organic compounds used as pesticides. The complexity of mixtures of pollutant organic compounds, their various modes of entering ecosystems, and their physical chemical forms are discussed. Important factors that influence bioavailability and disposition (e.g., organism-water partitioning, uptake via food, food web transfer) are reviewed. These factors include solubilities of chemicals; partitioning of chemicals between solid surfaces, colloids, and soluble phases; variables rates of sorption, desorption; and physiological status of organism. It appears that more emphasis on considering food as a source of uptake and bioaccumulation is important in benthic and epibenthic ecosystems when sediment-associated pollutants are a significant source of input to an aquatic ecosystem. Progress with mathematical models for exposure and uptake of contaminant chemicals is discussed briefly.

Farrington, J W

1991-01-01

346

Biogeochemical processes governing natural pyrite oxidation and release of Acid metalliferous drainage.  

PubMed

The oxidative dissolution of sulfide minerals (principally pyrite) is responsible for the majority of acid metalliferous drainage from mine sites, which represents a significant environmental problem worldwide. Understanding the complex biogeochemical processes governing natural pyrite oxidation is critical not only for solving this problem but also for understanding the industrial bioleaching of sulfide minerals. To this end, we conducted a simulated experiment of natural pyrite oxidative dissolution. Pyrosequencing analysis of the microbial community revealed a distinct succession across three stages. At the early stage, a newly proposed genus, Tumebacillus (which can use sodium thiosulfate and sulfite as the sole electron donors), dominated the microbial community. At the midstage, Alicyclobacillus (the fifth most abundant genus at the early stage) became the most dominant genus, whereas Tumebacillus was still ranked as the second most abundant. At the final stage, the microbial community was dominated by Ferroplasma (the tenth most abundant genus at the early stage). Our geochemical and mineralogical analyses indicated that exchangeable heavy metals increased as the oxidation progressed and that some secondary sulfate minerals (including jarosite and magnesiocopiapite) were formed at the final stage of the oxidation sequence. Additionally, we propose a comprehensive model of biogeochemical processes governing the oxidation of sulfide minerals. PMID:24730689

Chen, Ya-Ting; Li, Jin-Tian; Chen, Lin-Xing; Hua, Zheng-Shuang; Huang, Li-Nan; Liu, Jun; Xu, Bi-Bo; Liao, Bin; Shu, Wen-Sheng

2014-05-20

347

Scientific Posters from the DOE Subsurface Biogeochemical Research Program's Annual PI Meeting, 2012  

DOE Data Explorer

The Department of Energy's Subsurface Biogeochemical Research (SBR) program held its 7th annual Principal Investigator (PI) meeting on April 30-May 2, 2012 at the Wardman Park Hotel, Washington, DC. The Poster Session included the following scientific posters: • In Situ Generation of Iron-Chromium Precipitates for Long-Term Immobilization of Chromium at the Hanford Site • SLAC SFA: Biogeochemical Processes and Diffusive Transport Limitations Affecting the Stability of biogenic U(IV) • Formation and Stability of Uranium(VI) Phosphates under Groundwater Conditions • Development of Surface Complexation Models of Cr(VI) Adsorption on Soils, Sediments, and Model Mixtures of Kaolinite, Montmorillonite, g-Alumina, Hydrous Manganese and Ferric Oxides and Goethite • Radiochemically-Supported Microbial Communities: A Potential Mechanism for Biocolloid Production of Importance to Actinide Transport • Processes Affecting Iodine-127, 129 Speciation and Mobility in Two Contaminated DOE Plumes • Plutonium Speciation and Mobility through the Subsurface Environment: Nature of Organic Colloidal Carriers • Identification and Characterization of Microbial Proteins Important for Extracellular Electron Transfer Reactions

348

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

NASA Astrophysics Data System (ADS)

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

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

2005-12-01

349

Global Biogeochemical Fluxes Program for the Ocean Observatories Initiative: A Proposal. (Invited)  

NASA Astrophysics Data System (ADS)

The overarching emphasis of the Global Biogeochemical Flux Ocean Observatories Initiative is to assess the role of oceanic carbon, both living and non-, in the Earth climate system. Modulation of atmospheric CO2 and its influence on global climate is a function of the quantitative capacity of the oceans to sequester organic carbon into deep waters. Critical to our understanding of the role of the oceans in the global cycling of carbon are the quantitative dynamics in both time and space of the fixation of CO2 into organic matter by surface ocean primary production and removal of this carbon to deep waters via the “biological pump”. To take the next major step forward in advancing our understanding of the oceanic biological pump, a global observation program is required that: (i) greatly improves constraints on estimates of global marine primary production (PP), a critical factor in understanding the global CO2 cycle and for developing accurate estimates of export production (EP); (ii) explores the spatiotemporal links between PP, EP and the biogeochemical processes that attenuate particulate organic carbon (POC) flux; (iii) characterizes microbial community structure and dynamics both in the surface and deep ocean; (iv) develops a comprehensive picture of the chemical and biological processes that take place from the surface ocean to the sea floor; (v) provides unique time-series samples for detailed laboratory-based chemical and biological characterization and tracer studies that will enable connections to be made between the operation of the biological pump at present and in the geologic past. The primary goal is to provide high quality biological and biogeochemical observational data for the modeling and prediction efforts of the global CO2 cycle research community. Crucial to the realization of the GBF-OOI is the development of reliable, long-term, time-series ocean observation platforms capable of precise and controlled placement of sophisticated biogeochemical sensors/samplers, and in situ experimental systems at a wide range of depths, including close proximity to the sea surface. Significant opportunities exist to exploit sensor miniaturization in combination with recent exponential improvements in “omics” technologies for measurement of nucleic acids, proteins and metabolites with unprecedented throughput and resolution. We will discuss the goals, philosophy, principal experimental and technical approaches and operational challenges. We will outline proposed mooring systems as well as means for accurate, spatiotemporal assessment of: (i) primary production, (ii) constraint of POC export flux with season and depth, (iii) assessment of microbial and zooplankton community structure/function throughout the water column, and (iv) collection and preservation of particulate and water samples for land-based examination of temporal and vertical variability of specific tracers, isotopes, nutrients, DOC and related substances for even more precise measurements of environmental biogeochemical properties. The GBF-OOI will become our Hubble for the sea.

Ulmer, K. M.; Taylor, C.

2010-12-01

350

Light-Dependent Transcriptional Regulation of Genes of Biogeochemical Interest in the Diploid and Haploid Life Cycle Stages of Emiliania huxleyi? †  

PubMed Central

The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.

Richier, Sophie; Kerros, Marie-Emmanuelle; de Vargas, Colomban; Haramaty, Liti; Falkowski, Paul G.; Gattuso, Jean-Pierre

2009-01-01