Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

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

EPA Science Inventory

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

Biogeochemical Role of Subsurface Coherent Eddies in the Ocean: Tracer Cannonballs, Hypoxic Storms, and Microbial Stewpots?

NASA Astrophysics Data System (ADS)

Frenger, Ivy; Bianchi, Daniele; Stührenberg, Carolin; Oschlies, Andreas; Dunne, John; Deutsch, Curtis; Galbraith, Eric; Schütte, Florian

2018-02-01

Subsurface eddies are known features of ocean circulation, but the sparsity of observations prevents an assessment of their importance for biogeochemistry. Here we use a global eddying (0.1°) ocean-biogeochemical model to carry out a census of subsurface coherent eddies originating from eastern boundary upwelling systems (EBUS) and quantify their biogeochemical effects as they propagate westward into the subtropical gyres. While most eddies exist for a few months, moving over distances of hundreds of kilometers, a small fraction (<5%) of long-lived eddies propagates over distances greater than 1,000 km, carrying the oxygen-poor and nutrient-rich signature of EBUS into the gyre interiors. In the Pacific, transport by subsurface coherent eddies accounts for roughly 10% of the offshore transport of oxygen and nutrients in pycnocline waters. This "leakage" of subsurface waters can be a significant fraction of the transport by nutrient-rich poleward undercurrents and may contribute to the well-known reduction of productivity by eddies in EBUS. Furthermore, at the density layer of their cores, eddies decrease climatological oxygen locally by close to 10%, thereby expanding oxygen minimum zones. Finally, eddies represent low-oxygen extreme events in otherwise oxygenated waters, increasing the area of hypoxic waters by several percent and producing dramatic short-term changes that may play an important ecological role. Capturing these nonlocal effects in global climate models, which typically include noneddying oceans, would require dedicated parameterizations.

Biogeochemical Stability of Contaminants in the Subsurface Following In Situ Treatment

EPA Science Inventory

In recent years, innovative treatment technologies have emerged to meet groundwater cleanup goals. In many cases these methods take advantage of the redox behavior of contaminant species. For example, remedial technologies that strategically manipulate subsurface redox conditio...

A spatially explicit hydro-ecological modeling framework (BEPS-TerrainLab V2.0): Model description and test in a boreal ecosystem in Eastern North America

NASA Astrophysics Data System (ADS)

Govind, Ajit; Chen, Jing Ming; Margolis, Hank; Ju, Weimin; Sonnentag, Oliver; Giasson, Marc-André

2009-04-01

SummaryA spatially explicit, process-based hydro-ecological model, BEPS-TerrainLab V2.0, was developed to improve the representation of ecophysiological, hydro-ecological and biogeochemical processes of boreal ecosystems in a tightly coupled manner. Several processes unique to boreal ecosystems were implemented including the sub-surface lateral water fluxes, stratification of vegetation into distinct layers for explicit ecophysiological representation, inclusion of novel spatial upscaling strategies and biogeochemical processes. To account for preferential water fluxes common in humid boreal ecosystems, a novel scheme was introduced based on laboratory analyses. Leaf-scale ecophysiological processes were upscaled to canopy-scale by explicitly considering leaf physiological conditions as affected by light and water stress. The modified model was tested with 2 years of continuous measurements taken at the Eastern Old Black Spruce Site of the Fluxnet-Canada Research Network located in a humid boreal watershed in eastern Canada. Comparison of the simulated and measured ET, water-table depth (WTD), volumetric soil water content (VSWC) and gross primary productivity (GPP) revealed that BEPS-TerrainLab V2.0 simulates hydro-ecological processes with reasonable accuracy. The model was able to explain 83% of the ET, 92% of the GPP variability and 72% of the WTD dynamics. The model suggests that in humid ecosystems such as eastern North American boreal watersheds, topographically driven sub-surface baseflow is the main mechanism of soil water partitioning which significantly affects the local-scale hydrological conditions.

Linking Metabolism, Elemental Cycles, and Environmental Conditions in the Deep Biosphere: Growth of a Model Extremophile, Archaeoglobus fulgidus, Under High-Pressure Conditions

NASA Astrophysics Data System (ADS)

Oliver, G. C. M.; Cario, A.; Rogers, K. L.

2015-12-01

A majority of Earth's biosphere is hosted in subsurface environments where global-scale biogeochemical and energy cycles are driven by diverse microbial communities that operate on and are influenced by micro-scale environmental variables. While the subsurface hosts a variety of geochemical and geothermal conditions, elevated pressures are common to all subsurface ecosystems. Understanding how microbes adapt to and thrive in high-pressure environments is essential to linking microbial subsurface processes with global-scale cycles. Here we are using a model extremophile, Archaeoglobus fulgidus, to determine how elevated pressures affect the growth, metabolism, and physiology of subsurface microorganisms. A. fulgidus cycles carbon and sulfur via heterotrophic and autotrophic sulfate reduction in various high temperature and high-pressure niches including shallow marine vents, deep-sea hydrothermal vents, and deep oil reservoirs. Here we report the results of A. fulgidus growth experiments at optimum temperature, 83°C, and pressures up to 600 bars. Exponential growth was observed over the entire pressure range, though growth rates were diminished at 500 and 600 bars compared to ambient pressure experimental controls. At pressures up to 400 bars, cell density yields and growth rates were at least as high as ambient pressure controls. Elevated pressures and extended incubation times stimulated cell flocculation, a common stress response in this strain, and cellular morphology was affected at pressures exceeding 400 bars. These results suggest that A. fulgidus continues carbon, sulfur and energy cycling unaffected by elevated pressures up to 400 bars, representing a variety of subsurface environments. The ability of subsurface organisms to drive biogeochemical cycles at elevated pressures is a critical link between the surface and subsurface biospheres and understanding how species-scale processes operate under these conditions is a vital part of global-scale biogeochemical models.

Two-Relaxation-Time Lattice Boltzmann Method and its Application to Advective-Diffusive-Reactive Transport

DOE PAGES

Yan, Zhifeng; Yang, Xiaofan; Li, Siliang; ...

2017-09-05

The lattice Boltzmann method (LBM) based on single-relaxation-time (SRT) or multiple-relaxation-time (MRT) collision operators is widely used in simulating flow and transport phenomena. The LBM based on two-relaxation-time (TRT) collision operators possesses strengths from the SRT and MRT LBMs, such as its simple implementation and good numerical stability, although tedious mathematical derivations and presentations of the TRT LBM hinder its application to a broad range of flow and transport phenomena. This paper describes the TRT LBM clearly and provides a pseudocode for easy implementation. Various transport phenomena were simulated using the TRT LBM to illustrate its applications in subsurface environments.more » These phenomena include advection-diffusion in uniform flow, Taylor dispersion in a pipe, solute transport in a packed column, reactive transport in uniform flow, and bacterial chemotaxis in porous media. Finally, the TRT LBM demonstrated good numerical performance in terms of accuracy and stability in predicting these transport phenomena. Therefore, the TRT LBM is a powerful tool to simulate various geophysical and biogeochemical processes in subsurface environments.« less

Two-relaxation-time lattice Boltzmann method and its application to advective-diffusive-reactive transport

NASA Astrophysics Data System (ADS)

Yan, Zhifeng; Yang, Xiaofan; Li, Siliang; Hilpert, Markus

2017-11-01

The lattice Boltzmann method (LBM) based on single-relaxation-time (SRT) or multiple-relaxation-time (MRT) collision operators is widely used in simulating flow and transport phenomena. The LBM based on two-relaxation-time (TRT) collision operators possesses strengths from the SRT and MRT LBMs, such as its simple implementation and good numerical stability, although tedious mathematical derivations and presentations of the TRT LBM hinder its application to a broad range of flow and transport phenomena. This paper describes the TRT LBM clearly and provides a pseudocode for easy implementation. Various transport phenomena were simulated using the TRT LBM to illustrate its applications in subsurface environments. These phenomena include advection-diffusion in uniform flow, Taylor dispersion in a pipe, solute transport in a packed column, reactive transport in uniform flow, and bacterial chemotaxis in porous media. The TRT LBM demonstrated good numerical performance in terms of accuracy and stability in predicting these transport phenomena. Therefore, the TRT LBM is a powerful tool to simulate various geophysical and biogeochemical processes in subsurface environments.

Two-Relaxation-Time Lattice Boltzmann Method and its Application to Advective-Diffusive-Reactive Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Zhifeng; Yang, Xiaofan; Li, Siliang

The lattice Boltzmann method (LBM) based on single-relaxation-time (SRT) or multiple-relaxation-time (MRT) collision operators is widely used in simulating flow and transport phenomena. The LBM based on two-relaxation-time (TRT) collision operators possesses strengths from the SRT and MRT LBMs, such as its simple implementation and good numerical stability, although tedious mathematical derivations and presentations of the TRT LBM hinder its application to a broad range of flow and transport phenomena. This paper describes the TRT LBM clearly and provides a pseudocode for easy implementation. Various transport phenomena were simulated using the TRT LBM to illustrate its applications in subsurface environments.more » These phenomena include advection-diffusion in uniform flow, Taylor dispersion in a pipe, solute transport in a packed column, reactive transport in uniform flow, and bacterial chemotaxis in porous media. Finally, the TRT LBM demonstrated good numerical performance in terms of accuracy and stability in predicting these transport phenomena. Therefore, the TRT LBM is a powerful tool to simulate various geophysical and biogeochemical processes in subsurface environments.« less

Spectral induced polarization as a tool to map subsurface biogeochemical hot spots: a first laboratory evaluation in the Fe-S system

NASA Astrophysics Data System (ADS)

Nordsiek, Sven; Gilfedder, Ben; Frei, Sven

2017-04-01

Zones of intense biogeochemical reactivity (hot spots) arise in the saturated subsurface at the interface between regions with oxidizing and reducing conditions. Hot spots are both sinks and sources of different chemical compounds, thus they are of particular importance for element cycling in the subsurface. However, the investigation of hot spot structures is difficult, because they are not directly identifiable from the surface and can only be investigated by invasive methods in the subsurface. Additionally, they often form in sensitive wetland ecosystems where only non-destructive measurements are applicable to avoid significant degradation of these sensitive environments. Under these circumstances, geophysical methods may provide useful tools to identify biogeochemically active regions. One of the most important biogeochemical reactions in wetlands is the reduction of sulphate and formation and accumulation of FexSy minerals (where x and y delineate mineral stoichiometry). These reactions only occur in specific hot spots where specific chemical and microbial conditions are met. Within a research project concerning biogeochemical transformations and turnover in wetlands, we investigate the applicability of the geoelectrical method of spectral induced polarization (SIP) to locate and monitor regions containing polarizing FexSy particles as indicator for biogeochemical hot spots. After developing and testing a sample holder and a set of non-polarizing electrodes for laboratory SIP measurements, we performed experiments on natural soil samples taken from the hyporheic zone of a local river channel. The collected material originates from a location known for biogeochemical activity. The sample contains a high percentage of dark grayish/black sediment interpreted as FexSy, and possibly pyrite (FeS2). The material was homogenized and split into four samples. The FexSy concentration was adjusted to three different levels by oxidation using H2O2. For all samples we recorded the SIP spectra in the frequency range between 0.26 Hz and 25 Hz repeatedly. The sensitivity of SIP measurements to the FexSy content is promising. For a sample of the sediment saturated with its natural fluid (conductivity > 600 μS/cm), we observed phase shifts of more than 7 mrad at frequencies between 1 and 10 Hz. We expect a lower fluid conductivity and thus a larger maximum phase shift for measurements in wetlands. The application of the SIP method in field surveys at places with biogeochemical activity will be the next step in our study.

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates: BIOFILM DISTRIBUTION AND RATE SCALING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan

Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models, and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical propertiesmore » was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.« less

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

NASA Astrophysics Data System (ADS)

Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan; Bailey, Vanessa L.

2017-11-01

Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN

PubMed Central

Hammond, G E; Lichtner, P C; Mills, R T

2014-01-01

[1] To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer. After a brief introduction to the code's parallel layout and code design, PFLOTRAN's parallel performance (measured through strong and weak scalability analyses) is evaluated in the context of conceptual model layout, software and algorithmic design, and known hardware limitations. PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field. Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted. PMID:25506097

Evaluating the performance of parallel subsurface simulators: An illustrative example with PFLOTRAN.

PubMed

Hammond, G E; Lichtner, P C; Mills, R T

2014-01-01

[1] To better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code PFLOTRAN as it is applied to several realistic modeling scenarios run on the Jaguar supercomputer. After a brief introduction to the code's parallel layout and code design, PFLOTRAN's parallel performance (measured through strong and weak scalability analyses) is evaluated in the context of conceptual model layout, software and algorithmic design, and known hardware limitations. PFLOTRAN scales well (with regard to strong scaling) for three realistic problem scenarios: (1) in situ leaching of copper from a mineral ore deposit within a 5-spot flow regime, (2) transient flow and solute transport within a regional doublet, and (3) a real-world problem involving uranium surface complexation within a heterogeneous and extremely dynamic variably saturated flow field. Weak scalability is discussed in detail for the regional doublet problem, and several difficulties with its interpretation are noted.

2500 high-quality genomes reveal that the biogeochemical cycles of C, N, S and H are cross-linked by metabolic handoffs in the terrestrial subsurface

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Brown, C. T.; Hug, L. A.; Sharon, I.; Castelle, C. J.; Shelton, A.; Bonet, B.; Probst, A. J.; Thomas, B. C.; Singh, A.; Wilkins, M.; Williams, K. H.; Tringe, S. G.; Beller, H. R.; Brodie, E.; Hubbard, S. S.; Banfield, J. F.

2015-12-01

Microorganisms drive the transformations of carbon compounds in the terrestrial subsurface, a key reservoir of carbon on earth, and impact other linked biogeochemical cycles. Our current knowledge of the microbial ecology in this environment is primarily based on 16S rRNA gene sequences that paint a biased picture of microbial community composition and provide no reliable information on microbial metabolism. Consequently, little is known about the identity and metabolic roles of the uncultivated microbial majority in the subsurface. In turn, this lack of understanding of the microbial processes that impact the turnover of carbon in the subsurface has restricted the scope and ability of biogeochemical models to capture key aspects of the carbon cycle. In this study, we used a culture-independent, genome-resolved metagenomic approach to decipher the metabolic capabilities of microorganisms in an aquifer adjacent to the Colorado River, near Rifle, CO, USA. We sequenced groundwater and sediment samples collected across fifteen different geochemical regimes. Sequence assembly, binning and manual curation resulted in the recovery of 2,542 high-quality genomes, 27 of which are complete. These genomes represent 1,300 non-redundant organisms comprising both abundant and rare community members. Phylogenetic analyses involving ribosomal proteins and 16S rRNA genes revealed the presence of up to 34 new phyla that were hitherto unknown. Less than 11% of all genomes belonged to the 4 most commonly represented phyla that constitute 93% of all currently available genomes. Genome-specific analyses of metabolic potential revealed the co-occurrence of important functional traits such as carbon fixation, nitrogen fixation and use of electron donors and electron acceptors. Finally, we predict that multiple organisms are often required to complete redox pathways through a complex network of metabolic handoffs that extensively cross-link subsurface biogeochemical cycles.

Quantifying Subsurface Water and Heat Distribution and its Linkage with Landscape Properties in Terrestrial Environment using Hydro-Thermal-Geophysical Monitoring and Coupled Inverse Modeling

NASA Astrophysics Data System (ADS)

Dafflon, B.; Tran, A. P.; Wainwright, H. M.; Hubbard, S. S.; Peterson, J.; Ulrich, C.; Williams, K. H.

2015-12-01

Quantifying water and heat fluxes in the subsurface is crucial for managing water resources and for understanding the terrestrial ecosystem where hydrological properties drive a variety of biogeochemical processes across a large range of spatial and temporal scales. Here, we present the development of an advanced monitoring strategy where hydro-thermal-geophysical datasets are continuously acquired and further involved in a novel inverse modeling framework to estimate the hydraulic and thermal parameter that control heat and water dynamics in the subsurface and further influence surface processes such as evapotranspiration and vegetation growth. The measured and estimated soil properties are also used to investigate co-interaction between subsurface and surface dynamics by using above-ground aerial imaging. The value of this approach is demonstrated at two different sites, one in the polygonal shaped Arctic tundra where water and heat dynamics have a strong impact on freeze-thaw processes, vegetation and biogeochemical processes, and one in a floodplain along the Colorado River where hydrological fluxes between compartments of the system (surface, vadose zone and groundwater) drive biogeochemical transformations. Results show that the developed strategy using geophysical, point-scale and aerial measurements is successful to delineate the spatial distribution of hydrostratigraphic units having distinct physicochemical properties, to monitor and quantify in high resolution water and heat distribution and its linkage with vegetation, geomorphology and weather conditions, and to estimate hydraulic and thermal parameters for enhanced predictions of water and heat fluxes as well as evapotranspiration. Further, in the Colorado floodplain, results document the potential presence of only periodic infiltration pulses as a key hot moment controlling soil hydro and biogeochemical functioning. In the arctic, results show the strong linkage between soil water content, thermal parameters, thaw layer thickness and vegetation distribution. Overall, results of these efforts demonstrate the value of coupling various datasets at high spatial and temporal resolution to improve predictive understanding of subsurface and surface dynamics.

Lateral, vertical, and longitudinal connectivity of runoff source areas drive stream hydro-biogeochemical signals across a low relief drainage network

NASA Astrophysics Data System (ADS)

Zimmer, M. A.; McGlynn, B. L.

2017-12-01

Our understanding of the balance between longitudinal, lateral, and vertical expansion and contraction of reactive flowpaths and source areas in headwater catchments is limited. To address this, we utilized an ephemeral-to-perennial stream network in the Piedmont region of North Carolina, USA to gain new understanding about critical zone mechanisms that drive runoff generation and biogeochemical signals in both groundwater and stream water. Here, we used chemical and hydrometric data collected from zero through second order catchments to characterize spatial and temporal runoff and overland, shallow soil, and deep subsurface flow across characteristic landscape positions. Our results showed that the active stream network was driven by two superimposed runoff generation regimes that produced distinct hydro-biogeochemical signals at the catchment outlet. The baseflow runoff generation regime expanded and contracted the stream network seasonally through the rise and fall of the seasonal water table. Superimposed on this, event-activated source area contributions were driven by surficial and shallow subsurface flowpaths. The subsurface critical zone stratigraphy in this landscape coupled with the precipitation regime activated these shallow flowpaths frequently. This drove an increase in dissolved organic carbon (DOC) concentrations with increases in runoff across catchment scales. DOC-runoff relationship variability and spread was driven by the balance between runoff regimes as well as a seasonal depletion of DOC from shallow subsurface flowpath activation and annual replenishment from litterfall. From this, we suggest that the hydro-biogeochemical signals at larger catchment outlets can be driven by a balance of longitudinal, lateral, and vertical source area contributions, critical zone structure, and complex hydrological processes.

Spatially explicit simulation of hydrologically controlled carbon and nitrogen cycles and associated feedback mechanisms in a boreal ecosystem

NASA Astrophysics Data System (ADS)

Govind, Ajit; Chen, Jing Ming; Ju, Weimin

2009-06-01

Ecosystem models that simulate biogeochemical processes usually ignore hydrological controls that govern them. It is quite possible that topographically driven water fluxes significantly influence the spatial distribution of C sources and sinks because of their large contribution to the local water balance. To investigate this, we simulated biogeochemical processes along with the associated feedback mechanisms in a boreal ecosystem using a spatially explicit hydroecological model, boreal ecosystem productivity simulator (BEPS)-TerrainLab V2.0, that has a tight coupling of ecophysiological, hydrological, and biogeochemical processes. First, the simulated dynamics of snowpack, soil temperature, net ecosystem productivity (NEP), and total ecosystem respiration (TER) were validated with high-frequency measurements for 2 years. The model was able to explain 80% of the variability in NEP and 84% of the variability in TER. Further, we investigated the influence of topographically driven subsurface base flow on soil C and N cycling and on the spatiotemporal patterns of C sources and sinks using three hydrological modeling scenarios that differed in hydrological conceptualizations. In general, the scenarios that had nonexplicit hydrological representation overestimated NEP, as opposed to the scenario that had an explicit (realistic) representation. The key processes controlling the NEP differences were attributed to the combined effects of variations in photosynthesis (due to changes in stomatal conductance and nitrogen (N) availability), heterotrophic respiration, and autotrophic respiration, all of which occur simultaneously affecting NEP. Feedback relationships were also found to exacerbate the differences. We identified six types of NEP differences (biases), of which the most commonly found was due to an underestimation of the existing C sources, highlighting the vulnerability of regional-scale ecosystem models that ignore hydrological processes.

Volume reduction outweighs biogeochemical processes in controlling phosphorus treatment in aged detention systems

NASA Astrophysics Data System (ADS)

Shukla, Asmita; Shukla, Sanjay; Annable, Michael D.; Hodges, Alan W.

2017-08-01

Stormwater detention areas (SDAs) play an important role in treating end-of-the-farm runoff in phosphorous (P) limited agroecosystems. Phosphorus transport from the SDAs, including those through subsurface pathways, are not well understood. The prevailing understanding of these systems assumes that biogeochemical processes play the primary treatment role and that subsurface losses can be neglected. Water and P fluxes from a SDA located in a row-crop farm were measured for two years (2009-2011) to assess the SDA's role in reducing downstream P loads. The SDA treated 55% (497 kg) and 95% (205 kg) of the incoming load during Year 1 (Y1, 09-10) and Year 2 (Y2, 10-11), respectively. These treatment efficiencies were similar to surface water volumetric retention (49% in Y1 and 84% in Y2) and varied primarily with rainfall. Similar water volume and P retentions indicate that volume retention is the main process controlling P loads. A limited role of biogeochemical processes was supported by low to no remaining soil P adsorption capacity due to long-term drainage P input. The fact that outflow P concentrations (Y1 = 368.3 μg L- 1, Y2 = 230.4 μg L- 1) could be approximated by using a simple mixing of rainfall and drainage P input further confirmed the near inert biogeochemical processes. Subsurface P losses through groundwater were 304 kg (27% of inflow P) indicating that they are an important source for downstream P. Including subsurface P losses reduces the treatment efficiency to 35% (from 61%). The aboveground biomass in the SDA contained 42% (240 kg) of the average incoming P load suggesting that biomass harvesting could be a cost-effective alternative for reviving the role of biogeochemical processes to enhance P treatment in aged, P-saturated SDAs. The 20-year present economic value of P removal through harvesting was estimated to be 341,000, which if covered through a cost share or a payment for P treatment services program could be a positive outcome for both agriculture and public interests.

Volume reduction outweighs biogeochemical processes in controlling phosphorus treatment in aged detention systems.

PubMed

Shukla, Asmita; Shukla, Sanjay; Annable, Michael D; Hodges, Alan W

2017-08-01

Stormwater detention areas (SDAs) play an important role in treating end-of-the-farm runoff in phosphorous (P) limited agroecosystems. Phosphorus transport from the SDAs, including those through subsurface pathways, are not well understood. The prevailing understanding of these systems assumes that biogeochemical processes play the primary treatment role and that subsurface losses can be neglected. Water and P fluxes from a SDA located in a row-crop farm were measured for two years (2009-2011) to assess the SDA's role in reducing downstream P loads. The SDA treated 55% (497kg) and 95% (205kg) of the incoming load during Year 1 (Y1, 09-10) and Year 2 (Y2, 10-11), respectively. These treatment efficiencies were similar to surface water volumetric retention (49% in Y1 and 84% in Y2) and varied primarily with rainfall. Similar water volume and P retentions indicate that volume retention is the main process controlling P loads. A limited role of biogeochemical processes was supported by low to no remaining soil P adsorption capacity due to long-term drainage P input. The fact that outflow P concentrations (Y1=368.3μg L -1 , Y2=230.4μg L -1 ) could be approximated by using a simple mixing of rainfall and drainage P input further confirmed the near inert biogeochemical processes. Subsurface P losses through groundwater were 304kg (27% of inflow P) indicating that they are an important source for downstream P. Including subsurface P losses reduces the treatment efficiency to 35% (from 61%). The aboveground biomass in the SDA contained 42% (240kg) of the average incoming P load suggesting that biomass harvesting could be a cost-effective alternative for reviving the role of biogeochemical processes to enhance P treatment in aged, P-saturated SDAs. The 20-year present economic value of P removal through harvesting was estimated to be $341,000, which if covered through a cost share or a payment for P treatment services program could be a positive outcome for both agriculture and public interests. Copyright © 2017. Published by Elsevier B.V.

Preliminary forecasts of Pacific bigeye tuna population trends under the A2 IPCC scenario

NASA Astrophysics Data System (ADS)

Lehodey, P.; Senina, I.; Sibert, J.; Bopp, L.; Calmettes, B.; Hampton, J.; Murtugudde, R.

2010-07-01

An improved version of the spatial ecosystem and population dynamics model SEAPODYM was used to investigate the potential impacts of global warming on tuna populations. The model included an enhanced definition of habitat indices, movements, and accessibility of tuna predators to different vertically migrant and non-migrant micronekton functional groups. The simulations covered the Pacific basin (model domain) at a 2° × 2° geographic resolution. The structure of the model allows an evaluation from multiple data sources, and parameterization can be optimized by adjoint techniques and maximum likelihood using fishing data. A first such optimized parameterization was obtained for bigeye tuna ( Thunnus obesus) in the Pacific Ocean using historical catch data for the last 50 years and a hindcast from a coupled physical-biogeochemical model driven by the NCEP atmospheric reanalysis. The parameterization provided very plausible biological parameter values and a good fit to fishing data from the different fisheries, both within and outside the time period used for optimization. We then employed this model to forecast the future of bigeye tuna populations in the Pacific Ocean. The simulation was driven by the physical-biogeochemical fields predicted from a global marine biogeochemistry - climate simulation. This global simulation was performed with the IPSL climate model version 4 (IPSL-CM4) coupled to the oceanic biogeochemical model PISCES and forced by atmospheric CO 2, from historical records over 1860-2000, and under the SRES A2 IPCC scenario for the 21st century (i.e. atmospheric CO 2 concentration reaching 850 ppm in the year 2100). Potential future changes in distribution and abundance under the IPCC scenario are presented but without taking into account any fishing effort. The simulation showed an improvement in bigeye tuna spawning habitat both in subtropical latitudes and in the eastern tropical Pacific (ETP) where the surface temperature becomes optimal for bigeye tuna spawning. The adult feeding habitat also improved in the ETP due to the increase of dissolved oxygen concentration in the sub-surface allowing adults to access deeper forage. Conversely, in the Western Central Pacific the temperature becomes too warm for bigeye tuna spawning. The decrease in spawning is compensated by an increase of larvae biomass in subtropical regions. However, natural mortality of older stages increased due to lower habitat values (too warm surface temperatures, decreasing oxygen concentration in the sub-surface and less food). This increased mortality and the displacement of surviving fish to the eastern region led to stable then declining adult biomass at the end of the century.

Development of stream-subsurface flow module in sub-daily simulation of Escherichia coli using SWAT

NASA Astrophysics Data System (ADS)

Kim, Minjeong; Boithias, Laurie; Cho, Kyung Hwa; Silvera, Norbert; Thammahacksa, Chanthamousone; Latsachack, Keooudone; Rochelle-Newall, Emma; Sengtaheuanghoung, Oloth; Pierret, Alain; Pachepsky, Yakov A.; Ribolzi, Olivier

2017-04-01

Water contaminated with pathogenic bacteria poses a large threat to public health, especially in the rural areas in the tropics where sanitation and drinking water facilities are often lacking. Several studies have used the Soil and Water Assessment Tool (SWAT) to predict the export of in-stream bacteria at a watershed-scale. However, SWAT is limited to in-stream processes, such as die-off, resuspension and, deposition; and it is usually implemented on a daily time step using the SCS Curve Number method, making it difficult to explore the dynamic fate and transport of bacteria during short but intense events such as flash floods in tropical humid montane headwaters. To address these issues, this study implemented SWAT on an hourly time step using the Green-Ampt infiltration method, and tested the effects of subsurface flow (LATQ+GWQ in SWAT) on bacterial dynamics. We applied the modified SWAT model to the 60-ha Houay Pano catchment in Northern Laos, using sub-daily rainfall and discharge measurements, electric conductivity-derived fractions of overland and subsurface flows, suspended sediments concentrations, and the number of fecal indicator organism Escherichia coli monitored at the catchment outlet from 2011 to 2013. We also took into account land use change by delineating the watershed with the 3-year composite land use map. The results show that low subsurface flow of less than 1 mm recovered the underestimation of E. coli numbers during the dry season, while high subsurface flow caused an overestimation during the wet season. We also found that it is more reasonable to apply the stream-subsurface flow interaction to simulate low in-stream bacteria counts. Using fecal bacteria to identify and understand the possible interactions between overland and subsurface flows may well also provide some insight into the fate of other bacteria, such as those involved in biogeochemical fluxes both in-stream and in the adjacent soils and hyporheic zones.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammond, Glenn Edward; Bao, J; Huang, M

Hyporheic exchange is a critical mechanism shaping hydrological and biogeochemical processes along a river corridor. Recent studies on quantifying the hyporheic exchange were mostly limited to local scales due to field inaccessibility, computational demand, and complexity of geomorphology and subsurface geology. Surface flow conditions and subsurface physical properties are well known factors on modulating the hyporheic exchange, but quantitative understanding of their impacts on the strength and direction of hyporheic exchanges at reach scales is absent. In this study, a high resolution computational fluid dynamics (CFD) model that couples surface and subsurface flow and transport is employed to simulate hyporheicmore » exchanges in a 7-km long reach along the main-stem of the Columbia River. Assuming that the hyporheic exchange does not affect surface water flow conditions due to its negligible magnitude compared to the volume and velocity of river water, we developed a one-way coupled surface and subsurface water flow model using the commercial CFD software STAR-CCM+. The model integrates the Reynolds-averaged Navier-Stokes (RANS) equation solver with a realizable κ-ε two-layer turbulence model, a two-layer all y + wall treatment, and the volume of fluid (VOF) method, and is used to simulate hyporheic exchanges by tracking the free water-air interface as well as flow in the river and the subsurface porous media. The model is validated against measurements from acoustic Doppler current profiler (ADCP) in the stream water and hyporheic fluxes derived from a set of temperature profilers installed across the riverbed. The validated model is then employed to systematically investigate how hyporheic exchanges are influenced by surface water fluid dynamics strongly regulated by upstream dam operations, as well as subsurface structures (e.g. thickness of riverbed and subsurface formation layers) and hydrogeological properties (e.g. permeability). The results suggest that the thickness of riverbed alluvium layer is the dominant factor for reach-scale hyporheic exchanges, followed by the alluvium permeability, the depth of the underlying impermeable layer, and the assumption of hydrostatic pressure.« less

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

PubMed

Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

2016-08-01

Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantifying shallow subsurface water and heat dynamics using coupled hydrological-thermal-geophysical inversion

DOE PAGES

Tran, Anh Phuong; Dafflon, Baptiste; Hubbard, Susan S.; ...

2016-04-25

Improving our ability to estimate the parameters that control water and heat fluxes in the shallow subsurface is particularly important due to their strong control on recharge, evaporation and biogeochemical processes. The objectives of this study are to develop and test a new inversion scheme to simultaneously estimate subsurface hydrological, thermal and petrophysical parameters using hydrological, thermal and electrical resistivity tomography (ERT) data. The inversion scheme-which is based on a nonisothermal, multiphase hydrological model-provides the desired subsurface property estimates in high spatiotemporal resolution. A particularly novel aspect of the inversion scheme is the explicit incorporation of the dependence of themore » subsurface electrical resistivity on both moisture and temperature. The scheme was applied to synthetic case studies, as well as to real datasets that were autonomously collected at a biogeochemical field study site in Rifle, Colorado. At the Rifle site, the coupled hydrological-thermal-geophysical inversion approach well predicted the matric potential, temperature and apparent resistivity with the Nash-Sutcliffe efficiency criterion greater than 0.92. Synthetic studies found that neglecting the subsurface temperature variability, and its effect on the electrical resistivity in the hydrogeophysical inversion, may lead to an incorrect estimation of the hydrological parameters. The approach is expected to be especially useful for the increasing number of studies that are taking advantage of autonomously collected ERT and soil measurements to explore complex terrestrial system dynamics.« less

A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations

DOE PAGES

Scheibe, Timothy D.; Yang, Xiaofan; Chen, Xingyuan; ...

2015-06-01

Extensive research efforts have been invested in reducing model errors to improve the predictive ability of biogeochemical earth and environmental system simulators, with applications ranging from contaminant transport and remediation to impacts of biogeochemical elemental cycling (e.g., carbon and nitrogen) on local ecosystems and regional to global climate. While the bulk of this research has focused on improving model parameterizations in the face of observational limitations, the more challenging type of model error/uncertainty to identify and quantify is model structural error which arises from incorrect mathematical representations of (or failure to consider) important physical, chemical, or biological processes, properties, ormore » system states in model formulations. While improved process understanding can be achieved through scientific study, such understanding is usually developed at small scales. Process-based numerical models are typically designed for a particular characteristic length and time scale. For application-relevant scales, it is generally necessary to introduce approximations and empirical parameterizations to describe complex systems or processes. This single-scale approach has been the best available to date because of limited understanding of process coupling combined with practical limitations on system characterization and computation. While computational power is increasing significantly and our understanding of biological and environmental processes at fundamental scales is accelerating, using this information to advance our knowledge of the larger system behavior requires the development of multiscale simulators. Accordingly there has been much recent interest in novel multiscale methods in which microscale and macroscale models are explicitly coupled in a single hybrid multiscale simulation. A limited number of hybrid multiscale simulations have been developed for biogeochemical earth systems, but they mostly utilize application-specific and sometimes ad-hoc approaches for model coupling. We are developing a generalized approach to hierarchical model coupling designed for high-performance computational systems, based on the Swift computing workflow framework. In this presentation we will describe the generalized approach and provide two use cases: 1) simulation of a mixing-controlled biogeochemical reaction coupling pore- and continuum-scale models, and 2) simulation of biogeochemical impacts of groundwater – river water interactions coupling fine- and coarse-grid model representations. This generalized framework can be customized for use with any pair of linked models (microscale and macroscale) with minimal intrusiveness to the at-scale simulators. It combines a set of python scripts with the Swift workflow environment to execute a complex multiscale simulation utilizing an approach similar to the well-known Heterogeneous Multiscale Method. User customization is facilitated through user-provided input and output file templates and processing function scripts, and execution within a high-performance computing environment is handled by Swift, such that minimal to no user modification of at-scale codes is required.« less

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

NASA Astrophysics Data System (ADS)

Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

PHT3D-UZF: A reactive transport model for variably-saturated porous media

USGS Publications Warehouse

Wu, Ming Zhi; Post, Vincent E. A.; Salmon, S. Ursula; Morway, Eric D.; Prommer, H.

2016-01-01

A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns.

Mineral transformation and biomass accumulation associated with uranium bioremediation at Rifle, Colorado

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, L.; Steefel, C.I.; Williams, K.H.

2009-04-20

Injection of organic carbon into the subsurface as an electron donor for bioremediation of redox-sensitive contaminants like uranium often leads to mineral transformation and biomass accumulation, both of which can alter the flow field and potentially bioremediation efficacy. This work combines reactive transport modeling with a column experiment and field measurements to understand the biogeochemical processes and to quantify the biomass and mineral transformation/accumulation during a bioremediation experiment at a uranium contaminated site near Rifle, Colorado. We use the reactive transport model CrunchFlow to explicitly simulate microbial community dynamics of iron and sulfate reducers, and their impacts on reaction rates.more » The column experiment shows clear evidence of mineral precipitation, primarily in the form of calcite and iron monosulfide. At the field scale, reactive transport simulations suggest that the biogeochemical reactions occur mostly close to the injection wells where acetate concentrations are highest, with mineral precipitate and biomass accumulation reaching as high as 1.5% of the pore space. This work shows that reactive transport modeling coupled with field data can be an effective tool for quantitative estimation of mineral transformation and biomass accumulation, thus improving the design of bioremediation strategies.« less

Mineral transformation and biomass accumulation associated with uranium bioremediation at Rifle, Colorado.

PubMed

Li, Li; Steefel, Carl I; Williams, Kenneth H; Wilkins, Michael J; Hubbard, Susan S

2009-07-15

Injection of organic carbon into the subsurface as an electron donor for bioremediation of redox-sensitive contaminants like uranium often leads to mineral transformation and biomass accumulation, both of which can alter the flow field and potentially bioremediation efficacy. This work combines reactive transport modeling with a column experiment and field measurements to understand the biogeochemical processes and to quantify the biomass and mineral transformation/accumulation during a bioremediation experiment at a uranium contaminated site near Rifle, Colorado. We use the reactive transport model CrunchFlow to explicitly simulate microbial community dynamics of iron and sulfate reducers, and their impacts on reaction rates. The column experiment shows clear evidence of mineral precipitation, primarily in the form of calcite and iron monosulfide. At the field scale, reactive transport simulations suggest that the biogeochemical reactions occur mostly close to the injection wells where acetate concentrations are highest, with mineral precipitate and biomass accumulation reaching as high as 1.5% of the pore space. This work shows that reactive transport modeling coupled with field data can bean effective tool for quantitative estimation of mineral transformation and biomass accumulation, thus improving the design of bioremediation strategies.

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

USGS Publications Warehouse

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

2012-01-01

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

Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream-aquifer-land interactions (CP v1.0)

NASA Astrophysics Data System (ADS)

Bisht, Gautam; Huang, Maoyi; Zhou, Tian; Chen, Xingyuan; Dai, Heng; Hammond, Glenn E.; Riley, William J.; Downs, Janelle L.; Liu, Ying; Zachara, John M.

2017-12-01

A fully coupled three-dimensional surface and subsurface land model is developed and applied to a site along the Columbia River to simulate three-way interactions among river water, groundwater, and land surface processes. The model features the coupling of the Community Land Model version 4.5 (CLM4.5) and a massively parallel multiphysics reactive transport model (PFLOTRAN). The coupled model, named CP v1.0, is applied to a 400 m × 400 m study domain instrumented with groundwater monitoring wells along the Columbia River shoreline. CP v1.0 simulations are performed at three spatial resolutions (i.e., 2, 10, and 20 m) over a 5-year period to evaluate the impact of hydroclimatic conditions and spatial resolution on simulated variables. Results show that the coupled model is capable of simulating groundwater-river-water interactions driven by river stage variability along managed river reaches, which are of global significance as a result of over 30 000 dams constructed worldwide during the past half-century. Our numerical experiments suggest that the land-surface energy partitioning is strongly modulated by groundwater-river-water interactions through expanding the periodically inundated fraction of the riparian zone, and enhancing moisture availability in the vadose zone via capillary rise in response to the river stage change. Meanwhile, CLM4.5 fails to capture the key hydrologic process (i.e., groundwater-river-water exchange) at the site, and consequently simulates drastically different water and energy budgets. Furthermore, spatial resolution is found to significantly impact the accuracy of estimated the mass exchange rates at the boundaries of the aquifer, and it becomes critical when surface and subsurface become more tightly coupled with groundwater table within 6 to 7 meters below the surface. Inclusion of lateral subsurface flow influenced both the surface energy budget and subsurface transport processes as a result of river-water intrusion into the subsurface in response to an elevated river stage that increased soil moisture for evapotranspiration and suppressed available energy for sensible heat in the warm season. The coupled model developed in this study can be used for improving mechanistic understanding of ecosystem functioning and biogeochemical cycling along river corridors under historical and future hydroclimatic changes. The dataset presented in this study can also serve as a good benchmarking case for testing other integrated models.

Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream–aquifer–land interactions (CP v1.0)

DOE PAGES

Bisht, Gautam; Huang, Maoyi; Zhou, Tian; ...

2017-12-12

A fully coupled three-dimensional surface and subsurface land model is developed and applied to a site along the Columbia River to simulate three-way interactions among river water, groundwater, and land surface processes. The model features the coupling of the Community Land Model version 4.5 (CLM4.5) and a massively parallel multiphysics reactive transport model (PFLOTRAN). The coupled model, named CP v1.0, is applied to a 400 m × 400 m study domain instrumented with groundwater monitoring wells along the Columbia River shoreline. CP v1.0 simulations are performed at three spatial resolutions (i.e., 2, 10, and 20 m) over a 5-year periodmore » to evaluate the impact of hydroclimatic conditions and spatial resolution on simulated variables. Results show that the coupled model is capable of simulating groundwater–river-water interactions driven by river stage variability along managed river reaches, which are of global significance as a result of over 30 000 dams constructed worldwide during the past half-century. Our numerical experiments suggest that the land-surface energy partitioning is strongly modulated by groundwater–river-water interactions through expanding the periodically inundated fraction of the riparian zone, and enhancing moisture availability in the vadose zone via capillary rise in response to the river stage change. Meanwhile, CLM4.5 fails to capture the key hydrologic process (i.e., groundwater–river-water exchange) at the site, and consequently simulates drastically different water and energy budgets. Furthermore, spatial resolution is found to significantly impact the accuracy of estimated the mass exchange rates at the boundaries of the aquifer, and it becomes critical when surface and subsurface become more tightly coupled with groundwater table within 6 to 7 meters below the surface. Inclusion of lateral subsurface flow influenced both the surface energy budget and subsurface transport processes as a result of river-water intrusion into the subsurface in response to an elevated river stage that increased soil moisture for evapotranspiration and suppressed available energy for sensible heat in the warm season. The coupled model developed in this study can be used for improving mechanistic understanding of ecosystem functioning and biogeochemical cycling along river corridors under historical and future hydroclimatic changes. The dataset presented in this study can also serve as a good benchmarking case for testing other integrated models.« less

Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream–aquifer–land interactions (CP v1.0)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bisht, Gautam; Huang, Maoyi; Zhou, Tian

A fully coupled three-dimensional surface and subsurface land model is developed and applied to a site along the Columbia River to simulate three-way interactions among river water, groundwater, and land surface processes. The model features the coupling of the Community Land Model version 4.5 (CLM4.5) and a massively parallel multiphysics reactive transport model (PFLOTRAN). The coupled model, named CP v1.0, is applied to a 400 m × 400 m study domain instrumented with groundwater monitoring wells along the Columbia River shoreline. CP v1.0 simulations are performed at three spatial resolutions (i.e., 2, 10, and 20 m) over a 5-year period to evaluate themore » impact of hydroclimatic conditions and spatial resolution on simulated variables. Results show that the coupled model is capable of simulating groundwater–river-water interactions driven by river stage variability along managed river reaches, which are of global significance as a result of over 30 000 dams constructed worldwide during the past half-century. Our numerical experiments suggest that the land-surface energy partitioning is strongly modulated by groundwater–river-water interactions through expanding the periodically inundated fraction of the riparian zone, and enhancing moisture availability in the vadose zone via capillary rise in response to the river stage change. Meanwhile, CLM4.5 fails to capture the key hydrologic process (i.e., groundwater–river-water exchange) at the site, and consequently simulates drastically different water and energy budgets. Furthermore, spatial resolution is found to significantly impact the accuracy of estimated the mass exchange rates at the boundaries of the aquifer, and it becomes critical when surface and subsurface become more tightly coupled with groundwater table within 6 to 7 meters below the surface. Inclusion of lateral subsurface flow influenced both the surface energy budget and subsurface transport processes as a result of river-water intrusion into the subsurface in response to an elevated river stage that increased soil moisture for evapotranspiration and suppressed available energy for sensible heat in the warm season. The coupled model developed in this study can be used for improving mechanistic understanding of ecosystem functioning and biogeochemical cycling along river corridors under historical and future hydroclimatic changes. The dataset presented in this study can also serve as a good benchmarking case for testing other integrated models.« less

Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream–aquifer–land interactions (CP v1.0)

DOE PAGES

Bisht, Gautam; Huang, Maoyi; Zhou, Tian; ...

2017-01-01

A fully coupled three-dimensional surface and subsurface land model is developed and applied to a site along the Columbia River to simulate three-way interactions among river water, groundwater, and land surface processes. The model features the coupling of the Community Land Model version 4.5 (CLM4.5) and a massively parallel multiphysics reactive transport model (PFLOTRAN). The coupled model, named CP v1.0, is applied to a 400 m × 400 m study domain instrumented with groundwater monitoring wells along the Columbia River shoreline. CP v1.0 simulations are performed at three spatial resolutions (i.e., 2, 10, and 20 m) over a 5-year period to evaluate themore » impact of hydroclimatic conditions and spatial resolution on simulated variables. Results show that the coupled model is capable of simulating groundwater–river-water interactions driven by river stage variability along managed river reaches, which are of global significance as a result of over 30 000 dams constructed worldwide during the past half-century. Our numerical experiments suggest that the land-surface energy partitioning is strongly modulated by groundwater–river-water interactions through expanding the periodically inundated fraction of the riparian zone, and enhancing moisture availability in the vadose zone via capillary rise in response to the river stage change. Meanwhile, CLM4.5 fails to capture the key hydrologic process (i.e., groundwater–river-water exchange) at the site, and consequently simulates drastically different water and energy budgets. Furthermore, spatial resolution is found to significantly impact the accuracy of estimated the mass exchange rates at the boundaries of the aquifer, and it becomes critical when surface and subsurface become more tightly coupled with groundwater table within 6 to 7 meters below the surface. Inclusion of lateral subsurface flow influenced both the surface energy budget and subsurface transport processes as a result of river-water intrusion into the subsurface in response to an elevated river stage that increased soil moisture for evapotranspiration and suppressed available energy for sensible heat in the warm season. The coupled model developed in this study can be used for improving mechanistic understanding of ecosystem functioning and biogeochemical cycling along river corridors under historical and future hydroclimatic changes. The dataset presented in this study can also serve as a good benchmarking case for testing other integrated models.« less

Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream–aquifer–land interactions (CP v1.0)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bisht, Gautam; Huang, Maoyi; Zhou, Tian

A fully coupled three-dimensional surface and subsurface land model is developed and applied to a site along the Columbia River to simulate three-way interactions among river water, groundwater, and land surface processes. The model features the coupling of the Community Land Model version 4.5 (CLM4.5) and a massively parallel multiphysics reactive transport model (PFLOTRAN). The coupled model, named CP v1.0, is applied to a 400 m × 400 m study domain instrumented with groundwater monitoring wells along the Columbia River shoreline. CP v1.0 simulations are performed at three spatial resolutions (i.e., 2, 10, and 20 m) over a 5-year periodmore » to evaluate the impact of hydroclimatic conditions and spatial resolution on simulated variables. Results show that the coupled model is capable of simulating groundwater–river-water interactions driven by river stage variability along managed river reaches, which are of global significance as a result of over 30 000 dams constructed worldwide during the past half-century. Our numerical experiments suggest that the land-surface energy partitioning is strongly modulated by groundwater–river-water interactions through expanding the periodically inundated fraction of the riparian zone, and enhancing moisture availability in the vadose zone via capillary rise in response to the river stage change. Meanwhile, CLM4.5 fails to capture the key hydrologic process (i.e., groundwater–river-water exchange) at the site, and consequently simulates drastically different water and energy budgets. Furthermore, spatial resolution is found to significantly impact the accuracy of estimated the mass exchange rates at the boundaries of the aquifer, and it becomes critical when surface and subsurface become more tightly coupled with groundwater table within 6 to 7 meters below the surface. Inclusion of lateral subsurface flow influenced both the surface energy budget and subsurface transport processes as a result of river-water intrusion into the subsurface in response to an elevated river stage that increased soil moisture for evapotranspiration and suppressed available energy for sensible heat in the warm season. The coupled model developed in this study can be used for improving mechanistic understanding of ecosystem functioning and biogeochemical cycling along river corridors under historical and future hydroclimatic changes. The dataset presented in this study can also serve as a good benchmarking case for testing other integrated models.« less

The emergence of hydrogeophysics for improved understanding of subsurface processes over multiple scales

DOE PAGES

Binley, Andrew; Hubbard, Susan S.; Huisman, Johan A.; ...

2015-06-15

Geophysics provides a multidimensional suite of investigative methods that are transforming our ability to see into the very fabric of the subsurface environment, and monitor the dynamics of its fluids and the biogeochemical reactions that occur within it. Here we document how geophysical methods have emerged as valuable tools for investigating shallow subsurface processes over the past two decades and offer a vision for future developments relevant to hydrology and also ecosystem science. The field of “hydrogeophysics” arose in the late 1990s, prompted, in part, by the wealth of studies on stochastic subsurface hydrology that argued for better field-based investigativemore » techniques. These new hydrogeophysical approaches benefited from the emergence of practical and robust data inversion techniques, in many cases with a view to quantify shallow subsurface heterogeneity and the associated dynamics of subsurface fluids. Furthermore, the need for quantitative characterization stimulated a wealth of new investigations into petrophysical relationships that link hydrologically relevant properties to measurable geophysical parameters. Development of time-lapse approaches provided a new suite of tools for hydrological investigation, enhanced further with the realization that some geophysical properties may be sensitive to biogeochemical transformations in the subsurface environment, thus opening up the new field of “biogeophysics.” Early hydrogeophysical studies often concentrated on relatively small “plot-scale” experiments. More recently, however, the translation to larger-scale characterization has been the focus of a number of studies. In conclusion, geophysical technologies continue to develop, driven, in part, by the increasing need to understand and quantify key processes controlling sustainable water resources and ecosystem services.« less

The emergence of hydrogeophysics for improved understanding of subsurface processes over multiple scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Binley, Andrew; Hubbard, Susan S.; Huisman, Johan A.

Geophysics provides a multidimensional suite of investigative methods that are transforming our ability to see into the very fabric of the subsurface environment, and monitor the dynamics of its fluids and the biogeochemical reactions that occur within it. Here we document how geophysical methods have emerged as valuable tools for investigating shallow subsurface processes over the past two decades and offer a vision for future developments relevant to hydrology and also ecosystem science. The field of “hydrogeophysics” arose in the late 1990s, prompted, in part, by the wealth of studies on stochastic subsurface hydrology that argued for better field-based investigativemore » techniques. These new hydrogeophysical approaches benefited from the emergence of practical and robust data inversion techniques, in many cases with a view to quantify shallow subsurface heterogeneity and the associated dynamics of subsurface fluids. Furthermore, the need for quantitative characterization stimulated a wealth of new investigations into petrophysical relationships that link hydrologically relevant properties to measurable geophysical parameters. Development of time-lapse approaches provided a new suite of tools for hydrological investigation, enhanced further with the realization that some geophysical properties may be sensitive to biogeochemical transformations in the subsurface environment, thus opening up the new field of “biogeophysics.” Early hydrogeophysical studies often concentrated on relatively small “plot-scale” experiments. More recently, however, the translation to larger-scale characterization has been the focus of a number of studies. In conclusion, geophysical technologies continue to develop, driven, in part, by the increasing need to understand and quantify key processes controlling sustainable water resources and ecosystem services.« less

The emergence of hydrogeophysics for improved understanding of subsurface processes over multiple scales

PubMed Central

Hubbard, Susan S.; Huisman, Johan A.; Revil, André; Robinson, David A.; Singha, Kamini; Slater, Lee D.

2015-01-01

Abstract Geophysics provides a multidimensional suite of investigative methods that are transforming our ability to see into the very fabric of the subsurface environment, and monitor the dynamics of its fluids and the biogeochemical reactions that occur within it. Here we document how geophysical methods have emerged as valuable tools for investigating shallow subsurface processes over the past two decades and offer a vision for future developments relevant to hydrology and also ecosystem science. The field of “hydrogeophysics” arose in the late 1990s, prompted, in part, by the wealth of studies on stochastic subsurface hydrology that argued for better field‐based investigative techniques. These new hydrogeophysical approaches benefited from the emergence of practical and robust data inversion techniques, in many cases with a view to quantify shallow subsurface heterogeneity and the associated dynamics of subsurface fluids. Furthermore, the need for quantitative characterization stimulated a wealth of new investigations into petrophysical relationships that link hydrologically relevant properties to measurable geophysical parameters. Development of time‐lapse approaches provided a new suite of tools for hydrological investigation, enhanced further with the realization that some geophysical properties may be sensitive to biogeochemical transformations in the subsurface environment, thus opening up the new field of “biogeophysics.” Early hydrogeophysical studies often concentrated on relatively small “plot‐scale” experiments. More recently, however, the translation to larger‐scale characterization has been the focus of a number of studies. Geophysical technologies continue to develop, driven, in part, by the increasing need to understand and quantify key processes controlling sustainable water resources and ecosystem services. PMID:26900183

Residence-time framework for modeling multicomponent reactive transport in stream hyporheic zones

NASA Astrophysics Data System (ADS)

Painter, S. L.; Coon, E. T.; Brooks, S. C.

2017-12-01

Process-based models for transport and transformation of nutrients and contaminants in streams require tractable representations of solute exchange between the stream channel and biogeochemically active hyporheic zones. Residence-time based formulations provide an alternative to detailed three-dimensional simulations and have had good success in representing hyporheic exchange of non-reacting solutes. We extend the residence-time formulation for hyporheic transport to accommodate general multicomponent reactive transport. To that end, the integro-differential form of previous residence time models is replaced by an equivalent formulation based on a one-dimensional advection dispersion equation along the channel coupled at each channel location to a one-dimensional transport model in Lagrangian travel-time form. With the channel discretized for numerical solution, the associated Lagrangian model becomes a subgrid model representing an ensemble of streamlines that are diverted into the hyporheic zone before returning to the channel. In contrast to the previous integro-differential forms of the residence-time based models, the hyporheic flowpaths have semi-explicit spatial representation (parameterized by travel time), thus allowing coupling to general biogeochemical models. The approach has been implemented as a stream-corridor subgrid model in the open-source integrated surface/subsurface modeling software ATS. We use bedform-driven flow coupled to a biogeochemical model with explicit microbial biomass dynamics as an example to show that the subgrid representation is able to represent redox zonation in sediments and resulting effects on metal biogeochemical dynamics in a tractable manner that can be scaled to reach scales.

Subsurface Microbes Expanding the Tree of Life

ScienceCinema

Banfield, Jillian

2018-02-14

Jillian Banfield, Ph.D., UC Berkeley Professor and Berkeley Lab Earth Sciences Division staff scientist and long-time user of the DOE Joint Genome Institute’s resources shares her perspective on how the DOE JGI helps advance her research addressing knowledge gaps related to the roles of subsurface microbial communities in biogeochemical cycling. The video was filmed near the town of Rifle, Colorado at the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 sponsored by the DOE Office of Biological and Environmental Research.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

NASA Astrophysics Data System (ADS)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Predicting Mountainous Watershed Biogeochemical Dynamics, Including Response to Droughts and Early Snowmelt

NASA Astrophysics Data System (ADS)

Hubbard, S. S.; Williams, K. H.; Long, P.; Agarwal, D.; Banfield, J. F.; Beller, H. R.; Bouskill, N.; Brodie, E.; Maxwell, R. M.; Nico, P. S.; Steefel, C. I.; Steltzer, H.; Tokunaga, T. K.; Wainwright, H. M.

2016-12-01

Climate change, extreme weather, land-use change, and other perturbations are significantly reshaping interactions with in watersheds throughout the world. While mountainous watersheds are recognized as the water towers for the world, hydrological processes in watersheds also mediate biogeochemical processes that support all terrestrial life. Developing predictive understanding of watershed hydrological and biogeochemical functioning is challenging, as complex interactions occurring within a heterogeneous watershed can lead to a cascade of effects on downstream water availability and quality. Although these interactions can have significant implications for energy production, agriculture, water quality, and other benefits valued by society, uncertainty associated with predicting watershed function is high. The Watershed Function project aims to substantially reduce this uncertainty through developing a predictive understanding of how mountainous watersheds retain and release downgradient water, nutrients, carbon, and metals. In particular, the project is exploring how early snowmelt, drought, and other disturbances will influence mountainous watershed dynamics at seasonal to decadal timescales. The Watershed Function project is being carried out in a headwater mountainous catchment of the Upper Colorado River Basin, within a watershed characterized by significant gradients in elevation, vegetation and hydrogeology. A system-within system project perspective posits that the integrated watershed response to disturbances can be adequately predicted through consideration of interactions and feedbacks occurring within a limited number of subsystems, each having distinct vegetation-subsurface biogeochemical-hydrological characteristics. A key technological goal is the development of scale-adaptive simulation capabilities that can incorporate genomic information where and when it is useful for predicting the overall watershed response to disturbance. Through developing and integrating new microbial ecology, geochemical, hydrological, ecohydrological, computational and geophysical approaches, the project is developing new insights about biogeochemical dynamics from genome to watershed scales.

Influences of Coupled Hydrologic and Microbial Processes on River Corridor Biogeochemistry and Ecology

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Song, H. S.; Stegen, J.; Graham, E.; Bao, J.; Goldman, A.; Zhou, T.; Crump, A.; Hou, Z.; Hammond, G. E.; Chen, X.; Huang, M.; Zhang, X.; Nelson, W. C.; Garayburu-Caruso, V. A.

2017-12-01

The exchange of water between rivers and surrounding subsurface environments (hydrologic exchange flows or HEFs) is a vital aspect of river ecology and watershed function. HEFs play a key role in water quality, nutrient cycling, and ecosystem health, and they modulate water temperatures and enhance exchange of terrestrial and aquatic nutrients, which lead to elevated biogeochemical activity. However, these coupled hydrologic and microbiological processes are not well understood, particularly in the context of large managed river systems with highly variable discharge, and are poorly represented in system-scale quantitative models. Using the 75 km Hanford Reach of the Columbia River as the research domain, we apply high-resolution flow simulations supported by field observations to understand how variable river discharge interacts with hydromorphic and hydrogeologic structures to generate HEFs and distributions of subsurface residence times. We combine this understanding of hydrologic processes with microbiological activity measurements and reactive transport models to elucidate the holistic impacts of variable discharge on river corridor (surface and subsurface) ecosystems. In particular, our project seeks to develop and test new conceptual and numerical models that explicitly incorporate i) the character (chemical speciation and thermodynamics) of natural organic matter as it varies along flow paths and through mixing of groundwater and surface water, and ii) the history-dependent response of microbial communities to varying time scales of inundation associated with fluctuations in river discharge. The results of these high-resolution mechanistic models are guiding formulation and parameterization of reduced-order models applicable at reach to watershed scales. New understanding of coupled hydrology and microbiology in the river corridor will play a key role in reduction of uncertainties associated with major Earth system biogeochemical fluxes, improving predictions of environmental and human impacts on water quality and riverine ecosystems, and supporting environmentally responsible management of linked energy-water systems.

Project Work Plan: Sequestration of Strontium-90 Subsurface Contamination in the Hanford 100-N Area by Surface Infiltration of an Apatite Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szecsody, Jim E.

2006-04-30

We propose to develop an infiltration strategy that defines the precipitation rate of an apatite-forming solution and Sr-90 sequestration processes under variably saturated (low water content) conditions. We will develop this understanding through small-scale column studies, intermediate-scale two-dimensional (2-D) experiments, and numerical modeling to quantify individual and coupled processes associated with apatite formation and Sr-90 transport during and after infiltration of the Ca-citrate-PO4 solution. Development of capabilities to simulate these coupled biogeochemical processes during both injection and infiltration will be used to determine the most cost-effective means to emplace an in situ apatite barrier with a longevity of 300 yearsmore » to permanently sequester Sr-90 until it decays. Biogeochemical processes that will be investigated are citrate biodegradation and apatite precipitation rates at varying water contents as a function of water content. Coupled processes that will be investigated include the influence of apatite precipitation (which occupies pore space) on the hydraulic and transport properties of the porous media during infiltration.« less

Control of topography gradients on residence time distributions, mixing dynamics and reactive hotspot development

NASA Astrophysics Data System (ADS)

Bandopadhyay, Aditya; Le Borgne, Tanguy; Davy, Philippe

2017-04-01

Topography-driven subsurface flows are thought to play a central role in determining solute turnover and biogeochemical processes at different scales in the critical zone, including river-hyporheic zone exchanges, hillslope solute transport and reactions, and catchment biogeochemical cycles. Hydraulic head gradients, induced by topography gradients at different scales, generate a distribution of streamlines at depth, dictating the spatial distribution of redox sensitive species, the magnitude of surface water - ground water exchanges and ultimately the source/sink function of the subsurface. Flow velocities generally decrease with depth, leading to broad residence time distributions, which have been shown to affect river chemistry and geochemical reactions in catchments. In this presentation, we discuss the impact of topography-driven flows on mixing processes and the formation of localized reactive hotspots. For this, we solve analytically the coupled flow, mixing and reaction equations in two-dimensional vertical cross-sections of subsurface domains with different topography gradients. For a given topography gradient, we derive the spatial distribution of subsurface velocities, the rates of solute mixing accross streamlines and the induced kinetics of redox, precipitation and dissolution reactions using a Lagrangian approach (Le Borgne et al. 2014). We demonstrate that vertical velocity profiles driven by topography variations, act effectively as shear flows, hence stretching continuously the mixing fronts between recently infiltrated and resident water (Bandopadhyay et al. 2017). We thus derive analytical expressions for residence time distributions, mixing rates and kinetics of chemical reactions as a function of the topography gradients. We show that the rates dissolution and precipitation reactions are significantly enhanced by the existence of vertical velocity gradients and that reaction rates reach a maximum in a localized subsurface reactive layer, whose location and intensity depends on topography gradients. As a consequence of these findings, we discuss the links between topography variations, subsurface velocity gradients and biogeochemical processes in the critical zone. References: Bandopadhyay A., T. Le Borgne, Y. Méheust and M. Dentz (2017) Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damkohler numbers, Adv. in Water Resour. Vol. 100, p. 78-95 Le Borgne T., T. Ginn and M. Dentz (2014) Impact of Fluid Deformation on Mixing-Induced Chemical Reactions in Heterogeneous Flows, Geophys. Res. Lett., Vol. 41, 22, p. 7898-790

In-situ Subsurface Soil Analyzer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulmer, Chris

The Department of Energy’s (DOE’s) Terrestrial Ecosystem Science (TES) program is seeking improved sensor systems for monitoring hydro-biogeochemical processes in complex subsurface environments. The TES program is specifically interested in acquiring chemical and structural information regarding the type and nature of the hydration and redox states of subsurface chemical species. The technology should be able to perform on-site and real-time measurements to provide information not available using current sample acquisition and preservation processes. To address the needs of the DOE and the terrestrial science community, Physical Optics Corporation (POC) worked on the development of a new In-Situ Subsurface Soil Analyzermore » (ISSA) based on magnetic resonance technologies. Benchtop testing was performed to assess the feasibility of continuous wave electron pair resonance (CW-EPR) detection of chemical species in subsurface soil systems.« less

Opportunities and challenges in studies of deep life (Invited)

NASA Astrophysics Data System (ADS)

Edwards, K. J.

2010-12-01

Over the past two decades, there has been an increasing awareness within the geological, microbiological, and oceanographic communities of the potentially vast microbial biosphere that is harbored beneath the surface of the Earth. With this awareness has come a mounting effort to study this potential biome - to better quantify biomass abundance, activity, and biogeochemical activity. In the Earth system, the largest deep subsurface biome is also the least accessible - the deep ocean subsurface biosphere. The oceanic deep biosphere also has greatest potential for influencing global scale biogeochemical processes -the carbon and energy cycles for example, and other elemental cycles. To address these topics and mount interdisciplinary efforts to study the deep subsurface marine biosphere, we have recently formed a center in support integrative, collaborative investigations. The national science foundation Center for Dark Biosphere Investigations (C-DEBI), has been initiated for the explicit purpose of resolving the extent, function, dynamics and implications of the subseafloor biosphere. This talk will discuss C-DEBI science, with focus on some of the opportunities and challenges in the study of deep life in the ocean, and the role that C-DEBI will play in meeting them

Microbial activity in the marine deep biosphere: progress and prospects.

PubMed

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Microbial activity in the marine deep biosphere: progress and prospects

PubMed Central

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Functional Microbial Diversity Explains Groundwater Chemistry in a Pristine Aquifer

EPA Science Inventory

Microbial communities inhabiting anoxic aquifers catalyze critical biogeochemical reactions in the subsurface, yet little is known about how their community structure correlates with groundwater chemistry. In this study, we described the composition of microbial communities in th...

The Importance of Subsurface Production for Carbon Export - Evidence from Past Oceans

NASA Astrophysics Data System (ADS)

Kemp, A. E. S.

2016-02-01

The maxim of the geological concept of uniformitarianism is "the present is the key to the past", but in the context of our temporally and spatially minimal observational record of modern ocean biogeochemical processes, ancient ocean sediments may provide critical evidence of the key species involved in carbon flux. Specifically, laminated marine sediments that preserve the seasonal flux cycle represent "palaeo-sediment traps" that vastly expand our knowledge of the operations of the marine biological carbon pump. Several key subsurface-dwelling diatom taxa, hitherto thought to be biogeochemically insignificant, are dominant components of ancient marine sediments. For example, the sapropels and equivalent horizons that have accumulated in the Mediterranean over the past 5 million years, contain abundant rhizosolenid and hemiaulid diatoms. These deposits contain the highest concentrations of organic carbon and there is extensive evidence that this was produced by subsurface production in a deep chlorophyll maximum. The highly stratified conditions that led to this subsurface production and carbon flux are in contrast to prevailing views that have held upwelling systems as those with the highest potential for export in the global ocean. Similarly, studies of ancient "greenhouse" periods such as the Cretaceous, with highly stratified oceans and which are potential analogues for future climate change, show evidence for extensive subsurface production. Together with emerging evidence from stratified regions of the modern ocean, such as the subtropical gyres, insights from these ancient oceans suggest that a reappraisal is required of current views on key phytoplankton producers and their role the operation of the marine biological carbon pump.

TOUGHREACT Version 2.0: A simulator for subsurface reactive transport under non-isothermal multiphase flow conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, T.; Spycher, N.; Sonnenthal, E.

2010-08-01

TOUGHREACT is a numerical simulation program for chemically reactive non-isothermal flows of multiphase fluids in porous and fractured media, and was developed by introducing reactive chemistry into the multiphase fluid and heat flow simulator TOUGH2 V2. The first version of TOUGHREACT was released to the public through the U.S. Department of Energy's Energy Science and Technology Software Center (ESTSC) in August 2004. It is among the most frequently requested of ESTSC's codes. The code has been widely used for studies in CO{sub 2} geological sequestration, nuclear waste isolation, geothermal energy development, environmental remediation, and increasingly for petroleum applications. Over themore » past several years, many new capabilities have been developed, which were incorporated into Version 2 of TOUGHREACT. Major additions and improvements in Version 2 are discussed here, and two application examples are presented: (1) long-term fate of injected CO{sub 2} in a storage reservoir and (2) biogeochemical cycling of metals in mining-impacted lake sediments.« less

Biogeochemical characteristics of mesoscale eddies in the generation zone off Valparaíso, Chile

NASA Astrophysics Data System (ADS)

Villegas, Valerie; Cornejo, Marcela; Molina, Verónica; Silva, Nelson; Hormazábal, Samuel

2016-04-01

The coastal area off Valparaiso is characterized by an intense mesoscale activity associated with eddies, which transport highly productive-coastal waters to the oligotrophic areas of the Subtropical Gyre. Among these, the Intrathermocline Anticyclonic Eddies (ITE's) which are forming in the eastern South Pacific, transport low oxygen- and high nutrients- subsurface water of Equatorial Subsurface Water (ESSW). These eddies have been well characterized in terms of generation rate, direction, speed and water transport. However, biogeochemical conditions in their origin and its temporal variability are not well assessed. The present study aims to determine the variability, spatially and temporally, of the biogeochemical properties in the water column at the eddies generation zone, off Punta Ángeles, Valparaíso (33° S). For this, a monthly time series was conducted between January and August 2016 where a cross-shore transect with six-stations was deployed (from coast to 16 nm). Each station was sampled with CTD-OF, while only in station 5 (1300 m depth) was sampled in 16 depth for biogeochemical variables: nutrients (NO3-, NO2-, PO4-3, Si(OH)4), greenhouse gases (CO2, CH4 and N2O), chlorophyll a, stable isotopes in particulate organic material (13C, 15N), content of organic carbon and nitrogen in POM. The spatial and temporal distribution shows the presence of subsurface cores (100 - 300 m) with water with high salinity (> 34.7 psu) and low oxygen content (< 0.5 mLṡL-1), associated with mesoscale subsurface structures. The largest vertical and horizontal extension of these structures was observed in January 2015. These subsurface structures showed a significant deficit of reactive nitrogen (N* < -10 μM), nitrite accumulation (> 0.6 μM) and the highest supersaturations of CO2 (110 - 344%) and N2O (107 - 407%). Along with this, the eddies generation zone presented a temporal variability of air-sea gases fluxes with the highest in the austral summer and autumn (from 67.64 to 9.12 mmolṡm-2ṡd-1, from 3.00 to 0.94 μmolṡm-2ṡd-1, and from 19.62 to 5.77 μmolṡm-2ṡd-1, for CO2, CH4 and N2O, respectively), while between June and August, the ocean-atmosphere flows were close to equilibrium (from 0.09 to -1.93 mmolṡm-2ṡd-1, from 0.40 to 0.03 μmolṡm-2ṡd-1, and from 0,29 to -0.02 μmolṡm-2ṡd-1, for CO2, CH4 and N2O, respectively). Acknowledgment: This work is part of the PIA 037.474 Project (PUCV) and the Instituto Milenio de Oceanografía (IMO-Chile).

MINERALOGICAL PRESERVATION OF SOLID SAMPLES COLLECTED FROM ANOXIC SUBSURFACE ENVIRONMENTS

EPA Science Inventory

Remedial technologies utilized at hazardous waste sites for the treatment of metal and metalloid contaminants often take advantage of reduction-oxidation (redox) processes to reach ground water clean up goals. This is because redox reactions, in many cases, govern the biogeochem...

Low Elevation Old Channel Features of the Willamette River Floodplain Support High Subsurface Denitrification Rates

EPA Science Inventory

Background/Question/Methods: Large river floodplains are poor nitrate pollution buffers when polluted groundwater moves beneath biogeochemically retentive zones prior to entering the main channel. However, in floodplain regions with extensive backwaters and organic carbon acc...

Insights on multivariate updates of physical and biogeochemical ocean variables using an Ensemble Kalman Filter and an idealized model of upwelling

NASA Astrophysics Data System (ADS)

Yu, Liuqian; Fennel, Katja; Bertino, Laurent; Gharamti, Mohamad El; Thompson, Keith R.

2018-06-01

Effective data assimilation methods for incorporating observations into marine biogeochemical models are required to improve hindcasts, nowcasts and forecasts of the ocean's biogeochemical state. Recent assimilation efforts have shown that updating model physics alone can degrade biogeochemical fields while only updating biogeochemical variables may not improve a model's predictive skill when the physical fields are inaccurate. Here we systematically investigate whether multivariate updates of physical and biogeochemical model states are superior to only updating either physical or biogeochemical variables. We conducted a series of twin experiments in an idealized ocean channel that experiences wind-driven upwelling. The forecast model was forced with biased wind stress and perturbed biogeochemical model parameters compared to the model run representing the "truth". Taking advantage of the multivariate nature of the deterministic Ensemble Kalman Filter (DEnKF), we assimilated different combinations of synthetic physical (sea surface height, sea surface temperature and temperature profiles) and biogeochemical (surface chlorophyll and nitrate profiles) observations. We show that when biogeochemical and physical properties are highly correlated (e.g., thermocline and nutricline), multivariate updates of both are essential for improving model skill and can be accomplished by assimilating either physical (e.g., temperature profiles) or biogeochemical (e.g., nutrient profiles) observations. In our idealized domain, the improvement is largely due to a better representation of nutrient upwelling, which results in a more accurate nutrient input into the euphotic zone. In contrast, assimilating surface chlorophyll improves the model state only slightly, because surface chlorophyll contains little information about the vertical density structure. We also show that a degradation of the correlation between observed subsurface temperature and nutrient fields, which has been an issue in several previous assimilation studies, can be reduced by multivariate updates of physical and biogeochemical fields.

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

NASA Astrophysics Data System (ADS)

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

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

Geophysical characterisation of the groundwater-surface water interface

NASA Astrophysics Data System (ADS)

McLachlan, P. J.; Chambers, J. E.; Uhlemann, S. S.; Binley, A.

2017-11-01

Interactions between groundwater (GW) and surface water (SW) have important implications for water quantity, water quality, and ecological health. The subsurface region proximal to SW bodies, the GW-SW interface, is crucial as it actively regulates the transfer of nutrients, contaminants, and water between GW systems and SW environments. However, geological, hydrological, and biogeochemical heterogeneity in the GW-SW interface makes it difficult to characterise with direct observations. Over the past two decades geophysics has been increasingly used to characterise spatial and temporal variability throughout the GW-SW interface. Geophysics is a powerful tool in evaluating structural heterogeneity, revealing zones of GW discharge, and monitoring hydrological processes. Geophysics should be used alongside traditional hydrological and biogeochemical methods to provide additional information about the subsurface. Further integration of commonly used geophysical techniques, and adoption of emerging techniques, has the potential to improve understanding of the properties and processes of the GW-SW interface, and ultimately the implications for water quality and environmental health.

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

DOE PAGES

Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C.; ...

2013-08-27

Microorganisms in the subsurface represent a substantial but poorly understood component of the Earth’s biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as a ‘dark matter’ of the carbon and other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent to the Colorado River, CO, USA. No single organism represents more than ~1% of either community. Remarkably, many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative. The dominant organism in deeper sediment, RBG-1, is a member ofmore » a new phylum. On the basis of its reconstructed complete genome, RBG-1 is metabolically versatile. Its wide respiration-based repertoire may enable it to respond to the fluctuating redox environment close to the water table. We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations.« less

A New Approach to Predict Microbial Community Assembly and Function Using a Stochastic, Genome-Enabled Modeling Framework

NASA Astrophysics Data System (ADS)

King, E.; Brodie, E.; Anantharaman, K.; Karaoz, U.; Bouskill, N.; Banfield, J. F.; Steefel, C. I.; Molins, S.

2016-12-01

Characterizing and predicting the microbial and chemical compositions of subsurface aquatic systems necessitates an understanding of the metabolism and physiology of organisms that are often uncultured or studied under conditions not relevant for one's environment of interest. Cultivation-independent approaches are therefore important and have greatly enhanced our ability to characterize functional microbial diversity. The capability to reconstruct genomes representing thousands of populations from microbial communities using metagenomic techniques provides a foundation for development of predictive models for community structure and function. Here, we discuss a genome-informed stochastic trait-based model incorporated into a reactive transport framework to represent the activities of coupled guilds of hypothetical microorganisms. Metabolic pathways for each microbe within a functional guild are parameterized from metagenomic data with a unique combination of traits governing organism fitness under dynamic environmental conditions. We simulate the thermodynamics of coupled electron donor and acceptor reactions to predict the energy available for cellular maintenance, respiration, biomass development, and enzyme production. While `omics analyses can now characterize the metabolic potential of microbial communities, it is functionally redundant as well as computationally prohibitive to explicitly include the thousands of recovered organisms into biogeochemical models. However, one can derive potential metabolic pathways from genomes along with trait-linkages to build probability distributions of traits. These distributions are used to assemble groups of microbes that couple one or more of these pathways. From the initial ensemble of microbes, only a subset will persist based on the interaction of their physiological and metabolic traits with environmental conditions, competing organisms, etc. Here, we analyze the predicted niches of these hypothetical microbes and assess the ability of a stochastically assembled community of organisms to predict subsurface biogeochemical dynamics.

Numerical Modeling of Artificial Recharge: Determining Spatial/Temporal Sampling Resolution to Quantify Infiltration Rates and Effective Hydraulic Conductivity

NASA Astrophysics Data System (ADS)

Glose, T. J.; Hausner, M. B.; Lowry, C.

2016-12-01

The accurate, fine scale quantification of groundwater-surface water (GW-SW) interactions over large expanses in hydrologic systems is a fundamental need in order to accurately characterize critical zones of biogeochemical transformation and fluxes, as well as to provide insight into near-surface geologic heterogeneity. Paired fiber-optic distributed temperature sensing (FO-DTS) is a tool that is capable of synoptically sampling hydrologic systems, allowing GW-SW interactions to be examined at a fine scale over large distances. Within managed aquifer recharge (MAR) sites, differential recharge dynamics controlled by bed clogging and subsurface heterogeneity dictate the effectiveness of these sites at infiltrating water. Numerical modeling indicates that the use of paired FO-DTS in an MAR site can provide accurate quantification of flux at the GW-SW interface, as well as provide insight to the areal extent of geologic heterogeneity in the subsurface. However, the lateral and vertical separation of the fiber-optic cables is of vital importance. Here we present a 2-D, fully coupled groundwater flow and heat transport model with prescribed heterogeneity. Following a forward modeling approach, realizations simulating varying fiber-optic cable positioning, differential bed clogging, and hydraulic conductivity variability were analyzed over a suite of scenarios. The results from the model were then used as observations to calculate groundwater recharge rates and calibration targets for an inverse model to estimate subsurface heterogeneity.

Large fluctuations of dissolved oxygen in the Indian and Pacific oceans during Dansgaard-Oeschger oscillations caused by variations of North Atlantic Deep Water subduction

NASA Astrophysics Data System (ADS)

Schmittner, Andreas; Galbraith, Eric D.; Hostetler, Steven W.; Pedersen, Thomas F.; Zhang, Rong

2007-09-01

Paleoclimate records from glacial Indian and Pacific oceans sediments document millennial-scale fluctuations of subsurface dissolved oxygen levels and denitrification coherent with North Atlantic temperature oscillations. Yet the mechanism of this teleconnection between the remote ocean basins remains elusive. Here we present model simulations of the oxygen and nitrogen cycles that explain how changes in deepwater subduction in the North Atlantic can cause large and synchronous variations of oxygen minimum zones throughout the Northern Hemisphere of the Indian and Pacific oceans, consistent with the paleoclimate records. Cold periods in the North Atlantic are associated with reduced nutrient delivery to the upper Indo-Pacific oceans, thereby decreasing productivity. Reduced export production diminishes subsurface respiration of organic matter leading to higher oxygen concentrations and less denitrification. This effect of reduced oxygen consumption dominates at low latitudes. At high latitudes in the Southern Ocean and North Pacific, increased mixed layer depths and steepening of isopycnals improve ocean ventilation and oxygen supply to the subsurface. Atmospheric teleconnections through changes in wind-driven ocean circulation modify this basin-scale pattern regionally. These results suggest that changes in the Atlantic Ocean circulation, similar to those projected by climate models to possibly occur in the centuries to come because of anthropogenic climate warming, can have large effects on marine ecosystems and biogeochemical cycles even in remote areas.

Evidence of linked biogeochemical and hydrological processes in homogeneous and layered vadose zone systems

NASA Astrophysics Data System (ADS)

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

2010-12-01

Understanding chemical fate and transport in the vadose zone is critical to protect groundwater resources and preserve ecosystem health. However, prediction can be challenging due to the dynamic hydrologic and biogeochemical nature of the vadose zone. Additional controls on hydrobiogeochemical processes are added by subsurface structural heterogeneity. This study uses repacked soil column experiments to quantify linkages between microbial activity, geochemical cycling and hydrologic flow. Three “short” laboratory soil columns were constructed to evaluate the effects of soil layering: a homogenized medium-grained sand, homogenized organic-rich loam, and a sand-over-loam layered column. In addition, two “long” columns were constructed using either gamma-irradiated (sterilized) or untreated sediments to evaluate the effects of both soil layers and the presence of microorganisms. The long columns were packed identically; a medium-grained sand matrix with two vertically separated and horizontally offset lenses of organic-rich loam. In all 5 columns, downward and upward infiltration of water was evaluated to simulate rainfall and rising water table events respectively. In-situ colocated probes were used to measure soil water content, matric potential, Eh, major anions, ammonium, Fe2+, and total sulfide. Enhanced biogeochemical cycling was observed in the short layered column versus the short, homogeneous columns, and enumerations of iron and sulfate reducing bacteria were 1-2 orders of magnitude greater. In the long columns, microbial activity caused mineral bands and produced insoluble gases that impeded water flow through the pores of the sediment. Capillary barriers, formed around the lenses due to soil textural differences, retarded water flow rates through the lenses. This allowed reducing conditions to develop, evidenced by the production of Fe2+ and S2-. At the fringes of the lenses, Fe2+ oxidized to form Fe(III)-oxide bands that further retarded water flux. No such mineral bands developed in the sterilized column. As a consequence, water content in the lenses of the sterilized column was half that of the other column and flow rates through the lenses were an order of magnitude lower. This flow impedance limited the interaction and mixing of groundwater with infiltrating vadose zone water and led to the formation of geochemically distinct water masses residing in relatively close proximity to one another. Results provide a specific examples of the direct impact of biogeochemical cycling on water flow in the vadose zone and vice versa. In addition, these demonstrate that the presence of layers in vadose zone environments may be an important control on overall chemical fate and transport in subsurface systems.

Acidification of subsurface coastal waters enhanced by eutrophication

EPA Science Inventory

Uptake of fossil-fuel carbon dioxide (CO2) from the atmosphere has acidified the surface ocean by ~0.1 pH units and driven down the carbonate saturation state. Ocean acidification is a threat to marine ecosystems and may alter key biogeochemical cycles. Coastal oceans have also b...

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

USGS Publications Warehouse

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

2011-01-01

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

Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

NASA Astrophysics Data System (ADS)

Chen, M.; Kocar, B. D.

2016-12-01

Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

Genome-enabled Modeling of Microbial Biogeochemistry using a Trait-based Approach. Does Increasing Metabolic Complexity Increase Predictive Capabilities?

NASA Astrophysics Data System (ADS)

King, E.; Karaoz, U.; Molins, S.; Bouskill, N.; Anantharaman, K.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.; Brodie, E.

2015-12-01

The biogeochemical functioning of ecosystems is shaped in part by genomic information stored in the subsurface microbiome. Cultivation-independent approaches allow us to extract this information through reconstruction of thousands of genomes from a microbial community. Analysis of these genomes, in turn, gives an indication of the organisms present and their functional roles. However, metagenomic analyses can currently deliver thousands of different genomes that range in abundance/importance, requiring the identification and assimilation of key physiologies and metabolisms to be represented as traits for successful simulation of subsurface processes. Here we focus on incorporating -omics information into BioCrunch, a genome-informed trait-based model that represents the diversity of microbial functional processes within a reactive transport framework. This approach models the rate of nutrient uptake and the thermodynamics of coupled electron donors and acceptors for a range of microbial metabolisms including heterotrophs and chemolithotrophs. Metabolism of exogenous substrates fuels catabolic and anabolic processes, with the proportion of energy used for cellular maintenance, respiration, biomass development, and enzyme production based upon dynamic intracellular and environmental conditions. This internal resource partitioning represents a trade-off against biomass formation and results in microbial community emergence across a fitness landscape. Biocrunch was used here in simulations that included organisms and metabolic pathways derived from a dataset of ~1200 non-redundant genomes reflecting a microbial community in a floodplain aquifer. Metagenomic data was directly used to parameterize trait values related to growth and to identify trait linkages associated with respiration, fermentation, and key enzymatic functions such as plant polymer degradation. Simulations spanned a range of metabolic complexities and highlight benefits originating from simulations including a larger number of organisms that more appropriately reflect the in situ microbial community.

Hydrological and Climate Controls on Hyporheic Contributions to River Net Ecosystem Productivity

NASA Astrophysics Data System (ADS)

Newcomer, M. E.; Hubbard, S. S.; Fleckenstein, J. H.; Maier, U.; Schmidt, C.; Laube, G.; Chen, N.; Ulrich, C.; Dwivedi, D.; Steefel, C. I.; Rubin, Y.

2016-12-01

Hyporheic zone contributions to river net ecosystem productivity (NEP) can represent a substantial source or sink for organic and inorganic carbon (C). Hyporheic zone processes are estimated to vary with network location as a function of river-aquifer interactions as well as with climatic factors supporting riverbed gross primary productivity (GPP) and ecosystem respiration. Even though hyporheic zone NEP is hypothesized to be a significant budgetary component to river-aquifer biogeochemical cycling, models of river NEP often parameterize hyporheic zone contributions as a space-time constant input of CO2 to rivers, leading to overestimation of hyporheic zone NEP and underestimation of C storage. This assumption is problematic during the summer growing season, when GPP is largest and C is stored in surface and subsurface biomass. We investigated the dynamic role of hyporheic zone NEP using the MIN3P flow and reactive transport model with surface water GPP and ecosystem respiration simulated as a function of light, depth, temperature, pH, and atmospheric CO2. We simulated hyporheic zone NEP for low-order and high-order streams, which collectively represent a range of characteristic flow paths and subsurface residence times. Downscaled climate predictions of temperature and atmospheric CO2 representing carbon emission futures were used to force the models and to compare future and current hyporheic zone NEP. Our results show that river-aquifer flow conditions determine the relative role of the river as either a store or sink of C through direct contributions of O2 and dissolved organic content from river GPP. Modeled results show that high discharge, high order rivers are net stores of CO2 from the atmosphere; however this is dependent on perturbation events that allow stored C from summer GPP to be released (i.e. rising water tables during winter storms). Lacking a perturbation event, C remains in pore-water storage as dissolved CO2 and biomass. Conversely, low-discharge mountainous streams with continuous hyporheic zone flow represent a net source of CO2, with future temperature rises stimulating additional heterotrophic activity. Our work contributes to a better understanding of how river and hyporheic zone processes significantly influence biogeochemical cycling under changing climate conditions.

Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and themore » formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studies will be necessary to further establish the potential relationship(s) between viruses, cells, carbon, and metals/radionuclides to provide sufficient scientific understanding to incorporate coupled physical, chemical, and biological processes into agent based and reactive transport models.« less

Characterizing variable biogeochemical changes during the treatment of produced oilfield waste.

PubMed

Hildenbrand, Zacariah L; Santos, Inês C; Liden, Tiffany; Carlton, Doug D; Varona-Torres, Emmanuel; Martin, Misty S; Reyes, Michelle L; Mulla, Safwan R; Schug, Kevin A

2018-09-01

At the forefront of the discussions about climate change and energy independence has been the process of hydraulic fracturing, which utilizes large amounts of water, proppants, and chemical additives to stimulate sequestered hydrocarbons from impermeable subsurface strata. This process also produces large amounts of heterogeneous flowback and formation waters, the subsurface disposal of which has most recently been linked to the induction of anthropogenic earthquakes. As such, the management of these waste streams has provided a newfound impetus to explore recycling alternatives to reduce the reliance on subsurface disposal and fresh water resources. However, the biogeochemical characteristics of produced oilfield waste render its recycling and reutilization for production well stimulation a substantial challenge. Here we present a comprehensive analysis of produced waste from the Eagle Ford shale region before, during, and after treatment through adjustable separation, flocculation, and disinfection technologies. The collection of bulk measurements revealed significant reductions in suspended and dissolved constituents that could otherwise preclude untreated produced water from being utilized for production well stimulation. Additionally, a significant step-wise reduction in pertinent scaling and well-fouling elements was observed, in conjunction with notable fluctuations in the microbiomes of highly variable produced waters. Collectively, these data provide insight into the efficacies of available water treatment modalities within the shale energy sector, which is currently challenged with improving the environmental stewardship of produced water management. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

PubMed Central

Freedman, Adam J.E.; Tan, BoonFei

2017-01-01

Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Advances in interpretation of subsurface processes with time-lapse electrical imaging

USGS Publications Warehouse

Singha, Kaminit; Day-Lewis, Frederick D.; Johnson, Tim B.; Slater, Lee D.

2015-01-01

Electrical geophysical methods, including electrical resistivity, time-domain induced polarization, and complex resistivity, have become commonly used to image the near subsurface. Here, we outline their utility for time-lapse imaging of hydrological, geochemical, and biogeochemical processes, focusing on new instrumentation, processing, and analysis techniques specific to monitoring. We review data collection procedures, parameters measured, and petrophysical relationships and then outline the state of the science with respect to inversion methodologies, including coupled inversion. We conclude by highlighting recent research focused on innovative applications of time-lapse imaging in hydrology, biology, ecology, and geochemistry, among other areas of interest.

Advances in interpretation of subsurface processes with time-lapse electrical imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singha, Kamini; Day-Lewis, Frederick D.; Johnson, Timothy C.

2015-03-15

Electrical geophysical methods, including electrical resistivity, time-domain induced polarization, and complex resistivity, have become commonly used to image the near subsurface. Here, we outline their utility for time-lapse imaging of hydrological, geochemical, and biogeochemical processes, focusing on new instrumentation, processing, and analysis techniques specific to monitoring. We review data collection procedures, parameters measured, and petrophysical relationships and then outline the state of the science with respect to inversion methodologies, including coupled inversion. We conclude by highlighting recent research focused on innovative applications of time-lapse imaging in hydrology, biology, ecology, and geochemistry, among other areas of interest.

Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Truex, Michael J.; Lee, Brady D.; Johnson, Christian D.

The fate and transport of 129I in the environment and potential remediation technologies are currently being studied as part of environmental remediation activities at the Hanford Site. A conceptual model describing the nature and extent of subsurface contamination, factors that control plume behavior, and factors relevant to potential remediation processes is needed to support environmental remedy decisions. Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited. Thus, the conceptual model also needs to both describe known contaminant and biogeochemical process information and to identify aspects about which additional information needed to effectively support remedy decisions.more » this document summarizes the conceptual model of iodine behavior relevant to iodine in the subsurface environment at the Hanford site.« less

Large fluctuations of dissolved oxygen in the Indian and Pacific oceans during Dansgaard-Oeschger oscillations caused by variations of North Atlantic Deep Water subduction

USGS Publications Warehouse

Schmittner, A.; Galbraith, E.D.; Hostetler, S.W.; Pedersen, Thomas F.; Zhang, R.

2007-01-01

Paleoclimate records from glacial Indian and Pacific oceans sediments document millennial-scale fluctuations of subsurface dissolved oxygen levels and denitrification coherent with North Atlantic temperature oscillations. Yet the mechanism of this teleconnection between the remote ocean basins remains elusive. Here we present model simulations of the oxygen and nitrogen cycles that explain how changes in deepwater subduction in the North Atlantic can cause large and synchronous variations of oxygen minimum zones, throughout the Northern Hemisphere of the Indian and Pacific oceans, consistent with the paleoclimate records. Cold periods in the North Atlantic are associated with reduced nutrient delivery to the upper Indo-Pacific oceans, thereby decreasing productivity. Reduced export production diminishes subsurface respiration of organic matter leading to higher oxygen concentrations and less denitrification. This effect of reduced oxygen consumption dominates at low latitudes. At high latitudes in the Southern Ocean and North Pacific, increased mixed layer depths and steepening of isopycnals improve ocean ventilation and oxygen supply to the subsurface. Atmospheric teleconnections through changes in wind-driven ocean circulation modify this basin-scale pattern regionally. These results suggest that changes in the Atlantic Ocean circulation, similar to those projected by climate models to possibly occur in the centuries to come because of anthropogenic climate warming, can have large effects on marine ecosystems and biogeochemical cycles even in remote areas. Copyright 2007 by the American Geophysical Union.

Deep subsurface life in Bengal Fan sediments (IODP Exp. 354)

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Heuer, V. B.; Elvert, M.; Kallmeyer, J.; Kitte, J. A.; Wörmer, L.; Hinrichs, K. U.

2017-12-01

We collected Bengal Fan sediment samples along a 8°N transect during International Ocean Discovery Program Expedition 354 (February - March 2015, Singapore - Colombo, Sri Lanka) to study subseafloor life in this, as yet unstudied, area. Among other biogeochemical parameters, we quantified microbial biomass by analyzing prokaryotic cells using epifluorescence microscopy after detaching cells from the sediment, and bacterial endospores by analyzing the diagnostic biomarker dipicolinic acid (DPA) by detection of fluorescence of the terbium-DPA complex. To gain understanding of total microbial activity, we quantified hydrogen utilization potential of hydrogenase enzymes, which are ubiquitous in subsurface microorganisms, by using a tritium assay. We measured highest cell concentrations of ca. 108 cells g-1 in shallow sediments close to the seafloor. These concentrations are one to two orders of magnitude lower than in most marine continental margin settings [1]. Similar to the global trend [1], cell concentrations decreased with depth according to a power-law function. Endospore concentrations scattered between ca. 105 and 107 cells g-1 sediment at all sites and depths. We could not observe a clear relationship of endospore concentration and sediment depth; instead, it appears to be linked to lithology and total organic carbon content. Bulk Hydrogenase enzyme activity ranged from nmolar to μmolar range of H2 g-1d-1. Similar to previous observations [2], per-cell hydrogen utilization depends on vertical biogeochemical zones, which could be due to the differences in hydrogen utilization requirements/efficiency of the respective metabolic processes such as sulfate reduction, methanogenesis, fermentation etc. Bengal fan is highly dynamic due to channel and levee systems and the sediments are dominated by turbidites, thick sand layers and hemipelagic deposits, which may control biogeochemical zonation. Based on our microbial biomass and activity data, we suggest that the nature, quality and origin of sedimentary material influence the deep subsurface life. [1] Kallmeyer et al., (2012) PNAS 109(40), 16213-16216 [2] Adhikari et al., (2016) Frontiers in Microbiology 7:8

Scaling isotopic emissions and microbes across a permafrost thaw landscape

NASA Astrophysics Data System (ADS)

Varner, R. K.; Palace, M. W.; Saleska, S. R.; Bolduc, B.; Braswell, B. H., Jr.; Crill, P. M.; Chanton, J.; DelGreco, J.; Deng, J.; Frolking, S. E.; Herrick, C.; Hines, M. E.; Li, C.; McArthur, K. J.; McCalley, C. K.; Persson, A.; Roulet, N. T.; Torbick, N.; Tyson, G. W.; Rich, V. I.

2017-12-01

High latitude peatlands are a significant source of atmospheric methane. This source is spatially and temporally heterogeneous, resulting in a wide range of emission estimates for the atmospheric budget. Increasing atmospheric temperatures are causing degradation of underlying permafrost, creating changes in surface soil moisture, the surface and sub-surface hydrological patterns, vegetation and microbial communities, but the consequences to rates and magnitudes of methane production and emissions are poorly accounted for in global budgets. We combined field observations, multi-source remote sensing data and biogeochemical modeling to predict methane dynamics, including the fraction derived from hydrogenotrophic versus acetoclastic microbial methanogenesis across Stordalen mire, a heterogeneous discontinuous permafrost wetland located in northernmost Sweden. Using the field measurement validated Wetland-DNDC biogeochemical model, we estimated mire-wide CH4 and del13CH4 production and emissions for 2014 with input from field and unmanned aerial system (UAS) image derived vegetation maps, local climatology and water table from insitu and remotely sensed data. Model simulated methanogenic pathways correlate with sequence-based observations of methanogen community composition in samples collected from across the permafrost thaw landscape. This approach enables us to link below ground microbial community composition with emissions and indicates a potential for scaling across broad areas of the Arctic region.

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

NASA Astrophysics Data System (ADS)

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

2013-11-01

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.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Zhangshuan; Nelson, William C.; Stegen, James C.

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO 2, N 2 and N 2O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal rivermore » stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.« less

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

DOE PAGES

Hou, Zhangshuan; Nelson, William C.; Stegen, James C.; ...

2017-09-20

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO 2, N 2 and N 2O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal rivermore » stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.« less

Sensitivity of land surface modeling to parameters: An uncertainty quantification method applied to the Community Land Model

NASA Astrophysics Data System (ADS)

Ricciuto, D. M.; Mei, R.; Mao, J.; Hoffman, F. M.; Kumar, J.

2015-12-01

Uncertainties in land parameters could have important impacts on simulated water and energy fluxes and land surface states, which will consequently affect atmospheric and biogeochemical processes. Therefore, quantification of such parameter uncertainties using a land surface model is the first step towards better understanding of predictive uncertainty in Earth system models. In this study, we applied a random-sampling, high-dimensional model representation (RS-HDMR) method to analyze the sensitivity of simulated photosynthesis, surface energy fluxes and surface hydrological components to selected land parameters in version 4.5 of the Community Land Model (CLM4.5). Because of the large computational expense of conducting ensembles of global gridded model simulations, we used the results of a previous cluster analysis to select one thousand representative land grid cells for simulation. Plant functional type (PFT)-specific uniform prior ranges for land parameters were determined using expert opinion and literature survey, and samples were generated with a quasi-Monte Carlo approach-Sobol sequence. Preliminary analysis of 1024 simulations suggested that four PFT-dependent parameters (including slope of the conductance-photosynthesis relationship, specific leaf area at canopy top, leaf C:N ratio and fraction of leaf N in RuBisco) are the dominant sensitive parameters for photosynthesis, surface energy and water fluxes across most PFTs, but with varying importance rankings. On the other hand, for surface ans sub-surface runoff, PFT-independent parameters, such as the depth-dependent decay factors for runoff, play more important roles than the previous four PFT-dependent parameters. Further analysis by conditioning the results on different seasons and years are being conducted to provide guidance on how climate variability and change might affect such sensitivity. This is the first step toward coupled simulations including biogeochemical processes, atmospheric processes or both to determine the full range of sensitivity of Earth system modeling to land-surface parameters. This can facilitate sampling strategies in measurement campaigns targeted at reduction of climate modeling uncertainties and can also provide guidance on land parameter calibration for simulation optimization.

Dynamics of Reactive Microbial Hotspots in Concentration Gradient.

NASA Astrophysics Data System (ADS)

Hubert, A.; Farasin, J.; Tabuteau, H.; Dufresne, A.; Meheust, Y.; Le Borgne, T.

2017-12-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella capsiferriformans ES-2 as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. We measure bacterial activity and population growth locally in precisely known hydrodynamic and chemical environments. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We compare reactive microbial hotspot dynamics in our micromodels to classic growth laws and well-known growth parameters for the laboratory model bacteria Escherichia coli.We also discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

PubMed

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Dynamics of reactive microbial hotspots in concentration gradients

NASA Astrophysics Data System (ADS)

Hubert, Antoine; Farasin, Julien; Tabuteau, Hervé; Méheust, Yves; Le Borgne, Tanguy

2017-04-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as a quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. To quantify bacterial activity we use Fluorescein Diacetate (FDA) hydrolysis by bacterial enzymes which transforms FDA into Fluorescein, whose local concentration is measured optically. We thus measure bacterial activity locally from the time derivative of the measured fluorescence. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Improving Permafrost Hydrology Prediction Through Data-Model Integration

NASA Astrophysics Data System (ADS)

Wilson, C. J.; Andresen, C. G.; Atchley, A. L.; Bolton, W. R.; Busey, R.; Coon, E.; Charsley-Groffman, L.

2017-12-01

The CMIP5 Earth System Models were unable to adequately predict the fate of the 16GT of permafrost carbon in a warming climate due to poor representation of Arctic ecosystem processes. The DOE Office of Science Next Generation Ecosystem Experiment, NGEE-Arctic project aims to reduce uncertainty in the Arctic carbon cycle and its impact on the Earth's climate system by improved representation of the coupled physical, chemical and biological processes that drive how much buried carbon will be converted to CO2 and CH4, how fast this will happen, which form will dominate, and the degree to which increased plant productivity will offset increased soil carbon emissions. These processes fundamentally depend on permafrost thaw rate and its influence on surface and subsurface hydrology through thermal erosion, land subsidence and changes to groundwater flow pathways as soil, bedrock and alluvial pore ice and massive ground ice melts. LANL and its NGEE colleagues are co-developing data and models to better understand controls on permafrost degradation and improve prediction of the evolution of permafrost and its impact on Arctic hydrology. The LANL Advanced Terrestrial Simulator was built using a state of the art HPC software framework to enable the first fully coupled 3-dimensional surface-subsurface thermal-hydrology and land surface deformation simulations to simulate the evolution of the physical Arctic environment. Here we show how field data including hydrology, snow, vegetation, geochemistry and soil properties, are informing the development and application of the ATS to improve understanding of controls on permafrost stability and permafrost hydrology. The ATS is being used to inform parameterizations of complex coupled physical, ecological and biogeochemical processes for implementation in the DOE ACME land model, to better predict the role of changing Arctic hydrology on the global climate system. LA-UR-17-26566.

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

USGS Publications Warehouse

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

2012-01-01

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

Modelling biofilm-induced formation damage and biocide treatment in subsurface geosystems

PubMed Central

Ezeuko, C C; Sen, A; Gates, I D

2013-01-01

Biofilm growth in subsurface porous media, and its treatment with biocides (antimicrobial agents), involves a complex interaction of biogeochemical processes which provide non-trivial mathematical modelling challenges. Although there are literature reports of mathematical models to evaluate biofilm tolerance to biocides, none of these models have investigated biocide treatment of biofilms growing in interconnected porous media with flow. In this paper, we present a numerical investigation using a pore network model of biofilm growth, formation damage and biocide treatment. The model includes three phases (aqueous, adsorbed biofilm, and solid matrix), a single growth-limiting nutrient and a single biocide dissolved in the water. Biofilm is assumed to contain a single species of microbe, in which each cell can be a viable persister, a viable non-persister, or non-viable (dead). Persisters describe small subpopulation of cells which are tolerant to biocide treatment. Biofilm tolerance to biocide treatment is regulated by persister cells and includes ‘innate’ and ‘biocide-induced’ factors. Simulations demonstrate that biofilm tolerance to biocides can increase with biofilm maturity, and that biocide treatment alone does not reverse biofilm-induced formation damage. Also, a successful application of biological permeability conformance treatment involving geologic layers with flow communication is more complicated than simply engineering the attachment of biofilm-forming cells at desired sites. PMID:23164434

How old is streamwater? Open questions in catchment transit time conceptualization, modeling and analysis

Treesearch

J.J. McDonnell; K. McGuire; P. Aggarwal; K.J. Beven; D. Biondi; G. Destouni; S. Dunn; A. James; J. Kirchner; P. Kraft; S. Lyon; P. Maloszewski; B. Newman; L. Pfister; A. Rinaldo; A. Rodhe; T. Sayama; J. Seibert; K. Solomon; C. Soulsby; M. Stewart; D. Tetzlaff; C. Tobin; P. Troch; M. Weiler; A. Western; A. Wörman; S. Wrede

2010-01-01

The time water spends travelling subsurface through a catchment to the stream network (i.e. the catchment water transit time) fundamentally describes the storage, flow pathway heterogeneity and sources of water in a catchment. The distribution of transit times reflects how catchments retain and release water and solutes that in turn set biogeochemical conditions and...

Critical Zone Co-dynamics: Quantifying Interactions between Subsurface, Land Surface, and Vegetation Properties Using UAV and Geophysical Approaches

NASA Astrophysics Data System (ADS)

Dafflon, B.; Leger, E.; Peterson, J.; Falco, N.; Wainwright, H. M.; Wu, Y.; Tran, A. P.; Brodie, E.; Williams, K. H.; Versteeg, R.; Hubbard, S. S.

2017-12-01

Improving understanding and modelling of terrestrial systems requires advances in measuring and quantifying interactions among subsurface, land surface and vegetation processes over relevant spatiotemporal scales. Such advances are important to quantify natural and managed ecosystem behaviors, as well as to predict how watershed systems respond to increasingly frequent hydrological perturbations, such as droughts, floods and early snowmelt. Our study focuses on the joint use of UAV-based multi-spectral aerial imaging, ground-based geophysical tomographic monitoring (incl., electrical and electromagnetic imaging) and point-scale sensing (soil moisture sensors and soil sampling) to quantify interactions between above and below ground compartments of the East River Watershed in the Upper Colorado River Basin. We evaluate linkages between physical properties (incl. soil composition, soil electrical conductivity, soil water content), metrics extracted from digital surface and terrain elevation models (incl., slope, wetness index) and vegetation properties (incl., greenness, plant type) in a 500 x 500 m hillslope-floodplain subsystem of the watershed. Data integration and analysis is supported by numerical approaches that simulate the control of soil and geomorphic characteristic on hydrological processes. Results provide an unprecedented window into critical zone interactions, revealing significant below- and above-ground co-dynamics. Baseline geophysical datasets provide lithological structure along the hillslope, which includes a surface soil horizon, underlain by a saprolite layer and the fractured Mancos shale. Time-lapse geophysical data show very different moisture dynamics in various compartments and locations during the winter and growing season. Integration with aerial imaging reveals a significant linkage between plant growth and the subsurface wetness, soil characteristics and the topographic gradient. The obtained information about the organization and connectivity of the landscape is being transferred to larger regions using aerial imaging and will be used to constrain multi-scale, multi-physics hydro-biogeochemical simulations of the East River watershed response to hydrological perturbations.

Hierarchical Bayesian method for mapping biogeochemical hot spots using induced polarization imaging

DOE PAGES

Wainwright, Haruko M.; Flores Orozco, Adrian; Bucker, Matthias; ...

2016-01-29

In floodplain environments, a naturally reduced zone (NRZ) is considered to be a common biogeochemical hot spot, having distinct microbial and geochemical characteristics. Although important for understanding their role in mediating floodplain biogeochemical processes, mapping the subsurface distribution of NRZs over the dimensions of a floodplain is challenging, as conventional wellbore data are typically spatially limited and the distribution of NRZs is heterogeneous. In this work, we present an innovative methodology for the probabilistic mapping of NRZs within a three-dimensional (3-D) subsurface domain using induced polarization imaging, which is a noninvasive geophysical technique. Measurements consist of surface geophysical surveys andmore » drilling-recovered sediments at the U.S. Department of Energy field site near Rifle, CO (USA). Inversion of surface time domain-induced polarization (TDIP) data yielded 3-D images of the complex electrical resistivity, in terms of magnitude and phase, which are associated with mineral precipitation and other lithological properties. By extracting the TDIP data values colocated with wellbore lithological logs, we found that the NRZs have a different distribution of resistivity and polarization from the other aquifer sediments. To estimate the spatial distribution of NRZs, we developed a Bayesian hierarchical model to integrate the geophysical and wellbore data. In addition, the resistivity images were used to estimate hydrostratigraphic interfaces under the floodplain. Validation results showed that the integration of electrical imaging and wellbore data using a Bayesian hierarchical model was capable of mapping spatially heterogeneous interfaces and NRZ distributions thereby providing a minimally invasive means to parameterize a hydrobiogeochemical model of the floodplain.« less

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

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

PubMed

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

2016-09-15

We utilize N and C species concentration data along with δ(15)N values of NO3(-) and δ(13)C values of dissolved inorganic C to evaluate the stoichiometry of biogeochemical reactions (mineralization, nitrification, anammox, and denitrification) occurring within a subsurface wastewater plume that originates as treated wastewater injection and enters the coastal waters of Maui as submarine groundwater discharge. Additionally, we compare wastewater effluent time-series data, injection rates, and treatment history with submarine spring discharge time-series data. We find that heterotrophic denitrification is the primary mechanism of N loss within the groundwater plume and that chlorination for pathogen disinfection suppresses microbial activity in the aquifer responsible for N loss, resulting in increased coastal ocean N loading. Replacement of chlorination with UV disinfection may restore biogeochemical reactions responsible for N loss within the aquifer and return N-attenuating conditions in the effluent plume, reducing N loading to coastal waters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Trends and future challenges in sampling the deep terrestrial biosphere.

PubMed

Wilkins, Michael J; Daly, Rebecca A; Mouser, Paula J; Trexler, Ryan; Sharma, Shihka; Cole, David R; Wrighton, Kelly C; Biddle, Jennifer F; Denis, Elizabeth H; Fredrickson, Jim K; Kieft, Thomas L; Onstott, Tullis C; Peterson, Lee; Pfiffner, Susan M; Phelps, Tommy J; Schrenk, Matthew O

2014-01-01

Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Cumulative effects of wetland drainage on watershed-scale subsurface hydrologic connectivity

NASA Astrophysics Data System (ADS)

Creed, I. F.; Ameli, A.

2017-12-01

Subsurface hydrologic connectivity influences hydrological, biogeochemical and ecological responses within watersheds. However, information about the location, duration, and frequency of subsurface hydrologic connections within wetlandscapes and between wetlandscapes and streams is often not available. This leads to a lack of understanding of the potential effects of human modifications of the landscape, including wetland degradation and removal, on subsurface hydrologic connectivity and therefore watershed responses. Herein, we develop a computationally efficient, physically-based subsurface hydrologic connectivity model that explicitly characterizes the effects of wetland degradation and removal on the distribution, length, and timing of subsurface hydrologic connectivity within a wetland-dominated watershed in the Prairie Pothole Region of North America. We run the model using a time series of wetland inventories that reflect incremental wetland loss from 1962, to 1993, and to 2009. We also consider a potential future wetland loss scenario based on removal of all wetlands outside of the protected areas of the watershed. Our findings suggest that wetland degradation and removal over this period increased the average length, transit time, and frequency of subsurface hydrologic connections to the regional surface waters, resulting in decreased baseflow in the major river network. This study provides important insights that can be used by wetland managers and policy makers to support watershed-scale wetland protection and restoration plans to improve water resource management.

Biogeochemical evidence for subsurface hydrocarbon occurrence, Recluse oil field, Wyoming; preliminary results

USGS Publications Warehouse

Dalziel, Mary C.; Donovan, Terrence J.

1980-01-01

Anomalously high manganese-to-iron ratios occurring in pine needles and sage leaves over the Recluse oil field, Wyoming, suggest effects of petroleum microseepage on the plants. This conclusion is supported by iron and manganese concentrations in soils and carbon and oxygen isotope ratios in rock samples. Seeping hydrocarbons provided reducing conditions sufficient to enable divalent iron and manganese to be organically complexed or adsorbed on solids in the soils. These bound or adsorped elements in the divalent state are essential to plants, and the plants readily assimilate them. The magnitude of the plant anomalies, combined with the supportive isotopic and chemical evidence confirming petroleum leakage, makes a strong case for the use of plants as a biogeochemical prospecting tool.

SULFATE REDUCTION IN GROUNDWATER: CHARACTERIZATION AND APPLICATIONS FOR REMEDIATION

PubMed Central

Miao, Z.; Brusseau, M. L.; Carroll, K. C.; Carreón-Diazconti, C.; Johnson, B.

2013-01-01

Sulfate is ubiquitous in groundwater, with both natural and anthropogenic sources. Sulfate reduction reactions play a significant role in mediating redox conditions and biogeochemical processes for subsurface systems. They also serve as the basis for innovative in-situ methods for groundwater remediation. An overview of sulfate reduction in subsurface environments is provided, along with a brief discussion of characterization methods and applications for addressing acid mine drainage. We then focus on two innovative, in-situ methods for remediating sulfate-contaminated groundwater, the use of zero-valent iron (ZVI) and the addition of electron-donor substrates. The advantages and limitations associated with the methods are discussed, with examples of prior applications. PMID:21947714

Modeling the fate of nitrogen on the catchment scale using a spatially explicit hydro-biogeochemical simulation system

NASA Astrophysics Data System (ADS)

Klatt, S.; Butterbach-Bahl, K.; Kiese, R.; Haas, E.; Kraus, D.; Molina-Herrera, S. W.; Kraft, P.

2015-12-01

The continuous growth of the human population demands an equally growing supply for fresh water and food. As a result, available land for efficient agriculture is constantly diminishing which forces farmers to cultivate inferior croplands and intensify agricultural practices, e.g., increase the use of synthetic fertilizers. This intensification of marginal areas in particular will cause a dangerous rise in nitrate discharge into open waters or even drinking water resources. In order to reduce the amount of nitrate lost by surface runoff or lateral subsurface transport, bufferstrips have proved to be a valuable means. Current laws, however, promote rather static designs (i.e., width and usage) even though a multitude of factors, e.g., soil type, slope, vegetation and the nearby agricultural management, determines its effectiveness. We propose a spatially explicit modeling approach enabling to assess the effects of those factors on nitrate discharge from arable lands using the fully distributed hydrology model CMF coupled to the complex biogeochemical model LandscapeDNDC. Such a modeling scheme allows to observe the displacement of dissolved nutrients in both vertical and horizontal directions and serves to estimate both their uptake by the vegetated bufferstrip and loss to the environment. First results indicate a significant reduction of nitrate loss in the presence of a bufferstrip (2.5 m). We show effects induced by various buffer strip widths and plant cover on the nitrate retention.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

Saltmarsh restoration undoubtedly provides environmental enhancement, with vegetation quickly re-establishing following the breach of sea walls and subsequent tidal inundation of previously defended areas. Yet evidence increasingly suggests that the restored saltmarshes do not have the same biological characteristics as their natural counterparts (Mossman et al. 2012) and this may be in part be due to physicochemical parameters at the site including anoxia and poor drainage. Hence, restored saltmarshes may not offer the range and quality of ecosystem services anticipated. These environments will have been 'disturbed' by previous land use and there is little understanding of the impacts of this disturbance on the wider hydrogeomorphic and biogeochemical functioning in restored saltmarshes and the implications for saltmarsh vegetation development. This study examines linkages between physical sediment characteristics, sediment structure (using X-ray microtomography), sub-surface hydrology (using pressure transducers and time series analysis), and sediment and porewater geochemistry (major and trace elements, major anions) in sediment cores collected from undisturbed saltmarshes and those restored by de-embankment. Sub-surface sediments in restored saltmarshes have lower organic matter content, lower moisture content and higher bulk density than undisturbed sites. Using X-ray tomography a clear horizon can be observed which separates relict agricultural soils at depth with less dense and structureless sediments deposited since de-embankment. Ratios of open to closed pore space suggest that while undisturbed saltmarshes have the highest porosity, restored saltmarshes have larger void spaces, but limited pore connectivity. Sub-surface hydrological response to tidal flooding was subdued in the restored compared to the undisturbed site, suggesting that porewater flow may be impeded. Time series analysis indicated that flow pathways differ in restored saltmarsh sediments with preferential horizontal flows. The undisturbed saltmarsh displayed typical vertical geochemical sediment profiles. However, in the restored sites total Fe and Mn are elevated at depth indicating an absence of diagenetic cycling, whilst porewater sulphate and nitrate increased at depth suggesting that vertical solute transport is impeded in restored sites. In surface sediments, though total Hg concentrations are similar, Hg methylation rates are significantly higher than in the undisturbed saltmarsh suggesting that surface anoxia and poor drainage may result in increased mobilization and bioavailability of Hg. These findings have implications for the wider biogeochemical ecosystem services offered by saltmarsh restoration and the water-logged, anoxic conditions produced are unsuitable for seedling germination and plant growth. This highlights the need for integrated understanding of physical and biogeochemical processes.

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Donald; Nolan, Jason; Williams, Kenneth H.

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

DOE PAGES

Pan, Donald; Nolan, Jason; Williams, Kenneth H.; ...

2017-07-11

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Subsurface Conditions Controlling Uranium Incorporation in Iron Oxides: A Redox Stable Sink

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fendorf, Scott

2016-04-05

Toxic metals and radionuclides throughout the U.S. Department of Energy Complex pose a serious threat to ecosystems and to human health. Of particular concern is the redox-sensitive radionuclide uranium, which is classified as a priority pollutant in soils and groundwaters at most DOE sites owing to its large inventory, its health risks, and its mobility with respect to primary waste sources. The goal of this research was to contribute to the long-term mission of the Subsurface Biogeochemistry Program by determining reactions of uranium with iron (hydr)oxides that lead to long-term stabilization of this pervasive contaminant. The research objectives of thismore » project were thus to (1) identify the (bio)geochemical conditions, including those of the solid-phase, promoting uranium incorporation in Fe (hydr)oxides, (2) determine the magnitude of uranium incorporation under a variety of relevant subsurface conditions in order to quantify the importance of this pathway when in competition with reduction or adsorption; (3) identify the mechanism(s) of U(VI/V) incorporation in Fe (hydr)oxides; and (4) determine the stability of these phases under different biogeochemical (inclusive of redox) conditions. Our research demonstrates that redox transformations are capable of achieving U incorporation into goethite at ambient temperatures, and that this transformation occurs within days at U and Fe(II) concentrations that are common in subsurface geochemical environments with natural ferrihydrites—inclusive of those with natural impurities. Increasing Fe(II) or U concentration, or initial pH, made U(VI) reduction to U(IV) a more competitive sequestration pathway in this system, presumably by increasing the relative rate of U reduction. Uranium concentrations commonly found in contaminated subsurface environments are often on the order of 1-10 μM, and groundwater Fe(II) concentrations can reach exceed 1 mM in reduced zones of the subsurface. The redox-driven U(V) incorporation mechanism may help to explain U retention in some geologic materials, improving our understanding of U-based geochronology and the redox status of ancient geochemical environments. Additionally, U(VI) may be incorporated within silicate minerals though encapsulation of U-bearing iron oxides, leading to a redox stable solid. Our research detailing previously unrecognized mechanism of U incorporation within sediment minerals may even lead to new approaches for in situ contamination remediation techniques, and will help refine models of U fate and transport in reduced subsurface zones.« less

Evaluation of the transport matrix method for simulation of ocean biogeochemical tracers

NASA Astrophysics Data System (ADS)

Kvale, Karin F.; Khatiwala, Samar; Dietze, Heiner; Kriest, Iris; Oschlies, Andreas

2017-06-01

Conventional integration of Earth system and ocean models can accrue considerable computational expenses, particularly for marine biogeochemical applications. Offline numerical schemes in which only the biogeochemical tracers are time stepped and transported using a pre-computed circulation field can substantially reduce the burden and are thus an attractive alternative. One such scheme is the transport matrix method (TMM), which represents tracer transport as a sequence of sparse matrix-vector products that can be performed efficiently on distributed-memory computers. While the TMM has been used for a variety of geochemical and biogeochemical studies, to date the resulting solutions have not been comprehensively assessed against their online counterparts. Here, we present a detailed comparison of the two. It is based on simulations of the state-of-the-art biogeochemical sub-model embedded within the widely used coarse-resolution University of Victoria Earth System Climate Model (UVic ESCM). The default, non-linear advection scheme was first replaced with a linear, third-order upwind-biased advection scheme to satisfy the linearity requirement of the TMM. Transport matrices were extracted from an equilibrium run of the physical model and subsequently used to integrate the biogeochemical model offline to equilibrium. The identical biogeochemical model was also run online. Our simulations show that offline integration introduces some bias to biogeochemical quantities through the omission of the polar filtering used in UVic ESCM and in the offline application of time-dependent forcing fields, with high latitudes showing the largest differences with respect to the online model. Differences in other regions and in the seasonality of nutrients and phytoplankton distributions are found to be relatively minor, giving confidence that the TMM is a reliable tool for offline integration of complex biogeochemical models. Moreover, while UVic ESCM is a serial code, the TMM can be run on a parallel machine with no change to the underlying biogeochemical code, thus providing orders of magnitude speed-up over the online model.

Thinking outside the channel: modeling nitrogen cycling in networked river ecosystems

Treesearch

Ashley M. Helton; Geoffrey C. Poole; Judy L. Meyer; Wilfred M. Wollheim; Bruce J. Peterson; Patrick J. Mulholland; Emily S. Bernhardt; Jack A. Stanford; Clay Arango; Linda R. Ashkenas; Lee W. Cooper; Walter K. Dodds; Stanley V. Gregory; Robert O. Hall; Stephen K. Hamilton; Sherri L. Johnson; William H. McDowell; Jody D. Potter; Jennifer L. Tank; Suzanne M. Thomas; H. Maurice Valett; Jackson R. Webster; Lydia Zeglin

2011-01-01

Agricultural and urban development alters nitrogen and other biogeochemical cycles in rivers worldwide. Because such biogeochemical processes cannot be measured empirically across whole river networks, simulation models are critical tools for understanding river-network biogeochemistry. However, limitations inherent in current models restrict our ability to simulate...

Active Serpentinization and the Potential for a Diverse Subsurface Biosphere

NASA Astrophysics Data System (ADS)

Canovas, P. A.; Shock, E.

2013-12-01

The ubiquitous nature of serpentinization and the unique fluids it generates have major consequences for habitat generation, abiotic organic synthesis, and biosynthesis. The production of hydrogen from the anaerobic hydrolysis of ultramafic minerals sets the redox state of serpentinizing fluids to be thermodynamically favorable for these processes. Consequently, a host of specialized microbial populations and metabolisms can be sustained. Active low-temperature serpentinizing systems, such as the Samail ophiolite in Oman, offer an ideal opportunity to investigate biogeochemical processes during the alteration of ultramafic minerals. At the Samail ophiolite in particular, serpentinization may provide the potential for an active subsurface microbial community shielded from potentially unfavorable surface conditions. Support for this assertion comes from geochemical data including Mg, Ca, CH4 (aq), and H2 (aq) abundances indicating that methane is a product of serpentinization. To further investigate viable metabolic strategies, affinity calculations were performed on both the surface waters and the hyperalkaline springs, which may be considered as messengers of processes occurring in the subsurface. Almost all sites yield positive affinities (i.e., are thermodynamically favorable) for a diverse suite of serpentinization metabolisms including methanogenesis, anammox, and carbon monoxide, nitrate, and sulfate reduction with hydrogen, as well as anaerobic methanotrophy coupled to nitrate, nitrite, and sulfate reduction. Reaction path modeling was performed to ascertain the extent to which serpentinization and mixing of surface waters with hyperalkaline spring waters in the subsurface can generate suitable habitats. The serpentinization model simulates the reaction of pristine Oman harzburgite with surface water to quantify the redox state and generation of hyperalkaline spring water. Preliminary results show that water-rock ratios as high as 100 could effectively reduce the system and create a thermodynamic drive sufficient to convert all of the dissolved inorganic carbon into methane. This indicates that the system is poised to create the reducing conditions necessary to support a subsurface biosphere very early in the serpentinizing process, and that the subsurface biosphere could extend upwards to very near the surface. The mixing model simulates the percolation of surface water into the active serpentinization zone. During the mixing process, methane is calculated to be more stable than carbonate species until approximately 100g of surface water have been added to 1 kg of the serpentinizing fluid. These results suggest that unreacted surface water flowing directly into the serpentinizing zone can create the disequilibria necessary for methanogenesis, and possibly other metabolisms, to proceed while still maintaining the low redox state of the system. As long as the recharge to the hyperalkaline reservoir does not exceed ten percent of the reservoir, methanogenesis and other serpentinization metabolisms can thrive off the disequilibria generated through mixing.

Filling the gap: using non-invasive geophysical methods to monitor the processes leading to enhanced carbon turnover induced by periodic water table fluctuations

NASA Astrophysics Data System (ADS)

Mellage, A.; Pronk, G.; Atekwana, E. A.; Furman, A.; Rezanezhad, F.; Van Cappellen, P.

2017-12-01

Subsurface transition environments such as the capillary fringe are characterized by steep gradients in redox conditions. Spatial and temporal variations in electron acceptor and donor availability - driven by hydrological changes - may enhance carbon turnover, in some cases resulting in pulses of CO2-respiration. Filling the mechanistic knowledge gap between the hydrological driver and its biogeochemical effects hinges on our ability to monitor microbial activity and key geochemical markers at a high spatial and temporal resolution. However, direct access to subsurface biogeochemical processes is logistically difficult, invasive and usually expensive. In-line, non-invasive geophysical techniques - Spectral Induced Polarization (SIP) and Electrodic Potential (EP), specifically - offer a comparatively inexpensive alternative and can provide data with high spatial and temporal resolution. The challenge lies in linking electrical responses to specific changes in biogeochemical processes. We conducted SIP and EP measurements on a soil column experiment where an artificial soil mixture was subjected to monthly drainage and imbibition cycles. SIP responses showed a clear dependence on redox zonation and microbial abundance. Temporally variable responses exhibited no direct moisture dependence suggesting that the measured responses recorded changes in microbial activity and coincided with the depth interval over which enhanced carbon turnover was observed. EP measurements detected the onset of sulfate mineralization and mapped its depth zonation. SIP and EP signals thus detected enhanced microbial activity within the water table fluctuation zone as well as the timing of the development of specific reactive processes. These findings can be used to relate measured electrical signals to specific reaction pathways and help inform reactive transport models, increasing their predictive capabilities.

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

DOE PAGES

Hug, Laura A.; Thomas, Brian C.; Sharon, Itai; ...

2015-07-22

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla withmore » no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.« less

Linking Spectral Induced Polarization (SIP) and Subsurface Microbial Processes: Results from Sand Column Incubation Experiments.

PubMed

Mellage, Adrian; Smeaton, Christina M; Furman, Alex; Atekwana, Estella A; Rezanezhad, Fereidoun; Van Cappellen, Philippe

2018-02-20

Geophysical techniques, such as spectral induced polarization (SIP), offer potentially powerful approaches for in situ monitoring of subsurface biogeochemistry. The successful implementation of these techniques as monitoring tools for reactive transport phenomena, however, requires the deconvolution of multiple contributions to measured signals. Here, we present SIP spectra and complementary biogeochemical data obtained in saturated columns packed with alternating layers of ferrihydrite-coated and pure quartz sand, and inoculated with Shewanella oneidensis supplemented with lactate and nitrate. A biomass-explicit diffusion-reaction model is fitted to the experimental biogeochemical data. Overall, the results highlight that (1) the temporal response of the measured imaginary conductivity peaks parallels the microbial growth and decay dynamics in the columns, and (2) SIP is sensitive to changes in microbial abundance and cell surface charging properties, even at relatively low cell densities (<10 8 cells mL -1 ). Relaxation times (τ) derived using the Cole-Cole model vary with the dominant electron accepting process, nitrate or ferric iron reduction. The observed range of τ values, 0.012-0.107 s, yields effective polarization diameters in the range 1-3 μm, that is, 2 orders of magnitude smaller than the smallest quartz grains in the columns, suggesting that polarization of the bacterial cells controls the observed chargeability and relaxation dynamics in the experiments.

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

USGS Publications Warehouse

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

2014-01-01

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

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2.

PubMed

Jin, Qusheng; Kirk, Matthew F

2016-01-01

Geological carbon sequestration captures CO 2 from industrial sources and stores the CO 2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO 2 concentration. This study uses biogeochemical modeling to explore the influence of CO 2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO 2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO 2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO 2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO 2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2

PubMed Central

Jin, Qusheng; Kirk, Matthew F.

2016-01-01

Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses. PMID:27909425

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

A generic biogeochemical module for earth system models

NASA Astrophysics Data System (ADS)

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

2013-06-01

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.

Comparative Biogeochemical Cycles of Bioenergy Crops Reveal Nitrogen-Fixation and Low GHG Emissions in a Miscanthus x giganteus Agro-ecosystem

USDA-ARS?s Scientific Manuscript database

We evaluated the relative greenhouse gas mitigation potential of plant species considered as biofuel feedstock crops by simulating the biogeochemical processes associated with Miscanthus x giganteus, Panicum virgatum, Zea mays, and a mixed prairie community. DayCent model simulations for Miscanthus ...

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

NASA Astrophysics Data System (ADS)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.

2011-11-01

Field experiments at a former uranium mill tailings site have identified the potential for stimulating indigenous bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. This effectively removes uranium from solution resulting in groundwater concentrations below actionable standards. Three-dimensional, coupled variably-saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport rates and biogeochemical reaction rates that determine the location and magnitude of key reaction products. A comprehensive reaction network, developed largely throughmore » 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.« less

Improved simulation of poorly drained forests using Biome-BGC.

PubMed

Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E

2007-05-01

Forested wetlands and peatlands are important in boreal and terrestrial biogeochemical cycling, but most general-purpose forest process models are designed and parameterized for upland systems. We describe changes made to Biome-BGC, an ecophysiological process model, that improve its ability to simulate poorly drained forests. Model changes allowed for: (1) lateral water inflow from a surrounding watershed, and variable surface and subsurface drainage; (2) adverse effects of anoxic soil on decomposition and nutrient mineralization; (3) closure of leaf stomata in flooded soils; and (4) growth of nonvascular plants (i.e., bryophytes). Bryophytes were treated as ectohydric broadleaf evergreen plants with zero stomatal conductance, whose cuticular conductance to CO(2) was dependent on plant water content. Individual model changes were parameterized with published data, and ecosystem-level model performance was assessed by comparing simulated output to field data from the northern BOREAS site in Manitoba, Canada. The simulation of the poorly drained forest model exhibited reduced decomposition and vascular plant growth (-90%) compared with that of the well-drained forest model; the integrated bryophyte photosynthetic response accorded well with published data. Simulated net primary production, biomass and soil carbon accumulation broadly agreed with field measurements, although simulated net primary production was higher than observed data in well-drained stands. Simulated net primary production in the poorly drained forest was most sensitive to oxygen restriction on soil processes, and secondarily to stomatal closure in flooded conditions. The modified Biome-BGC remains unable to simulate true wetlands that are subject to prolonged flooding, because it does not track organic soil formation, water table changes, soil redox potential or anaerobic processes.

Assimilation of Ocean-Color Plankton Functional Types to Improve Marine Ecosystem Simulations

NASA Astrophysics Data System (ADS)

Ciavatta, S.; Brewin, R. J. W.; Skákala, J.; Polimene, L.; de Mora, L.; Artioli, Y.; Allen, J. I.

2018-02-01

We assimilated phytoplankton functional types (PFTs) derived from ocean color into a marine ecosystem model, to improve the simulation of biogeochemical indicators and emerging properties in a shelf sea. Error-characterized chlorophyll concentrations of four PFTs (diatoms, dinoflagellates, nanoplankton, and picoplankton), as well as total chlorophyll for comparison, were assimilated into a physical-biogeochemical model of the North East Atlantic, applying a localized Ensemble Kalman filter. The reanalysis simulations spanned the years 1998-2003. The skill of the reference and reanalysis simulations in estimating ocean color and in situ biogeochemical data were compared by using robust statistics. The reanalysis outperformed both the reference and the assimilation of total chlorophyll in estimating the ocean-color PFTs (except nanoplankton), as well as the not-assimilated total chlorophyll, leading the model to simulate better the plankton community structure. Crucially, the reanalysis improved the estimates of not-assimilated in situ data of PFTs, as well as of phosphate and pCO2, impacting the simulation of the air-sea carbon flux. However, the reanalysis increased further the model overestimation of nitrate, in spite of increases in plankton nitrate uptake. The method proposed here is easily adaptable for use with other ecosystem models that simulate PFTs, for, e.g., reanalysis of carbon fluxes in the global ocean and for operational forecasts of biogeochemical indicators in shelf-sea ecosystems.

Concentration-Discharge Relationships, Nested Reaction Fronts, and the Balance of Oxidative and Acid-Base Weathering Fluxes in an Alpine Catchment, East River, Colorado

NASA Astrophysics Data System (ADS)

Winnick, M.; Carroll, R. W. H.; Williams, K. H.; Maxwell, R. M.; Maher, K.

2016-12-01

Although important for solute production and transport, the varied interactions between biogeochemical processes and subsurface hydrology remain poorly characterized. We investigate these couplings in the headwaters of the East River, CO, a high-elevation shale-dominated catchment system in the Rocky Mountains, using concentration-discharge (C-Q) relationships for major cations, anions, and organic carbon. Dissolved organic carbon (DOC) displays a positive C-Q relationship with well-defined clockwise hysteresis, indicating the mobilization and depletion of DOC in the upper soil horizons and highlighting the importance of shallow flowpaths through the snowmelt period. Cation and anion concentrations demonstrate that carbonate weathering, which dominates solute fluxes, is promoted by both carbonic acid and sulfuric acid derived from oxidation of pyrite in the shale bedrock. Sulfuric acid weathering in the deep subsurface dominates during base flow conditions when waters have infiltrated below the hypothesized pyrite oxidation front, whereas carbonic acid weathering plays a dominant role during the snowmelt period as a result of shallow flowpaths. Differential C-Q relationships between solutes suggest that infiltrating waters approach calcite saturation before reaching the pyrite oxidation front, after which sulfuric acid reduces carbonate alkalinity. This increase in CO2(aq) at the expense of HCO3- results in outgassing of CO2 when waters equilibrate to surface conditions, and reduces the export of carbon and alkalinity from the East River by roughly 33% annually. Future changes in snowmelt dynamics that control the balance of carbonic and sulfuric acid weathering therefore have the capacity to substantially alter the cycling of carbon in the East River catchment. Ultimately, we demonstrate that differential C-Q relationships between major solutes can provide unique insights into the complex subsurface flow and biogeochemical dynamics that operate at catchment scales.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE PAGES

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.; ...

2016-01-22

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Snowmelt controls on concentration-discharge relationships and the balance of oxidative and acid-base weathering fluxes in an alpine catchment, East River, Colorado: ACID-BASE VERSUS OXIDATIVE WEATHERING FLUXES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winnick, Matthew J.; Carroll, Rosemary W. H.; Williams, Kenneth H.

Although important for riverine solute and nutrient fluxes, the connections between biogeochemical processes and subsurface hydrology remain poorly characterized. We investigate these couplings in the East River, CO, a high-elevation shale-dominated catchment in the Rocky Mountains, using concentration-discharge (C-Q) relationships for major cations, anions, and organic carbon. Dissolved organic carbon (DOC) displays a positive C-Q relationship with clockwise hysteresis, indicating mobilization and depletion of DOC in the upper soil horizons and emphasizing the importance of shallow flowpaths during snowmelt. Cation and anion concentrations demonstrate that carbonate weathering, which dominates solute fluxes, is promoted by both sulfuric acid derived from pyritemore » oxidation in the shale bedrock and carbonic acid derived from subsurface respiration. Sulfuric acid weathering dominates during baseflow conditions when waters infiltrate below the inferred pyrite oxidation front, whereas carbonic acid weathering plays a dominant role during snowmelt as a result of shallow flowpaths. Differential C-Q relationships between solutes suggest that infiltrating waters approach calcite saturation before reaching the pyrite oxidation front, after which sulfuric acid reduces carbonate alkalinity. This reduction in alkalinity results in CO 2 outgassing when waters equilibrate to surface conditions, and reduces the riverine export of carbon and alkalinity by roughly 33% annually. In conclusion, future changes in snowmelt dynamics that control the balance of carbonic and sulfuric acid weathering may substantially alter carbon cycling in the East River. Ultimately, we demonstrate that differential C-Q relationships between major solutes can provide unique insights into the complex subsurface flow and biogeochemical dynamics that operate at catchment scales.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Snowmelt controls on concentration-discharge relationships and the balance of oxidative and acid-base weathering fluxes in an alpine catchment, East River, Colorado: ACID-BASE VERSUS OXIDATIVE WEATHERING FLUXES

DOE PAGES

Winnick, Matthew J.; Carroll, Rosemary W. H.; Williams, Kenneth H.; ...

2017-03-01

Although important for riverine solute and nutrient fluxes, the connections between biogeochemical processes and subsurface hydrology remain poorly characterized. We investigate these couplings in the East River, CO, a high-elevation shale-dominated catchment in the Rocky Mountains, using concentration-discharge (C-Q) relationships for major cations, anions, and organic carbon. Dissolved organic carbon (DOC) displays a positive C-Q relationship with clockwise hysteresis, indicating mobilization and depletion of DOC in the upper soil horizons and emphasizing the importance of shallow flowpaths during snowmelt. Cation and anion concentrations demonstrate that carbonate weathering, which dominates solute fluxes, is promoted by both sulfuric acid derived from pyritemore » oxidation in the shale bedrock and carbonic acid derived from subsurface respiration. Sulfuric acid weathering dominates during baseflow conditions when waters infiltrate below the inferred pyrite oxidation front, whereas carbonic acid weathering plays a dominant role during snowmelt as a result of shallow flowpaths. Differential C-Q relationships between solutes suggest that infiltrating waters approach calcite saturation before reaching the pyrite oxidation front, after which sulfuric acid reduces carbonate alkalinity. This reduction in alkalinity results in CO 2 outgassing when waters equilibrate to surface conditions, and reduces the riverine export of carbon and alkalinity by roughly 33% annually. In conclusion, future changes in snowmelt dynamics that control the balance of carbonic and sulfuric acid weathering may substantially alter carbon cycling in the East River. Ultimately, we demonstrate that differential C-Q relationships between major solutes can provide unique insights into the complex subsurface flow and biogeochemical dynamics that operate at catchment scales.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Boyanov, Maxim I; Brulc, Jennifer M; Johnston, Eric R; Kemner, Kenneth M; Antonopoulos, Dionysios A

2016-01-01

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.

Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

NASA Astrophysics Data System (ADS)

Chang, C.; Li, M.; Yeh, G.

2010-12-01

The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

Microbial Reduction of Fe(III) and U(VI) in Aquifers: Simulations Exploring Coupled Effects of Heterogeneity and Fe(II) Sorption

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Fang, Y.; Roden, E. E.; Brooks, S. C.; Chien, Y.; Murray, C. J.

2004-05-01

Uranium is a significant groundwater contaminant at many former mining and processing sites. In its oxidized state, U(VI) is soluble and mobile, although strongly retarded by sorption to natural iron oxide surfaces. It has been demonstrated that commonly occurring subsurface microorganisms can reduce uranium and other metals when provided sufficient carbon as an electron donor. Reduced U(IV) precipitates as a solid phase; therefore biostimulation provides a potential strategy for in situ removal from contaminated groundwater. However, these biogeochemical reactions occur in the context of a complex heterogeneous environment in which flow and transport dynamics and abiotic reactions can have significant impacts. We have constructed a high-resolution numerical model of groundwater flow and multicomponent reactive transport that incorporates heterogeneity in hydraulic conductivity and initial Fe(III) distribution, microbial growth and transport dynamics, and effects of sorption or precipitation of biogenic Fe(II) on availability of Fe(III) as an electron acceptor. The biogeochemical reaction models and their parameters are based on laboratory experiments; the heterogeneous field-scale property distributions are based on interpretations of geophysical and other observations at a highly characterized field site. The model is being run in Monte Carlo mode to examine the controls that these factors exert on 1) the initial distribution of sorbed uranium in an oxic environment and 2) the reduction and immobilization of uranium upon introduction of a soluble electron donor.

Hyporheic zone as a bioreactor: sediment heterogeneity influencing biogeochemical processes

NASA Astrophysics Data System (ADS)

Perujo, Nuria; Romani, Anna M.; Sanchez-Vila, Xavier

2017-04-01

Mediterranean fluvial systems are characterized by frequent periods of low flow or even drought. During low flow periods, water from wastewater treatment plants (WWTPs) is proportionally large in fluvial systems. River water might be vertically transported through the hyporheic zone, and then porous medium acts as a complementary treatment system since, as water infiltrates, a suite of biogeochemical processes occurs. Subsurface sediment heterogeneity plays an important role since it influences the interstitial fluxes of the medium and drives biomass growing, determining biogeochemical reactions. In this study, WWTP water was continuously infiltrated for 3 months through two porous medium tanks: one consisting of 40 cm of fine sediment (homogeneous); and another comprised of two layers of different grain size sediments (heterogeneous), 20 cm of coarse sediment in the upper part and 20 cm of fine one in the bottom. Several hydrological, physicochemical and biological parameters were measured periodically (weekly at the start of the experiment and biweekly at the end). Analysed parameters include dissolved nitrogen, phosphorus, organic carbon, and oxygen all measured at the surface, and at 5, 20 and 40 cm depth. Variations in hydraulic conductivity with time were evaluated. Sediment samples were also analysed at three depths (surface, 20 and 40 cm) to determine bacterial density, chlorophyll content, extracellular polymeric substances, and biofilm function (extracellular enzyme activities and carbon substrate utilization profiles). Preliminary results suggest hydraulic conductivity to be the main driver of the differences in the biogeochemical processes occurring in the subsurface. At the heterogeneous tank, a low nutrient reduction throughout the whole medium is measured. In this medium, high hydraulic conductivity allows for a large amount of infiltrating water, but with a small residence time. Since some biological processes are largely time-dependent, small water residence time results in low nutrient reduction. Moreover, high nitrification and low ammonium concentration in the interface of the two grain-size layers are measured, probably related to high dissolved oxygen concentration at the coarse-fine sediment interface, further promoting accumulation of bacteria and algae. In contrast, the homogeneous tank shows low dissolved oxygen values and high denitrification in depth which could be related to lower overall hydraulic conductivity, as compared to the heterogeneous tank. The preliminary analysis of our results indicates a key role of hydraulic conductivity on biogeochemical processes in the porous medium but, at the same time that it is strongly interacting with sediment grain-size distribution and the development of biofilm. The final scope of this study is to know the interactions between physicochemical and biological components in sediments in order to understand in detail the biogeochemical processes occurring.

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

USGS Publications Warehouse

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

2008-01-01

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

Adapting to life: ocean biogeochemical modelling and adaptive remeshing

NASA Astrophysics Data System (ADS)

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

2013-11-01

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

Adapting to life: ocean biogeochemical modelling and adaptive remeshing

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wrighton, Kelly C.; Castelle, Cindy; Wilkins, Michael J.

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge, and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, Colorado, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via two acetate-based biostimulation treatments. Samples weremore » collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include genomes from a new phylum (ACD20), phylogenetically novel members of the Chloroflexi and Bacteroidetes, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER, and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate, and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen currency in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate, and iron reduction. Thus, fermentation carried out by previously unstudied members of sediment microbial communities may be an important driver of diverse subsurface biogeochemical cycles.« less

Mechanisms of Arsenic Mobilization and Attenuation in Subsurface Sediments

NASA Astrophysics Data System (ADS)

O'Day, P. A.; Illera, V.; Root, R.; Choi, S.; Vlassopoulos, D.

2007-12-01

This talk will review molecular mechanisms of As mobilization and attenuation in subsurface sediments using examples from recent field studies that represent a range in oxidation-redox (redox) potential. As a ubiquitous trace element in sediments, As speciation and fate is linked to the abundance and biogeochemical behavior of the generally more abundant redox-active elements Fe, S, and Mn. All four elements are subject to oxidation, reduction, and pH-dependent processes such as sorption, desorption, precipitation, and dissolution, and which may include both biotic and abiotic reaction steps. We have used spectroscopic interrogation and geochemical modeling to characterize As speciation in subsurface sediments in several contrasting environments, including high and low S and Fe settings. Aquifers most at risk for contamination by As include those that are rich in organic matter and nutrients, stimulating high rates of microbial reduction and creating anoxic conditions, but limited in labile or available S and/or Fe that remove As by precipitation or adsorption. In subsurface sediments with low labile S and Fe, laboratory experiments and spectroscopic studies suggest that sediment Mn minerals are important in the oxidation of sorbed As(III) to As(V), but that they have a limited oxidation capacity. Arsenic attenuation and mobilization in the subsurface are affected by seasonal variations when hydraulic conditions are influenced by surface infiltration, which may induce transitions from oxidized to reduced conditions (or vice versa) in porewater.

Using proteomic data to assess a genome-scale "in silico" model of metal reducing bacteria in the simulation of field-scale uranium bioremediation

NASA Astrophysics Data System (ADS)

Yabusaki, S.; Fang, Y.; Wilkins, M. J.; Long, P.; Rifle IFRC Science Team

2011-12-01

A series of field experiments in a shallow alluvial aquifer at a former uranium mill tailings site have demonstrated that indigenous bacteria can be stimulated with acetate to catalyze the conversion of hexavalent uranium in a groundwater plume to immobile solid-associated uranium in the +4 oxidation state. While this bioreduction of uranium has been shown to lower groundwater concentrations below actionable standards, a viable remediation methodology will need a mechanistic, predictive and quantitative understanding of the microbially-mediated reactions that catalyze the reduction of uranium in the context of site-specific processes, properties, and conditions. At the Rifle IFRC site, we are investigating the impacts on uranium behavior of pulsed acetate amendment, acetate-oxidizing iron and sulfate reducing bacteria, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. The simulation of three-dimensional, variably saturated flow and biogeochemical reactive transport during a uranium bioremediation field experiment includes a genome-scale in silico model of Geobacter sp. to represent the Fe(III) terminal electron accepting process (TEAP). The Geobacter in silico model of cell-scale physiological metabolic pathways is comprised of hundreds of intra-cellular and environmental exchange reactions. One advantage of this approach is that the TEAP reaction stoichiometry and rate are now functions of the metabolic status of the microorganism. The linkage of in silico model reactions to specific Geobacter proteins has enabled the use of groundwater proteomic analyses to assess the accuracy of the model under evolving hydrologic and biogeochemical conditions. In this case, the largest predicted fluxes through in silico model reactions generally correspond to high abundances of proteins linked to those reactions (e.g. the condensation reaction catalyzed by the protein citrate synthase that generates citrate from acetyl-CoA and oxaloacetate). Model discrepancies with the proteomic data, such as the prediction of shifts associated with nitrogen limitation, revealed pathways in the in silico code that could be modified to more accurately predict metabolic processes that occur in the subsurface. The potential outcome of this approach is the engineering of electron donor (e.g., acetate), terminal electron acceptor [e.g., U(VI)], and biogeochemical conditions that enhance the desired metabolic pathways of the target microorganism(s) to effect cost-effective uranium bioreduction.

Validation of an intermediate-complexity model for simulating marine biogeochemistry under anoxic conditions in the modern Black Sea

NASA Astrophysics Data System (ADS)

Romaniello, Stephen J.; Derry, Louis A.

2010-08-01

We test the ability of a new 1-D intermediate-complexity box model (ICBM) that includes process-based C, N, P, O, and S biogeochemistry to simulate profiles and fluxes of biogeochemically reactive species across a wide range of ocean redox states. The ICBM was developed to simulate whole ocean processes for paleoceanographic applications and has been tested with data from the modern global ocean. Here we adapt the circulation submodel of the ICBM to simulate water mass exchange and eddy diffusion processes in the Black Sea but make only very minor changes to the biogeochemical submodel. We force the model with estimated natural and anthropogenic inputs of tracers and nutrients to the Black Sea and compare the results of the simulations to modern observations. Ventilation of the Black Sea is modeled by depth-dependent entrainment of Cold Intermediate Layer water into Bosphorus plume water and subsequent intrusion into deep layers. The simulated profiles of circulation tracers θ, salinity, CFC-12, and radiocarbon agree well with available data, suggesting that the model does a reasonable job of representing physical exchange. Vertical profiles of biogeochemically active components are in good overall agreement with observations. The lack of trace metal (Mn and Fe) cycling in the model results in some discrepancies between the simulated profiles and observation across the suboxic zone; however, the overall redox balance is not sensitive to this difference. We compare modeled basin-wide biogeochemical fluxes to available estimates, but in a number of cases uncertainties in modern budgets limit our ability to test the model rigorously. In agreement with earlier work we find that fixed N losses via thiodenitrification are likely a major pathway in the Black Sea N cycle. Overall, the same biogeochemical submodel used to simulate the modern global ocean appears to perform well in simulating Black Sea processes without requiring significant modification. The ability of a single model to perform across a wide range of redox states is an important prerequisite for applying the ICBM to deep time paleoceanographic problems. The model source code is available as MATLAB™ 7 m-files provided as auxiliary material.

The Shale Hills Critical Zone Observatory for Embedded Sensing and Simulation

NASA Astrophysics Data System (ADS)

Duffy, C.; Davis, K.; Kane, T.; Boyer, E.

2009-04-01

The future of environmental observing systems will utilize embedded sensor networks with continuous real-time measurement of hydrologic, atmospheric, biogeochemical, and ecological variables across diverse terrestrial environments. Embedded environmental sensors, benefitting from advances in information sciences, networking technology, materials science, computing capacity, and data synthesis methods, are undergoing revolutionary change. It is now possible to field spatially-distributed, multi-node sensor networks that provide density and spatial coverage previously accessible only via numerical simulation. At the same time, computational tools are advancing rapidly to the point where it is now possible to simulate the physical processes controlling individual parcels of water and solutes through the complete terrestrial water cycle. Our goal for the Penn State Critical Zone Observatory is to apply environmental sensor arrays, integrated hydrologic models deployed and coordinated at a testbed within the Penn State Experimental Forest. The NSF-funded CZO is designed to observe the detailed space and time complexities of the water and energy cycle for a watershed and ultimately the river basin for all physical states and fluxes (groundwater, soil moisture, temperature, streamflow, latent heat, snowmelt, chemistry, isotopes etc.). Presently fully-coupled physical models are being developed that link the atmosphere-land-vegetation-subsurface system into a fully-coupled distributed system. During the last 5 years the Penn State Integrated Hydrologic Modeling System has been under development as an open-source community modeling project funded by NSF EAR/GEO and NSF CBET/ENG. PIHM represents a strategy for the formulation and solution of fully-coupled process equations at the watershed and river basin scales, and includes a tightly coupled GIS tool for data handling, domain decomposition, optimal unstructured grid generation, and model parameterization. (PIHM; http://sourceforge.net/projects/pihmmodel/; http://sourceforge.net/projects/pihmgis/ ) The CZO sensor and simulation system is being developed to have the following elements: 1) extensive, spatially-distributed smart sensor networks to gather intensive soil, geologic, hydrologic, geochemical and isotopic data; 2) spatially-explicit multiphysics models/solutions of the land-subsurface-vegetation-atmosphere system; and 3) parallel/distributed, adaptive algorithms for rapidly simulating the states of the watershed at high resolution, and 4) signal processing tools for data mining and parameter estimation. The prototype proposed sensor array and simulation system proposed is demonstrated with preliminary results from our first year.

Biogeochemical control points in a water-limited critical zone

NASA Astrophysics Data System (ADS)

Chorover, J.; Brooks, P. D.; Gallery, R. E.; McIntosh, J. C.; Olshansky, Y.; Rasmussen, C.

2017-12-01

The routing of water and carbon through complex terrain is postulated to control structure evolution in the sub-humid critical zone of the southwestern US. By combining measurements of land-atmosphere exchange, ecohydrologic partitioning, and subsurface biogeochemistry, we seek to quantify how a heterogeneous (in time and space) distribution of "reactants" impacts both short-term (sub-)catchment response (e.g., pore and surface water chemical dynamics) and long-term landscape evolution (e.g., soil geochemistry/morphology and regolith weathering depth) in watersheds underlain by rhyolite and schist. Instrumented pedons in convergent, planar, and divergent landscape positions show distinct depth-dependent responses to precipitation events. Wetting front propagation, dissolved carbon flux and associated biogeochemical responses (e.g., pulses of CO2 production, O2 depletion, solute release) vary with topography, revealing the influence of lateral subsidies of water and carbon. The impacts of these episodes on the evolution of porous media heterogeneity is being investigated by statistical analysis of pore water chemistry, chemical/spectroscopic studies of solid phase organo-mineral products, sensor-derived water characteristic curves, and quantification of co-located microbial community activity/composition. Our results highlight the interacting effects of critical zone structure and convergent hydrologic flows in the evolution of biogeochemical control points.

Hyporheic Interfaces Serve as Ecological Control Points for Mountainous Landscape Biological Productivity

NASA Astrophysics Data System (ADS)

Newcomer, M. E.; Dwivedi, D.; Raberg, J.; Fox, P. M.; Nico, P. S.; Wainwright, H. M.; Conrad, M. E.; Bill, M.; Bouskill, N.; Williams, K. H.; Hubbard, S.; Steefel, C. I.

2017-12-01

Riverine systems in snow-dominated mountainous regions often express complex biogeochemistry and river nutrient indicators as a function of hydrologic variability. In early spring, meltwater infiltration from a ripened snowpack creates a hydrological gradient through hillslopes, floodplains, and hyporheic zones. During this time, these systems are more-or-less a passive filter that allows the rising limb of the hydrograph to display chemo-dynamic relationships (inversely proportional) with solutes and nutrients. During the growing season, temperatures, plants, microbes, and hydrologic gradients shift dramatically and activate hyporheic-zone biogeochemistry as a major control on water nutrient degradation. Hyporheic biogeochemical reliance on the timing of meltwater infiltration and the possibility of a longer vernal window under future climate change indicates the importance of hyporheic cycling as the dominant ecological control point on carbon and nitrogen fluxes and transformations. The objective of our study is to develop a predictive understanding of the subsurface and surface controls on hyporheic biogeochemical behavior through data-model integration. Data from our 2017 field campaign in the East River, Colorado, a pristine, mountainous watershed, were taken at key times during the rising, peak, falling, and dry limb of the hydrograph. Throughout multiple locations across this spatial and temporal gradient, we measured surface and subsurface gases, geochemistry, isotopes, and hydrological flow conditions and used this data to constrain a numerical flow and reactive transport model of the hyporheic zone that included microbial and flow feedback dynamics. Our data coupled with the predictive power of our numerical model reveal that the hyporheic zone serves dual roles throughout the year—as a net source of nutrients and solutes during the early vernal phase, shifting to a net sink of nutrients during the summer dry season. The possibility of a future lengthened vernal window motivates a better understanding of the role each ecological control point plays in processing landscape biological productivity and for understanding biogeochemical cycling in riverine systems.

Simulation and validation of concentrated subsurface lateral flow paths in an agricultural landscape

NASA Astrophysics Data System (ADS)

Zhu, Q.; Lin, H. S.

2009-08-01

The importance of soil water flow paths to the transport of nutrients and contaminants has long been recognized. However, effective means of detecting concentrated subsurface flow paths in a large landscape are still lacking. The flow direction and accumulation algorithm based on single-direction flow algorithm (D8) in GIS hydrologic modeling is a cost-effective way to simulate potential concentrated flow paths over a large area once relevant data are collected. This study tested the D8 algorithm for simulating concentrated lateral flow paths at three interfaces in soil profiles in a 19.5-ha agricultural landscape in central Pennsylvania, USA. These interfaces were (1) the interface between surface plowed layers of Ap1 and Ap2 horizons, (2) the interface with subsoil water-restricting clay layer where clay content increased to over 40%, and (3) the soil-bedrock interface. The simulated flow paths were validated through soil hydrologic monitoring, geophysical surveys, and observable soil morphological features. The results confirmed that concentrated subsurface lateral flow occurred at the interfaces with the clay layer and the underlying bedrock. At these two interfaces, the soils on the simulated flow paths were closer to saturation and showed more temporally unstable moisture dynamics than those off the simulated flow paths. Apparent electrical conductivity in the soil on the simulated flow paths was elevated and temporally unstable as compared to those outside the simulated paths. The soil cores collected from the simulated flow paths showed significantly higher Mn content at these interfaces than those away from the simulated paths. These results suggest that (1) the D8 algorithm is useful in simulating possible concentrated subsurface lateral flow paths if used with appropriate threshold value of contributing area and sufficiently detailed digital elevation model (DEM); (2) repeated electromagnetic surveys can reflect the temporal change of soil water storage and thus is a useful indicator of possible subsurface flow path over a large area; and (3) observable Mn distribution in soil profiles can be used as a simple indicator of water flow paths in soils and over the landscape; however, it does require sufficient soil sampling (by excavation or augering) to possibly infer landscape-scale subsurface flow paths. In areas where subsurface interface topography varies similarly with surface topography, surface DEM can be used to simulate potential subsurface lateral flow path reasonably so the cost associated with obtaining depth to subsurface water-restricting layer can be minimized.

Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P; Czerwinski, Ken; Russell, Charles E

2010-07-13

This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Bruckner, Jim; Fisher, Jen

2010-09-01

This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program’s Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Beyond The Blueprint: Development Of Genome-Informed Trait-Based Models For Prediction Of Microbial Dynamics And Biogeochemical Rates

NASA Astrophysics Data System (ADS)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Johnson, J. N.; Bouskill, N.; Hug, L. A.; Thomas, B. C.; Castelle, C. J.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.

2014-12-01

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

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

EPA Science Inventory

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

Physical and biogeochemical variability in Todos Santos Bay, northwestern Baja California, derived from a numerical NPZD model

NASA Astrophysics Data System (ADS)

Cruz-Rico, Jorge; Rivas, David

2018-07-01

A physical-biogeochemical Nitrate-Phytoplankton-Zooplankton-Detritus (NPZD) numerical model is used to study the variability of coastal phytoplankton biomass in northwestern Baja California and the Todos Santos Bay (TSB), a region of high socioeconomic importance located in the southern California Current System. The model reproduces adequately the most important oceanographic features of the study area, like the coastal chlorophyll-a (Chl-a) maxima and thermal gradients in the regions of enhanced coastal upwelling. The variability of Chl-a in the TSB is influenced by the activity of El Niño-Southern Oscillation (ENSO) and decadal modes of the Pacific, e.g., the Pacific Decadal Oscillation (PDO) and the North Pacific Gyre Oscillation (NPGO). From de multi-year model simulation (2004-2011), this large-scale influence is remarkable in two contrasting anomalous years. The year 2006 was anomalously warm and with low Chl-a levels, associated with warm phases of ENSO and PDO and a weakening of the NPGO. These climatic anomalies caused a strong stratification and weak upwelling around the TSB, which induced a poor nutrient input into the Bay and a deep and weak subsurface Chl-a maximum (SCM) during summer. The year 2011, on the other hand, was a cold year with enhanced upwelling during the spring, associated with cold phases of ENSO and PDO and an intensification of the NPGO. These conditions also caused a weak stratification and an intense nutrient transport into the TSB and hence a shallower and stronger SCM.

Identification of land use and other anthropogenic impacts on nitrogen cycling using stable isotopes and distributed hydrologic modeling

NASA Astrophysics Data System (ADS)

O'Connell, M. T.; Macko, S. A.

2017-12-01

Reactive modeling of sources and processes affecting the concentration of NO3- and NH4+ in natural and anthropogenically influenced surface water can reveal unexpected characteristics of the systems. A distributed hydrologic model, TREX, is presented that provides opportunities to study multiscale effects of nitrogen inputs, outputs, and changes. The model is adapted to run on parallel computing architecture and includes the geochemical reaction module PhreeqcRM, which enables calculation of δ15N and δ18O from biologically mediated transformation reactions in addition to mixing and equilibration. Management practices intended to attenuate nitrate in surface and subsurface waters, in particular the establishment of riparian buffer zones, are variably effective due to spatial heterogeneity of soils and preferential flow through buffers. Accounting for this heterogeneity in a fully distributed biogeochemical model allows for more efficient planning and management practices. Highly sensitive areas within a watershed can be identified based on a number of spatially variable parameters, and by varying those parameters systematically to determine conditions under which those areas are under more or less critical stress. Responses can be predicted at various scales to stimuli ranging from local changes in cropping regimes to global shifts in climate. This work presents simulations of conditions showing low antecedent nitrogen retention versus significant contribution of old nitrate. Nitrogen sources are partitioned using dual isotope ratios and temporally varying concentrations. In these two scenarios, we can evaluate the efficiency of source identification based on spatially explicit information, and model effects of increasing urban land use on N biogeochemical cycling.

Shifts in Geochemical Parameters and Greenhouse Gas Fluxes following Insect-Induced Tree Mortality

NASA Astrophysics Data System (ADS)

Brouillard, B.; Mikkelson, K. M.; Berryman, E.; Sharp, J.; Leonard, L.; Vega, M.

2016-12-01

Extensive insect infestations and resultant expansive tree mortality are occurring globally due in part to warmer temperatures and persistent drought. These forest disturbances are expected to cause shifts in the biogeochemical cycle due to the cessation of below ground root outputs, changes in soil microbial communities, hydrologic perturbations, and altered woody material deposits to the forest floor. To better understand biogeochemical alterations and resolve potentially conflicting findings, we studied a lodgepole pine forest recently impacted by mountain pine beetles to determine the response of subsurface geochemical parameters and gaseous flux to the effects of surrounding tree mortality. While many parameters were found to be significantly different under recently killed trees compared to their healthy counterparts (pH, soil moisture, C/N-species), notable biogeochemically relevant parameters displayed shifts that tracked with the level of surrounding tree mortality. For instance, aromatic carbon (TSUVA) and CO2 respiration were found to have an increasing linear response under grey trees as the surrounding tree mortality within an 8m radius also increased. Rather than a linear increase, ammonium and nitrogen associated bacterial communities displayed a threshold effect, not increasing until a certain level of tree mortality of approximately 40% was surpassed. Gas flux was also correlated to measured parameters in three near surface soil horizons to determine drivers of CO2 and N2O release and their interactions with biogeochemical cycles. Collectively, these results aid in elucidating the extent of forest mortality required to overcome compensatory terrestrial biogeochemical processes. A heightened understanding of these shifts will aid the scientific and resource management community through enhanced predictive understanding of greenhouse gas release or potential water quality impacts following forest disturbance.

Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea.

PubMed

Becker, Kevin W; Elling, Felix J; Schröder, Jan M; Lipp, Julius S; Goldhammer, Tobias; Zabel, Matthias; Elvert, Marcus; Overmann, Jörg; Hinrichs, Kai-Uwe

2018-03-09

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia-oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition. Importance Microorganisms play crucial roles in global biogeochemical cycles. Yet, we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy and anoxygenic photosynthesis in defined geochemical zones. Copyright © 2018 American Society for Microbiology.

Method of imaging the electrical conductivity distribution of a subsurface

DOEpatents

Johnson, Timothy C.

2017-09-26

A method of imaging electrical conductivity distribution of a subsurface containing metallic structures with known locations and dimensions is disclosed. Current is injected into the subsurface to measure electrical potentials using multiple sets of electrodes, thus generating electrical resistivity tomography measurements. A numeric code is applied to simulate the measured potentials in the presence of the metallic structures. An inversion code is applied that utilizes the electrical resistivity tomography measurements and the simulated measured potentials to image the subsurface electrical conductivity distribution and remove effects of the subsurface metallic structures with known locations and dimensions.

Concentration-discharge relationships to understand the interplay between hydrological and biogeochemical processes: insights from data analysis and numerical experiments in headwater catchments.

NASA Astrophysics Data System (ADS)

De Dreuzy, J. R.; Marçais, J.; Moatar, F.; Minaudo, C.; Courtois, Q.; Thomas, Z.; Longuevergne, L.; Pinay, G.

2017-12-01

Integration of hydrological and biogeochemical processes led to emerging patterns at the catchment scale. Monitoring in rivers reflects the aggregation of these effects. While discharge time series have been measured for decades, high frequency water quality monitoring in rivers now provides prominent measurements to characterize the interplay between hydrological and biogeochemical processes, especially to infer the processes that happen in the heterogeneous subsurface. However, we still lack frameworks to relate observed patterns to specific processes, because of the "organized complexity" of hydrological systems. Indeed, it is unclear what controls, for example, patterns in concentration-discharge (C/Q) relationships due to non-linear processes and hysteresis effects. Here we develop a non-intensive process-based model to test how the integration of different landforms (i.e. geological heterogeneities and structures, topographical features) with different biogeochemical reactivity assumptions (e.g. reactive zone locations) can shape the overall water quality time series. With numerical experiments, we investigate typical patterns in high frequency C/Q relationships. In headwater basins, we found that typical hysteretic patterns in C/Q relationships observed in data time series can be attributed to differences in water and solute locations stored across the hillslope. At the catchment scale though, these effects tend to average out by integrating contrasted hillslopes' landforms. Together these results suggest that information contained in headwater water quality monitoring can be used to understand how hydrochemical processes determine downstream conditions.

A Centimeter-Scale Investigation of Geochemical Hotspots in a Soil Lysimeter

NASA Astrophysics Data System (ADS)

Umanzor, M.; Wang, Y.; Dontsova, K.; Chorover, J.; Troch, P. A. A.

2016-12-01

Studying the co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative for improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. Hotspots may form in porous media that is undergoing biogeochemical weathering at locations where reactants accumulate to threshold values along hydrologic flow paths. This is expected to occur in weatherable silicate media, like granular basalt. To examine such processes during incipient soil formation, we constructed a sloping weighing lysimeter 2-m in length, 0.5-m in width and 1-m in depth. Mini-LEO was filled with crushed granular basalt rock with a known initial chemical composition. After 18 months of irrigation and intensive hydrological study, the model "landscape" was divided into a 3D matrix of 324 voxels and excavated. Collected samples were subjected to detailed hydro-bio-geochemical analysis to assess the formation of geochemical heterogeneity. A five-step sequential extraction was employed to characterize incongruent mineral weathering, and its relation to the spatial distribution of microbial composition (in a related study). The changes in Fe and Mn concentration and speciation along the lysimeter length and depth (as measured by each step of the sequential extraction) was quantified to characterize spatial distribution of weathering processes. Results are being used to assist in understanding not only spatial and temporal distribution of basalt weathering on the slope, but also, connections between hydrological and biogeochemical cycles that lead to formation of hotspots.

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

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Natural and drought scenarios in an east central Amazon forest: Fidelity of the Community Land Model 3.5 with three biogeochemical models

NASA Astrophysics Data System (ADS)

Sakaguchi, Koichi; Zeng, Xubin; Christoffersen, Bradley J.; Restrepo-Coupe, Natalia; Saleska, Scott R.; Brando, Paulo M.

2011-03-01

Recent development of general circulation models involves biogeochemical cycles: flows of carbon and other chemical species that circulate through the Earth system. Such models are valuable tools for future projections of climate, but still bear large uncertainties in the model simulations. One of the regions with especially high uncertainty is the Amazon forest where large-scale dieback associated with the changing climate is predicted by several models. In order to better understand the capability and weakness of global-scale land-biogeochemical models in simulating a tropical ecosystem under the present day as well as significantly drier climates, we analyzed the off-line simulations for an east central Amazon forest by the Community Land Model version 3.5 of the National Center for Atmospheric Research and its three independent biogeochemical submodels (CASA', CN, and DGVM). Intense field measurements carried out under Large Scale Biosphere-Atmosphere Experiment in Amazonia, including forest response to drought from a throughfall exclusion experiment, are utilized to evaluate the whole spectrum of biogeophysical and biogeochemical aspects of the models. Our analysis shows reasonable correspondence in momentum and energy turbulent fluxes, but it highlights three processes that are not in agreement with observations: (1) inconsistent seasonality in carbon fluxes, (2) biased biomass size and allocation, and (3) overestimation of vegetation stress to short-term drought but underestimation of biomass loss from long-term drought. Without resolving these issues the modeled feedbacks from the biosphere in future climate projections would be questionable. We suggest possible directions for model improvements and also emphasize the necessity of more studies using a variety of in situ data for both driving and evaluating land-biogeochemical models.

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes.

PubMed

Itävaara, M; Salavirta, H; Marjamaa, K; Ruskeeniemi, T

2016-01-01

Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities. Copyright © 2016 Elsevier Inc. All rights reserved.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

DOE Office of Scientific and Technical Information (OSTI.GOV)

Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.

2015-03-01

We explored the impact of the starting community composition and structure on ecosystem response to perturbations using organic carbon amendment experiments. Subsurface sediment was partitioned into flow-through columns, and the microbial communities were initially stimulated in situ by addition of acetate as a carbon and electron donor source. This drove community richness and evenness down, and pushed the system into a new biogeochemical state characterized by iron reduction. Reconstructed near-full-length 16S rRNA gene sequence analysis indicated a concomitant enrichment of Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After 10 to 12 days, acetate was exchange for lactate in a subset of columns.more » Following the clear onset of sulfate reduction (35 days after acetate-amendment), acetate was substituted for lactate in additional columns. Acetatestimulated communities differed markedly during each biogeochemical regime and at each lactate-switch. Regardless, however, of when communities were switched to lactate, they followed comparable trajectories with respect to composition and structure, with convergence evident one week after each switch, and marked after one month of lactate amendment. During sulfate reduction all treatments were enriched in Firmicutes and a number of species likely involved in sulfate reduction (notably Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum). Lactate treatments were distinguished by substantially lower relative abundances of Desulfotomaculum and Bacteroidetes, and enrichments of Psychrosinus and Clostridiales species. Results imply that the structure of the starting community was not significant in controlling organism selection in community succession.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wainwright, Haruko M.; Flores Orozco, Adrian; Bucker, Matthias

In floodplain environments, a naturally reduced zone (NRZ) is considered to be a common biogeochemical hot spot, having distinct microbial and geochemical characteristics. Although important for understanding their role in mediating floodplain biogeochemical processes, mapping the subsurface distribution of NRZs over the dimensions of a floodplain is challenging, as conventional wellbore data are typically spatially limited and the distribution of NRZs is heterogeneous. In this work, we present an innovative methodology for the probabilistic mapping of NRZs within a three-dimensional (3-D) subsurface domain using induced polarization imaging, which is a noninvasive geophysical technique. Measurements consist of surface geophysical surveys andmore » drilling-recovered sediments at the U.S. Department of Energy field site near Rifle, CO (USA). Inversion of surface time domain-induced polarization (TDIP) data yielded 3-D images of the complex electrical resistivity, in terms of magnitude and phase, which are associated with mineral precipitation and other lithological properties. By extracting the TDIP data values colocated with wellbore lithological logs, we found that the NRZs have a different distribution of resistivity and polarization from the other aquifer sediments. To estimate the spatial distribution of NRZs, we developed a Bayesian hierarchical model to integrate the geophysical and wellbore data. In addition, the resistivity images were used to estimate hydrostratigraphic interfaces under the floodplain. Validation results showed that the integration of electrical imaging and wellbore data using a Bayesian hierarchical model was capable of mapping spatially heterogeneous interfaces and NRZ distributions thereby providing a minimally invasive means to parameterize a hydrobiogeochemical model of the floodplain.« less

LLNL SFA OBER SBR FY17 Program Management and Performance Report: Subsurface Biogeochemistry of Actinides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kersting, Annie B.

A major scientific challenge in environmental sciences is to identify the dominant processes controlling actinide transport in the environment. It is estimated that currently, over 2200 metric tons of anthropogenic plutonium (Pu) has accumulated worldwide, a number that increases yearly with additional spent nuclear fuel (Ewing et al., 2010). Plutonium has been shown to migrate on the scale of kilometers, giving way to a critical concern that the fundamental biogeochemical processes that control its behavior in the subsurface are not well understood (Kersting et al. 1999; Novikov et al. 2006; Santschi et al. 2002). Neptunium (Np) is less prevalent inmore » the environment; however, it is predicted to be a significant long-term dose contributor in high-level nuclear waste. Our focus on Np chemistry in this Science Plan is intended to help formulate a better understanding of Pu redox transformations in the environment and clarify the differences between the two long-lived actinides. The research approach of our Science Plan combines (1) Fundamental Mechanistic Studies that identify and quantify biogeochemical processes that control actinide behavior in solution and on solids, (2) Field Integration Studies that investigate the transport characteristics of Pu and test our conceptual understanding of actinide transport, and (3) Actinide Research Capabilities that allow us to achieve the objectives of this Scientific Focus Area (SFA) and provide new opportunities for advancing actinide environmental chemistry. These three Research Thrusts form the basis of our SFA Science Program.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kersting, Annie B.; Zavarin, Mavrik

A major scientific challenge in environmental sciences is to identify the dominant processes controlling actinide transport in the environment. It is estimated that currently, over 2200 metric tons of plutonium (Pu) have been deposited in the subsurface worldwide, a number that increases yearly with additional spent nuclear fuel (Ewing et al., 2010). Plutonium has been shown to migrate on the scale of kilometers, giving way to a critical concern that the fundamental biogeochemical processes that control its behavior in the subsurface are not well understood (Kersting et al., 1999; Novikov et al., 2006; Santschi et al., 2002). Neptunium (Np) ismore » less prevalent in the environment; however, it is predicted to be a significant long-term dose contributor in high-level nuclear waste. Our focus on Np chemistry in this Science Plan is intended to help formulate a better understanding of Pu redox transformations in the environment and clarify the differences between the two long-lived actinides. The research approach of our Science Plan combines (1) Fundamental Mechanistic Studies that identify and quantify biogeochemical processes that control actinide behavior in solution and on solids, (2) Field Integration Studies that investigate the transport characteristics of Pu and test our conceptual understanding of actinide transport, and (3) Actinide Research Capabilities that allow us to achieve the objectives of this Scientific Focus Area (SFA and provide new opportunities for advancing actinide environmental chemistry. These three Research Thrusts form the basis of our SFA Science Program (Figure 1).« less

Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Ham, Baknoon; Hwang, Yunho; Shim, Moojoon; Lee, Soonjae

2018-01-15

Subsurface biogeochemistry and contaminant dynamics during the remediation of diesel-contamination by in-situ soil flushing were investigated at a site located in a coastal region. An in-situ sampler containing diesel-contaminated soils separated into two size fractions (<0.063- and <2-mm) was utilized in two monitoring wells: DH1 (located close to the injection and extraction wells for in-situ soil flushing) and DH2 (located beyond sheet piles placed to block the transport of leaked diesel). Total petroleum hydrocarbon (TPH) concentrations and biogeochemical properties were monitored both in soil and groundwater for six months. A shift occurred in the groundwater type from Ca-HCO 3 to Na-Cl due to seawater intrusion during intense pumping, while the concentrations of Ni, Cu, Co, V, Cr, and Se increased substantially following surfactant (TWEEN 80) injection. The in-situ sampler with fine particles was more sensitive to variations in conditions during the remedial soil flushing process. In both wells, soil TPH concentrations in the <0.063-mm fraction were much higher than those in the <2-mm fraction. Increases in soil TPH in DH1 were consistent with the expected outcomes following well pumping and surfactant injection used to enhance TPH extraction. However, the number of diesel-degrading microorganisms decreased after surfactant injection. 16S-rRNA gene-based analysis also showed that the community composition and diversity depended on both particle size and diesel contamination. The multidisciplinary approach to the contaminated site assessments showed that soil flushing with surfactant enhanced diesel extraction, but negatively impacted in-situ diesel biodegradation as well as groundwater quality. The results also suggest that the in-situ sampler can be an effective monitoring tool for subsurface biogeochemistry as well as contaminant dynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

AquaDiva: Understanding the Link between the Surface and Subsurface Biogeosphere

NASA Astrophysics Data System (ADS)

Trumbore, S.; Küsel, K.; Totsche, K. U.; Schwab, V.; Herrmann, M.; Nowak, M. E.; Gleixner, G.

2017-12-01

In the collaborative research project AquaDiva, we combine hydrogeochemical, metagemonic and biogeochemical tools to understand how the complex interactions between geologic setting and surface land use influence the function and biodiversity of the subsurface, especially ground water ecosystems. At the Hainich Critical Zone Exploratory in central Germany, we investigate soil and seepage waters in recharge areas and aquifers in a fractured limestone setting characterized by a dynamic water infiltration regime. Within the Exploratory, we have so far identified three distinct biogeochemical zones in which land use and lithologic differences combine to give rise to surprisingly different biotic communities and hydrogeochemical properties with different degrees of connection to the surface. Here we will focus on how we have combined carbon isotopic, organic biomarkers such as phospholipid fatty acids, and `omics' approaches to determine (i) how deep soil-borne microorganisms can be traced into the subsurface, and (ii) which energy sources sustain microbial life in oligotrophic limestone aquifers. With increasing travel distance to the surface, there is a decline in the abundance of microbes, with less than 5% of the taxa identified overlapping with those identified in the soils. Dissolved organic matter also is altered as it passes through soils, demonstrating an overall increase in molecular weight and a change in molecular makeup as well as radiocarbon content. Using the radiocarbon signature (corrected for the influence of carbonate dissolution), as a way to identify if organic C is being supplied recently by plants, atmosphere sources of energy for communities within the aquifer differ for the identified biogeochemical zones and include (i) dominance of inputs of fresh organic carbon from the surface feeding heterotrophy in oxygenic environments; (ii) CO2 fixation linked to nitrogen and sulfur cycling in anoxic environments and (iii) rock-derived organic matter that enters the food web and supplies up to a quarter of the carbon recycled by heterotrophic groundwater microbial communities. The degree of importance of these metabolisms, and therefore their connection to the surface is different in the three zones, with the importance of internal cycling and rock-derived organic matter as a C source surprisingly higher in anoxic aquifers. The second major goal of AquaDiva is to determine the impact of individual precipitation events on the groundwater. Initial results show dramatic effects of singular precipitation events, particularly of events during snowmelt season when the major recharge takes place. Observed large fluctuations in the water table have been linked to changes in the vertical distribution of oxygen and events of carbonate dissolution/precipitation can be identified based on variations of CO2 and O2. Ongoing research in AquaDiva seeks to better quantify the rates of groundwater movement and mixing as a way of further understanding how the emergent subsurface properties can be better linked to processes of transport and transformation within the Critical Zone.

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...

Bottom RedOx Model (BROM v.1.1): a coupled benthic-pelagic model for simulation of water and sediment biogeochemistry

NASA Astrophysics Data System (ADS)

Yakushev, Evgeniy V.; Protsenko, Elizaveta A.; Bruggeman, Jorn; Wallhead, Philip; Pakhomova, Svetlana V.; Yakubov, Shamil Kh.; Bellerby, Richard G. J.; Couture, Raoul-Marie

2017-02-01

Interactions between seawater and benthic systems play an important role in global biogeochemical cycling. Benthic fluxes of some chemical elements (e.g., C, N, P, O, Si, Fe, Mn, S) alter the redox state and marine carbonate system (i.e., pH and carbonate saturation state), which in turn modulate the functioning of benthic and pelagic ecosystems. The redox state of the near-bottom layer in many regions can change with time, responding to the supply of organic matter, physical regime, and coastal discharge. We developed a model (BROM) to represent key biogeochemical processes in the water and sediments and to simulate changes occurring in the bottom boundary layer. BROM consists of a transport module (BROM-transport) and several biogeochemical modules that are fully compatible with the Framework for the Aquatic Biogeochemical Models, allowing independent coupling to hydrophysical models in 1-D, 2-D, or 3-D. We demonstrate that BROM is capable of simulating the seasonality in production and mineralization of organic matter as well as the mixing that leads to variations in redox conditions. BROM can be used for analyzing and interpreting data on sediment-water exchange, and for simulating the consequences of forcings such as climate change, external nutrient loading, ocean acidification, carbon storage leakage, and point-source metal pollution.

Biofilm-induced calcium carbonate precipitation: application in the subsurface

NASA Astrophysics Data System (ADS)

Phillips, A. J.; Eldring, J.; Lauchnor, E.; Hiebert, R.; Gerlach, R.; Mitchell, A. C.; Esposito, R.; Cunningham, A. B.; Spangler, L.

2012-12-01

We have investigated mitigation strategies for sealing high permeability regions, like fractures, in the subsurface. This technology has the potential to, for example, improve the long-term security of geologically-stored carbon dioxide (CO2) by sealing fractures in cap rocks or to mitigate leakage pathways to prevent contamination of overlying aquifers from hydraulic fracturing fluids. Sealing technologies using low-viscosity fluids are advantageous since they potentially reduce the necessary injection pressures and increase the radius of influence around injection wells. In this technology, aqueous solutions and suspensions are used to promote microbially-induced mineral precipitation which can be applied in subsurface environments. To this end, a strategy was developed to twice seal a hydraulically fractured, 74 cm (2.4') diameter Boyles Sandstone core, collected in North-Central Alabama, with biofilm-induced calcium carbonate (CaCO3) precipitates under ambient pressures. Sporosarcina pasteurii biofilms were established and calcium and urea containing reagents were injected to promote saturation conditions favorable for CaCO3 precipitation followed by growth reagents to resuscitate the biofilm's ureolytic activity. Then, in order to evaluate this process at relevant deep subsurface pressures, a novel high pressure test vessel was developed to house the 74 cm diameter core under pressures as high as 96 bar (1,400 psi). After determining that no impact to the fracture permeability occurred due to increasing overburden pressure, the fractured core was sealed under subsurface relevant pressures relating to 457 meters (1,500 feet) below ground surface (44 bar (650 psi) overburden pressure). After fracture sealing under both ambient and subsurface relevant pressure conditions, the sandstone core withstood three times higher well bore pressure than during the initial fracturing event, which occurred prior to biofilm-induced CaCO3 mineralization. These studies suggest biofilm-induced CaCO3 precipitation technologies may potentially seal and strengthen high permeability regions or fractures (either natural or induced) in the subsurface. Novel high pressure test vessel to investigate biogeochemical processes under relevant subsurface scales and pressures.

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

PubMed Central

Sheik, Cody S.; Reese, Brandi Kiel; Twing, Katrina I.; Sylvan, Jason B.; Grim, Sharon L.; Schrenk, Matthew O.; Sogin, Mitchell L.; Colwell, Frederick S.

2018-01-01

Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset. PMID:29780369

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

PubMed

Sheik, Cody S; Reese, Brandi Kiel; Twing, Katrina I; Sylvan, Jason B; Grim, Sharon L; Schrenk, Matthew O; Sogin, Mitchell L; Colwell, Frederick S

2018-01-01

Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium , Aquabacterium , Ralstonia , and Acinetobacter . While the top five most frequently observed genera were Pseudomonas , Propionibacterium , Acinetobacter , Ralstonia , and Sphingomonas . The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth's deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.

Investigating ebullition in a sand column using dissolved gas analysis and reactive transport modeling

USGS Publications Warehouse

Amos, Richard T.; Mayer, K. Ulrich

2006-01-01

Ebullition of gas bubbles through saturated sediments can enhance the migration of gases through the subsurface, affect the rate of biogeochemical processes, and potentially enhance the emission of important greenhouse gases to the atmosphere. To better understand the parameters controlling ebullition, methanogenic conditions were produced in a column experiment and ebullition through the column was monitored and quantified through dissolved gas analysis and reactive transport modeling. Dissolved gas analysis showed rapid transport of CH4 vertically through the column at rates several times faster than the bromide tracer and the more soluble gas CO2, indicating that ebullition was the main transport mechanism for CH4. An empirically derived formulation describing ebullition was integrated into the reactive transport code MIN3P allowing this process to be investigated on the REV scale in a complex geochemical framework. The simulations provided insights into the parameters controlling ebullition and show that, over the duration of the experiment, 36% of the CH4 and 19% of the CO2 produced were transported to the top of the column through ebullition.

Characterization and consequences of intermittent sediment oxygenation by macrofauna: interpretation of high-resolution data sets

NASA Astrophysics Data System (ADS)

Meile, C. D.; Dwyer, I.; Zhu, Q.; Polerecky, L.; Volkenborn, N.

2017-12-01

Mineralization of organic matter in marine sediments leads to the depletion of oxygen, while activities of infauna introduce oxygenated seawater to the subsurface. In permeable sediments solutes can be transported from animals and their burrows into the surrounding sediment through advection over several centimeters. The intermittency of pumping leads to a spatially heterogeneous distribution of oxidants, with the temporal dynamics depending on sediment reactivity and activity patterns of the macrofauna. Here, we present results from a series of experiments in which these dynamics are studied at high spatial and temporal resolution using planar optodes. From O2, pH and pCO2 optode data, we quantify rates of O2 consumption and dissolved inorganic carbon production, as well alkalinity dynamics, with millimeter-scale resolution. Simulating intermittent irrigation by imposed pumping patterns in thin aquaria, we derive porewater flow patterns, which together with the production and consumption rates cause the chemical distributions and the establishment of reaction fronts. Our analysis thus establishes a quantitative connection between the locally dynamic redox conditions relevant for biogeochemical transformations and macroscopic observations commonly made with sediment cores.

Trends and Future Challenges in Sampling the Deep Terrestrial Biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Daly, Rebecca; Mouser, Paula J.

2014-09-12

Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on “Trends and Future Challenges in Sampling The Deep Subsurface” was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty,more » and sponsored by The Ohio State University and the Sloan Foundation’s Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.« less

A hydrogeomorphic river network model predicts where and why hyporheic exchange is important in large basins

USGS Publications Warehouse

Gomez-Velez, Jesus D.; Harvey, Judson

2014-01-01

Hyporheic exchange has been hypothesized to have basin-scale consequences; however, predictions throughout river networks are limited by available geomorphic and hydrogeologic data and by models that can analyze and aggregate hyporheic exchange flows across large spatial scales. We developed a parsimonious but physically based model of hyporheic flow for application in large river basins: Networks with EXchange and Subsurface Storage (NEXSS). We applied NEXSS across a broad range of geomorphic diversity in river reaches and synthetic river networks. NEXSS demonstrates that vertical exchange beneath submerged bed forms rather than lateral exchange through meanders dominates hyporheic fluxes and turnover rates along river corridors. Per kilometer, low-order streams have a biogeochemical potential at least 2 orders of magnitude larger than higher-order streams. However, when biogeochemical potential is examined per average length of each stream order, low- and high-order streams were often found to be comparable. As a result, the hyporheic zone's intrinsic potential for biogeochemical transformations is comparable across different stream orders, but the greater river miles and larger total streambed area of lower order streams result in the highest cumulative impact from low-order streams. Lateral exchange through meander banks may be important in some cases but generally only in large rivers.

A hydrogeomorphic river network model predicts where and why hyporheic exchange is important in large basins

NASA Astrophysics Data System (ADS)

Gomez-Velez, Jesus D.; Harvey, Judson W.

2014-09-01

Hyporheic exchange has been hypothesized to have basin-scale consequences; however, predictions throughout river networks are limited by available geomorphic and hydrogeologic data and by models that can analyze and aggregate hyporheic exchange flows across large spatial scales. We developed a parsimonious but physically based model of hyporheic flow for application in large river basins: Networks with EXchange and Subsurface Storage (NEXSS). We applied NEXSS across a broad range of geomorphic diversity in river reaches and synthetic river networks. NEXSS demonstrates that vertical exchange beneath submerged bed forms rather than lateral exchange through meanders dominates hyporheic fluxes and turnover rates along river corridors. Per kilometer, low-order streams have a biogeochemical potential at least 2 orders of magnitude larger than higher-order streams. However, when biogeochemical potential is examined per average length of each stream order, low- and high-order streams were often found to be comparable. As a result, the hyporheic zone's intrinsic potential for biogeochemical transformations is comparable across different stream orders, but the greater river miles and larger total streambed area of lower order streams result in the highest cumulative impact from low-order streams. Lateral exchange through meander banks may be important in some cases but generally only in large rivers.

Synoptic-to-planetary scale wind variability enhances phytoplankton biomass at ocean fronts

NASA Astrophysics Data System (ADS)

Whitt, D. B.; Taylor, J. R.; Lévy, M.

2017-06-01

In nutrient-limited conditions, phytoplankton growth at fronts is enhanced by winds, which drive upward nutrient fluxes via enhanced turbulent mixing and upwelling. Hence, depth-integrated phytoplankton biomass can be 10 times greater at isolated fronts. Using theory and two-dimensional simulations with a coupled physical-biogeochemical ocean model, this paper builds conceptual understanding of the physical processes driving upward nutrient fluxes at fronts forced by unsteady winds with timescales of 4-16 days. The largest vertical nutrient fluxes occur when the surface mixing layer penetrates the nutricline, which fuels phytoplankton in the mixed layer. At a front, mixed layer deepening depends on the magnitude and direction of the wind stress, cross-front variations in buoyancy and velocity at the surface, and potential vorticity at the base of the mixed layer, which itself depends on past wind events. Consequently, mixing layers are deeper and more intermittent in time at fronts than outside fronts. Moreover, mixing can decouple in time from the wind stress, even without other sources of physical variability. Wind-driven upwelling also enhances depth-integrated phytoplankton biomass at fronts; when the mixed layer remains shallower than the nutricline, this results in enhanced subsurface phytoplankton. Oscillatory along-front winds induce both oscillatory and mean upwelling. The mean effect of oscillatory vertical motion is to transiently increase subsurface phytoplankton over days to weeks, whereas slower mean upwelling sustains this increase over weeks to months. Taken together, these results emphasize that wind-driven phytoplankton growth is both spatially and temporally intermittent and depends on a diverse combination of physical processes.

An autotrophic H 2 -oxidizing, nitrate-respiring, Tc(VII)-reducing A cidovorax sp. isolated from a subsurface oxic-anoxic transition zone: H 2 -oxidizing, Tc-reducing Acidovorax spp.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ji-Hoon; Fredrickson, James K.; Plymale, Andrew E.

2015-04-08

Increasing concentrations of H 2 with depth were observed across a geologic unconformity and associated redox transition zone in the subsurface at the Hanford Site in south-central Washington, USA. An opposing gradient characterized by decreasing O 2 and nitrate concentrations was consistent with microbial-catalyzed biogeochemical processes. Sterile sand was incubated in situ within a multi-level sampler placed across the redox transition zone to evaluate the potential for Tc(VII) reduction and for enrichment of H 2-oxidizing denitrifiers capable of reducing Tc(VII). H 2-driven TcO 4- reduction was detected in sand incubated at all depths but was strongest in material from amore » depth of 17.1 m. Acidovorax spp. were isolated from H 2-nitrate enrichments from colonized sand from 15.1 m, with one representative, strain JHL-9, subsequently characterized. JHL-9 grew on acetate with either O 2 or nitrate as electron acceptor (data not shown) and on medium with bicarbonate, H 2 and nitrate. JHL-9 also reduced pertechnetate (TcO 4-) under denitrifying conditions with H 2 as the electron donor. H 2-oxidizing Acidovorax spp. in the subsurface at Hanford and other locations may contribute to the maintenance of subsurface redox gradients and offer the potential for Tc(VII) reduction.« less

Stress management skills in the subsurface: H2 stress on thermophilic heterotrophs and methanogens

NASA Astrophysics Data System (ADS)

Topcuoglu, B. D.; Holden, J. F.

2017-12-01

Marine hyperthermophilic heterotrophs and methanogens belonging to the Thermococcales and Methanococcales are often found in subsurface environments such as coal and shale beds, marine sediments, and oil reservoirs where they encounter H2 stress conditions. It is important to study the H2 stress survival strategies of these organisms and their cooperation with one another for survival to better understand their biogeochemical impact in hot subsurface environments. In this study, we have shown that H2 inhibition changed the growth kinetics and the transcriptome of Thermococcus paralvinellae. We observed a significant decrease in batch phase growth rates and cell concentrations with high H2 background. Produced metabolite production measurements, RNA-seq analyses of differentially expressed genes and in silico experiments we performed with the T. paralvinellae metabolic model showed that T. paralvinellae produces formate by a formate hydrogenlyase to survive H2 inhibition. We have also shown that H2 limitation caused a significant decrease in batch phase growth rates and methane production rates of the methanogen, Methanocaldococcus jannaschii. H2 stress of both organisms can be ameliorated by syntrophic growth. H2 syntrophy was demonstrated in microcosm incubations for a natural assemblage of Thermococcus and hyperthermophilic methanogens present in hydrothermal fluid samples. This project aims to describe how a hyperthermophilic heterotroph and a hyperthermophilic methanogen eliminate H2 stress and explore cooperation among thermophiles in the hot subsurface.

Groundwater Salinity Simulation of a Subsurface Reservoir in Taiwan

NASA Astrophysics Data System (ADS)

Fang, H. T.

2015-12-01

The subsurface reservoir is located in Chi-Ken Basin, Pescadores (a group islands located at western part of Taiwan). There is no river in these remote islands and thus the freshwater supply is relied on the subsurface reservoir. The basin area of the subsurface reservoir is 2.14 km2 , discharge of groundwater is 1.27×106m3 , annual planning water supplies is 7.9×105m3 , which include for domestic agricultural usage. The annual average temperature is 23.3oC, average moisture is 80~85%, annual average rainfall is 913 mm, but ET rate is 1975mm. As there is no single river in the basin; the major recharge of groundwater is by infiltration. Chi-Ken reservoir is the first subsurface reservoir in Taiwan. Originally, the water quality of the reservoir is good. The reservoir has had the salinity problem since 1991 and it became more and more serious from 1992 until 1994. Possible reason of the salinity problem was the shortage of rainfall or the leakage of the subsurface barrier which caused the seawater intrusion. The present study aimed to determine the leakage position of subsurface barrier that caused the salinity problem. In order to perform the simulation for different possible leakage position of the subsurface reservoir, a Groundwater Modeling System (GMS) is used to define soils layer data, hydro-geological parameters, initial conditions, boundary conditions and the generation of three dimension meshes. A three dimension FEMWATER(Yeh , 1996) numerical model was adopted to find the possible leakage position of the subsurface barrier and location of seawater intrusion by comparing the simulation of different possible leakage with the observations. 1.By assuming the leakage position in the bottom of barrier, the simulated numerical result matched the observation better than the other assumed leakage positions. It showed that the most possible leakage position was at the bottom of the barrier. 2.The research applied three dimension FEMWATER and GMS as an interface to input parameter. The simulation of water level and chloride concentration already showed the real situation, and the result can be applied to the future study of the Chi-Ken subsurface reservoir salinity problems.

Using a spatially-distributed hydrologic biogeochemistry model with nitrogen transport to study the spatial variation of carbon stocks and fluxes in a Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Shi, Y.; Eissenstat, D. M.; He, Y.; Davis, K. J.

2017-12-01

Most current biogeochemical models are 1-D and represent one point in space. Therefore, they cannot resolve topographically driven land surface heterogeneity (e.g., lateral water flow, soil moisture, soil temperature, solar radiation) or the spatial pattern of nutrient availability. A spatially distributed forest biogeochemical model with nitrogen transport, Flux-PIHM-BGC, has been developed by coupling a 1-D mechanistic biogeochemical model Biome-BGC (BBGC) with a spatially distributed land surface hydrologic model, Flux-PIHM, and adding an advection dominated nitrogen transport module. Flux-PIHM is a coupled physically based model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model, and is augmented by adding a topographic solar radiation module. Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as land surface heterogeneities caused by topography. In the coupled Flux-PIHM-BGC model, each Flux-PIHM model grid couples a 1-D BBGC model, while nitrogen is transported among model grids via surface and subsurface water flow. In each grid, Flux-PIHM provides BBGC with soil moisture, soil temperature, and solar radiation, while BBGC provides Flux-PIHM with spatially-distributed leaf area index. The coupled Flux-PIHM-BGC model has been implemented at the Susquehanna/Shale Hills Critical Zone Observatory. The model-predicted aboveground vegetation carbon and soil carbon distributions generally agree with the macro patterns observed within the watershed. The importance of abiotic variables (including soil moisture, soil temperature, solar radiation, and soil mineral nitrogen) in predicting aboveground carbon distribution is calculated using a random forest. The result suggests that the spatial pattern of aboveground carbon is controlled by the distribution of soil mineral nitrogen. A Flux-PIHM-BGC simulation without the nitrogen transport module is also executed. The model without nitrogen transport fails in predicting the spatial patterns of vegetation carbon, which indicates the importance of having a nitrogen transport module in spatially distributed ecohydrologic modeling.

Linking Surface Topography Variations To Subsurface Mixing And Reaction Patterns

NASA Astrophysics Data System (ADS)

Le Borgne, T.; Bandopadhyay, A.; Davy, P.

2017-12-01

Fluctuations in surface topography generate nested streamline patterns in the subsurface over scales ranging from millimeters to kilometers. Because solute residence times can be very different for each streamlines, these patterns exert a strong control on biogeochemical reactions. While this effect has been quantified in reactive transport models, solute transfer across streamlines has been generally neglected. Yet, this process can lead to significant solute dilution and may trigger reactions by mixing water with different chemical compositions. Considering topography-driven subsurface flow cells of different sizes, we show that the resulting streamline structures act as shear flows, with shear rates that can vary over orders of magnitude depending on scale, permeability and hydraulic head gradient. This leads to the formation of localized layers of enhanced dilution and reaction, where mixing rates can be orders of magnitude larger than diffusion limited rates (Bandopadhyay et al. under review). We develop a theoretical model that predicts the depth and magnitude of these mixing hotspots and quantifies the resulting exports of conservative and reactive chemical species at discharge locations. We discuss consequences of these findings by applying this model at hyporheic zone, hillslope, and catchment scales.

Chemotaxis and flow disorder shape microbial dispersion in porous media

NASA Astrophysics Data System (ADS)

De Anna, Pietro; Yawata, Yutaka; Stocker, Roman; Juanes, Ruben

2017-04-01

Bacteria drive a plethora of natural processes in the subsurface, consuming organic matter and catalysing chemical reactions that are key to global elemental cycles. These macro-scale consequences result from the collective action of individual bacteria at the micro-scale, which are modulated by the highly heterogeneous subsurface environment, dominated by flow disorder and strong chemical gradients. Yet, despite the generally recognized importance of these microscale processes, microbe-host medium interaction at the pore scale remain poorly characterized and understood. Here, we introduce a microfluidic model system to directly image and quantify the role of cell motility on bacterial dispersion and residence time in confined, porous, media. Using the soil-dwelling bacterium Bacillus subtilis and the common amino acid serine as a resource, we observe that chemotaxis in highly disordered and confined physico-chemical environment affords bacteria an increase in their ability to persistently occupy the host medium. Our findings illustrate that the interplay between bacterial behaviour and pore-scale disorder in fluid velocity and nutrient concentration directly impacts the residence time, transport and bio-geo-chemical transformation rates of biota in the subsurface, and thus likely the processes they mediate.

Optimizing the Hydrological and Biogeochemical Simulations on a Hillslope with Stony Soil

NASA Astrophysics Data System (ADS)

Zhu, Q.

2017-12-01

Stony soils are widely distributed in the hilly area. However, traditional pedotransfer functions are not reliable in predicting the soil hydraulic parameters for these soils due to the impacts of rock fragments. Therefore, large uncertainties and errors may exist in the hillslope hydrological and biogeochemical simulations in stony soils due to poor estimations of soil hydraulic parameters. In addition, homogenous soil hydraulic parameters are usually used in traditional hillslope simulations. However, soil hydraulic parameters are spatially heterogeneous on the hillslope. This may also cause the unreliable simulations. In this study, we obtained soil hydraulic parameters using five different approaches on a tea hillslope in Taihu Lake basin, China. These five approaches included (1) Rossetta predicted and spatially homogenous, (2) Rossetta predicted and spatially heterogeneous), (3) Rossetta predicted, rock fragment corrected and spatially homogenous, (4) Rossetta predicted, rock fragment corrected and spatially heterogeneous, and (5) extracted from observed soil-water retention curves fitted by dual-pore function and spatially heterogeneous (observed). These five sets of soil hydraulic properties were then input into Hydrus-3D and DNDC to simulate the soil hydrological and biogeochemical processes. The aim of this study is testing two hypotheses. First, considering the spatial heterogeneity of soil hydraulic parameters will improve the simulations. Second, considering the impact of rock fragment on soil hydraulic parameters will improve the simulations.

Modeling nitrogen loading in a small watershed in southwest China using a DNDC model with hydrological enhancements

NASA Astrophysics Data System (ADS)

Deng, J.; Zhou, Z.; Zhu, B.; Zheng, X.; Li, C.; Wang, X.; Jian, Z.

2011-10-01

The degradation of water quality has been observed worldwide, and inputs of nitrogen (N), along with other nutrients, play a key role in the process of contamination. The quantification of N loading from non-point sources at a watershed scale has long been a challenge. Process-based models have been developed to address this problem. Because N loading from non-point sources result from interactions between biogeochemical and hydrological processes, a model framework must include both types of processes if it is to be useful. This paper reports the results of a study in which we integrated two fundamental hydrologic features, the SCS (Soil Conservation Service) curve function and the MUSLE (Modified Universal Soil Loss), into a biogeochemical model, the DNDC. The SCS curve equation and the MUSLE are widely used in hydrological models for calculating surface runoff and soil erosion. Equipped with the new added hydrologic features, DNDC was substantially enhanced with the new capacity of simulating both vertical and horizontal movements of water and N at a watershed scale. A long-term experimental watershed in Southwest China was selected to test the new version of the DNDC. The target watershed's 35.1 ha of territory encompass 19.3 ha of croplands, 11.0 ha of forest lands, 1.1 ha of grassplots, and 3.7 ha of residential areas. An input database containing topographic data, meteorological conditions, soil properties, vegetation information, and management applications was established and linked to the enhanced DNDC. Driven by the input database, the DNDC simulated the surface runoff flow, the subsurface leaching flow, the soil erosion, and the N loadings from the target watershed. The modeled water flow, sediment yield, and N loading from the entire watershed were compared with observations from the watershed and yielded encouraging results. The sources of N loading were identified by using the results of the model. In 2008, the modeled runoff-induced loss of total N from the watershed was 904 kg N yr-1, of which approximately 67 % came from the croplands. The enhanced DNDC model also estimated the watershed-scale N losses (1391 kg N yr-1) from the emissions of the N-containing gases (ammonia, nitrous oxide, nitric oxide, and dinitrogen). Ammonia volatilization (1299 kg N yr-1) dominated the gaseous N losses. The study indicated that process-based biogeochemical models such as the DNDC could contribute more effectively to watershed N loading studies if the hydrological components of the models were appropriately enhanced.

Modeling nitrogen loading in a small watershed in Southwest China using a DNDC model with hydrological enhancements

NASA Astrophysics Data System (ADS)

Deng, J.; Zhou, Z.; Zhu, B.; Zheng, X.; Li, C.; Wang, X.; Jian, Z.

2011-07-01

The degradation of water quality has been observed worldwide, and inputs of nitrogen (N), along with other nutrients, play a key role in the process of contamination. The quantification of N loading from non-point sources at a watershed scale has long been a challenge. Process-based models have been developed to address this problem. Because N loading from non-point sources result from interactions between biogeochemical and hydrological processes, a model framework must include both types of processes if it is to be useful. This paper reports the results of a study in which we integrated two fundamental hydrologic features, the SCS (Soil Conservation Service) curve function and the MUSLE (Modified Universal Soil Loss), into a biogeochemical model, the DNDC. The SCS curve equation and the MUSLE are widely used in hydrological models for calculating surface runoff and soil erosion. Equipped with the new added hydrologic features, DNDC was substantially enhanced with the new capacity of simulating both vertical and horizontal movements of water and N at a watershed scale. A long-term experimental watershed in Southwest China was selected to test the new version of the DNDC. The target watershed's 35.1 ha of territory encompass 19.3 ha of croplands, 11.0 ha of forest lands, 1.1 ha of grassplots, and 3.7 ha of residential areas. An input database containing topographic data, meteorological conditions, soil properties, vegetation information, and management applications was established and linked to the enhanced DNDC. Driven by the input database, the DNDC simulated the surface runoff flow, the subsurface leaching flow, the soil erosion, and the N loadings from the target watershed. The modeled water flow, sediment yield, and N loading from the entire watershed were compared with observations from the watershed and yielded encouraging results. The sources of N loading were identified by using the results of the model. In 2008, the modeled runoff-induced loss of total N from the watershed was 904 kg N yr-1, of which approximately 67 % came from the croplands. The enhanced DNDC model also estimated the watershed-scale N losses (1391 kg N yr-1) from the emissions of the N-containing gases (ammonia, nitrous oxide, nitric oxide, and dinitrogen). Ammonia volatilization (1299 kg N yr-1) dominated the gaseous N losses. The study indicated that process-based biogeochemical models such as the DNDC could contribute more effectively to watershed N loading studies if the hydrological components of the models were appropriately enhanced.

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

A quantitative assessment of methane cycling in Hikurangi Margin sediments (New Zealand) using geophysical imaging and biogeochemical modeling

NASA Astrophysics Data System (ADS)

Luo, Min; Dale, Andrew W.; Haffert, Laura; Haeckel, Matthias; Koch, Stephanie; Crutchley, Gareth; De Stigter, Henko; Chen, Duofu; Greinert, Jens

2016-12-01

Takahe seep, located on the Opouawe Bank, Hikurangi Margin, is characterized by a well-defined subsurface seismic chimney structure ˜80,500 m2 in area. Subseafloor geophysical data based on acoustic anomaly layers indicated the presence of gas hydrate and free gas layers within the chimney structure. Reaction-transport modeling was applied to porewater data from 11 gravity cores to constrain methane turnover rates and benthic methane fluxes in the upper 10 m. Model results show that methane dynamics were highly variable due to transport and dissolution of ascending gas. The dissolution of gas (up to 3761 mmol m-2 yr-1) dwarfed the rate of methanogenesis within the simulated sediment column (2.6 mmol m-2 yr-1). Dissolved methane is mainly consumed by anaerobic oxidation of methane (AOM) at the base of the sulfate reduction zone and trapped by methane hydrate formation below it, with maximum rates in the central part of the chimney (946 and 2420 mmol m-2 yr-1, respectively). A seep-wide methane budget was constrained by combining the biogeochemical model results with geophysical data and led to estimates of AOM rates, gas hydrate formation, and benthic dissolved methane fluxes of 3.68 × 104 mol yr-1, 73.85 × 104 mol yr-1, and 1.19 × 104 mol yr-1, respectively. A much larger flux of methane probably escapes in gaseous form through focused bubble vents. The approach of linking geochemical model results with spatial geophysical data put forward here can be applied elsewhere to improve benthic methane turnover rates from limited single spot measurements to larger spatial scales.

Quantifying Km-scale Hydrological Exchange Flows under Dynamic Flows and Their Influences on River Corridor Biogeochemistry

NASA Astrophysics Data System (ADS)

Chen, X.; Song, X.; Shuai, P.; Hammond, G. E.; Ren, H.; Zachara, J. M.

2017-12-01

Hydrologic exchange flows (HEFs) in rivers play vital roles in watershed ecological and biogeochemical functions due to their strong capacity to attenuate contaminants and process significant quantities of carbon and nutrients. While most of existing HEF studies focus on headwater systems with the assumption of steady-state flow, there is lack of understanding of large-scale HEFs in high-order regulated rivers that experience high-frequency stage fluctuations. The large variability of HEFs is a result of interactions between spatial heterogeneity in hydrogeologic properties and temporal variation in river discharge induced by natural or anthropogenic perturbations. Our 9-year spatially distributed dataset (water elevation, specific conductance, and temperature) combined with mechanistic hydrobiogeochemical simulations have revealed complex spatial and temporal dynamics in km-scale HEFs and their significant impacts on contaminant plume mobility and hyporheic biogeochemical processes along the Hanford Reach. Extended multidirectional flow behaviors of unconfined, river corridor groundwater were observed hundreds of meters inland from the river shore resulting from discharge-dependent HEFs. An appropriately sized modeling domain to capture the impact of regional groundwater flow as well as knowledge of subsurface structures controlling intra-aquifer hydrologic connectivity were essential to realistically model transient storage in this large-scale river corridor. This work showed that both river water and mobile groundwater contaminants could serve as effective tracers of HEFs, thus providing valuable information for evaluating and validating the HEF models. Multimodal residence time distributions with long tails were resulted from the mixture of long and short exchange pathways, which consequently impact the carbon and nutrient cycling within the river corridor. Improved understanding of HEFs using integrated observational and modeling approaches sheds light on developing fundamental understanding of the influences of HEFs on water quality, nutrient dynamics, and ecosystem health in dynamic river corridor systems.

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

USDA-ARS?s Scientific Manuscript database

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

Reactive transport codes for subsurface environmental simulation

DOE PAGES

Steefel, C. I.; Appelo, C. A. J.; Arora, B.; ...

2014-09-26

A general description of the mathematical and numerical formulations used in modern numerical reactive transport codes relevant for subsurface environmental simulations is presented. The formulations are followed by short descriptions of commonly used and available subsurface simulators that consider continuum representations of flow, transport, and reactions in porous media. These formulations are applicable to most of the subsurface environmental benchmark problems included in this special issue. The list of codes described briefly here includes PHREEQC, HPx, PHT3D, OpenGeoSys (OGS), HYTEC, ORCHESTRA, TOUGHREACT, eSTOMP, HYDROGEOCHEM, CrunchFlow, MIN3P, and PFLOTRAN. The descriptions include a high-level list of capabilities for each of themore » codes, along with a selective list of applications that highlight their capabilities and historical development.« less

Organic and Inorganic Carbon in the Rio Tinto (Spain) Deep Subsurface System: a Possible Model for Subsurface Carbon and Lithoautotrophs on Mars.

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Stoker, C. R.; MARTE Science Team

2007-12-01

The subsurface is the key environment for searching for life on planets lacking surface life. Subsurface ecosystems are of great relevance to astrobiology including the search for past/present life on Mars. Conditions on the Martian surface do not support biological activity but the subsurface might preserve organics and host subsurface life [1]. A key requirement for the analysis of subsurface samples on Mars is the ability to characterize organic vs. inorganic carbon pools. This information is needed to determine if the sample contains organic material of biological origin and/ or to establish if pools of inorganic carbon can support subsurface biospheres. The Mars Analog Rio Tinto Experiment (MARTE) performed deep drilling of cores i.e., down to 165-m depth, in a volcanically-hosted-massive-sulfide deposit at Rio Tinto, Spain, which is considered an important analog of the Sinus Meridiani site on Mars. Results from MARTE suggest the existence of a relatively complex subsurface life including aerobic and anaerobic chemoautotrophs, and strict anaerobic methanogens sustained by Fe and S minerals in anoxic conditions, which is an ideal model analog for a deep subsurface Martian environment. We report here on the distribution of organic (C-org: 0.01-0.3Wt% and inorganic carbon (IC = 0.01-7.0 Wt%) in a subsurface rock system including weathered/oxidized i.e., gossan, and unaltered pyrite stockwork. Cores were analyzed from 3 boreholes (BH-4, BH-7, and BH-8) that penetrated down to a depth of ~165 m into massive sulfide. Nearsurface phyllosilicate rich-pockets contain the highest amounts of organics (0.3Wt%) [2], while the deeper rocks contain the highest amount of carbonates. Assessing the amount of C pools available throughout the RT subsurface brings key insight on the type of trophic system sustaining its microbial ecosystem (i.e., heterotrophs vs. autotrophs) and the biogeochemical relationships that characterize a new type of subsurface biosphere at RT. This potentially novel biosphere on Earth could be used as a model to test for extant and extinct life on Mars. Furthermore, having found carbonates in an hyperacidic system (pH ~2.3) brings new insights on the possible occurrence of deep carbonates deposits under low-pH condition on Mars. [1] Boston, P.J., et al., 1992. Icarus 95,300-308; Bonaccorsi, Stoker and Sutter, 2007 Accepted with review in Astrobiology.

Isotopic Evidence for the Evolution of Subsurface Nitrate in the Western Equatorial Pacific

NASA Astrophysics Data System (ADS)

Lehmann, Nadine; Granger, Julie; Kienast, Markus; Brown, Kevin S.; Rafter, Patrick A.; Martínez-Méndez, Gema; Mohtadi, Mahyar

2018-03-01

Subsurface waters from both hemispheres converge in the Western Equatorial Pacific (WEP), some of which form the Equatorial Undercurrent (EUC) that influences equatorial Pacific productivity across the basin. Measurements of nitrogen (N) and oxygen (O) isotope ratios in nitrate (δ15NNO3 and δ18ONO3), the isotope ratios of dissolved inorganic carbon (δ13CDIC), and complementary biogeochemical tracers reveal that northern and southern WEP waters have distinct biogeochemical histories. Organic matter remineralization plays an important role in setting the nutrient characteristics on both sides of the WEP. However, remineralization in the northern WEP contributes a larger concentration of the nutrients, consistent with the older "age" of northern thermocline-depth and intermediate-depth waters. Remineralization introduces a relatively low δ15NNO3 to northern waters, suggesting the production of sinking organic matter by N2 fixation at the surface—consistent with the notion that N2 fixation is quantitatively important in the North Pacific. In contrast, remineralization contributes elevated δ15NNO3 to the southern WEP thermocline, which we hypothesize to derive from the vertical flux of high-δ15N material at the southern edge of the equatorial upwelling. This signal potentially masks any imprint of N2 fixation from South Pacific waters. The observations further suggest that the intrusion of high δ15NNO3 and δ18ONO3 waters from the eastern margins is more prominent in the northern than southern WEP. Together, these north-south differences enable the examination of the hemispheric inputs to the EUC, which appear to derive predominantly from southern hemisphere waters.

iTOUGH2: A multiphysics simulation-optimization framework for analyzing subsurface systems

NASA Astrophysics Data System (ADS)

Finsterle, S.; Commer, M.; Edmiston, J. K.; Jung, Y.; Kowalsky, M. B.; Pau, G. S. H.; Wainwright, H. M.; Zhang, Y.

2017-11-01

iTOUGH2 is a simulation-optimization framework for the TOUGH suite of nonisothermal multiphase flow models and related simulators of geophysical, geochemical, and geomechanical processes. After appropriate parameterization of subsurface structures and their properties, iTOUGH2 runs simulations for multiple parameter sets and analyzes the resulting output for parameter estimation through automatic model calibration, local and global sensitivity analyses, data-worth analyses, and uncertainty propagation analyses. Development of iTOUGH2 is driven by scientific challenges and user needs, with new capabilities continually added to both the forward simulator and the optimization framework. This review article provides a summary description of methods and features implemented in iTOUGH2, and discusses the usefulness and limitations of an integrated simulation-optimization workflow in support of the characterization and analysis of complex multiphysics subsurface systems.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-12-01

The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 1010 or 107 cells g soil-1 or rock-1, or ml water-1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and free-living decomposers have been studied extensively in soil habitats, where they occur up to 103 cells g soil-1, little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

Influence of Assimilation of Subsurface Temperature Measurements on Simulations of Equatorial Undercurrent and South Equatorial Current Along the Pacific Equator

NASA Technical Reports Server (NTRS)

Halpern, David; Leetmaan, Ants; Reynolds, Richard W.; Ji, Ming

1997-01-01

Equatorial Pacific current and temperature fields were simulated with and without assimilation of subsurface temperature measurements for April 1992 - March 1995, and compared with moored bouy and research vessel current measurements.

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

Treesearch

Jianbo Cui; Changsheng Li; Carl Trettin

2005-01-01

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

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processesmore » receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. Furthermore, the results also demonstrate the sensitivity of surface based ERT measurements to those changes over time.« less

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

DOE PAGES

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

2016-09-22

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processesmore » receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. Furthermore, the results also demonstrate the sensitivity of surface based ERT measurements to those changes over time.« less

Structure of peat soils and implications for biogeochemical processes and hydrological flow

NASA Astrophysics Data System (ADS)

Rezanezhad, F.; McCarter, C. P. R.; Gharedaghloo, B.; Kleimeier, C.; Milojevic, T.; Liu, H.; Weber, T. K. D.; Price, J. S.; Quinton, W. L.; Lenartz, B.; Van Cappellen, P.

2017-12-01

Permafrost peatlands contain globally important amounts of soil organic carbon and play major roles in global water, nutrient and biogeochemical cycles. The structure of peatland soils (i.e., peat) are highly complex with unique physical and hydraulic properties; where significant, and only partially reversible, shrinkage occurs during dewatering (including water table fluctuations), compression and/or decomposition. These distinct physical and hydraulic properties controls water flow, which in turn affect reactive and non-reactive solute transport (such as, sorption or degradation) and biogeochemical functions. Additionally, peat further attenuates solute migration through molecular diffusion into the inactive pores of Sphagnum dominated peat. These slow, diffusion-limited solute exchanges between the pore regions may give rise to pore-scale chemical gradients and heterogeneous distributions of microbial habitats and activity in peat soils. Permafrost peat plateaus have the same essential subsurface characteristics as other widely organic soil-covered peatlands, where the hydraulic conductivity is related to the degree of decomposition and soil compression. Increasing levels of decomposition correspond with a reduction of effective pore diameter and consequently restrict water and solute flow (by several orders of magnitude in hydraulic conductivity between the ground surface and a depth of 50 cm). In this presentation, we present the current knowledge of key physical and hydraulic properties related to the structure of globally available peat soils and discuss their implications for water storage, flow and the migration of solutes.

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer

NASA Astrophysics Data System (ADS)

Danczak, Robert; Yabusaki, Steven; Williams, Kenneth; Fang, Yilin; Hobson, Chad; Wilkins, Michael

2016-05-01

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a six-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species in reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.

Researchers Mine Information from Next-Generation Subsurface Flow Simulations

DOE PAGES

Gedenk, Eric D.

2015-12-01

A research team based at Virginia Tech University leveraged computing resources at the US Department of Energy's (DOE's) Oak Ridge National Laboratory to explore subsurface multiphase flow phenomena that can't be experimentally observed. Using the Cray XK7 Titan supercomputer at the Oak Ridge Leadership Computing Facility, the team took Micro-CT images of subsurface geologic systems and created two-phase flow simulations. The team's model development has implications for computational research pertaining to carbon sequestration, oil recovery, and contaminant transport.

Sedimentary silicon isotope indicates the Kuroshio subsurface upwelling in the East China Sea

NASA Astrophysics Data System (ADS)

Zhao, Y.; Yang, S.; Su, N.

2017-12-01

The Kuroshio as the western boundary current of the North Pacific subtropical circulation, originates from east of the Philippine Islands, and flows northeastward along the eastern coast of Taiwan. It's subsurface water intrudes the East China Sea (ECS) and forms a typical upwelling on the inner shelf, which may play an important role in the material and heat transport, biogeochemical process and marine ecosystem of the ECS.To date, most previous studies on the Kuroshio subsurface upwelling focuse on the seasonal and interannual variations, and few researches touch on the upwelling evolution in the geologic past. In this study, eight short sediment cores were taken along the ECS inner shelf (upwelling area), which allow us to reconstruct the upwelling history over the last several hundred years. Although conventional indexes of oceanographic changes, such as salinity, temperature and hydrogen and oxygen isotope, provide valuable constraints on the modern oceanic circulation and water mass movements, how to reconstruct them from geologic records is always a challenging work. In this contribution, we present the data of stable silicon isotope, biogenic opal, diatom assemblages, element geochemistry and stable carbon and nitrogen isotopes of these core sediments, and aim to decipher the Kuroshio subsurface upwelling history on the ECS shelf. We will also illustrate the difference in δ30Si signals between small (<30 um) and large (>150 um) diatom fractions, and test whether it is an effective indicator for paleo-upwelling intensity.

Underground Habitats in the Río Tinto Basin: A Model for Subsurface Life Habitats on Mars

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Prieto-Ballesteros, Olga; Rodríguez, Nuria; Gómez, Felipe; Amils, Ricardo; Gómez-Elvira, Javier; Stoker, Carol R.

2008-10-01

A search for evidence of cryptic life in the subsurface region of a fractured Paleozoic volcanosedimentary deposit near the source waters of the Río Tinto River (Iberian pyrite belt, southwest Spain) was carried out by Mars Astrobiology Research and Technology Experiment (MARTE) project investigators in 2003 and 2004. This conventional deep-drilling experiment is referred to as the MARTE ground truth drilling project. Boreholes were drilled at three sites, and samples from extracted cores were analyzed with light microscopy, scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy. Core leachates were analyzed with ion chromatography, and borehole fluids were analyzed with ion and gas chromatography. Key variables of the groundwater system (e.g. , pO2, pH, and salinity) exhibit huge ranges probably due to surficial oxygenation of overall reducing waters, physical mixing of waters, and biologically mediated water-rock interactions. Mineral distribution is mainly driven by the pH of subsurface solutions, which range from highly acidic to neutral. Borehole fluids contain dissolved gases such as CO2, CH4, and H2. SEM-EDS analyses of core samples revealed evidence of microbes attacking pyrite. The Río Tinto alteration mechanisms may be similar to subsurface weathering of the martian crust and provide insights into the possible (bio)geochemical cycles that may have accompanied underground habitats in extensive early Mars volcanic regions and associated sulfide ores.

Development of Enabling Scientific Tools to Characterize the Geologic Subsurface at Hanford

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kenna, Timothy C.; Herron, Michael M.

2014-07-08

This final report to the Department of Energy provides a summary of activities conducted under our exploratory grant, funded through U.S. DOE Subsurface Biogeochemical Research Program in the category of enabling scientific tools, which covers the period from July 15, 2010 to July 14, 2013. The main goal of this exploratory project is to determine the parameters necessary to translate existing borehole log data into reservoir properties following scientifically sound petrophysical relationships. For this study, we focused on samples and Ge-based spectral gamma logging system (SGLS) data collected from wells located in the Hanford 300 Area. The main activities consistedmore » of 1) the analysis of available core samples for a variety of mineralogical, chemical and physical; 2) evaluation of selected spectral gamma logs, environmental corrections, and calibration; 3) development of algorithms and a proposed workflow that permits translation of log responses into useful reservoir properties such as lithology, matrix density, porosity, and permeability. These techniques have been successfully employed in the petroleum industry; however, the approach is relatively new when applied to subsurface remediation. This exploratory project has been successful in meeting its stated objectives. We have demonstrated that our approach can lead to an improved interpretation of existing well log data. The algorithms we developed can utilize available log data, in particular gamma, and spectral gamma logs, and continued optimization will improve their application to ERSP goals of understanding subsurface properties.« less

Underground habitats in the Río Tinto basin: a model for subsurface life habitats on Mars.

PubMed

Fernández-Remolar, David C; Prieto-Ballesteros, Olga; Rodríguez, Nuria; Gómez, Felipe; Amils, Ricardo; Gómez-Elvira, Javier; Stoker, Carol R

2008-10-01

A search for evidence of cryptic life in the subsurface region of a fractured Paleozoic volcanosedimentary deposit near the source waters of the Río Tinto River (Iberian pyrite belt, southwest Spain) was carried out by Mars Astrobiology Research and Technology Experiment (MARTE) project investigators in 2003 and 2004. This conventional deep-drilling experiment is referred to as the MARTE ground truth drilling project. Boreholes were drilled at three sites, and samples from extracted cores were analyzed with light microscopy, scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy. Core leachates were analyzed with ion chromatography, and borehole fluids were analyzed with ion and gas chromatography. Key variables of the groundwater system (e.g., pO(2), pH, and salinity) exhibit huge ranges probably due to surficial oxygenation of overall reducing waters, physical mixing of waters, and biologically mediated water-rock interactions. Mineral distribution is mainly driven by the pH of subsurface solutions, which range from highly acidic to neutral. Borehole fluids contain dissolved gases such as CO(2), CH(4), and H(2). SEM-EDS analyses of core samples revealed evidence of microbes attacking pyrite. The Río Tinto alteration mechanisms may be similar to subsurface weathering of the martian crust and provide insights into the possible (bio)geochemical cycles that may have accompanied underground habitats in extensive early Mars volcanic regions and associated sulfide ores.

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

DOE PAGES

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

2016-08-11

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

Multi `omics reveals role of phenotypic plasticity in governing biogeochemical hotspots within the groundwater-surface water (hyporheic) mixing zone

NASA Astrophysics Data System (ADS)

Graham, E.; Tfaily, M. M.; Crump, A.; Arntzen, E.; Romero, E. B.; Goldman, A. E.; Resch, T.; Kennedy, D.; Nelson, W. C.; Stegen, J.

2017-12-01

Subsurface groundwater-surface water mixing zones (hyporheic zones) contain spatially heterogeneous hotspots of enhanced biogeochemical activity that contribute disproportionately to river corridor function. We have a poor understanding of the processes governing hotspots, but recent advances have enabled greater mechanistic understanding. We employ a suite of ultra-high resolution measurements to investigate the mechanisms underlying biogeochemical cycles in hyporheic zone hotspots. We use Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), metagenomic shotgun sequencing, and mass spectrometry of metaproteomes to characterize metabolite structure and metabolic transformations, microbiome structure and functional potential, and expressed microbiome functions in hyporheic sediments from the Columbia River in central Washington State. Surprisingly, microbiome structure and function in biogeochemical hotspots were indistinguishable from low-activity sediments. Metabolites were uncorrelated to protein expression but strongly related to aerobic respiration. Hotspot metabolites were distinguished by high molecular weight compounds and protein-, lignin-, and lipid-like molecules. Although the most common metabolic transformations were similar between hotspots and low-activity samples, hotspots contained a greater proportion of rare pathways, which in turn were correlated to metabolism. Our results contradicted our expectations that hotspots would be characterized by a unique microbiome with distinct physiology. Instead, our results indicate that microbial phenotypic plasticity underlies elevated hyporheic zone function, whereby the activity of rare pathways is stimulated by substrate availability. We therefore hypothesize that microbiome plasticity couples meso- (e.g., local root distribution) and macro-scale (e.g., landscape vegetation) resource heterogeneity to ecosystem-scale function. This indicates a need to mechanistically understand and represent microbiome physiological plasticity in predictive hydrobiogeochemical models that include the hyporheic zone.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

PubMed

Daly, Rebecca A; Borton, Mikayla A; Wilkins, Michael J; Hoyt, David W; Kountz, Duncan J; Wolfe, Richard A; Welch, Susan A; Marcus, Daniel N; Trexler, Ryan V; MacRae, Jean D; Krzycki, Joseph A; Cole, David R; Mouser, Paula J; Wrighton, Kelly C

2016-09-05

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that methylamine cycling supports methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while sulfide generation from thiosulfate represents a poorly recognized corrosion mechanism inmore » shales. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.« less

Remote Sensing of Subsurface Microbial Transformations

NASA Astrophysics Data System (ADS)

Williams, K. H.; Ntarlagiannis, D.; Slater, L.; Long, P.; Dohnalkova, A.; Hubbard, S. S.; Banfield, J. F.

2004-12-01

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to detect microbial dynamics in real time with high spatial resolution. Here we have used non-invasive geophysical methods to monitor biomineralization and related processes during biostimulation at both laboratory and field scales. Alterations in saturated sediment characteristics resulting from microbe-mediated transformations were concomitant with changes in complex resistivity, spontaneous potential, and acoustic wave signatures. Variability in complex resistivity and acoustic wave amplitudes appears tied to the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. In contrast, time-varying spontaneous potentials appear primarily sensitive to the electrochemical gradients resulting from metabolic pathways, such as iron- and sulfate-reduction. Furthermore, they enable us to track mobile fronts of active respiration that arise due to microbial chemotaxis. In this way, geophysical data may be used to image the distribution of mineral precipitates, biomass, and biogeochemical fronts evolving over time and suggest the ability to remotely monitor contaminated aquifers undergoing bioremediation.

Coupled charge migration and fluid mixing in reactive fronts

NASA Astrophysics Data System (ADS)

Ghosh, Uddipta; Bandopadhyay, Aditya; Jougnot, Damien; Le Borgne, Tanguy; Meheust, Yves

2017-04-01

Quantifying fluid mixing in subsurface environments and its consequence on biogeochemical reactions is of paramount importance owing to its role in processes such as contaminant migration, aquifer remediation, CO2 sequestration or clogging processes, to name a few (Dentz et al. 2011). The presence of strong velocity gradients in porous media is expected to lead to enhanced diffusive mixing and augmented reaction rates (Le Borgne et al. 2014). Accurate in situ imaging of subsurface reactive solute transport and mixing remains to date a challenging proposition: the opacity of the medium prevents optical imaging and field methods based on tracer tests do not provide spatial information. Recently developed geophysical methods based on the temporal monitoring of electrical conductivity and polarization have shown promises for mapping and monitoring biogeochemical reactions in the subsurface although it remains challenging to decipher the multiple sources of electrical signals (e.g. Knight et al. 2010). In this work, we explore the coupling between fluid mixing, reaction and charge migration in porous media to evaluate the potential of mapping reaction rates from electrical measurements. To this end, we develop a new theoretical framework based on a lamellar mixing model (Le Borgne et al. 2013) to quantify changes in electrical mobility induced by chemical reactions across mixing fronts. Electrical conductivity and induced polarization are strongly dependent on the concentration of ionic species, which in turn depend on the local reaction rates. Hence, our results suggest that variation in real and complex electrical conductivity may be quantitatively related to the mixing and reaction dynamics. Thus, the presented theory provides a novel upscaling framework for quantifying the coupling between mixing, reaction and charge migration in heterogeneous porous media flows. References: Dentz. et al., Mixing, spreading and reaction in heterogeneous media: A brief review J. Contam. Hydrol. 120-121, 1 (2011). Le Borgne et al. Impact of Fluid Deformation on Mixing-Induced Chemical Reactions in heterogeneous Flows, Geophys. Res. Lett. 41, 7898 (2014). Knight, et al., Geophysics at the interface: Response of geophysical properties to solid-fluid, fluid-fluid, and solid-solid interfaces. Rev. Geophys. 48, (2010). Le Borgne et al. (2013) Stretching, coalescence and mixing in porous media, Phys. Rev. Lett., 110, 204501

Carbon Characteristics and Biogeochemical Processes of Uranium Accumulating Organic Matter Rich Sediments in the Upper Colorado River Basin

NASA Astrophysics Data System (ADS)

Boye, K.; Noel, V.; Tfaily, M. M.; Dam, W. L.; Bargar, J.; Fendorf, S. E.

2015-12-01

Uranium plume persistence in groundwater aquifers is a problem on several former ore processing sites on floodplains in the upper Colorado River Basin. Earlier observations by our group and others at the Old Rifle Site, CO, have noted that U concentrations are highest in organic rich, fine-grained, and, therefore, diffusion limited sediment material. Due to the constantly evolving depositional environments of floodplains, surficial organic matter may become buried at various stages of decomposition, through sudden events such as overbank flooding and through the slower progression of river meandering. This creates a discontinuous subsurface distribution of organic-rich sediments, which are hotspots for microbial activity and thereby central to the subsurface cycling of contaminants (e.g. U) and biologically relevant elements (e.g. C, N, P, Fe). However, the organic matter itself is poorly characterized. Consequently, little is known about its relevance in driving biogeochemical processes that control U fate and transport in the subsurface. In an investigation of soil/sediment cores from five former uranium ore processing sites on floodplains distributed across the Upper Colorado River Basin we confirmed consistent co-enrichment of U with organic-rich layers in all profiles. However, using C K-edge X-ray Absorption Spectroscopy (XAS) coupled with Fourier-Transformed Ion-Cyclotron-Resonance Mass-Spectroscopy (FT-ICR-MS) on bulk sediments and density-separated organic matter fractions, we did not detect any chemical difference in the organic rich sediments compared to the surrounding coarser-grained aquifer material within the same profile, even though there were differences in organic matter composition between the 5 sites. This suggests that U retention and reduction to U(IV) is independent of C chemical composition on the bulk scale. Instead it appears to be the abundance of organic matter in combination with a limited O2 supply in the fine-grained material that stimulate anaerobic microbial processes responsible for U enrichment. Thus, the chemical composition of organic matter is subordinate to the physical environment and total organic matter content in controlling U reduction and retention processes.

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Stegen, James C.

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE PAGES

Graham, Emily B.; Stegen, James C.

2017-11-01

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Fracture Mechanics Analyses of Subsurface Defects in Reinforced Carbon-Carbon Joggles Subjected to Thermo-Mechanical Loads

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Raju, Ivatury S.; Song, Kyongchan

2011-01-01

Coating spallation events have been observed along the slip-side joggle region of the Space Shuttle Orbiter wing-leading-edge panels. One potential contributor to the spallation event is a pressure build up within subsurface voids or defects due to volatiles or water vapor entrapped during fabrication, refurbishment, or normal operational use. The influence of entrapped pressure on the thermo-mechanical fracture-mechanics response of reinforced carbon-carbon with subsurface defects is studied. Plane-strain simulations with embedded subsurface defects are performed to characterize the fracture mechanics response for a given defect length when subjected to combined elevated-temperature and subsurface-defect pressure loadings to simulate the unvented defect condition. Various subsurface defect locations of a fixed-length substrate defect are examined for elevated temperature conditions. Fracture mechanics results suggest that entrapped pressure combined with local elevated temperatures have the potential to cause subsurface defect growth and possibly contribute to further material separation or even spallation. For this anomaly to occur, several unusual circumstances would be required making such an outcome unlikely but plausible.

Modeling physical and biogeochemical controls over carbon accumulation in a boreal forest soil

USGS Publications Warehouse

Carrasco, J.J.; Neff, J.C.; Harden, J.W.

2006-01-01

Boreal soils are important to the global C cycle owing to large C stocks, repeated disturbance from fire, and the potential for permafrost thaw to expose previously stable, buried C. To evaluate the primary mechanisms responsible for both short- and long-term C accumulation in boreal soils, we developed a multi-isotope (12,14C) Soil C model with dynamic soil layers that develop through time as soil organic matter burns and reaccumulates. We then evaluated the mechanisms that control organic matter turnover in boreal regions including carbon input rates, substrate recalcitrance, soil moisture and temperature, and the presence of historical permafrost to assess the importance of these factors in boreal C accumulation. Results indicate that total C accumulation is controlled by the rate of carbon input, decomposition rates, and the presence of historical permafrost. However, unlike more temperate ecosystems, one of the key mechanisms involved in C preservation in boreal soils examined here is the cooling of subsurface soil layers as soil depth increases rather than increasing recalcitrance in subsurface soils. The propagation of the 14C bomb spike into soils also illustrates the importance of historical permafrost and twentieth century warming in contemporary boreal soil respiration fluxes. Both 14C and total C simulation data also strongly suggest that boreal SOM need not be recalcitrant to accumulate; the strong role of soil temperature controls on boreal C accumulation at our modeling test site in Manitoba, Canada, indicates that carbon in the deep organic soil horizons is probably relatively labile and thus subject to perturbations that result from changing climatic conditions in the future. Copyright 2006 by the American Geophysical Union.

Drivers of the Seasonal Carbon Cycle in the Coastal Gulf of Alaska

NASA Astrophysics Data System (ADS)

Pilcher, D.; Siedlecki, S. A.; Hermann, A. J.; Coyle, K. O.; Mathis, J. T.

2016-02-01

The Coastal Gulf of Alaska serves as a significant carbon sink annually, but varies seasonally from net carbon efflux in winter, to net carbon uptake from spring through fall. This significant uptake of anthropogenic CO2 combined with the naturally cold, low calcium carbonate surface waters is expected to accelerate ocean acidification. Observational evidence has already detected subsurface aragonite undersaturation, likely resulting from carbon remineralization of sinking organic matter. Other processes such as storm-induced vertical mixing, glacial runoff, temperature change, and nutrient supply can further modify the carbon cycle. Improving knowledge of these seasonal processes is critical for the region's fisheries that provide substantial ecosystem services and can be adversely impacted by sub-optimal aragonite saturation conditions. We use a regional model of the Coastal Gulf of Alaska coupled to an ecosystem model with full carbonate chemistry to investigate the physical and biogeochemical mechanisms that drive the seasonal carbon cycle. Boundary conditions are set from the coarser Northeast Pacific model, with alkalinity and carbon concentrations determined from empirical relationships with salinity. Model output from a 2009 hindcast simulation is compared to observations of alkalinity and dissolved inorganic carbon concentrations for model verification and to elucidate seasonal mechanisms.

Biological data assimilation for parameter estimation of a phytoplankton functional type model for the western North Pacific

NASA Astrophysics Data System (ADS)

Hoshiba, Yasuhiro; Hirata, Takafumi; Shigemitsu, Masahito; Nakano, Hideyuki; Hashioka, Taketo; Masuda, Yoshio; Yamanaka, Yasuhiro

2018-06-01

Ecosystem models are used to understand ecosystem dynamics and ocean biogeochemical cycles and require optimum physiological parameters to best represent biological behaviours. These physiological parameters are often tuned up empirically, while ecosystem models have evolved to increase the number of physiological parameters. We developed a three-dimensional (3-D) lower-trophic-level marine ecosystem model known as the Nitrogen, Silicon and Iron regulated Marine Ecosystem Model (NSI-MEM) and employed biological data assimilation using a micro-genetic algorithm to estimate 23 physiological parameters for two phytoplankton functional types in the western North Pacific. The estimation of the parameters was based on a one-dimensional simulation that referenced satellite data for constraining the physiological parameters. The 3-D NSI-MEM optimized by the data assimilation improved the timing of a modelled plankton bloom in the subarctic and subtropical regions compared to the model without data assimilation. Furthermore, the model was able to improve not only surface concentrations of phytoplankton but also their subsurface maximum concentrations. Our results showed that surface data assimilation of physiological parameters from two contrasting observatory stations benefits the representation of vertical plankton distribution in the western North Pacific.

Effect of Co-Contaminants Uranium and Nitrate on Iodine Remediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szecsody, James E.; Lee, Brady D.; Lawter, Amanda R.

The objective of this study is to evaluate the significance of co-contaminants on the migration and transformation of iodine species in the Hanford subsurface environment. These impacts are relevant because remedies that target individual contaminants like iodine, may not only impact the fate and transport of other contaminants in the subsurface, but also inhibit the effectiveness of a targeted remedy. For example, iodine (as iodate) co-precipitates with calcite, and has been identified as a potential remedy because it immobilizes iodine. Since uranium also co-precipitates with calcite in field sediments, the presence of uranium may also inhibit iodine co-precipitation. Another potentiallymore » significant impact from co-existing contaminants is iodine and nitrate. The presence of nitrate has been shown to promote biogeochemical reduction of iodate to iodide, thereby increasing iodine species subsurface mobility (as iodide exhibits less sorption). Hence, this study reports on both laboratory batch and column experiments that investigated a) the change in iodate uptake mass and rate of uptake into precipitating calcite due to the presence of differing amounts of uranium, b) the amount of change of the iodate bio-reduction rate due to the presence of differing nitrate concentrations, and c) whether nitrite can reduce iodate in the presence of microbes and/or minerals acting as catalysts.« less

Modeling Phosphorus Losses through Surface Runoff and Subsurface Drainage Using ICECREAM.

PubMed

Qi, Hongkai; Qi, Zhiming; Zhang, T Q; Tan, C S; Sadhukhan, Debasis

2018-03-01

Modeling soil phosphorus (P) losses by surface and subsurface flow pathways is essential in developing successful strategies for P pollution control. We used the ICECREAM model to simultaneously simulate P losses in surface and subsurface flow, as well as to assess effectiveness of field practices in reducing P losses. Monitoring data from a mineral-P-fertilized clay loam field in southwestern Ontario, Canada, were used for calibration and validation. After careful adjustment of model parameters, ICECREAM was shown to satisfactorily simulate all major processes of surface and subsurface P losses. When the calibrated model was used to assess tillage and fertilizer management scenarios, results point to a 10% reduction in total P losses by shifting autumn tillage to spring, and a 25.4% reduction in total P losses by injecting fertilizer rather than broadcasting. Although the ICECREAM model was effective in simulating surface and subsurface P losses when thoroughly calibrated, further testing is needed to confirm these results with manure P application. As illustrated here, successful use of simulation models requires careful verification of model routines and comprehensive calibration to ensure that site-specific processes are accurately represented. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Need to improve SWMM's subsurface flow routing algorithm for green infrastructure modeling

EPA Science Inventory

SWMM can simulate various subsurface flows, including groundwater (GW) release from a subcatchment to a node, percolation out of storage units and low impact development (LID) controls, and rainfall derived inflow and infiltration (RDII) at a node. Originally, the subsurface flow...

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states frommore » PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of changes subsurface electrical conductivity, in both the saturated and unsaturated zones, arising from water table changes and from river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev .« less

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

NASA Astrophysics Data System (ADS)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

2017-02-01

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev.

Distribution of microbial biomass and potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment.

PubMed

Lin, Xueju; Kennedy, David; Peacock, Aaron; McKinley, James; Resch, Charles T; Fredrickson, James; Konopka, Allan

2012-02-01

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.

Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment

PubMed Central

Lin, Xueju; Kennedy, David; Peacock, Aaron; McKinley, James; Resch, Charles T.; Fredrickson, James

2012-01-01

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling. PMID:22138990

A dynamic organic soil biogeochemical model for simulating the effects of wildfire on soil environmental conditions and carbon dynamics of black spruce forests

Treesearch

Shuhua Yi; A. David McGuire; Eric Kasischke; Jennifer Harden; Kristen Manies; Michelle Mack; Merritt Turetsky

2010-01-01

Ecosystem models have not comprehensively considered how interactions among fire disturbance, soil environmental conditions, and biogeochemical processes affect ecosystem dynamics in boreal forest ecosystems. In this study, we implemented a dynamic organic soil structure in the Terrestrial Ecosystem Model (DOS-TEM) to investigate the effects of fire on soil temperature...

Influence of PAHs among other coastal environmental variables on total and PAH-degrading bacterial communities.

PubMed

Sauret, Caroline; Tedetti, Marc; Guigue, Catherine; Dumas, Chloé; Lami, Raphaël; Pujo-Pay, Mireille; Conan, Pascal; Goutx, Madeleine; Ghiglione, Jean-François

2016-03-01

We evaluated the relative impact of anthropogenic polycyclic aromatic hydrocarbons (PAHs) among biogeochemical variables on total, metabolically active, and PAH bacterial communities in summer and winter in surface microlayer (SML) and subsurface seawaters (SSW) across short transects along the NW Mediterranean coast from three harbors, one wastewater effluent, and one nearshore observatory reference site. At both seasons, significant correlations were found between dissolved total PAH concentrations and PAH-degrading bacteria that formed a gradient from the shore to nearshore waters. Accumulation of PAH degraders was particularly high in the SML, where PAHs accumulated. Harbors and wastewater outfalls influenced drastically and in a different way the total and active bacterial community structure, but they only impacted the communities from the nearshore zone (<2 km from the shore). By using direct multivariate statistical analysis, we confirmed the significant effect of PAH concentrations on the spatial and temporal dynamic of total and active communities in this area, but this effect was putted in perspective by the importance of other biogeochemical variables.

Modifying WEPP to improve streamflow simulation in a Pacific Northwest watershed

Treesearch

A. Srivastava; M. Dobre; J. Q. Wu; W. J. Elliot; E. A. Bruner; S. Dun; E. S. Brooks; I. S. Miller

2013-01-01

The assessment of water yield from hillslopes into streams is critical in managing water supply and aquatic habitat. Streamflow is typically composed of surface runoff, subsurface lateral flow, and groundwater baseflow; baseflow sustains the stream during the dry season. The Water Erosion Prediction Project (WEPP) model simulates surface runoff, subsurface lateral flow...

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

USGS Publications Warehouse

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

2009-01-01

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

Mercury and methylmercury stream concentrations in a Coastal Plain watershed: A multi-scale simulation analysis

USGS Publications Warehouse

Knightes, Christopher D.; Golden, Heather E.; Journey, Celeste A.; Davis, Gary M.; Conrads, Paul; Marvin-DiPasquale, Mark; Brigham, Mark E.; Bradley, Paul M.

2014-01-01

Mercury is a ubiquitous global environmental toxicant responsible for most US fish advisories. Processes governing mercury concentrations in rivers and streams are not well understood, particularly at multiple spatial scales. We investigate how insights gained from reach-scale mercury data and model simulations can be applied at broader watershed scales using a spatially and temporally explicit watershed hydrology and biogeochemical cycling model, VELMA. We simulate fate and transport using reach-scale (0.1 km2) study data and evaluate applications to multiple watershed scales. Reach-scale VELMA parameterization was applied to two nested sub-watersheds (28 km2 and 25 km2) and the encompassing watershed (79 km2). Results demonstrate that simulated flow and total mercury concentrations compare reasonably to observations at different scales, but simulated methylmercury concentrations are out-of-phase with observations. These findings suggest that intricacies of methylmercury biogeochemical cycling and transport are under-represented in VELMA and underscore the complexity of simulating mercury fate and transport.

Performance Analysis and Scaling Behavior of the Terrestrial Systems Modeling Platform TerrSysMP in Large-Scale Supercomputing Environments

NASA Astrophysics Data System (ADS)

Kollet, S. J.; Goergen, K.; Gasper, F.; Shresta, P.; Sulis, M.; Rihani, J.; Simmer, C.; Vereecken, H.

2013-12-01

In studies of the terrestrial hydrologic, energy and biogeochemical cycles, integrated multi-physics simulation platforms take a central role in characterizing non-linear interactions, variances and uncertainties of system states and fluxes in reciprocity with observations. Recently developed integrated simulation platforms attempt to honor the complexity of the terrestrial system across multiple time and space scales from the deeper subsurface including groundwater dynamics into the atmosphere. Technically, this requires the coupling of atmospheric, land surface, and subsurface-surface flow models in supercomputing environments, while ensuring a high-degree of efficiency in the utilization of e.g., standard Linux clusters and massively parallel resources. A systematic performance analysis including profiling and tracing in such an application is crucial in the understanding of the runtime behavior, to identify optimum model settings, and is an efficient way to distinguish potential parallel deficiencies. On sophisticated leadership-class supercomputers, such as the 28-rack 5.9 petaFLOP IBM Blue Gene/Q 'JUQUEEN' of the Jülich Supercomputing Centre (JSC), this is a challenging task, but even more so important, when complex coupled component models are to be analysed. Here we want to present our experience from coupling, application tuning (e.g. 5-times speedup through compiler optimizations), parallel scaling and performance monitoring of the parallel Terrestrial Systems Modeling Platform TerrSysMP. The modeling platform consists of the weather prediction system COSMO of the German Weather Service; the Community Land Model, CLM of NCAR; and the variably saturated surface-subsurface flow code ParFlow. The model system relies on the Multiple Program Multiple Data (MPMD) execution model where the external Ocean-Atmosphere-Sea-Ice-Soil coupler (OASIS3) links the component models. TerrSysMP has been instrumented with the performance analysis tool Scalasca and analyzed on JUQUEEN with processor counts on the order of 10,000. The instrumentation is used in weak and strong scaling studies with real data cases and hypothetical idealized numerical experiments for detailed profiling and tracing analysis. The profiling is not only useful in identifying wait states that are due to the MPMD execution model, but also in fine-tuning resource allocation to the component models in search of the most suitable load balancing. This is especially necessary, as with numerical experiments that cover multiple (high resolution) spatial scales, the time stepping, coupling frequencies, and communication overheads are constantly shifting, which makes it necessary to re-determine the model setup with each new experimental design.

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Minjing; Qian, Wei-jun; Gao, Yuqian

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes asmore » time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates« less

Depositionally controlled recycling of iron and sulfur in marine sediments and its isotopic consequences

NASA Astrophysics Data System (ADS)

Riedinger, N.; Formolo, M.; Arnold, G. L.; Vossmeyer, A.; Henkel, S.; Sawicka, J.; Kasten, S.; Lyons, T. W.

2011-12-01

The continental margin off Uruguay and Argentina is characterized by highly dynamic depositional conditions. This variable depositional regime significantly impacts the biogeochemical cycles of iron and sulfur. Mass deposit related redeposition of reduced minerals can lead to the reoxidation of these phases and thus to an overprint of their geochemical primary signatures. Due to rapid burial these oxidized phases are still present in deeper subsurface sediments. To study the effects of sediment relocation on the sulfur and iron inventory we collected shallow and deep subsurface sediment samples via multicorer and gravity cores, respectively, in the western Argentine Basin during the RV Meteor Expedition M78/3 in May-July 2009. The samples were retrieved from shelf, slope and deep basin sites. The concentration and sulfur isotope composition of acid volatile sulfur (AVS), chromium reducible sulfur (CRS), elemental sulfur and total organic sulfur were determined. Furthermore, sequential iron extraction techniques were applied assess the distribution of iron oxide phases within the sediment. The investigated sediments are dominated by terrigenous inputs, with high amounts of reactive ferric iron minerals and only low concentrations of calcium carbonate. Total organic carbon concentrations show strong variation in the shallow subsurface sediments ranging between approximately 0.7 and 6.4 wt% for different sites. These concentrations do not correlate with water depths. Pore water accumulations of hydrogen sulfide are restricted to an interval at the sulfate-methane transition (SMT) zone a few meters below the sediment surface. In these deeper subsurface sediments pyrite is precipitated in this zone of hydrogen sulfide excess, whereas the accumulation of authigenic AVS and elemental sulfur (up to 2000 ppm) occurs at the upper and lower boundary of the sulfidic zone due the reaction of iron oxides with limited amounts of sulfide. Furthermore, our preliminary results indicate that there is a link between modern deposition in the shallow subsurface sediments and the long-term signals being buried and preserved in the deep subsurface layers. The data show that the burial of elemental sulfur into deep subsurface sediments can fuel the deep biosphere and has consequences for isotopic overprints tied, for example, to oxidation and disproportionation processes in the deeper sediments.

Simulating global and local surface temperature changes due to Holocene anthropogenic land cover change

NASA Astrophysics Data System (ADS)

He, F.; Vavrus, S. J.; Kutzbach, J. E.; Ruddiman, W. F.; Kaplan, J. O.; Krumhardt, K. M.

2015-12-01

Surface albedo changes from anthropogenic land cover change (ALCC) represent the second-largest negative radiative forcing behind aerosol during the industrial era. Using a new reconstruction of ALCC during the Holocene era by Kaplan et al. [2011], we quantify the local and global temperature response induced by Holocene ALCC in the Community Climate System Model, version 4 (CCSM4). With 1-degree resolution of the CCSM4 slab-ocean model,we find that Holocene ALCC cause a global cooling of 0.17 °C due to the biogeophysical effects of land-atmosphere exchange of momentum, moisture, radiative and heat fluxes. On the global scale, the biogeochemical effects of Holocene ALCC from carbon emissions dominate the biogeophysical effects by causing 0.9 °C global warming. The net effects of Holocene ALCC amount to a global warming of 0.73 °C during the pre-industrial era, which is comparable to the ~0.8 °C warming during industrial times. On local to regional scales, such as parts of Europe, North America and Asia, the biogeophysical effects of Holocene ALCC are significant and comparable to the biogeochemical effect. The lack of ocean dynamics in the 1° CCSM4 slab-ocean simulations could underestimate the climate sensitivity because of the lack of feedbacks from ocean heat transport [Kutzbach et al., 2013; Manabe and Bryan, 1985]. In 1° CCSM4 fully coupled simulations, the climate sensitivity is ~65% larger than the 1° CCSM4 slab-ocean simulations during the Holocene (5.3 °C versus 3.2 °C) [Kutzbach et al., 2013]. With this greater climate sensitivity, the biogeochemical effects of Holocene ALCC could have caused a global warming of ~1.5 °C, and the net biogeophysical and biogeochemical effects of Holocene ALCC could cause a global warming of 1.2 °C during the preindustrial era in our simulations, which is 50% higher than the global warming of ~0.8 °C during industrial times.

A multi-scale experimental and simulation approach for fractured subsurface systems

NASA Astrophysics Data System (ADS)

Viswanathan, H. S.; Carey, J. W.; Frash, L.; Karra, S.; Hyman, J.; Kang, Q.; Rougier, E.; Srinivasan, G.

2017-12-01

Fractured systems play an important role in numerous subsurface applications including hydraulic fracturing, carbon sequestration, geothermal energy and underground nuclear test detection. Fractures that range in scale from microns to meters and their structure control the behavior of these systems which provide over 85% of our energy and 50% of US drinking water. Determining the key mechanisms in subsurface fractured systems has been impeded due to the lack of sophisticated experimental methods to measure fracture aperture and connectivity, multiphase permeability, and chemical exchange capacities at the high temperature, pressure, and stresses present in the subsurface. In this study, we developed and use microfluidic and triaxial core flood experiments required to reveal the fundamental dynamics of fracture-fluid interactions. In addition we have developed high fidelity fracture propagation and discrete fracture network flow models to simulate these fractured systems. We also have developed reduced order models of these fracture simulators in order to conduct uncertainty quantification for these systems. We demonstrate an integrated experimental/modeling approach that allows for a comprehensive characterization of fractured systems and develop models that can be used to optimize the reservoir operating conditions over a range of subsurface conditions.

Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments

PubMed Central

Yanagawa, Katsunori; Tani, Atsushi; Yamamoto, Naoya; Hachikubo, Akihiro; Kano, Akihiro; Matsumoto, Ryo; Suzuki, Yohey

2016-01-01

The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxidation to CO2 surpassed methanol assimilation and methanogenesis from CO2/H2 and methanol. Nevertheless, a significant decrease in methanol was not observed after the incubation, and this was attributed to the microbial production of methanol in parallel with its consumption. These results suggest that microbial reactions play an important role in the sources and sinks of methanol in subseafloor sediments. PMID:27301420

Hydrologic and Biogeochemical Connections between Uplands and Streams in Contrasting Landscapes

NASA Astrophysics Data System (ADS)

Shanley, J. B.; Webb, R. M.; Hjerdt, K. N.; Sebestyen, S. D.; Peters, N. E.; Burns, D. A.; Aulenbach, B. T.; Campbell, D. H.; Clow, D. W.; Mast, M. A.; Walker, J. F.; Hunt, R. J.; Troester, J. W.; Larsen, M. C.

2004-12-01

We used combinations of hydrometric, chemical, and isotopic evidence to evaluate linkages between upland and riparian zones at the 5 small watersheds of the U.S. Geological Survey Water Energy and Biogeochemical Budget (WEBB) program. These sites span a broad range of climate and topography. At Sleepers River, Vermont, snowmelt induced the water table on hillslopes to rise into the highly transmissive upper soil. The close timing of the groundwater and stream hydrographs suggests a large contribution of hillslope water to the stream. However, the chemistry of these upland groundwaters indicates that only limited areas of convergent groundwater flow directly contribute to streamflow. At Panola Mountain, Georgia, a thin saturated zone develops on the hillslope during large rainstorms. This hillslope groundwater is chemically distinct from riparian groundwater, and transits the riparian zone near land surface with little mixing. Based on chemical mixing analysis, the hillslope contributes up to 30% of the streamwater during moderate to large-sized rainstorms. The Trout Lake site in Wisconsin is a low-lying landscape in highly conductive sandy glacial outwash.Hillslope water chemistry is considerably more dilute (i.e. less evolved) than the regional groundwater that supplies baseflow. The lack of chemical response in streamwater during storms suggests that hillslope water makes a minimal contribution relative to regional groundwater flow. In the alpine/subalpine watershed of Loch Vale, Colorado, much of the subsurface flow occurs on steep slopes of talus. Water in the talus flow has a wide range of residence times. The talus deposits are biogeochemically active and play an important role in maintaining summer baseflow, regulating seasonal changes in streamwater chemistry, and exporting nitrogen from atmospheric deposition. The tropical Icacos watershed in the Luquillo mountains of Puerto Rico receives 4 meters of rainfall annually and has high physical and chemical weathering rates. Streamwater chemistry during baseflow is strongly controlled by groundwater interaction with weathered bedrock. Most hillslope runoff occurs through near-surface macropores with limited soil interaction. This source dominates during storms resulting in stream chemistry that resembles that of the extremely dilute precipitation.We will compare these field observations at each site with the aid of TOPMODEL-based simulation of residence times and observed water quality on the hillslope and riparian saturated zones.

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

PubMed Central

Lau, Maggie C. Y.; Cameron, Connor; Magnabosco, Cara; Brown, C. Titus; Schilkey, Faye; Grim, Sharon; Hendrickson, Sarah; Pullin, Michael; Sherwood Lollar, Barbara; van Heerden, Esta; Kieft, Thomas L.; Onstott, Tullis C.

2014-01-01

Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes. PMID:25400621

A strategy to sample nutrient dynamics across the terrestrial-aquatic interface at NEON sites

NASA Astrophysics Data System (ADS)

Hinckley, E. S.; Goodman, K. J.; Roehm, C. L.; Meier, C. L.; Luo, H.; Ayres, E.; Parnell, J.; Krause, K.; Fox, A. M.; SanClements, M.; Fitzgerald, M.; Barnett, D.; Loescher, H. W.; Schimel, D.

2012-12-01

The construction of the National Ecological Observatory Network (NEON) across the U.S. creates the opportunity for researchers to investigate biogeochemical transformations and transfers across ecosystems at local-to-continental scales. Here, we examine a subset of NEON sites where atmospheric, terrestrial, and aquatic observations will be collected for 30 years. These sites are located across a range of hydrological regimes, including flashy rain-driven, shallow sub-surface (perched, pipe-flow, etc), and deep groundwater, which likely affect the chemical forms and quantities of reactive elements that are retained and/or mobilized across landscapes. We present a novel spatial and temporal sampling design that enables researchers to evaluate long-term trends in carbon, nitrogen, and phosphorus biogeochemical cycles under these different hydrological regimes. This design focuses on inputs to the terrestrial system (atmospheric deposition, bulk precipitation), transfers (soil-water and groundwater sources/chemistry), and outputs (surface water, and evapotranspiration). We discuss both data that will be collected as part of the current NEON design, as well as how the research community can supplement the NEON design through collaborative efforts, such as providing additional datasets, including soil biogeochemical processes and trace gas emissions, and developing collaborative research networks. Current engagement with the research community working at the terrestrial-aquatic interface is critical to NEON's success as we begin construction, to ensure that high-quality, standardized and useful data are not only made available, but inspire further, cutting-edge research.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE PAGES

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.; ...

2016-05-11

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a 6-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Thus, reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.« less

Tracing Nitrogen Sources in Forested Catchments Under Varying Flow Conditions: Seasonal and Event Scale Patterns

NASA Astrophysics Data System (ADS)

Sebestyen, S. D.; Shanley, J. B.; Boyer, E. W.; Kendall, C.

2004-12-01

Our ability to assess how stream nutrient concentrations respond to biogeochemical transformations and stream flow dynamics is often limited by datasets that do not include all flow conditions that occur over event, monthly, seasonal, and yearly time scales. At the Sleepers River Research Watershed in northeastern Vermont, USA, nitrate, DOC (dissolved organic carbon), and major ion concentrations were measured on samples collected over a wide range of flow conditions from summer 2002 through summer 2004. Nutrient flushing occurred at the W-9 catchment and high-frequency sampling revealed critical insights into seasonal and event-scale controls on nutrient concentrations. In this seasonally snow-covered catchment, the earliest stage of snowmelt introduced nitrogen directly to the stream from the snowpack. As snowmelt progressed, the source of stream nitrate shifted to flushing of soil nitrate along shallow subsurface flow paths. In the growing season, nitrogen flushing to streams varied with antecedent moisture conditions. More nitrogen was available to flush to streams when antecedent moisture was lowest, and mobile nitrogen stores in the landscape regenerated under baseflow conditions on times scales as short as 7 days. Leaf fall was another critical time when coupled hydrological and biogeochemical processes controlled nutrient fluxes. With the input of labile organic carbon from freshly decomposing leaves, nitrate concentrations declined sharply in response to in-stream immobilization or denitrification. These high-resolution hydrochemical data from multiple flow regimes are identifying "hot spots" and "hot moments" of biogeochemical and hydrological processes that control nutrient fluxes in streams.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a 6-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Thus, reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.« less

From terrestrial to aquatic fluxes: Integrating stream dynamics within a dynamic global vegetation modeling framework

NASA Astrophysics Data System (ADS)

Hoy, Jerad; Poulter, Benjamin; Emmett, Kristen; Cross, Molly; Al-Chokhachy, Robert; Maneta, Marco

2016-04-01

Integrated terrestrial ecosystem models simulate the dynamics and feedbacks between climate, vegetation, disturbance, and hydrology and are used to better understand biogeography and biogeochemical cycles. Extending dynamic vegetation models to the aquatic interface requires coupling surface and sub-surface runoff to catchment routing schemes and has the potential to enhance how researchers and managers investigate how changes in the environment might impact the availability of water resources for human and natural systems. In an effort towards creating such a coupled model, we developed catchment-based hydrologic routing and stream temperature model to pair with LPJ-GUESS, a dynamic global vegetation model. LPJ-GUESS simulates detailed stand-level vegetation dynamics such as growth, carbon allocation, and mortality, as well as various physical and hydrologic processes such as canopy interception and through-fall, and can be applied at small spatial scales, i.e., 1 km. We demonstrate how the coupled model can be used to investigate the effects of transient vegetation dynamics and CO2 on seasonal and annual stream discharge and temperature regimes. As a direct management application, we extend the modeling framework to predict habitat suitability for fish habitat within the Greater Yellowstone Ecosystem, a 200,000 km2 region that provides critical habitat for a range of aquatic species. The model is used to evaluate, quantitatively, the effects of management practices aimed to enhance hydrologic resilience to climate change, and benefits for water storage and fish habitat in the coming century.

Mars Analog Rio Tinto Experiment (MARTE): 2003 Drilling Campaign to Search for a Subsurface Biosphere at Rio Tinto Spain

NASA Astrophysics Data System (ADS)

Stoker, C.; Dunagan, S.; Stevens, T.; Amils, R.; Gómez-Elvira, J.; Fernández, D.; Hall, J.; Lynch, K.; Cannon, H.; Zavaleta, J.; Glass, B.; Lemke, L.

2004-03-01

The results of an drilling experiment to search for a subsurface biosphere in a pyritic mineral deposit at Rio Tinto, Spain, are described. The experiment provides ground truth for a simulation of a Mars drilling mission to search for subsurface life.

Effect of subsurface heterogeneity on free-product recovery from unconfined aquifers

NASA Astrophysics Data System (ADS)

Kaluarachchi, Jagath J.

1996-03-01

Free-product record system designs for light-hydrocarbon-contaminated sites were investigated to evaluate the effects of subsurface heterogeneity using a vertically integrated three-phase flow model. The input stochastic variable of the areal flow analysis was the log-intrinsic permeability and it was generated using the Turning Band method. The results of a series of hypothetical field-scale simulations showed that subsurface heterogeneity has a substantial effect on free-product recovery predictions. As the heterogeneity increased, the recoverable oil volume decreased and the residual trapped oil volume increased. As the subsurface anisotropy increased, these effects together with free- and total-oil contaminated areas were further enhanced. The use of multiple-stage water pumping was found to be insignificant compared to steady uniform pumping due to reduced recovery efficiency and increased residual oil volume. This observation was opposite to that produced under homogeneous scenarios. The effect of subsurface heterogeneity was enhanced at relatively low water pumping rates. The difference in results produced by homogeneous and heterogeneous simulations was substantial, indicating greater attention should be paid in modeling free-product recovery systems with appropriate subsurface heterogeneity.

Simulating oil droplet dispersal from the Deepwater Horizon spill with a Lagrangian approach

USGS Publications Warehouse

North, Elizabeth W.; Schlag, Zachary; Adams, E. Eric; Sherwood, Christopher R.; He, Ruoying; Hyun, Hoon; Socolofsky, Scott A.

2011-01-01

An analytical multiphase plume model, combined with time-varying flow and hydrographic fields generated by the 3-D South Atlantic Bight and Gulf of Mexico model (SABGOM) hydrodynamic model, were used as input to a Lagrangian transport model (LTRANS), to simulate transport of oil droplets dispersed at depth from the recent Deepwater Horizon MC 252 oil spill. The plume model predicts a stratification-dominated near field, in which small oil droplets detrain from the central plume containing faster rising large oil droplets and gas bubbles and become trapped by density stratification. Simulated intrusion (trap) heights of ∼ 310–370 m agree well with the midrange of conductivity-temperature-depth observations, though the simulated variation in trap height was lower than observed, presumably in part due to unresolved variability in source composition (percentage oil versus gas) and location (multiple leaks during first half of spill). Simulated droplet trajectories by the SABGOM-LTRANS modeling system showed that droplets with diameters between 10 and 50 μm formed a distinct subsurface plume, which was transported horizontally and remained in the subsurface for >1 month. In contrast, droplets with diameters ≥90 μm rose rapidly to the surface. Simulated trajectories of droplets ≤50 μm in diameter were found to be consistent with field observations of a southwest-tending subsurface plume in late June 2010 reported by Camilli et al. [2010]. Model results suggest that the subsurface plume looped around to the east, with potential subsurface oil transport to the northeast and southeast. Ongoing work is focusing on adding degradation processes to the model to constrain droplet dispersal.

Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation

PubMed Central

2011-01-01

Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH4+ production during urea hydrolysis were incorporated in the model and captured critical changes in the major metal species. The electrical phase increases were potentially due to ion exchange processes that modified charge structure at mineral/water interfaces. Our study revealed the potential of geophysical monitoring for geochemical changes during urea hydrolysis and the advantages of combining multiple approaches to understand complex biogeochemical processes in the subsurface. PMID:21943229

Impact of atmospheric forcing on heat content variability in the sub-surface layer in the Japan/East Sea, 1948-2009

NASA Astrophysics Data System (ADS)

Stepanov, Dmitry; Gusev, Anatoly; Diansky, Nikolay

2016-04-01

Based on numerical simulations the study investigates impact of atmospheric forcing on heat content variability of the sub-surface layer in Japan/East Sea (JES), 1948-2009. We developed a model configuration based on a INMOM model and atmospheric forcing extracted from the CORE phase II experiment dataset 1948-2009, which enables to assess impact of only atmospheric forcing on heat content variability of the sub-surface layer of the JES. An analysis of kinetic energy (KE) and total heat content (THC) in the JES obtained from our numerical simulations showed that the simulated circulation of the JES is being quasi-steady state. It was found that the year-mean KE variations obtained from our numerical simulations are similar those extracted from the SODA reanalysis. Comparison of the simulated THC and that extracted from the SODA reanalysis showed significant consistence between them. An analysis of numerical simulations showed that the simulated circulation structure is very similar that obtained from the PALACE floats in the intermediate and abyssal layers in the JES. Using empirical orthogonal function analysis we studied spatial-temporal variability of the heat content of the sub-surface layer in the JES. Based on comparison of the simulated heat content variations with those obtained from natural observations an assessment of the atmospheric forcing impact on the heat content variability was obtained. Using singular value decomposition analysis we considered relationships between the heat content variability and wind stress curl as well as sensible heat flux in winter. It was established the major role of sensible heat flux in decadal variability of the heat content of the sub-surface layer in the JES. The research was supported by the Russian Foundation for Basic Research (grant N 14-05-00255) and the Council on the Russian Federation President Grants (grant N MK-3241.2015.5)

Computational Evaluation of Mg–Salen Compounds as Subsurface Fluid Tracers: Molecular Dynamics Simulations in Toluene–Water Mixtures and Clay Mineral Nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.

Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less

Computational Evaluation of Mg–Salen Compounds as Subsurface Fluid Tracers: Molecular Dynamics Simulations in Toluene–Water Mixtures and Clay Mineral Nanopores

DOE PAGES

Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.

2018-04-11

Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less

Variation of subsurface chlorophyll maximum layer from the vertical profiler and in-situ observation in the eastern coastal region of Korea (the East/Japan Sea)

NASA Astrophysics Data System (ADS)

Son, Y. T.; Chang, K. I.; Nam, S.; Kang, D. J.

2016-02-01

Coastal monitoring buoy (called it as ESROB) has been continually operated to monitor meteorological (wind, air temperature, air pressure, PAR) and oceanic properties (temperature, salinity, current, chlorophyll fluorescence, DO, turbidity) using equipment such as CTD, fluorometer and WQM (Water Quality Monitor) in the eastern coastal region of Korea (the East/Japan Sea) since April 2011. The ESROB produced temporal evolution of physical and biogeochemical parameters of the water column with high resolution of 10 min interval. In order to understand horizontal influence of physical and biogeochemical parameters on variation of subsurface chlorophyll maximum layer (SCM), interdisciplinary in-situ surveys with small R/V in the study area for about week were conducted in June/October 2014 and in May 2015. A wirewalker, a wave-driven vertically profiling platform (Rainville and Pinkel 2001), was also deployed at two points (about 30 m and 80 m water depth) along cross-shore direction with the ESROB for about one or two weeks with in-situ survey durations. The wirewalker was equipped with CTD, turbidity and chlorophyll a fluorometer profiler, which was completed approximately every 3 10 minute depending on sea surface state. The SCM was observed in almost every deployment nearest coast, except for June in 2014, with variation of semi- and diurnal time periods. Temporal evolution of the wirewalker showed that disappearance and reoccurrence of the SCM within the water column in October 2014, which was associated with vertical mixing induced by strong wind stress. Low salinity plume in the surface layer and shoaling of bottom cold water were concurrently observed after homogeneous water column, affecting another condition to the vertical distribution of chlorophyll a in this coastal region. Moreover in-situ observation with densely points and temporal interval for 1 day revealed that distribution with high concentration of chlorophyll a on isopycnal was association with the horizontal local circulation that has influence on stability (vertical stratification and shear) of the water column. Optical and biogeochemical parameter analyzed from the water samples, affecting on the variation of chlorophyll a concentration within the water column, will be also discussed in the presentation of Ocean Science Meeting.

[Correlation of substrate structure and hydraulic characteristics in subsurface flow constructed wetlands].

PubMed

Bai, Shao-Yuan; Song, Zhi-Xin; Ding, Yan-Li; You, Shao-Hong; He, Shan

2014-02-01

The correlation of substrate structure and hydraulic characteristics was studied by numerical simulation combined with experimental method. The numerical simulation results showed that the permeability coefficient of matrix had a great influence on hydraulic efficiency in subsurface flow constructed wetlands. The filler with a high permeability coefficient had a worse flow field distribution in the constructed wetland with single layer structure. The layered substrate structure with the filler permeability coefficient increased from surface to bottom could avoid the short-circuited flow and dead-zones, and thus, increased the hydraulic efficiency. Two parallel pilot-scale constructed wetlands were built according to the numerical simulation results, and tracer experiments were conducted to validate the simulation results. The tracer experiment result showed that hydraulic characteristics in the layered constructed wetland were obviously better than that in the single layer system, and the substrate effective utilization rates were 0.87 and 0.49, respectively. It was appeared that numerical simulation would be favorable for substrate structure optimization in subsurface flow constructed wetlands.

Geoelectrical monitoring of simulated subsurface leakage to support high-hazard nuclear decommissioning at the Sellafield Site, UK.

PubMed

Kuras, Oliver; Wilkinson, Paul B; Meldrum, Philip I; Oxby, Lucy S; Uhlemann, Sebastian; Chambers, Jonathan E; Binley, Andrew; Graham, James; Smith, Nicholas T; Atherton, Nick

2016-10-01

A full-scale field experiment applying 4D (3D time-lapse) cross-borehole Electrical Resistivity Tomography (ERT) to the monitoring of simulated subsurface leakage was undertaken at a legacy nuclear waste silo at the Sellafield Site, UK. The experiment constituted the first application of geoelectrical monitoring in support of decommissioning work at a UK nuclear licensed site. Images of resistivity changes occurring since a baseline date prior to the simulated leaks revealed likely preferential pathways of silo liquor simulant flow in the vadose zone and upper groundwater system. Geophysical evidence was found to be compatible with historic contamination detected in permeable facies in sediment cores retrieved from the ERT boreholes. Results indicate that laterally discontinuous till units forming localized hydraulic barriers substantially affect flow patterns and contaminant transport in the shallow subsurface at Sellafield. We conclude that only geophysical imaging of the kind presented here has the potential to provide the detailed spatial and temporal information at the (sub-)meter scale needed to reduce the uncertainty in models of subsurface processes at nuclear sites. Copyright © 2016 British Geological Survey, NERC. Published by Elsevier B.V. All rights reserved.

Mineral Influence on Microbial Survival During Carbon Sequestration

NASA Astrophysics Data System (ADS)

Santillan, E. U.; Shanahan, T. M.; Wolfe, W. W.; Bennett, P.

2012-12-01

CO2 sequestered in a deep saline aquifer will perturb subsurface biogeochemistry by acidifying the groundwater and accelerating mineral diagenesis. Subsurface microbial communities heavily influence geochemistry through their metabolic processes, such as with dissimilatory iron reducing bacteria (DIRB). However, CO2 also acts as a sterilant and will perturb these communities. We investigated the role of mineralogy and its effect on the survival of microbes at high PCO2 conditions using the model DIRB Shewanella oneidensis MR-1. Batch cultures of Shewanella were grown to stationary phase and exposed to high PCO2 using modified Parr reactors. Cell viability was then determined by plating cultures after exposure. Results indicate that at low PCO2 (2 bar), growth and iron reduction are decreased and cell death occurs within 1 hour when exposed to CO2 pressures of 10 bar or greater. Further, fatty acid analysis indicates microbial lipid degradation with C18 fatty acids being the slowest lipids to degrade. When cultures were grown in the presence of rocks or minerals representative of the deep subsurface such as carbonates and silicates and exposed to 25 bar CO2, survival lasted beyond 2 hours. The most effective protecting substratum was quartz sandstone, with cultures surviving beyond 8 hours of CO2 exposure. Scanning electron microscope images reveal biofilm formation on the mineral surfaces with copious amounts of extracellular polymeric substances (EPS) present. EPS from these biofilms acts as a reactive barrier to the CO2, slowing the penetration of CO2 into cells and resulting in increased survival. When biofilm cultures were grown with Al and As to simulate the release of toxic metals from minerals such as feldspars and clays, survival time decreased, indicating mineralogy may also enhance microbial death. Biofilms were then grown on iron-coated quartz sand to determine conversely what influence biofilms may have on mineral dissolution during CO2 perturbation. Growth media was allowed to flow through a sand-packed column at a constant flow rate with pulses of liquid CO2 injected directly into the column. Preliminary data of dissolved iron measured from the effluent indicates that biofilm columns show a slight increase in dissolved iron concentrations before and after CO2 exposure in comparison to abiotic columns. These findings imply the important relationship between microbes and minerals during CO2 sequestration. The ability minerals have to contribute to the selection of microbes has important consequences to the survival of different microbial populations in the subsurface and the consequent biogeochemical changes that may happen.

Enhanced Remedial Amendment Delivery through Fluid Viscosity Modifications: Experiments and numerical simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong, Lirong; Oostrom, Martinus; Wietsma, Thomas W.

2008-07-29

Abstract Heterogeneity is often encountered in subsurface contamination characterization and remediation. Low-permeability zones are typically bypassed when remedial fluids are injected into subsurface heterogeneous aquifer systems. Therefore, contaminants in the bypassed areas may not be contacted by the amendments in the remedial fluid, which may significantly prolong the remediation operations. Laboratory experiments and numerical studies have been conducted to develop the Mobility-Controlled Flood (MCF) technology for subsurface remediation and to demonstrate the capability of this technology in enhancing the remedial amendments delivery to the lower permeability zones in heterogeneous systems. Xanthan gum, a bio-polymer, was used to modify the viscositymore » of the amendment-containing remedial solutions. Sodium mono-phosphate and surfactant were the remedial amendment used in this work. The enhanced delivery of the amendments was demonstrated in two-dimensional (2-D) flow cell experiments, packed with heterogeneous systems. The impact of polymer concentration, fluid injection rate, and permeability contract in the heterogeneous systems has been studied. The Subsurface Transport over Multiple Phases (STOMP) simulator was modified to include polymer-induced shear thinning effects. Shear rates of polymer solutions were computed from pore-water velocities using a relationship proposed in the literature. Viscosity data were subsequently obtained from empirical viscosity-shear rate relationships derived from laboratory data. The experimental and simulation results clearly show that the MCF technology is capable of enhancing the delivery of remedial amendments to subsurface lower permeability zones. The enhanced delivery significantly improved the NAPL removal from these zones and the sweeping efficiency on a heterogeneous system was remarkably increased when a polymer fluid was applied. MCF technology is also able to stabilize the fluid displacing front when there is a density difference between the fluids. The modified STOMP simulator was able to predict the experimental observed fluid displacing behavior. The simulator may be used to predict the subsurface remediation performance when a shear thinning fluid is used to remediate a heterogeneous system.« less

Controls on Nitrous Oxide Emissions from the Hyporheic Zones of Streams.

PubMed

Quick, Annika M; Reeder, W Jeffery; Farrell, Tiffany B; Tonina, Daniele; Feris, Kevin P; Benner, Shawn G

2016-11-01

The magnitude and mechanisms of nitrous oxide (N 2 O) release from rivers and streams are actively debated. The complex interactions of hydrodynamic and biogeochemical controls on emissions of this important greenhouse gas preclude prediction of when and where N 2 O emissions will be significant. We present observations from column and large-scale flume experiments supporting an integrative model of N 2 O emissions from stream sediments. Our results show a distinct, replicable, pattern of nitrous oxide generation and consumption dictated by subsurface (hyporheic) residence times and biological nitrogen reduction rates. Within this model, N 2 O emission from stream sediments requires subsurface residence times (and microbially mediated reduction rates) be sufficiently long (and fast reacting) to produce N 2 O by nitrate reduction but also sufficiently short (or slow reacting) to limit N 2 O conversion to dinitrogen gas. Most subsurface exchange will not result in N 2 O emissions; only specific, intermediate, residence times (reaction rates) will both produce and release N 2 O to the stream. We also confirm previous observations that elevated nitrate and declining organic carbon reactivity increase N 2 O production, highlighting the importance of associated reaction rates in controlling N 2 O accumulation. Combined, these observations help constrain when N 2 O release will occur, providing a predictive link between stream geomorphology, hydrodynamics, and N 2 O emissions.

A review on vegetation models and applicability to climate simulations at regional scale

NASA Astrophysics Data System (ADS)

Myoung, Boksoon; Choi, Yong-Sang; Park, Seon Ki

2011-11-01

The lack of accurate representations of biospheric components and their biophysical and biogeochemical processes is a great source of uncertainty in current climate models. The interactions between terrestrial ecosystems and the climate include exchanges not only of energy, water and momentum, but also of carbon and nitrogen. Reliable simulations of these interactions are crucial for predicting the potential impacts of future climate change and anthropogenic intervention on terrestrial ecosystems. In this paper, two biogeographical (Neilson's rule-based model and BIOME), two biogeochemical (BIOME-BGC and PnET-BGC), and three dynamic global vegetation models (Hybrid, LPJ, and MC1) were reviewed and compared in terms of their biophysical and physiological processes. The advantages and limitations of the models were also addressed. Lastly, the applications of the dynamic global vegetation models to regional climate simulations have been discussed.

Hydrologic and biogeochemical controls of river subsurface solutes under agriculturally enhanced ground water flow

USGS Publications Warehouse

Wildman, R.A.; Domagalski, Joseph L.; Hering, J.G.

2009-01-01

The relative influences of hydrologic processes and biogeochemistry on the transport and retention of minor solutes were compared in the riverbed of the lower Merced River (California, USA). The subsurface of this reach receives ground water discharge and surface water infiltration due to an altered hydraulic setting resulting from agricultural irrigation. Filtered ground water samples were collected from 30 drive point locations in March, June, and October 2004. Hydrologic processes, described previously, were verified by observations of bromine concentrations; manganese was used to indicate redox conditions. The separate responses of the minor solutes strontium, barium, uranium, and phosphorus to these influences were examined. Correlation and principal component analyses indicate that hydrologic processes dominate the distribution of trace elements in the ground water. Redox conditions appear to be independent of hydrologic processes and account for most of the remaining data variability. With some variability, major processes are consistent in two sampling transects separated by 100 m. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

NASA Astrophysics Data System (ADS)

Beller, H. R.; Han, R.; Karaoz, U.; Lim, H.; Brodie, E. L.

2012-12-01

Pelosinus species are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with Hanford 100H aquifer sediment (constituting 80% of the total bacterial population in the columns). Strain HCF1 ferments lactate to propionate and acetate (a complete fermentation pathway was identified in the genome) and its genome encodes both [NiFe]- and [FeFe]-hydrogenases for H2 cycling. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides. In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of nitrate reductases and hydrogenases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

The subsurface geology of Río Tinto: material examined during a simulated Mars drilling mission for the Mars Astrobiology Research and Technology Experiment (MARTE).

PubMed

Prieto-Ballesteros, Olga; Martínez-Frías, Jesús; Schutt, John; Sutter, Brad; Heldmann, Jennifer L; Bell, Mary Sue; Battler, Melissa; Cannon, Howard; Gómez-Elvira, Javier; Stoker, Carol R

2008-10-01

The 2005 Mars Astrobiology Research and Technology Experiment (MARTE) project conducted a simulated 1-month Mars drilling mission in the Río Tinto district, Spain. Dry robotic drilling, core sampling, and biological and geological analytical technologies were collectively tested for the first time for potential use on Mars. Drilling and subsurface sampling and analytical technologies are being explored for Mars because the subsurface is the most likely place to find life on Mars. The objectives of this work are to describe drilling, sampling, and analytical procedures; present the geological analysis of core and borehole material; and examine lessons learned from the drilling simulation. Drilling occurred at an undisclosed location, causing the science team to rely only on mission data for geological and biological interpretations. Core and borehole imaging was used for micromorphological analysis of rock, targeting rock for biological analysis, and making decisions regarding the next day's drilling operations. Drilling reached 606 cm depth into poorly consolidated gossan that allowed only 35% of core recovery and contributed to borehole wall failure during drilling. Core material containing any indication of biology was sampled and analyzed in more detail for its confirmation. Despite the poorly consolidated nature of the subsurface gossan, dry drilling was able to retrieve useful core material for geological and biological analysis. Lessons learned from this drilling simulation can guide the development of dry drilling and subsurface geological and biological analytical technologies for future Mars drilling missions.

The Subsurface Geology of Río Tinto: Material Examined During a Simulated Mars Drilling Mission for the Mars Astrobiology Research and Technology Experiment (MARTE)

NASA Astrophysics Data System (ADS)

Prieto-Ballesteros, Olga; Martínez-Frías, Jesús; Schutt, John; Sutter, Brad; Heldmann, Jennifer L.; Bell Johnson, Mary Sue; Battler, Melissa; Cannon, Howard; Gómez-Elvira, Javier; Stoker, Carol R.

2008-10-01

The 2005 Mars Astrobiology Research and Technology Experiment (MARTE) project conducted a simulated 1-month Mars drilling mission in the Río Tinto district, Spain. Dry robotic drilling, core sampling, and biological and geological analytical technologies were collectively tested for the first time for potential use on Mars. Drilling and subsurface sampling and analytical technologies are being explored for Mars because the subsurface is the most likely place to find life on Mars. The objectives of this work are to describe drilling, sampling, and analytical procedures; present the geological analysis of core and borehole material; and examine lessons learned from the drilling simulation. Drilling occurred at an undis closed location, causing the science team to rely only on mission data for geological and biological interpretations. Core and borehole imaging was used for micromorphological analysis of rock, targeting rock for biological analysis, and making decisions regarding the next day's drilling operations. Drilling reached 606 cm depth into poorly consolidated gossan that allowed only 35% of core recovery and contributed to borehole wall failure during drilling. Core material containing any indication of biology was sampled and analyzed in more detail for its confirmation. Despite the poorly consolidated nature of the subsurface gossan, dry drilling was able to retrieve useful core material for geological and biological analysis. Lessons learned from this drilling simulation can guide the development of dry drilling and subsurface geological and biological analytical technologies for future Mars drilling missions.

Mercury and methylmercury stream concentrations in a Coastal Plain watershed: a multi-scale simulation analysis.

PubMed

Knightes, C D; Golden, H E; Journey, C A; Davis, G M; Conrads, P A; Marvin-DiPasquale, M; Brigham, M E; Bradley, P M

2014-04-01

Mercury is a ubiquitous global environmental toxicant responsible for most US fish advisories. Processes governing mercury concentrations in rivers and streams are not well understood, particularly at multiple spatial scales. We investigate how insights gained from reach-scale mercury data and model simulations can be applied at broader watershed scales using a spatially and temporally explicit watershed hydrology and biogeochemical cycling model, VELMA. We simulate fate and transport using reach-scale (0.1 km(2)) study data and evaluate applications to multiple watershed scales. Reach-scale VELMA parameterization was applied to two nested sub-watersheds (28 km(2) and 25 km(2)) and the encompassing watershed (79 km(2)). Results demonstrate that simulated flow and total mercury concentrations compare reasonably to observations at different scales, but simulated methylmercury concentrations are out-of-phase with observations. These findings suggest that intricacies of methylmercury biogeochemical cycling and transport are under-represented in VELMA and underscore the complexity of simulating mercury fate and transport. Published by Elsevier Ltd.

Imaging lateral groundwater flow in the shallow subsurface using stochastic temperature fields

NASA Astrophysics Data System (ADS)

Fairley, Jerry P.; Nicholson, Kirsten N.

2006-04-01

Although temperature has often been used as an indication of vertical groundwater movement, its usefulness for identifying horizontal fluid flow has been limited by the difficulty of obtaining sufficient data to draw defensible conclusions. Here we use stochastic simulation to develop a high-resolution image of fluid temperatures in the shallow subsurface at Borax Lake, Oregon. The temperature field inferred from the geostatistical simulations clearly shows geothermal fluids discharging from a group of fault-controlled hydrothermal springs, moving laterally through the subsurface, and mixing with shallow subsurface flow originating from nearby Borax Lake. This interpretation of the data is supported by independent geochemical and isotopic evidence, which show a simple mixing trend between Borax Lake water and discharge from the thermal springs. It is generally agreed that stochastic simulation can be a useful tool for extracting information from complex and/or noisy data and, although not appropriate in all situations, geostatistical analysis may provide good definition of flow paths in the shallow subsurface. Although stochastic imaging techniques are well known in problems involving transport of species, e.g. delineation of contaminant plumes from soil gas survey data, we are unaware of previous applications to the transport of thermal energy for the purpose of inferring shallow groundwater flow.

Freeze-Thaw Cycles and Soil Biogeochemistry: Implications for Greenhouse Gas emission

NASA Astrophysics Data System (ADS)

Rezanezhad, F.; Milojevic, T.; Oh, D. H.; Parsons, C. T.; Smeaton, C. M.; Van Cappellen, P.

2016-12-01

Freeze-thaw cycles represent a major natural climate forcing acting on soils at middle and high latitudes. Repeated freezing and thawing of soils changes their physical properties, geochemistry, and microbial community structure, which together govern the biogeochemical cycling of carbon and nutrients. In this presentation, we focus on how freeze-thaw cycles regulate carbon and nitrogen cycling and how these transformations influence greenhouse gas (GHG) fluxes. We present a novel approach, which combines the acquisition of physical and chemical data in a newly developed experimental soil column system. This system simulates realistic soil temperature profiles during freeze-thaw cycles. A high-resolution, Multi-Fiber Optode (MuFO) microsensor technique was used to detect oxygen (O2) continuously in the column at multiple depths. Surface and subsurface changes to gas and aqueous phase chemistry were measured to delineate the pathways and quantify soil respiration rates during freeze-thaw cycles. The results indicate that the time-dependent release of GHG from the soil surface is influenced by a combination of two key factors. Firstly, fluctuations in temperature and O2 availability affect soil biogeochemical activity and GHG production. Secondly, the recurrent development of a physical ice barrier prevents exchange of gaseous compounds between the soil and atmosphere during freezing conditions; removal of this barrier during thaw conditions increases GHG fluxes. During freezing, O2 levels in the unsaturated zone decreased due to restricted gas exchange with the atmosphere. As the soil thawed, O2 penetrated deeper into the soil enhancing the aerobic mineralization of organic carbon and nitrogen. Additionally, with the onset of thawing a pulse of gas flux occurred, which is attributed to the build-up of respiratory gases in the pore space during freezing. The latter implies enhanced anaerobic respiration as O2 supply ceases when the upper soil layer freezes.

Cumulative Significance of Hyporheic Exchange and Biogeochemical Processing in River Networks

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Modeling microbial reaction rates in a submarine hydrothermal vent chimney wall

NASA Astrophysics Data System (ADS)

LaRowe, Douglas E.; Dale, Andrew W.; Aguilera, David R.; L'Heureux, Ivan; Amend, Jan P.; Regnier, Pierre

2014-01-01

The fluids emanating from active submarine hydrothermal vent chimneys provide a window into subseafloor processes and, through mixing with seawater, are responsible for steep thermal and compositional gradients that provide the energetic basis for diverse biological communities. Although several models have been developed to better understand the dynamic interplay of seawater, hydrothermal fluid, minerals and microorganisms inside chimney walls, none provide a fully integrated approach to quantifying the biogeochemistry of these hydrothermal systems. In an effort to remedy this, a fully coupled biogeochemical reaction-transport model of a hydrothermal vent chimney has been developed that explicitly quantifies the rates of microbial catalysis while taking into account geochemical processes such as fluid flow, solute transport and oxidation-reduction reactions associated with fluid mixing as a function of temperature. The metabolisms included in the reaction network are methanogenesis, aerobic oxidation of hydrogen, sulfide and methane and sulfate reduction by hydrogen and methane. Model results indicate that microbial catalysis is generally fastest in the hottest habitable portion of the vent chimney (77-102 °C), and methane and sulfide oxidation peak near the seawater-side of the chimney. The fastest metabolisms are aerobic oxidation of H2 and sulfide and reduction of sulfate by H2 with maximum rates of 140, 900 and 800 pmol cm-3 d-1, respectively. The maximum rate of hydrogenotrophic methanogenesis is just under 0.03 pmol cm-3 d-1, the slowest of the metabolisms considered. Due to thermodynamic inhibition, there is no anaerobic oxidation of methane by sulfate (AOM). These simulations are consistent with vent chimney metabolic activity inferred from phylogenetic data reported in the literature. The model developed here provides a quantitative approach to describing the rates of biogeochemical transformations in hydrothermal systems and can be used to constrain the role of microbial activity in the deep subsurface.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fenn, Mark E.; Driscoll, Charles; Zhou, Qingtao

2015-01-01

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

Biogeochemical metabolic modeling of methanogenesis by Methanosarcina barkeri

NASA Astrophysics Data System (ADS)

Jensvold, Z. D.; Jin, Q.

2015-12-01

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

Mercury mass balance in Lake Michigan--the knowns and unknowns

EPA Science Inventory

LM2-Mercury, a mercury mass balance model, was developed to simulate and evaluate the transport, fate, and biogeochemical transformations of mercury in Lake Michigan. The model simulates total suspended solids (TSS), disolved organic carbon (DOC), and total, elemental, divalent, ...

Environmental Assessment for Selection and Operation of the Proposed Field Research Centers for the Natural and Accelerated Bioremediation Research (NABIR) Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

N /A

2000-04-18

The US Department of Energy (DOE) Office of Biological and Environmental Research (OBER), within the Office of Science (SC), proposes to add a Field Research Center (FRC) component to the existing Natural and Accelerated Bioremediation Research (NABIR) Program. The NABIR Program is a ten-year fundamental research program designed to increase the understanding of fundamental biogeochemical processes that would allow the use of bioremediation approaches for cleaning up DOE's contaminated legacy waste sites. An FRC would be integrated with the existing and future laboratory and field research and would provide a means of examining the fundamental biogeochemical processes that influence bioremediationmore » under controlled small-scale field conditions. The NABIR Program would continue to perform fundamental research that might lead to promising bioremediation technologies that could be demonstrated by other means in the future. For over 50 years, DOE and its predecessor agencies have been responsible for the research, design, and production of nuclear weapons, as well as other energy-related research and development efforts. DOE's weapons production and research activities generated hazardous, mixed, and radioactive waste products. Past disposal practices have led to the contamination of soils, sediments, and groundwater with complex and exotic mixtures of compounds. This contamination and its associated costs and risks represents a major concern to DOE and the public. The high costs, long duration, and technical challenges associated with remediating the subsurface contamination at DOE sites present a significant need for fundamental research in the biological, chemical, and physical sciences that will contribute to new and cost-effective solutions. One possible low-cost approach for remediating the subsurface contamination of DOE sites is through the use of a technology known as bioremediation. Bioremediation has been defined as the use of microorganisms to biodegrade or biotransform hazardous organic contaminants to environmentally safe levels in soils, subsurface materials, water, sludges, and residues.. While bioremediation technology is promising, DOE managers and non-DOE scientists have recognized that the fundamental scientific information needed to develop effective bioremediation technologies for cleanup of the legacy waste sites is lacking in many cases. DOE believes that field-based research is needed to realize the full potential of bioremediation. The Department of Energy faces a unique set of challenges associated with cleaning up waste at its former weapons production and research sites. These sites contain complex mixtures of contaminants in the subsurface, including radioactive compounds. In many cases, the fundamental field-based scientific information needed to develop safe and effective remediation and cleanup technologies is lacking. DOE needs fundamental research on the use of microorganisms and their products to assist DOE in the decontamination and cleanup of its legacy waste sites. The existing NABIR program to-date has focused on fundamental scientific research in the laboratory. Because subsurface hydrologic and geologic conditions at contaminated DOE sites cannot easily be duplicated in a laboratory, however, the DOE needs a field component to permit existing and future laboratory research results to be field-tested on a small scale in a controlled outdoor setting. Such field-testing needs to be conducted under actual legacy waste field conditions representative of those that DOE is most in need of remediating. Ideally, these field conditions should be as representative as practicable of the types of subsurface contamination conditions that resulted from legacy wastes from the nuclear weapons program activities. They should also be representative of the types of hydrologic and geologic conditions that exist across the DOE complex.« less

Hydrological and associated biogeochemical consequences of rapid global warming during the Paleocene-Eocene Thermal Maximum

NASA Astrophysics Data System (ADS)

Carmichael, Matthew J.; Inglis, Gordon N.; Badger, Marcus P. S.; Naafs, B. David A.; Behrooz, Leila; Remmelzwaal, Serginio; Monteiro, Fanny M.; Rohrssen, Megan; Farnsworth, Alexander; Buss, Heather L.; Dickson, Alexander J.; Valdes, Paul J.; Lunt, Daniel J.; Pancost, Richard D.

2017-10-01

The Paleocene-Eocene Thermal Maximum (PETM) hyperthermal, 56 million years ago (Ma), is the most dramatic example of abrupt Cenozoic global warming. During the PETM surface temperatures increased between 5 and 9 °C and the onset likely took < 20 kyr. The PETM provides a case study of the impacts of rapid global warming on the Earth system, including both hydrological and associated biogeochemical feedbacks, and proxy data from the PETM can provide constraints on changes in warm climate hydrology simulated by general circulation models (GCMs). In this paper, we provide a critical review of biological and geochemical signatures interpreted as direct or indirect indicators of hydrological change at the PETM, explore the importance of adopting multi-proxy approaches, and present a preliminary model-data comparison. Hydrological records complement those of temperature and indicate that the climatic response at the PETM was complex, with significant regional and temporal variability. This is further illustrated by the biogeochemical consequences of inferred changes in hydrology and, in fact, changes in precipitation and the biogeochemical consequences are often conflated in geochemical signatures. There is also strong evidence in many regions for changes in the episodic and/or intra-annual distribution of precipitation that has not widely been considered when comparing proxy data to GCM output. Crucially, GCM simulations indicate that the response of the hydrological cycle to the PETM was heterogeneous - some regions are associated with increased precipitation - evaporation (P - E), whilst others are characterised by a decrease. Interestingly, the majority of proxy data come from the regions where GCMs predict an increase in PETM precipitation. We propose that comparison of hydrological proxies to GCM output can be an important test of model skill, but this will be enhanced by further data from regions of model-simulated aridity and simulation of extreme precipitation events.

An open, object-based modeling approach for simulating subsurface heterogeneity

NASA Astrophysics Data System (ADS)

Bennett, J.; Ross, M.; Haslauer, C. P.; Cirpka, O. A.

2017-12-01

Characterization of subsurface heterogeneity with respect to hydraulic and geochemical properties is critical in hydrogeology as their spatial distribution controls groundwater flow and solute transport. Many approaches of characterizing subsurface heterogeneity do not account for well-established geological concepts about the deposition of the aquifer materials; those that do (i.e. process-based methods) often require forcing parameters that are difficult to derive from site observations. We have developed a new method for simulating subsurface heterogeneity that honors concepts of sequence stratigraphy, resolves fine-scale heterogeneity and anisotropy of distributed parameters, and resembles observed sedimentary deposits. The method implements a multi-scale hierarchical facies modeling framework based on architectural element analysis, with larger features composed of smaller sub-units. The Hydrogeological Virtual Reality simulator (HYVR) simulates distributed parameter models using an object-based approach. Input parameters are derived from observations of stratigraphic morphology in sequence type-sections. Simulation outputs can be used for generic simulations of groundwater flow and solute transport, and for the generation of three-dimensional training images needed in applications of multiple-point geostatistics. The HYVR algorithm is flexible and easy to customize. The algorithm was written in the open-source programming language Python, and is intended to form a code base for hydrogeological researchers, as well as a platform that can be further developed to suit investigators' individual needs. This presentation will encompass the conceptual background and computational methods of the HYVR algorithm, the derivation of input parameters from site characterization, and the results of groundwater flow and solute transport simulations in different depositional settings.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

NASA Astrophysics Data System (ADS)

Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

2009-12-01

The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration of plutonium in the subsurface.

Insight from Genomics on Biogeochemical Cycles in a Shallow-Sea Hydrothermal System

NASA Astrophysics Data System (ADS)

Lu, G. S.; Amend, J.

2015-12-01

Shallow-sea hydrothermal ecosystems are dynamic, high-energy systems influenced by sunlight and geothermal activity. They provide accessible opportunities for investigating thermophilic microbial biogeochemical cycles. In this study, we report biogeochemical data from a shallow-sea hydrothermal system offshore Paleochori Bay, Milos, Greece, which is characterized by a central vent covered by white microbial mats with hydrothermally influenced sediments extending into nearby sea grass area. Geochemical analysis and deep sequencing provide high-resolution information on the geochemical patterns, microbial diversity and metabolic potential in a two-meter transect. The venting fluid is elevated in temperature (~70oC), low in pH (~4), and enriched in reduced species. The geochemical pattern shows that the profile is affected by not only seawater dilution but also microbial regulation. The microbial community in the deepest section of vent core (10-12 cm) is largely dominated by thermophilic archaea, including a methanogen and a recently described Crenarcheon. Mid-core (6-8 cm), the microbial community in the venting area switches to the hydrogen utilizer Aquificae. Near the sediment-water interface, anaerobic Firmicutes and Actinobacteria dominate, both of which are commonly associated with subsurface and hydrothermal sites. All other samples are dominated by diverse Proteobacteria. The sulfate profile is strongly correlated with the population size of delta- and episilon-proteobactia. The dramatic decrease in concentrations of As and Mn in pore fluids as a function of distance from the vent suggests that in addition to seawater dilution, microorganisms are likely transforming these and other ions through a combination of detoxification and catabolism. In addition, high concentrations of dissolved Fe are only measurable in the shallow sea grass area, suggesting that iron-transforming microorganisms are controlling Fe mobility, and promoting biomineralization. Taken together, these samples represent the effects of submarine venting on sediment microbial communities both vertically and horizontally in the predicted fluid flow path, and will provide a detailed investigation of genetic potential for biogeochemical cycling at Paleochori Bay.

Long-term ERT monitoring of biogeochemical changes of an aged hydrocarbon contamination.

PubMed

Caterina, David; Flores Orozco, Adrian; Nguyen, Frédéric

2017-06-01

Adequate management of contaminated sites requires information with improved spatio-temporal resolution, in particular to assess bio-geochemical processes, such as the transformation and degradation of contaminants, precipitation of minerals or changes in groundwater geochemistry occurring during and after remediation procedures. Electrical Resistivity Tomography (ERT), a geophysical method sensitive to pore-fluid and pore-geometry properties, permits to gain quasi-continuous information about subsurface properties in real-time and has been consequently widely used for the characterization of hydrocarbon-impacted sediments. However, its application for the long-term monitoring of processes accompanying natural or engineered bioremediation is still difficult due to the poor understanding of the role that biogeochemical processes play in the electrical signatures. For in-situ studies, the task is further complicated by the variable signal-to-noise ratio and the variations of environmental parameters leading to resolution changes in the electrical images. In this work, we present ERT imaging results for data collected over a period of two years on a site affected by a diesel fuel contamination and undergoing bioremediation. We report low electrical resistivity anomalies in areas associated to the highest contaminant concentrations likely due transformations of the contaminant due to microbial activity and accompanying release of metabolic products. We also report large seasonal variations of the bulk electrical resistivity in the contaminated areas in correlation with temperature and groundwater level fluctuations. However, the amplitude of bulk electrical resistivity variations largely exceeds the amplitude expected given existing petrophysical models. Our results suggest that the variations in electrical properties are mainly controlled by microbial activity which in turn depends on soil temperature and hydrogeological conditions. Therefore, ERT can be suggested as a promising tool to track microbial activity during bioremediation even though further research is still needed to completely understand the bio-geochemical processes involved and their impact on electrical signatures. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-term ERT monitoring of biogeochemical changes of an aged hydrocarbon contamination

NASA Astrophysics Data System (ADS)

Caterina, David; Flores Orozco, Adrian; Nguyen, Frédéric

2017-06-01

Adequate management of contaminated sites requires information with improved spatio-temporal resolution, in particular to assess bio-geochemical processes, such as the transformation and degradation of contaminants, precipitation of minerals or changes in groundwater geochemistry occurring during and after remediation procedures. Electrical Resistivity Tomography (ERT), a geophysical method sensitive to pore-fluid and pore-geometry properties, permits to gain quasi-continuous information about subsurface properties in real-time and has been consequently widely used for the characterization of hydrocarbon-impacted sediments. However, its application for the long-term monitoring of processes accompanying natural or engineered bioremediation is still difficult due to the poor understanding of the role that biogeochemical processes play in the electrical signatures. For in-situ studies, the task is further complicated by the variable signal-to-noise ratio and the variations of environmental parameters leading to resolution changes in the electrical images. In this work, we present ERT imaging results for data collected over a period of two years on a site affected by a diesel fuel contamination and undergoing bioremediation. We report low electrical resistivity anomalies in areas associated to the highest contaminant concentrations likely due transformations of the contaminant due to microbial activity and accompanying release of metabolic products. We also report large seasonal variations of the bulk electrical resistivity in the contaminated areas in correlation with temperature and groundwater level fluctuations. However, the amplitude of bulk electrical resistivity variations largely exceeds the amplitude expected given existing petrophysical models. Our results suggest that the variations in electrical properties are mainly controlled by microbial activity which in turn depends on soil temperature and hydrogeological conditions. Therefore, ERT can be suggested as a promising tool to track microbial activity during bioremediation even though further research is still needed to completely understand the bio-geochemical processes involved and their impact on electrical signatures.

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

PubMed

Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling. © 2016 John Wiley & Sons Ltd.

Nutrient transports in the Baltic Sea - results from a 30-year physical-biogeochemical reanalysis

NASA Astrophysics Data System (ADS)

Liu, Ye; Meier, H. E. Markus; Eilola, Kari

2017-04-01

Long-term oxygen and nutrient transports in the Baltic Sea are reconstructed using the Swedish Coastal and Ocean Biogeochemical model (SCOBI) coupled to the Rossby Centre Ocean model (RCO). Two simulations with and without data assimilation covering the period 1970-1999 are carried out. Here, the weakly coupled scheme with the Ensemble Optimal Interpolation (EnOI) method is adopted to assimilate observed profiles in the reanalysis system. The reanalysis shows considerable improvement in the simulation of both oxygen and nutrient concentrations relative to the free run. Further, the results suggest that the assimilation of biogeochemical observations has a significant effect on the simulation of the oxygen-dependent dynamics of biogeochemical cycles. From the reanalysis, nutrient transports between sub-basins, between the coastal zone and the open sea, and across latitudinal and longitudinal cross sections are calculated. Further, the spatial distributions of regions with nutrient import or export are examined. Our results emphasize the important role of the Baltic proper for the entire Baltic Sea, with large net transport (export minus import) of nutrients from the Baltic proper into the surrounding sub-basins (except the net phosphorus import from the Gulf of Riga and the net nitrogen import from the Gulf of Riga and Danish Straits). In agreement with previous studies, we found that the Bothnian Sea imports large amounts of phosphorus from the Baltic proper that are retained in this sub-basin. For the calculation of sub-basin budgets, the location of the lateral borders of the sub-basins is crucial, because net transports may change sign with the location of the border. Although the overall transport patterns resemble the results of previous studies, our calculated estimates differ in detail considerably.

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

NASA Astrophysics Data System (ADS)

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

2003-12-01

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

Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions.

PubMed

Pearce, Carolyn I; Wilkins, Michael J; Zhang, Changyong; Heald, Steve M; Fredrickson, Jim K; Zachara, John M

2012-08-07

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced in the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting reoxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.

Scenario simulation based assessment of subsurface energy storage

NASA Astrophysics Data System (ADS)

Beyer, C.; Bauer, S.; Dahmke, A.

2014-12-01

Energy production from renewable sources such as solar or wind power is characterized by temporally varying power supply. The politically intended transition towards renewable energies in Germany („Energiewende") hence requires the installation of energy storage technologies to compensate for the fluctuating production. In this context, subsurface energy storage represents a viable option due to large potential storage capacities and the wide prevalence of suited geological formations. Technologies for subsurface energy storage comprise cavern or deep porous media storage of synthetic hydrogen or methane from electrolysis and methanization, or compressed air, as well as heat storage in shallow or moderately deep porous formations. Pressure build-up, fluid displacement or temperature changes induced by such operations may affect local and regional groundwater flow, geomechanical behavior, groundwater geochemistry and microbiology. Moreover, subsurface energy storage may interact and possibly be in conflict with other "uses" like drinking water abstraction or ecological goods and functions. An utilization of the subsurface for energy storage therefore requires an adequate system and process understanding for the evaluation and assessment of possible impacts of specific storage operations on other types of subsurface use, the affected environment and protected entities. This contribution presents the framework of the ANGUS+ project, in which tools and methods are developed for these types of assessments. Synthetic but still realistic scenarios of geological energy storage are derived and parameterized for representative North German storage sites by data acquisition and evaluation, and experimental work. Coupled numerical hydraulic, thermal, mechanical and reactive transport (THMC) simulation tools are developed and applied to simulate the energy storage and subsurface usage scenarios, which are analyzed for an assessment and generalization of the imposed THMC-processes, mutual effects and influences on protected entities. The scenario analyses allow the deduction of monitoring concepts as well as a first methodology for large scale spatial planning of the geological subsurface. This concept is illustrated for different storage options and their impacts in space and time.

Carbonate Platform Development and Stromatolite Morphogenesis: Constraints on Environmental and Biological Evolution

NASA Technical Reports Server (NTRS)

Grotzinger, John P.

2002-01-01

Work this past year has focused on the globally significant events of faunal turnover, tectonic reorganization, and biogeochemical change that closely coincided with the Precambrian-Cambrian boundary in the Sultanate oilman. Higher temporal and chronostratigraphic resolution are required in order to answer this question. Stratigraphic sections must contain fossils, volcanic rocks, and abundant carbonates with little or no diagenetic overprint. The Ara Group of the South Oman Salt Basin presents such a succession - with carbonate rocks tightly enclosed in a protective envelope of impermeable halite, these rocks have likely never exchanged with younger fluids. Our work has had two thrusts. The first pertains to the geochemistry of the Athel Formation, a deep water deposit formed at the Precambrian-Cambrian boundary which contains unique records of ocean anoxia for that time interval. This unit is important because it will enable tighter focus on the links which existed between global biogeochemical events and episodes of faunal extinction and radiation. The second direction involves a comparison of terminal Proterozoic thrombolites between Oman (subsurface) and Namibia (outcrop). These thrombolites are important not only as significant deposits of ancient microbial communities, but because they formed the key substrate for growth of the oldest calcified metazoans - Cloudina and Namacalathus.

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

NASA Technical Reports Server (NTRS)

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

Finding the best windows: An apparent environmental threshold determines which diffuse flows are dominated by subsurface microbes

NASA Astrophysics Data System (ADS)

Olins, H. C.; Rogers, D.; Scholin, C. A.; Preston, C. J.; Vidoudez, C.; Ussler, W.; Pargett, D.; Jensen, S.; Roman, B.; Birch, J. M.; Girguis, P. R.

2014-12-01

Hydrothermal vents are hotspots of microbial primary productivity often described as "windows into the subsurface biosphere." High temperature vents have received the majority of research attention, but cooler diffuse flows are as, if not more, important a source of heat and chemicals to the overlying ocean. We studied patterns of in situ gene expression and co-registered geochemistry in order to 1) describe the diversity and physiological poise of active microbial communities that span thermal and geochemical gradients from active diffuse flow to background vent field seawater, and 2) determine to what extent seawater or subsurface microbes were active throughout this environment. Analyses of multiple metatranscriptomes from 5 geochemically distinct sites (some from samples preserved in situ) show that proximate diffuse flows showed strikingly different transcription profiles. Specifically, caldera background and some diffuse flows were similar, both dominated by seawater-derived Gammaproteobacteria despite having distinct geochemistries. Intra-field community shows evidence of increased primary productivity throughout the entire vent field and not just at individual diffuse flows. In contrast, a more spatially limited, Epsilonproteobacteria-dominated transcription profile from the most hydrothermally-influenced diffuse flow appeared to be driven by the activity of vent-endemic microbes, likely reflecting subsurface microbial activity. We suggest that the microbial activity within many diffuse flow vents is primarily attributable to seawater derived Gammaproteobacterial sulfur oxidizers, while in certain other flows vent-endemic Epsilonproteobactiera are most active. These data reveal a diversity in microbial activity at diffuse flows that has not previously been recognized, and reshapes our thinking about the relative influence that different microbial communities may have on local processes (such as primary production) and potentially global biogeochemical cycles.

Corn stover harvest increases herbicide movement to subsurface drains: RZWQM simulations

USGS Publications Warehouse

Shipitalo, Martin J.; Malone, Robert W.; Ma, Liwang; Nolan, Bernard T.; Kanwar, Rameshwar S.; Shaner, Dale L.; Pederson, Carl H.

2016-01-01

BACKGROUND Crop residue removal for bioenergy production can alter soil hydrologic properties and the movement of agrochemicals to subsurface drains. The Root Zone Water Quality Model (RZWQM), previously calibrated using measured flow and atrazine concentrations in drainage from a 0.4 ha chisel-tilled plot, was used to investigate effects of 50 and 100% corn (Zea mays L.) stover harvest and the accompanying reductions in soil crust hydraulic conductivity and total macroporosity on transport of atrazine, metolachlor, and metolachlor oxanilic acid (OXA). RESULTS The model accurately simulated field-measured metolachlor transport in drainage. A 3-yr simulation indicated that 50% residue removal decreased subsurface drainage by 31% and increased atrazine and metolachlor transport in drainage 4 to 5-fold when surface crust conductivity and macroporosity were reduced by 25%. Based on its measured sorption coefficient, ~ 2-fold reductions in OXA losses were simulated with residue removal. CONCLUSION RZWQM indicated that if corn stover harvest reduces crust conductivity and soil macroporosity, losses of atrazine and metolachlor in subsurface drainage will increase due to reduced sorption related to more water moving through fewer macropores. Losses of the metolachlor degradation product OXA will decrease due to the more rapid movement of the parent compound into the soil.

Review and analysis of strengths and weaknesses of agro-ecosystem models for simulating C and N fluxes.

PubMed

Brilli, Lorenzo; Bechini, Luca; Bindi, Marco; Carozzi, Marco; Cavalli, Daniele; Conant, Richard; Dorich, Cristopher D; Doro, Luca; Ehrhardt, Fiona; Farina, Roberta; Ferrise, Roberto; Fitton, Nuala; Francaviglia, Rosa; Grace, Peter; Iocola, Ileana; Klumpp, Katja; Léonard, Joël; Martin, Raphaël; Massad, Raia Silvia; Recous, Sylvie; Seddaiu, Giovanna; Sharp, Joanna; Smith, Pete; Smith, Ward N; Soussana, Jean-Francois; Bellocchi, Gianni

2017-11-15

Biogeochemical simulation models are important tools for describing and quantifying the contribution of agricultural systems to C sequestration and GHG source/sink status. The abundance of simulation tools developed over recent decades, however, creates a difficulty because predictions from different models show large variability. Discrepancies between the conclusions of different modelling studies are often ascribed to differences in the physical and biogeochemical processes incorporated in equations of C and N cycles and their interactions. Here we review the literature to determine the state-of-the-art in modelling agricultural (crop and grassland) systems. In order to carry out this study, we selected the range of biogeochemical models used by the CN-MIP consortium of FACCE-JPI (http://www.faccejpi.com): APSIM, CERES-EGC, DayCent, DNDC, DSSAT, EPIC, PaSim, RothC and STICS. In our analysis, these models were assessed for the quality and comprehensiveness of underlying processes related to pedo-climatic conditions and management practices, but also with respect to time and space of application, and for their accuracy in multiple contexts. Overall, it emerged that there is a possible impact of ill-defined pedo-climatic conditions in the unsatisfactory performance of the models (46.2%), followed by limitations in the algorithms simulating the effects of management practices (33.1%). The multiplicity of scales in both time and space is a fundamental feature, which explains the remaining weaknesses (i.e. 20.7%). Innovative aspects have been identified for future development of C and N models. They include the explicit representation of soil microbial biomass to drive soil organic matter turnover, the effect of N shortage on SOM decomposition, the improvements related to the production and consumption of gases and an adequate simulations of gas transport in soil. On these bases, the assessment of trends and gaps in the modelling approaches currently employed to represent biogeochemical cycles in crop and grassland systems appears an essential step for future research. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (3DFATMIC) Model

EPA Pesticide Factsheets

This model simulates subsurface flow, fate and transport of contaminants that are undergoing chemical or biological transformations. The model is applicable to transient conditions in both saturated and unsaturated zones.

Two-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (2DFATMIC) Model

EPA Pesticide Factsheets

This model simulates subsurface flow, fate, and transport of contaminants that are undergoing chemical or biological transformations. This model is applicable to transient conditions in both saturated and unsaturated zones.

On the effects of subsurface parameters on evaporite dissolution (Switzerland)

NASA Astrophysics Data System (ADS)

Zidane, Ali; Zechner, Eric; Huggenberger, Peter; Younes, Anis

2014-05-01

Uncontrolled subsurface evaporite dissolution could lead to hazards such as land subsidence. Observed subsidences in a study area of Northwestern Switzerland were mainly due to subsurface dissolution (subrosion) of evaporites such as halite and gypsum. A set of 2D density driven flow simulations were evaluated along 1000 m long and 150 m deep 2D cross sections within the study area that is characterized by tectonic horst and graben structures. The simulations were conducted to study the effect of the different subsurface parameters that could affect the dissolution process. The heterogeneity of normal faults and its impact on the dissolution of evaporites is studied by considering several permeable faults that include non-permeable areas. The mixed finite element method (MFE) is used to solve the flow equation, coupled with the multipoint flux approximation (MPFA) and the discontinuous Galerkin method (DG) to solve the diffusion and the advection parts of the transport equation.

Hyperresolution Global Land Surface Modeling: Meeting a Grand Challenge for Monitoring Earth's Terrestrial Water

NASA Technical Reports Server (NTRS)

Wood, Eric F.; Roundy, Joshua K.; Troy, Tara J.; van Beek, L. P. H.; Bierkens, Marc F. P.; 4 Blyth, Eleanor; de Roo, Ad; Doell. Petra; Ek, Mike; Famiglietti, James;

Hyperresolution global land surface modeling: Meeting a grand challenge for monitoring Earth's terrestrial water

NASA Astrophysics Data System (ADS)

Wood, Eric F.; Roundy, Joshua K.; Troy, Tara J.; van Beek, L. P. H.; Bierkens, Marc F. P.; Blyth, Eleanor; de Roo, Ad; DöLl, Petra; Ek, Mike; Famiglietti, James; Gochis, David; van de Giesen, Nick; Houser, Paul; Jaffé, Peter R.; Kollet, Stefan; Lehner, Bernhard; Lettenmaier, Dennis P.; Peters-Lidard, Christa; Sivapalan, Murugesu; Sheffield, Justin; Wade, Andrew; Whitehead, Paul

2011-05-01

Monitoring Earth's terrestrial water conditions is critically important to many hydrological applications such as global food production; assessing water resources sustainability; and flood, drought, and climate change prediction. These needs have motivated the development of pilot monitoring and prediction systems for terrestrial hydrologic and vegetative states, but to date only at the rather coarse spatial resolutions (˜10-100 km) over continental to global domains. Adequately addressing critical water cycle science questions and applications requires systems that are implemented globally at much higher resolutions, on the order of 1 km, resolutions referred to as hyperresolution in the context of global land surface models. This opinion paper sets forth the needs and benefits for a system that would monitor and predict the Earth's terrestrial water, energy, and biogeochemical cycles. We discuss six major challenges in developing a system: improved representation of surface-subsurface interactions due to fine-scale topography and vegetation; improved representation of land-atmospheric interactions and resulting spatial information on soil moisture and evapotranspiration; inclusion of water quality as part of the biogeochemical cycle; representation of human impacts from water management; utilizing massively parallel computer systems and recent computational advances in solving hyperresolution models that will have up to 109 unknowns; and developing the required in situ and remote sensing global data sets. We deem the development of a global hyperresolution model for monitoring the terrestrial water, energy, and biogeochemical cycles a "grand challenge" to the community, and we call upon the international hydrologic community and the hydrological science support infrastructure to endorse the effort.

Information content of in situ and remotely sensed chlorophyll-a: Learning from size-structured phytoplankton model

NASA Astrophysics Data System (ADS)

Laiolo, Leonardo; Matear, Richard; Baird, Mark E.; Soja-Woźniak, Monika; Doblin, Martina A.

2018-07-01

Chlorophyll-a measurements in the form of in situ observations and satellite ocean colour products are commonly used in data assimilation to calibrate marine biogeochemical models. Here, a two size-class phytoplankton biogeochemical model, with a 0D configuration, was used to simulate the surface chlorophyll-a dynamics (simulated surface Chl-a) for cyclonic and anticyclonic eddies off East Australia. An optical model was then used to calculate the inherent optical properties from the simulation and convert them into remote-sensing reflectance (Rrs). Subsequently, Rrs was used to produce a satellite-like estimate of the simulated surface Chl-a concentrations through the MODIS OC3M algorithm (simulated OC3M Chl-a). Identical parameter optimisation experiments were performed through the assimilation of the two separate datasets (simulated surface Chl-a and simulated OC3M Chl-a), with the purpose of investigating the contrasting information content of simulated surface Chl-a and remotely-sensed data sources. The results we present are based on the analysis of the distribution of a cost function, varying four parameters of the biogeochemical model. In our idealized experiments the simulated OC3M Chl-a product is a poor proxy for the total simulated surface Chl-a concentration. Furthermore, our result show the OC3M algorithm can underestimate the simulated chlorophyll-a concentration in offshore eddies off East Australia (Case I waters), because of the weak relationship between large-sized phytoplankton and remote-sensing reflectance. Although Case I waters are usually characteristic of oligotrophic environments, with a photosynthetic community typically represented by relatively small-sized phytoplankton, mesoscale features such as eddies can generate seasonally favourable conditions for a photosynthetic community with a greater proportion of large phytoplankton cells. Furthermore, our results show that in mesoscale features such as eddies, in situ chlorophyll-a observations and the ocean colour products can carry different information related to phytoplankton sizes. Assimilating both remote-sensing reflectance and measurements of in situ chlorophyll-a concentration reduces the uncertainty of the parameter values more than either data set alone, thus reducing the spread of acceptable solutions, giving an improved simulation of the natural environment.

Abiotic/biotic coupling in the rhizosphere: a reactive transport modeling analysis

USGS Publications Warehouse

Lawrence, Corey R.; Steefel, Carl; Maher, Kate

2014-01-01

A new generation of models is needed to adequately simulate patterns of soil biogeochemical cycling in response changing global environmental drivers. For example, predicting the influence of climate change on soil organic matter storage and stability requires models capable of addressing complex biotic/abiotic interactions of rhizosphere and weathering processes. Reactive transport modeling provides a powerful framework simulating these interactions and the resulting influence on soil physical and chemical characteristics. Incorporation of organic reactions in an existing reactive transport model framework has yielded novel insights into soil weathering and development but much more work is required to adequately capture root and microbial dynamics in the rhizosphere. This endeavor provides many advantages over traditional soil biogeochemical models but also many challenges.

SeSBench - An initiative to benchmark reactive transport models for environmental subsurface processes

NASA Astrophysics Data System (ADS)

Jacques, Diederik

2017-04-01

As soil functions are governed by a multitude of interacting hydrological, geochemical and biological processes, simulation tools coupling mathematical models for interacting processes are needed. Coupled reactive transport models are a typical example of such coupled tools mainly focusing on hydrological and geochemical coupling (see e.g. Steefel et al., 2015). Mathematical and numerical complexity for both the tool itself or of the specific conceptual model can increase rapidly. Therefore, numerical verification of such type of models is a prerequisite for guaranteeing reliability and confidence and qualifying simulation tools and approaches for any further model application. In 2011, a first SeSBench -Subsurface Environmental Simulation Benchmarking- workshop was held in Berkeley (USA) followed by four other ones. The objective is to benchmark subsurface environmental simulation models and methods with a current focus on reactive transport processes. The final outcome was a special issue in Computational Geosciences (2015, issue 3 - Reactive transport benchmarks for subsurface environmental simulation) with a collection of 11 benchmarks. Benchmarks, proposed by the participants of the workshops, should be relevant for environmental or geo-engineering applications; the latter were mostly related to radioactive waste disposal issues - excluding benchmarks defined for pure mathematical reasons. Another important feature is the tiered approach within a benchmark with the definition of a single principle problem and different sub problems. The latter typically benchmarked individual or simplified processes (e.g. inert solute transport, simplified geochemical conceptual model) or geometries (e.g. batch or one-dimensional, homogeneous). Finally, three codes should be involved into a benchmark. The SeSBench initiative contributes to confidence building for applying reactive transport codes. Furthermore, it illustrates the use of those type of models for different environmental and geo-engineering applications. SeSBench will organize new workshops to add new benchmarks in a new special issue. Steefel, C. I., et al. (2015). "Reactive transport codes for subsurface environmental simulation." Computational Geosciences 19: 445-478.

Subsurface conditions in hydrothermal vents inferred from diffuse flow composition, and models of reaction and transport

NASA Astrophysics Data System (ADS)

Larson, B. I.; Houghton, J. L.; Lowell, R. P.; Farough, A.; Meile, C. D.

2015-08-01

Chemical gradients in the subsurface of mid-ocean ridge hydrothermal systems create an environment where minerals precipitate and dissolve and where chemosynthetic organisms thrive. However, owing to the lack of easy access to the subsurface, robust knowledge of the nature and extent of chemical transformations remains elusive. Here, we combine measurements of vent fluid chemistry with geochemical and transport modeling to give new insights into the under-sampled subsurface. Temperature-composition relationships from a geochemical mixing model are superimposed on the subsurface temperature distribution determined using a heat flow model to estimate the spatial distribution of fluid composition. We then estimate the distribution of Gibb's free energies of reaction beneath mid oceanic ridges and by combining flow simulations with speciation calculations estimate anhydrite deposition rates. Applied to vent endmembers observed at the fast spreading ridge at the East Pacific Rise, our results suggest that sealing times due to anhydrite formation are longer than the typical time between tectonic and magmatic events. The chemical composition of the neighboring low temperature flow indicates relatively uniform energetically favorable conditions for commonly inferred microbial processes such as methanogenesis, sulfate reduction and numerous oxidation reactions, suggesting that factors other than energy availability may control subsurface microbial biomass distribution. Thus, these model simulations complement fluid-sample datasets from surface venting and help infer the chemical distribution and transformations in subsurface flow.

Depth dependency of neutron density produced by cosmic rays in the lunar subsurface

NASA Astrophysics Data System (ADS)

Ota, S.; Sihver, L.; Kobayashi, S.; Hasebe, N.

2014-11-01

Depth dependency of neutrons produced by cosmic rays (CRs) in the lunar subsurface was estimated using the three-dimensional Monte Carlo particle and heavy ion transport simulation code, PHITS, incorporating the latest high energy nuclear data, JENDL/HE-2007. The PHITS simulations of equilibrium neutron density profiles in the lunar subsurface were compared with the measurement by Apollo 17 Lunar Neutron Probe Experiment (LNPE). Our calculations reproduced the LNPE data except for the 350-400 mg/cm2 region under the improved condition using the CR spectra model based on the latest observations, well-tested nuclear interaction models with systematic cross section data, and JENDL/HE-2007.

Marine Biogeochemistry Under The Influence of Fish And Fisheries: An Ecosystem Modeling Study

NASA Astrophysics Data System (ADS)

Disa, Deniz; Akoglu, Ekin; Salihoglu, Baris

2017-04-01

The ocean and the marine ecosystems are important controllers of the global carbon cycle. They play a pivotal role in capturing atmospheric carbon into the ocean body, transforming it into organic carbon through photosynthesis and transporting it to the depths of the ocean. Fish, which has a significant role in the marine food webs, is thought to have a considerable impact on carbon export. More specifically, fish has a control on plankton dynamics as a predator, it provides nutrient to the ecosystem by its metabolic activities and it has the ability of moving actively and transporting materials. Fishing is also expected to impact carbon cycle because it directly changes the fish biomasses. However, how fish impacts the biogeochemistry of marine ecosystems is not studied extensively. The aim of this study is to analyze the impact of fish and fisheries on marine biogeochemical processes by setting up an end-to-end model, which simulates lower and higher tropic levels of marine ecosystems simultaneously. For this purpose, a one dimensional biogeochemical model simulating lower tropic level dynamics (e.g. carbon export, nutrient cycles) and an food web model simulating fisheries exploitation and higher tropic level dynamics were online and two-way coupled. Representing the marine ecosystem from one end to the other, the coupled model served as a tool for the analysis of fishing impacts on marine biogeochemical dynamics. Results obtained after incorporation of higher trophic level model changed the plankton compositions and enhanced detritus pools and increased carbon export. Additionally, our model showed that active movement of fish contributed to transport of carbon from surface to the deeper parts of the ocean. Moreover, results after applying different fishing intensities indicated that changes in fisheries exploitation levels directly influence the marine nutrient cycles and hence, the carbon export. Depending on the target and the intensity of fisheries, considerable changes in the biogeochemical responses observed. In conclusion, unlike the models that do not represent the fish explicitly, we demonstrate how marine biogeochemical processes are impacted by the activity of fish assemblages and fisheries exploitation.

Quantifying the influence of the terrestrial biosphere on glacial-interglacial climate dynamics

NASA Astrophysics Data System (ADS)

Davies-Barnard, Taraka; Ridgwell, Andy; Singarayer, Joy; Valdes, Paul

2017-10-01

The terrestrial biosphere is thought to be a key component in the climatic variability seen in the palaeo-record. It has a direct impact on surface temperature through changes in surface albedo and evapotranspiration (so-called biogeophysical effects) and, in addition, has an important indirect effect through changes in vegetation and soil carbon storage (biogeochemical effects) and hence modulates the concentrations of greenhouse gases in the atmosphere. The biogeochemical and biogeophysical effects generally have opposite signs, meaning that the terrestrial biosphere could potentially have played only a very minor role in the dynamics of the glacial-interglacial cycles of the late Quaternary. Here we use a fully coupled dynamic atmosphere-ocean-vegetation general circulation model (GCM) to generate a set of 62 equilibrium simulations spanning the last 120 kyr. The analysis of these simulations elucidates the relative importance of the biogeophysical versus biogeochemical terrestrial biosphere interactions with climate. We find that the biogeophysical effects of vegetation account for up to an additional -0.91 °C global mean cooling, with regional cooling as large as -5 °C, but with considerable variability across the glacial-interglacial cycle. By comparison, while opposite in sign, our model estimates of the biogeochemical impacts are substantially smaller in magnitude. Offline simulations show a maximum of +0.33 °C warming due to an increase of 25 ppm above our (pre-industrial) baseline atmospheric CO2 mixing ratio. In contrast to shorter (century) timescale projections of future terrestrial biosphere response where direct and indirect responses may at times cancel out, we find that the biogeophysical effects consistently and strongly dominate the biogeochemical effect over the inter-glacial cycle. On average across the period, the terrestrial biosphere has a -0.26 °C effect on temperature, with -0.58 °C at the Last Glacial Maximum. Depending on assumptions made about the destination of terrestrial carbon under ice sheets and where sea level has changed, the average terrestrial biosphere contribution over the last 120 kyr could be as much as -50 °C and -0.83 °C at the Last Glacial Maximum.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aleman, S.E.

This report documents a finite element code designed to model subsurface flow and contaminant transport, named FACT. FACT is a transient three-dimensional, finite element code designed to simulate isothermal groundwater flow, moisture movement, and solute transport in variably saturated and fully saturated subsurface porous media.

Revising Hydrology of a Land Surface Model

NASA Astrophysics Data System (ADS)

Le Vine, Nataliya; Butler, Adrian; McIntyre, Neil; Jackson, Christopher

2015-04-01

Land Surface Models (LSMs) are key elements in guiding adaptation to the changing water cycle and the starting points to develop a global hyper-resolution model of the terrestrial water, energy and biogeochemical cycles. However, before this potential is realised, there are some fundamental limitations of LSMs related to how meaningfully hydrological fluxes and stores are represented. An important limitation is the simplistic or non-existent representation of the deep subsurface in LSMs; and another is the lack of connection of LSM parameterisations to relevant hydrological information. In this context, the paper uses a case study of the JULES (Joint UK Land Environmental Simulator) LSM applied to the Kennet region in Southern England. The paper explores the assumptions behind JULES hydrology, adapts the model structure and optimises the coupling with the ZOOMQ3D regional groundwater model. The analysis illustrates how three types of information can be used to improve the model's hydrology: a) observations, b) regionalized information, and c) information from an independent physics-based model. It is found that: 1) coupling to the groundwater model allows realistic simulation of streamflows; 2) a simple dynamic lower boundary improves upon JULES' stationary unit gradient condition; 3) a 1D vertical flow in the unsaturated zone is sufficient; however there is benefit in introducing a simple dual soil moisture retention curve; 4) regionalized information can be used to describe soil spatial heterogeneity. It is concluded that relatively simple refinements to the hydrology of JULES and its parameterisation method can provide a substantial step forward in realising its potential as a high-resolution multi-purpose model.

Gypsies in the palace: Experimentalist's view on the use of 3-D physics-based simulation of hillslope hydrological response

USGS Publications Warehouse

James, A.L.; McDonnell, Jeffery J.; Tromp-Van Meerveld, I.; Peters, N.E.

2010-01-01

As a fundamental unit of the landscape, hillslopes are studied for their retention and release of water and nutrients across a wide range of ecosystems. The understanding of these near-surface processes is relevant to issues of runoff generation, groundwater-surface water interactions, catchment export of nutrients, dissolved organic carbon, contaminants (e.g. mercury) and ultimately surface water health. We develop a 3-D physics-based representation of the Panola Mountain Research Watershed experimental hillslope using the TOUGH2 sub-surface flow and transport simulator. A recent investigation of sub-surface flow within this experimental hillslope has generated important knowledge of threshold rainfall-runoff response and its relation to patterns of transient water table development. This work has identified components of the 3-D sub-surface, such as bedrock topography, that contribute to changing connectivity in saturated zones and the generation of sub-surface stormflow. Here, we test the ability of a 3-D hillslope model (both calibrated and uncalibrated) to simulate forested hillslope rainfall-runoff response and internal transient sub-surface stormflow dynamics. We also provide a transparent illustration of physics-based model development, issues of parameterization, examples of model rejection and usefulness of data types (e.g. runoff, mean soil moisture and transient water table depth) to the model enterprise. Our simulations show the inability of an uncalibrated model based on laboratory and field characterization of soil properties and topography to successfully simulate the integrated hydrological response or the distributed water table within the soil profile. Although not an uncommon result, the failure of the field-based characterized model to represent system behaviour is an important challenge that continues to vex scientists at many scales. We focus our attention particularly on examining the influence of bedrock permeability, soil anisotropy and drainable porosity on the development of patterns of transient groundwater and sub-surface flow. Internal dynamics of transient water table development prove to be essential in determining appropriate model parameterization. ?? 2010 John Wiley & Sons, Ltd.

Regolith-atmosphere exchange of water in Mars' recent past

NASA Astrophysics Data System (ADS)

Steele, Liam J.; Balme, Matthew R.; Lewis, Stephen R.

2017-03-01

We investigate the exchange of water vapour between the regolith and atmosphere of Mars, and how it varies with different orbital parameters, atmospheric dust contents and surface water ice reservoirs. This is achieved through the coupling of a global circulation model (GCM) and a regolith diffusion model. GCM simulations are performed for hundreds of Mars years, with additional one-dimensional simulations performed for 50 kyr. At obliquities ɛ =15∘ and 30°, the thermal inertia and albedo of the regolith have more control on the subsurface water distribution than changes to the eccentricity or solar longitude of perihelion. At ɛ =45∘ , atmospheric water vapour abundances become much larger, allowing stable subsurface ice to form in the tropics and mid-latitudes. The circulation of the atmosphere is important in producing the subsurface water distribution, with increased water content in various locations due to vapour transport by topographically-steered flows and stationary waves. As these circulation patterns are due to topographic features, it is likely the same regions will also experience locally large amounts of subsurface water at different epochs. The dustiness of the atmosphere plays an important role in the distribution of subsurface water, with a dusty atmosphere resulting in a wetter water cycle and increased stability of subsurface ice deposits.

Two-Relaxation-Time Lattice Boltzmann Method for Advective-Diffusive-Reactive Transport

NASA Astrophysics Data System (ADS)

Yan, Z.; Hilpert, M.

2016-12-01

The lattice Boltzmann method (LBM) has been applied to study a wide range of reactive transport in porous and fractured media. The single-relaxation-time (SRT) LBM, employing single relaxation time, is the most popular LBM due to its simplicity of understanding and implementation. Nevertheless, the SRT LBM may suffer from numerical instability for small value of the relaxation time. By contrast, the multiple-relaxation-time (MRT) LBM, employing multiple relaxation times, can improve the numerical stability through tuning the multiple relaxation times, but the complexity of implementing this method restricts its applications. The two-relaxation-time (TRT) LBM, which employs two relaxation times, combines the advantages of SRT and MRT LBMs. The TRT LBM can produce simulations with better accuracy and stability than the SRT one, and is easier to implement than the MRT one. This work evaluated the numerical accuracy and stability of the TRT method by comparing the simulation results with analytical solutions of Gaussian hill transport and Taylor dispersion under different advective velocities. The accuracy generally increased with the tunable relaxation time τ, and the stability first increased and then decreased as τ increased, showing an optimal TRT method emerging the best numerical stability. The free selection of τ enabled the TRT LBM to simulate the Gaussian hill transport and Taylor dispersion under relatively high advective velocity, under which the SRT LBM suffered from numerical instability. Finally, the TRT method was applied to study the contaminant degradation by chemotactic microorganisms in porous media, which acted as a reprehensive of reactive transport in this study, and well predicted the evolution of microorganisms and degradation of contaminants for different transport scenarios. To sum up, the TRT LBM produced simulation results with good accuracy and stability for various advective-diffusive-reactive transport through tuning the relaxation time τ, illustrating its potential to study various biogeochemical behaviors in the subsurface environment.

A reduced-order modeling approach to represent subgrid-scale hydrological dynamics for land-surface simulations: application in a polygonal tundra landscape

DOE PAGES

Pau, G. S. H.; Bisht, G.; Riley, W. J.

2014-09-17

Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO 2, CH 4) exchanges with the atmosphere range from the molecular scale (pore-scale O 2 consumption) to tens of kilometers (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a reduced-order modeling (ROM) technique known as "proper orthogonal decomposition mapping method" thatmore » reconstructs temporally resolved fine-resolution solutions based on coarse-resolution solutions. We developed four different methods and applied them to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface–subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 10 3) with very small relative approximation error (< 0.1%) for 2 validation years not used in training the ROM. We also demonstrate that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training data set with relatively good accuracy (< 1.7% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. By coupling the ROMs constructed at different scales together hierarchically, this method has the potential to efficiently increase the resolution of land models for coupled climate simulations to spatial scales consistent with mechanistic physical process representation.« less

Vadose Zone Fate and Transport Simulation of Chemicals Associated with Coal Seam Gas Extraction

NASA Astrophysics Data System (ADS)

Simunek, J.; Mallants, D.; Jacques, D.; Van Genuchten, M.

2017-12-01

The HYDRUS-1D and HYDRUS (2D/3D) computer software packages are widely used finite element models for simulating the one-, and two- or three-dimensional movement of water, heat, and multiple solutes in variably-saturated media, respectively. While the standard HYDRUS models consider only the fate and transport of individual solutes or solutes subject to first-order degradation reactions, several specialized HYDRUS add-on modules can simulate far more complex biogeochemical processes. The objective of this presentation is to provide an overview of the HYDRUS models and their add-on modules, and to demonstrate applications of the software to the subsurface fate and transport of chemicals involved in coal seam gas extraction and water management operations. One application uses the standard HYDRUS model to evaluate the natural soil attenuation potential of hydraulic fracturing chemicals and their transformation products in case of an accidental release. By coupling the processes of retardation, first-order degradation and convective-dispersive transport of the biocide bronopol and its degradation products, we demonstrated how natural attenuation reduces initial concentrations by more than a factor of hundred in the top 5 cm of the vadose zone. A second application uses the UnsatChem module to explore the possible use of coal seam gas produced water for sustainable irrigation. Simulations with different irrigation waters (untreated, amended with surface water, and reverse osmosis treated) provided detailed results regarding chemical indicators of soil and plant health, notably SAR, EC and sodium concentrations. A third application uses the coupled HYDRUS-PHREEQC module to analyze trace metal transport involving cation exchange and surface complexation sorption reactions in the vadose zone leached with coal seam gas produced water following some accidental water release scenario. Results show that the main process responsible for trace metal migration is complexation of naturally present trace metals with inorganic ligands such as (bi)carbonate that enter the soil upon infiltration with alkaline produced water.

Application of model abstraction techniques to simulate transport in soils

USDA-ARS?s Scientific Manuscript database

Successful understanding and modeling of contaminant transport in soils is the precondition of risk-informed predictions of the subsurface contaminant transport. Exceedingly complex models of subsurface contaminant transport are often inefficient. Model abstraction is the methodology for reducing th...

Linkage of mike she to wetland-dndc for carbon budgeting and anaerobic biogeochemistry simulation

Treesearch

Jianbo Cui; Changsheng Li; Ge Sun; Carl Trettin

2005-01-01

This study reports the linkage between MIKE SHE and Wetland-DNDC for carbon dynamics and greenhouse gases (GHGs) emissions simulation in forested wetland.Wet1and-DNDC was modified by parameterizing management measures, refining anaerobic biogeochemical processes, and was linked to the hydrological model - MIKE SHE. As a preliminary application, we simulated the effect...

DayCent model simulations for estimating soil carbon dynamics and greenhouse gas fluxes from agricultural production systems

USDA-ARS?s Scientific Manuscript database

DayCent is a biogeochemical model of intermediate complexity used to simulate carbon, nutrient, and greenhouse gas fluxes for crop, grassland, forest, and savanna ecosystems. Model inputs include: soil texture and hydraulic properties, current and historical land use, vegetation cover, daily maximum...

A mercury transport and fate model (LM2-mercury) for mass budget assessment of mercury cycling in Lake Michigan

EPA Science Inventory

LM2-Mercury, a mercury mass balance model, was developed to simulate and evaluate the transport, fate, and biogeochemical transformations of mercury in Lake Michigan. The model simulates total suspended solids (TSS), disolved organic carbon (DOC), and total, elemental, divalent, ...

Using a spatially-distributed hydrologic biogeochemistry model to study the spatial variation of carbon processes in a Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Shi, Y.; Eissenstat, D. M.; Davis, K. J.; He, Y.

2016-12-01

Forest carbon processes are affected by, among other factors, soil moisture, soil temperature, soil nutrients and solar radiation. Most of the current biogeochemical models are 1-D and represent one point in space. Therefore, they cannot resolve the topographically driven hill-slope land surface heterogeneity or the spatial pattern of nutrient availability. A spatially distributed forest ecosystem model, Flux-PIHM-BGC, has been developed by coupling a 1-D mechanistic biogeochemical model Biome-BGC (BBGC) with a spatially distributed land surface hydrologic model, Flux-PIHM. Flux-PIHM is a coupled physically based model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model. Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as the land surface heterogeneities caused by topography. In the coupled Flux-PIHM-BGC model, each Flux-PIHM model grid couples a 1-D BBGC model, while soil nitrogen is transported among model grids via subsurface water flow. In each grid, Flux-PIHM provides BBGC with soil moisture, soil temperature, and solar radiation information, while BBGC provides Flux-PIHM with leaf area index. The coupled Flux-PIHM-BGC model has been implemented at the Susquehanna/Shale Hills critical zone observatory (SSHCZO). Model results suggest that the vegetation and soil carbon distribution is primarily constrained by nitorgen availability (affected by nitorgen transport via topographically driven subsurface flow), and also constrained by solar radiation and root zone soil moisture. The predicted vegetation and soil carbon distribution generally agrees with the macro pattern observed within the watershed. The coupled ecosystem-hydrologic model provides an important tool to study the impact of topography on watershed carbon processes, as well as the impact of climate change on water resources.

Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences.

PubMed

Zhang, Xiaoying; Hu, Bill X; Ren, Hejun; Zhang, Jin

2018-08-15

The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity. Copyright © 2018 Elsevier B.V. All rights reserved.

How do local and remote processes affect the distribution of iron in the Atlantic Ocean?

NASA Astrophysics Data System (ADS)

Tagliabue, A.; Boyd, P.; Rijkenberg, M. J. A.; Williams, R. G.

2016-02-01

Iron (Fe) plays an important role in governing the magnitudes and patterns of primary productivity, nitrogen fixation and phytoplankton community composition across the Atlantic Ocean. Variations in the supply of Fe to surface waters across the mixed layer interface, over seasonal to annual to decadal scales, are underpinned by it's vertical profile. Traditionally, nutrient profiles are understood in terms of surface depletion and subsurface regeneration, but for Fe this is more complicated due to the role of scavenging and organic complexation by ligands, as well as subsurface sources. This means that the Fe profile may be controlled locally, by sinking, regeneration and scavenging or remotely, by the upstream conditions of subducted water masses. Subduction drives the transfer of Fe across the interface between winter mixed layer and the ocean interior, but has received little attention thus far. Via the subduction of watermasses with distinct biogeochemical signatures to low latitudes, remote processes can regulate the Atlantic Ocean Fe distribution at local scales. Specifically, the formation of mode waters with excess Fe binding ligands (positive L*) enable these waters to stabilise any Fe flux from regeneration that would otherwise be lost by scavenging. The pattern of mode water ventilation then highlights those regions of the ocean where local processes are able to influence the Fe profile. Local process that augment L*, such as the production of ligands during particle regeneration, can also interact with the larger scale ventilation signature but do not alter the main trends. By applying our framework to recent GEOTRACES datasets over the Atlantic Ocean we are able to highlight regions where the Fe profile is forced locally or remotely, thereby providing an important process-based constraint on the biogeochemical models we rely on for future projections. Furthermore, we are able to appraise how the varying influence of local and remote processes drives the degree of agreement in the vertical profiles of Fe and macronutrients, which then sets the degree of surface water Fe limitation.

The Shale Hills Sensorium for Embedded Sensors, Simulation, & Visualization: A Prototype for Land-Vegetation-Atmosphere Interactions

NASA Astrophysics Data System (ADS)

Duffy, C.

2008-12-01

The future of environmental observing systems will utilize embedded sensor networks with continuous real- time measurement of hydrologic, atmospheric, biogeochemical, and ecological variables across diverse terrestrial environments. Embedded environmental sensors, benefitting from advances in information sciences, networking technology, materials science, computing capacity, and data synthesis methods, are undergoing revolutionary change. It is now possible to field spatially-distributed, multi-node sensor networks that provide density and spatial coverage previously accessible only via numerical simulation. At the same time, computational tools are advancing rapidly to the point where it is now possible to simulate the physical processes controlling individual parcels of water and solutes through the complete terrestrial water cycle. Our goal for the Penn State Critical Zone Observatory is to apply environmental sensor arrays, integrated hydrologic models, and state-of-the-art visualization deployed and coordinated at a testbed within the Penn State Experimental Forest. The Shale Hills Hydro_Sensorium prototype proposed here is designed to observe land-atmosphere interactions in four-dimensional (space and time). The term Hydro_Sensorium implies the totality of physical sensors, models and visualization tools that allow us to perceive the detailed space and time complexities of the water and energy cycle for a watershed or river basin for all physical states and fluxes (groundwater, soil moisture, temperature, streamflow, latent heat, snowmelt, chemistry, isotopes etc.). This research will ultimately catalyze the study of complex interactions between the land surface, subsurface, biological and atmospheric systems over a broad range of scales. The sensor array would be real-time and fully controllable by remote users for "computational steering" and data fusion. Presently fully-coupled physical models are being developed that link the atmosphere-land-vegetation-subsurface system into a fully-coupled distributed system. During the last 5 years the Penn State Integrated Hydrologic Modeling System has been under development as an open-source community modeling project funded by NSF EAR/GEO and NSF CBET/ENG. PIHM represents a strategy for the formulation and solution of fully-coupled process equations at the watershed and river basin scales, and includes a tightly coupled GIS tool for data handling, domain decomposition, optimal unstructured grid generation, and model parameterization. The sensor and simulation system has the following elements: 1) extensive, spatially-distributed, non- invasive, smart sensor networks to gather massive geologic, hydrologic, and geochemical data; 2) stochastic information fusion methods; 3) spatially-explicit multiphysics models/solutions of the land-vegetation- atmosphere system; and 4) asynchronous, parallel/distributed, adaptive algorithms for rapidly simulating the states of a basin at high resolution, 5) signal processing tools for data mining and parameter estimation, and 6) visualization tools. The prototype proposed sensor array and simulation system proposed here will offer a coherent new approach to environmental predictions with a fully integrated observing system design. We expect that the Shale Hills Hydro_Sensorium may provide the needed synthesis of information and conceptualization necessary to advance predictive understanding in complex hydrologic systems.

One multi-media environmental system with linkage between meteorology/ hydrology/ air quality models and water quality model

NASA Astrophysics Data System (ADS)

Tang, C.; Lynch, J. A.; Dennis, R. L.

2016-12-01

The biogeochemical processing of nitrogen and associated pollutants is driven by meteorological and hydrological processes in conjunction with pollutant loading. There are feedbacks between meteorology and hydrology that will be affected by land-use change and climate change. Changes in meteorology will affect pollutant deposition. It is important to account for those feedbacks and produce internally consistent simulations of meteorology, hydrology, and pollutant loading to drive the (watershed/water quality) biogeochemical models. In this study, the ecological response to emission reductions in streams in the Potomac watershed was evaluated. Firstly, we simulated the deposition by using the fully coupled Weather Research & Forecasting (WRF) model and the Community Multiscale Air Quality (CAMQ) model; secondly, we created the hydrological data by the offline linked Variable Infiltration Capacity (VIC) model and the WRF model. Lastly, we investigated the water quality by one comprehensive/environment model, namely the linkage of CMAQ, WRF, VIC and the Model of Acidification of Groundwater In Catchment (MAGIC) model from 2002 to 2010.The simulated results (such as NO3, SO4, and SBC) fit well to the observed values. The linkage provides a generally accurate, well-tested tool for evaluating sensitivities to varying meteorology and environmental changes on acidification and other biogeochemical processes, with capability to comprehensively explore strategic policy and management design.

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

NASA Astrophysics Data System (ADS)

Wu, Y.; Blodau, C.

2013-08-01

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

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

NASA Astrophysics Data System (ADS)

Wu, Y.; Blodau, C.

2013-03-01

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

Biogeochemical reactive transport of carbon, nitrogen and iron in the hyporheic zone

NASA Astrophysics Data System (ADS)

Dwivedi, D.; Steefel, C. I.; Newcomer, M. E.; Arora, B.; Spycher, N.; Hammond, G. E.; Moulton, J. D.; Fox, P. M.; Nico, P. S.; Williams, K. H.; Dafflon, B.; Carroll, R. W. H.

2017-12-01

To understand how biogeochemical processes in the hyporheic zone influence carbon and nitrogen cycling as well as stream biogeochemistry, we developed a biotic and abiotic reaction network and integrated it into a reactive transport simulator - PFLOTRAN. Three-dimensional reactive flow and transport simulations were performed to describe the hyporheic exchange of fluxes from and within an intra-meander region encompassing two meanders of East River in the East Taylor watershed, Colorado. The objectives of this study were to quantify (1) the effect of transience on the export of carbon, nitrogen, and iron; and (2) the biogeochemical transformation of nitrogen and carbon species as a function of the residence time. The model was able to capture reasonably well the observed trends of nitrate and dissolved oxygen values that decreased as well as iron (Fe (II)) values that increased along the meander centerline away from the stream. Hyporheic flow paths create lateral redox zonation within intra-meander regions, which considerably impact nitrogen export into the stream system. Simulation results further demonstrated that low water conditions lead to higher levels of dissolved iron in groundwater, which (Fe (II)> 80%) is exported to the stream on the downstream side during high water conditions. An important conclusion from this study is that reactive transport models representing spatial and temporal heterogeneities are required to identify important factors that contribute to the redox gradients at riverine scales.

Nonlinear Interactions between Climate and Atmospheric Carbon Dioxide Drivers of Terrestrial and Marine Carbon Cycle Changes

NASA Astrophysics Data System (ADS)

Hoffman, F. M.; Randerson, J. T.; Moore, J. K.; Goulden, M.; Fu, W.; Koven, C.; Swann, A. L. S.; Mahowald, N. M.; Lindsay, K. T.; Munoz, E.

2017-12-01

Quantifying interactions between global biogeochemical cycles and the Earth system is important for predicting future atmospheric composition and informing energy policy. We applied a feedback analysis framework to three sets of Historical (1850-2005), Representative Concentration Pathway 8.5 (2006-2100), and its extension (2101-2300) simulations from the Community Earth System Model version 1.0 (CESM1(BGC)) to quantify drivers of terrestrial and ocean responses of carbon uptake. In the biogeochemically coupled simulation (BGC), the effects of CO2 fertilization and nitrogen deposition influenced marine and terrestrial carbon cycling. In the radiatively coupled simulation (RAD), the effects of rising temperature and circulation changes due to radiative forcing from CO2, other greenhouse gases, and aerosols were the sole drivers of carbon cycle changes. In the third, fully coupled simulation (FC), both the biogeochemical and radiative coupling effects acted simultaneously. We found that climate-carbon sensitivities derived from RAD simulations produced a net ocean carbon storage climate sensitivity that was weaker and a net land carbon storage climate sensitivity that was stronger than those diagnosed from the FC and BGC simulations. For the ocean, this nonlinearity was associated with warming-induced weakening of ocean circulation and mixing that limited exchange of dissolved inorganic carbon between surface and deeper water masses. For the land, this nonlinearity was associated with strong gains in gross primary production in the FC simulation, driven by enhancements in the hydrological cycle and increased nutrient availability. We developed and applied a nonlinearity metric to rank model responses and driver variables. The climate-carbon cycle feedback gain at 2300 was 42% higher when estimated from climate-carbon sensitivities derived from the difference between FC and BGC than when derived from RAD. We re-analyzed other CMIP5 model results to quantify the effects of such nonlinearities on their projected climate-carbon cycle feedback gains.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ginn, Timothy R.; Weathers, Tess

Biogeochemical modeling using PHREEQC2 and a streamtube ensemble approach is utilized to understand a well-to-well subsurface treatment system at the Vadose Zone Research Park (VZRP) near Idaho Falls, Idaho. Treatment involves in situ microbially-mediated ureolysis to induce calcite precipitation for the immobilization of strontium-90. PHREEQC2 is utilized to model the kinetically-controlled ureolysis and consequent calcite precipitation. Reaction kinetics, equilibrium phases, and cation exchange are used within PHREEQC2 to track pH and levels of calcium, ammonium, urea, and calcite precipitation over time, within a series of one-dimensional advective-dispersive transport paths creating a streamtube ensemble representation of the well-to-well transport. An understandingmore » of the impact of physical heterogeneities within this radial flowfield is critical for remediation design; we address this via the streamtube approach: instead of depicting spatial extents of solutes in the subsurface we focus on their arrival distribution at the control well(s). Traditionally, each streamtube maintains uniform velocity; however in radial flow in homogeneous media, the velocity within any given streamtube is spatially-variable in a common way, being highest at the input and output wells and approaching a minimum at the midpoint between the wells. This idealized velocity variability is of significance in the case of ureolytically driven calcite precipitation. Streamtube velocity patterns for any particular configuration of injection and withdrawal wells are available as explicit calculations from potential theory, and also from particle tracking programs. To approximate the actual spatial distribution of velocity along streamtubes, we assume idealized radial non-uniform velocity associated with homogeneous media. This is implemented in PHREEQC2 via a non-uniform spatial discretization within each streamtube that honors both the streamtube’s travel time and the idealized “fast-slow-fast” pattern of non-uniform velocity along the streamline. Breakthrough curves produced by each simulation are weighted by the path-respective flux fractions (obtained by deconvolution of tracer tests conducted at the VZRP) to obtain the flux-average of flow contributions to the observation well.« less

Quantifying the Interactions Between Soil Thermal Characteristics, Soil Physical Properties, Hydro-geomorphological Conditions and Vegetation Distribution in an Arctic Watershed

NASA Astrophysics Data System (ADS)

Dafflon, B.; Leger, E.; Robert, Y.; Ulrich, C.; Peterson, J. E.; Soom, F.; Biraud, S.; Tran, A. P.; Hubbard, S. S.

2017-12-01

Improving understanding of Arctic ecosystem functioning and parameterization of process-rich hydro-biogeochemical models require advances in quantifying ecosystem properties, from the bedrock to the top of the canopy. In Arctic regions having significant subsurface heterogeneity, understanding the link between soil physical properties (incl. fraction of soil constituents, bedrock depth, permafrost characteristics), thermal behavior, hydrological conditions and landscape properties is particularly challenging yet is critical for predicting the storage and flux of carbon in a changing climate. This study takes place in Seward Peninsula Watersheds near Nome AK and Council AK, which are characterized by an elevation gradient, shallow bedrock, and discontinuous permafrost. To characterize permafrost distribution where the top of permafrost cannot be easily identified with a tile probe (due to rocky soil and/or large thaw layer thickness), we developed a novel technique using vertically resolved thermistor probes to directly sense the temperature regime at multiple depths and locations. These measurements complement electrical imaging, seismic refraction and point-scale data for identification of the various thermal behavior and soil characteristics. Also, we evaluate linkages between the soil physical-thermal properties and the surface properties (hydrological conditions, geomorphic characteristics and vegetation distribution) using UAV-based aerial imaging. Data integration and analysis is supported by numerical approaches that simulate hydrological and thermal processes. Overall, this study enables the identification of watershed structure and the links between various subsurface and landscape properties in representative Arctic watersheds. Results show very distinct trends in vertically resolved soil temperature profiles and strong lateral variations over tens of meters that are linked to zones with various hydrological conditions, soil properties and vegetation types. The interaction between these zones is of strong interest to understand the evolution of the landscape and the permafrost distribution. The obtained information is expected to be useful for improving predictions of Arctic ecosystem feedbacks to climate.

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

NASA Astrophysics Data System (ADS)

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

2003-01-01

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

Production and export in a global ocean ecosystem model

NASA Astrophysics Data System (ADS)

Palmer, J. R.; Totterdell, I. J.

2001-05-01

The Hadley Centre Ocean Carbon Cycle (HadOCC) model is a coupled physical-biogeochemical model of the ocean carbon cycle. It features an explicit representation of the marine ecosystem, which is assumed to be limited by nitrogen availability. The biogeochemical compartments are dissolved nutrient, total CO 2, total alkalinity, phytoplankton, zooplankton and detritus. The results of the standard simulation are presented. The annual primary production predicted by the model ( 47.7 Gt C yr -1) compares well to the estimates made by Longhurst et al. (1995, J. Plankton Res., 17, 1245) and Antoine et al. (1996, Global Biogeochem. Cycles, 10, 57). The HadOCC model finds high production in the sub-polar North Pacific and North Atlantic Oceans, and around the Antarctic convergence, and low production in the sub-tropical gyres. However in disagreement with the observations of Longhurst et al. and Antoine et al., the model predicts very high production in the eastern equatorial Pacific Ocean. The export flux of carbon in the model agrees well with data from deep-water sediment traps. In order to examine the factors controlling production in the ocean, additional simulations have been run. A nutrient-restoring simulation confirms that the areas with the highest primary production are those with the greatest nutrient supply. A reduced wind-stress experiment demonstrates that the high production found in the equatorial Pacific is driven by excessive upwelling of nutrient-rich water. Three further simulations show that nutrient supply at high latitudes, and hence production there, is sensitive to the parameters and climatological forcings of the mixed layer sub-model.

Enhanced recharge rates and altered recharge sensitivity to climate variability through subsurface heterogeneity

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Gleeson, Tom; Wada, Yoshihide; Wagener, Thorsten

2017-04-01

Karst aquifers in Europe are an important source of fresh water contributing up to half of the total drinking water supply in some countries. Karstic groundwater recharge is one of the most important components of the water balance of karst systems as it feeds the karst aquifers. Presently available large-scale hydrological models do not consider karst heterogeneity adequately. Projections of current and potential future groundwater recharge of Europe's karst aquifers are therefore unclear. In this study we compare simulations of present (1991-2010) and future (2080-2099) recharge using two different models to simulate groundwater recharge processes. One model includes karst processes (subsurface heterogeneity, lateral flow and concentrated recharge), while the other is based on the conceptual understanding of common hydrological systems (homogeneous subsurface, saturation excess overland flow). Both models are driven by the bias-corrected 5 GCMs of the ISI-MIP project (RCP8.5). To further assess sensitivity of groundwater recharge to climate variability, we calculate the elasticity of recharge rates to annual precipitation, temperature and average intensity of rainfall events, which is the median change of recharge that corresponds to the median change of these climate variables within the present and future time period, respectively. Our model comparison shows that karst regions over Europe have enhanced recharge rates with greater inter-annual variability compared to those with more homogenous subsurface properties. Furthermore, the heterogeneous representation shows stronger elasticity concerning climate variability than the homogeneous subsurface representation. This difference tends to increase towards the future. Our results suggest that water management in regions with heterogeneous subsurface can expect a higher water availability than estimated by most of the current large-scale simulations, while measures should be taken to prepare for increasingly variable groundwater recharge rates.

Nutrient pressures and legacies in a small agricultural karst catchment

NASA Astrophysics Data System (ADS)

Fenton, Owen; Mellander, Per-Erik; Daly, Karen; Wall, David P.; Jahangir, Mohammad M.; Jordan, Phil; Hennessey, Deirdre; Huebsch, Manuela; Blum, Philipp; Vero, Sara; Richards, Karl G.

2017-04-01

Catchments with short subsurface hydrologic time lags are commonly at risk for leached losses of nitrogen (N) and phosphorus (P). Such catchments are suitable for testing the efficacy of mitigation measures as management changes. In some sites, however, N and P may be retained in the soil and subsoil layers, and then leached, mobilised or attenuated over time. This biogeochemical time lag may therefore have enduring effects on the water quality. The aim of this study was to improve the understanding of N and P retention, attenuation and distribution of subsurface pathway in an intensively managed agricultural karst catchment with an oxidised aquifer setting, and also to inform how similar sites can be managed in the future. Results showed that in the years pre-2000 slurry from an on-site integrated pig production unit had been applied at rates of 33 t/ha annually, which supplied approximately 136 kg/ha total N and approximately 26 kg/ha total P annually. This practice contributed to large quantities of N (total N and NH4-N) and elevated soil test P (Morgan extractable P), present to a depth of 1 m. This store was augmented by recent surpluses of 263 kg N/ha, with leached N to groundwater of 82.5 kg N/ha and only 2.5 kg N/ha denitrified in the aquifer thereafter. Sub hourly spring data showed the largest proportion of N loss from small (54-88%) and medium fissure pathways (7- 21%) with longer hydrologic time lags, with smallest loads from either large fissure (1-13%) or conduit (1-10%) pathways with short hydrologic time lags (reaction time at the spring from onset of a rainfall event is within hours). Although soils were saturated in P and in mobile forms to 0.5 m, dissolved reactive P concentrations in groundwater remained low due to Ca and Mg limestone chemistry. Under these conditions a depletion of the legacy store, with no further inputs, would take approximately 50 years and with NO3-N concentrations in the source area dropping to levels that could sustain groundwater NO3-N concentrations below admissible levels within 9 years. Biogeochemical time lags (decades) are longer than hydrologic time lags on this site (months to years). Future management should target farm surpluses that maintain a legacy store at or below a soil organic N mass of ca. 20 kg N/ha. Incorporation of biogeochemical and hydrologic time lag principles into future water quality regulations will provide regulators with realistic expectations when implementing policies.

Fluid pressure responses for a Devil's Slide-like system: problem formulation and simulation

USGS Publications Warehouse

Thomas, Matthew A.; Loague, Keith; Voss, Clifford I.

2015-01-01

This study employs a hydrogeologic simulation approach to investigate subsurface fluid pressures for a landslide-prone section of the central California, USA, coast known as Devil's Slide. Understanding the relative changes in subsurface fluid pressures is important for systems, such as Devil's Slide, where slope creep can be interrupted by episodic slip events. Surface mapping, exploratory core, tunnel excavation records, and dip meter data were leveraged to conceptualize the parameter space for three-dimensional (3D) Devil's Slide-like simulations. Field observations (i.e. seepage meter, water retention, and infiltration experiments; well records; and piezometric data) and groundwater flow simulation (i.e. one-dimensional vertical, transient, and variably saturated) were used to design the boundary conditions for 3D Devil's Slide-like problems. Twenty-four simulations of steady-state saturated subsurface flow were conducted in a concept-development mode. Recharge, heterogeneity, and anisotropy are shown to increase fluid pressures for failure-prone locations by up to 18.1, 4.5, and 1.8% respectively. Previous estimates of slope stability, driven by simple water balances, are significantly improved upon with the fluid pressures reported here. The results, for a Devil's Slide-like system, provide a foundation for future investigations

Modeling seasonal variability of carbonate system parameters at the sediment -water interface in the Baltic Sea (Gdansk Deep)

NASA Astrophysics Data System (ADS)

Protsenko, Elizaveta; Yakubov, Shamil; Lessin, Gennady; Yakushev, Evgeniy; Sokołowski, Adam

2017-04-01

A one-dimensional fully-coupled benthic pelagic biogeochemical model BROM (Bottom RedOx Model) was used for simulations of seasonal variability of biogeochemical parameters in the upper sediment, Bottom Boundary Layer and the water column in the Gdansk Deep of the Baltic Sea. This model represents key biogeochemical processes of transformation of C, N, P, Si, O, S, Mn, Fe and the processes of vertical transport in the water column and the sediments. The hydrophysical block of BROM was forced by the output calculated with model GETM (General Estuarine Transport Model). In this study we focused on parameters of carbonate system at Baltic Sea, and mainly on their distributions near the sea-water interface. For validating of BROM we used field data (concentrations of main nutrients at water column and porewater of upper sediment) from the Gulf of Gdansk. The model allowed us to simulate the baseline ranges of seasonal variability of pH, Alkalinity, TIC and calcite/aragonite saturation as well as vertical fluxes of carbon in a region potentially selected for the CCS storage. This work was supported by project EEA CO2MARINE and STEMM-CCS.

Experimental and simulated ultrasonic characterization of complex damage in fused silica.

PubMed

Martin, L Peter; Chambers, David H; Thomas, Graham H

2002-02-01

The growth of a laser-induced, surface damage site in a fused silica window was monitored by the ultrasonic pulse-echo technique. The laser damage was grown using 12-ns pulses of 1.053-microm wavelength light at a fluence of approximately 27 J/cm2. The ultrasonic data were acquired after each pulse of the laser beam for 19 pulses. In addition, optical images of the surface and subsurface damage shape were recorded after each pulse of the laser. The ultrasonic signal amplitude exhibited variations with the damage size, which were attributed to the subsurface morphology of the damage site. A mechanism for the observed ultrasonic data based on the interaction of the ultrasound with cracks radiating from the damage site was tested using two-dimensional numerical simulations. The simulated results exhibit qualitatively similar characteristics to the experimental data and demonstrate the usefulness of numerical simulation as an aid for ultrasonic signal interpretation. The observed sensitivity to subsurface morphology makes the ultrasonic methodology a promising tool for monitoring laser damage in large aperture laser optics used in fusion energy research.

Active subsurface cellular function in the Baltic Sea Basin, IODP Exp 347

NASA Astrophysics Data System (ADS)

Reese, B. K.; Zinke, L. A.; Bird, J. T.; Lloyd, K. G.; Marshall, I.; Amend, J.; Jørgensen, B. B.

2016-12-01

The Baltic Sea Basin is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of global temperature fluctuations over the course of several hundred thousand years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates (100-500 cm/1000 y) make this an ideal setting to understand the microbial structure of a deep biosphere community in a high-organic matter environment. The responses of deep sediment microbial communities to variations in conditions during and after deposition are poorly understood. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further define the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

Microbiological, Geochemical and Hydrologic Processes Controlling Uranium Mobility: An Integrated Field Scale Subsurface Research Challenge Site at Rifle, Colorado, February 2011 to January 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Philip E.; Banfield, Jill; Chandler, Darrell P.

The Rifle IFRC continued to make excellent progress during the last 12 months. As noted above, a key field experiment (Best Western) was performed during 2011 as a logical follow-on to the Super 8 field experiment preformed in 2010. In the Super 8 experiment, we successfully combined desorption and bioreduction and deployed a number of novel tracer techniques to enhance our ability to interpret the biogeochemistry of the experiment. In the Best Western experiment, we used the same experimental plot (Plot C) as was used for Super 8. The overarching objective of the Best Western field experiment was to comparedmore » the impacts of abiotic vs. biotic increases in alkalinity and to assess the mass of the sorbed pool of U(VI) at Rifle at the field scale. Both of these objectives were met. Preliminary analysis of the data indicate that the underlying biogeochemical data sets were obtained that will support a mechanistic understanding of the underlying processes, including remarkable insight into previously unrecognized microbial processes taking place during acetate amendment of the subsurface for a second time.« less

Subsurface chlorophyll maximum layers: enduring enigma or mystery solved?

PubMed

Cullen, John J

2015-01-01

The phenomenon of subsurface chlorophyll maximum layers (SCMLs) is not a unique ecological response to environmental conditions; rather, a broad range of interacting processes can contribute to the formation of persistent layers of elevated chlorophyll a concentration (Chl) that are nearly ubiquitous in stratified surface waters. Mechanisms that contribute to the formation and maintenance of the SCMLs include a local maximum in phytoplankton growth rate near the nutricline, photoacclimation of pigment content that leads to elevated Chl relative to phytoplankton biomass at depth, and a range of physiologically influenced swimming behaviors in motile phytoplankton and buoyancy control in diatoms and cyanobacteria that can lead to aggregations of phytoplankton in layers, subject to grazing and physical control. A postulated typical stable water structure characterizes consistent patterns in vertical profiles of Chl, phytoplankton biomass, nutrients, and light across a trophic gradient structured by the vertical flux of nutrients and characterized by the average daily irradiance at the nutricline. Hypothetical predictions can be tested using a nascent biogeochemical global ocean observing system. Partial results to date are generally consistent with predictions based on current knowledge, which has strong roots in research from the twentieth century.

MICROSCALE METABOLIC, REDOX AND ABIOTIC REACTIONS IN HANFORD 300 AREA SUBSURFACE SEDIMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beyenal, Haluk; McLEan, Jeff; Majors, Paul

2013-11-14

The Hanford 300 Area is a unique site due to periodic hydrologic influence of river water resulting in changes in groundwater elevation and flow direction. This area is also highly subject to uranium remobilization, the source of which is currently believed to be the region at the base of the vadose zone that is subject to period saturation due to the changes in the water levels in the Columbia River. We found that microbial processes and redox and abiotic reactions which operate at the microscale were critical to understanding factors controlling the macroscopic fate and transport of contaminants in themore » subsurface. The combined laboratory and field research showed how microscale conditions control uranium mobility and how biotic, abiotic and redox reactions relate to each other. Our findings extended the current knowledge to examine U(VI) reduction and immobilization using natural 300 Area communities as well as selected model organisms on redox-sensitive and redox-insensitive minerals. Using innovative techniques developed specifically to probe biogeochemical processes at the microscale, our research expanded our current understanding of the roles played by mineral surfaces, bacterial competition, and local biotic, abiotic and redox reaction rates on the reduction and immobilization of uranium.« less

Microbial diversity in Cenozoic sediments recovered from the Lomonosov Ridge in the Central Arctic basin.

PubMed

Forschner, Stephanie R; Sheffer, Roberta; Rowley, David C; Smith, David C

2009-03-01

The current understanding of microbes inhabiting deeply buried marine sediments is based largely on samples collected from continental shelves in tropical and temperate latitudes. The geographical range of marine subsurface coring was expanded during the Integrated Ocean Drilling Program Arctic Coring Expedition (IODP ACEX). This expedition to the ice-covered central Arctic Ocean successfully cored the entire 428 m sediment stack on the Lomonosov Ridge during August and September 2004. The recovered cores vary from siliciclastic sediment low in organic carbon (< 0.2%) to organic rich ( approximately 3%) black sediments that rapidly accumulated in the early middle Eocene. Three geochemical environments were characterized based on chemical analyses of porewater: an upper ammonium oxidation zone, a carbonate dissolution zone and a deep (> 200 m below sea floor) sulfate reduction zone. The diversity of microbes within each zone was assessed using 16S rRNA phylogenetic markers. Bacterial 16S rRNA genes were successfully amplified from each of the biogeochemical zones, while archaea was only amplified from the deep sulfate reduction zone. The microbial communities at each zone are phylogenetically different and are most closely related to those from other deep subsurface environments.

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru

PubMed Central

Biddle, Jennifer F.; Lipp, Julius S.; Lever, Mark A.; Lloyd, Karen G.; Sørensen, Ketil B.; Anderson, Rika; Fredricks, Helen F.; Elvert, Marcus; Kelly, Timothy J.; Schrag, Daniel P.; Sogin, Mitchell L.; Brenchley, Jean E.; Teske, Andreas; House, Christopher H.; Hinrichs, Kai-Uwe

2006-01-01

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea. PMID:16505362

Mars Analog Rio Tinto Experiment (MARTE): 2003 Drilling Campaign to Search for a Subsurface Biosphere at Rio Tinto Spain

NASA Technical Reports Server (NTRS)

Stoker, Carol; Dunagan, Stephen; Stevens, Todd; Amils, Ricardo; Gomez-Elvira, Javier; Fernandez, David; Hall, James; Lynch, Kennda; Cannon, Howard; Zavaleta, Jhony

2004-01-01

The MARTE (Mars Astrobiology Research and Technology Experiment) project, an ASTEP field experiment, is exploring for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Tinto River- or Rio Tinto- in southwestern Spain. It is also demonstrating technology needed to search for a subsurface biosphere on Mars. The project has three primary objectives: (1) search for and characterize subsurface life at Rio Tinto along with the physical and chemical properties and sustaining energy sources of its environment, (2) perform a high fidelity simulation of a robotic Mars drilling mission to search for life, and (3) demonstrate the drilling, sample handling, and instrument technologies relevant to searching for life on Mars. The simulation of the robotic drilling mission is guided by the results of the aseptic drilling campaign to search for life at Rio Tinto. This paper describes results of the first phase of the aseptic drilling campaign.

Simulating pathways of subsurface oil in the Faroe-Shetland Channel using an ocean general circulation model.

PubMed

Main, C E; Yool, A; Holliday, N P; Popova, E E; Jones, D O B; Ruhl, H A

2017-01-15

Little is known about the fate of subsurface hydrocarbon plumes from deep-sea oil well blowouts and their effects on processes and communities. As deepwater drilling expands in the Faroe-Shetland Channel (FSC), oil well blowouts are a possibility, and the unusual ocean circulation of this region presents challenges to understanding possible subsurface oil pathways in the event of a spill. Here, an ocean general circulation model was used with a particle tracking algorithm to assess temporal variability of the oil-plume distribution from a deep-sea oil well blowout in the FSC. The drift of particles was first tracked for one year following release. Then, ambient model temperatures were used to simulate temperature-mediated biodegradation, truncating the trajectories of particles accordingly. Release depth of the modeled subsurface plumes affected both their direction of transport and distance travelled from their release location, and there was considerable interannual variability in transport. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

A locally conservative stabilized continuous Galerkin finite element method for two-phase flow in poroelastic subsurfaces

NASA Astrophysics Data System (ADS)

Deng, Q.; Ginting, V.; McCaskill, B.; Torsu, P.

2017-10-01

We study the application of a stabilized continuous Galerkin finite element method (CGFEM) in the simulation of multiphase flow in poroelastic subsurfaces. The system involves a nonlinear coupling between the fluid pressure, subsurface's deformation, and the fluid phase saturation, and as such, we represent this coupling through an iterative procedure. Spatial discretization of the poroelastic system employs the standard linear finite element in combination with a numerical diffusion term to maintain stability of the algebraic system. Furthermore, direct calculation of the normal velocities from pressure and deformation does not entail a locally conservative field. To alleviate this drawback, we propose an element based post-processing technique through which local conservation can be established. The performance of the method is validated through several examples illustrating the convergence of the method, the effectivity of the stabilization term, and the ability to achieve locally conservative normal velocities. Finally, the efficacy of the method is demonstrated through simulations of realistic multiphase flow in poroelastic subsurfaces.

Discriminative Random Field Models for Subsurface Contamination Uncertainty Quantification

NASA Astrophysics Data System (ADS)

Arshadi, M.; Abriola, L. M.; Miller, E. L.; De Paolis Kaluza, C.

2017-12-01

Application of flow and transport simulators for prediction of the release, entrapment, and persistence of dense non-aqueous phase liquids (DNAPLs) and associated contaminant plumes is a computationally intensive process that requires specification of a large number of material properties and hydrologic/chemical parameters. Given its computational burden, this direct simulation approach is particularly ill-suited for quantifying both the expected performance and uncertainty associated with candidate remediation strategies under real field conditions. Prediction uncertainties primarily arise from limited information about contaminant mass distributions, as well as the spatial distribution of subsurface hydrologic properties. Application of direct simulation to quantify uncertainty would, thus, typically require simulating multiphase flow and transport for a large number of permeability and release scenarios to collect statistics associated with remedial effectiveness, a computationally prohibitive process. The primary objective of this work is to develop and demonstrate a methodology that employs measured field data to produce equi-probable stochastic representations of a subsurface source zone that capture the spatial distribution and uncertainty associated with key features that control remediation performance (i.e., permeability and contamination mass). Here we employ probabilistic models known as discriminative random fields (DRFs) to synthesize stochastic realizations of initial mass distributions consistent with known, and typically limited, site characterization data. Using a limited number of full scale simulations as training data, a statistical model is developed for predicting the distribution of contaminant mass (e.g., DNAPL saturation and aqueous concentration) across a heterogeneous domain. Monte-Carlo sampling methods are then employed, in conjunction with the trained statistical model, to generate realizations conditioned on measured borehole data. Performance of the statistical model is illustrated through comparisons of generated realizations with the `true' numerical simulations. Finally, we demonstrate how these realizations can be used to determine statistically optimal locations for further interrogation of the subsurface.

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

NASA Technical Reports Server (NTRS)

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

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

The Development of 3d Sub-Surface Mapping Scheme and its Application to Martian Lobate Debris Aprons

NASA Astrophysics Data System (ADS)

Baik, H.; Kim, J.

2017-07-01

The Shallow Subsurface Radar (SHARAD), a sounding radar equipped on the Mars Reconnaissance Orbiter (MRO), has produced highly valuable information about the Martian subsurface. In particular, the complicated substructures of Mars such as polar deposit, pedestal crater and the other geomorphic features involving possible subsurface ice body has been successfully investigated by SHARAD. In this study, we established a 3D subsurface mapping strategy employing the multiple SHARAD profiles. A number of interpretation components of SHARAD signals were integrated into a subsurface mapping scheme using radargram information and topographic data, then applied over a few mid latitude Lobate Debris Aprons (LDAs). From the identified subsurface layers of LDA, and the GIS data base incorporating the other interpretation outcomes, we are expecting to trace the origin of LDAs. Also, the subsurface mapping scheme developed in this study will be further applied to other interesting Martian geological features such as inter crater structures, aeolian deposits and fluvial sediments. To achieve higher precision sub-surface mapping, the clutter simulation employing the high resolution topographic data and the upgraded clustering algorithms assuming multiple sub-surface layers will be also developed.

Physical-Biological-Optics Model Development and Simulation for the Pacific Ocean and Monterey Bay, California

DTIC Science & Technology

2011-09-30

and easy to apply in large-scale physical-biogeochemical simulations. We also collaborate with Dr. Curt Mobley at Sequoia Scientific for the second...we are collaborating with Dr. Curtis Mobley of Sequoia Scientific on improving the link between the radiative transfer model (EcoLight) within the

Effect of electrochemical corrosion on the subsurface microstructure evolution of a CoCrMo alloy in albumin containing environment

NASA Astrophysics Data System (ADS)

Wang, Zhongwei; Yan, Yu; Su, Yanjing; Qiao, Lijie

2017-06-01

The subsurface microstructures of metallic implants play a key role in bio-tribocorrosion. Due to wear or change of local environment, the implant surface can have inhomogeneous electrochemical corrosion properties. In this work, the effect of electrochemical corrosion conditions on the subsurface microstructure evolution of CoCrMo alloys for artificial joints was investigated. Transmission electron microscope (TEM) was employed to observe the subsurface microstructures of worn areas at different applied potentials in a simulated physiological solution. The results showed that applied potentials could affect the severity of the subsurface deformation not only by changing the surface passivation but also affecting the adsorption of protein on the alloy surface.

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

El Nino and the Global Ocean Observing System

NASA Technical Reports Server (NTRS)

Halpern, David

1999-01-01

Until a decade ago, an often-quoted expression in oceanography is that very few observations are recorded throughout the ocean. Now, the sentiment is no longer valid in the uppermost 10% of the tropical Pacific Ocean nor at the surface of the global ocean. One of the remarkable legacies of the 1985-1994 Tropical Oceans Global Atmosphere (TOGA) Program is an in situ marine meteorological and upper oceanographic measurement array throughout the equatorial Pacific to monitor the development and maintenance of El Nino episodes. The TOGA Observing System, which initially consisted of moored- and drifting-buoy arrays, a network of commercial ships, and coastal and island stations, now includes a constellation of satellites and data-assimilating models to simulate subsurface oceanographic conditions. The El Nino and La Nina tropical Pacific Ocean observing system represents the initial phase of an integrated global ocean observing system. Remarkable improvements have been made in ocean model simulation of subsurface currents, but some problems persist. For example, the simulation of the South Equatorial Current (SEC) remains an important challenge in the 2S-2N Pacific equatorial wave guide. During El Nino the SEC at the equator is reduced and sometimes the direction is reversed, becoming eastward. Both conditions allow warm water stored in the western Pacific to invade the eastern region, creating an El Nino episode. Assimilation of data is a tenet of faith to correct simulation errors caused by deficiencies in surface fluxes (especially wind stress) and parameterizations of subgrid-scale physical processes. In the first of two numerical experiments, the Pacific SEC was simulated with and without assimilation of subsurface temperature data. Along the equator, a very weak SEC occurred throughout the eastern Pacific, independent of assimilation of data. However, as displayed in the diagram, in the western Pacific there was no satisfactory agreement between the two simulations. To help determine reliability of the simulated SEC in the western Pacific, current measurements recorded during the 9-19 October 1994 voyage of the French research vessel L'Atalante are also shown in the diagram. With data assimilation, the simulated SEC was in much better agreement with L'Atalante observations. The simulated SEC with data assimilation was far from perfect, in part because of the sparsity of subsurface temperature observations. In the next experiment, TOPEX/POSEIDON sea surface height data in combination with subsurface temperatures will be assimilated to assess further improvement of the simulation of the SEC.

Fronts and eddies: Engines for biogeochemical variability of the Central Red Sea during winter-spring periods

NASA Astrophysics Data System (ADS)

Zarokanellos, Nikolaos; Jones, Burton

2017-04-01

The central Red Sea (CRS) has been shown to be characterized by significant eddy activity throughout the year. In winter, weakened stratification may lead to enhanced vertical exchange contributing to physical and biogeochemical processes. In winter 2014-2015 we began an extended glider time series to monitor a region in the northern CRS where eddy activity is significant. Remote sensing and glider observations that include CTD, oxygen, CDOM and chlorophyll fluorescence, and multi-wavelength optical backscatter, have been used to characterize the effects of winter mixing and eddy activity in this region. During winter, deep mixing driven by surface cooling and strong winds combined with eddy features, can supply nutrients into the upper layer dramatically modifies the environment from its typically stratified conditions. These mixing events disperse the phytoplankton from the deep chlorophyll maximum throughout the upper mixed layer, and increase the chlorophyll signature detected by ocean color imagery. In addition to the mixing, cyclonic eddies in the region can enhance the vertical displacement of deeper, nutrient containing water toward the euphotic zone contributing to increased chlorophyll concentration and biological productivity. Remote sensing analyses indicate that these eddies also contribute to significant horizontal dispersion including the exchange between the open sea and coastal coral reef ecosystems. During the winter mixing periods, diel fluctuations in phytoplankton biomass have been observed indicative of solar driven plankton dynamics. The biogeochemical response to the subsurface physical processes provides a sensitive indicator to the processes that result from the mixing and eddy dynamics - processes that are not necessarily detectable via remote sensing. In order to understand the seasonal responses, but also the interannual influences on these processes, sustained in situ autonomous platform measurements are essential.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a six-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments. Frontiers in Earth Science Journal Impact & Description - ResearchGate - Impact Rankings ( 2015 and 2016 ). Available from: https://www.researchgate.net/journal/2296-6463_Frontiers_in_Earth_Science [accessed Jul 25, 2016].« less

Structural adjustment for accurate conditioning in large-scale subsurface systems

NASA Astrophysics Data System (ADS)

Tahmasebi, Pejman

2017-03-01

Most of the current subsurface simulation approaches consider a priority list for honoring the well and any other auxiliary data, and eventually adopt a middle ground between the quality of the model and conditioning it to hard data. However, as the number of datasets increases, such methods often produce undesirable features in the subsurface model. Due to their high flexibility, subsurface modeling based on training images (TIs) is becoming popular. Providing comprehensive TIs remains, however, an outstanding problem. In addition, identifying a pattern similar to those in the TI that honors the well and other conditioning data is often difficult. Moreover, the current subsurface modeling approaches do not account for small perturbations that may occur in a subsurface system. Such perturbations are active in most of the depositional systems. In this paper, a new methodology is presented that is based on an irregular gridding scheme that accounts for incomplete TIs and minor offsets. Use of the methodology enables one to use a small or incomplete TI and adaptively change the patterns in the simulation grid in order to simultaneously honor the well data and take into account the effect of the local offsets. Furthermore, the proposed method was used on various complex process-based models and their structures are deformed for matching with the conditioning point data. The accuracy and robustness of the proposed algorithm are successfully demonstrated by applying it to models of several complex examples.

Modeling of Near-Surface Leakage and Seepage of CO2 for Risk Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oldenburg, Curtis M.; Unger, Andre A.J.

2004-02-18

The injection of carbon dioxide (CO2) into deep geologic carbon sequestration sites entails risk that CO2 will leak away from the primary storage formation and migrate upwards to the unsaturated zone from which it can seep out of the ground. We have developed a coupled modeling framework called T2CA for simulating CO2 leakage and seepage in the subsurface and in the atmospheric surface layer. The results of model simulations can be used to calculate the two key health, safety, and environmental (HSE) risk drivers, namely CO2 seepage flux and nearsurface CO2 concentrations. Sensitivity studies for a subsurface system with amore » thick unsaturated zone show limited leakage attenuation resulting in correspondingly large CO2 concentrations in the shallow subsurface. Large CO2 concentrations in the shallow subsurface present a risk to plant and tree roots, and to humans and other animals in subsurface structures such as basements or utility vaults. Whereas CO2 concentrations in the subsurface can be high, surfacelayer winds reduce CO2 concentrations to low levels for the fluxes investigated. We recommend more verification and case studies be carried out with T2CA, along with the development of extensions to handle additional scenarios such as calm conditions, topographic effects, and catastrophic surface-layer discharge events.« less

Surface segregation in a binary mixture of ionic liquids: Comparison between high-resolution RBS measurements and moleculardynamics simulations.

PubMed

Nakajima, Kaoru; Nakanishi, Shunto; Chval, Zdeněk; Lísal, Martin; Kimura, Kenji

2016-11-14

Surface structure of equimolar mixture of 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C 2 C 1 Im][Tf 2 N]) and 1-ethyl-3-methylimidazolium tetrafluoroborate ([C 2 C 1 Im][BF 4 ]) is studied using high-resolution Rutherford backscattering spectroscopy (HRBS) and molecular dynamics (MD) simulations. Both HRBS and MD simulations show enrichment of [Tf 2 N] in the first molecular layer although the degree of enrichment observed by HRBS is more pronounced than that predicted by the MD simulation. In the subsurface region, MD simulation shows a small depletion of [Tf 2 N] while HRBS shows a small enrichment here. This discrepancy is partially attributed to the artifact of the MD simulations. Since the number of each ion is fixed in a finite-size simulation box, surface enrichment of particular ion results in its artificial depletion in the subsurface region.

Surface segregation in a binary mixture of ionic liquids: Comparison between high-resolution RBS measurements and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Nakajima, Kaoru; Nakanishi, Shunto; Chval, Zdeněk; Lísal, Martin; Kimura, Kenji

2016-11-01

Surface structure of equimolar mixture of 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C2C1Im][Tf2N]) and 1-ethyl-3-methylimidazolium tetrafluoroborate ([C2C1Im][BF4]) is studied using high-resolution Rutherford backscattering spectroscopy (HRBS) and molecular dynamics (MD) simulations. Both HRBS and MD simulations show enrichment of [Tf2N] in the first molecular layer although the degree of enrichment observed by HRBS is more pronounced than that predicted by the MD simulation. In the subsurface region, MD simulation shows a small depletion of [Tf2N] while HRBS shows a small enrichment here. This discrepancy is partially attributed to the artifact of the MD simulations. Since the number of each ion is fixed in a finite-size simulation box, surface enrichment of particular ion results in its artificial depletion in the subsurface region.

Reimplementation of the Biome-BGC model to simulate successional change.

PubMed

Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E; Thornton, Peter E

2005-04-01

Biogeochemical process models are increasingly employed to simulate current and future forest dynamics, but most simulate only a single canopy type. This limitation means that mixed stands, canopy succession and understory dynamics cannot be modeled, severe handicaps in many forests. The goals of this study were to develop a version of Biome-BGC that supported multiple, interacting vegetation types, and to assess its performance and limitations by comparing modeled results to published data from a 150-year boreal black spruce (Picea mariana (Mill.) BSP) chronosequence in northern Manitoba, Canada. Model data structures and logic were modified to support an arbitrary number of interacting vegetation types; an explicit height calculation was necessary to prioritize radiation and precipitation interception. Two vegetation types, evergreen needle-leaf and deciduous broadleaf, were modeled based on site-specific meteorological and physiological data. The new version of Biome-BGC reliably simulated observed changes in leaf area, net primary production and carbon stocks, and should be useful for modeling the dynamics of mixed-species stands and ecological succession. We discuss the strengths and limitations of Biome-BGC for this application, and note areas in which further work is necessary for reliable simulation of boreal biogeochemical cycling at a landscape scale.

MODELING THREE-DIMENSIONAL SUBSURFACE FLOW, FATE AND TRANSPORT OF MICROBES AND CHEMICALS (3DFATMIC)

EPA Science Inventory

A three-dimensional model simulating the subsurface flow, microbial growth and degradation, microbial-chemical reaction, and transport of microbes and chemicals has been developed. he model is designed to solve the coupled flow and transport equations. asically, the saturated-uns...

Biotic and abiotic retention, recycling and remineralization of metals in the ocean

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boyd, Philip W.; Ellwood, Michael J.; Tagliabue, Alessandro

Trace metals shape both the biogeochemical functioning and biological structure of oceanic provinces. Trace metal biogeochemistry has primarily focused on modes of external supply of metals from aeolian, hydrothermal, sedimentary and other sources. However, metals also undergo internal transformations such as abiotic and biotic retention, recycling and remineralization. The role of these internal transformations in metal biogeochemical cycling is now coming into focus. First, the retention of metals by biota in the surface ocean for days, weeks or months depends on taxon-specific metal requirements of phytoplankton, and on their ultimate fate: that is, viral lysis, senescence, grazing and/or export tomore » depth. Rapid recycling of metals in the surface ocean can extend seasonal productivity by maintaining higher levels of metal bioavailability compared to the influence of external metal input alone. As metal-containing organic particles are exported from the surface ocean, different metals exhibit distinct patterns of remineralization with depth. These patterns are mediated by a wide range of physicochemical and microbial processes such as the ability of particles to sorb metals, and are influenced by the mineral and organic characteristics of sinking particles. We conclude that internal metal transformations play an essential role in controlling metal bioavailability, phytoplankton distributions and the subsurface resupply of metals.« less

Modeling subsurface stormflow initiation in low-relief landscapes

NASA Astrophysics Data System (ADS)

Hopp, Luisa; Vaché, Kellie B.; Rhett Jackson, C.; McDonnell, Jeffrey J.

2015-04-01

Shallow lateral subsurface flow as a runoff generating mechanism at the hillslope scale has mostly been studied in steeper terrain with typical hillside angles of 10 - 45 degrees. These studies have shown that subsurface stormflow is often initiated at the interface between a permeable upper soil layer and a lower conductivity impeding layer, e.g. a B horizon or bedrock. Many studies have identified thresholds of event size and soil moisture states that need to be exceeded before subsurface stormflow is initiated. However, subsurface stormflow generation on low-relief hillslopes has been much less studied. Here we present a modeling study that investigates the initiation of subsurface stormflow on low-relief hillslopes in the Upper Coastal Plain of South Carolina, USA. Hillslopes in this region typically have slope angles of 2-5 degrees. Topsoils are sandy, underlain by a low-conductivity sandy clay loam Bt horizon. Subsurface stormflow has only been intercepted occasionally in a 120 m long trench, and often subsurface flow was not well correlated with stream signals, suggesting a disconnect between subsurface flow on the hillslopes and stream flow. We therefore used a hydrologic model to better understand which conditions promote the initiation of subsurface flow in this landscape, addressing following questions: Is there a threshold event size and soil moisture state for producing lateral subsurface flow? What role does the spatial pattern of depth to the impeding clay layer play for subsurface stormflow dynamics? We reproduced a section of a hillslope, for which high-resolution topographic data and depth to clay measurements were available, in the hydrologic model HYDRUS-3D. Soil hydraulic parameters were based on experimentally-derived data. The threshold analysis was first performed using hourly climate data records for 2009-2010 from the study site to drive the simulation. For this period also trench measurements of subsurface flow were available. In addition, we also ran a longer-term simulation, using daily climate data for a nine year period to include more variable climate conditions in the threshold analysis. The model captured the observed subsurface flow instances very well. The threshold analysis indicated that the occurrence of subsurface stormflow uncommon, with a large proportion of the water perching above the clay layer percolating vertically into the clay layer. Event sizes of approximately 70-80 mm were required for initiating subsurface stormflow. The hourly data from 2009-2010 was subsequently used to test if the actual spatial distribution of depth to clay is a major control for the occurrence and magnitude of lateral subsurface flow. Results suggest that in this low-relief landscape also a spatially uniform mean depth to clay reproduces well the hydrologic behavior.

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

PubMed

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

2015-08-01

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

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

PubMed Central

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

2015-01-01

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

Efficiency of small scale carbon mitigation by patch iron fertilization

NASA Astrophysics Data System (ADS)

Sarmiento, J. L.; Slater, R. D.; Dunne, J.; Gnanadesikan, A.; Hiscock, M. R.

2010-11-01

While nutrient depletion scenarios have long shown that the high-latitude High Nutrient Low Chlorophyll (HNLC) regions are the most effective for sequestering atmospheric carbon dioxide, recent simulations with prognostic biogeochemical models have suggested that only a fraction of the potential drawdown can be realized. We use a global ocean biogeochemical general circulation model developed at GFDL and Princeton to examine this and related issues. We fertilize two patches in the North and Equatorial Pacific, and two additional patches in the Southern Ocean HNLC region north of the biogeochemical divide and in the Ross Sea south of the biogeochemical divide. We evaluate the simulations using observations from both artificial and natural iron fertilization experiments at nearby locations. We obtain by far the greatest response to iron fertilization at the Ross Sea site, where sea ice prevents escape of sequestered CO2 during the wintertime, and the CO2 removed from the surface ocean by the biological pump is carried into the deep ocean by the circulation. As a consequence, CO2 remains sequestered on century time-scales and the efficiency of fertilization remains almost constant no matter how frequently iron is applied as long as it is confined to the growing season. The second most efficient site is in the Southern Ocean. The North Pacific site has lower initial nutrients and thus a lower efficiency. Fertilization of the Equatorial Pacific leads to an expansion of the suboxic zone and a striking increase in denitrification that causes a sharp reduction in overall surface biological export production and CO2 uptake. The impacts on the oxygen distribution and surface biological export are less prominent at other sites, but nevertheless still a source of concern. The century time scale retention of iron in this model greatly increases the long-term biological response to iron addition as compared with simulations in which the added iron is rapidly scavenged from the ocean.

A process-oriented hydro-biogeochemical model enabling simulation of gaseous carbon and nitrogen emissions and hydrologic nitrogen losses from a subtropical catchment.

PubMed

Zhang, Wei; Li, Yong; Zhu, Bo; Zheng, Xunhua; Liu, Chunyan; Tang, Jialiang; Su, Fang; Zhang, Chong; Ju, Xiaotang; Deng, Jia

2018-03-01

Quantification of nitrogen losses and net greenhouse gas (GHG) emissions from catchments is essential for evaluating the sustainability of ecosystems. However, the hydrologic processes without lateral flows hinder the application of biogeochemical models to this challenging task. To solve this issue, we developed a coupled hydrological and biogeochemical model, Catchment Nutrients Management Model - DeNitrification-DeComposition Model (CNMM-DNDC), to include both vertical and lateral mass flows. By incorporating the core biogeochemical processes (including decomposition, nitrification, denitrification and fermentation) of the DNDC into the spatially distributed hydrologic framework of the CNMM, the simulation of lateral water flows and their influences on nitrogen transportation can be realized. The CNMM-DNDC was then calibrated and validated in a small subtropical catchment belonged to Yanting station with comprehensive field observations. Except for the calibration of water flows (surface runoff and leaching water) in 2005, stream discharges of water and nitrate in 2007, the model validations of soil temperature, soil moisture, crop yield, water flows in 2006 and associated nitrate loss, fluxes of methane, ammonia, nitric oxide and nitrous oxide, and stream discharges of water and nitrate in 2008 were statistically in good agreement with the observations. Meanwhile, our initial simulation of the catchment showed scientific predictions. For instance, it revealed the following: (i) dominant ammonia volatilization among the losses of nitrogenous gases (accounting for 11-21% of the applied annual fertilizer nitrogen in croplands); (ii) hotspots of nitrate leaching near the main stream; and (iii) a net GHG sink function of the catchment. These results implicate the model's promising capability of predicting ecosystem productivity, hydrologic nitrogen loads, losses of gaseous nitrogen and emissions of GHGs, which could be used to provide strategies for establishing sustainable catchments. In addition, the model's capability would be further proved by applying in other catchments with different backgrounds. Copyright © 2017. Published by Elsevier B.V.

Evaluating the effect of oceanic striations on biogeochemistry in the eastern South Pacific

NASA Astrophysics Data System (ADS)

Auger, P. A.; Belmadani, A.; Donoso, D.; Hormazabal, S.

2017-12-01

In recent years, quasi-zonal mesoscale jet-like features or striations have been ubiquitously detected in the time-mean circulation of the world ocean using satellite altimetry and in situ data. Most likely the result of some organization of the mesoscale eddy field such as preferred eddy tracks, these striations may be able to advect and mix physical properties. Yet, their impact on biogeochemistry has not been assessed yet. Off central Chile, the interaction between striations and sharp background gradients of biogeochemical properties may spatially structure biogeochemistry, with potential implications for marine ecosystems. For instance, striations may affect the mean horizontal distribution of surface phytoplankton biomass in the coastal transition zone (CTZ), or the structure and variability of the oxygen-minimum zone (OMZ). Here, we evaluate the expression of striations in satellite records of ocean color and in a set of numerically simulated biogeochemical tracers off central Chile (chlorophyll, carbon, primary production, oxygen, nutrients), averaged over the surface productive layer, the OMZ at intermediate depths or the water column. A multi-decadal hindcast simulation of the physical-biogeochemical dynamics was run over the period 1984-2013 using the ROMS-PISCES (for Regional Oceanic Modeling System - Pelagic Interactions Scheme for Carbon and Ecosystem Studies) platform at an eddy-resolving resolution. Satellite data and model outputs are spatially high-pass filtered to remove the large-scale signal and evaluate the match between striations and biogeochemical tracer anomalies in the model and observations. The effect of striations on the mean shape of the zonal gradient of phytoplankton biomass in the CTZ between eutrophic coastal waters and oligotrophic offshore waters is then deduced. The fraction of tracer anomalies due to striations is quantified, and the structuring roles of stationary and transient striations are respectively explored by matching striations and biogeochemical tracers on moving frames of variable widths from 6 months to several years.

San Francisco Bay nutrients and plankton dynamics as simulated by a coupled hydrodynamic-ecosystem model

NASA Astrophysics Data System (ADS)

Liu, Qianqian; Chai, Fei; Dugdale, Richard; Chao, Yi; Xue, Huijie; Rao, Shivanesh; Wilkerson, Frances; Farrara, John; Zhang, Hongchun; Wang, Zhengui; Zhang, Yinglong

2018-06-01

An open source coupled physical-biogeochemical model is developed for San Francisco Bay (SFB) to study nutrient cycling and plankton dynamics as well as to assist ecosystem based management and risk assessment. The biogeochemical model in this study is based on the Carbon, Silicate and Nitrogen Ecosystem (CoSiNE) model, and coupled to the unstructured grid, Semi-Implicit Cross-scale Hydroscience Integrated System Model (SCHISM). The SCHISM-CoSiNE model reproduces the spatial and temporal variability in nutrients and plankton biomass, and its physical and biogeochemical performance is successfully tested using comparisons with shipboard and fixed station observations. The biogeochemical characteristics of the SFB during wet and dry years are investigated by changing the input of the major rivers. River discharges from the Sacramento and San Joaquin Rivers affect the phytoplankton biomass in North SFB through both advection and dilution of nutrient (including ammonium, NH4) concentrations in the river. The reduction in residence time caused by increased inflows can result in decreased biomass accumulation, while the corresponding reduction in NH4 concentration favors the growth of biomass. In addition, the model is used to make a series of sensitivity experiments to examine the response of SFB to changes in 1) nutrient loading from rivers and wastewater treatment plants (WWTPs), 2) a parameter (ψ) defining NH4 inhibition of nitrate (NO3) uptake by phytoplankton, 3) bottom grazing and 4) suspended sediment concentration. The model results show that changes in NH4 input from rivers or WWTPs affect the likelihood of phytoplankton blooms via NH4 inhibition and that the choice of ψ is critical. Bottom grazing simulated here as increased plankton mortality demonstrates the potential for bivalve reduction of chlorophyll biomass and the need to include bivalve grazing in future models. Furthermore, the model demonstrates the need to include sediments and their contribution to turbidity and availability of light. This biogeochemical model is suitable for other estuaries with similar ecological issues and anthropogenic stressors.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

The research described below was conducted on Fourchon Beach, a coastal headland consisting of nine miles of fairly pristine sandy beaches and dunes, backed by wetlands and tidal channels, located between Belle Pass tidal inlet on the west and Elmer's Island on the east in Lafourche Parish, Louisiana. MC252 oil first arrived in large quantities on Fourchon Beach on or around May 20, 2010. A unique oil form created under these conditions was an aggregate of sand and emulsified oil, typically 0.1-10 cm in diameter, termed small surface residue balls (SSRBs). The work from this project made critical measurements on the factors controlling biodegradability of these SSRB aggregates. SSRB aggregates were sampled across transects perpendicular to the beach from the intertidal to the supratidal. Areas in the supratidal that were sampled initially were set aside for research purposes and not altered by any clean-up activities. Chemical composition of SSRBs was measured including concentrations of n-alkanes, PAHs, hopanes, nutrients (nitrate, nitrite, ammonium and orthophosphate measured on water extracts of SSRBs), and electron acceptor concentrations (O2 microprofiles measured on intact SSRBs and sulfate). Physical characterization of the SSRBs including length and area dimensions, mass, density, porosity, moisture content, and salinity using standard methods. Microbial characterization of SSRBs was also conducted using denaturing gradient gel electrophoresis and sequencing of dominant bands. SSRBs were sampled from various locations across the beach profile deposited by 2 significant tropical events in 2010; Hurricane Alex and TS Bonnie, and one event in 2011, TS Lee. Sampling focused on comparing and contrasting impacts of biogeochemistry on weathering of oil stranded in three beach microenvironments; supratidal surface; subtidal subsurface which is permanently inundated and intertidal subsurface samples which are intermittently inundated. The three types of oil are dramatically different in appearance and have a distinctive chemical signature indicative of different rates of weathering. Supratidal surface samples were depleted in n-alkanes and lower-molecular weight PAHs. Geochemically, aggregates located in these environments had low salinities (1.3-1.5 ppt), O2 at near saturation throughout the aggregates and nutrient concentrations (N and P) significantly lower than SSRBs deposited in the intertidal and subtidal. Intertidal and subtidal subsurface oil samples were characterized by elevated nutrient concentrations and salinities consistent with regular seawater inundation. Complete inundation leads to O2 consumption in the aggregates after several days. Despite the presence of elevated nutrients, PAHs and n-alkanes were comparatively unweathered in the subtidal subsurface samples consistent with O2 limitations. Sequences of known PAH degraders were isolated from the supratidal and intertidal aggregates. The results to be presented support the hypothesis that SSRBs deposited at different locations on the beach have different biogeochemical characteristics . These characteristics are due, in part, to their location on the landscape.

An intermediate-scale model for thermal hydrology in low-relief permafrost-affected landscapes

DOE PAGES

Jan, Ahmad; Coon, Ethan T.; Painter, Scott L.; ...

2017-07-10

Integrated surface/subsurface models for simulating the thermal hydrology of permafrost-affected regions in a warming climate have recently become available, but computational demands of those new process-rich simu- lation tools have thus far limited their applications to one-dimensional or small two-dimensional simulations. We present a mixed-dimensional model structure for efficiently simulating surface/subsurface thermal hydrology in low-relief permafrost regions at watershed scales. The approach replaces a full three-dimensional system with a two-dimensional overland thermal hydrology system and a family of one-dimensional vertical columns, where each column represents a fully coupled surface/subsurface thermal hydrology system without lateral flow. The system is then operatormore » split, sequentially updating the overland flow system without sources and the one-dimensional columns without lateral flows. We show that the app- roach is highly scalable, supports subcycling of different processes, and compares well with the corresponding fully three-dimensional representation at significantly less computational cost. Those advances enable recently developed representations of freezing soil physics to be coupled with thermal overland flow and surface energy balance at scales of 100s of meters. Furthermore developed and demonstrated for permafrost thermal hydrology, the mixed-dimensional model structure is applicable to integrated surface/subsurface thermal hydrology in general.« less

Changes in Chesapeake Bay Hypoxia over the Past Century

NASA Astrophysics Data System (ADS)

Friedrichs, M. A.; Kaufman, D. E.; Najjar, R.; Tian, H.; Zhang, B.; Yao, Y.

2016-02-01

The Chesapeake Bay, one of the world's largest estuaries, is among the many coastal systems where hypoxia is a major concern and where dissolved oxygen thus represents a critical factor in determining the health of the Bay's ecosystem. Over the past century, the population of the Chesapeake Bay region has almost quadrupled, greatly modifying land cover and management practices within the watershed. Simultaneously, the Chesapeake Bay has been experiencing a high degree of climate change, including increases in temperature, precipitation, and precipitation intensity. Together, these changes have resulted in significantly increased riverine nutrient inputs to the Bay. In order to examine how interdecadal changes in riverine nitrogen input affects biogeochemical cycling and dissolved oxygen concentrations in Chesapeake Bay, a land-estuarine-ocean biogeochemical modeling system has been developed for this region. Riverine inputs of nitrogen to the Bay are computed from a terrestrial ecosystem model (the Dynamic Land Ecosystem Model; DLEM) that resolves riverine discharge variability on scales of days to years. This temporally varying discharge is then used as input to the estuarine-carbon-biogeochemical model embedded in the Regional Modeling System (ROMS), which provides estimates of the oxygen concentrations and nitrogen fluxes within the Bay as well as advective exports from the Bay to the adjacent Mid-Atlantic Bight shelf. Simulation results from this linked modeling system for the present (early 2000s) have been extensively evaluated with in situ and remotely sensed data. Longer-term simulations are used to isolate the effect of increased riverine nitrogen loading on dissolved oxygen concentrations and biogeochemical cycling within the Chesapeake Bay.

Translucent Radiosity: Efficiently Combining Diffuse Inter-Reflection and Subsurface Scattering.

PubMed

Sheng, Yu; Shi, Yulong; Wang, Lili; Narasimhan, Srinivasa G

2014-07-01

It is hard to efficiently model the light transport in scenes with translucent objects for interactive applications. The inter-reflection between objects and their environments and the subsurface scattering through the materials intertwine to produce visual effects like color bleeding, light glows, and soft shading. Monte-Carlo based approaches have demonstrated impressive results but are computationally expensive, and faster approaches model either only inter-reflection or only subsurface scattering. In this paper, we present a simple analytic model that combines diffuse inter-reflection and isotropic subsurface scattering. Our approach extends the classical work in radiosity by including a subsurface scattering matrix that operates in conjunction with the traditional form factor matrix. This subsurface scattering matrix can be constructed using analytic, measurement-based or simulation-based models and can capture both homogeneous and heterogeneous translucencies. Using a fast iterative solution to radiosity, we demonstrate scene relighting and dynamically varying object translucencies at near interactive rates.

The simulated climate of the Last Glacial Maximum and insights into the global carbon cycle.

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R.; Lenton, A.; Phipps, S. J.; Chase, Z.; Etheridge, D. M.

2016-12-01

The ocean's ability to store large quantities of carbon, combined with the millennial longevity over which this reservoir is overturned, has implicated the ocean as a key driver of glacial-interglacial climates. However, the combination of processes that cause an accumulation of carbon within the ocean during glacial periods is still under debate. Here we present simulations of the Last Glacial Maximum (LGM) using the CSIRO Mk3L-COAL Earth System Model to test the contribution of key biogeochemical processes to ocean carbon storage. For the coupled LGM simulation, we find that significant cooling (3.2 °C), expanded minimum (Northern Hemisphere: 105 %; Southern Hemisphere: 225 %) and maximum (Northern Hemisphere: 145 %; Southern Hemisphere: 120 %) sea ice cover, and a reorganisation of the overturning circulation caused significant changes in ocean biogeochemical fields. The coupled LGM simulation stores an additional 322 Pg C in the deep ocean relative to the Pre-Industrial (PI) simulation. However, 839 Pg C is lost from the upper ocean via equilibration with a lower atmospheric CO2 concentration, causing a net loss of 517 Pg C relative to the PI simulation. The LGM deep ocean also experiences an oxygenation (>100 mmol O2 m-3) and deepening of the aragonite saturation depth (> 2,000 m deeper) at odds with proxy reconstructions. Hence, these physical changes cannot in isolation produce plausible biogeochemistry nor the required drawdown of atmospheric CO2 of 80-100 ppm at the LGM. With modifications to key biogeochemical processes, which include an increased export of organic matter due to a simulated release from iron limitation, a deepening of remineralisation and decreased inorganic carbon export driven by cooler temperatures, we find that the carbon content in the glacial oceanic reservoir can be increased (326 Pg C) to a level that is sufficient to explain the reduction in atmospheric and terrestrial carbon at the LGM (520 ± 400 Pg C). These modifications also go some way to reconcile simulated export production, aragonite saturation state and oxygen fields with those that have been reconstructed by proxy measurements, thereby implicating past changes in ocean biogeochemistry as an essential driver of the climate system.

Corn stover harvest increases herbicide movement to subsurface drains – Root Zone Water Quality Model simulations

USDA-ARS?s Scientific Manuscript database

BACKGROUND: Removal of crop residues for bioenergy production can alter soil hydrologic properties, but there is little information on its impact on transport of herbicides and their degradation products to subsurface drains. The Root Zone Water Quality Model, previously calibrated using measured fl...

The Search for Subsurface Life on Mars: Results from the MARTE Analog Drill Experiment in Rio Tinto, Spain

NASA Astrophysics Data System (ADS)

Stoker, C. R.; Lemke, L. G.; Cannon, H.; Glass, B.; Dunagan, S.; Zavaleta, J.; Miller, D.; Gomez-Elvira, J.

2006-03-01

The Mars Analog Research and Technology (MARTE) experiment has developed an automated drilling system on a simulated Mars lander platform including drilling, sample handling, core analysis and down-hole instruments relevant to searching for life in the Martian subsurface.

3DHYDROGEOCHEM: A 3-DIMENSIONAL MODEL OF DENSITY-DEPENDENT SUBSURFACE FLOW AND THERMAL MULTISPECIES-MULTICOMPONENT HYDROGEOCHEMICAL TRANSPORT

EPA Science Inventory

This report presents a three-dimensional finite-element numerical model designed to simulate chemical transport in subsurface systems with temperature effect taken into account. The three-dimensional model is developed to provide (1) a tool of application, with which one is able...

Corn stover harvest increases herbicide movement to subsurface drains - Root Zone Water Quality Model simulations.

PubMed

Shipitalo, Martin J; Malone, Robert W; Ma, Liwang; Nolan, Bernard T; Kanwar, Rameshwar S; Shaner, Dale L; Pederson, Carl H

2016-06-01

Crop residue removal for bioenergy production can alter soil hydrologic properties and the movement of agrochemicals to subsurface drains. The Root Zone Water Quality Model (RZWQM), previously calibrated using measured flow and atrazine concentrations in drainage from a 0.4 ha chisel-tilled plot, was used to investigate effects of 50 and 100% corn (Zea mays L.) stover harvest and the accompanying reductions in soil crust hydraulic conductivity and total macroporosity on transport of atrazine, metolachlor and metolachlor oxanilic acid (OXA). The model accurately simulated field-measured metolachlor transport in drainage. A 3 year simulation indicated that 50% residue removal reduced subsurface drainage by 31% and increased atrazine and metolachlor transport in drainage 4-5-fold when surface crust conductivity and macroporosity were reduced by 25%. Based on its measured sorption coefficient, approximately twofold reductions in OXA losses were simulated with residue removal. The RZWQM indicated that, if corn stover harvest reduces crust conductivity and soil macroporosity, losses of atrazine and metolachlor in subsurface drainage will increase owing to reduced sorption related to more water moving through fewer macropores. Losses of the metolachlor degradation product OXA will decrease as a result of the more rapid movement of the parent compound into the soil. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Predicting marine physical-biogeochemical variabilities in the Gulf of Mexico and southeastern U.S. shelf sea

NASA Astrophysics Data System (ADS)

He, R.; Zong, H.; Xue, Z. G.; Fennel, K.; Tian, H.; Cai, W. J.; Lohrenz, S. E.

2017-12-01

An integrated terrestrial-ocean ecosystem modeling system is developed and used to investigate marine physical-biogeochemical variabilities in the Gulf of Mexico and southeastern US shelf sea. Such variabilities stem from variations in the shelf circulation, boundary current dynamics, impacts of climate variability, as well as growing population and associated land use practices on transport of carbon and nutrients within terrestrial systems and their delivery to the coastal ocean. We will report our efforts in evaluating the performance of the coupled modeling system via extensive model and data comparisons, as well as findings from a suite of case studies and scenario simulations. Long-term model simulation results are used to quantify regional ocean circulation dynamics, nitrogen budget and carbon fluxes. Their corresponding sub-regional differences are also characterized and contrasted.

The Effects of Mineral Matrices and Extraction Method on Quantification of Bacterial Phospholipid Fatty Acids.

NASA Astrophysics Data System (ADS)

Ford, S. E.; McKelvie, J. R. M.; Sherwood Lollar, B.; Slater, G. F.

2017-12-01

Understanding the distribution, abundances and metabolic activities of microbial life in the subsurface is fundamental to our understanding of biogeochemical cycling on Earth. Given that the most likely environments for life to still exist, or be preserved, on other planets and moons in the solar system are in the subsurface, a better understanding of subsurface life on Earth is also a key factor in our ability to search for life beyond the Earth. While we have made progress in investigating life in the continental subsurface in recent years, significant challenges remain. In particular, the low biomass abundance, heterogeneous distribution of biomass, and the potential for matrix effects during sampling and analysis mean that further development and optimization of methods to study subsurface life are needed. Phospholipid fatty acids (PLFA) are a useful biosignature of extant, viable microbial communities that are applied in a wide range of environments. Here we test the sensitivity of two methods of PLFA analysis (modified Bligh and Dyer, Microwave Assisted Extraction) to detect known numbers of cells doped into two distinct matrices (bentonite, crushed granite). Samples were prepared by adding known cellular concentrations of Basciullus subtilis subtilis (ATCC 6051) to crushed bentonite, or to granite, respectively, to create dilution series. Samples were extracted for PLFA using a dichloromethane-methanol modified Bligh & Dyer (mBD) or Microwave Assisted Extraction (MAE) and then quantified using GC - MS and GC - FID. Pure culture extractions yielded a linearly decreasing trend to the level of the process blank. The ratio of cells to PLFA for this trend was 2.4x104 +/- 1.9x104 cells/pmol at the lower end of the generic range of 2 to 6 x105 cells/pmol. For bentonite the PLFA results were lower than for the pure culture. PLFA results for bentonite followed a linear trend at higher concentrations, but departed from this at low concentrations indicating the potential for interference for low biomass samples. The ratio of cells to PLFA for the bentonite was to 6.2x104 +/- 4.5x104 cells/pmol, at the upper end of generic range. Ongoing comparison of the efficiency of microwave extraction and the effect of different matrices (e.g. granite) aims to optimize detection of PLFA for low biomass samples relevant to subsurface systems.

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

NASA Astrophysics Data System (ADS)

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

2008-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2005-12-01

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.

How deep can surface signals be traced in the critical zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape

NASA Astrophysics Data System (ADS)

Küsel, Kirsten; Totsche, Kai; Trumbore, Susan; Lehmann, Robert; Steinhäuser, Christine; Herrmann, Martina

2016-04-01

The Earth's Critical Zone (CZ) is a thin living layer connecting atmosphere and geosphere, including aquifers. Humans live in the CZ and benefit from the vital supporting services it provides. However, the CZ is increasingly impacted by human activities including land and resource use, pollution and climate change. Recent interest in uniting the many disciplines studying this complex domain has initiated an international network of research infrastructure platforms that allow access to the CZ in a range of geologic settings. In this paper a new such infrastructure platform associated with the Collaborative Research Center AquaDiva is described, that uniquely seeks to combine CZ research with detailed investigation of the functional biodiversity of the subsurface. Overall, AquaDiva aims to test hypotheses about how water connects surface conditions set by land cover and land management to the biota and biogeochemical functions in the subsurface. With long-term and continuous observations, hypotheses about how seasonal variations and extreme events at the surface impact subsurface processes, community structure and function, are tested. AquaDiva has established the Hainich Critical Zone Exploratory (CZE) in central Germany in an alkaline geological setting of German Triassic Muschelkalk formations. The Hainich CZE includes specialized monitoring wells to access the vadose zone and two main groundwater complexes in limestone and marlstone parent materials along a ~6 km transect spanning forest, pasture and agricultural land uses. Initial results demonstrate fundamental differences in the biota and biogeochemistry of the two aquifer complexes that trace back to the land uses in their respective recharge areas. They also show the importance of antecedent conditions on the impact of precipitation events on responses in terms of groundwater dynamics, chemistry and ecology. Thus we find signals of surface land use and events can be detected in the subsurface CZ. Future research will expand to a second CZE in contrasting siliciclastic parent rock, to evaluate the relative importance of parent material lithology versus surface conditions for the emergent characteristics of the subsurface CZ and biodiversity. The Hainich CZE is open to researchers who bring new questions that the research platform can help answer.

Thermodynamic Cconstraints on Coupled Carbonate-Pyrite Weathering Dynamics and Carbon Fluxes

NASA Astrophysics Data System (ADS)

Winnick, M.; Maher, K.

2017-12-01

Chemical weathering within the critical zone regulates global biogeochemical cycles, atmospheric composition, and the supply of key nutrients to terrestrial and aquatic ecosystems. Recent studies suggest that thermodynamic limits on solute production act as a first-order control on global chemical weathering rates; however, few studies have addressed the factors that set these thermodynamic limits in natural systems. In this presentation, we investigate the effects of soil CO2 concentrations and pyrite oxidation rates on carbonate dissolution and associated carbon fluxes in the East River watershed in Colorado, using concentration-discharge relationships and thermodynamic constraints. Within the shallow subsurface, soil respiration rates and moisture content determine the extent of carbonic acid-promoted carbonate dissolution through their modulation of soil pCO2 and the balance of open- v. closed-system weathering processes. At greater depths, pyrite oxidation generates sulfuric acid, which alters the approach to equilibrium of infiltrating waters. Through comparisons of concentration-discharge data and reactive transport model simulations, we explore the conditions that determine whether sulfuric acid reacts to dissolve additional carbonate mineral or instead reacts with alkalinity already in solution - the balance of which determines watershed carbon flux budgets. Our study highlights the importance of interactions between the chemical structure of the critical zone and the hydrologic regulation of flowpaths in determining concentration-discharge relationships and overall carbon fluxes.

Pore-Scale Characterization of Biogeochemical Controls on Iron and Uranium Speciation under Flow Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearce, Carolyn I.; Wilkins, Michael J.; Zhang, Changyong

2012-09-17

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray Microprobe and X-ray Absorption Spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced inmore » the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting re-oxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.« less

LIRAS mission for lunar exploration by microwave interferometric radiometer: Moon's subsurface characterization, emission model and numerical simulator

NASA Astrophysics Data System (ADS)

Pompili, Sara; Silvio Marzano, Frank; Di Carlofelice, Alessandro; Montopoli, Mario; Talone, Marco; Crapolicchio, Raffaele; L'Abbate, Michelangelo; Varchetta, Silvio; Tognolatti, Piero

2013-04-01

The "Lunar Interferometric Radiometer by Aperture Synthesis" (LIRAS) mission is promoted by the Italian Space Agency and is currently in feasibility phase. LIRAS' satellite will orbit around the Moon at a height of 100 km, with a revisiting time period lower than 1 lunar month and will be equipped with: a synthetic aperture radiometer for subsurface sounding purposes, working at 1 and 3 GHz, and a real aperture radiometer for near-surface probing, working at 12 and 24 GHz. The L-band payload, representing a novel concept for lunar exploration, is designed as a Y-shaped thinned array with three arms less than 2.5 m long. The main LIRAS objectives are high-resolution mapping and vertical sounding of the Moon subsurface by applying the advantages of the antenna aperture synthesis technique to a multi-frequency microwave passive payload. The mission is specifically designed to achieve spatial resolutions less than 10 km at surface and to retrieve thermo-morphological properties of the Moon subsurface within 5 m of depth. Among LIRAS products are: lunar near-surface brightness temperature, subsurface brightness temperature gross profile, subsurface regolith thickness, density and average thermal conductivity, detection index of possible subsurface discontinuities (e.g. ice presence). The following study involves the preliminary design of the LIRAS payload and the electromagnetic and thermal characterization of the lunar subsoil through the implementation of a simulator for reproducing the LIRAS measurements in response to observations of the Moon surface and subsurface layers. Lunar physical data, collected after the Apollo missions, and LIRAS instrument parameters are taken as input for the abovementioned simulator, called "LIRAS End-to-end Performance Simulator" (LEPS) and obtained by adapting the SMOS End-to-end Performance Simulator to the different instrumental, orbital, and geophysical LIRAS characteristics. LEPS completely simulates the behavior of the satellite when it becomes operational providing the extrapolation of lunar brightness temperature maps in both Antenna frame (the cosine domain) and on the Moon surface and allowing an accurate analysis of the instrument performance. The Moon stratigraphy is reproduced in LEPS environment through three scenarios: a macro-layer of regolith; two subsequent macro-layers of regolith and rock; three subsequent macro-layers of regolith, ice and rock, respectively. These scenarios are studied using an incoherent approach, taking into account the interaction between the upwelling and downwelling radiation contributions from each layer to model the resulting brightness temperature at the surface level. It has been considered that the radiative behavior of the Moon varies over time, depending on solar illumination conditions, and it is also function of the material properties, layer thickness and specific position on the lunar crust; moreover it has been examined its variation with frequency, observation angle, and polarization. Using the proposed emission model it has been possible to derive a digital thermal model in the microwave frequency of the Moon, allowing in-depth analysis of the lunar soil consistency; this collected information could be related with a lunar digital elevation model in order to achieve global coverage information on topological aspects. The main results of the study will be presented at the conference.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Partitioning Tracer Test for Detection, Estimation, and Remediation Performance Assessment of Subsurface Nonaqueous Phase Liquids

NASA Astrophysics Data System (ADS)

Jin, Minquan; Delshad, Mojdeh; Dwarakanath, Varadarajan; McKinney, Daene C.; Pope, Gary A.; Sepehrnoori, Kamy; Tilburg, Charles E.; Jackson, Richard E.

1995-05-01

In this paper we present a partitioning interwell tracer test (PITT) technique for the detection, estimation, and remediation performance assessment of the subsurface contaminated by nonaqueous phase liquids (NAPLs). We demonstrate the effectiveness of this technique by examples of experimental and simulation results. The experimental results are from partitioning tracer experiments in columns packed with Ottawa sand. Both the method of moments and inverse modeling techniques for estimating NAPL saturation in the sand packs are demonstrated. In the simulation examples we use UTCHEM, a comprehensive three-dimensional, chemical flood compositional simulator developed at the University of Texas, to simulate a hypothetical two-dimensional aquifer with properties similar to the Borden site contaminated by tetrachloroethylene (PCE), and we show how partitioning interwell tracer tests can be used to estimate the amount of PCE contaminant before remedial action and as the remediation process proceeds. Tracer tests results from different stages of remediation are compared to determine the quantity of PCE removed and the amount remaining. Both the experimental (small-scale) and simulation (large-scale) results demonstrate that PITT can be used as an innovative and effective technique to detect and estimate the amount of residual NAPL and for remediation performance assessment in subsurface formations.

Partitioning tracer test for detection, estimation, and remediation performance assessment of subsurface nonaqueous phase liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, M.; Delshad, M.; Dwarakanath, V.

1995-05-01

In this paper we present a partitioning interwell tracer test (PITT) technique for the detection, estimation, and remediation performance assessment of the subsurface contaminated by nonaqueous phase liquids (NAPLs). We demonstrate the effectiveness of this technique by examples of experimental and simulation results. The experimental results are from partitioning tracer experiments in columns packed with Ottawa sand. Both the method of moments and inverse modeling techniques for estimating NAPL saturation in the sand packs are demonstrated. In the simulation examples we use UTCHEM, a comprehensive three-dimensional, chemical flood compositional simulator developed at the University of Texas, to simulate a hypotheticalmore » two-dimensional aquifer with properties similar to the Borden site contaminated by tetrachloroethylene (PCE), and we show how partitioning interwell tracer tests can be used to estimate the amount of PCE contaminant before remedial action and as the remediation process proceeds. Tracer test results from different stages of remediation are compared to determine the quantity of PCE removed and the amount remaining. Both the experimental (small-scale) and simulation (large-scale) results demonstrate that PITT can be used as an innovative and effective technique to detect and estimate the amount of residual NAPL and for remediation performance assessment in subsurface formations. 43 refs., 10 figs., 1 tab.« less

Simulation Based Exploration of Critical Zone Dynamics in Intensively Managed Landscapes

NASA Astrophysics Data System (ADS)

Kumar, P.

2017-12-01

The advent of high-resolution measurements of topographic and (vertical) vegetation features using areal LiDAR are enabling us to resolve micro-scale ( 1m) landscape structural characteristics over large areas. Availability of hyperspectral measurements is further augmenting these LiDAR data by enabling the biogeochemical characterization of vegetation and soils at unprecedented spatial resolutions ( 1-10m). Such data have opened up novel opportunities for modeling Critical Zone processes and exploring questions that were not possible before. We show how an integrated 3-D model at 1m grid resolution can enable us to resolve micro-topographic and ecological dynamics and their control on hydrologic and biogeochemical processes over large areas. We address the computational challenge of such detailed modeling by exploiting hybrid CPU and GPU computing technologies. We show results of moisture, biogeochemical, and vegetation dynamics from studies in the Critical Zone Observatory for Intensively managed Landscapes (IMLCZO) in the Midwestern United States.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Simulated laser fluorosensor signals from subsurface chlorophyll distributions

NASA Technical Reports Server (NTRS)

Venable, D. D.; Khatun, S.; Punjabi, A.; Poole, L.

1986-01-01

A semianalytic Monte Carlo model has been used to simulate laser fluorosensor signals returned from subsurface distributions of chlorophyll. This study assumes the only constituent of the ocean medium is the common coastal zone dinoflagellate Prorocentrum minimum. The concentration is represented by Gaussian distributions in which the location of the distribution maximum and the standard deviation are variable. Most of the qualitative features observed in the fluorescence signal for total chlorophyll concentrations up to 1.0 microg/liter can be accounted for with a simple analytic solution assuming a rectangular chlorophyll distribution function.

Biogenic uraninite precipitation and its reoxidation by iron(III) (hydr)oxides: A reaction modeling approach

NASA Astrophysics Data System (ADS)

Spycher, Nicolas F.; Issarangkun, Montarat; Stewart, Brandy D.; Sevinç Şengör, S.; Belding, Eileen; Ginn, Tim R.; Peyton, Brent M.; Sani, Rajesh K.

2011-08-01

One option for immobilizing uranium present in subsurface contaminated groundwater is in situ bioremediation, whereby dissimilatory metal-reducing bacteria and/or sulfate-reducing bacteria are stimulated to catalyze the reduction of soluble U(VI) and precipitate it as uraninite (UO 2). This is typically accomplished by amending groundwater with an organic electron donor. It has been shown, however, that once the electron donor is entirely consumed, Fe(III) (hydr)oxides can reoxidize biogenically produced UO 2, thus potentially impeding cleanup efforts. On the basis of published experiments showing that such reoxidation takes place even under highly reducing conditions (e.g., sulfate-reducing conditions), thermodynamic and kinetic constraints affecting this reoxidation are examined using multicomponent biogeochemical simulations, with particular focus on the role of sulfide and Fe(II) in solution. The solubility of UO 2 and Fe(III) (hydr)oxides are presented, and the effect of nanoscale particle size on stability is discussed. Thermodynamically, sulfide is preferentially oxidized by Fe(III) (hydr)oxides, compared to biogenic UO 2, and for this reason the relative rates of sulfide and UO 2 oxidation play a key role on whether or not UO 2 reoxidizes. The amount of Fe(II) in solution is another important factor, with the precipitation of Fe(II) minerals lowering the Fe +2 activity in solution and increasing the potential for both sulfide and UO 2 reoxidation. The greater (and unintuitive) UO 2 reoxidation by hematite compared to ferrihydrite previously reported in some experiments can be explained by the exhaustion of this mineral from reaction with sulfide. Simulations also confirm previous studies suggesting that carbonate produced by the degradation of organic electron donors used for bioreduction may significantly increase the potential for UO 2 reoxidation through formation of uranyl carbonate aqueous complexes.

Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics

NASA Astrophysics Data System (ADS)

Boutchko, Rostyslav; Rayz, Vitaliy L.; Vandehey, Nicholas T.; O'Neil, James P.; Budinger, Thomas F.; Nico, Peter S.; Druhan, Jennifer L.; Saloner, David A.; Gullberg, Grant T.; Moses, William W.

2012-01-01

This paper presents experimental and modeling aspects of applying nuclear emission tomography to study fluid flow in laboratory packed porous media columns of the type frequently used in geophysics, geochemistry and hydrology research. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are used as non-invasive tools to obtain dynamic 3D images of radioactive tracer concentrations. Dynamic sequences obtained using 18F-FDG PET are used to trace flow through a 5 cm diameter × 20 cm tall sand packed column with and without an impermeable obstacle. In addition, a custom-made rotating column setup placed in a clinical two-headed SPECT camera is used to image 99mTc-DTPA tracer propagation in a through-flowing column (10 cm diameter × 30 cm tall) packed with recovered aquifer sediments. A computational fluid dynamics software package FLUENT is used to model the observed flow dynamics. Tracer distributions obtained in the simulations in the smaller column uniformly packed with sand and in the column with an obstacle are remarkably similar to the reconstructed images in the PET experiments. SPECT results demonstrate strongly non-uniform flow patterns for the larger column slurry-packed with sub-surface sediment and slow upward flow. In the numerical simulation of the SPECT study, two symmetric channels with increased permeability are prescribed along the column walls, which result in the emergence of two well-defined preferential flow paths. Methods and results of this work provide new opportunities in hydrologic and biogeochemical research. The primary target application for developed technologies is non-destructive, non-perturbing, quantitative imaging of flow dynamics within laboratory scale porous media systems.

Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics.

PubMed

Boutchko, Rostyslav; Rayz, Vitaliy L; Vandehey, Nicholas T; O'Neil, James P; Budinger, Thomas F; Nico, Peter S; Druhan, Jennifer L; Saloner, David A; Gullberg, Grant T; Moses, William W

2012-01-01

This paper presents experimental and modeling aspects of applying nuclear emission tomography to study fluid flow in laboratory packed porous media columns of the type frequently used in geophysics, geochemistry and hydrology research. Positron emission tomography (PET) and single photon emission computed tomography (SPECT) are used as non-invasive tools to obtain dynamic 3D images of radioactive tracer concentrations. Dynamic sequences obtained using 18 F-FDG PET are used to trace flow through a 5 cm diameter × 20 cm tall sand packed column with and without an impermeable obstacle. In addition, a custom-made rotating column setup placed in a clinical two-headed SPECT camera is used to image 99m Tc-DTPA tracer propagation in a through-flowing column (10 cm diameter × 30 cm tall) packed with recovered aquifer sediments. A computational fluid dynamics software package FLUENT is used to model the observed flow dynamics. Tracer distributions obtained in the simulations in the smaller column uniformly packed with sand and in the column with an obstacle are remarkably similar to the reconstructed images in the PET experiments. SPECT results demonstrate strongly non-uniform flow patterns for the larger column slurry-packed with sub-surface sediment and slow upward flow. In the numerical simulation of the SPECT study, two symmetric channels with increased permeability are prescribed along the column walls, which result in the emergence of two well-defined preferential flow paths. Methods and results of this work provide new opportunities in hydrologic and biogeochemical research. The primary target application for developed technologies is non-destructive, non-perturbing, quantitative imaging of flow dynamics within laboratory scale porous media systems.

Observationally-based Metrics of Ocean Carbon and Biogeochemical Variables are Essential for Evaluating Earth System Model Projections

NASA Astrophysics Data System (ADS)

Russell, J. L.; Sarmiento, J. L.

2017-12-01

The Southern Ocean is central to the climate's response to increasing levels of atmospheric greenhouse gases as it ventilates a large fraction of the global ocean volume. Global coupled climate models and earth system models, however, vary widely in their simulations of the Southern Ocean and its role in, and response to, the ongoing anthropogenic forcing. Due to its complex water-mass structure and dynamics, Southern Ocean carbon and heat uptake depend on a combination of winds, eddies, mixing, buoyancy fluxes and topography. Understanding how the ocean carries heat and carbon into its interior and how the observed wind changes are affecting this uptake is essential to accurately projecting transient climate sensitivity. Observationally-based metrics are critical for discerning processes and mechanisms, and for validating and comparing climate models. As the community shifts toward Earth system models with explicit carbon simulations, more direct observations of important biogeochemical parameters, like those obtained from the biogeochemically-sensored floats that are part of the Southern Ocean Carbon and Climate Observations and Modeling project, are essential. One goal of future observing systems should be to create observationally-based benchmarks that will lead to reducing uncertainties in climate projections, and especially uncertainties related to oceanic heat and carbon uptake.

Crystal Orientation Effect on the Subsurface Deformation of Monocrystalline Germanium in Nanometric Cutting.

PubMed

Lai, Min; Zhang, Xiaodong; Fang, Fengzhou

2017-12-01

Molecular dynamics simulations of nanometric cutting on monocrystalline germanium are conducted to investigate the subsurface deformation during and after nanometric cutting. The continuous random network model of amorphous germanium is established by molecular dynamics simulation, and its characteristic parameters are extracted to compare with those of the machined deformed layer. The coordination number distribution and radial distribution function (RDF) show that the machined surface presents the similar amorphous state. The anisotropic subsurface deformation is studied by nanometric cutting on the (010), (101), and (111) crystal planes of germanium, respectively. The deformed structures are prone to extend along the 110 slip system, which leads to the difference in the shape and thickness of the deformed layer on various directions and crystal planes. On machined surface, the greater thickness of subsurface deformed layer induces the greater surface recovery height. In order to get the critical thickness limit of deformed layer on machined surface of germanium, the optimized cutting direction on each crystal plane is suggested according to the relevance of the nanometric cutting to the nanoindentation.

Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Truex, Michael J.; Lee, Brady D.; Johnson, Christian D.

Isotopes of iodine were generated during plutonium production within the nine production reactors at the U.S. Department of Energy Hanford Site. The short half-life 131I that was released from the fuel into the atmosphere during the dissolution process (when the fuel was dissolved) in the Hanford Site 200 Area is no longer present at concentrations of concern in the environment. The long half-life 129I generated at the Hanford Site during reactor operations was (1) stored in single-shell and double-shell tanks, (2) discharged to liquid disposal sites (e.g., cribs and trenches), (3) released to the atmosphere during fuel reprocessing operations, ormore » (4) captured by off-gas absorbent devices (silver reactors) at chemical separations plants (PUREX, B-Plant, T-Plant, and REDOX). Releases of 129I to the subsurface have resulted in several large, though dilute, plumes in the groundwater. There is also 129I remaining in the vadose zone beneath disposal or leak locations. The fate and transport of 129I in the environment and potential remediation technologies are currently being studied as part of environmental remediation activities at the Hanford Site. A conceptual model describing the nature and extent of subsurface contamination, factors that control plume behavior, and factors relevant to potential remediation processes is needed to support environmental remedy decisions. Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited. In addition, its behavior in subsurface is different from that of other more common and important contaminants (e.g., U, Cr and Tc) in terms of sorption (adsorption and precipitation), and aqueous phase species transformation via redox reactions. Thus, the conceptual model also needs to both describe known contaminant and biogeochemical process information and identify aspects about which additional information is needed to effectively support remedy decisions.« less

Evaluating the Competitive Use of the Subsurface: The Influence of Energy Storage and Production in Groundwater

NASA Astrophysics Data System (ADS)

Helmig, R.; Becker, B.; Flemisch, B.

2015-12-01

The natural subsurface is gaining in importance for a variety of engineering applications related to energy supply. At the same time it is already utilized in many ways. On the one hand, the subsurface with its groundwater system represents the most important source of drinking water; on the other hand, it contains natural resources such as petroleum, natural gas and coal. In recent years, the subsurface has been gaining importance as a resource of energy and as an energy and waste repository. It can serve as a short-, medium- or long-term storage medium for energy in various forms, e.g. in the form of methane (CH4), hydrogen (H2) or compressed air. The subsurface is also attracting increasing interest as a natural source of energy, regarding, for instance, the extraction of fossil methane by hydraulic fracturing or the utilization of geothermal energy as a renewable energy source. As a result, with increasing exploitation, resource conflicts are becoming more and more common and complex. Modeling concepts for simulating multiphase flow that can reproduce the high complexity of the underlying processes in an efficient way need to be developed. The application of these model concepts is of great importance with respect to feasibility, risk analysis, storage capacity and sensitivity issues. This talk will give an overview on possible utilization conflicts in subsurface systems and how the groundwater is affected. It will focus on presenting fundamental properties and functions of a compositional multiphase system in a porous medium and introduce basic multiscale and multiphysics concepts as well as formulate conser­vation laws for simulating energy storage in the subsurface. Large-scale simulations that show the general applicability of the modeling concepts of such complicated natural systems, especially the impact on the groundwater of simultaneously using geothermal energy and storing chemical and thermal energy, and how such real large-scale systems provide a good environment for balancing the efficiency potential and possible weaknesses of the approaches will be discussed.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2013-08-14

Subsurface bacteria including sulfate reducing bacteria (SRB) reduce soluble U(VI) to insoluble U(IV) with subsequent precipitation of UO 2. We have shown that SRB reduce U(VI) to nanometer-sized UO 2 particles (1-5 nm) which are both intra- and extracellular, with UO 2 inside the cell likely physically shielded from subsequent oxidation processes. We evaluated the UO 2 nanoparticles produced by Desulfovibrio desulfuricans G20 under growth and non-growth conditions in the presence of lactate or pyruvate and sulfate, thiosulfate, or fumarate, using ultrafiltration and HR-TEM. Results showed that a significant mass fraction of bioreduced U (35-60%) existed as a mobile phasemore » when the initial concentration of U(VI) was 160 µM. Further experiments with different initial U(VI) concentrations (25 - 900 M) in MTM with PIPES or bicarbonate buffers indicated that aggregation of uraninite depended on the initial concentrations of U(VI) and type of buffer. It is known that under some conditions SRB-mediated UO 2 nanocrystals can be reoxidized (and thus remobilized) by Fe(III)-(hydr)oxides, common constituents of soils and sediments. To elucidate the mechanism of UO 2 reoxidation by Fe(III) (hydr)oxides, we studied the impact of Fe and U chelating compounds (citrate, NTA, and EDTA) on reoxidation rates. Experiments were conducted in anaerobic batch systems in PIPES buffer. Results showed EDTA significantly accelerated UO 2 reoxidation with an initial rate of 9.5 M day-1 for ferrihydrite. In all cases, bicarbonate increased the rate and extent of UO 2 reoxidation with ferrihydrite. The highest rate of UO 2 reoxidation occurred when the chelator promoted UO 2 and Fe(III) (hydr)oxide dissolution as demonstrated with EDTA. When UO 2 dissolution did not occur, UO 2 reoxidation likely proceeded through an aqueous Fe(III) intermediate as observed for both NTA and citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO 2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO 2 reoxidation as Fe(III) oxidizes HS– preferentially over UO 2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO 2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO 2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network.« less

Effect of Freeze-Thaw Cycles on Soil Nitrogen Reactive Transport in a Polygonal Arctic Tundra Ecosystem at Barrow AK Using 3-D Coupled ALM-PFLOTRAN

NASA Astrophysics Data System (ADS)

Yuan, F.; Wang, G.; Painter, S. L.; Tang, G.; Xu, X.; Kumar, J.; Bisht, G.; Hammond, G. E.; Mills, R. T.; Thornton, P. E.; Wullschleger, S. D.

2017-12-01

In Arctic tundra ecosystem soil freezing-thawing is one of dominant physical processes through which biogeochemical (e.g., carbon and nitrogen) cycles are tightly coupled. Besides hydraulic transport, freezing-thawing can cause pore water movement and aqueous species gradients, which are additional mechanisms for soil nitrogen (N) reactive-transport in Tundra ecosystem. In this study, we have fully coupled an in-development ESM(i.e., Advanced Climate Model for Energy, ACME)'s Land Model (ALM) aboveground processes with a state-of-the-art massively parallel 3-D subsurface thermal-hydrology and reactive transport code, PFLOTRAN. The resulting coupled ALM-PFLOTRAN model is a Land Surface Model (LSM) capable of resolving 3-D soil thermal-hydrological-biogeochemical cycles. This specific version of PFLOTRAN has incorporated CLM-CN Converging Trophic Cascade (CTC) model and a full and simple but robust soil N cycle. It includes absorption-desorption for soil NH4+ and gas dissolving-degasing process as well. It also implements thermal-hydrology mode codes with three newly-modified freezing-thawing algorithms which can greatly improve computing performance in regarding to numerical stiffness at freezing-point. Here we tested the model in fully 3-D coupled mode at the Next Generation Ecosystem Experiment-Arctic (NGEE-Arctic) field intensive study site at the Barrow Environmental Observatory (BEO), AK. The simulations show that: (1) synchronous coupling of soil thermal-hydrology and biogeochemistry in 3-D can greatly impact ecosystem dynamics across polygonal tundra landscape; and (2) freezing-thawing cycles can add more complexity to the system, resulting in greater mobility of soil N vertically and laterally, depending upon local micro-topography. As a preliminary experiment, the model is also implemented for Pan-Arctic region in 1-D column mode (i.e. no lateral connection), showing significant differences compared to stand-alone ALM. The developed ALM-PFLOTRAN coupling codes embeded within ESM will be used for Pan-Arctic regional evaluation of climate change-caused ecosystem responses and their feedbacks to climate system at various scales.

Modeling critical zone processes in intensively managed environments

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Le, Phong; Woo, Dong; Yan, Qina

2017-04-01

Processes in the Critical Zone (CZ), which sustain terrestrial life, are tightly coupled across hydrological, physical, biochemical, and many other domains over both short and long timescales. In addition, vegetation acclimation resulting from elevated atmospheric CO2 concentration, along with response to increased temperature and altered rainfall pattern, is expected to result in emergent behaviors in ecologic and hydrologic functions, subsequently controlling CZ processes. We hypothesize that the interplay between micro-topographic variability and these emergent behaviors will shape complex responses of a range of ecosystem dynamics within the CZ. Here, we develop a modeling framework ('Dhara') that explicitly incorporates micro-topographic variability based on lidar topographic data with coupling of multi-layer modeling of the soil-vegetation continuum and 3-D surface-subsurface transport processes to study ecological and biogeochemical dynamics. We further couple a C-N model with a physically based hydro-geomorphologic model to quantify (i) how topographic variability controls the spatial distribution of soil moisture, temperature, and biogeochemical processes, and (ii) how farming activities modify the interaction between soil erosion and soil organic carbon (SOC) dynamics. To address the intensive computational demand from high-resolution modeling at lidar data scale, we use a hybrid CPU-GPU parallel computing architecture run over large supercomputing systems for simulations. Our findings indicate that rising CO2 concentration and air temperature have opposing effects on soil moisture, surface water and ponding in topographic depressions. Further, the relatively higher soil moisture and lower soil temperature contribute to decreased soil microbial activities in the low-lying areas due to anaerobic conditions and reduced temperatures. The decreased microbial relevant processes cause the reduction of nitrification rates, resulting in relatively lower nitrate concentration. Results from geomorphologic model also suggest that soil erosion and deposition plays a dominant role in SOC both above- and below-ground. In addition, tillage can change the amplitude and frequency of C-N oscillation. This work sheds light in developing practical means for reducing soil erosion and carbon loss when the landscape is affected by human activities.

Quantifying hyporheic exchange dynamics in a highly regulated large river reach.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammond, Glenn Edward; Zhou, T; Huang, M

Hyporheic exchange is an important mechanism taking place in riverbanks and riverbed sediments, where river water and shallow groundwater mix and interact with each other. The direction, magnitude, and residence time of the hyporheic flux that penetrates the river bed are critical for biogeochemical processes such as carbon and nitrogen cycling, and biodegradation of organic contaminants. Many approaches including field measurements and numerical methods have been developed to quantify the hyporheic exchanges in relatively small rivers. However, the spatial and temporal distributions of hyporheic exchanges in a large, regulated river reach remain less explored due to the large spatial domains,more » complexity of geomorphologic features and subsurface properties, and the great pressure gradient variations at the riverbed created by dam operations.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pau, G. S. H.; Bisht, G.; Riley, W. J.

Existing land surface models (LSMs) describe physical and biological processes that occur over a wide range of spatial and temporal scales. For example, biogeochemical and hydrological processes responsible for carbon (CO 2, CH 4) exchanges with the atmosphere range from the molecular scale (pore-scale O 2 consumption) to tens of kilometers (vegetation distribution, river networks). Additionally, many processes within LSMs are nonlinearly coupled (e.g., methane production and soil moisture dynamics), and therefore simple linear upscaling techniques can result in large prediction error. In this paper we applied a reduced-order modeling (ROM) technique known as "proper orthogonal decomposition mapping method" thatmore » reconstructs temporally resolved fine-resolution solutions based on coarse-resolution solutions. We developed four different methods and applied them to four study sites in a polygonal tundra landscape near Barrow, Alaska. Coupled surface–subsurface isothermal simulations were performed for summer months (June–September) at fine (0.25 m) and coarse (8 m) horizontal resolutions. We used simulation results from three summer seasons (1998–2000) to build ROMs of the 4-D soil moisture field for the study sites individually (single-site) and aggregated (multi-site). The results indicate that the ROM produced a significant computational speedup (> 10 3) with very small relative approximation error (< 0.1%) for 2 validation years not used in training the ROM. We also demonstrate that our approach: (1) efficiently corrects for coarse-resolution model bias and (2) can be used for polygonal tundra sites not included in the training data set with relatively good accuracy (< 1.7% relative error), thereby allowing for the possibility of applying these ROMs across a much larger landscape. By coupling the ROMs constructed at different scales together hierarchically, this method has the potential to efficiently increase the resolution of land models for coupled climate simulations to spatial scales consistent with mechanistic physical process representation.« less

A Reactive Transport Model for the Distribution and Age of Carbon in Soils and Sediments Through Direct Simulation of the Stable and Radiogenic Isotopologues

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Lawrence, C. R.

2015-12-01

We present a reactive transport (RT) approach to link hydrologic transport, geochemical transformations and microbial activity influencing the magnitude and residence time of different carbon pools under variably saturated conditions. This model explicitly simulates the simultaneous transport, transformation, fractionation and decay of the three isotopes of carbon (12C, 13C and 14C) through a mechanistic framework. This is demonstrated with a modification of the CrunchTope multi-component RT software to extend the isotope-specific versions of both microbially-mediated and transition state theory (TST) rate laws to accommodate a three-isotope system. In addition both aqueous and solid phase decay of 14C are tracked, yielding in an implicit means of accounting for the 13C/12C correction in normalized radiocarbon ages. The capacity of this approach to quantify the storage and flux of carbon through subsurface compartments is demonstrated using two examples distinguished by timescale. The first considers a simplified flow path in which an influent containing labile organic carbon is distributed by biogenic reduction and mineralization into a suite of reaction products. The residence time of these pools and their characteristic stable isotope ratios are tracked through a variety of transient processes occurring at short timescales (e.g. months). These include a change in fluid flow rate, a limitation of ammonium supporting anabolic growth and an influx of oxygenated fluid. The second example considers the distribution of carbon over the timescale of soil development (e.g., millennia), using a dataset of stable isotope ratios and radiocarbon ages of organic and inorganic carbon present in both dissolved and solid phases from a soil chronosequence near Santa Cruz, CA. The results of these model simulations suggest the promise of this tool for improving our understanding of coupling between hydrologic transport and biogeochemical reactions in soils.

The Role of Subsurface Properties on Transport of Water and Trace Gases: 1D Simulations at Selected Mars Landing Sites.

NASA Astrophysics Data System (ADS)

Karatekin, O.; Gloesener, E.; Dehant, V. M. A.

2017-12-01

In this work, water ice stability and water vapour transport through porous martian subsurface are studied using a 1D diffusive model. The role of adsorption on water transfer in martian conditions is investigated as well as the range of parameters that have the largest effect on gas transport. In addition, adsorption kinetics is considered to examine its influence on the water vapor exchange between the subsurface and the atmosphere. As methane has been detected in the martian atmosphere, the subsurface model is then used to study methane diffusion in the CH4/CO2/H2O system from variable depths under the surface. The results of subsurface gas transport at selected locations/landing sites are shown and implications for present/future observations are discussed.

Project Introduction for SUBSEA: Systematic Underwater Biogeochemical Science and Exploration Analog

NASA Astrophysics Data System (ADS)

Nawotniak, S. E. K.; Lim, D. S. S.; German, C. R.; Shock, E. L.; Huber, J. A.; Breier, J. A.

2018-05-01

NASA SUBSEA studies low T, low P seamounts via integrated volcanology, geochemistry, and microbiology as an analog for Enceladus. Research done in telerobotic space exploration simulation. First cruise is Loihi in August 2018.

Simulating the biogeochemical cycles in cypress wetland-pine upland ecosystems at a landscape scale with the wetland-DNDC model

Treesearch

G. Sun; C. Li; C. Tretting; J. Lu; S.G. McNulty

2005-01-01

A modeling framework (Wetland-DNDC) that described forested wetland ecosystem processes has been developed and validated with data from North America and Europe. The model simulates forest photosynthesis, respiration, carbon allocation, and liter production, soil organic matter (SOM) turnover, trace gas emissions, and N leaching. Inputs required by Wetland-DNDC...

Bacterial transformation and biodegradation processes simulation in horizontal subsurface flow constructed wetlands using CWM1-RETRASO.

PubMed

Llorens, Esther; Saaltink, Maarten W; Poch, Manel; García, Joan

2011-01-01

The performance and reliability of the CWM1-RETRASO model for simulating processes in horizontal subsurface flow constructed wetlands (HSSF CWs) and the relative contribution of different microbial reactions to organic matter (COD) removal in a HSSF CW treating urban wastewater were evaluated. Various different approaches with diverse influent configurations were simulated. According to the simulations, anaerobic processes were more widespread in the simulated wetland and contributed to a higher COD removal rate [72-79%] than anoxic [0-1%] and aerobic reactions [20-27%] did. In all the cases tested, the reaction that most contributed to COD removal was methanogenesis [58-73%]. All results provided by the model were in consonance with literature and experimental field observations, suggesting a good performance and reliability of CWM1-RETRASO. According to the good simulation predictions, CWM1-RETRASO is the first mechanistic model able to successfully simulate the processes described by the CWM1 model in HSSF CWs. Copyright © 2010 Elsevier Ltd. All rights reserved.

Effectiveness of Hydraulic Parameterization Strategies for Simulating Moisture Dynamics in a Deep Semi-Arid Vadose Zone

NASA Astrophysics Data System (ADS)

Zhang, Y.; Schaap, M. G.

2012-12-01

Over the past fifteen years, the University of Arizona has carried out four controlled infiltration experiments in a 3600 m2, 15 meter deep vadose zone (Maricopa, Arizona) in which the evolution of moisture content (9 wells, 25 cm resolution), and matric potential (27 locations) was monitored and the subsurface stratigraphy, texture (1042 samples), and bulk density (251 samples) was characterized. In order to simulate the subsurface moisture dynamics it is necessary to define the 3D structure of the subsurface hydraulic characteristics (i.e. moisture retention and hydraulic functions). Several simple to complex strategies are possible ranging from stratigraphy based layering using hydraulic parameters derived from core samples to sophisticated numerical inversions based on 3D geostatistics and site-specific pedotransfer functions. A range of approaches will be evaluated on objective metrics that quantify how well the observed moisture dynamics are matched by simulations. We will evaluate the worth of auxiliary data such as observed matric potentials and quantity the number of texture samples needed to arrive at effective descriptions of subsurface structure. In addition, we will discuss more subjective metrics that evaluate the relative effort involved and estimate monetary cost of each method. While some of the results will only be valid for the studied site, some general conclusions will be possible about the effectiveness of particular methods for other semi-arid sites.

Microbial production and oxidation of methane in deep subsurface

NASA Astrophysics Data System (ADS)

Kotelnikova, Svetlana

2002-10-01

The goal of this review is to summarize present studies on microbial production and oxidation of methane in the deep subterranean environments. Methane is a long-living gas causing the "greenhouse" effect in the planet's atmosphere. Earlier, the deep "organic carbon poor" subsurface was not considered as a source of "biogenic" methane. Evidence of active methanogenesis and presence of viable methanogens including autotrophic organisms were obtained for some subsurface environments including water-flooded oil-fields, deep sandy aquifers, deep sea hydrothermal vents, the deep sediments and granitic groundwater at depths of 10 to 2000 m below sea level. As a rule, the deep subterranean microbial populations dwell at more or less oligotrophic conditions. Molecular hydrogen has been found in a variety of subsurface environments, where its concentrations were significantly higher than in the tested surface aquatic environments. Chemolithoautotrophic microorganisms from deep aquifers that could grow on hydrogen and carbon dioxide can act as primary producers of organic carbon, initiating heterotrophic food chains in the deep subterranean environments independent of photosynthesis. "Biogenic" methane has been found all over the world. On the basis of documented occurrences, gases in reservoirs and older sediments are similar and have the isotopic character of methane derived from CO 2 reduction. Groundwater representing the methanogenic end member are characterized by a relative depletion of dissolved organic carbon (DOC) in combination with an enrichment in 13C in inorganic carbon, which is consistent with the preferential reduction of 12CO 2 by autotrophic methanogens or acetogens. The isotopic composition of methane formed via CO 2 reduction is controlled by the δ13C of the original CO 2 substrate. Literature data shows that CH 4 as heavy as -40‰ or -50‰ can be produced by the microbial reduction of isotopically heavy CO 2. Produced methane may be oxidized microbially to carbon dioxide. Microbial methane oxidation is a biogeochemical process that limits the release of methane, a greenhouse gas from anaerobic environments. Anaerobic methane oxidation plays an important role in marine sediments. Similar processes may take place in deep subsurface and thus fuel the deep microbial community. Organisms or consortia responsible for anaerobic methane oxidation have not yet been cultured, although diverse aerobic methanotrophs have been isolated from a variety of underground niches. The presence of aerobic methanotrophs in the anoxic subsurface remains to be explained. The presence of methane in the deep subsurface have been shown all over the world. The flux of gases between the deep subsurface and the atmosphere is driven by the concentration gradient from depth to the atmosphere. However, methane is consumed by methanotrophs on the way of its evolution in oxidized environments and is transformed to organic form, available for further microbial processing. When the impact of subsurface environments to global warming is estimated, it is necessary to take into account the activity of methane-producing Archaea and methane-oxidizing biofilters in groundwater. Microbial production and oxidation of methane is involved in the carbon cycle in the deep subsurface environments.

Influence of cutting parameters on the depth of subsurface deformed layer in nano-cutting process of single crystal copper.

PubMed

Wang, Quanlong; Bai, Qingshun; Chen, Jiaxuan; Su, Hao; Wang, Zhiguo; Xie, Wenkun

2015-12-01

Large-scale molecular dynamics simulation is performed to study the nano-cutting process of single crystal copper realized by single-point diamond cutting tool in this paper. The centro-symmetry parameter is adopted to characterize the subsurface deformed layers and the distribution and evolution of the subsurface defect structures. Three-dimensional visualization and measurement technology are used to measure the depth of the subsurface deformed layers. The influence of cutting speed, cutting depth, cutting direction, and crystallographic orientation on the depth of subsurface deformed layers is systematically investigated. The results show that a lot of defect structures are formed in the subsurface of workpiece during nano-cutting process, for instance, stair-rod dislocations, stacking fault tetrahedron, atomic clusters, vacancy defects, point defects. In the process of nano-cutting, the depth of subsurface deformed layers increases with the cutting distance at the beginning, then decreases at stable cutting process, and basically remains unchanged when the cutting distance reaches up to 24 nm. The depth of subsurface deformed layers decreases with the increase in cutting speed between 50 and 300 m/s. The depth of subsurface deformed layer increases with cutting depth, proportionally, and basically remains unchanged when the cutting depth reaches over 6 nm.

Near-Field Resonance Microwave Tomography and Holography

NASA Astrophysics Data System (ADS)

Gaikovich, K. P.; Smirnov, A. I.; Yanin, D. V.

2018-02-01

We develop the methods of electromagnetic computer near-field microwave tomography of distributed subsurface inhomogeneities of complex dielectric permittivity and of holography (shape retrieval) of internally homogeneous subsurface objects. The methods are based on the solution of the near-field inverse scattering problem from measurements of the resonance-parameter variations of microwave probes above the medium surface. The capabilities of the proposed diagnostic technique are demonstrated in the numerical simulation for sensors with a cylindrical capacitor as a probe element, the edge capacitance of which is sensitive to subsurface inhomogeneities.

Combined effects of hydrologic alteration and cyprinid fish in mediating biogeochemical processes in a Mediterranean stream.

PubMed

Rubio-Gracia, Francesc; Almeida, David; Bonet, Berta; Casals, Frederic; Espinosa, Carmen; Flecker, Alexander S; García-Berthou, Emili; Martí, Eugènia; Tuulaikhuu, Baigal-Amar; Vila-Gispert, Anna; Zamora, Lluis; Guasch, Helena

2017-12-01

Flow regimes are important drivers of both stream community and biogeochemical processes. However, the interplay between community and biogeochemical responses under different flow regimes in streams is less understood. In this study, we investigated the structural and functional responses of periphyton and macroinvertebrates to different densities of the Mediterranean barbel (Barbus meridionalis, Cyprinidae) in two stream reaches differing in flow regime. The study was conducted in Llémena Stream, a small calcareous Mediterranean stream with high nutrient levels. We selected a reach with permanent flow (permanent reach) and another subjected to flow regulation (regulated reach) with periods of flow intermittency. At each reach, we used in situ cages to generate 3 levels of fish density. Cages with 10 barbels were used to simulate high fish density (>7indm -2 ); cages with open sides were used as controls (i.e. exposed to actual fish densities of each stream reach) thus having low fish density; and those with no fish were used to simulate the disappearance of fish that occurs with stream drying. Differences in fish density did not cause significant changes in periphyton biomass and macroinvertebrate density. However, phosphate uptake by periphyton was enhanced in treatments lacking fish in the regulated reach with intermittent flow but not in the permanent reach, suggesting that hydrologic alteration hampers the ability of biotic communities to compensate for the absence of fish. This study indicates that fish density can mediate the effects of anthropogenic alterations such as flow intermittence derived from hydrologic regulation on stream benthic communities and associated biogeochemical processes, at least in eutrophic streams. Copyright © 2017. Published by Elsevier B.V.

Biogeochemistry of natural ponds in agricultural landscape: Lessons learned from modeling a kettle hole in Northeast Germany.

PubMed

Onandia, Gabriela; Lischeid, Gunnar; Kalettka, Thomas; Kleeberg, Andreas; Omari, Mohamed; Premke, Katrin; Arhonditsis, George B

2018-09-01

Kettle holes, small shallow ponds of glacial origin, represent hotspots for biodiversity and biogeochemical cycling. They abound in the young moraine landscape of Northeast Germany, potentially modulating element fluxes in a region where intensive agriculture prevails. The Rittgarten kettle hole, with semi-permanent hydroperiod and a surrounding reed belt, can be considered as a representative case study for such systems. Aiming to provide insights into the biogeochemical processes driving nutrient and primary producer dynamics in the Rittgarten kettle hole, we developed a mechanistic model that simulates the carbon, nitrogen, phosphorus and oxygen, phytoplankton, and free-floating macrophyte biomass dynamics. After model calibration and sensitivity analysis, our modeling exercise quantified the simulated nutrient fluxes associated with all the major biogeochemical processes considered by the model. Seasonality of nutrient concentrations, magnitude of primary productivity rates, and biogeochemical process characterization in the pond were reasonably reproduced by the model from July 2013 to July 2014. Our results suggest that the establishment of a phytoplankton community well-adapted to low light availability, together with the differential use of N and P from free-floating macrophytes and phytoplankton can explain their coexistence in kettle holes. Sediment nutrient release along with decomposition of decaying submerged macrophyte are essential drivers of internal nutrient cycling in kettle holes. Our results also suggest that the Rittgarten kettle hole act as a net source of CO 2 to the atmosphere on an annual scale, which offers a testable hypothesis for kettle holes with structural and functional similarities. We conclude by discussing the need to shed light on the effects of water level fluctuations on nutrient dynamics and biological succession patterns, as well as the relative importance of external sources and internal nutrient recycling mechanisms. Copyright © 2018 Elsevier B.V. All rights reserved.

Modeling biogeochemical responses of vegetation to ENSO: comparison and analysis on subgrid PFT patches

NASA Astrophysics Data System (ADS)

Xu, M.; Hoffman, F. M.

2016-12-01

The El Niño Southern Oscillation (ENSO) is an important interannual climate variability and has significant consequences and impacts on the global biosphere. The responses of vegetation to ENSO are highly heterogeneous and generally depend on the biophysical and biochemical characteristics associated with model plant functional types (PFTs). The modeled biogeochemical variables from Earth System Models (ESMs) are generally grid averages consisting of several PFTs within a gridcell, which will lead to difficulties in directly comparing them with site observations and large uncertainties in studying their responses to large scale climate variability. In this study, we conducted a transient ENSO simulation for the previoustwo decades from 1995 to 2020 using the DOE ACME v0.3 model. It has a comprehensive terrestrial biogeochemistry model that is fully coupled with a sophisticated atmospheric model with an advanced spectral element dynamical core. The model was driven by the NOAA optimum interpolation sea surface temperature (SST) for contemporary years and CFS v2 nine-month seasonal predicted and reconstructed SST for future years till to 2020. We saved the key biogeochemical variables in the subgrid PFT patches and compared them with site observations directly. Furthermore, we studied the biogeochemical responses of terrestrial vegetation to two largest ENSO events (1997-1998 and 2015-2016) for different PFTs. Our results show that it is useful and meaningful to compare and analyze model simulations in subgrid patches. The comparison and analysis not only gave us the details of responses of terrestrial ecosystem to global climate variability under changing climate, but also the insightful view on the model performance on the PFT level.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Shallow subsurface storm flow in a forested headwater catchment: Observations and modeling using a modified TOPMODEL

USGS Publications Warehouse

Scanlon, Todd M.; Raffensperger, Jeff P.; Hornberger, George M.; Clapp, Roger B.

2000-01-01

Transient, perched water tables in the shallow subsurface are observed at the South Fork Brokenback Run catchment in Shenandoah National Park, Virginia. Crest piezometers installed along a hillslope transect show that the development of saturated conditions in the upper 1.5 m of the subsurface is controlled by total precipitation and antecedent conditions, not precipitation intensity, although soil heterogeneities strongly influence local response. The macroporous subsurface storm flow zone provides a hydrological pathway for rapid runoff generation apart from the underlying groundwater zone, a conceptualization supported by the two‐storage system exhibited by hydrograph recession analysis. A modified version of TOPMODEL is used to simulate the observed catchment dynamics. In this model, generalized topographic index theory is applied to the subsurface storm flow zone to account for logarithmic storm flow recessions, indicative of linearly decreasing transmissivity with depth. Vertical drainage to the groundwater zone is required, and both subsurface reservoirs are considered to contribute to surface saturation.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Lateral and subsurface flows impact arctic coastal plain lake water budgets

USGS Publications Warehouse

Koch, Joshua C.

2016-01-01

Arctic thaw lakes are an important source of water for aquatic ecosystems, wildlife, and humans. Many recent studies have observed changes in Arctic surface waters related to climate warming and permafrost thaw; however, explaining the trends and predicting future responses to warming is difficult without a stronger fundamental understanding of Arctic lake water budgets. By measuring and simulating surface and subsurface hydrologic fluxes, this work quantified the water budgets of three lakes with varying levels of seasonal drainage, and tested the hypothesis that lateral and subsurface flows are a major component of the post-snowmelt water budgets. A water budget focused only on post-snowmelt surface water fluxes (stream discharge, precipitation, and evaporation) could not close the budget for two of three lakes, even when uncertainty in input parameters was rigorously considered using a Monte Carlo approach. The water budgets indicated large, positive residuals, consistent with up to 70% of mid-summer inflows entering lakes from lateral fluxes. Lateral inflows and outflows were simulated based on three processes; supra-permafrost subsurface inflows from basin-edge polygonal ground, and exchange between seasonally drained lakes and their drained margins through runoff and evapotranspiration. Measurements and simulations indicate that rapid subsurface flow through highly conductive flowpaths in the polygonal ground can explain the majority of the inflow. Drained lakes were hydrologically connected to marshy areas on the lake margins, receiving water from runoff following precipitation and losing up to 38% of lake efflux to drained margin evapotranspiration. Lateral fluxes can be a major part of Arctic thaw lake water budgets and a major control on summertime lake water levels. Incorporating these dynamics into models will improve our ability to predict lake volume changes, solute fluxes, and habitat availability in the changing Arctic.

Large-scale assessment of present day and future groundwater recharge and its sensitivity to climate variability in Europe's karst regions

NASA Astrophysics Data System (ADS)

Hartmann, A. J.; Gleeson, T. P.; Wagener, T.; Wada, Y.

2016-12-01

Karst aquifers in Europe are an important source of fresh water contributing up to half of the total drinking water supply in some countries. Karstic groundwater recharge is one of the most important components of the water balance of karst systems as it feeds the karst aquifers. Presently available large-scale hydrological models do not consider karst heterogeneity adequately. Projections of current and potential future groundwater recharge of Europe's karst aquifers are therefore unclear. In this study we compare simulations of present (1991-2010) and future (2080-2099) recharge using two different models to simulate groundwater recharge processes. One model includes karst processes (subsurface heterogeneity, lateral flow and concentrated recharge), while the other is based on the conceptual understanding of common hydrological systems (homogeneous subsurface, saturation excess overland flow). Both models are driven by the bias-corrected 5 GCMs of the ISI-MIP project (RCP8.5). To further assess sensitivity of groundwater recharge to climate variability, we calculate the elasticity of recharge rates to annual precipitation, temperature and average intensity of rainfall events, which is the median change of recharge that corresponds to the median change of these climate variables within the present and future time period, respectively. Our model comparison shows that karst regions over Europe have enhanced recharge rates with greater inter-annual variability compared to those with more homogenous subsurface properties. Furthermore, the heterogeneous representation shows stronger elasticity concerning climate variability than the homogeneous subsurface representation. This difference tends to increase towards the future. Our results suggest that water management in regions with heterogeneous subsurface can expect a higher water availability than estimated by most of the current large-scale simulations, while measures should be taken to prepare for increasingly variable groundwater recharge rates.

3DHYDROGEOCHEM: A 3-DIMENSIONAL MODEL OF DENSITY-DEPENDENT SUBSURFACE FLOW AND THERMAL MULTISPECIES-MULTICOMPONENT HYDROGEOCHEMICAL TRANSPORT (EPA/600/SR-98/159)

EPA Science Inventory

This report presents a three-dimensional finite-element numerical model designed to simulate chemical transport in subsurface systems with temperature effect taken into account. The three-dimensional model is developed to provide (1) a tool of application, with which one is able ...

The Multi-Scale Mass Transfer Processes Controlling Natural Attenuation and Engineered Remediation: An IFC Focused on Hanford’s 300 Area Uranium Plume Quality Assurance Project Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fix, N. J.

The purpose of the project is to conduct research at an Integrated Field-Scale Research Challenge Site in the Hanford Site 300 Area, CERCLA OU 300-FF-5 (Figure 1), to investigate multi-scale mass transfer processes associated with a subsurface uranium plume impacting both the vadose zone and groundwater. The project will investigate a series of science questions posed for research related to the effect of spatial heterogeneities, the importance of scale, coupled interactions between biogeochemical, hydrologic, and mass transfer processes, and measurements/approaches needed to characterize a mass-transfer dominated system. The research will be conducted by evaluating three (3) different hypotheses focused onmore » multi-scale mass transfer processes in the vadose zone and groundwater, their influence on field-scale U(VI) biogeochemistry and transport, and their implications to natural systems and remediation. The project also includes goals to 1) provide relevant materials and field experimental opportunities for other ERSD researchers and 2) generate a lasting, accessible, and high-quality field experimental database that can be used by the scientific community for testing and validation of new conceptual and numerical models of subsurface reactive transport.« less

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points: Microbial community succession and disturbance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.

2014-04-18

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacteriummore » and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.« less

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2017-04-01

Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms associated with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochemistry. Based on our results, we propose a conceptualization of hyporheic zone metabolism in which increased organic carbon concentrations during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochemistry and its influence over riverine ecosystem function. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

PubMed Central

Robador, Alberto; Jungbluth, Sean P.; LaRowe, Douglas E.; Bowers, Robert M.; Rappé, Michael S.; Amend, Jan P.; Cowen, James P.

2015-01-01

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling. PMID:25642212

The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal.

PubMed

Kuippers, Gina; Boothman, Christopher; Bagshaw, Heath; Ward, Michael; Beard, Rebecca; Bryan, Nicholas; Lloyd, Jonathan R

2018-06-08

Intermediate level radioactive waste (ILW) generally contains a heterogeneous range of organic and inorganic materials, of which some are encapsulated in cement. Of particular concern are cellulosic waste items, which will chemically degrade under the conditions predicted during waste disposal, forming significant quantities of isosaccharinic acid (ISA), a strongly chelating ligand. ISA therefore has the potential to increase the mobility of a wide range of radionuclides via complex formation, including Ni-63 and Ni-59. Although ISA is known to be metabolized by anaerobic microorganisms, the biodegradation of metal-ISA complexes remains unexplored. This study investigates the fate of a Ni-ISA complex in Fe(III)-reducing enrichment cultures at neutral pH, representative of a microbial community in the subsurface. After initial sorption of Ni onto Fe(III)oxyhydroxides, microbial ISA biodegradation resulted in >90% removal of the remaining Ni from solution when present at 0.1 mM, whereas higher concentrations of Ni proved toxic. The microbial consortium associated with ISA degradation was dominated by close relatives to Clostridia and Geobacter species. Nickel was preferentially immobilized with trace amounts of biogenic amorphous iron sulfides. This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from the groundwater in the subsurface geosphere surrounding a geodisposal facility.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pelletier, Jon D.; Broxton, Patrick D.; Hazenberg, Pieter

Earth’s terrestrial near-subsurface environment can be divided into relatively porous layers of soil, intact regolith, and sedimentary deposits above unweathered bedrock. Variations in the thicknesses of these layers control the hydrologic and biogeochemical responses of landscapes. Currently, Earth System Models approximate the thickness of these relatively permeable layers above bedrock as uniform globally, despite the fact that their thicknesses vary systematically with topography, climate, and geology. To meet the need for more realistic input data for models, we developed a high-resolution gridded global data set of the average thicknesses of soil, intact regolith, and sedimentary deposits within each 30 arcsecmore » (~ 1 km) pixel using the best available data for topography, climate, and geology as input. Our data set partitions the global land surface into upland hillslope, upland valley bottom, and lowland landscape components and uses models optimized for each landform type to estimate the thicknesses of each subsurface layer. On hillslopes, the data set is calibrated and validated using independent data sets of measured soil thicknesses from the U.S. and Europe and on lowlands using depth to bedrock observations from groundwater wells in the U.S. As a result, we anticipate that the data set will prove useful as an input to regional and global hydrological and ecosystems models.« less

Subsurface phytoplankton layers in the Arctic Ocean

NASA Astrophysics Data System (ADS)

Tremblay, J. E.

2016-02-01

Recent observations underscored the near-ubiquitous presence of subsurface chlorophyll maxima (SCM) and their potential importance for total primary production (PP) and pelagic food webs in perennially stratified waters of the Arctic Ocean. The contribution of SCM layers to annual PP is particularly important in oligotrophic areas, where modest nutrient supply to the upper euphotic zone results in weak or short-lived phytoplankton blooms near the surface. The large amount of nutrients present in the Pacific halocline relative to comparable depths in the Atlantic sector of the Arctic may also foster particularly productive SCM along the path of Pacific water. The association between strongly stratified conditions and the SCM in today's Arctic Ocean has broad relevance in providing a glimpse into the future of other oceans whose vertical stratification progressively rises with water temperature and freshwater content. In this regard, there is much to learn on the photosynthetic and nutritive ecology of SCM layers, whose biogeochemical significance depends on the extent to which they rely on allochthonous nitrogen (new production), their contribution to carbon biomass and their ability to influence air-sea CO2 exchange. Here we report on several years of eco-physiological investigations of SCM across the Arctic Ocean, with an aim to provide a basis of comparison with the ecology of SCM in other ocean areas.

Review on airflow in unsaturated zones induced by natural forcings

NASA Astrophysics Data System (ADS)

Kuang, Xingxing; Jiao, Jiu Jimmy; Li, Hailong

2013-10-01

Subsurface airflow in unsaturated zones induced by natural forcings is of importance in many environmental and engineering fields, such as environmental remediation, water infiltration and groundwater recharge, coastal soil aeration, mine and tunnel ventilation, and gas exchange between soil and atmosphere. This review synthesizes the published literature on subsurface airflow driven by natural forcings such as atmospheric pressure fluctuations, topographic effect, water table fluctuations, and water infiltration. The present state of knowledge concerning the mechanisms, analytical and numerical models, and environmental and engineering applications related to the naturally occurring airflow is discussed. Airflow induced by atmospheric pressure fluctuations is studied the most because of the applications to environmental remediation and transport of trace gases from soil to atmosphere, which are very important in understanding biogeochemical cycling and global change. Airflow induced by infiltration is also an extensively investigated topic because of its implications in rainfall infiltration and groundwater recharge. Airflow induced by water table fluctuations is important in coastal areas because it plays an important role in coastal environmental remediation and ecological systems. Airflow induced by topographic effect is studied the least. However, it has important applications in unsaturated zone gas transport and natural ventilation of mines and tunnels. Finally, the similarities and differences in the characteristics of the air pressure and airflow are compared and future research efforts are recommended.

Biogeography of serpentinite-hosted microbial ecosystems

NASA Astrophysics Data System (ADS)

Brazelton, W.; Cardace, D.; Fruh-Green, G.; Lang, S. Q.; Lilley, M. D.; Morrill, P. L.; Szponar, N.; Twing, K. I.; Schrenk, M. O.

2012-12-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). To date, however, the "serpentinite microbiome" is poorly constrained- almost nothing is known about the microbial diversity endemic to rocks actively undergoing serpentinization. Through the Census of Deep Life, we have obtained 16S rRNA gene pyrotag sequences from fluids and rocks from serpentinizing ophiolites in California, Canada, and Italy. The samples include high pH serpentinite springs, presumably representative of deeper environments within the ophiolite complex, wells which directly access subsurface aquifers, and rocks obtained from drill cores into serpentinites. These data represent a unique opportunity to examine biogeographic patterns among a restricted set of microbial taxa that are adapted to similar environmental conditions and are inhabiting sites with related geological histories. In general, our results point to potentially H2-utilizing Betaproteobacteria thriving in shallow, oxic-anoxic transition zones and anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These general taxonomic and biogeochemical trends were also observed in seafloor Lost City hydrothermal chimneys, indicating that we are beginning to identify a core serpentinite microbial community that spans marine and continental settings.

Effects of tillage and application rate on atrazine transport to subsurface drainage: Evaluation of RZWQM using a six-year field study

USGS Publications Warehouse

Malone, Robert W.; Nolan, Bernard T.; Ma, Liwang; Kanwar, Rameshwar S.; Pederson, Carl H.; Heilman, Philip

2014-01-01

Well tested agricultural system models can improve our understanding of the water quality effects of management practices under different conditions. The Root Zone Water Quality Model (RZWQM) has been tested under a variety of conditions. However, the current model's ability to simulate pesticide transport to subsurface drain flow over a long term period under different tillage systems and application rates is not clear. Therefore, we calibrated and tested RZWQM using six years of data from Nashua, Iowa. In this experiment, atrazine was spring applied at 2.8 (1990–1992) and 0.6 kg/ha/yr (1993–1995) to two 0.4 ha plots with different tillage (till and no-till). The observed and simulated average annual flow weighted atrazine concentrations (FWAC) in subsurface drain flow from the no-till plot were 3.7 and 3.2 μg/L, respectively for the period with high atrazine application rates, and 0.8 and 0.9 μg/L, respectively for the period with low application rates. The 1990–1992 observed average annual FWAC difference between the no-till and tilled plot was 2.4 μg/L while the simulated difference was 2.1 μg/L. These observed and simulated differences for 1993–1995 were 0.1 and 0.1 μg/L, respectively. The Nash–Sutcliffe model performance statistic (EF) for cumulative atrazine flux to subsurface drain flow was 0.93 for the no-till plot testing years (1993–1995), which is comparable to other recent model tests. The value of EF is 1.0 when simulated data perfectly match observed data. The order of selected parameter sensitivity for RZWQM simulated FWAC was atrazine partition coefficient > number of macropores > atrazine half life in soil > soil hydraulic conductivity. Simulations from 1990 to 1995 with four different atrazine application rates applied at a constant rate throughout the simulation period showed concentrations in drain flow for the no-till plot to be twice those of the tilled plot. The differences were more pronounced in the early simulation period (1990–1992), partly because of the characteristics of macropore flow during large storms. The results suggest that RZWQM is a promising tool to study pesticide transport to subsurface drain flow under different tillage systems and application rates over several years, the concentrations of atrazine in drain flow can be higher with no-till than tilled soil over a range of atrazine application rates, and atrazine concentrations in drain flow are sensitive to the macropore flow characteristics under different tillage systems and rainfall timing and intensity.

Application of the Quadrupole Method for Simulation of Passive Thermography

NASA Technical Reports Server (NTRS)

Winfree, William P.; Zalameda, Joseph N.; Gregory, Elizabeth D.

2017-01-01

Passive thermography has been shown to be an effective method for in-situ and real time nondestructive evaluation (NDE) to measure damage growth in a composite structure during cyclic loading. The heat generation by subsurface flaw results in a measurable thermal profile at the surface. This paper models the heat generation as a planar subsurface source and calculates the resultant temperature profile at the surface using a three dimensional quadrupole. The results of the model are compared to finite element simulations of the same planar sources and experimental data acquired during cyclic loading of composite specimens.

Impact of Subsurface Heterogeneities on nano-Scale Zero Valent Iron Transport

NASA Astrophysics Data System (ADS)

Krol, M. M.; Sleep, B. E.; O'Carroll, D. M.

2011-12-01

Nano-scale zero valent iron (nZVI) has been applied as a remediation technology at sites contaminated with chlorinated compounds and heavy metals. Although laboratory studies have demonstrated high reactivity for the degradation of target contaminants, the success of nZVI in the field has been limited due to poor subsurface mobility. When injected into the subsurface, nZVI tends to aggregate and be retained by subsurface soils. As such nZVI suspensions need to be stabilized for increased mobility. However, even with stabilization, soil heterogeneities can still lead to non-uniform nZVI transport, resulting in poor distribution and consequently decreased degradation of target compounds. Understanding how nZVI transport can be affected by subsurface heterogeneities can aid in improving the technology. This can be done with the use of a numerical model which can simulate nZVI transport. In this study CompSim, a finite difference groundwater model, is used to simulate the movement of nZVI in a two-dimensional domain. CompSim has been shown in previous studies to accurately predict nZVI movement in the subsurface, and is used in this study to examine the impact of soil heterogeneity on nZVI transport. This work also explores the impact of different viscosities of the injected nZVI suspensions (corresponding to different stabilizing polymers) and injection rates on nZVI mobility. Analysis metrics include travel time, travel distance, and average nZVI concentrations. Improving our understanding of the influence of soil heterogeneity on nZVI transport will lead to improved field scale implementation and, potentially, to more effective remediation of contaminated sites.

Electrical imaging of subsurface nanoparticle propagation for in-situ groundwater remediation

NASA Astrophysics Data System (ADS)

Flores Orozco, Adrián; Gallistl, Jakob; Schmid, Doris; Micic Batka, Vesna; Bücker, Matthias; Hofmann, Thilo

2017-04-01

Application of nanoparticles has emerged as a promising in situ remediation technology for the remediation of contaminated groundwater, particularly for areas difficult to access by other remediation techniques. The performance of nanoparticle injections, as a foremost step within this technology, is usually assessed through the geochemical analysis of soil and groundwater samples. This approach is not well suited for a real-time monitoring, and often suffers from a poor spatio-temporal resolution and only provides information from areas close to the sampling points. To overcome these limitations we propose the application of non-invasive Induced Polarization (IP) imaging, a geophysical method that provides information on the electrical properties of the subsurface. The analysis of temporal changes in the electrical images allows tracking the propagation of the injected nanoparticle suspension and detection of the induced bio-geochemical changes in the subsurface. Here, we present IP monitoring results for data collected during the injection of Nano-Goethite particles (NGP) used for simulation of biodegradation of a BTEX plume (i.e., benzene, toluene, ethylbenzene, and xylene) at the Spolchemie II site, CZ. Frequency-domain IP measurements were collected parallel to the groundwater flow direction and centred on the NGP injection point. Pre-injection imaging results revealed high electrical conductivities (> 10 S/m) and negligible polarization effects in the BTEX-contaminated part of the saturated zone (below 5 m depth). The apparently contradictory observation - BTEX compounds are poor electrical conductors - can be explained by the release of carbonic acids (a metabolic by-product of the biodegradation of hydrocarbons), which leads to an increase of the electrical conductivity. Post-injection images revealed a significant decrease (> 50%) of the electrical conductivity, with even larger changes in the proximity of the injection points, most likely due to the relatively high resistivity of the NGP suspension. This is in line with geochemical data from both the injected NGP suspension and the groundwater samples. Furthermore, temporal changes in the IP images are consistent with variations in total iron concentration in groundwater (a proxy for the NGP concentration) as well as in situ groundwater parameters, such as pH and oxidation-reduction potential. Our results demonstrate the applicability of IP imaging for the real-time monitoring of nanoparticle injection, as well as of the accompanying geochemical changes. Part of this research is funded by the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no 309517.

Modeling the time-varying interaction between surface water and groundwater bodies

NASA Astrophysics Data System (ADS)

Gliege, Steffen; Steidl, Jörg; Lischeid, Gunnar; Merz, Christoph

2016-04-01

The countless kettle holes (small lakes) in the Late Pleistocene landscapes of Northern Europe have important ecological and hydrological functions. On the one hand they act as depressions in which water and solutes of mainly agriculturally used catchments accumulate. On the other hand they operate as biochemical reactors with respect to greenhouse gas emissions, carbon sequestration, and as major sinks for nutrients and contaminants. Even small kettle holes often are hydraulically connected to the uppermost groundwater system: Groundwater discharges into the kettle hole on one side, and the aquifer is recharged from the kettle hole water body on the other side. Thus kettle hole biogeochemical processes are both affected by groundwater and vice versa. Groundwater flow direction and velocity into and out of the kettle hole often is not stable over time. Groundwater flow direction might reverse at the downstream part, resulting in repeated recycling of groundwater and corresponding solute turnover within the kettle holes. A sound understanding of this intricate interplay is a necessary prerequisite for better understanding of the biogeochemistry of this terrestrial-aquatic interface. A numerical experiment was used to quantify the lateral solute exchange between a kettle hole and the surrounding groundwater. A vertical cross section through the real existing catchment of a kettle hole was chosen. Glacial till represents the lower boundary. The heterogeneity of the subsurface was reproduced by various parameterizations of the soil hydraulic properties as well as varying the thickness of the unconfined aquifer or the lateral boundary conditions. In total 24 different parameterizations were implemented in the modeling software HydroGeoSphere (HGS). HGS is suitable to calculate the fluid exchange between surface and subsurface simultaneously and in a physically based way. The simulation runs were done for the period from November 1994 to October 2014. All results were analyzed with regard to the intensity and duration of water exchange between kettle hole and surrounding groundwater. Finally the three variants with the smallest, average and largest number of days where water flow is directed from kettle hole to groundwater were chosen to extend the scope of this study to include solute transport. Therefore a non-reactive substance was injected at the kettle hole bed. As a result, the fluid dynamics and the spread of water flowing from surface to subsurface and vice versa could be closely monitored. Finally, the choice of these variants provides information on the range of distances and duration of water exchange between kettle hole and surrounding groundwater.

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

DOE PAGES

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

2016-02-05

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

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

PubMed

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

2014-02-04

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Evaluating the spatial distribution of water balance in a small watershed, Pennsylvania

NASA Astrophysics Data System (ADS)

Yu, Zhongbo; Gburek, W. J.; Schwartz, F. W.

2000-04-01

A conceptual water-balance model was modified from a point application to be distributed for evaluating the spatial distribution of watershed water balance based on daily precipitation, temperature and other hydrological parameters. The model was calibrated by comparing simulated daily variation in soil moisture with field observed data and results of another model that simulates the vertical soil moisture flow by numerically solving Richards' equation. The impacts of soil and land use on the hydrological components of the water balance, such as evapotranspiration, soil moisture deficit, runoff and subsurface drainage, were evaluated with the calibrated model in this study. Given the same meteorological conditions and land use, the soil moisture deficit, evapotranspiration and surface runoff increase, and subsurface drainage decreases, as the available water capacity of soil increases. Among various land uses, alfalfa produced high soil moisture deficit and evapotranspiration and lower surface runoff and subsurface drainage, whereas soybeans produced an opposite trend. The simulated distribution of various hydrological components shows the combined effect of soil and land use. Simulated hydrological components compare well with observed data. The study demonstrated that the distributed water balance approach is efficient and has advantages over the use of single average value of hydrological variables and the application at a single point in the traditional practice.

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stegen, James C.; Johnson, Tim; Fredrickson, James K.

The hyporheic corridor (HC) is a critical component of riverine ecosystems that encompasses the river-11 groundwater continuum. The mixing of groundwater (GW) with river water (RW) in the HC can 12 stimulate biogeochemical activity, and here we (i) propose a novel thermodynamic mechanism 13 underlying this phenomenon, and (ii) reveal broader impacts on dissolved organic carbon (DOC) 14 biogeochemistry and microbial ecology. We show that thermodynamically-favorable DOC 15 accumulates in GW despite decreases in DOC concentration along subsurface flow paths, and that RW 16 contains less thermodynamically-favorable DOC, but at higher concentrations. This indicates that DOC 17 in GW ismore » protected from microbial oxidation by low total energy contained within the DOC pool, while 18 RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-19 RW mixing overcomes these protection mechanisms and stimulates respiration. Mixing models 20 coupled with time-lapse electrical resistance tomography revealed that stimulated respiration leads 21 to tipping points in spatiotemporal dynamics of DOC across the HC. Further, shifts in DOC speciation 22 and biochemical pathways were associated with shifts in microbiome composition, highlighting 23 feedbacks among hydrology, DOC biochemistry, and microbial ecology. These results reveal that 24 previously unrecognized thermodynamic-based mechanisms regulated by GW-RW mixing can strongly 25 influence biogeochemical and microbial dynamics in riverine ecosystems.« less

U(VI) bioreduction with emulsified vegetable oil as the electron donor--microcosm tests and model development.

PubMed

Tang, Guoping; Wu, Wei-Min; Watson, David B; Parker, Jack C; Schadt, Christopher W; Shi, Xiaoqing; Brooks, Scott C

2013-04-02

We conducted microcosm tests and biogeochemical modeling to study U(VI) reduction in contaminated sediments amended with emulsified vegetable oil (EVO). Indigenous microorganisms in the sediments degraded EVO and stimulated Fe(III), U(VI), and sulfate reduction, and methanogenesis. Acetate concentration peaked in 100-120 days in the EVO microcosms versus 10-20 days in the oleate microcosms, suggesting that triglyceride hydrolysis was a rate-limiting step in EVO degradation and subsequent reactions. Acetate persisted 50 days longer in oleate- and EVO- than in ethanol-amended microcosms, indicating that acetate-utilizing methanogenesis was slower in the oleate and EVO than ethanol microcosms. We developed a comprehensive biogeochemical model to couple EVO hydrolysis, production, and oxidation of long-chain fatty acids (LCFA), glycerol, acetate, and hydrogen, reduction of Fe(III), U(VI) and sulfate, and methanogenesis with growth and decay of multiple functional microbial groups. By estimating EVO, LCFA, and glycerol degradation rate coefficients, and introducing a 100 day lag time for acetoclastic methanogenesis for oleate and EVO microcosms, the model approximately matched observed sulfate, U(VI), and acetate concentrations. Our results confirmed that EVO could stimulate U(VI) bioreduction in sediments and the slow EVO hydrolysis and acetate-utilizing methanogens growth could contribute to longer term bioreduction than simple substrates (e.g., ethanol, acetate, etc.) in the subsurface.

Geochemical response to hydrologic change along land-sea interfaces

NASA Astrophysics Data System (ADS)

Michael, H. A.; Yu, X.; LeMonte, J. J.; Sparks, D. L.; Kim, K. H.; Heiss, J.; Ullman, W. J.; Guimond, J. A.; Seyfferth, A.

2016-12-01

Coastal groundwater-surface water interfaces are hotspots of geochemical activity, where reactants contributed by different sources come in contact. Reactions that occur along these land-sea boundaries have important effects on fluxes and cycling of carbon, nutrients, and contaminants. Hydrologic perturbations can alter interactions by promoting mixing, changing redox state, and altering subsurface residence times during which reactions may occur. We present examples from field and modeling investigations along the Delaware coastline that illustrate the impacts of hydrologic fluctuations on geochemical conditions and fluxes in different coastal environments. Along the highly populated Wilmington coastline, soils are contaminated with heavy metals from legacy industrial practices. We show with continuous redox monitoring and sampling over tidal to seasonal timescales that arsenic is mobilized and immobilized in response to hydrologic change. Along a beach, modeling and long-term monitoring show the influence of tidal to seasonal changes in the mixing zone between discharging fresh groundwater and seawater in the intertidal beach aquifer and associated impacts on biogeochemical reactivity and denitrification. In a saltmarsh, hydrologic changes alter carbon dynamics, with implications for the discharge of dissolved organic carbon to the ocean and export of carbon dioxide and methane to the atmosphere. Understanding the impacts of hydrologic changes on both long and short timescales is essential for improving our ability to predict the global biogeochemical impacts of a changing climate.

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

DOE PAGES

Stegen, James C.; Johnson, Tim; Fredrickson, James K.; ...

2018-02-08

The hyporheic corridor (HC) is a critical component of riverine ecosystems that encompasses the river-11 groundwater continuum. The mixing of groundwater (GW) with river water (RW) in the HC can 12 stimulate biogeochemical activity, and here we (i) propose a novel thermodynamic mechanism 13 underlying this phenomenon, and (ii) reveal broader impacts on dissolved organic carbon (DOC) 14 biogeochemistry and microbial ecology. We show that thermodynamically-favorable DOC 15 accumulates in GW despite decreases in DOC concentration along subsurface flow paths, and that RW 16 contains less thermodynamically-favorable DOC, but at higher concentrations. This indicates that DOC 17 in GW ismore » protected from microbial oxidation by low total energy contained within the DOC pool, while 18 RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-19 RW mixing overcomes these protection mechanisms and stimulates respiration. Mixing models 20 coupled with time-lapse electrical resistance tomography revealed that stimulated respiration leads 21 to tipping points in spatiotemporal dynamics of DOC across the HC. Further, shifts in DOC speciation 22 and biochemical pathways were associated with shifts in microbiome composition, highlighting 23 feedbacks among hydrology, DOC biochemistry, and microbial ecology. These results reveal that 24 previously unrecognized thermodynamic-based mechanisms regulated by GW-RW mixing can strongly 25 influence biogeochemical and microbial dynamics in riverine ecosystems.« less

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

Describing interactions between surface and subsurface flow processes is important to adequately define water flow in natural systems. Since overland flow generation is highly influenced by rainfall and infiltration, both highly spatially heterogeneous processes, overland flow is unsteady and varies spatially. The prediction of overland flow needs to include an appropriate description of the interactions between the surface and subsurface flow. Coupling surface and subsurface water flow is a challenging task. Different approaches have been developed during the last few years, each having its own advantages and disadvantages. A new approach by Weill et al. (2009) to couple overland flow and subsurface flow based on a generalized Richards equation was implemented into the well-known subsurface flow model HYDRUS-2D (Šimůnek et al., 2011). This approach utilizes the one-dimensional diffusion wave equation to model overland flow. The diffusion wave model is integrated in HYDRUS-2D by replacing the terms of the Richards equation in a pre-defined runoff layer by terms defining the diffusion wave equation. Using this approach, pressure and flux continuity along the interface between both flow domains is provided. This direct coupling approach provides a strong coupling of both systems based on the definition of a single global system matrix to numerically solve the coupled flow problem. The advantage of the direct coupling approach, compared to the loosely coupled approach, is supposed to be a higher robustness, when many convergence problems can be avoided (Takizawa et al., 2014). The HYDRUS-2D implementation was verified using a) different test cases, including a direct comparison with the results of Weill et al. (2009), b) an analytical solution of the kinematic wave equation, and c) the results of a benchmark test of Maxwell et al. (2014), that included several known coupled surface subsurface flow models. Additionally, a sensitivity analysis evaluating the effects of various model parameters on simulated overland flow (while considering or neglecting the effects of subsurface flow) was carried out to verify the applicability of the model to different problems. The model produced reasonable results in describing the diffusion wave approximation and its interactions with subsurface flow processes. The model could handle coupled surface-subsurface processes for conditions involving runoff generated by infiltration excess, saturation excess, or run-on, as well as a combination of these runoff generating processes. Several standard features of the HYDRUS 2D model, such as root water uptake and evaporation from the soil surface, as well as evaporation from runoff layer, can still be considered by the new model. The code required relatively small time steps when overland flow was active, resulting in long simulation times, and sometimes produced poor mass balance. The model nevertheless showed potential to be a useful tool for addressing various issues related to irrigation research and to natural generation of overland flow at the hillslope scale. Maxwell, R., Putti, M., Meyerhoff, S., Delf, J., Ferguson, I., Ivanov, V., Kim, J., Kolditz, O., Kollet, S., Kumar, M., Lopez, S., Niu, J., Paniconi, C., Park, Y.-J., Phanikumar, M., Shen, C., Sudicky, E., and Sulis, M. (2014). Surface-subsurface model intercomparison: A first set of benchmark results to diagnose integrated hydrology and feedbacks. Water Resourc. Res., 50:1531-1549. Šimůnek, J., van Genuchten, M. T., and Šejna, M. (2011). The HYDRUS Software Package for Simulating Two- and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Media. Technical Manual, Version 2.0, PC Progress, Prague, Czech Republic. Takizawa, K., Bazilevs Y., Tezduyar, T. E., Long, C.C., Marsden, A. L. and Schjodt.K., Patient-Specific Cardiovascular Fluid Mechanics Analysis with the ST and ALE-VMS Method in Idelsohn, S. R. (2014). Numerical Simulations of Coupled Problems in Engineering. Springer. Weill, S., Mouche, E., and Patin, J. (2009). A generalized Richards equation for surface/subsurface flow modelling. Journal of Hydrology, 366:9-20.

Puget Sound Applications of the VELMA Ecohydrological Model

EPA Science Inventory

This seminar will present an overview of EPA’s Visualizing Ecosystem Land Management Assessments (VELMA) model and its applications in the Puget Sound Basin. Topics will include a description of how VELMA simulates the interaction of hydrological and biogeochemical processe...

Biogeochemical Reactions Under Simulated Europa Ocean Conditions

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

Subsurface Scattered Photons: Friend or Foe? Improving visible light laser altimeter elevation estimates, and measuring surface properties using subsurface scattered photons

NASA Astrophysics Data System (ADS)

Greeley, A.; Kurtz, N. T.; Neumann, T.; Cook, W. B.; Markus, T.

2016-12-01

Photon counting laser altimeters such as MABEL (Multiple Altimeter Beam Experimental Lidar) - a single photon counting simulator for ATLAS (Advanced Topographical Laser Altimeter System) - use individual photons with visible wavelengths to measure their range to target surfaces. ATLAS, the sole instrument on NASA's upcoming ICESat-2 mission, will provide scientists a view of Earth's ice sheets, glaciers, and sea ice with unprecedented detail. Precise calibration of these instruments is needed to understand rapidly changing parameters such as sea ice freeboard, and to measure optical properties of surfaces like snow covered ice sheets using subsurface scattered photons. Photons that travel through snow, ice, or water before scattering back to an altimeter receiving system travel farther than photons taking the shortest path between the observatory and the target of interest. These delayed photons produce a negative elevation bias relative to photons scattered directly off these surfaces. We use laboratory measurements of snow surfaces using a flight-tested laser altimeter (MABEL), and Monte Carlo simulations of backscattered photons from snow to estimate elevation biases from subsurface scattered photons. We also use these techniques to demonstrate the ability to retrieve snow surface properties like snow grain size.

Viral Tracer Studies Indicate Contamination of Marine Waters by Sewage Disposal Practices in Key Largo, Florida

PubMed Central

Paul, J. H.; Rose, J. B.; Brown, J.; Shinn, E. A.; Miller, S.; Farrah, S. R.

1995-01-01

Domestic wastewater disposal practices in the Florida Keys are primarily limited to on-site disposal systems such as septic tanks, injection wells, and illegal cesspits. Poorly treated sewage is thus released into the highly porous subsurface Key Largo limestone matrix. To investigate the fate and transport of sewage in the subsurface environment and the potential for contamination of marine surface waters, we employed bacteriophages as tracers in a domestic septic system and a simulated injection well in Key Largo, Florida. Transport of bacteriophage (Phi)HSIC-1 from the septic tank to adjacent surface canal waters and outstanding marine waters occurred in as little as 11 and 23 h, respectively. Transport of the Salmonella phage PRD1 from the simulated injection well to a canal adjacent to the injection site occurred in 11.2 h. Estimated rates of migration of viral tracers ranged from 0.57 to 24.2 m/h, over 500-fold greater than flow rates measured previously by subsurface flow meters in similar environments. These results suggest that current on-site disposal practices can lead to contamination of the subsurface and surface marine waters in the Keys. PMID:16535046

Viral tracer studies indicate contamination of marine waters by sewage disposal practices in key largo, Florida.

PubMed

Paul, J H; Rose, J B; Brown, J; Shinn, E A; Miller, S; Farrah, S R

1995-06-01

Domestic wastewater disposal practices in the Florida Keys are primarily limited to on-site disposal systems such as septic tanks, injection wells, and illegal cesspits. Poorly treated sewage is thus released into the highly porous subsurface Key Largo limestone matrix. To investigate the fate and transport of sewage in the subsurface environment and the potential for contamination of marine surface waters, we employed bacteriophages as tracers in a domestic septic system and a simulated injection well in Key Largo, Florida. Transport of bacteriophage (Phi)HSIC-1 from the septic tank to adjacent surface canal waters and outstanding marine waters occurred in as little as 11 and 23 h, respectively. Transport of the Salmonella phage PRD1 from the simulated injection well to a canal adjacent to the injection site occurred in 11.2 h. Estimated rates of migration of viral tracers ranged from 0.57 to 24.2 m/h, over 500-fold greater than flow rates measured previously by subsurface flow meters in similar environments. These results suggest that current on-site disposal practices can lead to contamination of the subsurface and surface marine waters in the Keys.

Potential Elevation Biases for Laser Altimeters from Subsurface Scattered Photons: Laboratory and Model Exploration of Green Light Scattering in Snow

NASA Astrophysics Data System (ADS)

Greeley, A.; Neumann, T.; Markus, T.; Kurtz, N. T.; Cook, W. B.

2015-12-01

Existing visible light laser altimeters such as MABEL (Multiple Altimeter Beam Experimental Lidar) - a single photon counting simulator for ATLAS (Advanced Topographic Laser Altimeter System) on NASA's upcoming ICESat-2 mission - and ATM (Airborne Topographic Mapper) on NASA's Operation IceBridge mission provide scientists a view of Earth's ice sheets, glaciers, and sea ice with unprecedented detail. Precise calibration of these instruments is needed to understand rapidly changing parameters like sea ice freeboard and to measure optical properties of surfaces like snow covered ice sheets using subsurface scattered photons. Photons travelling into snow, ice, or water before scattering back to the altimeter receiving system (subsurface photons) travel farther and longer than photons scattering off the surface only, causing a bias in the measured elevation. We seek to identify subsurface photons in a laboratory setting using a flight-tested laser altimeter (MABEL) and to quantify their effect on surface elevation estimates for laser altimeter systems. We also compare these estimates with previous laboratory measurements of green laser light transmission through snow, as well as Monte Carlo simulations of backscattered photons from snow.

Testing the Joint UK Land Environment Simulator (JULES) for flood forecasting

NASA Astrophysics Data System (ADS)

Batelis, Stamatios-Christos; Rosolem, Rafael; Han, Dawei; Rahman, Mostaquimur

2017-04-01

Land Surface Models (LSM) are based on physics principles and simulate the exchanges of energy, water and biogeochemical cycles between the land surface and lower atmosphere. Such models are typically applied for climate studies or effects of land use changes but as the resolution of LSMs and supporting observations are continuously increasing, its representation of hydrological processes need to be addressed adequately. For example, changes in climate and land use can alter the hydrology of a region, for instance, by altering its flooding regime. LSMs can be a powerful tool because of their ability to spatially represent a region with much finer resolution. However, despite such advantages, its performance has not been extensively assessed for flood forecasting simply because its representation of typical hydrological processes, such as overland flow and river routing, are still either ignored or roughly represented. In this study, we initially test the Joint UK Land Environment Simulator (JULES) as a flood forecast tool focusing on its river routing scheme. In particular, JULES river routing parameterization is based on the Rapid Flow Model (RFM) which relies on six prescribed parameters (two surface and two subsurface wave celerities, and two return flow fractions). Although this routing scheme is simple, the prescription of its six default parameters is still too generalized. Our aim is to understand the importance of each RFM parameter in a series of JULES simulations at a number of catchments in the UK for the 2006-2015 period. This is carried out, for instance, by making a number of assumptions of parameter behaviour (e.g., spatially uniform versus varying and/or temporally constant or time-varying parameters within each catchment). Hourly rainfall radar in combination with the CHESS (Climate, Hydrological and Ecological research Support System) meteorological daily data both at 1 km2 resolution are used. The evaluation of the model is based on hourly runoff data provided by the National River Flood Archive using a number of model performance metrics. We use a calibrated conceptually-based lumped model, more typically applied in flood studies, as a benchmark for our analysis.

Optimization of buffer injection for the effective bioremediation of chlorinated solvents in aquifers

NASA Astrophysics Data System (ADS)

Brovelli, A.; Robinson, C.; Barry, A.; Kouznetsova, I.; Gerhard, J.

2008-12-01

Various techniques have been proposed to enhance biologically-mediated reductive dechlorination of chlorinated solvents in the subsurface, including the addition of fermentable organic substrate for the generation of H2 as an electron donor. One rate-limiting factor for enhanced dechlorination is the pore fluid pH. Organic acids and H+ ions accumulate in dechlorination zones, generating unfavorable conditions for microbial activity (pH < 6.5). The pH variation is a nonlinear function of the amount of reduced chlorinated solvents, and is affected by the organic material fermented, the chemical composition of the pore fluid and the soil's buffering capacity. Consequently, in some cases enhanced remediation schemes rely on buffer injection (e.g., bicarbonate) to alleviate this problem, particularly in the presence of solvent nonaqueous phase liquid (NAPL) source zones. However, the amount of buffer required - particularly in complex, evolving biogeochemical environments - is not well understood. To investigate this question, this work builds upon a geochemical numerical model (Robinson et al., Science of the Total Environment, submitted), which computes the amount of additional buffer required to maintain the pH at a level suitable for bacterial activity for batch systems. The batch model was coupled to a groundwater flow/solute transport/chemical reaction simulator to permit buffer optimization computations within the context of flowing systems exhibiting heterogeneous hydraulic, physical and chemical properties. A suite of simulations was conducted in which buffer optimization was examined within the bounds of the minimum concentration necessary to sustain a pH favorable to microbial activity and the maximum concentration to avoid excessively high pH values (also not suitable to bacterial activity) and mineral precipitation (e.g., calcite, which may lead to pore-clogging). These simulations include an examination of the sensitivity of this buffer concentration range to aquifer heterogeneity and groundwater velocity. This work is part of SABRE (Source Area BioREmediation), a collaborative international research project that aims to evaluate and improve enhanced bioremediation of chlorinated solvent source zones. In this context, numerical simulations are supporting the upscaling of the technique, including identifying the most appropriate buffer injection strategies for field applications

Quantifying induced effects of subsurface renewable energy storage

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Beyer, Christof; Pfeiffer, Tilmann; Boockmeyer, Anke; Popp, Steffi; Delfs, Jens-Olaf; Wang, Bo; Li, Dedong; Dethlefsen, Frank; Dahmke, Andreas

2015-04-01

New methods and technologies for energy storage are required for the transition to renewable energy sources. Subsurface energy storage systems such as salt caverns or porous formations offer the possibility of hosting large amounts of energy or substance. When employing these systems, an adequate system and process understanding is required in order to assess the feasibility of the individual storage option at the respective site and to predict the complex and interacting effects induced. This understanding is the basis for assessing the potential as well as the risks connected with a sustainable usage of these storage options, especially when considering possible mutual influences. For achieving this aim, in this work synthetic scenarios for the use of the geological underground as an energy storage system are developed and parameterized. The scenarios are designed to represent typical conditions in North Germany. The types of subsurface use investigated here include gas storage and heat storage in porous formations. The scenarios are numerically simulated and interpreted with regard to risk analysis and effect forecasting. For this, the numerical simulators Eclipse and OpenGeoSys are used. The latter is enhanced to include the required coupled hydraulic, thermal, geomechanical and geochemical processes. Using the simulated and interpreted scenarios, the induced effects are quantified individually and monitoring concepts for observing these effects are derived. This presentation will detail the general investigation concept used and analyze the parameter availability for this type of model applications. Then the process implementation and numerical methods required and applied for simulating the induced effects of subsurface storage are detailed and explained. Application examples show the developed methods and quantify induced effects and storage sizes for the typical settings parameterized. This work is part of the ANGUS+ project, funded by the German Ministry of Education and Research (BMBF).

Benthic contributions to Adriatic and Mediterranean biogeochemical cycles

NASA Astrophysics Data System (ADS)

Capet, Arthur; Lazzari, Paolo; Spagnoli, Federico; Bolzon, Giorgio; Solidoro, Cosimo

2017-04-01

The 3D biogeochemical BFM-OGSTM implementation currently exploited operationally in the Copernicus Marine Environment Monitoring Services Mediterranean Sea Monitoring and Forecasting Centre (CMEMS-Med-MFC; Lazzari et al., 2010) has been complemented with a benthic component. The approach followed that of (Capet et al 2016) and involved a vertically integrated benthic module accounting for the effect of environmental bottom conditions on diagenetic rates (aerobic mineralization, denitrification, nitrification) through transfer functions as well as the effect of waves and bottom currents on sediment deposition and resuspension. A balanced climatological year is simulated for various values of the resuspension parameters, using specifically calibrated transfer functions for the Adriatic Sea and generic formulations for the rest of the Mediterranean basin. The results serves the mapping of distinct provinces of the Adriatic Sea based on the benthic contributions biogeochemical budgets and the seasonal variability of benthic-pelagic fluxes. The differences with the non-benthic reference simulation are highlighted in details regarding the Adriatic, and more generally for the entire Mediterranean Sea. Lazzari, P., Teruzzi, A., Salon, S., Campagna, S., Calonaci, C., Colella, S., Tonani, M., Crise, A. (2010). Pre-operational short-term forecasts for Mediterranean Sea biogeochemistry. Ocean Science, 6(1), 25-39. Capet, A., Meysman, F. J., Akoumianaki, I., Soetaert, K., & Grégoire, M. (2016). Integrating sediment biogeochemistry into 3D oceanic models: A study of benthic-pelagic coupling in the Black Sea. Ocean Modelling, 101, 83-100.

BIO ARGO floats: tools for operational monitoring of the Black Sea

NASA Astrophysics Data System (ADS)

Palazov, Atanas; Slabakova, Violeta; Peneva, Elisaveta; Stanev, Emil

2014-05-01

The assessment of ecological status in the context of the Water Framework Directive (WFD) and Marine Strategy Framework Directive (MSFD) requires comprehensive knowledge and understanding of the physical and biogeochemical processes that determine the functioning of marine ecosystems. One of the main challenges however is the need of data with frequency relevant to the spatial and temporal scales of the ecological processes. The majority of in situ observations that are commonly used for ecological monitoring of the Black Sea are generally based on near-shore monitoring programs or irregular oceanographic cruises that provide either non-synoptic, coarse resolution realizations of large scale processes or detailed, but time and site specific snapshots of local features. These gaps can be filled by two independent sources: satellite observation and profiling floats. In fact satellite ocean color sensors allows for determination at synoptic scale of water quality parameters through its absorption properties. However the satellite ocean color methods have a number of limitations such as: measurements can only be made during daylight hours; require cloud-free conditions and are sensitive to atmospheric aerosols; provide information only for the upper layer of the ocean (approximately the depth of 10% incident light); algorithms developed for global applications are a source of large uncertainties in the marginal seas and costal areas. These constrains of the optical remote sensing observations can be avoided by using miniature biogeochemical sensors and autonomous platforms that offer remarkable perspectives for observing the "biological" ocean, notably at critical spatiotemporal scales which have been out of reach until recently (Claustre et al., 2010). In the frame of "E-AIMS: Euro-Argo Improvements for the GMES marine Service" 7 EC FP project two Bio Argo floats were deployed in the Black Sea. Beside the traditionally CTD the floats were equipped with biogeochemical sensors (oxygen, irradiance, chl-a and backscattering). The selection of the deployment locations was limited only to the Bulgarian Black Sea waters, so that the optimal deployment strategy that has been chosen was the floats to be deployed in the maximum distant positions from each other along the Black Sea geostrophic current at depth ~ 1800 m. Coincident biogeochemical and in-water radiometric measurements were collected at the time of each float deployment to ensure intercalibration of the instruments mounted on the floats and as well as to find empirical relationship between optical data and biogeochemical variables. The data obtained form Bio floats will be used to: investigate the seasonal evolution of oxygen in the upper layers, including the subsurface oxygen maximum; study the seasonal and inter annual dynamics of phytoplankton blooms in the deeper Black Sea; cross validation of satellite derived Chl-a and backscattering. References: Claustre et al. (2010). Bio-optical profiling floats as new observational tools for biogeochemical and ecosystem studies: potential synergies with ocean color remote sensing. Proceedings of the "OceanObs'09: Sustained Ocean Observations and Information for Society" Conference, Venice/Italy.

Sources and fates of heavy metals in a mining-impacted stream: Temporal variability and the role of iron oxides

PubMed Central

Schaider, Laurel A.; Senn, David B.; Estes, Emily R.; Brabander, Daniel J.; Shine, James P.

2014-01-01

Heavy metal contamination of surface waters at mining sites often involves complex interactions of multiple sources and varying biogeochemical conditions. We compared surface and subsurface metal loading from mine waste pile runoff and mine drainage discharge and characterized the influence of iron oxides on metal fate along a 0.9-km stretch of Tar Creek (Oklahoma, USA), which drains an abandoned Zn/Pb mining area. The importance of each source varied by metal: mine waste pile runoff contributed 70% of Cd, while mine drainage contributed 90% of Pb, and both sources contributed similarly to Zn loading. Subsurface inputs accounted for 40% of flow and 40-70% of metal loading along this stretch. Streambed iron oxide aggregate material contained highly elevated Zn (up to 27,000 μg g−1), Pb (up to 550 μg g−1) and Cd (up to 200 μg g−1) and was characterized as a heterogeneous mixture of iron oxides, fine-grain mine waste, and organic material. Sequential extractions confirmed preferential sequestration of Pb by iron oxides, as well as substantial concentrations of Zn and Cd in iron oxide fractions, with additional accumulation of Zn, Pb, and Cd during downstream transport. Comparisons with historical data show that while metal concentrations in mine drainage have decreased by more than an order of magnitude in recent decades, the chemical composition of mine waste pile runoff has remained relatively constant, indicating less attenuation and increased relative importance of pile runoff. These results highlight the importance of monitoring temporal changes at contaminated sites associated with evolving speciation and simultaneously addressing surface and subsurface contamination from both mine waste piles and mine drainage. PMID:24867708

The impact of multi-decadal sub-surface circulation changes on sea surface chlorophyll patterns in the tropical Pacific

NASA Astrophysics Data System (ADS)

Schollaert Uz, S.; Busalacchi, A. J.; Smith, T. M.; Evans, M. N.; Brown, C.; Hackert, E. C.; Wang, X.

2016-12-01

The tropical Pacific is a region of strong forcing where physical oceanography primarily controls biological variability over the seasonal to interannual time scales observed since dedicated ocean color satellite remote sensing began in 1997. To quantify how multi-decadal, climate-scale changes impact marine biological dynamics, we used the correlation with sea-surface temperature and height to reconstruct a 50-year time series of surface chlorophyll concentrations. The reconstruction demonstrates greatest skill away from the coast and within 10o of the equator where chlorophyll variance is greatest and primarily associated with El Niño Southern Oscillation (ENSO) dynamics and secondarily associated with decadal variability. We observe significant basin-wide differences between east and central Pacific events when the El Niño events are strong: chlorophyll increases with La Niña and decreases with El Niño, with larger declines east of 180o for remotely-forced east Pacific events and west of 180o for locally-forced central Pacific events. Chlorophyll variations also reflect the physical dynamics of Pacific decadal variability with small but significant differences between cool and warm eras: consistent with advection variability west of 180o and likely driven by subsurface changes in the nutricline depth between 110-140oW. Comparisons with output from a fully-coupled biogeochemical model support the hypothesis that this anomalous region is controlled by lower frequency changes in subsurface circulation patterns that transport nutrients to the surface. Basin-wide chlorophyll distributions exhibiting spatial heterogeneity in response to multi-decadal climate forcing imply similar long-term changes in phytoplankton productivity, with implications for the marine food web and the ocean's role as a carbon sink.

The formation of a subsurface anticyclonic eddy in the Peru-Chile Undercurrent and its impact on the near-coastal salinity, oxygen, and nutrient distributions

NASA Astrophysics Data System (ADS)

Thomsen, Soeren; Kanzow, Torsten; Krahmann, Gerd; Greatbatch, Richard J.; Dengler, Marcus; Lavik, Gaute

2016-01-01

The formation of a subsurface anticyclonic eddy in the Peru-Chile Undercurrent (PCUC) in January and February 2013 is investigated using a multiplatform four-dimensional observational approach. Research vessel, multiple glider, and mooring-based measurements were conducted in the Peruvian upwelling regime near 12°30'S. The data set consists of >10,000 glider profiles and repeated vessel-based hydrography and velocity transects. It allows a detailed description of the eddy formation and its impact on the near-coastal salinity, oxygen, and nutrient distributions. In early January, a strong PCUC with maximum poleward velocities of ˜0.25 m/s at 100-200 m depth was observed. Starting on 20 January, a subsurface anticyclonic eddy developed in the PCUC downstream of a topographic bend, suggesting flow separation as the eddy formation mechanism. The eddy core waters exhibited oxygen concentration of <1 μmol/kg, an elevated nitrogen deficit of ˜17 μmol/L, and potential vorticity close to zero, which seemed to originate from the bottom boundary layer of the continental slope. The eddy-induced across-shelf velocities resulted in an elevated exchange of water masses between the upper continental slope and the open ocean. Small-scale salinity and oxygen structures were formed by along-isopycnal stirring, and indications of eddy-driven oxygen ventilation of the upper oxygen minimum zone were observed. It is concluded that mesoscale stirring of solutes and the offshore transport of eddy core properties could provide an important coastal open ocean exchange mechanism with potentially large implications for nutrient budgets and biogeochemical cycling in the oxygen minimum zone off Peru.

Mars Analog Research and Technology Experiment (MARTE): A Simulated Mars Drilling Mission to Search for Subsurface Life at the Rio Tinto, Spain

NASA Technical Reports Server (NTRS)

Stoker, Carol; Lemke, Larry; Mandell, Humboldt; McKay, David; George, Jeffrey; Gomez-Alvera, Javier; Amils, Ricardo; Stevens, Todd; Miller, David

2003-01-01

The MARTE (Mars Astrobiology Research and Technology Experiment) project was selected by the new NASA ASTEP program, which supports field experiments having an equal emphasis on Astrobiology science and technology development relevant to future Astrobiology missions. MARTE will search for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Tinto River in southwestern Spain while also demonstrating technology needed to search for a subsurface biosphere on Mars. The experiment is informed by the strategy for searching for life on Mars.

Hydrological modelling in sandstone rocks watershed

NASA Astrophysics Data System (ADS)

Ponížilová, Iva; Unucka, Jan

2015-04-01

The contribution is focused on the modelling of surface and subsurface runoff in the Ploučnice basin. The used rainfall-runoff model is HEC-HMS comprising of the method of SCS CN curves and a recession method. The geological subsurface consisting of sandstone is characterised by reduced surface runoff and, on the contrary, it contributes to subsurface runoff. The aim of this paper is comparison of the rate of influence of sandstone on reducing surface runoff. The recession method for subsurface runoff was used to determine the subsurface runoff. The HEC-HMS model allows semi- and fully distributed approaches to schematisation of the watershed and rainfall situations. To determine the volume of runoff the method of SCS CN curves is used, which results depend on hydrological conditions of the soils. The rainfall-runoff model assuming selection of so-called methods of event of the SCS-CN type is used to determine the hydrograph and peak flow rate based on simulation of surface runoff in precipitation exceeding the infiltration capacity of the soil. The recession method is used to solve the baseflow (subsurface) runoff. The method is based on the separation of hydrograph to direct runoff and subsurface or baseflow runoff. The study area for the simulation of runoff using the method of SCS CN curves to determine the hydrological transformation is the Ploučnice basin. The Ploučnice is a hydrologically significant river in the northern part of the Czech Republic, it is a right tributary of the Elbe river with a total basin area of 1.194 km2. The average value of CN curves for the Ploučnice basin is 72. The geological structure of the Ploučnice basin is predominantly formed by Mesozoic sandstone. Despite significant initial loss of rainfall the basin response to the causal rainfall was demonstrated by a rapid rise of the surface runoff from the watershed and reached culmination flow. Basically, only surface runoff occures in the catchment during the initial phase of this extreme event. The increase of the baseflow runoff is slower and remains constant after reaching a certain level. The rise of the baseflow runoff is showed in a descending part of the hydrograph. The recession method in this case shows almost 20 hours delay. Results from the HEC-HMS prove availability of both methods for the runoff modeling in this type of catchment. When simulating extreme short-term rainfall-runoff episodes, the influence of geological subsurface is not significant, but it is manifested. Using more relevant rainfall events would bring more satisfactory results.

Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.

PubMed

Averill, Colin

2014-10-01

Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate. © 2014 John Wiley & Sons Ltd/CNRS.

Understanding the Day Cent model: Calibration, sensitivity, and identifiability through inverse modeling

USGS Publications Warehouse

Necpálová, Magdalena; Anex, Robert P.; Fienen, Michael N.; Del Grosso, Stephen J.; Castellano, Michael J.; Sawyer, John E.; Iqbal, Javed; Pantoja, Jose L.; Barker, Daniel W.

2015-01-01

The ability of biogeochemical ecosystem models to represent agro-ecosystems depends on their correct integration with field observations. We report simultaneous calibration of 67 DayCent model parameters using multiple observation types through inverse modeling using the PEST parameter estimation software. Parameter estimation reduced the total sum of weighted squared residuals by 56% and improved model fit to crop productivity, soil carbon, volumetric soil water content, soil temperature, N2O, and soil3NO− compared to the default simulation. Inverse modeling substantially reduced predictive model error relative to the default model for all model predictions, except for soil 3NO− and 4NH+. Post-processing analyses provided insights into parameter–observation relationships based on parameter correlations, sensitivity and identifiability. Inverse modeling tools are shown to be a powerful way to systematize and accelerate the process of biogeochemical model interrogation, improving our understanding of model function and the underlying ecosystem biogeochemical processes that they represent.

A Search for Life in the Subsurface At Rio Tinto Spain, An Analog To Searching For Life On Mars.

NASA Astrophysics Data System (ADS)

Stoker, C. R.

2003-12-01

Most familiar life forms on Earth live in the surface biosphere where liquid water, sunlight, and the essential chemical elements for life are abundant. However, such environments are not found on Mars or anywhere else in the solar system. On Mars, the surface environmental conditions of pressure and temperature prevent formation of liquid water. Furthermore, conditions at the Martian surface are unfavorable to life due to intense ultraviolet radiation and strong oxidizing compounds that destroy organic compounds. However, subsurface liquid water on Mars has been predicted on theoretical grounds. The recent discovery of near surface ground ice by the Mars Odyssey mission, and the abundant evidence for recent Gully features observed by the Mars Global Surveyor mission strengthen the case for subsurface liquid water on Mars. Thus, the strategy for searching for life on Mars points to drilling to the depth of liquid water, bringing samples to the surface and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. The MARTE (Mars Astrobiology Research and Technology Experiment) project is a field experiment focused on searching for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Rio Tinto, a river in southwestern Spain while also demonstrating technology relevant to searching for a subsurface biosphere on Mars. The Tinto river is located in the Iberian Pyrite belt, one of the largest deposits of sulfide minerals in the world. The surface (river) system is an acidic extreme environment produced and maintained by microbes that metabolize sulfide minerals and produce sulfuric acid as a byproduct. Evidence suggests that the river is a surface manifestation of an underground biochemical reactor. Organisms found in the river are capable of chemoautotrophic metabolism using sulfide and ferric iron mineral substrates, suggesting these organisms could thrive in groundwater which is the source of the Rio Tinto. The MARTE project will simulate the search for subsurface life on Mars using a drilling system developed for future Mars flight to accomplish subsurface access. Augmenting the drill are robotic systems for extracting the cores from the drill head and performing analysis using a suite of instruments to understand the composition, mineralogy, presence of organics, and to search for life signatures in subsurface samples. A robotic bore-hole inspection system will characterize borehole properties in situ. A Mars drilling mission simulation including remote operation of the drilling, sample handling, and instruments and interpretation of results by a remote science team will be performed. This simulated mission will be augmented by manual methods of drilling, sample handling, and sample analysis to fully document the subsurface, prevent surface microbial contamination, identify subsurface biota, and compare what can be learned with robotically-operated instruments. The first drilling campaign in the MARTE project takes place in September 2003 and is focused on characterizing the microbiology of the subsurface at Rio Tinto using conventional drilling, sample handling and laboratory analysis techniques. Lessons learned from this "ground truth" drilling campaign will guide the development of robotic systems and instruments needed for searching for life underground on Mars.

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

PubMed Central

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

2014-01-01

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

Simulating land-atmosphere feedbacks and response to widespread forest disturbance: The role of lower boundary configuration and dynamic water table in meteorological modeling

NASA Astrophysics Data System (ADS)

Forrester, M.; Maxwell, R. M.; Bearup, L. A.; Gochis, D.

2017-12-01

Numerical meteorological models are frequently used to diagnose land-atmosphere interactions and predict large-scale response to extreme or hazardous events, including widespread land disturbance or perturbations to near-surface moisture. However, few atmospheric modeling platforms consider the impact that dynamic groundwater storage, specifically 3D subsurface flow, has on land-atmosphere interactions. In this study, we use the Weather Research and Forecasting (WRF) mesoscale meteorological model to identify ecohydrologic and land-atmosphere feedbacks to disturbance by the mountain pine beetle (MPB) over the Colorado Headwaters region. Disturbance simulations are applied to WRF with various lower boundary configurations: Including default Noah land surface model soil moisture representation; a version of WRF coupled to ParFlow (PF), an integrated groundwater-surface water model that resolves variably saturated flow in the subsurface; and WRF coupled to PF in a static water table version, simulating only vertical and no lateral subsurface flow. Our results agree with previous literature showing MPB-induced reductions in canopy transpiration in all lower boundary scenarios, as well as energy repartitioning, higher water tables, and higher planetary boundary layer over infested regions. Simulations show that expanding from local to watershed scale results in significant damping of MPB signal as unforested and unimpacted regions are added; and, while deforestation appears to have secondary feedbacks to planetary boundary layer and convection, these slight perturbations to cumulative summer precipitation are insignificant in the context of ensemble methodologies. Notably, the results suggest that groundwater representation in atmospheric modeling affects the response intensity of a land disturbance event. In the WRF-PF case, energy and atmospheric processes are more sensitive to disturbance in regions with higher water tables. Also, when dynamic subsurface hydrology is removed, WRF simulates a greater response to MPB at the land-atmosphere interface, including greater changes to daytime skin temperature, Bowen ratio and near-surface humidity. These findings highlight lower boundary representations in computational meteorology and numerical land-atmosphere modeling.

Carbon Tetrachloride Flow and Transport in the Subsurface of the 216-Z-9 Trench at the Hanford Site

NASA Astrophysics Data System (ADS)

Oostrom, M.; Rockhold, M.; Truex, M.; Thorne, P.; Last, G.; Rohay, V.

2006-12-01

Three-dimensional modeling was conducted with layered and heterogeneous models to enhance the conceptual model of CT distribution in the vertical and lateral direction beneath the 216-Z-9 trench and to investigate the effects of soil vapor extraction (SVE). This work supports the U.S. Department of Energy's (DOE's) efforts to characterize the nature and distribution of CT in the 200 West Area and subsequently select an appropriate final remedy. Simulations targeted migration of dense, nonaqueous phase liquid (DNAPL) consisting of CT and co-disposed organics in the subsurface beneath the 216-Z-9 trench as a function of the properties and distribution of subsurface sediments and of the properties and disposal history of the waste. Simulations of CT migration were conducted using the Subsurface Transport Over Multiple Phases (STOMP) simulator. Simulation results support a conceptual model for CT distribution where CT in the DNAPL phase is expected to have migrated primarily in a vertical direction below the disposal trench. Presence of small-scale heterogeneities tends to limit the extent of vertical migration of CT DNAPL due to enhanced retention of DNAPL compared to more homogeneous conditions, but migration is still predominantly in the vertical direction. Results also show that the Cold Creek units retain more CT DNAPL within the vadose zone than other hydrologic unit during SVE. A considerable amount of the disposed CT DNAPL may have partitioned to the vapor and subsequently water and sorbed phases. Presence of small-scale heterogeneities tends to increase the amount of volatilization. Any continued migration of CT from the vadose zone to the groundwater is likely through interaction of vapor phase CT with the groundwater and not through continued DNAPL migration. The results indicated that SVE appears to be an effective technology for vadose zone remediation, but additional effort is needed to improve simulation of the SVE process.

FINAL REPORT: Mechanistically-Base Field Scale Models of Uranium Biogeochemistry from Upscaling Pore-Scale Experiments and Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Brian D.

2013-11-04

Biogeochemical reactive transport processes in the subsurface environment are important to many contemporary environmental issues of significance to DOE. Quantification of risks and impacts associated with environmental management options, and design of remediation systems where needed, require that we have at our disposal reliable predictive tools (usually in the form of numerical simulation models). However, it is well known that even the most sophisticated reactive transport models available today have poor predictive power, particularly when applied at the field scale. Although the lack of predictive ability is associated in part with our inability to characterize the subsurface and limitations inmore » computational power, significant advances have been made in both of these areas in recent decades and can be expected to continue. In this research, we examined the upscaling (pore to Darcy and Darcy to field) the problem of bioremediation via biofilms in porous media. The principle idea was to start with a conceptual description of the bioremediation process at the pore scale, and apply upscaling methods to formally develop the appropriate upscaled model at the so-called Darcy scale. The purpose was to determine (1) what forms the upscaled models would take, and (2) how one might parameterize such upscaled models for applications to bioremediation in the field. We were able to effectively upscale the bioremediation process to explain how the pore-scale phenomena were linked to the field scale. The end product of this research was to produce a set of upscaled models that could be used to help predict field-scale bioremediation. These models were mechanistic, in the sense that they directly incorporated pore-scale information, but upscaled so that only the essential features of the process were needed to predict the effective parameters that appear in the model. In this way, a direct link between the microscale and the field scale was made, but the upscaling process helped inform potential users of the model what kinds of information would be needed to accurately characterize the system.« less

Novel applications for biogeophysics: Prospects for detecting key subseafloor geomicrobiological processes or habitats

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Ntarlagiannis, D.

2007-05-01

The new subdiscipline of biogeophysics has focused mostly on the geophysical signatures of microbial processes in contaminated subsurface environments usually undergoing remediation. However, the use of biogeophysics to examine the biogeochemistry of marine sediments has not yet been well-integrated into conceptual models that describe subseafloor processes. Current examples of geophysical measurements that have been used to detect geomicrobiological processes or infer their location in the seafloor include sound surveillance system (SOSUS)-derived data that detect seafloor eruptive events, deep and shallow cross-sectional seismic surveys that determine the presence of hydraulically conductive zones or gas-bearing sediments (e.g., bottom-simulating reflectors or bubble-rich strata), and thermal profiles. One possible area for innovative biogeophysical characterization of the seafloor involves determining the depth of the sulfate-methane interface (SMI) in locations where sulfate diffuses from the seawater and methane emanates from subsurface strata. The SMI demarcates a stratum where microbially-driven anaerobic methane oxidation (AMO) is dependent upon methane as an electron donor and sulfate as an electron acceptor. AMO is carried out by a recently defined, unique consortium of microbes that metabolically temper the flux of methane into the overlying seawater. The depth of the SMI is, respectively, shallow or deep according to whether a high or low rate of methane flux occurs from the deep sediments. Presently, the SMI can only be determined by direct measurements of methane and sulfate concentrations in the interstitial waters or by molecular biological techniques that target the microbes responsible for creating the SMI. Both methods require collection and considerable analysis of sediment samples. Therefore, detection of the SMI by non-destructive methods would be advantageous. As a key biogeochemical threshold in marine sediments, the depth of the SMI defines methane charge in marine sediments, whether it is from dissolved methane or from methane hydrates. As such, a biogeophysical strategy for determining SMI depth would represent an important contribution to assessing methane charge with respect to climate change, sediment stability, or potential energy resources.

Parameter-induced uncertainty quantification of crop yields, soil N2O and CO2 emission for 8 arable sites across Europe using the LandscapeDNDC model

NASA Astrophysics Data System (ADS)

Santabarbara, Ignacio; Haas, Edwin; Kraus, David; Herrera, Saul; Klatt, Steffen; Kiese, Ralf

2014-05-01

When using biogeochemical models to estimate greenhouse gas emissions at site to regional/national levels, the assessment and quantification of the uncertainties of simulation results are of significant importance. The uncertainties in simulation results of process-based ecosystem models may result from uncertainties of the process parameters that describe the processes of the model, model structure inadequacy as well as uncertainties in the observations. Data for development and testing of uncertainty analisys were corp yield observations, measurements of soil fluxes of nitrous oxide (N2O) and carbon dioxide (CO2) from 8 arable sites across Europe. Using the process-based biogeochemical model LandscapeDNDC for simulating crop yields, N2O and CO2 emissions, our aim is to assess the simulation uncertainty by setting up a Bayesian framework based on Metropolis-Hastings algorithm. Using Gelman statistics convergence criteria and parallel computing techniques, enable multi Markov Chains to run independently in parallel and create a random walk to estimate the joint model parameter distribution. Through means distribution we limit the parameter space, get probabilities of parameter values and find the complex dependencies among them. With this parameter distribution that determines soil-atmosphere C and N exchange, we are able to obtain the parameter-induced uncertainty of simulation results and compare them with the measurements data.

Improved global simulation of groundwater-ecosystem interactions via tight coupling of a dynamic global ecosystem model and a global hydrological model

NASA Astrophysics Data System (ADS)

Braakhekke, Maarten; Rebel, Karin; Dekker, Stefan; Smith, Benjamin; Sutanudjaja, Edwin; van Beek, Rens; van Kampenhout, Leo; Wassen, Martin

2017-04-01

In up to 30% of the global land surface ecosystems are potentially influenced by the presence of a shallow groundwater table. In these regions upward water flux by capillary rise increases soil moisture availability in the root zone, which has a strong effect on evapotranspiration, vegetation dynamics, and fluxes of carbon and nitrogen. Most global hydrological models and several land surface models simulate groundwater table dynamics and their effects on land surface processes. However, these models typically have relatively simplistic representation of vegetation and do not consider changes in vegetation type and structure. Dynamic global vegetation models (DGVMs), describe land surface from an ecological perspective, combining detailed description of vegetation dynamics and structure, and biogeochemical processes and are thus more appropriate to simulate the ecological and biogeochemical effects of groundwater interactions. However, currently virtually all DGVMs ignore these effects, assuming that water tables are too deep to affect soil moisture in the root zone. We have implemented a tight coupling between the dynamic global ecosystem model LPJ-GUESS and the global hydrological model PCR-GLOBWB, which explicitly simulates groundwater dynamics. This coupled model allows us to explicitly account for groundwater effects on terrestrial ecosystem processes at global scale. Results of global simulations indicate that groundwater strongly influences fluxes of water, carbon and nitrogen, in many regions, adding up to a considerable effect at the global scale.

Impact of transient soil water simulation to estimated nitrogen leaching and emission at high- and low-deposition forest sites in southern California

Treesearch

Yuan Yuan; Thomas Meixner; Mark E. Fenn; Jirka Simunek

2011-01-01

Soil water dynamics and drainage are key abiotic factors controlling losses of atmospherically deposited N in Southern California. In this paper soil N leaching and trace gaseous emissions simulated by the DAYCENT biogeochemical model using its original semi‐dynamic water flow module were compared to that coupled with a finite element transient water flow...

System dynamics modeling of nitrogen removal in a stormwater infiltration basin with biosorption-activated media.

PubMed

Xuan, Zhemin; Chang, Ni-Bin; Wanielista, Martin P; Williams, Evan Shane

2013-07-01

Stormwater infiltration basins, one of the typical stormwater best management practices, are commonly constructed for surface water pollution control, flood mitigation, and groundwater restoration in rural or residential areas. These basins have soils with better infiltration capacity than the native soil; however, the ever-increasing contribution of nutrients to groundwater from stormwater due to urban expansion makes existing infiltration basins unable to meet groundwater quality criteria related to environmental sustainability and public health. This issue requires retrofitting current infiltration basins for flood control as well as nutrient control before the stormwater enters the groundwater. An existing stormwater infiltration basin in north-central Florida was selected, retrofitted, and monitored to identify subsurface physiochemical and biological processes during 2007-2010 to investigate nutrient control processes. This implementation in the nexus of contaminant hydrology and ecological engineering adopted amended soil layers packed with biosorption activated media (BAM; tire crumb, silt, clay, and sand) to perform nutrient removal in a partitioned forebay using a berm. This study presents an infiltration basin-nitrogen removal (IBNR) model, a system dynamics model that simulates nitrogen cycling in this BAM-based stormwater infiltration basin with respect to changing hydrologic conditions and varying dissolved nitrogen concentrations. Modeling outputs of IBNR indicate that denitrification is the biogeochemical indicator in the BAM layer that accounted for a loss of about one third of the total dissolved nitrogen mass input. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Modeling the relative importance of nutrient and carbon loads ...

EPA Pesticide Factsheets

The Louisiana continental shelf (LCS) in the northern Gulf of Mexico experiences bottom water hypoxia in the summer. In order to gain a more fundamental understanding of the controlling factors leading to hypoxia, the Gulf of Mexico Dissolved Oxygen Model (GoMDOM) was applied to this area to simulate dissolved oxygen concentrations in the water as a function of various nutrient loadings. The model is a numerical, biogeochemical, three-dimensional ecological model that receives its physical transport data from the Navy Coastal Ocean Model (NCOM-LCS). GoMDOM was calibrated to a large set of nutrient, phytoplankton, dissolved oxygen, sediment nutrient flux, sediment oxygen demand (SOD), primary production, and respiration data collected in 2006 and corroborated with field data collected in 2003. The primary objective was to use the model to estimate a nutrient load reduction of both nitrogen and phosphorus necessary to reduce the size of the hypoxic area to 5,000 km2, a goal established in the 2008 Gulf of Mexico Hypoxia Action Plan prepared by the Mississippi River/Gulf of Mexico Watershed Nutrient Task Force. Using the year 2006 as a test case, the model results suggest that the nitrogen and phosphorus load reduction from the Atchafalaya and Mississippi River basins would need to be reduced by 64% to achieve the target hypoxia area. The Louisiana continental shelf (LCS) in the northern part of the Gulf of Mexico has a history of subsurface hypoxia in the summer.

Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.

Assessing Forest Carbon Response to Climate Change and Disturbances Using Long-term Hydro-climatic Observations and Simulations

NASA Astrophysics Data System (ADS)

Trettin, C.; Dai, Z.; Amatya, D. M.

2014-12-01

Long-term climatic and hydrologic observations on the Santee Experimental Forest in the lower coastal plain of South Carolina were used to estimate long-term changes in hydrology and forest carbon dynamics for a pair of first-order watersheds. Over 70 years of climate data indicated that warming in this forest area in the last decades was faster than the global mean; 35+ years of hydrologic records showed that forest ecosystem succession three years following Hurricane Hugo caused a substantial change in the ratio of runoff to precipitation. The change in this relationship between the paired watersheds was attributed to altered evapotranspiration processes caused by greater abundance of pine in the treatment watershed and regeneration of the mixed hardwood-pine forest on the reference watershed. The long-term records and anomalous observations are highly valuable for reliable calibration and validation of hydrological and biogeochemical models capturing the effects of climate variability. We applied the hydrological model MIKESHE that showed that runoff and water table level are sensitive to global warming, and that the sustained warming trends can be expected to decrease stream discharge and lower the mean water table depth. The spatially-explicit biogeochemical model Forest-DNDC, validated using biomass measurements from the watersheds, was used to assess carbon dynamics in response to high resolution hydrologic observation data and simulation results. The simulations showed that the long-term spatiotemporal carbon dynamics, including biomass and fluxes of soil carbon dioxide and methane were highly regulated by disturbance regimes, climatic conditions and water table depth. The utility of linked-modeling framework demonstrated here to assess biogeochemical responses at the watershed scale suggests applications for assessing the consequences of climate change within an urbanizing forested landscape. The approach may also be applicable for validating large-scale models.

Regulation of pesticide degradation in the detritusphere

NASA Astrophysics Data System (ADS)

Pagel, Holger; Poll, Christian; Ingwersen, Joachim; Ditterich, Franziska; Gebala, Aurelia; Kandeler, Ellen; Streck, Thilo

2015-04-01

The detritusphere is a microbial hot spot of C turnover and degradation of pesticides in soils. We aimed at an improved understanding of the regulation mechanisms, which are responsible for stimulated degradation of the herbicide MCPA (2-Methyl-4-chlorophenoxyacetic acid) in response to increased C availability in the detritusphere. We combined a microcosm experiment with biogeochemical modeling and linked genetic information on abundances of total bacteria, fungi and specific pesticide degraders in soil to the coupled biogeochemical dynamics of C and MCPA. As a result of diffusive and convective C transport from litter into the adjacent soil we found increased dissolved organic C (DOC) in soil up to a 6 mm distance to litter (detritusphere). In the detritusphere, we observed increased microbial C and accelerated MCPA degradation. These dynamics were accurately reproduced by the model. Whereas the observed increase of bacteria and pesticide degrader populations in the detritusphere was simulated satisfactorily, the model could not reproduce the steep increase of fungi indicated by the fungal marker gene. Our simulations suggest that bacterial MCPA degraders mostly benefited from high-quality DOC, whereas fungal activity and growth were specifically stimulated by low-quality DOC. According to the simulations, MCPA was predominantly degraded via fungal co-metabolism. Our study demonstrates that biogeochemical processes in soil hotspots are regulated by the interaction of transport processes and microbial dynamics. It further reveals that mathematical modelling is as powerful tool to gain comprehensive insight into the microbial regulation of matter cycling in soil. Genetic information has a high potential to parameterize and evaluate complex mechanistic models, but model approaches must be improved based on extended information on gene dynamics at the cellular level.

Sedimentary particulate iron: the missing micronutrients ?

NASA Astrophysics Data System (ADS)

Beghoura, Houda; Gorgues, Thomas; Aumont, Olivier; Planquette, Hélène

2017-04-01

Iron is known to regulate the marine primary production and to impact the structure of ecosystems. Indeed, iron is the limiting nutrient for the phytoplankton growth over about 30% of the global ocean. However, the nature of the external sources of iron to the ocean and their quantification remain uncertain. Among these external sources, the sediment sources have been recently shown to be underestimated. Besides, since the operationally defined dissolved iron (which is the sum of truly dissolved and colloidal iron) was traditionally assumed to be the only form available to phytoplankton and bacteria, most studies have focused on the supply of dissolved iron to the ocean, the role of the particulate fraction of iron being largely ignored. This traditional view has been recently challenged, noticeably, by observational evidences. Indeed, in situ observations have shown that large amounts of particulate iron are being resuspended from continental margins to the open ocean thanks to fine grained particles' transport over long distances. A fraction of this particulate iron may dissolve and thereby fuel the phytoplankton growth. The magnitude of the sedimentary sources of particulate iron and the releasing processes affecting this iron phase are not yet well constrained or quantified. As a consequence, the role of sedimentary particulate iron in the biogeochemical cycles is still unclear despite its potentially major widespread importance. Here, we propose a modeling exercise to assess the first order impacts of this newly considered particulate sedimentary iron on global ocean biogeochemistry. We designed global experiments with a coupled dynamical-biogeochemical model (NEMO-PISCES). First, a control simulation that includes only a sediment source of iron in the dissolved phase has been run. Then, this control simulation is being compared with simulations, in which we include a sediment source of iron in both phases (dissolved as well as particulate). Those latter simulations have been performed using a range of particulate iron dissolution rates (from published studies and laboratory experiment results) that will permit to test the sensitivity of the biogeochemical response.

Global simulation of interactions between groundwater and terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Braakhekke, M. C.; Rebel, K.; Dekker, S. C.; Smith, B.; Van Beek, L. P.; Sutanudjaja, E.; van Kampenhout, L.; Wassen, M. J.

2016-12-01

In many places in the world ecosystems are influenced by the presence of a shallow groundwater table. In these regions upward water flux due to capillary rise increases soil moisture availability in the root zone, which has strong positive effect on evapotranspiration. Additionally it has important consequences for vegetation dynamics and fluxes of carbon and nitrogen. Under water limited conditions shallow groundwater stimulates vegetation productivity, and soil organic matter decomposition while under saturated conditions groundwater may have a negative effect on these processes due to lack of oxygen. Furthermore, since plant species differ with respect to their root distribution, preference for moisture conditions, and resistance to oxygen stress, shallow groundwater also influences vegetation type. Finally, processes such as denitrification and methane production occur under strictly anaerobic conditions and are thus strongly influenced by moisture availability. Most global hydrological models and several land surface models simulate groundwater table dynamics and their effects on land surface processes. However, these models typically have relatively simplistic representation of vegetation and do not consider changes in vegetation type and structure and are therefore less suitable to represent effects of groundwater on biogeochemical fluxes. Dynamic global vegetation models (DGVMs), describe land surface from an ecological perspective, combining detailed description of vegetation dynamics and structure and biogeochemical processes. These models are thus more appropriate to simulate the ecological and biogeochemical effects of groundwater interactions. However, currently virtually all DGVMs ignore these effects, assuming that water tables are too deep to affect soil moisture in the root zone. We have implemented a tight coupling between the dynamic global ecosystem model LPJ-GUESS and the global hydrological model PCR-GLOBWB. Using this coupled model we aim to study the influence of shallow groundwater on terrestrial ecosystem processes. We will present results of global simulations to demonstrate the effects on C, N, and water fluxes.

Spatially explicit simulation of peatland hydrology and carbon dioxide exchange: Influence of mesoscale topography

NASA Astrophysics Data System (ADS)

Sonnentag, O.; Chen, J. M.; Roulet, N. T.; Ju, W.; Govind, A.

2008-06-01

Carbon dynamics in peatlands are controlled, in large part, by their wetness as defined by water table depth and volumetric liquid soil moisture content. A common type of peatland is raised bogs that typically have a multiple-layer canopy of vascular plants over a Sphagnum moss ground cover. Their convex form restricts water supply to precipitation and water is shed toward the margins, usually by lateral subsurface flow. The hydraulic gradient for lateral subsurface flow is governed by the peat surface topography at the mesoscale (˜200 m to 5 km). To investigate the influence of mesoscale topography on wetness, evapotranspiration (ET), and gross primary productivity (GPP) in a bog during the snow-free period, we compare the outputs of a further developed version of the daily Boreal Ecosystem Productivity Simulator (BEPS) with observations made at the Mer Bleue peatland, located near Ottawa, Canada. Explicitly considering mesoscale topography, simulated total ET and GPP correlate well with measured ET (r = 0.91) and derived gross ecosystem productivity (GEP; r = 0.92). Both measured ET and derived GEP are simulated similarly well when mesoscale topography is neglected, but daily simulated values are systematically underestimated by about 10% and 12% on average, respectively, due to greater wetness resulting from the lack of lateral subsurface flow. Owing to the differences in moss surface conductances of water vapor and carbon dioxide with increasing moss water content, the differences in the spatial patterns of simulated total ET and GPP are controlled by the mesotopographic position of the moss ground cover.

Linking Water Pathways and Sources of Dissolved Organic Matter at the Hillslope Scale: A 24-Day Sprinkling Experiment

NASA Astrophysics Data System (ADS)

van Verseveld, W. J.; Graham, C. B.; Barnard, H. R.; McDonnell, J. J.; Lajtha, K.; Brooks, R. J.; Bond, B. J.

2006-12-01

The link between water flow paths, dissolved organic matter (DOM) sources and DOM production is poorly understood. The few investigations that have explored such relations in forest systems have relied passively on natural rainfall and drainage events. As a result, it has been difficult to identify the first order controls on water- biogeochemical processes. While we often assume an unlimited supply of DOM in our hydro-biogeochemical models, few studies have explicitly tested this. This work reports on a 24-day sprinkler experiment in Watershed-10 at the H.J. Andrews Experimental Forest in Oregon, USA. Our research objectives were: (1) To quantify the labile DOM pool in the upper soil layers at the hillslope scale, (2) To resolve the dominant flowpath at the hillslope scale that flush DOM from the soil profile to the stream channel, and (3) quantify the mixing between sprinkler water and hillslope subsurface flux. We injected 0,8 L of 100% deuterium into the sprinkler water for 24 hours and sampled soil and groundwater at daily to 2 days intervals throughout the 24 day experiment. We extracted 10 soil samples each week from the test hillslope and an adjacent similar reference plot and incubated them to quantify potential N mineralization and supply of organic carbon and nitrogen. Preliminary results suggested that DOM was transport-limited during the sprinkler experiment. Shallow lateral flow through the unsaturated zone; at 30 cm depth was very likely the dominant DOM pathway to the stream for the first two days (and 95 mm of sprinkled water) of the sprinkler experiment. After more than 4 days (and 395 mm of sprinkled water), saturation occurred at 100 cm, and deeper flowpaths became activated. These results challenge many of the assumptions in hydro-biogeochemical models where an unlimited supply of DOM is usually assumed.

Cations and microbial indicators: strong relationships in waters of urban/mixed land use watersheds of Southwest, VA

NASA Astrophysics Data System (ADS)

Steele, M.; Badgley, B.

2016-12-01

Background The salinity and composition of salts in freshwater streams, rivers, and waterbodies varies substantially, often impacted by human urban, agricultural, and mining land uses. While extreme fluctuations in salinity have been shown to influence both microbial communities and biogeochemical cycles, the differential effects of specific ion species at low salinity levels is poorly understood. The objective of this study was to examine the relationship between water chemistry and microbial water quality indicators. We collected weekly grab samples from nine sub-watersheds in Southwest Virginia. Samples were measured for standard physical and chemical properties: dissolved oxygen, temperature, specific conductance, pH, calcium, magnesium, potassium, chloride, fluoride, sulfate, nitrogen species, phosphorus, and dissolved organic carbon. In addition, three types of microbial fecal indicators were measured: total coliforms, E. coli, and HF183 (a human specific genomic marker). Results The relationships within and between water chemistry and water quality indicators are complex and frequently co-correlated. Concentrations of traditional biogeochemical elements (N, P, C) were less strongly related to water quality indicators than were Ca, Mg, Na in watersheds. Ca and Mg were strongly correlated with total coliforms, r2 = 0.88 and r2 = 0.86 respectively. While potassium is very strongly related to E. coli (r2 = 0.96). Currently, we cannot reasonably explain these relationships by the land use composition or common sources within the landscape. The human specific fecal indicator was not well correlated with other microbial water quality indicators, and yet found ubiquitously across the developed watersheds and most strongly correlated with sodium concentrations (r2 = 0.84). The results suggest that 1) wastewater via subsurface flowpaths may more broadly impact surface water chemistry and quality than expected, and 2) that cation chemistry may influence the microbial community and serve as a mediator of watershed biogeochemical cycling.

From mountains to the ocean: quantifying connectivity along the river corridor

NASA Astrophysics Data System (ADS)

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

2015-12-01

Rivers are the landscape's arteries; they convey water, solutes, energy, and living organisms from the hillslopes, floodplains, aquifers, and atmosphere to the oceans. As water moves along this complex circulatory system, it is continuously exchanged with the surrounding alluvial aquifer, termed hyporheic exchange, which strongly conditions and constrains the biogeochemical evolution of water at the local scale with basin-scale consequences. Over the last two decades, considerable efforts have focused on the use of detailed mathematical models to explore the hydrodynamics and biogeochemical effect of hyporheic exchange at the scale of individual channel morphologies. While these efforts are essential to gain mechanistic understanding, their computational demand makes them impractical for basin applications. In this talk, a parsimonious but physically based model of hyporheic flow for application in large river basins is presented: Networks with EXchange and Subsurface Storage (NEXSS). At the core of NEXSS are the up-scaling of detailed mathematical models and a characterization of the channel geometry, geomorphic features, and related hydraulic drivers based on scaling equations from the literature and readily accessible information such as river discharge, width, grain size, sinuosity, channel slope, and regional groundwater gradients. As a proof-of-concept, we use NEXSS to characterize the spatial and temporal variability of hyporheic exchange and denitrification potential along the Mississippi River basin. This modeling approach allows us to map the location of critical hot spots for biogeochemical transformation, their geomorphic drivers, and cumulative effect. Finally, we discuss new avenues to incorporate exchange with floodplains and ponded waters, which also play a key role in water quality along the river corridor. This new modeling approach is critical to transition from purely empirical continental models of water quality to hybrid approaches that incorporate fundamental physics and take advantage of available hydrogeomorphic data. In particular, hybrid models will be instrumental for predicting outcomes of river basin management practices under present and future socio-economic and climatic conditions.