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1

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

NASA Astrophysics Data System (ADS)

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.

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

2008-07-01

2

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

SciTech Connect

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

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

2008-02-25

3

A Coupled Surface/Subsurface Model for Hydrological Drought Investigations  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

4

Saturated area dynamics and streamflow generation from coupled surface-subsurface simulations and field observations  

NASA Astrophysics Data System (ADS)

A distributed physically-based model describing coupled surface-subsurface flows is applied to an instrumented catchment to investigate the links between runoff generation processes and the dynamics of saturated areas. The spatial characterization of the system is obtained through geophysical measurements and in situ observations. The model is able to reproduce the dynamics of the system through the calibration of only few parameters with a clear physical interpretation, providing a solid basis for our numerical investigations. Such investigations demonstrate the important control exerted by surface topography on the time evolution of saturated area patterns, mainly mediated by topographic curvature, that dictates both the dominant streamflow generation process at the local scale and the connection-disconnection dynamics of saturated areas. The relation between hillslope water storage and streamflow, Q = f(V), is shown to be highly hysteretical and dependent on the mean saturation of the catchment: higher degrees of saturation tend to yield one-to-one relationships between streamflow and water storage. On the contrary, streamflow-water storage relations are importantly affected by the specific configuration of saturated areas connected to the outlet when the system is far from complete saturation. This observation contradicts common assumptions of a one-to-one relationship Q = f(V) often used to justify widely observed power-law Q vs. dQ/dt recession curves. Furthermore, even when Q = f(V) becomes unique at high degrees of saturation, no power-law form emerged in our runs, speculatively because of the small size of the catchment formed by a single incision and the corresponding hillslope.

Weill, S.; Altissimo, M.; Cassiani, G.; Deiana, R.; Marani, M.; Putti, M.

2013-09-01

5

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

PubMed

Coastal aquifers are complex hydrologic systems because many physical processes interact: (i) variably saturated flow, (ii) spatial-temporal fluid density variations, (iii) tidal fluctuations, (iv) storm surges overtopping dykes, and (v) surface runoff of storm water. The HydroGeoSphere model is used to numerically simulate coastal flow dynamics, assuming a fully coupled surface-subsurface approach, accounting for all processes listed above. The diffusive wave approximation of the St. Venant equation is used to describe surface flow. Surface flow and salt transport are fully coupled with subsurficial variably saturated, variable-density flow and salt transport through mathematical terms that represent exchange of fluid mass and solute mass, respectively. Tides and storm surges induce a time-variant head that is applied to nodes of the surface domain. The approach is applied to real cases of tide and storm surge events. Tide simulation results confirm the existence of a recirculating zone, forming beneath the upper part of the intertidal zone. By monitoring the exchange fluid flux rates through the beach, it was found that the major inflow to the aquifer takes place at the upper part of the intertidal zone, which explains the formation of the recirculating zone. The recirculating zone is forming particularly during rising tide. Results from a storm surge simulation show that plume fingers develop below the flooded land surface. Natural remediation by seaward flowing freshwater is relatively slow, such that reducing the salt concentration in the aquifer down to drinking water standards takes up to 10 years. PMID:23603354

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

2013-06-01

6

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

NASA Astrophysics Data System (ADS)

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

Yang, Jie; Graf, Thomas

2013-04-01

7

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

8

Characterization of Coupled Hydrologic-Biogeochemical Processes Using Geophysical Data  

SciTech Connect

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

Hubbard, Susan

2005-06-01

9

Coupling a terrestrial biogeochemical model to the common land model  

SciTech Connect

A terrestrial biogeochemical model (CASACNP) was coupled to a land surface model (the Common Land Model, CoLM) to simulate the dynamics of carbon substrate in soil and its limitation on soil respiration. The combined model, CoLM-CASACNP, was able to predict long-term carbon sources and sinks that CoLM alone could not. The coupled model was tested using measurements of belowground respiration and surface fluxes from two forest ecosystems. The combined model simulated reasonably well the diurnal and seasonal variations of net ecosystem carbon exchange, as well as seasonal variation in the soil respiration rate of both the forest sites chosen for this study. However, the agreement between model simulations and actual measurements was poorer under dry conditions. The model should be tested against more measurements before being applied globally to investigate the feedbacks between the carbon cycle and climate change.

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

2011-01-01

10

Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Co-Metabolism  

SciTech Connect

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

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

2006-04-05

11

Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloroethylene Co-Metabolism  

SciTech Connect

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

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

2006-06-01

12

Simulation of land-atmosphere gaseous exchange using a coupled land surface-biogeochemical model  

NASA Astrophysics Data System (ADS)

It is important to develop and evaluate biogeochemical models that on the one hand represent vegetation and soil dynamics and on the other hand provide energy and water fluxes in a temporal resolution suitable for biogeochemical processes. In this study, we present a consistent coupling between a common land surface model (CLM3.0) and a recently developed biogeochemical model (TOUGHREACT-N). The model TOUGHREACT-N (TR-N) is one of the few process-based models that simulate green house gases fluxes by using an implicit scheme to solve the diffusion equations governing soil heat and water fluxes. By coupling with CLM3.0, we have significantly improved TR-N by including realistic representations of surface water, energy, and momentum exchanges, through the use of improved formulations for soil evaporation, plant transpiration, vegetation growth, and plant nitrogen uptake embedded in CLM3.0. The coupled CLMTR-N model is a first step for a full coupling of land surface and biogeochemical processes. The model is evaluated with measurements of soil temperature, soil water content, and N2O and N2 gaseous emission data from fallow, corn, and forest sites in Venezuela. The results demonstrate that the CLMTR-N model simulates realistic diurnal variation of soil temperature, soil water content, and N gaseous fluxes. For example, mean differences between predicted and observed midday near-surface soil water content were 8, 11, and 4 % in July, August, and September. The sensitivity of the biogeochemical processes and resulting N emissions to variation in environmental drivers is high, which indicates the need to calculate biogeochemical processes in, at least, two hourly time steps using dynamically updated (rather than daily averaged) soil environmental conditions. The development in CLMTR-N of such a complex representation of processes will allow us to characterize relevant processes and simplifications appropriate for regional to global-scale coupled biogeochemical and climate models.

Gu, C.; Riley, W. J.; Perez, T. J.; Pan, L.

2009-12-01

13

HBGC123D: a high-performance computer model of coupled hydrogeological and biogeochemical processes  

Microsoft Academic Search

Groundwater flow and transport models have been used to assist management of subsurface water resources and water quality. The needs of more efficient use of technical and financial resources have recently motivated the development of more effective remediation techniques and complex models of coupled hydrogeological and biogeochemical processes. We present a high-performance computer model of the coupled processes, HBGC123D. The

Jin P. Gwo; Eduardo F D’Azevedo; Hartmut Frenzel; Melanie Mayes; Gour-Tsyh Yeh; Philip M. Jardine; Karen M. Salvagee; Forrest M. Hoffman

2001-01-01

14

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

Microsoft Academic Search

Weathering of As-bearing rocks in the Himalayas has resulted in the transport of sediments down major river systems such as the Brahmaputra, Ganges, Red, Irrawaddy, and Mekong. Groundwater in these river basins commonly has As concentrations exceeding the World Health Organization's recommended drinking water limit (10 mug L-1) by more than an order of magnitude. Coupling of hydrology and biogeochemical

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

2008-01-01

15

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

16

Biogeochemical cycle in the Arctic with a global coupled sea ice-ocean-ecosystem model  

NASA Astrophysics Data System (ADS)

In the Arctic Ocean, both phytoplankton and sea ice algae are important contributors to the primary production and modulators of biogeochemical cycle. A global coupled ice-ocean-ecosystem model was established to investigate ice-ocean biogeochemical cycle and the ice-ocean ecosystem modules are fully coupled in the physical model POP-CICE (Parallel Ocean Program- Los Alamos Sea Ice Model). The model results are compared with various observations and the focus here are on the perspectives of the ice and ocean primary production and nutrients cycling in the Arctic Regions. The modeled sea ice algal carbon production shows reasonable seasonal successions of blooms from the subarctic toward the central Arctic and is in the comparable ranges of observations in the Chukchi Sea and the total amount in the pan-Arctic Regions. The phytoplankton blooms in the ocean starts with ice-edge blooms in the marginal ice zone, especially on shelf regions where nutrients concentrations are high. The ocean primary production is one order higher than the ice algal production in the subarctic seas and the shelf regions of the Arctic, while both are low in the central arctic due to nutrient limitation. The model reproduced the spatial distribution of the annual carbon production levels in the upper 100m of the Arctic Ocean. The DMS and DMSP concentrations are calculated in both sea ice and ocean, and preliminary results of the seasonal cycle of DMS, DMSP concentrations and fluxes at the air-sea interface are shown.

Jin, Meibing; Deal, Clara; Elliott, Scott; Hunke, Elizabeth; Maltrud, Mathew

2010-05-01

17

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

NASA Astrophysics Data System (ADS)

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

Wu, Y.; Blodau, C.

2013-03-01

18

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

NASA Astrophysics Data System (ADS)

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

Wu, Y.; Blodau, C.

2013-08-01

19

Hydro-biogeochemical coupling beneath a large polythermal Arctic glacier: Implications for subice sheet biogeochemistry  

NASA Astrophysics Data System (ADS)

We analyze the interannual chemical and isotopic composition of runoff from a large, high Arctic valley glacier over a 5 year period, during which drainage evolved from a long-residence-time drainage system feeding an artesian subglacial upwelling (SGU) at the glacier terminus to a shorter-residence-time drainage system feeding an ice-marginal channel (IMC). Increased icemelt inputs to the SGU are thought to have triggered this evolution. This sequence of events provides a unique opportunity to identify coupling between subglacial hydrology and biogeochemical processes within drainage systems of differing residence time. The biogeochemistry of the SGU is consistent with prolonged contact between meltwaters and subglacial sediments, in which silicate dissolution is enhanced, anoxic processes (e.g., sulphate reduction) prevail, and microbially generated CO2 and sulphide oxidation drive mineral dissolution. Solute in the IMC was mainly derived from moraine pore waters which are added to the channel via extraglacial streams. These pore waters acquire solute predominantly via sulphide oxidation coupled to carbonate/silicate dissolution. We present the first evidence that microbially mediated processes may contribute a substantial proportion (80% in this case) of the total glacial solute flux, which includes coupling between microbial CO2-generation and silicate/carbonate dissolution. The latter suggests the presence of biofilms in subglacial/ice-marginal sediments, where local perturbation of the geochemical environment by release of protons, organic acids, and ligands stimulates mineral dissolution. These data enable inferences to be made regarding biogeochemical processes in longer-residence-time glacial systems, with implications for the future exploration of Antarctic subglacial lakes and other wet-based ice sheet environments.

Wadham, J. L.; Tranter, M.; Hodson, A. J.; Hodgkins, R.; Bottrell, S.; Cooper, R.; Raiswell, R.

2010-11-01

20

Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models  

SciTech Connect

This final report summarizes research undertaken collaboratively between Princeton University, the NOAA Geophysical Fluid Dynamics Laboratory on the Princeton University campus, the State University of New York at Stony Brook, and the University of California, Los Angeles between September 1, 2000, and November 30, 2006, to do fundamental research on ocean iron fertilization as a means to enhance the net oceanic uptake of CO2 from the atmosphere. The approach we proposed was to develop and apply a suite of coupled physical-ecological-biogeochemical models in order to (i) determine to what extent enhanced carbon fixation from iron fertilization will lead to an increase in the oceanic uptake of atmospheric CO2 and how long this carbon will remain sequestered (efficiency), and (ii) examine the changes in ocean ecology and natural biogeochemical cycles resulting from iron fertilization (consequences). The award was funded in two separate three-year installments: • September 1, 2000 to November 30, 2003, for a project entitled “Ocean carbon sequestration by fertilization: An integrated biogeochemical assessment.” A final report was submitted for this at the end of 2003 and is included here as Appendix 1. • December 1, 2003 to November 30, 2006, for a follow-on project under the same grant number entitled “Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models.” This report focuses primarily on the progress we made during the second period of funding subsequent to the work reported on in Appendix 1. When we began this project, we were thinking almost exclusively in terms of long-term fertilization over large regions of the ocean such as the Southern Ocean, with much of our focus being on how ocean circulation and biogeochemical cycling would interact to control the response to a given fertilization scenario. Our research on these types of scenarios, which was carried out largely during the first three years of our project, led to several major new insights on the interaction between ocean biogeochemistry and circulation. This work, which is described in the following Section II on “Large scale fertilization,” has continued to appear in the literature over the past few years, including two high visibility papers in Nature. Early on in the first three years of our project, it became clear that small "patch-scale" fertilizations over limited regions of order 100 km diameter were much more likely than large scale fertilization, and we carried out a series of idealized patch fertilization simulations reported on in Gnanadesikan et al. (2003). Based on this paper and other results we had obtained by the end of our first three-year grant, we identified a number of important issues that needed to be addressed in the second three-year period of this grant. Section III on “patch fertilization” discusses the major findings of this phase of our research, which is described in two major manuscripts that will be submitted for publication in the near future. This research makes use of new more realistic ocean ecosystem and iron cycling models than our first paper on this topic. We have several major new insights into what controls the efficiency of iron fertilization in the ocean. Section IV on “model development” summarizes a set of papers describing the progress that we made on improving the ecosystem models we use for our iron fertilization simulations.

Jorge L. Sarmiento - Princeton PI, Anand Gnanadesikan - Princeton Co-I, Nicolas Gruber - UCLA PI, Xin Jin - UCLA PostDoc, Robert Armstrong - SUNY /Stony Brook Consultant

2007-06-21

21

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

SciTech Connect

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

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

2006-06-01

22

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

PubMed

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

Lu, Chaoqun; Tian, Hanqin

2013-02-01

23

Coupled modeling of transport and biogeochemical processes in aquifers - Model requirements, strength and limitations  

NASA Astrophysics Data System (ADS)

Microbially mediated geochemical changes in aquifers may trigger a series of secondary reactions that include aqueous and surface complexation, ion exchange, and mineral dissolution-precipitation. Due to the coupled nature and the multitude of processes involved it is often difficult to identify the reactions controlling the system's overall evolution. Numerical models can be a useful component for identifying gaps and inconsistencies in conceptual models and for performing a more quantitative investigation of these systems. Suitable computer codes must allow for a general description of transport and reaction processes to facilitate the investigation of site-specific conditions. In recent years significant advances have been made in terms of model generality and applicability. Major advances include the consideration of mass balance equations for reactants and reaction products, the integration of biodegradation and thermodynamic models, and the development of novel approaches for simulating biogeochemical processes and reactive transport under variably saturated conditions. MIN3P is one of the codes capable of simulating coupled biogeochemical and hydrological processes on an increasingly mechanistic level. The simulation of column experiments and a hypothetical case study at the field scale illustrate how reactive transport modeling can be used. Modeling column experiments can be particularly fruitful, because detailed data can be collected to support the mechanistic approach. However, analysis of conceptual models is also beneficial on the field scale. The case study considered here describes natural attenuation of a petroleum hydrocarbon spill in an unconfined aquifer by multiple electron acceptors. The simulations also consider geochemical reactions triggered by contaminant degradation including the re-oxidation of reaction products during transport away from the source area. Comparing the results to contaminant plumes described in the literature suggests that geochemical trends can be described well for most reactants and reaction products. However, this would not have been possible without considering re-oxidation reactions. Remaining discrepancies with observed plumes suggest that mixing occurs between mobile plume water and stagnant background water along the flow path away from the source area. Simulations that make use of a dual porosity formulation provide a more realistic evolution of the concentrations of components such as O2, Fe(II) and CH4. The example is also useful in highlighting some of the model limitations, which include extensive data requirements to provide model constraints and non-unique results for components involved in several reactions.

Mayer, K.

2003-12-01

24

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

25

Finite volume integrated surface-subsurface flow modeling on nonorthogonal grids  

NASA Astrophysics Data System (ADS)

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

An, Hyunuk; Yu, Soonyoung

2014-03-01

26

Towards coupled physical-biogeochemical models of the ocean carbon cycle  

NASA Technical Reports Server (NTRS)

The purpose of this review is to discuss the critical gaps in our knowledge of ocean dynamics and biogeochemical cycles. It is assumed that the ultimate goal is the design of a model of the earth system that can predict the response to changes in the external forces driving climate.

Rintoul, Stephen R.

1992-01-01

27

Study of the Tagus estuarine plume using coupled hydro and biogeochemical models  

NASA Astrophysics Data System (ADS)

Plumes of buoyant water produced by inflow from rivers and estuaries are common on the continental shelf. Buoyancy associated with estuarine waters is a key mediating factor in the transport and transformation of dissolved and particulate materials in coastal margins. The offshore displacement of the plume is influenced greatly by the local alongshore wind, which will tend to advect the plume either offshore or onshore, consistently with the Ekman transport. Other factor affecting the propagation of an estuarine plume is the freshwater inflow on the landward boundary. In this paper, a coupled three-dimensional ocean circulation and biogeochemical model with realistic high and low frequency forcing is used to get insight on how the Tagus River plume responds to wind and freshwater discharge during winter and spring. A nesting approach based on the MOHID numerical system was implemented for the Tagus estuary near shelf. Realistic hindcast simulations were performed, covering a period from January to June 2007. Model results were evaluated using in-situ and satellite imagery data. The numerical model was implemented using a three level nesting model. The model domain includes the whole Portuguese coast, the Tagus estuary near shelf and the Tagus River estuary, using a realistic coastline and bottom topography. River discharge and wind forcing are considered as landward and surface boundary conditions, respectively. Initial ocean stratification is from the MERCATOR solution. Ambient shelf conditions include tidal motion. As a prior validation, models outputs of salinity and water temperature were compared to available data (January 30th and May 30th, 2007) and were found minor differences between model outputs and data. On January 30th, outside the estuary, the model results reveal a stratified water column, presenting salinity stratification of the order of 3-4. The model also reproduces the hydrography for the May 30th observations. In May, near the Tagus mouth, measurements show low salinity stratification (when compared to the January observations). During this month, stratification is mainly due to water temperature. In general, the correlation between water temperature from the model and satellite data, reveals values higher than 0.5 (significant values) for the whole simulation period, presenting high correlations (about 0.8) in January and February, when the plume propagation is mainly controlled by the estuarine discharge. The correlation between the model results of suspended sediments and the satellite data (suspended matter) presents significant values (higher than 0.5) for almost the whole simulation period. On the shelf, near the Tagus mouth, the export of estuarine waters forms a plume which is highly influenced by the geography of the coastline, inducing a plume trajectory very close to shore. Northern winds events cause a displacement of the coastally trapped plume, driving a new offshore plume. The relaxation of the northern wind regime pushes back the coastal jet toward the coast, propagating estuarine water to the north along the coastline. The model was also able to reproduce the effect of the estuary plume over the coastal surface chlorophyll patterns observed remotely and the in situ chlorophyll and nutrient profiles, especially in the periods of low wind intensity. In periods of persistent Northerly winds the effect of the Sintra Mountains Ridge over the wind field tend to be underestimated. This leads to a southerly transport by the model slightly more intense than the one observed remotely.

Vaz, Nuno; Leitão, Paulo C.; Juliano, Manuela; Mateus, Marcos; Dias, João. Miguel; Neves, Ramiro

2010-05-01

28

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

29

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

30

Ocean chlorophyll response to two types of El Niño events in an ocean-biogeochemical coupled model  

NASA Astrophysics Data System (ADS)

Based on a long-term simulation of an ocean-biogeochemical coupled model, we investigate the biogeochemical response to the two types of El Niño events, a Cold Tongue (CT)-El Niño and a Warm Pool (WP)-El Niño, in which a local maximum of anomalous sea surface temperature (SST) is located in the eastern and central tropical Pacific. Our model is able to reasonably simulate the characteristics of the biological variables in a way comparable to the observations. During the developing period, anomalous low chlorophyll appears in the eastern Pacific, while it appears in the central Pacific in the WP-El Niño. The difference in the spatial-temporal response of chlorophyll for the two types of El Niño events is mainly due to the eastward zonal advection of upper ocean currents, which plays a role in bringing nutrient-poor water from the western Pacific. During the decaying period of the WP-El Niño, anomalous high chlorophyll appears concurrently with anomalous low SST in the eastern Pacific. Conversely, anomalous high chlorophyll appears in the central Pacific prior to the decaying period of the CT-El Niño. In particular, the anomalous low sea level from the northwestern Pacific shifts to the southern equatorial region during the decaying period of the CT-El Niño. This drives anticyclonic boundary currents which enhance the Equatorial Undercurrent, playing a role in the supply of nutrients to the central equatorial Pacific, resulting in an increase in chlorophyll concentration in the same region.

Lee, Kie-Woung; Yeh, Sang-Wook; Kug, Jong-Seong; Park, Jong-Yeon

2014-02-01

31

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

NASA Technical Reports Server (NTRS)

A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model are determined from the influences of circulation and turbulence dynamics, irradiance availability. and the interactions among three functional phytoplankton groups (diatoms. chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (greater than 1000 km) model chlorophyll results are in overall agreement with CZCS pigments in many global regions. Seasonal variability observed in the CZCS is also represented in the model. Synoptic scale (100-1000 km) comparisons of imagery are generally in conformance although occasional departures are apparent. Model nitrate distributions agree with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicates that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on synoptic scales. This is especially true given that initial conditions are homogenous chlorophyll fields. The success of the model in producing a reasonable representation of chlorophyll and nutrient distributions and seasonal variability in the global oceans is attributed to the application of a generalized, processes-driven approach as opposed to regional parameterization and the existence of multiple phytoplankton groups with different physiological and physical properties. These factors enable the model to simultaneously represent many aspects of the great diversity of physical, biological, chemical, and radiative environments encountered in the global oceans.

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

2000-01-01

32

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

SciTech Connect

A scheme is described for the computation of terrestrial biogeochemical trace gas fluxes in the context of a general circulation model. This hierarchical system flux scheme (HSFS) incorporates five major components: (1) a general circulation model (GCM), which provides a medium-resolution (i.e., 1{degrees} by 1{degrees}) simulation of the atmospheric circulation; (2) a procedure for identifying regions of defined homogeneity of surface type within GCM grid cells; (3) a set of surface process models, to be run within each homogeneous region, which include a biophysical model, the Biosphere Atmospheric Transfer Scheme (BATS), and a biogeochemical model (BGCM); (4) an interpolation/integration system that transfers information between the GCM and surface process models with finer resolution; and (5) an interactive data array based on a geographic information system (GIS), which provides land characteristic information via the interpolator. The goals of this detailed investigation are to compute the local and global sensitivities of trace gas fluxes to GCM and BATS variables, the effects of trace gas fluxes on global climate, and the effects of global climate on specific biomes.

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

1994-04-01

33

Methods to evaluate CaCO3 cycle modules in coupled global biogeochemical ocean models  

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

34

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

35

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

NASA Astrophysics Data System (ADS)

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

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

2007-12-01

36

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

NASA Technical Reports Server (NTRS)

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

Gregg, Watson W.

1999-01-01

37

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

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

38

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

USGS Publications Warehouse

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

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

2014-01-01

39

Optimal Underground Extraction of Coal at Shallow Cover Beneath Surface\\/Subsurface Objects: Indian Practices  

Microsoft Academic Search

Summary  Considering ground instability problems of underground coal mines at shallow covers, this paper reviews and describes problems\\u000a of optimal extraction of coal stuck below surface\\/subsurface constraints at Indian coal fields. Importance of thickness and\\u000a quality of inter-burden between the working horizon and surface\\/subsurface constraints is discussed from a ground movement\\u000a point of view during optimisation of coal recovery by underground

Rajendra Singh; P. K. Mandal; A. K. Singh; R. Kumar; A. Sinha

2008-01-01

40

Aggregate-scale spatial heterogeneity in reductive transformation of ferrihydrite resulting from coupled biogeochemical and physical processes  

NASA Astrophysics Data System (ADS)

Iron (hydr)oxides are ubiquitous in soils and sediments and play a dominant role in the geochemistry of surface and subsurface environments. Their fate depends on local environmental conditions, which in structured soils may vary significantly over short distances due to mass-transfer limitations on solute delivery and metabolite removal. In the present study, artificial soil aggregates were used to investigate the coupling of physical and biogeochemical processes affecting the spatial distribution of iron (Fe) phases resulting from reductive transformation of ferrihydrite. Spherical aggregates made of ferrihydrite-coated sand were inoculated with the dissimilatory Fe-reducing bacterium Shewanella putrefaciens strain CN-32, and placed into a flow reactor, the reaction cell simulates a diffusion-dominated soil aggregate surrounded by an advective flow domain. The spatial and temporal evolution of secondary mineralization products resulting from dissimilatory Fe reduction of ferrihydrite were followed within the aggregates in response to a range of flow rates and lactate concentrations. Strong radial variations in the distribution of secondary phases were observed owing to diffusively controlled delivery of lactate and efflux of Fe(II) and bicarbonate. In the aggregate cortex, only limited formation of secondary Fe phases were observed over 30 d of reaction, despite high rates of ferrihydrite reduction. Under all flow conditions tested, ferrihydrite transformation was limited in the cortex (70-85 mol.% Fe remained as ferrihydrite) because metabolites such as Fe(II) and bicarbonate were efficiently removed in outflow solutes. In contrast, within the inner fractions of the aggregate, limited mass-transfer results in metabolite (Fe(II) and bicarbonate) build-up and the consummate transformation of ferrihydrite - only 15-40 mol.% Fe remained as ferrihydrite after 30 d of reaction. Goethite/lepidocrocite, and minor amounts of magnetite, formed in the aggregate mid-section and interior at low lactate concentration (0.3 mM) after 30 d of reaction. Under high lactate (3 mM) concentration, magnetite was observed only as a transitory phase, and rather goethite/lepidocrocite and siderite were the dominant secondary mineralization products. Our results illustrate the importance of slow diffusive transport of both electron donor and metabolites concentrations and concomitant biogeochemical reactions within soils and sediments, giving rise to heterogeneous products over small spatial (?m) scale.

Pallud, C.; Masue-Slowey, Y.; Fendorf, S.

2010-05-01

41

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

Microsoft Academic Search

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

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

2007-01-01

42

Spatial and temporal dynamics of biogeochemical processes in the Fraser River, Canada : a coupled organic-inorganic perspective  

E-print Network

The great geologic and climatic diversity of the Fraser River basin in southwestern Canada render it an excellent location for understanding biogeochemical cycling of sediments and terrigenous organic carbon in a relatively ...

Voss, Britta Marie

2014-01-01

43

A skill assessment of the biogeochemical model REcoM2 coupled to the finite element sea-ice ocean model (FESOM 1.3)  

NASA Astrophysics Data System (ADS)

In coupled ocean-biogeochemical models, the choice of numerical schemes in the ocean circulation component can have a large influence on the distribution of the biological tracers. Biogeochemical models are traditionally coupled to ocean general circulation models (OGCMs), which are based on dynamical cores employing quasi regular meshes, and therefore utilize limited spatial resolution in a global setting. An alternative approach is to use an unstructured-mesh ocean model, which allows variable mesh resolution. Here, we present initial results of a coupling between the Finite Element Sea-ice Ocean Model (FESOM) and the biogeochemical model REcoM2, with special focus on the Southern Ocean. Surface fields of nutrients, chlorophyll a and net primary production were compared to available data sets with focus on spatial distribution and seasonal cycle. The model produced realistic spatial distributions, especially regarding net primary production and chlorophyll a, whereas the iron concentration became too low in the Pacific Ocean. The modelled net primary production was 32.5 Pg C yr-1 and the export production 6.1 Pg C yr-1. This is lower than satellite-based estimates, mainly due to the excessive iron limitation in the Pacific along with too little coastal production. Overall, the model performed better in the Southern Ocean than on the global scale, though the assessment here is hindered by the lower availability of observations. The modelled net primary production was 3.1 Pg C yr-1 in the Southern Ocean and the export production 1.1 Pg C yr-1. All in all, the combination of a circulation model on an unstructured grid with an ocean biogeochemical model shows similar performance to other models at non-eddy-permitting resolution. It is well suited for studies of the Southern Ocean, but on the global scale deficiencies in the Pacific Ocean would have to be taken into account.

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

2014-07-01

44

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

45

Variability in surface-subsurface hydrologic interactions and implications for nutrient retention in an arid-land stream  

NASA Astrophysics Data System (ADS)

Hydrologic interactions among biogeochemically active stream subsystems affect material export downstream. We combined a conservative tracer addition with measurements of water table elevation and nutrient concentrations of surface and subsurface water to examine hydrologic interactions among surface and subsurface subsystems and their implications for stream biogeochemistry. We injected bromide (Br-) into a 400-m reach of Sycamore Creek, a losing stream in central Arizona, for 15 d and monitored changes in concentration in three subsystems: surface, parafluvial, and riparian zones. Additionally, we collected water samples from these subsystems for nutrient analyses. Water flowed from surface to subsurface zones as expected in this losing stream, but a significant amount of subsurface water (17% of surface discharge in the reach) returned to the surface. Within the parafluvial subsystem, median transport time (Tmed) in two gravel bars differed substantially (from 2 to 30 h and from 6 to >300 h, respectively, for upper and lower bars), and varied significantly with depth in the lower bar (mean (±SE) Tmed = 190 ± 20 h at 30 cm compared to 101 ± 18 h at 110 cm). Flow paths from the surface to parafluvial and riparian zones, and subsequently back to the surface stream, differ from patterns in mesic areas, where water moves laterally and vertically towards the surface stream. Estimates of nutrient retention for the stream reach varied four fold in response to simulated changes in lateral subsurface connections and the configuration of subsystems. Thus at this scale, accurate nutrient budgets require an understanding of surface-subsurface connections and hydrologic parameters.

Dent, C. Lisa; Grimm, Nancy B.; Martí, EugèNia; Edmonds, Jennifer W.; Henry, Julia Curro; Welter, Jill R.

2007-12-01

46

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

SciTech Connect

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

Crawford, Ronald L; Paszczynski, Andrzej J

2010-02-19

47

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

NASA Astrophysics Data System (ADS)

In coupled biogeochmical-ocean models, the choice of numerical schemes in the ocean circulation component can have a large influence on the distribution of the biological tracers. Biogeochemical models are traditionally coupled to ocean general circulation models (OGCMs), which are based on dynamical cores employing quasi-regular meshes, and therefore utilize limited spatial resolution in a global setting. An alternative approach is to use an unstructured-mesh ocean model, which allows variable mesh resolution. Here, we present initial results of a coupling between the Finite Element Sea Ice-Ocean Model (FESOM) and the biogeochemical model REcoM2 (Regulated Ecosystem Model 2), with special focus on the Southern Ocean. Surface fields of nutrients, chlorophyll a and net primary production (NPP) were compared to available data sets with a focus on spatial distribution and seasonal cycle. The model produces realistic spatial distributions, especially regarding NPP and chlorophyll a, whereas the iron concentration becomes too low in the Pacific Ocean. The modelled NPP is 32.5 Pg C yr-1 and the export production 6.1 Pg C yr-1, which is lower than satellite-based estimates, mainly due to excessive iron limitation in the Pacific along with too little coastal production. The model performs well in the Southern Ocean, though the assessment here is hindered by the lower availability of observations. The modelled NPP is 3.1 Pg C yr-1 in the Southern Ocean and the export production 1.1 Pg C yr-1. All in all, the combination of a circulation model on an unstructured grid with a biogeochemical-ocean model shows similar performance to other models at non-eddy-permitting resolution. It is well suited for studies of the Southern Ocean, but on the global scale deficiencies in the Pacific Ocean would have to be taken into account.

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

2014-11-01

48

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

49

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

USGS Publications Warehouse

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

Alexander, R.B.; Böhlke, J.K.; Boyer, E.W.; David, M.B.; Harvey, J.W.; Mulholland, P.J.; Seitzinger, S.P.; Tobias, C.R.; Tonitto, C.; Wollheim, W.M.

2009-01-01

50

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

NASA Technical Reports Server (NTRS)

A coupled ocean general circulation, biogeochemical, and radiative model was constructed to evaluate and understand the nature of seasonal variability of chlorophyll and nutrients in the global oceans. Biogeochemical processes in the model were determined from the influences of circulation and turbulence dynamics, irradiance availability, and the interactions among three functional phytoplankton groups (diatoms, chlorophytes, and picoplankton) and three nutrients (nitrate, ammonium, and silicate). Basin scale (>1000 km) model chlorophyll seasonal distributions were statistically positively correlated with CZCS chlorophyll in 10 of 12 major oceanographic regions, and with SeaWiFS in all 12. Notable disparities in magnitudes occurred, however, in the tropical Pacific, the spring/summer bloom in the Antarctic, autumn in the northern high latitudes, and during the southwest monsoon in the North Indian Ocean. Synoptic scale (100-1000 km) comparisons of satellite and in situ data exhibited broad agreement, although occasional departures were apparent. Model nitrate distributions agreed with in situ data, including seasonal dynamics, except for the equatorial Atlantic. The overall agreement of the model with satellite and in situ data sources indicated that the model dynamics offer a reasonably realistic simulation of phytoplankton and nutrient dynamics on basin and synoptic scales.

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

2000-01-01

51

Effects of forest management on biogeochemical functions in southern forested wetlands  

Microsoft Academic Search

Southern forested wetlands perform two important biogeochemical functions on the landscape: 1) nutrient (N and P), removal\\u000a from incident surface, subsurface, and ground waters, and 2) export of organic carbon and associated nutrients to aquatic\\u000a ecosystems downstream. In addition to P sediment deposition, which can range from 1.6 to 36.0 kg ha?1 yr?1 P, denitrification of NO3-N (0.5 to 350

Mark R. Walbridge; B. Graeme Lockaby

1994-01-01

52

Biogeochemical processes controlling methane in gassy coastal sediments—Part 1. A model coupling organic matter flux to gas production, oxidation and transport  

NASA Astrophysics Data System (ADS)

A new kinetic model has been developed for predicting biogeochemical processes occurring in gassy, anoxic sediments dominated by sulfate reduction (SR), methane production (MP), and methane oxidation (MO). The model is composed of mass conservation equations in which reaction rates are balanced by diffusive and advective transport. It directly couples bio-geochemical zones using error functions that serve as a toggle to simulate cessation of sulfate reduction, initiation of methane production and oxidation, and production of gaseous methane when in situ solubility is exceeded. Model-derived sulfate and methane concentration distributions combined with kinetic rate expressions are used to calculate rates of SR, MP and MO. Application of the model to gassy coastal and estuarine sediments reveals the extreme sensitivity of predicted methane distributions to the flux ( FG) and degradation rate constant ( kG) of reactive organic matter. Sulfate and methane concentrations from Eckernförde Bay in the Kiel Bight of the German Baltic Sea, and Cape Lookout Bight and the White Oak River Estuary of North Carolina, USA, can be predicted accurately from independently determined ( FG) values. Comparison of model-predicted results with a complete set of measured summertime concentration and rate data from the Cape Lookout site shows that introduction of 10-40% variations in individual rate parameters produce readily observable discrepancies in model results. In general, increases in the magnitude of FG and decreases in kG at the same total sediment accumulation rate increase the relative importance of methanogenesis in total organic matter remineralization as a result of more rapid depletion of dissolved pore water sulfate closer to the sediment-water interface. The predictive capabilities of the model should prove useful when concentration, rate, or flux measurements are not available.

Martens, Christopher S.; Albert, Daniel B.; Alperin, Marc J.

1998-12-01

53

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

54

Simulation of radar echoes from Mars' surface/subsurface and inversion of surface media parameters  

NASA Astrophysics Data System (ADS)

A two-layer model of Mars' regolith/bedrock media with a cratered rough surface/subsurface is presented for radar echo simulation of planetary exploration research. The numerical approach of geometric ray tracing for the scattering of rough surfaces, which is digitized by the triangulated network, is applied to the calculation of the scattering and imaging simulation of radar range echoes. Numerical simulations of a cratered rough surface generated by the Monte Carlo method are used to analyze the functional dependence of radar range echoes at 1-50 MHz center frequencies upon the surface/subsurface feature and the parameters of the layering media, that is, layer depth and dielectric properties. The radar range echoes from two areas of the real Mars surface, which is described by digital elevation model data with a resolution of 1 m × 1 m and a vertical error of less than 1 m, are also simulated and analyzed. Based on these simulations, this study presents a numerical imaging test of radar sounder at center frequencies 1-50 MHz for exploration of different dielectric regolith and bedrock media. The channel 50 MHz with high resolution might be an optimal frequency. Finally, inversion of the dielectric constants of the two-layer media and the regolith layer thickness are developed.

Liu, Chuan; Ye, Hongxia; Jin, Ya-Qiu

2014-07-01

55

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

NASA Technical Reports Server (NTRS)

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

Watson, Gregg W.

2000-01-01

56

Temporal coupling between surface and deep ocean biogeochemical processes in contrasting subtropical and subantarctic water masses, southwest Pacific Ocean  

Microsoft Academic Search

Surface to deep-ocean coupling was investigated in subtropical (STW) and subantarctic (SAW) waters off eastern New Zealand. Moorings, comprising a near-surface fluorometer, temperature loggers, current meters, and sediment trap at 1500 m depth, were deployed at 41° and 46°40?S along 178°30?E between October 2000 and October 2001. Locally validated, remotely sensed data provided areal estimates of surface chlorophyll that were

Scott D. Nodder; Philip W. Boyd; Stephen M. Chiswell; Matthew H. Pinkerton; Janet M. Bradford-Grieve; Malcolm J. N. Greig

2005-01-01

57

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

58

Temporal coupling between surface and deep ocean biogeochemical processes in contrasting subtropical and subantarctic water masses, southwest Pacific Ocean  

NASA Astrophysics Data System (ADS)

Surface to deep-ocean coupling was investigated in subtropical (STW) and subantarctic (SAW) waters off eastern New Zealand. Moorings, comprising a near-surface fluorometer, temperature loggers, current meters, and sediment trap at 1500 m depth, were deployed at 41° and 46°40'S along 178°30'E between October 2000 and October 2001. Locally validated, remotely sensed data provided areal estimates of surface chlorophyll that were representative of 1997-2004 annual cycles. In STW, early spring chlorophyll peaks were coupled with deposition of labile (molar C:N˜7-8), bio-siliceous organic matter. Low winter chlorophyll concentrations were associated with high particulate organic carbon (POC) fluxes of moderately refractory material (C:N˜9-10). This indicates that winter flux was affected by heterotrophic recycling processes (zooplankton exuviae, fecal pellets) and/or slowly sinking particles from the preceding autumn. Deep-ocean POC fluxes off New Zealand were similar to global estimates and Tasman Sea (0.8 cf. 1.0 g C m-2 yr-1). Elevated biogenic silica and lithogenic fluxes probably reflect processes within a warm-core eddy near an eroding landmass, rather than STW in general. In SAW, POC and biogenic silica flux peaks occurred in spring with moderate surface chlorophyll concentrations. Decoupling between high chlorophyll and low flux in summer may reflect near-surface organic matter recycling by the microbial-dominated ecosystem. In spring, moderate chlorophyll levels in SAW, high POC and silica flux, and high C:N ratios (9-13) indicate some coupling with upper water column processes. SAW, east of New Zealand, was characterized by low POC (0.2 g C m-2 yr-1), high biogenic silica, and low carbonate fluxes, unlike other subantarctic sites, which are dominated by carbonate deposition with fivefold higher POC flux.

Nodder, Scott D.; Boyd, Philip W.; Chiswell, Stephen M.; Pinkerton, Matthew H.; Bradford-Grieve, Janet M.; Greig, Malcolm J. N.

2005-12-01

59

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

60

Global Biogeochemical Cycles and the Physical Climate System  

NSDL National Science Digital Library

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

Fred Mackenzie

1999-01-01

61

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

62

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

SciTech Connect

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

Mulholland, Patrick J [ORNL; Alexander, Richard [U.S. Geological Survey; Bohlke, John [U.S. Geological Survey; Boyer, Elizabeth [Pennsylvania State University; Harvey, Judson [U.S. Geological Survey; Seitzinger, Sybil [Rutgers University; Tobias, Craig [University of North Carolina, Wilmington; Tonitto, Christina [Cornell University; Wollheim, Wilfred [University of New Hampshire

2009-01-01

63

A dynamic marine iron cycle module coupled to the University of Victoria Earth System Model: the Kiel Marine Biogeochemical Model 2 (KMBM2) for UVic 2.9  

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

64

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

PubMed

Past, present, and possible future changes in the Baltic Sea acid-base and oxygen balances were studied using different numerical experiments and a catchment-sea model system in several scenarios including business as usual, medium scenario, and the Baltic Sea Action Plan. New CO2 partial pressure data provided guidance for improving the marine biogeochemical model. Continuous CO2 and nutrient measurements with high temporal resolution helped disentangle the biogeochemical processes. These data and modeling indicate that traditional understandings of the nutrient availability-organic matter production relationship do not necessarily apply to the Baltic Sea. Modeling indicates that increased nutrient loads will not inhibit future Baltic Sea acidification; instead, increased mineralization and biological production will amplify the seasonal surface pH cycle. The direction and magnitude of future pH changes are mainly controlled by atmospheric CO2 concentration. Apart from decreasing pH, we project a decreasing calcium carbonate saturation state and increasing hypoxic area. PMID:24414804

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

2014-02-01

65

Soil Biogeochemical Cycles  

NSDL National Science Digital Library

This group activity charges students with teaching their colleagues about the biogeochemical cycle of one key soil element (e.g., either C, N, S, P, Ca, or Fe). Students are given a single class period to summarize their knowledge and to develop a lesson that includes (1) an organized, 5-8 minute oral presentation, (2) a graphical, conceptual model of their assigned element's soil-biogeochemical cycle, and (3) a list of discussion questions with which to engage their colleagues on the other teams. A second class session is used to refine and to expand upon the submitted models as necessary.

Colin Robins

66

Biogeochemical Processes in Microbial Ecosystems  

NASA Technical Reports Server (NTRS)

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial population, and their metabolic properties. Photosynthetic microbial mats offer an opportunity to define holistic functionality at the millimeter scale. At the same time, their Biogeochemistry contributes to environmental processes on a planetary scale. These mats are possibly direct descendents of the most ancient biological communities; communities in which oxygenic photosynthesis might have been invented. Mats provide one of the best natural systems to study how microbial populations associate to control dynamic biogeochemical gradients. These are self-sustaining, complete ecosystems in which light energy absorbed over a diel (24 hour) cycle drives the synthesis of spatially-organized, diverse biomass. Tightly-coupled microorganisms in the mat have specialized metabolisms that catalyze transformations of carbon, nitrogen. sulfur, and a host of other elements.

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

2001-01-01

67

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

SciTech Connect

This final report summarizes research undertaken collaboratively between Princeton University, the NOAA Geophysical Fluid Dynamics Laboratory on the Princeton University campus, the State University of New York at Stony Brook, and the University of California, Los Angeles between September 1, 2000, and November 30, 2006, to do fundamental research on ocean iron fertilization as a means to enhance the net oceanic uptake of CO2 from the atmosphere. The approach we proposed was to develop and apply a suite of coupled physical-ecologicalbiogeochemical models in order to (i) determine to what extent enhanced carbon fixation from iron fertilization will lead to an increase in the oceanic uptake of atmospheric CO2 and how long this carbon will remain sequestered (efficiency), and (ii) examine the changes in ocean ecology and natural biogeochemical cycles resulting from iron fertilization (consequences). The award was funded in two separate three-year installments: • September 1, 2000 to November 30, 2003, for a project entitled “Ocean carbon sequestration by fertilization: An integrated biogeochemical assessment.” A final report was submitted for this at the end of 2003 and is included here as Appendix 1. • December 1, 2003 to November 30, 2006, for a follow-on project under the same grant number entitled “Carbon sequestration by patch fertilization: A comprehensive assessment using coupled physical-ecological-biogeochemical models.” This report focuses primarily on the progress we made during the second period of funding subsequent to the work reported on in Appendix 1. When we began this project, we were thinking almost exclusively in terms of long-term fertilization over large regions of the ocean such as the Southern Ocean, with much of our focus being on how ocean circulation and biogeochemical cycling would interact to control the response to a given fertilization scenario. Our research on these types of scenarios, which was carried out largely during the first three years of our project, led to several major new insights on the interaction between ocean biogeochemistry and circulation. This work, which is described in 2 the following Section II on “Large scale fertilization,” has continued to appear in the literature over the past few years, including two high visibility papers in Nature. Early on in the first three years of our project, it became clear that small "patch-scale" fertilizations over limited regions of order 100 km diameter were much more likely than large scale fertilization, and we carried out a series of idealized patch fertilization simulations reported on in Gnanadesikan et al. (2003). Based on this paper and other results we had obtained by the end of our first three-year grant, we identified a number of important issues that needed to be addressed in the second three-year period of this grant. Section III on “patch fertilization” discusses the major findings of this phase of our research, which is described in two major manuscripts that will be submitted for publication in the near future. This research makes use of new more realistic ocean ecosystem and iron cycling models than our first paper on this topic. We have several major new insights into what controls the efficiency of iron fertilization in the ocean. Section IV on “model development” summarizes a set of papers describing the progress that we made on improving the ecosystem models we use for our iron fertilization simulations.

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

2007-06-21

68

Biogeochemical cycling and remote sensing  

NASA Technical Reports Server (NTRS)

The present investigation is concerned with the role of remote sensing in the analysis of biochemical cycling. A general review is provided of the interest of NASA in biochemical cycling, taking into account an assessment of the state and dynamics of the pools and fluxes of four major elements (carbon, nitrogen, phosphorus, sulfur), an understanding of the coupling and interaction of the biosphere and the atmosphere, and an understanding of the biosphere and the oceans. Attention is given to biogeochemical cycling science issues, the potential remote sensing role, the vegetation type, aspects of vegetation structure, the leaf area index, the canopy height, functional relationships, environmental and soil variables, questions of experimental design, sampling sites and ground data, and radiometric data and analysis.

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

1984-01-01

69

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

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

70

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

71

Cave Formation: Biogeochemical Cycles  

NSDL National Science Digital Library

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

72

The influence of the groundwater table dynamics on the land surface-subsurface interactions  

NASA Astrophysics Data System (ADS)

The terrestrial hydrological cycle comprises complex processes in the subsurface, land surface and atmosphere. These processes interact at different space-time scales, resulting in a non-linear system behavior with two-way feedback between different compartments. In order to understand the overall mechanisms of the hydrological cycle, it is important to study the space-time variance of different processes and their influence on the mass and energy balance components of the coupled water and energy cycles. In this study, the coupled subsurface-land surface model ParFlow.CLM is applied over a ~28,000 km2 model domain encompassing the Rur catchment, Germany, to simulate the fluxes and states of the coupled water and energy cycles. The model is forced by hourly atmospheric data from the COSMO-DE model (numerical weather prediction system of the German Weather Service) over the years 2009 and 2010. The space-time variability in different processes of the coupled water and energy cycles over the Rur catchment has been studied previously using the same modeling platform. The simulation results demonstrate that the land surface is exposed to a dual boundary forcing of the atmosphere and the free groundwater transforming the spatial and temporal structures of both forcings, which is reflected in distinct patterns in the moisture and energy fluxes. In this study, we perform multiple model runs considering different temporal variations in the lower boundary condition (e.g., monthly, seasonally, and yearly) conserving the average spatial heterogeneity to study explicitly the influence of temporal groundwater table dynamics on the land surface mass and energy balance components. Analyzing the model results across different time scales using statistical, geostatistical, and wavelet transform techniques demonstrate that the temporal variation in the lower boundary condition influences the land surface mass and energy balance components, especially under moisture limited conditions. The lower boundary condition is influenced by the processes in the atmosphere, as the variance in the atmospheric forcing affects the groundwater table dynamics after being filtered for smaller scale variability by the land surface and subsurface. The time series analysis suggests that the variability in the lower boundary condition and land surface processes (e.g., evaportanspiration) are generally in phase for a shallow groundwater table, while a phase shift is evident for deeper water tables, which has been discussed in a number of previous studies. Utilizing multi-year simulation results, we test the hypothesis that for increasing phase shifts and amplitudes in water table fluctuations, seasonal impacts of groundwater dynamics on the land surface energy fluxes can be predicted quantitatively at the yearly time scale.

Rahman, Mostaquimur; Kollet, Stefan; Sulis, Mauro

2014-05-01

73

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

74

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

SciTech Connect

Subsurface bacteria including sulfate reducing bacteria (SRB) reduce soluble U(VI) to insoluble U(IV) with subsequent precipitation of UO2. We have shown that SRB reduce U(VI) to nanometer-sized UO2 particles (1-5 nm) which are both intra- and extracellular, with UO2 inside the cell likely physically shielded from subsequent oxidation processes. We evaluated the UO2 nanoparticles produced by Desulfovibrio desulfuricans G20 under growth and non-growth conditions in the presence of lactate or pyruvate and sulfate, thiosulfate, or fumarate, using ultrafiltration and HR-TEM. Results showed that a significant mass fraction of bioreduced U (35-60%) existed as a mobile phase when the initial concentration of U(VI) was 160 µM. Further experiments with different initial U(VI) concentrations (25 - 900 ?M) in MTM with PIPES or bicarbonate buffers indicated that aggregation of uraninite depended on the initial concentrations of U(VI) and type of buffer. It is known that under some conditions SRB-mediated UO2 nanocrystals can be reoxidized (and thus remobilized) by Fe(III)-(hydr)oxides, common constituents of soils and sediments. To elucidate the mechanism of UO2 reoxidation by Fe(III) (hydr)oxides, we studied the impact of Fe and U chelating compounds (citrate, NTA, and EDTA) on reoxidation rates. Experiments were conducted in anaerobic batch systems in PIPES buffer. Results showed EDTA significantly accelerated UO2 reoxidation with an initial rate of 9.5?M day-1 for ferrihydrite. In all cases, bicarbonate increased the rate and extent of UO2 reoxidation with ferrihydrite. The highest rate of UO2 reoxidation occurred when the chelator promoted UO2 and Fe(III) (hydr)oxide dissolution as demonstrated with EDTA. When UO2 dissolution did not occur, UO2 reoxidation likely proceeded through an aqueous Fe(III) intermediate as observed for both NTA and citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO2 reoxidation as Fe(III) oxidizes HS– preferentially over UO2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network.

Peyton, Brent M. [Montana State University; Timothy, Ginn R. [University of California Davis; Sani, Rajesh K. [South Dakota School of Mines and Technology

2013-08-14

75

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

SciTech Connect

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

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

2013-09-30

76

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

NASA Astrophysics Data System (ADS)

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.

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

2014-12-01

77

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

NASA Astrophysics Data System (ADS)

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

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

2013-05-01

78

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

79

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

SciTech Connect

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

Miller, N.L.

1993-12-31

80

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

SciTech Connect

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

Miller, N.L.

1993-01-01

81

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

NASA Astrophysics Data System (ADS)

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

Bisht, G.; Riley, W. J.

2014-11-01

82

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

83

National Wetlands Biogeochemical Database (NWBD)  

NSDL National Science Digital Library

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

84

Biogeochemical Cycles in Degraded Lands  

NASA Technical Reports Server (NTRS)

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

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

2003-01-01

85

Biogeochemical Cycles in Degraded Lands  

NASA Technical Reports Server (NTRS)

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

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

2004-01-01

86

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

NASA Astrophysics Data System (ADS)

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

Powell, H.; McKnight, D. M.

2009-12-01

87

Global Biogeochemical Cycles Global biogeochemical cycles can be defined as any of the natural circulation pathways  

E-print Network

not well known. Global Carbon and Nutrient Cycles. The biogeochemical cycle of carbon and nutrientsGlobal Biogeochemical Cycles Global biogeochemical cycles can be defined as any of the natural) components of the biosphere and back to the nonliving again. Research on the biogeochemical cycles focuses

Winguth, Arne

88

Benthic Exchange and Biogeochemical Cycling in Permeable Sediments  

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

89

Biogeochemical Processes in Microbial Ecosystems  

NASA Technical Reports Server (NTRS)

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

DesMarais, David J.

2001-01-01

90

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

91

Ocean fronts drive marine fishery production and biogeochemical cycling  

PubMed Central

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

Woodson, C. Brock; Litvin, Steven Y.

2015-01-01

92

Ocean fronts drive marine fishery production and biogeochemical cycling.  

PubMed

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

Woodson, C Brock; Litvin, Steven Y

2015-02-10

93

Modeling the biogeochemical seasonal cycle in the Strait of Gibraltar  

NASA Astrophysics Data System (ADS)

A physical-biological coupled model was used to estimate the effect of the physical processes at the Strait of Gibraltar over the biogeochemical features of the Atlantic Inflow (AI) towards the Mediterranean Sea. This work was focused on the seasonal variation of the biogeochemical patterns in the AI and the role of the Strait; including primary production and phytoplankton features. As the physical model is 1D (horizontal) and two-layer, different integration methods for the primary production in the Biogeochemical Fluxes Model (BFM) have been evaluated. An approach based on the integration of a production-irradiance function was the chosen method. Using this Plankton Functional Type model (BFM), a simplified phytoplankton seasonal cycle in the AI was simulated. Main results included a principal bloom in spring dominated by nanoflagellates, whereas minimum biomass (mostly picophytoplankton) was simulated during summer. Physical processes occurring in the Strait could trigger primary production and raise phytoplankton biomass (during spring and autumn), mainly due to two combined effects. First, in the Strait a strong interfacial mixing (causing nutrient supply to the upper layer) is produced, and, second, a shoaling of the surface Atlantic layer occurs eastward. Our results show that these phenomena caused an integrated production of 105 g C m- 2 year- 1 in the eastern side of the Strait, and would also modify the proportion of the different phytoplankton groups. Nanoflagellates were favored during spring/autumn while picophytoplankton is more abundant in summer. Finally, AI could represent a relevant source of nutrients and biomass to Alboran Sea, fertilizing the upper layer of this area with 4.95 megatons nitrate year- 1 (79.83 gigamol year- 1) and 0.44 megatons C year- 1. A main advantage of this coupled model is the capability of solving relevant high-resolution processes as the tidal forcing without expensive computing requirements, allowing to assess the effect of these phenomena on the biogeochemical patterns at longer time scales.

Ramírez-Romero, E.; Vichi, M.; Castro, M.; Macías, J.; Macías, D.; García, C. M.; Bruno, M.

2014-11-01

94

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

95

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

96

Tidal sands as biogeochemical reactors  

NASA Astrophysics Data System (ADS)

Sandy sediments of continental shelves and most beaches are often thought of as geochemical deserts because they are usually poor in organic matter and other reactive substances. The present study focuses on analyses of dissolved biogenic compounds of surface seawater and pore waters of Aquitanian coastal beach sediments. To quantitatively assess the biogeochemical reactions, we collected pore waters at low tide on tidal cross-shore transects unaffected by freshwater inputs. We recorded temperature, salinity, oxygen saturation state, and nutrient concentrations. These parameters were compared to the values recorded in the seawater entering the interstitial environment during floods. Cross-shore topography and position of piezometric level at low tide were obtained from kinematics GPS records. Residence time of pore waters was estimated by a tracer approach, using dissolved silica concentration and kinetics estimate of quartz dissolution with seawater. Kinetics parameters were based on dissolved silica concentration monitoring during 20-day incubations of sediment with seawater. We found that seawater that entered the sediment during flood tides remained up to seven tidal cycles within the interstitial environment. Oxygen saturation of seawater was close to 100%, whereas it was as low as 80% in pore waters. Concentrations of dissolved nutrients were higher in pore waters than in seawater. These results suggest that aerobic respiration occurred in the sands. We propose that mineralised organic matter originated from planktonic material that infiltrated the sediment with water during flood tides. Therefore, the sandy tidal sediment of the Aquitanian coast is a biogeochemical reactor that promotes or accelerates remineralisation of coastal pelagic primary production. Mass balance calculations suggest that this single process supplies about 37 kmol of nitrate and 1.9 kmol of dissolved inorganic phosphorus (DIP) to the 250-km long Aquitanian coast during each semi-diurnal tidal cycle. It represents about 1.5% of nitrate and 5% of DIP supplied by the nearest estuary.

Anschutz, Pierre; Smith, Thomas; Mouret, Aurélia; Deborde, Jonathan; Bujan, Stéphane; Poirier, Dominique; Lecroart, Pascal

2009-08-01

97

Proterozoic ocean redox and biogeochemical stasis  

PubMed Central

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

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

2013-01-01

98

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

NASA Technical Reports Server (NTRS)

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

Levine, J. S.; Allario, F.

1982-01-01

99

Characterization of terrestrial ecosystems for biogeochemical studies using remote sensing  

NASA Technical Reports Server (NTRS)

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

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

1983-01-01

100

Modeling the biogeochemical cycling of nitrogen and phosphorus in the Eastern Mediterranean Sea: 1950-2000  

E-print Network

Modeling the biogeochemical cycling of nitrogen and phosphorus in the Eastern Mediterranean Sea and remains ultra-oligotrophic. A mass balance model of the coupled N & P cycles synthesizing our conceptual in the model confirms that nitrogen fixation plays a minor role, in agreement with field measurements

Simon, Emmanuel

101

Managing biogeochemical cycles to reduce greenhouse gases  

SciTech Connect

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

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

2012-01-01

102

Introduction to special section: Transport and transformation of biogeochemically important  

E-print Network

Introduction to special section: Transport and transformation of biogeochemically important), Introduction to special section: Transport and transformation of biogeochemically important materials Superior the Keweenaw Interdisciplinary Transport Experiment in Superior (KITES) focused on a region

103

Microbial diversity and biogeochemical cycling in soda lakes.  

PubMed

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments. PMID:25156418

Sorokin, Dimitry Y; Berben, Tom; Melton, Emily Denise; Overmars, Lex; Vavourakis, Charlotte D; Muyzer, Gerard

2014-09-01

104

Biogeochemical redox processes and their impact on contaminant dynamics.  

PubMed

Life and element cycling on Earth is directly related to electron transfer (or redox) reactions. An understanding of biogeochemical redox processes is crucial for predicting and protecting environmental health and can provide new opportunities for engineered remediation strategies. Energy can be released and stored by means of redox reactions via the oxidation of labile organic carbon or inorganic compounds (electron donors) by microorganisms coupled to the reduction of electron acceptors including humic substances, iron-bearing minerals, transition metals, metalloids, and actinides. Environmental redox processes play key roles in the formation and dissolution of mineral phases. Redox cycling of naturally occurring trace elements and their host minerals often controls the release or sequestration of inorganic contaminants. Redox processes control the chemical speciation, bioavailability, toxicity, and mobility of many major and trace elements including Fe, Mn, C, P, N, S, Cr, Cu, Co, As, Sb, Se, Hg, Tc, and U. Redox-active humic substances and mineral surfaces can catalyze the redox transformation and degradation of organic contaminants. In this review article, we highlight recent advances in our understanding of biogeochemical redox processes and their impact on contaminant fate and transport, including future research needs. PMID:20000681

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

2010-01-01

105

Temporal dynamics of biogeochemical processes at the Norman Landfill site  

USGS Publications Warehouse

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

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

2013-01-01

106

Temporal dynamics of biogeochemical processes at the Norman Landfill site  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

107

Global Change: A Biogeochemical Perspective  

NASA Technical Reports Server (NTRS)

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

Mcelroy, M.

1983-01-01

108

Biogeochemical Processes and Implications for Nutrient Cycling  

Microsoft Academic Search

Summary The availability and cycling of nutrients is determined by an interaction of physical, chemical, and biological processes in an ecosystem. This interaction of processes, collectively known as biogeochemistry, is important as it determines the forms, transformations, and ultimate fate of nutrients in a given system. This chapter focuses on biogeochemical processes in springs and spring runs with an examination

Patrick W. Inglett; Kanika S. Inglett; K. Ramesh Reddy

109

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

PubMed

Soil beneath a stormwater infiltration basin receiving runoff from a 23 ha predominantly residential watershed in north-central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop an innovative stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO(3)(-)/Cl(-)) ratios for the shallow groundwater indicates that prior to using BAM, NO(3)(-) concentrations were substantially influenced by nitrification or variations in NO(3)(-) input. In contrast, for the new basin utilizing BAM, NO(3)(-)/Cl(-) ratios indicate minor nitrification and NO(3)(-) losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest that NO(3)(-) losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by the increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO(4)(3-)) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO(4)(3-)/Cl(-) ratios for shallow groundwater indicate predominantly minor increases and decreases in PO(4)(3-) with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had undergone little biogeochemical transformation. Observed nitrogen and phosphorus losses demonstrate the potential, as well as the future research needs to improve performance, of the innovative stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure. PMID:22742948

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

2012-08-15

110

BIOGEOCHEMICAL STUDIES OF PHOTOSYNTHETIC MICROBIAL MATS AND THEIR BIOTA  

NASA Technical Reports Server (NTRS)

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

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

2005-01-01

111

Biogeochemical modelling of the tropical Pacific Ocean. I: Seasonal and interannual variability  

Microsoft Academic Search

A coupled physical–biogeochemical model has been developed in order to study physical–biological interactions in the tropical Pacific Ocean on seasonal-to-interannual timescales. The model incorporates both iron- and nitrogen-limited phytoplankton growth, and succession of phytoplankton size classes in accordance with the “ecumenical” iron hypothesis. The model shows a strong El Niño–Southern Oscillation component to phytoplankton variability in the central equatorial Pacific

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

2001-01-01

112

Calcium Isotopes as Tracers of Biogeochemical Processes  

Microsoft Academic Search

\\u000a The prevalence of calcium as a major cation in surface and oceanic environments, the necessity of calcium in the functioning\\u000a of living cells and bone growth, and the large spread in mass between calcium isotopes all suggest that calcium isotope biogeochemistry\\u000a can be an important avenue of insight into past and present biogeochemical cycling processes. In the following chapter, we

Laura C. Nielsen; Jennifer L. Druhan; Wenbo Yang; Shaun T. Brown; Donald J. DePaolo

113

Apparatus for Cold, Pressurized Biogeochemical Experiments  

NASA Technical Reports Server (NTRS)

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

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

2010-01-01

114

Monterey Bay Time Series Biogeochemical Data  

NSDL National Science Digital Library

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

115

Eastern Mediterranean biogeochemical flux model - Simulations of the pelagic ecosystem  

NASA Astrophysics Data System (ADS)

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

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

2009-02-01

116

Reanalysis of biogeochemical properties in the Mediterranean Sea  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

117

The NEON Aquatic Network: Expanding the Availability of Biogeochemical Data  

NASA Astrophysics Data System (ADS)

Aquatic ecosystems are facing unprecedented pressure from climate change and land-use practices. Invasive species, whether plant, animal, insect or microbe present additional threat to aquatic ecosystem services. There are significant scientific challenges to understanding how these forces will interact to affect aquatic ecosystems, as the flow of energy and materials in the environment is driven by multivariate and non-linear biogeochemical cycles. The National Ecological Observatory Network (NEON) will collect and provide observational data across multiple scales. Sites were selected to maximize representation of major North American ecosystems using a multivariate geographic clustering method that partitioned the continental US, AK, HI, and Puerto Rico into 20 eco-climatic domains. The NEON data collection systems and methods are designed to yield standardized, near real-time data subjected to rigorous quality controls prior to public dissemination through an online data portal. NEON will collect data for 30 years to facilitate spatial-temporal analysis of environmental responses and drivers of ecosystem change, ranging from local through continental scales. Here we present the NEON Aquatic Network, a multi-parameter network consisting of a combination of in situ sensor and observational data. This network will provide data to examine biogeochemical, biological, hydrologic and geomorphic metrics at 36 sites, which are a combination of small 1st/2nd order wadeable streams, large rivers and lakes. A typical NEON Aquatic site will host up to two in-stream sensor sets designed to collect near-continuous water quality data (e.g. pH/ORP, temperature, conductivity, dissolved oxygen, CDOM) along with up to 8 shallow groundwater monitoring wells (level, temp., cond.), and a local meteorological station (e.g. 2D wind speed, PAR, barometric pressure, temperature, net radiation). These coupled sensor suites will be complemented by observational data (e.g. water/sediment chemistry, aquatic organisms, geomorphology). The aquatic network will produce ~212 low-level data products for each site. NEON will produce several higher level data products such as measurements of whole-stream metabolism, gross primary productivity, ecosystem respiration, and fluxes of nitrogen, phosphorous and carbon that will enable users to analyze processes on a gross scale. These data may be integrated with NEON's terrestrial and airborne networks to bridge the gap between aquatic and terrestrial biogeochemical research. The NEON Aquatic Network is poised to greatly expand our ability to create more robust biogeochemical models. For example, hydrologic and stable isotope data will allow investigation of terrestrial-aquatic carbon flux. Constraints provided by NEON's terrestrial and atmospheric data concurrent with remotely sensed data will facilitate the scaling to regional and continental scales, potentially leading to greater accuracy in the global carbon budget. The NEON Aquatic Network represents a powerful tool that will give the scientific community access to standardized data over spatiotemporal scales that are needed to answer fundamental questions about natural ecological variability and responses to changes in the environment.

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

2013-12-01

118

Biogeochemical Cycles of Carbon and Sulfur  

NASA Technical Reports Server (NTRS)

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

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

2002-01-01

119

Global Biology Research Program: Biogeochemical Processes in Wetlands  

NASA Technical Reports Server (NTRS)

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

Bartlett, D. S. (editor)

1984-01-01

120

The role of plants in the Hg biogeochemical cycle  

E-print Network

atomic number 80 Liquid at room temperature Ubiquitous Important Hg facts · Mercury is ubiquitous? The Hg biogeochemical cycle The influence of plants on the Hg biogeochemical cycle Mercury ­ Element it in everything · Mercury is a global pollutant #12;2 What are uses? Occupational exposure What are issues? Me

Nowak, Robert S.

121

Winners and losers: Ecological and biogeochemical changes in a  

E-print Network

changes are driven by a balance between two impacts of a warming climate: higher metabolic rates (theWinners and losers: Ecological and biogeochemical changes in a warming ocean* Stephanie Dutkiewicz, Jeffery R. Scott and Mick J. Follows *Reprinted from Global Biogeochemical Cycles, 27(2): 463

122

Diel biogeochemical processes in terrestrial waters  

USGS Publications Warehouse

Many biogeochemical processes in rivers and lakes respond to the solar photocycle and produce persistent patterns of measureable phenomena that exhibit a day-night, or 24-h, cycle. Despite a large body of recent literature, the mechanisms responsible for these diel fluctuations are widely debated, with a growing consensus that combinations of physical, chemical, and biological processes are involved. These processes include streamflow variation, photosynthesis and respiration, plant assimilation, and reactions involving photochemistry, adsorption and desorption, and mineral precipitation and dissolution. Diel changes in streamflow and water properties such as temperature, pH, and dissolved oxygen concentration have been widely recognized, and recently, diel studies have focused more widely by considering other constituents such as dissolved and particulate trace metals, metalloids, rare earth elements, mercury, organic matter, dissolved inorganic carbon (DIC), and nutrients. The details of many diel processes are being studied using stable isotopes, which also can exhibit diel cycles in response to microbial metabolism, photosynthesis and respiration, or changes in phase, speciation, or redox state. In addition, secondary effects that diel cycles might have, for example, on biota or in the hyporheic zone are beginning to be considered. This special issue is composed primarily of papers presented at the topical session "Diurnal Biogeochemical Processes in Rivers, Lakes, and Shallow Groundwater" held at the annual meeting of the Geological Society of America in October 2009 in Portland, Oregon. This session was organized because many of the growing number of diel studies have addressed just a small part of the full range of diel cycling phenomena found in rivers and lakes. This limited focus is understandable because (1) fundamental aspects of many diel processes are poorly understood and require detailed study, (2) the interests and expertise of individual scientists typically do not encompass the wide diversity and range of processes that produce diel cycles, and (3) the logistics of making field measurements for 24-h periods has limited recognition and understanding of these important cycles. Thus, the topical session brought together hydrologists, biologists, geochemists, and ecologists to discuss field studies, laboratory experiments, theoretical modeling, and measurement techniques related to diel cycling. Hopefully with the cross-disciplinary synergy developed at the session as well as by this special issue, a more comprehensive understanding of the interrelationships between the diel processes will be developed. Needless to say, understanding diel processes is critical for regulatory agencies and the greater scientific community. And perhaps more importantly, expanded knowledge of biogeochemical cycling may lead to better predictions of how aquatic ecosystems might react to changing conditions of contaminant loading, eutrophication, climate change, drought, industrialization, development, and other variables.

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

2011-01-01

123

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

124

Oceanographic and Biogeochemical Insights from Diatom Genomes  

NASA Astrophysics Data System (ADS)

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

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

2010-01-01

125

The biogeochemical heterogeneity of tropical forests.  

PubMed

Tropical forests are renowned for their biological diversity, but also harbor variable combinations of soil age, chemistry and susceptibility to erosion or tectonic uplift. Here we contend that the combined effects of this biotic and abiotic diversity promote exceptional biogeochemical heterogeneity at multiple scales. At local levels, high plant diversity creates variation in chemical and structural traits that affect plant production, decomposition and nutrient cycling. At regional levels, myriad combinations of soil age, soil chemistry and landscape dynamics create variation and uncertainty in limiting nutrients that do not exist at higher latitudes. The effects of such heterogeneity are not well captured in large-scale estimates of tropical ecosystem function, but we suggest new developments in remote sensing can help bridge the gap. PMID:18582987

Townsend, Alan R; Asner, Gregory P; Cleveland, Cory C

2008-08-01

126

Carbohydrates as indicators of biogeochemical processes  

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

127

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

128

Modeling Interactions of Surface-Subsurface Flow Using a Free-Surface Overland Flow Boundary Condition in a Parallel Flow Simulator  

SciTech Connect

Models incorporating interactions between surface and subsurface flow are commonly based on the conductance concept that presumes a distinct interface at the land surface, separating the surface from the subsurface domain. In these models the subsurface and surface domains are linked via an exchange flux that depends upon the magnitude and direction of the hydraulic gradient across the interface and a proportionality constant (a measure of the hydraulic connectivity). Because experimental evidence of such a distinct interface is often lacking in the field, a more general coupled modeling approach would be preferable. We present a more general approach that incorporates a two-dimensional overland flow simulator into the parallel three-dimensional variably saturated subsurface flow code ParFlow developed at LLNL. This overland flow simulator takes the form of an upper, free-surface boundary condition and is, thus, fully integrated without relying on the conductance concept. Another advantage of this approach is the efficient parallelism of ParFlow, which is exploited by the overland flow simulator. Several verification and simulation examples are presented that focus on the two main processes of runoff production: excess infiltration and saturation. The usefulness of our approach is demonstrated in an application of the model to an urban watershed. The influence of heterogeneity of the shallow subsurface on overland flow and transport is also examined. The results show the uncertainty in flow and transport predictions due to heterogeneity. This is important in determining, for example, total maximum daily loads of surface water systems.

Kollet, S J; Maxwell, R M

2005-10-25

129

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

PubMed

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

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

2013-02-01

130

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

NASA Astrophysics Data System (ADS)

Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from the atmosphere, influencing global climate changes. Integration of these processes into Earth system models (e.g., community land models (CLMs)), however, currently faces three major challenges: (1) extensive efforts are required to modify modeling structures and to rewrite computer programs to incorporate new or updated processes as new knowledge is being generated, (2) computational cost is prohibitively expensive to simulate biogeochemical processes in land models due to large variations in the rates of biogeochemical processes, and (3) various mathematical representations of biogeochemical processes exist to incorporate different aspects of fundamental mechanisms, but systematic evaluation of the different mathematical representations is difficult, if not impossible. To address these challenges, we propose a new computational framework to easily incorporate physical and biogeochemical processes into land models. The new framework consists of a new biogeochemical module, Next Generation BioGeoChemical Module (NGBGC), version 1.0, with a generic algorithm and reaction database so that new and updated processes can be incorporated into land models without the need to manually set up the ordinary differential equations to be solved numerically. The reaction database consists of processes of nutrient flow through the terrestrial ecosystems in plants, litter, and soil. This framework facilitates effective comparison studies of biogeochemical cycles in an ecosystem using different conceptual models under the same land modeling framework. The approach was first implemented in CLM and benchmarked against simulations from the original CLM-CN code. A case study was then provided to demonstrate the advantages of using the new approach to incorporate a phosphorus cycle into CLM. To our knowledge, the phosphorus-incorporated CLM is a new model that can be used to simulate phosphorus limitation on the productivity of terrestrial ecosystems. The method presented here could in theory be applied to simulate biogeochemical cycles in other Earth system models.

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

2013-11-01

131

Organic geochemistry and stable isotope constraints on Precambrian biogeochemical processes  

E-print Network

Details of the biogeochemical cycles and the dominant mechanisms present in Precambrian remain heavily debated topics. The events of the Late Proterozoic onset to glaciations and what types of early life existed in the ...

Thomas, Katherine S., S.M. Massachusetts Institute of Technology

2011-01-01

132

Climate change effects on watershed hydrological and biogeochemical processes  

EPA Science Inventory

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

133

Doctoral Defense "Biogeochemical evaluation of disposal options for arsenic-  

E-print Network

Doctoral Defense "Biogeochemical evaluation of disposal options for arsenic- bearing wastes Lutgarde Raskin Professor, Civil & Environmental Engineering Arsenic contamination of drinking water of arsenic removal technologies requires disposal options for produced wastes that limit the release

Kamat, Vineet R.

134

Archaea in Biogeochemical Pierre Offre, Anja Spang, and Christa Schleper  

E-print Network

Keywords archaea, biogeochemical cycles, metabolism, carbon, nitrogen, sulfur Abstract Archaea constitute. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445 Sulfur Cycle and the combined metabolisms of all life forms (96). These self-organized nutrient cycles, which are increasingly

Saleska, Scott

135

Plant Nitrogen Uptake in Terrestrial Biogeochemical Models  

NASA Astrophysics Data System (ADS)

Most terrestrial biogeochemical models featured in the last Intergovernmental Panel on Climate Change (IPPC) Assessment Report highlight the importance of the terrestrial Carbon sequestration and feedbacks between the terrestrial Carbon cycle and the climate system. However, these models have been criticized for overestimating predicted Carbon sequestration and its potential climate feedback when calculating the rate of future climate change because they do not account for the Carbon sequestration constraints caused by nutrient limitation, particularly Nitrogen (N). This is particularly relevant considering the existence of a substantial deficit of Nitrogen for plants in most areas of the world. To date, most climate models assume that plants have access to as much Nitrogen as needed, but ignore the nutrient requirements for new vegetation growth. Determining the natural demand and acquisition for Nitrogen and its associated resource optimization is key when accounting for the Carbon sequestration constrains caused by nutrient limitation. The few climate models that include C-N dynamics have illustrated that the stimulation of plant growth over the coming century may be significantly smaller than previously predicted. However, models exhibit wide differences in their predictive accuracy and lead to widely diverging and inconsistent projections accounting for an uncertain Carbon sequestration decrease due to Nitrogen limitation ranging from 7 to 64%. This reduction in growth is partially offset by an increase in the availability of nutrients resulting from an accelerated rate of decomposition of dead plants and other organic matter that occurring with a rise in temperature. However, this offset does not counterbalance the reduced level of plant growth calculated by natural nutrient limitations. Additionally, Nitrogen limitation is also expected to become more pronounced in some ecosystems as atmospheric CO2 concentration increases; resulting in less new growth and higher atmospheric CO2 concentrations than originally expected. This study compares the differences in the predictions of alternative models of plant N uptake found in different terrestrial biogeochemical models with the predictions from a new N-uptake model developed under the Joint UK Land Environment Simulator (JULES) framework. We implement a methodology for the construction, parameterization and evaluation of N uptake models to fully decompose all the N uptake component processes in terms of their parameter uncertainty and the accuracy of their predictions with respect to different empirical data sets. Acknowledgements This work has been funded by the European Commission FP7-PEOPLE-ITN-2008 Marie Curie Action: "Greencycles II: FP7-PEOPLE-ITN-2008 Marie Curie Action: "Networks for Initial Training"

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

2013-12-01

136

Plant Nitrogen Uptake in Terrestrial Biogeochemical Models  

NASA Astrophysics Data System (ADS)

Most terrestrial biogeochemical models featured in the last Intergovernmental Panel on Climate Change (IPPC) Assessment Report highlight the importance of the terrestrial Carbon sequestration and feedbacks between the terrestrial Carbon cycle and the climate system. However, these models have been criticized for overestimating predicted Carbon sequestration and its potential climate feedback when calculating the rate of future climate change because they do not account for the Carbon sequestration constraints caused by nutrient limitation, particularly Nitrogen (N). This is particularly relevant considering the existence of a substantial deficit of Nitrogen for plants in most areas of the world. To date, most climate models assume that plants have access to as much Nitrogen as needed, but ignore the nutrient requirements for new vegetation growth. Determining the natural demand and acquisition for Nitrogen and its associated resource optimization is key when accounting for the Carbon sequestration constrains caused by nutrient limitation. The few climate models that include C-N dynamics have illustrated that the stimulation of plant growth over the coming century may be two to three times smaller than previously predicted. This reduction in growth is partially offset by an increase in the availability of nutrients resulting from an accelerated rate of decomposition of dead plants and other organic matter that occurring with a rise in temperature. However, this offset does not counterbalance the reduced level of plant growth calculated by natural nutrient limitations. Additionally, Nitrogen limitation is also expected to become more pronounced in some ecosystems as atmospheric CO2 concentration increases; resulting in less new growth and higher atmospheric CO2 concentrations than originally expected. This study compares alternative models of plant N uptake as found in different terrestrial biogeochemical models against field measurements, and introduces a new N-uptake model to the Joint UK Land Environment Simulator (JULES).. Acknowledgements This work has been funded by the European Commission FP7-PEOPLE-ITN-2008 Marie Curie Action: "Greencycles II: FP7-PEOPLE-ITN-2008 Marie Curie Action: "Networks for Initial Training"

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

2013-04-01

137

Searching for Biogeochemical Cycles on Mars  

NASA Technical Reports Server (NTRS)

The search for life on Mars clearly benefits from a rigorous, yet broad, definition of life that compels us to consider all possible lines of evidence for a martian biosphere. Recent studies in microbial ecology illustrate that the classic definition of life should be expanded beyond the traditional definition of a living cell. The traditional defining characteristics of life are threefold. First, life is capable of metabolism, that is, it performs chemical reactions that utilize energy and also synthesize its cellular constituents. Second, life is capable of self-replication. Third, life can evolve in order to adapt to environmental changes. An expanded, ecological definition of life also recognizes that life is a community of organisms that must interact with their nonliving environment through processes called biogeochemical cycles. This regenerative processing maintains, in an aqueous conditions, a dependable supply of nutrients and energy for growth. In turn, life can significantly affect those processes that control the exchange of materials between the atmosphere, ocean, and upper crust. Because metabolic processes interact directly with the environment, they can alter their surroundings and thus leave behind evidence of life. For example, organic matter is produced from single-carbon-atom precursors for the biosynthesis of cellular constituents. This leads to a reservoir of reduced carbon in sediments that, in turn, can affect the oxidation state of the atmosphere. The harvesting of chemical energy for metabolism often employs oxidation-reduction reactions that can alter the chemistry and oxidation state of the redox-sensitive elements carbon, sulfur, nitrogen, iron, and manganese. Have there ever been biogeochemical cycles on Mars? Certain key planetary processes can offer clues. Active volcanism provides reduced chemical species that biota can use for organic synthesis. Volcanic carbon dioxide and methane can serve as greenhouse gases. Thus the persistence of volcanism on Mars may well have influenced the persistence of a martian biosphere. The geologic processing of the crust can affect the availability of nutrients and also control the deposition of minerals that could have served as a medium for the preservation of fossil information. Finally, the activity of liquid water is crucial to life. Was there ever an Earth-like hydrologic cycle with rainfall? Has aqueous activity instead been restricted principally to hydrothermal activity below the surface? To what extent did the inorganic chemistry driven by sunlight and hydrothermal activity influence organic chemistry (prebiotic chemical evolution)? This paper addresses these and other key questions.

DesMarais, David J.

1997-01-01

138

Redox regime shifts in microbially-mediated biogeochemical cycles  

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

139

Dynamic biogeochemical provinces in the global ocean  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

140

Understanding oceanic migrations with intrinsic biogeochemical markers.  

PubMed

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

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

2009-01-01

141

Understanding Oceanic Migrations with Intrinsic Biogeochemical Markers  

PubMed Central

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

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

2009-01-01

142

Redox chemistry in the phosphorus biogeochemical cycle.  

PubMed

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

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

2014-10-28

143

Redox chemistry in the phosphorus biogeochemical cycle  

PubMed Central

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

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

2014-01-01

144

SYM01or -Arsenic in Soil and Groundwater Environment:Biogeochemical Interactions Proc. 7th Intern. Conf. on the Biogeochem. of Trace Elements; Uppsala '03  

E-print Network

#12;SYM01or - Arsenic in Soil and Groundwater Environment:Biogeochemical Interactions Proc. 7th #12;SYM01or - Arsenic in Soil and Groundwater Environment:Biogeochemical Interactions Proc. 7th Intern Intern. Conf. on the Biogeochem. of Trace Elements; Uppsala '03 In-Situ Speciation of Arsenic

Sparks, Donald L.

145

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

PubMed

With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles. PMID:23744573

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

2013-10-01

146

A generic biogeochemical module for earth system models  

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

147

Restoration of biogeochemical function in mangrove forests  

USGS Publications Warehouse

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

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

2000-01-01

148

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

SciTech Connect

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

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

2013-11-13

149

Ecosystem biogeochemical function and services in an urbanizing desert region  

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

150

Biogeochemical drivers of phosphatase activity in salt marsh sediments  

NASA Astrophysics Data System (ADS)

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

Freitas, Joana; Duarte, Bernardo; Caçador, Isabel

2014-10-01

151

Impact of resolved scales on global marine biogeochemical models  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

152

Aerosol indirect effect on biogeochemical cycles and climate.  

PubMed

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

Mahowald, Natalie

2011-11-11

153

Oceanic ventilation and biogeochemical cycling: Understanding the physical mechanisms that produce realistic distributions of tracers and  

E-print Network

Oceanic ventilation and biogeochemical cycling: Understanding the physical mechanisms that produce circulation support different rates of ventilation, which in turn produce different distributions. Matsumoto, J. L. Sarmiento, R. D. Slater, and P. S. Swathi (2004), Oceanic ventilation and biogeochemical

Matsumoto, Katsumi

154

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

NASA Astrophysics Data System (ADS)

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

Bala, G.; Narayanappa, D.

2013-12-01

155

Modelling biogeochemical tracer transport in sea ice due to gravity drainage  

NASA Astrophysics Data System (ADS)

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

Hitchen, Joseph; Wells, Andrew

2014-05-01

156

Modeling carbon cycle responses to tree mortality: linking microbial and biogeochemical changes  

NASA Astrophysics Data System (ADS)

Amid a worldwide increase in tree mortality, mountain pine beetles (Dendroctonus ponderosae Hopkins) have killed billions of trees from Mexico to Alaska in the last 13 years. This mortality is predicted to influence important carbon, water and energy balance feedbacks on the Earth system. We studied changes in soil biogeochemical cycling and microbial community structure after tree mortality. We show, using a decade long chronosequence, that tree mortality causes no increase in total respiration from local to watershed scales, with corresponding changes in biogeochemical pools of nitrogen and phosphorus. We also found comparable declines in both gross primary productivity and respiration suggesting little change in net flux. We tested the mechanisms controlling these patterns using an ecosystem model; contrasting a simplified microbial subroutine with a 'dead soil' model. We coupled our modeling work with direct measurements of microbial biomass, enzyme kinetics and community structure. The transitory recovery of respiration 6-7 years after mortality was associated with increased microbial biomass, increased incorporation of leaf litter carbon into soil organic matter, and was followed by a secondary decline in respiration during years 8-10. Our findings are consistent with the mechanism of reduced input of new carbon causing a decline in microbial biomass rather than an increased output of older carbon.

Moore, D. J.; Trahan, N. A.; Dynes, E. L.; Zobitz, J. M.; Gallery, R.

2013-12-01

157

Integrating turbulent flow, biogeochemical, and poromechanical processes in rippled coastal sediment (Invited)  

NASA Astrophysics Data System (ADS)

Coastal sediments are the locus of multiple coupled processes. Turbulent flow associated with waves and currents induces porewater flow through sediment leading to fluid exchange with the water column. This porewater flow is determined by the hydraulic and elastic properties of the sediment. Porewater flow also ultimately controls biogeochemical reactions in the sediment whose rates depend on delivery of reactants and export of products. We present results from numerical modeling studies directed at integrating these processes with the goal of shedding light on these complex environments. We show how denitrification rates inside ripples are largest at intermediate permeability which represents the optimal balance of reactant delivery and anoxic conditions. It is clear that nutrient cycling and distribution within the sediment is strongly dependent on the character of the multidimensional flow field inside of sediment. More recent studies illustrate the importance of the elastic properties of the saturated sediment on modulating fluid exchange between the water column and the sediment when pressure fluctuations along the sediment-water interface occur at the millisecond scale. Pressure fluctuations occur at this temporal scale due to turbulence and associated shedding of vortices due to the ripple geometry. This suggests that biogeochemical cycling may also be affected by these high-frequency elastic effects. Future studies should be directed towards this and should take advantage of modeling tools such as those we present.

Cardenas, M. B.; Cook, P. L.; Jiang, H.; Traykovski, P.

2010-12-01

158

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

NASA Astrophysics Data System (ADS)

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

Bieroza, Magdalena; Heathwaite, Louise

2013-04-01

159

EFFECTS OF INCREASED SOLAR ULTRAVIOLET RADIATION ON BIOGEOCHEMICAL CYCLES  

EPA Science Inventory

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

160

Biogeochemical study of organic substances in Antarctic lakes  

Microsoft Academic Search

The features of organic constituents in Antarctic lakes and ponds of the McMurdo, Syowa and Vestfold oases are summarised from a biogeochemical viewpoint. Total organic carbon or dissolved organic carbon contents in saline lakewaters are generally extremely high and much higher than those in freshwater lakes. The concentrations and\\/or compositions of hydrocarbons, fatty acids, sterols, phenolic acids and hydroxy acids

Genki I. Matsumoto

1989-01-01

161

Editorial: Organic wastes in soils: Biogeochemical and Environmental Aspects  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

162

Biogeochemical Changes Accompanying Woody Plant Encroachment in a Subtropical Savanna  

Microsoft Academic Search

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

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

2001-01-01

163

Probing the Biogeochemical Behavior of Technetium Using a  

E-print Network

Probing the Biogeochemical Behavior of Technetium Using a Novel Nuclear Imaging Approach G A V I N 13, 2009. Accepted April 1, 2009. Dynamic -camera imaging of radiotracer technetium (99m Tc) wasusedtoassesstheimpactofbiostimulationofmetal-reducing bacteria on technetium mobility at 10-12 mol L-1 concentrations in sediments. Addition

Burke, Ian

164

Physical Ecosystem Engineers as Agents of Biogeochemical Heterogeneity  

NSDL National Science Digital Library

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

JORGE L. GUTIÃ?Â?RREZ and CLIVE G. JONES (; )

2006-03-01

165

Submarine Groundwater Discharge Driving Mechanisms and Biogeochemical Aspects  

Microsoft Academic Search

Submarine groundwater discharge (SGD) is an important pathway for trace element and nutrient cycling in the coastal ocean. I use a combination of hydrological and geochemical tracer observations to gain insights into the natural and anthropogenic mechanisms driving SGD into coastal water bodies. Nutrient measurements in a subterranean estuary (STE) were used to discuss the biogeochemical controls of SGD endmember

Isaac R. Santos

2008-01-01

166

The identification and biogeochemical interpretation of fossil magnetotactic bacteria  

E-print Network

The identification and biogeochemical interpretation of fossil magnetotactic bacteria Robert E. Available online 14 August 2007. Abstract Magnetotactic bacteria, which most commonly live within the oxic, specifically magnetite or greigite. The crystals cause the bacteria to orient themselves passively with respect

167

PHOTOREACTIONS IN SURFACE WATERS AND THEIR ROLE IN BIOGEOCHEMICAL CYCLES  

EPA Science Inventory

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

168

Past and present of sediment and carbon biogeochemical cycling models  

NASA Astrophysics Data System (ADS)

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

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

2004-05-01

169

Past and present of sediment and carbon biogeochemical cycling models  

NASA Astrophysics Data System (ADS)

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

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

170

Vesicomyid Clams Alter Biogeochemical Processes at Pacific Methane Seeps  

NASA Astrophysics Data System (ADS)

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

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

2007-12-01

171

Earth's Early Biosphere and the Biogeochemical Carbon Cycle  

NASA Technical Reports Server (NTRS)

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

DesMarais, David

2004-01-01

172

Developing biogeochemical tracers of apatite weathering by ectomycorrhizal fungi  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

173

Adapting to life: ocean biogeochemical modelling and adaptive remeshing  

NASA Astrophysics Data System (ADS)

An outstanding problem in biogeochemical modelling of the ocean is that many of the key processes occur intermittently at small scales, such as the sub-mesoscale, that are not well represented in global ocean models. 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.

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

2013-11-01

174

Adapting to life: ocean biogeochemical modelling and adaptive remeshing  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

175

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

NASA Astrophysics Data System (ADS)

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

Podymov, O.

2009-04-01

176

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

PubMed

This paper uses the findings from a column study to develop a reactive model for exploring the interactions occurring in leachate-contaminated soils. The changes occurring in the concentrations of acetic acid, sulphate, suspended and attached biomass, Fe(II), Mn(II), calcium, carbonate ions, and pH in the column are assessed. The mathematical model considers geochemical equilibrium, kinetic biodegradation, precipitation-dissolution reactions, bacterial and substrate transport, and permeability reduction arising from bacterial growth and gas production. A two-step sequential operator splitting method is used to solve the coupled transport and biogeochemical reaction equations. The model gives satisfactory fits to experimental data and the simulations show that the transport of metals in soil is controlled by multiple competing biotic and abiotic reactions. These findings suggest that bioaccumulation and gas formation, compared to chemical precipitation, have a larger influence on hydraulic conductivity reduction. PMID:17996980

Singhal, Naresh; Islam, Jahangir

2008-02-19

177

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

NASA Technical Reports Server (NTRS)

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

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

1989-01-01

178

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

179

Aquifer/aquitard interfaces: Mixing zones that enhance biogeochemical reactions  

USGS Publications Warehouse

Several important biogeochemical reactions are known to occur near the interface between aquifer and aquitard sediments. These reactions include O2 reduction; denitrification; and Fe3+, SO42-, and CO2 (methanogenesis) reduction. In some settings, these reactions occur on the aquitard side of the interface as electron acceptors move from the aquifer into the electron-donor-enriched aquitard. In other settings, these reactions occur on the aquifer side of the interface as electron donors move from the aquitard into the electron-acceptor-enriched, or microorganism-enriched, aquifer. Thus, the aquifer/aquitard interface represents a mixing zone capable of supporting greater microbial activity than either hydrogeologic unit alone. The extent to which biogeochemical reactions proceed in the mixing zone and the width of the mixing zone depend on several factors, including the abundance and solubility of electron acceptors and donors on either side of the interface and the rate at which electron acceptors and donors react and move across the interface. Biogeochemical reactions near the aquifer/aquitard interface can have a substantial influence on the chemistry of water in aquifers and on the chemistry of sediments near the interface.

McMahon, P.B.

2001-01-01

180

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

181

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

182

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

PubMed

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

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

2011-11-01

183

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

NASA Astrophysics Data System (ADS)

The turbid tropical Cointzio reservoir, located in the Trans Mexican Volcanic Belt (TMVB), behaves as a warm monomictic water body (area = 6 km2, capacity 66 Mm3, residence time ~ 1 year). It is strategic for the drinking water supply of the city of Morelia, capital of the state of Michoacán, and for downstream irrigation during the dry season. This reservoir is a perfect example of a human-impacted system since its watershed is mainly composed of degraded volcanic soils and is subjected to high erosion processes and agricultural loss. The reservoir is threatened by sediment accumulation and nutrients originating from untreated waters in the upstream watershed. The high content of very fine clay particles and the lack of water treatment plants lead to serious episodes of eutrophication (up to 70 ?g chl. a L-1), high levels of turbidity (Secchi depth < 30 cm) and a long period of anoxia (from May to October). Based on intensive field measurements in 2009 (deposited sediment, benthic chamber, water vertical profiles, reservoir inflow and outflow) we determined suspended sediment (SS), carbon (C), nitrogen (N) and phosphorus (P) mass balances. Watershed SS yields were estimated at 35 t km2 y-1 of which 89-92 % were trapped in the Cointzio reservoir. As a consequence the reservoir has already lost 25 % of its initial storage capacity since its construction in 1940. Nutrient mass balances showed that 50 % and 46 % of incoming P and N were retained by sedimentation, and mainly eliminated through denitrification respectively. Removal of C by 30 % was also observed both by sedimentation and through gas emission. To complete field data analyses we examined the ability of vertical one dimensional (1DV) numerical models (Aquasim biogeochemical model coupled with k-? mixing model) to reproduce the main biogeochemical cycles in the Cointzio reservoir. The model can describe all the mineralization processes both in the water column and in the sediment. The values of the entire mass balance of nutrients and of the mineralization rates (denitrification and aerobic benthic mineralization) calculated from the model fitted well to the field measurements. Furthermore, this analysis indicates that the benthic mineralizations are the dominant processes involved in the nutrients release. This is the first implementation of a biogeochemical model applied to a highly productive reservoir in the TMVB in order to estimate nutrients release from sediments. It could be used for scenarios of reduction of eutrophication in the reservoir. This study provides a good example of the behavior of a small tropical reservoir under intense human pressure and it will help stakeholders to adopt appropriate strategies for the management of turbid tropical reservoirs.

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

2014-05-01

184

Modeling the influence of oxygenated inflows on the biogeochemical structure of the Gotland Sea, central Baltic Sea: Changes in the distribution of manganese  

NASA Astrophysics Data System (ADS)

A coupled hydrodynamic-biogeochemical one-dimensional O-N-S-P-Mn-Fe-model based on the RedOx Layer Model, (ROLM) and the General Ocean Turbulence Model (GOTM) is used to simulate basic changes in the biogeochemical water column structure in transition phases between oxic and anoxic conditions in a marginal sea. Organic matter (OM) formation and decay, the reduction and oxidation of species of nitrogen, sulfur, manganese, iron, and the transformation of phosphorus species are parameterized in the model. The influence of oxygenated intrusions on the vertical biogeochemical structure of the central Gotland Basin of the Baltic Sea is modeled. The model-produced simulations demonstrate that a complete ventilation of the Gotland Deep bottom water caused by massive inflows of oxygenated North Sea water has led to substantial changes in the vertical biogeochemical structure of the basin. During the inflow events large amounts of iron and manganese precipitate and vanish from the water column. In addition redox reactions are accelerated and bacterial growth leads to an increase of particulate matter content and consequent sedimentation of particles. During reestablishment of anoxic conditions, the structure of the water column is unbalanced. This is partly due to the absence of Mn species that play a dominant role in the oxidation-reduction reactions at the pelagic redox interfaces. This unbalanced structure can serve as a biotope for the development of untypical microbial redox-cline reactions (i.e. anammox). According to our model simulations, the reestablishment of steady state biogeochemical conditions following a complete flushing takes ˜1.5 years.

Yakushev, E. V.; Kuznetsov, I. S.; Podymov, O. I.; Burchard, H.; Neumann, T.; Pollehne, F.

2011-04-01

185

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

PubMed

Rivers are an important source of mercury (Hg) to marine ecosystems. Based on an analysis of compiled observations, we estimate global present-day Hg discharges from rivers to ocean margins are 27 ± 13 Mmol a(-1) (5500 ± 2700 Mg a(-1)), of which 28% reaches the open ocean and the rest is deposited to ocean margin sediments. Globally, the source of Hg to the open ocean from rivers amounts to 30% of atmospheric inputs. This is larger than previously estimated due to accounting for elevated concentrations in Asian rivers and variability in offshore transport across different types of estuaries. Riverine inputs of Hg to the North Atlantic have decreased several-fold since the 1970s while inputs to the North Pacific have increased. These trends have large effects on Hg concentrations at ocean margins but are too small in the open ocean to explain observed declines of seawater concentrations in the North Atlantic or increases in the North Pacific. Burial of Hg in ocean margin sediments represents a major sink in the global Hg biogeochemical cycle that has not been previously considered. We find that including this sink in a fully coupled global biogeochemical box model helps to balance the large anthropogenic release of Hg from commercial products recently added to global inventories. It also implies that legacy anthropogenic Hg can be removed from active environmental cycling on a faster time scale (centuries instead of millennia). Natural environmental Hg levels are lower than previously estimated, implying a relatively larger impact from human activity. PMID:25066365

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

2014-08-19

186

Using isotopes to understand linked hydrological, biological, and biogeochemical processes (Invited)  

NASA Astrophysics Data System (ADS)

Isotopes have many applications for understanding linked processes in ecosystems. Stable isotopes in particular are powerful tools because of their sensitivity to particular sources, transformations, and flow processes. Although less commonly used in an ecohydrological context, radioactive isotopes can also be valuable especially when questions related to groundwater or catchment residence times are involved. In this presentation, we will illustrate how isotopes can improve understanding of linked processes in ecosystems. For example, investigations of linked vadose zone/plant/atmosphere systems using deuterium and oxygen-18 show that both vertical and horizontal spatial variability of isotope values can provide important clues to understand how evaporation and transpiration partitioning varies across the landscape and how these processes impact water flow and pore water chemistry. The links to pore water chemistry are important because they show how strongly coupled vadose zone flow and transport, plant water use, and biogeochemical processes can be. Over the last few decades the use of isotopes has transformed understanding of linked hydrological, biological, and biogeochemical processes from both conceptual and quantitative viewpoints. In addition, recent advances in laboratory- and field-analysis methods for stable isotopes using laser absorption based methods have already had large impacts on scientific research and such impacts will almost certainly grow in the next few years. However, there are still important research questions and deficiencies in our sampling and analytical capabilities remain. These issues significantly hamper efforts to make better quantitative estimates of important fluxes (evaporation being one example). We conclude by discussing some of the key areas that require further development including issues related to the use of isotopes to quantify evaporation and evaporation/transpiration partitioning.

Newman, B. D.; Aggarwal, P. K.; Araguas-Araguas, L.; Groening, M.; Poeltenstein, L.; Tanweer, A.

2010-12-01

187

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

188

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

189

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

190

BIOGEOCHEMICAL ECOLOGY OF AQUACULTURE PONDS A DISSERTATION SUBMITIED TO THE GRADUATE DIVISION OF THE  

E-print Network

BIOGEOCHEMICAL ECOLOGY OF AQUACULTURE PONDS A DISSERTATION SUBMITIED TO THE GRADUATE DIVISION production and consumption were applied in shrimp aquaculture ponds which served as convenient model systems

Luther, Douglas S.

191

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

PubMed

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

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

2013-10-15

192

Circulation and biogeochemical processes in the East China Sea and the vicinity of Taiwan: an overview and a brief synthesis  

NASA Astrophysics Data System (ADS)

The East China Sea shelf (including the Yellow Sea and the Bohai Sea) is a very challenging system for hydrodynamic and biogeochemical studies due to its complicated physical and chemical forcing. It receives much attention because of its capacity for absorbing atmospheric CO 2 in spite of large riverine fluxes of terrigenous carbon. This volume reports field observations and modeling studies during the Kuroshio Edge Exchange Processes and ensuing projects, which are a part of the continental margins study in the Joint Global Ocean Flux Study. A 3-D numerical model has been developed to simulate the climatological circulation in the East China Sea. The model result is supported by observations in the seas around Taiwan. The significance of inflow from the Taiwan Strait is emphasized. Geochemical tracers prove useful in understanding the water and material transport. Biogeochemical studies suggest very efficient recycling of organic carbon by bacterial and protozoan consumption in the shelf water, but a finite amount of particulate organic carbon with a significant terrigenous fraction is exported from the shelf. The fine-grained sediments in the inner shelf appear to be an important source of organic carbon for export. Future studies are needed to improve our understanding of key physical and biogeochemcial processes, to develop coupled physical-biogeochemical models, and to catch and survey the elusive spring algal bloom. A tantalizing goal of our ongoing effort is to document or even to predict future changes in the East China Sea shelf caused by the operation of the Three-Gorge Dam, which is under construction in the middle reach of the Yangtze River.

Liu, Kon-Kee; Peng, Tsung-Hung; Shaw, Ping-Tung; Shiah, Fuh-Kwo

2003-03-01

193

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

PubMed Central

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

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

2013-01-01

194

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

PubMed

Biogeochemical dynamics in the vadose zone are poorly understood due to the transient nature of chemical and hydrologic conditions but are nonetheless critical to understanding chemical fate and transport. This study explored the effects of a soil layer on linked geochemical, hydrological, and microbiological processes. Three laboratory soil columns were constructed: a homogenized medium-grained sand, a homogenized organic-rich loam, and a sand-over-loam layered column. Upward and downward infiltration of water was evaluated during experiments to simulate rising water table and rainfall events, respectively. In situ collocated probes measured soil water content, matric potential, and Eh. Water samples collected from the same locations were analyzed for Br, Cl, NO, SO, NH, Fe, and total sulfide. Compared with homogeneous columns, the presence of a soil layer altered the biogeochemistry and water flow of the system considerably. Enhanced biogeochemical cycling was observed in the layered column over the texturally homogeneous soil columns. Enumerations of iron- and sulfate-reducing bacteria showed 1 to 2 orders of magnitude greater community numbers in the layered column. Mineral and soil aggregate composites were most abundant near the soil-layer interface, the presence of which likely contributed to an observed order-of-magnitude decrease in hydraulic conductivity. These findings show that quantifying coupled hydrologic-biogeochemical processes occurring at small-scale soil interfaces is critical to accurately describing and predicting chemical changes at the larger system scale. These findings also provide justification for considering soil layering in contaminant fate and transport models because of its potential to increase biodegradation or to slow the rate of transport of contaminants. PMID:22031578

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

2011-01-01

195

Reversible redox chemistry of quinones: impact on biogeochemical cycles.  

PubMed

The role of quinone biomolecules and quinone moieties of natural organic matter (NOM) as the electron transfer mediator in essential biogeochemical processes such as iron bioreduction and contaminant degradation has received considerable interests in the past decade. Hypothesized electron shuttling mechanism must be evaluated based on the availability and stability of quinones under a given environmental setting. The goal of this review is to examine the source, reactivity, and fate of potential quinone catalysts with respect to chemical interactions (e.g., with other quinones and nucleophiles) that will inevitably occur in complex environmental media. We will first discuss natural and anthropogenic sources of quinones in aqueous environments, and fundamental transformation pathways including cross reaction, autoxidation, and addition reactions. We will then assess how the described sources (molecular structure) and transformation pathways (stability) will impact the ability of a quinone molecule to catalyze a biogeochemical process. Thermodynamics and kinetics of electron transfer reactions with both the electron donor (e.g., hydrogen sulfide as a bulk reductant) and the terminal electron acceptor (e.g., nitroaromatic explosives in contaminant degradation), and stability towards irreversible side reactions are the key factors determining the geochemical conditions under which the catalysis by a quinone molecule will be operative. PMID:19665164

Uchimiya, Minori; Stone, Alan T

2009-10-01

196

Salt Marsh Sediment Biogeochemical Response to the BP Blowout.  

PubMed

The impact of the blowout on salt marshes was investigated by observing the biogeochemistry in salt marsh sediments along the Gulf Coast. High sulfide levels due to hydrocarbon loading, increased microbial activity, and microbial community shifts can lead to plant browning and mortality. Sediment biogeochemical processes that degrade enriched carbon pools through sulfate reduction are primarily responsible for the biodegradation of spilled hydrocarbons. An assessment of the impact of contamination on salt marshes at Skiff Island, LA, and Cat Island, Marsh Point, and Saltpan Island, MS, was achieved through sediment electrode profiling, microbial community profiling, and quantification of hydrocarbon contamination, which captured the spatial sedimentary biogeochemical response that affects salt marsh productivity. At western locations (Skiff and Cat Islands), total petroleum hydrocarbons (TPHs) ranged from 2183 to 2996 mg kg, which was more than double the TPH concentration observed at eastern locales. At eastern study locations (e.g., Marsh Point), sedimentary pore-water HS concentrations were higher (maximum value = 231 mg L) and detected further up in the sediment column than at western locales (e.g., Skiff Island). Similarly, anaerobic and aerobic microbial activity, as measured by C substrate utilization profiles and well-color development, was as high or higher at eastern locations as compared with western locations. These results indicate that other factors besides location or degree of contamination, perhaps sedimentary dynamics and physical processes specific to each marsh, should be considered when determining salt marsh response to hydrocarbon contamination. PMID:25603266

Mills, Calista G; McNeal, Karen S

2014-09-01

197

Global changes in biogeochemical cycles in response to human activities  

NASA Technical Reports Server (NTRS)

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

Moore, Berrien, III; Melillo, Jerry

1994-01-01

198

Hydro-biogeochemical Controls on Geophysical Signatures (Invited)  

NASA Astrophysics Data System (ADS)

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

Atekwana, E. A.

2013-12-01

199

BIOGEOCHEMICAL GRADIENTS AS A FRAMEWORK FOR UNDERSTANDING WASTE SITE EVOLUTION  

SciTech Connect

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

Denham, M; Karen Vangelas, K

2008-10-17

200

Subsurface Biogeochemical Research FY11 Second Quarter Performance Measure  

SciTech Connect

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

Scheibe, Timothy D.

2011-03-31

201

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

Microsoft Academic Search

This review summarizes biogeochemical processes that operate on diel, or 24-h, time scales in streams and the changes in aqueous chemistry that are associated with these processes. Some biogeochemical processes, such as those producing diel cycles of dissolved O2 and pH, were the first to be studied, whereas processes producing diel concentration cycles of a broader spectrum of chemical species

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

2011-01-01

202

Biogeochemical evolution of cryoconite holes on Canada Glacier, Taylor Valley, Antarctica  

E-print Network

Biogeochemical evolution of cryoconite holes on Canada Glacier, Taylor Valley, Antarctica Elizabeth 2007. [1] The cryoconite holes of the McMurdo Dry Valleys are simple, closed biogeochemical systems involving water, ice, mineral and organic debris, which serve as ecosystems for consortia of microorganisms

Fountain, Andrew G.

203

Afforestation alters the composition of functional genes in soil and biogeochemical processes in South American grasslands  

Microsoft Academic Search

Soil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacent Eucalyptus plantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial

Sean T. Berthrong; Christopher Warren Schadt; Gervasio Pineiro; Robert B. Jackson

2009-01-01

204

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

Microsoft Academic Search

This study aims to investigate the control of arsenic distribution by biogeochemical processes in the Indian Sundarban mangrove ecosystem and the importance of this ecosystem as an arsenic source for surrounding coastal water. The As(V)\\/As(III) ratio was found to be significantly lower in both surface and pore waters compared to sea water, which could be attributed to biogeochemical interconversion of

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

2009-01-01

205

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

EPA Science Inventory

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

206

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

SciTech Connect

In the past three centuries, human perturbations of the environment have affected the biogeochemical behavior of the global carbon cycle and that of the other three nutrient elements closely coupled to carbon: nitrogen, phosphorus, and sulfur. The partitioning of anthropogenic CO{sub 2} among its various sinks in the past, for the present, and for projections into the near future is controlled by the interactions of these four elemental cycles within the major environmental domains of the land, atmosphere, coastal oceanic zone, and open ocean. The authors analyze the past, present, and future behavior of the global carbon cycle using the Terrestrial-Ocean-aTmosphere Ecosystem Model (TOTEM), a unique process-based model of the four global coupled biogeochemical cycles of carbon, nitrogen, phosphorus, and sulfur. They find that during the past 300 yrs, anthropogenic CO{sub 2} was mainly stored in the atmosphere and in the open ocean. Human activities on land caused an enhanced loss of mass from the terrestrial organic matter reservoirs (phytomass and humus) mainly through deforestation and consequently increased humus remineralization, erosion, and transport to the coastal margins by rivers and runoff. Photosynthetic uptake by the terrestrial phytomass was enhanced owing to fertilization by increasing atmospheric CO{sub 2} concentrations and supported by nutrients remineralized from organic matter. TOTEM results indicate that through most of the past 300 yrs, the loss of C from deforestation and other land-use activities was greater than the gain from the enhanced photosynthetic uptake. Since pre-industrial time (since 1700), the net flux of CO{sub 2} from the coastal waters has decreased by 40%, from 0.20 Gt C/yr to 0.12 Gt C/yr. TOTEM analyses of atmospheric CO{sub 2} concentrations for the 21st century were based on the fossil-fuel emission projections of IPCC (business as usual scenario) and of the more restrictive UN 1997 Kyoto Protocol. By the mid-21st century, the projected atmospheric CO{sub 2} concentrations range from about 550 ppmv (TOTEM, based on IPCC projected emissions) to 510 ppmv (IPCC projection) and to 460 ppmv (TOTEM, based on the Kyoto Protocol reduced emissions).

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

1999-07-01

207

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

SciTech Connect

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

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

2011-11-01

208

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

Technology Transfer Automated Retrieval System (TEKTRAN)

The General Ensemble Biogeochemical Modeling System (GEMS) was developed for a proper integration of well-established ecosystem biogeochemical models with various spatial databases to simulate biogeochemical cycles over large areas. Major driving variables include land cover and land use, climate, s...

209

Linking soil and sediment properties for research on biogeochemical cycles  

NASA Astrophysics Data System (ADS)

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

Kuhn, Nikolaus J.

2013-04-01

210

Andreae is New Editor of Global Biogeochemical Cycles  

NASA Astrophysics Data System (ADS)

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

Andreae, Meinrat O.

2004-10-01

211

Reconstructing disturbances and their biogeochemical consequences over multiple timescales  

USGS Publications Warehouse

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

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

2014-01-01

212

A GIS approach to conducting biogeochemical research in wetlands  

NASA Technical Reports Server (NTRS)

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

Brannon, David P.; Irish, Gary J.

1985-01-01

213

Applications of synchrotron techniques in biogeochemical and geomicrobiological research  

NASA Astrophysics Data System (ADS)

Synchrotron methods are useful for examining the chemistry, speciation and distribution of elements such as Fe and Mn within environmental samples. Techniques such as x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and x-ray fluorescence (XRF) are routinely used at synchrotrons worldwide, by both academic and industrial users. It can be a challenge for potential users to identify where these methods will be useful to them. Here, I will present an overview of techniques available for geomicrobiologists at the Canadian Light Source (CLS). I will provide examples of the use of synchrotron tools in geomicrobiological projects, as well as examples of where CLS scientists have worked with mining companies to use these tools to address challenges in the mining industry. An overview of the CLS Green Mining Program will also be provided; our research group is conducting biogeochemical research that contributes to developing sustainable mining practices.

McBeth, J. M.

2013-12-01

214

Biogeochemical consequences of an oxygenated intrusion into an anoxic fjord  

PubMed Central

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

2014-01-01

215

Biogeochemical evolution of a landfill leachate plume, Norman, Oklahoma  

USGS Publications Warehouse

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

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

2011-01-01

216

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

PubMed

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

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

2011-01-01

217

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

218

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

219

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

PubMed Central

The availability of micronutrients is a key factor that affects primary productivity in High Nutrient Low Chlorophyll (HNLC) regions of the Southern Ocean. Nutrient supply is governed by a range of physical, chemical and biological processes, and there are significant feedbacks within the ecosystem. It has been suggested that baleen whales form a crucial part of biogeochemical cycling processes through the consumption of nutrient-rich krill and subsequent defecation, but data on their contribution are scarce. We analysed the concentration of iron, cadmium, manganese, cobalt, copper, zinc, phosphorus and carbon in baleen whale faeces and muscle, and krill tissue using inductively coupled plasma mass spectrometry. Metal concentrations in krill tissue were between 20 thousand and 4.8 million times higher than typical Southern Ocean HNLC seawater concentrations, while whale faecal matter was between 276 thousand and 10 million times higher. These findings suggest that krill act as a mechanism for concentrating and retaining elements in the surface layer, which are subsequently released back into the ocean, once eaten by whales, through defecation. Trace metal to carbon ratios were also higher in whale faeces compared to whale muscle indicating that whales are concentrating carbon and actively defecating trace elements. Consequently, recovery of the great whales may facilitate the recycling of nutrients via defecation, which may affect productivity in HNLC areas. PMID:25469984

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

2014-01-01

220

Biogeochemical implications of comparative growth rates of Emiliania huxleyi and Coccolithus species  

NASA Astrophysics Data System (ADS)

Coccolithophores are a diverse and biogeochemically important group of phytoplankton in terms of the production and export of calcite, yet the comparative physiology and ecology of species other than the ubiquitous Emiliania huxleyi is poorly understood. Despite assumptions that Emiliania huxleyi is a fast growing species, we found it had comparable growth rates (0.16-0.85 d-1) with strains of Coccolithus pelagicus and Coccolithus braarudii when grown under identical temperature and light conditions. A recently isolated Arctic strain of C. pelagicus (RCC4092) exhibited only a 12% slower growth rate, on average, than a recently isolated Arctic strain of E. huxleyi (RCC3533), over a temperature range of 6-12 °C. Established temperate strains of E. huxleyi and C. braarudii (RCC1228 and RCC1198) exhibited a slightly larger difference in growth rates, with E. huxleyi growing 28% faster on average than C. braarudii over a temperature range of 12-19 °C. Coupled with the 30-80 times higher cellular calcite content of C. pelagicus and C. braarudii compared to E. huxleyi, this suggests that Coccolithus species could be major calcite producers in mixed populations. The relative abundance of coccolithophore species is key for determining which species will dominate calcite production in mixed communities growing at similar rates. Field samples from the North Atlantic show that C. pelagicus is in a high enough relative abundance in 69% of samples collected in the spring and summer of 2010 to be a larger source of calcite production than E. huxleyi.

Daniels, C. J.; Sheward, R. M.; Poulton, A. J.

2014-07-01

221

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

PubMed

The availability of micronutrients is a key factor that affects primary productivity in High Nutrient Low Chlorophyll (HNLC) regions of the Southern Ocean. Nutrient supply is governed by a range of physical, chemical and biological processes, and there are significant feedbacks within the ecosystem. It has been suggested that baleen whales form a crucial part of biogeochemical cycling processes through the consumption of nutrient-rich krill and subsequent defecation, but data on their contribution are scarce. We analysed the concentration of iron, cadmium, manganese, cobalt, copper, zinc, phosphorus and carbon in baleen whale faeces and muscle, and krill tissue using inductively coupled plasma mass spectrometry. Metal concentrations in krill tissue were between 20 thousand and 4.8 million times higher than typical Southern Ocean HNLC seawater concentrations, while whale faecal matter was between 276 thousand and 10 million times higher. These findings suggest that krill act as a mechanism for concentrating and retaining elements in the surface layer, which are subsequently released back into the ocean, once eaten by whales, through defecation. Trace metal to carbon ratios were also higher in whale faeces compared to whale muscle indicating that whales are concentrating carbon and actively defecating trace elements. Consequently, recovery of the great whales may facilitate the recycling of nutrients via defecation, which may affect productivity in HNLC areas. PMID:25469984

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

2014-01-01

222

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

223

Mechanistic site-based emulation of a global ocean biogeochemical model for parametric analysis and calibration  

NASA Astrophysics Data System (ADS)

Biogeochemical ocean circulation models used to investigate the role of plankton ecosystems in global change rely on adjustable parameters to compensate for missing biological complexity. In principle, optimal parameter values can be estimated by fitting models to observational data, including satellite ocean colour products such as chlorophyll that achieve good spatial and temporal coverage of the surface ocean. However, comprehensive parametric analyses require large ensemble experiments that are computationally infeasible with global 3-D simulations. Site-based simulations provide an efficient alternative but can only be used to make reliable inferences about global model performance if robust quantitative descriptions of their relationships with the corresponding 3-D simulations can be established. The feasibility of establishing such a relationship is investigated for an intermediate complexity biogeochemistry model (MEDUSA) coupled with a widely-used global ocean model (NEMO). A site-based mechanistic emulator is constructed for surface chlorophyll output from this target model as a function of model parameters. The emulator comprises an array of 1-D simulators and a statistical quantification of the uncertainty in their predictions. The unknown parameter-dependent biogeochemical environment, in terms of initial tracer concentrations and lateral flux information required by the simulators, is a significant source of uncertainty. It is approximated by a mean environment derived from a small ensemble of 3-D simulations representing variability of the target model behaviour over the parameter space of interest. The performance of two alternative uncertainty quantification schemes is examined: a direct method based on comparisons between simulator output and a sample of known target model "truths" and an indirect method that is only partially reliant on knowledge of target model output. In general, chlorophyll records at a representative array of oceanic sites are well reproduced. The use of lateral flux information reduces the 1-D simulator error considerably, consistent with a major influence of advection at some sites. Emulator robustness is assessed by comparing actual error distributions with those predicted. With the direct uncertainty quantification scheme, the emulator is reasonably robust over all sites. The indirect uncertainty quantification scheme is less reliable at some sites but scope for improving its performance is identified. The results demonstrate the strong potential of the emulation approach to improve the effectiveness of site-based methods. This represents important progress towards establishing a robust site-based capability that will allow comprehensive parametric analyses to be achieved for improving global models and quantifying uncertainty in their predictions.

Hemmings, J. C. P.; Challenor, P. G.; Yool, A.

2014-09-01

224

A model of biogeochemical cycles of carbon, nitrogen and phosphorus including symbiotic nitrogen fixation and phosphatase production.  

NASA Astrophysics Data System (ADS)

Global climate models have not yet considered the effects of nutrient cycles and limitation when forecasting carbon uptake by the terrestrial biosphere into the future. Using the principle of resource optimization, we here develop a new theory by which C, N and P cycles interact. Our model is able to replicate the observed responses of net primary production to nutrient additions in N-limited, N and P co-limited, and P-limited environments. Our framework identifies a new pathway by which N2 fixers can alter P availability: by investing in N-rich phosphorus liberation enzymes (phosphatases), fixers can greatly accelerate soil P availability and its cycling rates. This is critical for the successive invasion and establishment of N2 fixers into an N limited environment. We conclude that our model can be used to examine nutrient limitation broadly, and thus offers promise for coupling the biogeochemical system of C, N, and P to broader climate-system models.

Wang, Y.; Houlton, B.; Field, C. B.

2006-12-01

225

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

NASA Astrophysics Data System (ADS)

On April 20, 2010, the drilling rig Deepwater Horizon exploded in the Gulf of Mexico, resulting in the release of approximately 5 million barrels of crude oil into the environment. Oil and its associated trace metals have been demonstrated to have a detrimental effect on coastal wetland ecosystems. Wetlands are particularly susceptible to oil contamination because they are composed largely of fine-grained sediments, which have a high capacity to adsorb organic matter and metals. The biogeochemical cycling of trace metals can be strongly influenced by microbial activity, specifically those of sulfate- and iron-reducing bacteria. Microbial activity may be enhanced by an increase in amounts of organic matter such as oil. This research incorporates an assessment of levels of trace metals and associated biogeochemical changes from ten coastal marshes in Alabama, Mississippi, and Louisiana. These sampling sites range in their pollution levels from pristine to highly contaminated. A total digestion analysis of wetland sediments shows higher concentrations of certain trace metals (e.g., Ni, Cu, Pb, Zn, Sr, Co, V, Ba, Hg, As) in heavily-oiled areas compared to less-affected and pristine sites. Due to chemical complexation among organic compounds and metals, crude oils often contain elevated levels (up to hundreds of mg/kg) of trace metals At the heavily-oiled Louisiana sites (e.g., Bay Jimmy, Bayou Dulac, Bay Batiste), elevated levels of metals and total organic carbon have been found in sediments down to depths of 30 cm. Clearly the contamination is not limited to shallow sediments and oil, along with various associated metals, may be invading into deeper (pre-industrial) portions of the marsh sediments. Pore-waters extracted from contaminated sediments are characterized by very high levels of reduced sulfur (up to 80 mg/kg), in contrast to fairly low ferrous iron concentrations (<0.02 mg/kg). The influx of oil into the wetlands might provide the initial substrate and carbon source for stimulating sulfate-reducing bacteria. The high sulfur levels, coupled with the low levels of iron, indicate that iron-reducing bacteria are outcompeted by sulfate reducers in oiled salt marshes. Moreover, pore-water pH values show a general increasing trend (ranging from 6.6 to 8.0) with depth, possibly reflecting the combined effects of bacterial sulfate reduction and saltwater intrusion at depth. Despite high levels of trace metals in bulk sediments, concentrations of trace metals dissolved in pore-waters are generally low. It is very likely that high organic matter content and bacterially-mediated sulfate reduction promote metal retention through the formation of sulfide solids. Framboidal pyrites, as well as other sulfides, have been identified, and are currently undergoing XRD, SEM, and EDAX analyses. Continued research is needed to monitor possible re-mobilization of trace metals in changing redox and biogeochemical conditions.

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

2011-12-01

226

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

NASA Astrophysics Data System (ADS)

A new biogeochemical model has been developed and coupled to a three-dimensional physical model in the Pacific Ocean. With the explicitly represented dissolved organic pools, this new model is able to link key biogeochemical processes with optical processes. Model validation against satellite and in situ data indicates the model is robust in reproducing general biogeochemical and optical features. Colored dissolved organic matter (CDOM) has been suggested to play an important role in regulating underwater light field. With the coupled model, physical and biological regulations of CDOM in the euphotic zone are analyzed. Model results indicate seasonal variability of CDOM is mostly determined by biological processes, while the importance of physical regulation manifests in the annual mean terms. Without CDOM attenuating light, modeled depth-integrated primary production is about 10% higher than the control run when averaged over the entire basin, while this discrepancy is highly variable in space with magnitudes reaching higher than 100% in some locations. With CDOM dynamics integrated in physical-biological interactions, a new mechanism by which physical processes affect biological processes is suggested, namely, physical transport of CDOM changes water optical properties, which can further modify underwater light field and subsequently affect the distribution of phytoplankton chlorophyll. This mechanism tends to occur in the entire Pacific basin but with strong spatial variability, implying the importance of including optical processes in the coupled physical-biogeochemical model. If ammonium uptake is sufficient to permit utilization of DOM, that is, UB??-U{U}/{U}-{(1-r_b)}/{RB}, then bacteria uptake of DOM has the form of FB=(1-r_b){U}/{RB}, bacteria respiration, SB=r_b×U, remineralization by bacteria, EB=UC{UN}/{UC}-{(1-r_b)}/{RB}. If EB > 0, then UB = 0; otherwise, UB = -EB. If there is insufficient ammonium, that is, UB?<-U{U}/{U}-{(1-r_b)}/{RB}, then bacteria uptake of ammonia is obtained by, UB=UB?, bacteria uptake of DOM, FB=U+UB, bacteria respiration, SB=RBFB{r_b}/{1-r_b}, remineralization by bacteria, EB=-UB. CDOM photolysis (Bissett et al., 1999a): UVLDOC=a(410)×RtUVLDOC×{PAR(0)}/{410}×exp?z0Kd(300)dz, UVSDOC=a(410)×RtUVSDOC×{PAR(0)}/{410}×exp?z0Kd(300)dz, UVLDIC=a(410)×RtUVLDIC×{PAR(0)}/{410}×exp?z0Kd(300)dz, UVSDIC=a(410)×RtUVSDIC×{PAR(0)}/{410}×exp?z0Kd(300)dz, a(410)=acdoc?×CLDOC, a(410)=acdoc?×CSDOC, Kd(300)=[a(410)+a(410)]×exp[0.0145×(410-300)]+0.154. The dissolution rate for biogenic silica (Jiang et al., 2003): D=(0.19T/25+0.01)×exp(0.069(T-25)). The air-sea flux of CO2 is calculated using the transfer velocity-wind speed relationships from Wanninkhof (1992): air-sea CO flux=0.31U2(660S{()sea-()air}, where U is the wind speed at sea surface and Sc is the Schmidt number for CO2 that can be calculated as: Sc=2073.1-125.62T+3.6276T2-0.043219T3, S is the solubility of CO2 and (pCO2)air is the partial pressure of CO2 in the air. In the model, we set a spatially uniform distribution of (pCO2)air observed at the Mauna Loa Observatory (Keeling et al., 1976).Dissolved oxygen (DO) is modeled using constant oxygen-to-nitrate and oxygen-to-ammonium ratios. At the surface, air-sea exchange of O2 is calculated as: O flux=0.31U2(660(DOsat-DO), where DOsat is the saturation concentration of DO calculated from temperature and salinity. So2 is the Schmidt number for O2 that can be calculated as follows: So2=1638.0-81.83T+1.483T2-0.008004T3.

Xiu, Peng; Chai, Fei

2014-03-01

227

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

NASA Astrophysics Data System (ADS)

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

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

2008-03-01

228

COUPLED REACTIVE TRANSPORT MODELING BASED ON THE NEW BIOGEOCHEMICAL CODE HP1  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

229

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....

230

Long-term controls on ocean phosphorus and oxygen in a global biogeochemical model  

Microsoft Academic Search

Sedimentary phosphorus dynamics are included in a global biogeochemical modelIncreases in phosphorus river inputs promote the expansion of ocean suboxiaPreferential P regeneration enhances the expansion of ocean suboxia

V. Palastanga; C. P. Slomp; C. Heinze

2011-01-01

231

An Investigation of Linked Physical And Biogeochemical Processes In Heterogeneous Soils In The Vadose Zone  

E-print Network

column, enhanced biogeochemical cycling was observed over the texturally homogeneous soil columns. Enumerations of Fe(III) and SO42- reducing microorganisms also show 1-2 orders of magnitude greater community numbers in the layered column. The greatest...

Hansen, David Joseph

2012-10-19

232

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...

233

CALIBRATION OF SUBSURFACE BATCH AND REACTIVE-TRANSPORT MODELS INVOLVING COMPLEX BIOGEOCHEMICAL PROCESSES  

EPA Science Inventory

In this study, the calibration of subsurface batch and reactive-transport models involving complex biogeochemical processes was systematically evaluated. Two hypothetical nitrate biodegradation scenarios were developed and simulated in numerical experiments to evaluate the perfor...

234

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

EPA Science Inventory

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

235

Global Biogeochemical Implications of Mercury Discharges from Rivers and Sediment Burial  

E-print Network

, Massachusetts 02138, United States § Department of Environmental Sciences, Jozef Stefan Institute, 1000, Massachusetts 02139, United States U.S. Geological Survey, Middleton, Wisconsin 53562, United StatesGlobal Biogeochemical Implications of Mercury Discharges from Rivers and Sediment Burial Helen M

Jacob, Daniel J.

236

Spatial heterogeneity in biogeochemical transport on Arctic hill slopes  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

237

BRIE: The Penn State Biogeochemical Research Initiative for Education  

NASA Astrophysics Data System (ADS)

Few scientists are prepared to address the interdisciplinary challenges of biogeochemical research due to disciplinary differences in vocabulary, technique, and scientific paradigm. Thus scientists and engineers trained in traditional disciplines bring a restricted view to the study of environmental systems, which can limit their ability to exploit new techniques and opportunities for scientific advancement. Although the literature is effusive with enthusiasm for interdisciplinary approaches to biogeochemistry, there remains the basic difficulty of cross-training geological and biological scientists. The NSF-IGERT funded Biogeochemical Research Initiative for Education (BRIE) program at Penn State is specifically designed to break down both disciplinary and institutional barriers and it has fostered cross-disciplinary collaboration and training since 1999. Students and faculty are drawn from environmental engineering, geochemistry, soil science, chemistry and microbiology, and the program is regarded on the Penn State campus as a successful example of how interdisciplinary science can best be promoted. There are currently 23 Ph.D. students funded by the program, with an additional 7 affiliated students. At present, a total of 6 students have completed doctoral degrees, and they have done so within normal timeframes. The program is "discipline-plus," whereby students enroll in traditional disciplinary degree programs, and undertake broad training via 12 credits of graduate coursework in other departments. Students are co-advised by faculty from different disciplines, and engage in interdisciplinary research facilitated by research "credit cards." Funding is available for international research experiences, travel to meetings, and other opportunities for professional development. Students help institutionalize interdisciplinary training by designing and conducting a teaching module that shares their expertise with a class in another department or discipline. Community building through social activities and scientific forums is a priority in both the undergraduate and graduate programs. In addition, entering Ph.D. students build cohort identity by taking a course that introduces them to BRIE faculty and research facilities through hands-on laboratory and field-based research activities. The BRIE undergraduate summer internship program has provided interdisciplinary research opportunities for a total of 35 students over the past five summers. This program aims to recruit students to the Ph.D. program, and at present, two Ph.D. students have entered this way. Our efforts have focused on attracting students from under-represented groups. Diversity in this program has been above national norms: and summer students have include 10 (29 %) African-American or Hispanic-American students, and 25 (over 70 %) females. The Ph.D. students and graduates are 50% female, with three students from minority populations.

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

2003-12-01

238

Suspended Particles: Their Role in Estuarine Biogeochemical Cycles  

NASA Astrophysics Data System (ADS)

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

Turner, A.; Millward, G. E.

2002-12-01

239

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

240

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

USGS Publications Warehouse

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.

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

2009-01-01

241

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

USGS Publications Warehouse

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

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

2011-01-01

242

Biogeochemical effects of seawater restoration to diked salt marshes  

USGS Publications Warehouse

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

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

1997-01-01

243

Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”?†  

PubMed Central

The genus of Marinobacter is one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content of Marinobacter aquaeolei VT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many “opportunitrophic” genetic characteristics and strategies that M. aquaeolei has adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential of M. aquaeolei and its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles. PMID:21335390

Singer, Esther; Webb, Eric A.; Nelson, William C.; Heidelberg, John F.; Ivanova, Natalia; Pati, Amrita; Edwards, Katrina J.

2011-01-01

244

Biogeochemical conditions determine virulence of black band disease in corals.  

PubMed

The microenvironmental dynamics of the microbial mat of black band disease (BBD) and its less virulent precursor, cyanobacterial patch (CP), were extensively profiled using microsensors under different light intensities with respect to O(2), pH and H(2)S. BBD mats exhibited vertical stratification into an upper phototrophic and lower anoxic and sulphidic zone. At the progression front of BBD lesions, high sulphide levels up to 4977??M were measured in darkness along with lower than ambient levels of pH (7.43±0.20). At the base of the coral-BBD microbial mat, conditions were hypoxic or anoxic depending on light intensity exposure. In contrast, CP mats did not exhibit strong microchemical stratification with mostly supersaturated oxygen conditions throughout the mats at all light intensities and with levels of pH generally higher than in BBD. Two of three replicate CP mats were devoid of sulphide, while the third replicate showed only low levels of sulphide (up to 42??M) present in darkness and at intermediate light levels. The level of oxygenation and sulphide correlated well with lesion migration rates, that is virulence of the mats, which were greater in BBD than in CP. The results suggest that biogeochemical microgradients of BBD shaped by the complex microbial community, rather than a defined pathogen, are the major trigger for high virulence and the associated derived coral mortality of this disease. PMID:22318304

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

2012-08-01

245

Biogeochemical conditions determine virulence of black band disease in corals  

PubMed Central

The microenvironmental dynamics of the microbial mat of black band disease (BBD) and its less virulent precursor, cyanobacterial patch (CP), were extensively profiled using microsensors under different light intensities with respect to O2, pH and H2S. BBD mats exhibited vertical stratification into an upper phototrophic and lower anoxic and sulphidic zone. At the progression front of BBD lesions, high sulphide levels up to 4977??M were measured in darkness along with lower than ambient levels of pH (7.43±0.20). At the base of the coral–BBD microbial mat, conditions were hypoxic or anoxic depending on light intensity exposure. In contrast, CP mats did not exhibit strong microchemical stratification with mostly supersaturated oxygen conditions throughout the mats at all light intensities and with levels of pH generally higher than in BBD. Two of three replicate CP mats were devoid of sulphide, while the third replicate showed only low levels of sulphide (up to 42??M) present in darkness and at intermediate light levels. The level of oxygenation and sulphide correlated well with lesion migration rates, that is virulence of the mats, which were greater in BBD than in CP. The results suggest that biogeochemical microgradients of BBD shaped by the complex microbial community, rather than a defined pathogen, are the major trigger for high virulence and the associated derived coral mortality of this disease. PMID:22318304

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

2012-01-01

246

Feedbacks between hydrological heterogeneity and bioremediation induced biogeochemical transformations  

SciTech Connect

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

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

2009-04-15

247

Seasonal pelagic biogeochemical processes in a scottish fjordic system  

NASA Astrophysics Data System (ADS)

Seasonal changes in the concentrations of heterotrophic and autotrophic biomass, nutrients, dissolved oxygen and particulate organic matter were examined within the water column at 3 locations in the Firth of Clyde, a fjordic environment off the west coast of Scotland. One site was located in the inner part of the fjord, directly influenced by freshwater inputs from the River Clyde. The second site was well representative of the main basin of the fjord. The third site was located at the entrance of the fjord. This fjord was one of the 6 sites studied as part of the current OAERRE EU FP5 research programme. The main objective of this project was to understand the physical, biogeochemical and biological processes, and their interactions, that contribute to the eutrophication of coastal marine regions of restricted exchange. The spatial and temporal variability of the studied parameters and their interactions are discussed in relation to the main hydrodynamic characteristics and microbial activity (photosynthetic, bacterial and respiration activity) within the fjord. Overall, the study seeks to identify the main environmental factors triggering changes in the balance between the heterotrophic and autotrophic components of the pelagic system. This is an essential step to predict the consequences and fate of anthropogenic inputs within a coastal system of restricted exchange.

Fouilland, E.; Jones, K.; Leakey, R.; Slater, J.; Brand, T.; Cunningham, A.

2003-04-01

248

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

249

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

250

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

PubMed Central

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

Taillefert, Martial; Neuhuber, Stephanie; Bristow, Gwendolyn

2007-01-01

251

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

252

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

NASA Astrophysics Data System (ADS)

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

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

2008-12-01

253

Biogeochemical Modeling of the Second Rise of Oxygen  

NASA Astrophysics Data System (ADS)

The rise of atmospheric oxygen set the tempo for the evolution of complex life on Earth. Oxygen levels are thought to have increased in two broad steps: one step occurred in the Archean ~ 2.45 Ga (the Great Oxidation Event or GOE), and another step occured in the Neoproterozoic ~750-580 Ma (the Neoprotoerozoic Oxygenation Event or NOE). During the NOE, oxygen levels increased from ~1-10% of the present atmospheric level (PAL) (Holland, 2006), to ~15% PAL in the late Neoproterozoic, to ~100% PAL later in the Phanerozoic. Complex life requires O2, so this transition allowed complex life to evolve. We seek to understand what caused the NOE. To explore causes for the NOE, we build upon the biogeochemical model of Claire et al. (2006), which calculates the redox evolution of the atmosphere, ocean, biosphere, and crust in the Archean through to the early Proterozoic. In this model, the balance between oxygenconsuming and oyxgen-producing fluxes evolves over time such that at ~2.4 Ga, the rapidly acting sources of oxygen outweigh the rapidly-acting sinks. Or, in other words, at ~2.4 Ga, the flux of oxygen from organic carbon burial exceeds the sinks of oxygen from reaction with reduced volcanic and metamoprphic gases. The model is able to drive oxygen levels to 1-10% PAL in the Proterozoic; however, the evolving redox fluxes in the model cannot explain how oxygen levels pushed above 1-10% in the late Proterozoic. The authors suggest that perhaps another buffer, such as sulfur, is needed to describe Proterozoic and Phanerozoic redox evolution. Geologic proxies show that in the Proterozoic, up to 10% of the deep ocean may have been sulfidic. With this ocean chemistry, the global sulfur cycle would have worked differently than it does today. Because the sulfur and oxygen cycles interact, the oxygen concentration could have permanently changed due to an evolving sulfur cycle (in combination with evolving redox fluxes associated with other parts of the oxygen cycle and carbon cycles). To determine how fluxes of sulfur, carbon, and oxygen define oxygen levels before, during, and after the NOE, we add a sulfur cycle to the biogeochemical model of Claire et al. (2006). Understanding processes that impact the evolution of atmospheric oxygen on Earth is key to diagnosing the habitability of other planets because it is possible that other planets undergo a similar evolution. If a sulfidic deep ocean was instrumental in driving oxygen levels to modern values, then it would be valuable to remotely detect a sulfide-rich ocean on another planet. One such remotely-detectable signature could be the color of a sulfide-rich ocean. For example, Gallardo and Espinoza (2008) have hypothesized that a sulfidic ocean may be have been blacker in color. Even if a sulfidic ocean is not key to oxygenation, detecting a planet in transition--that is, a planet with intermediate levels of oxygen co-existing with higher levels of reduced gases - would be important for diagnosing habitability.

Smith, M. L.; Catling, D.; Claire, M.; Zahnle, K.

2014-03-01

254

Subglacial (bio)geochemical weathering and the unexplored Antarctic system  

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

255

Biogeochemical characterisation of a coal tar distillate plume.  

PubMed

The distillation of acidified coal tars for up to 50 years has given rise to a phenol plume approximately 500 m long, 50 m deep and containing up to 15 g l(-1) dissolved organic carbon (DOC) in the Triassic Sandstones aquifer. A conceptual biogeochemical model based on chemical and microbiological analysis of groundwater samples has been developed as a preliminary to more detailed studies of the controls on natural attenuation. While the development of redox zones and the production of methane and carbon dioxide provide evidence of natural attenuation, it appears that degradation is slow. The existence of sulphate in the plume indicates that this electron acceptor has not been depleted and that consequently methanogenesis is probably limited. Based on a simple estimate of sulphate input concentration, a half-life of about 15 years has been estimated for sulphate reduction. Geochemical modelling predicts that increased alkalinity within the plume has not led to carbonate precipitation, and thus within the limits of accuracy of the measurement, alkalinity may reflect the degree of biodegradation. This implies a loss of around 18% of the DOC over a 30-year period. Despite limited degradation, microbial studies show that there are diverse microbial communities in the aquifer with the potential for both anaerobic and aerobic biodegradation. Microbial activity was found to be greatest at the leading edge of the plume where DOC concentrations are 60 mg l(-1) or less, but activity could still be observed in more contaminated samples even though cells could not be cultured. The study suggests that degradation may be limited by the high phenol concentrations within the core of the plume, but that once diluted by dispersion, natural attenuation may proceed. More detailed studies to confirm these initial findings are identified and form the basis of associated papers. PMID:11820470

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

2001-12-15

256

Constraining Ocean Biogeochemical Models with Dissolved Iron Observations  

NASA Astrophysics Data System (ADS)

Iron is a limiting factor to biological activity in some ocean regions and plays a vital role in oceanic biogeochemistry. We analyze a global database of dissolved iron measurements to better understand marine iron cycling and its relation to atmospheric and continental sources. The observational data are heavily weighted towards the upper ocean, with 68% from the upper 103m and 88% from the upper 502m, and towards the Northern Hemisphere (75%). In the deep ocean iron is clustered together within a relatively narrow range (0.2-1.0 nM) when margin-influenced data are excluded. In the upper ocean (< 500m) iron concentrations are much more variable, but generally low (< 0.4 nM) except in the high dust input regions of the North Atlantic and North Indian oceans. The lowest concentrations are seen in the Southern Ocean and the Equatorial Pacific. Observed iron distributions are correlated with atmospheric dust deposition in a non- linear fashion reflecting variable particle scavenging and biological uptake. We compare the dissolved iron observations with output from a Biogeochemical Elemental Cycling (BEC) ocean model. Scavenging of iron by particles is parameterized as a function of particle concentration and ambient dissolved iron concentrations. The model output was in general agreement with the field data (r = 0.77, for 103-502 m depths). At lower iron concentrations (< 0.3 nM) the model was biased high relative to observations. Future work will focus on improving the BEC iron cycling parameterizations utilizing the observational database.

Braucher, L.; Moore, J. K.

2006-12-01

257

Biogeochemical controls on hexavalent chromium formation in estuarine sediments.  

PubMed

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

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

2013-08-01

258

Microbial Reduction of Ferrous Arsenate: Biogeochemical Implications for Arsenic Mobilization  

SciTech Connect

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

Babechuk, M.; Weisener, C.G.; Fryer, B.; Paktunc, D.; Maunders, C.; (Windsor); (CCM); (McMaster U.)

2010-11-12

259

Biogeochemical indicators of elevated nitrogen deposition in semiarid Mediterranean ecosystems.  

PubMed

Nitrogen (N) deposition has doubled the natural N inputs received by ecosystems through biological N fixation and is currently a global problem that is affecting the Mediterranean regions. We evaluated the existing relationships between increased atmospheric N deposition and biogeochemical indicators related to soil chemical factors and cryptogam species across semiarid central, southern, and eastern Spain. The cryptogam species studied were the biocrust-forming species Pleurochaete squarrosa (moss) and Cladonia foliacea (lichen). Sampling sites were chosen in Quercus coccifera (kermes oak) shrublands and Pinus halepensis (Aleppo pine) forests to cover a range of inorganic N deposition representative of the levels found in the Iberian Peninsula (between 4.4 and 8.1 kg N ha(-1) year(-1)). We extended the ambient N deposition gradient by including experimental plots to which N had been added for 3 years at rates of 10, 20, and 50 kg N ha(-1) year(-1). Overall, N deposition (extant plus simulated) increased soil inorganic N availability and caused soil acidification. Nitrogen deposition increased phosphomonoesterase (PME) enzyme activity and PME/nitrate reductase (NR) ratio in both species, whereas the NR activity was reduced only in the moss. Responses of PME and NR activities were attributed to an induced N to phosphorus imbalance and to N saturation, respectively. When only considering the ambient N deposition, soil organic C and N contents were positively related to N deposition, a response driven by pine forests. The PME/NR ratios of the moss were better predictors of N deposition rates than PME or NR activities alone in shrublands, whereas no correlation between N deposition and the lichen physiology was observed. We conclude that integrative physiological measurements, such as PME/NR ratios, measured on sensitive species such as P. squarrosa, can provide useful data for national-scale biomonitoring programs, whereas soil acidification and soil C and N storage could be useful as additional corroborating ecosystem indicators of chronic N pollution. PMID:24894911

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

2014-09-01

260

Expanding the Role of Reactive Transport Modeling in Biogeochemical Sciences  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

261

Do microbial numbers count? Quantifying the regulation of biogeochemical fluxes by population size and cellular activity.  

PubMed

In order to enhance understanding of the interrelationships among community members and between them and their environment, the concept of regulation analysis is extended from biochemistry into microbial ecology. Ecological regulation analysis quantifies how biogeochemical fluxes are regulated by the microorganisms performing the process; the degree to which changes in fluxes are due to changes in population size and to changes in activity cell(-1) (cellular activity). Regulation analysis requires data on biogeochemical fluxes and the numbers of cells through which these fluxes run. Its application to five biogeochemical processes (aerobic methane oxidation, aerobic nitrite oxidation, methanogenesis, sulfate reduction and reductive dehalogenation) revealed that in general, but not always, flux was primarily regulated by cellular activity, i.e. by changes in the size and properties of the enzyme pool and in the concentrations of substrates and metabolites. Thus, it is often not sufficient to count the numbers of cells performing a particular step in a biogeochemical process in order to estimate its flux. Ecological regulation analysis can be extended to address which aspects of cellular activity require quantification in order to describe biogeochemical fluxes better. Its application is discussed in the context of the complexity of microbial communities (e.g. functional redundancy) and their functioning. PMID:17614962

Röling, Wilfred F M

2007-11-01

262

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

263

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

NASA Astrophysics Data System (ADS)

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

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

2003-12-01

264

Extracellular enzyme activity and biogeochemical cycling in restored prairies  

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

265

Biogeochemical features of aquatic plants in the Selenga River delta  

NASA Astrophysics Data System (ADS)

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

Shinkareva, Galina; Lychagin, Mikhail

2014-05-01

266

Biogeochemical controls on new production in the tropical Pacific  

NASA Astrophysics Data System (ADS)

Sources of variability in new production (NP) measured during nine cruises in the tropical Pacific Ocean are examined with respect to other biological and chemical properties. NP measured along the equator during the Zonal Flux and Flupac cruises using 15NO 3 incubation methods is presented in this paper and compared to similar data from seven previously published cruises to the tropical Pacific. The Zonal Flux cruise found a strong zonal gradient of increasing NP to the east that followed increasing nitrate inventories. NP values ranged from 0.8 and 3.8 mmol N m -2 d -1 from 165°E to 150°W, respectively. During the 7-day Flupac Time Series II at 150°W, NP measurements also showed strong variability, ranging from 1.9 to 3.6 mmol N m -2 d -1, despite relatively uniform nitrate. Both cruises observed a previously measured but seldom discussed trend for f-ratios to increase substantially at the limits of the euphotic zone (0.1% E0). Multiple linear regression (MLR) analyses of areal, depth-integrated data from 121 stations in the tropical Pacific previously have showed that variability in primary production (or chlorophyll), ammonium, nitrate and temperature together could "explain" 79% of the variability in NP (Aufdenkampe et al., Global Biogeochem. Cycles 15 (2001) 101). In the present study, the MLR method was extended to depth specific data, where the same variables were shown to explain 77% of nitrate uptake variability. MLR was then used to investigate differences between individual cruises in the relationships of NP to these variables. Similar to MLR results with combined data from all cruises, MLR of individual cruises also found primary production (or chlorophyll), ammonium and nitrate to be consistently the best variables to explain variability in areal NP, exhibiting R2 values from 0.45 to 0.92. However, nitrate is consistently a much stronger predictor of NP within cruises than between cruises. Other lines of evidence—including plots of each property vs. NP and vs. standard residuals of the all-cruise MLR, and differences in MLR partial slopes for individual cruises—together demonstrate that the relationship of NP to nitrate exhibits subtle but real differences from one cruise to the next. Zonal Flux and Flupac sampled the two extremes of this observed NP-to-nitrate variability.

Aufdenkampe, Anthony K.; McCarthy, James J.; Navarette, Claudie; Rodier, Martine; Dunne, John; Murray, James W.

267

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)

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.

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

268

Decadal variability in biogeochemical models: Comparison with a 50-year ocean colour dataset  

NASA Astrophysics Data System (ADS)

Assessing the skill of biogeochemical models to hindcast past variability is challenging, yet vital in order to assess their ability to predict biogeochemical change. However, the validation of decadal variability is limited by the sparsity of consistent, long-term biological datasets. The Phytoplankton Colour Index (PCI) product from the Continuous Plankton Recorder survey, which has been sampling the North Atlantic since 1948, is an example of such a dataset. Converting the PCI to chlorophyll values using SeaWiFS data allows a direct comparison with model output. Here we validate decadal variability in chlorophyll from the GFDL TOPAZ model. The model demonstrates skill at reproducing interannual variability, but cannot simulate the regime shifts evident in the PCI data. Comparison of the model output, data and climate indices highlights under-represented processes that it may be necessary to include in future biogeochemical models in order to accurately simulate decadal variability in ocean ecosystems.

Henson, Stephanie A.; Raitsos, Dionysios; Dunne, John P.; McQuatters-Gollop, Abigail

2009-11-01

269

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

PubMed

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

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

2014-12-01

270

An offline unstructured biogeochemical model (UBM) for complex estuarine and coastal environments  

SciTech Connect

Due to increased pollutant loads and water use from coastal development and population growth, occurrences of low-dissolved oxygen and "hypoxic zones" have increased. Reports of fish kills and water quality impairment are also becoming more frequent in many coastal waters. Water quality managers and regulatory agencies rely on numerical modeling tools to quantify the relative contributions of anthropogenic and "natural" pollutant loads (nutrients and biochemical oxygen demand) on dissolved oxygen levels and use the results for remedial activities and source control. The ability to conduct seasonlong simulations with sufficient nearshore resolution is therefore a key requirement. Mesh flexibility and the ability to increase site specific resolution without disturbing the larger domain setup and calibration are critical. The objective of this effort was to develop a robust biogeochemical model suitable for simulation of water quality dynamics including dissolved oxygen in complex coastal environments with multiple tidal channels, tidal flats, and density-driven circulation using unstructured-grid formulation. This paper presents an offline unstructured biogeochemical model that uses the Finite Volume Coastal Ocean Model (FVCOM) discretization of the study domain and the corresponding hydrodynamic solution to drive biogeochemical kinetics based on a water quality model CE-QUAL-ICM. In this paper, the linkage between selected hydrodynamic and water quality models is subjected to several scalar transport and biogeochemical module tests (plume transport and dilution, BOD/DO sag, and phytoplankton/nutrients reaction), and results are compared to their analytical solutions as part of model validation. A preliminary application of the biogeochemical model with a year-long simulation of Hood Canal basin in Puget Sound, USA, is presented as an example and a test of the tool in a real estuary setting. The model reproduced the dynamics and seasonal variations in the biogeochemical state variables and was used to test short-term wind-driven dynamics that could influence dissolved oxygen concentrations in Hood Canal.

Kim, Tae Yun; Khangaonkar, Tarang

2012-05-01

271

The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle.  

PubMed

Many iron (Fe) redox processes that were previously assumed to be purely abiotic, such as photochemical Fe reactions, are now known to also be microbially mediated. Owing to this overlap, discerning whether biotic or abiotic processes control Fe redox chemistry is a major challenge for geomicrobiologists and biogeochemists alike. Therefore, to understand the network of reactions within the biogeochemical Fe cycle, it is necessary to determine which abiotic or microbially mediated reactions are dominant under various environmental conditions. In this Review, we discuss the major microbially mediated and abiotic reactions in the biogeochemical Fe cycle and provide an integrated overview of biotic and chemically mediated redox transformations. PMID:25329406

Melton, Emily D; Swanner, Elizabeth D; Behrens, Sebastian; Schmidt, Caroline; Kappler, Andreas

2014-12-01

272

Biogeochemical Budgets in a Mediterranean Catchment with High Rates of Atmospheric N Deposition – Importance of Scale and Temporal Asynchrony  

Microsoft Academic Search

In this study biogeochemical export in a set of catchments that vary from 6 ha to almost 1500 ha is investigated. Studying catchments across this large range of scales enables us to investigate the scale dependence and fundamental processes controlling catchment biogeochemical export that would not have been possible with a more limited data set. The Devil Canyon catchment, in the San

Thomas Meixner; Mark Fenn

2004-01-01

273

GLOBAL BIOGEOCHEMICAL CYCLES, VOL. ???, XXXX, DOI:10.1029/, Global Dry Deposition of Nitrogen Dioxide and1  

E-print Network

GLOBAL BIOGEOCHEMICAL CYCLES, VOL. ???, XXXX, DOI:10.1029/, Global Dry Deposition of Nitrogen central roles in biogeochemical24 cycles. Nitrogen oxides (NOx=NO+NO2) and SO2 are emitted, annual dry deposition to land estimated from OMI as NO2 contributes12 1.5 ± 0.5 Tg of nitrogen and as SO2

Martin, Randall

274

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

275

Implied Nutrient Transport into the Southern Ocean in IPCC-AR4 Coupled Climate Models  

Microsoft Academic Search

The ventilation of Southern Ocean deep water regulates climate through carbon and heat uptake and transport, yet published Southern Ocean transport estimates from data differ widely. Simulations of the biogeochemical cycling of the Southern Ocean vary widely and are especially sensitive to the underlying physical circulation. We address this uncertainty by analyzing coupled climate model simulations of the late 20th

S. J. Everatt; P. J. Goodman; J. L. Russell

2010-01-01

276

Biogeochemical Redox Processes and their Impact on Contaminant Dynamics  

E-print Network

) by microorganisms coupled to the reduction of electron acceptors including humic substances, iron-bearing minerals, Mn, C, P, N, S, Cr, Cu, Co, As, Sb, Se, Hg, Tc, and U. Redox-active humic substances and mineral minerals, and Fe sulfides. Redox-active functional groups associated with humic substances and mineral

Sparks, Donald L.

277

MULTICOMPONENT BIOGEOCHEMICAL TRANSPORT MODELING USING THE HYDRUS COMPUTER SOFTWARE PACKAGES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Contaminant transport in the subsurface is generally affected by a large number of nonlinear and often interactive physical, chemical and biological processes. Simulating these processes requires a coupled reactive transport code that integrates the physical processes of water flow and advective-dis...

278

Spatial and temporal controls on biogeochemical indicators at the small-scale interface between a contaminated aquifer and wetland surface water  

E-print Network

This high-resolution biogeochemical study investigated spatial and temporal variability in the mixing interface zones within a wetland-aquifer system near a municipal landfill in the city of Norman, Oklahoma. Steep biogeochemical gradients...

Baez-Cazull, Susan Enid

2009-05-15

279

Biogeochemical dynamics of pollutants in Insitu groundwater remediation systems  

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

280

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

281

Coupling TOUGH2 with CLM3: Developing a Coupled Land Surface andSubsurface Model  

SciTech Connect

An understanding of the hydrologic interactions among atmosphere, land surface, and subsurface is one of the keys to understanding the water cycling system that supports life on earth. The inherent coupled processes and complex feedback structures among subsystems make such interactions difficult to simulate. In this paper, we present a model that simulates the land surface and subsurface hydrologic response to meteorological forcing. This model combines a state-of-the-art land-surface model, the NCAR Community Land Model version 3 (CLM3), with a variably saturated groundwater model, TOUGH2, through an internal interface that includes flux and state variables shared by the two submodels. Specifically, TOUGH2 uses infiltration, evaporation, and root-uptake rates, calculated by CLM3, as source/sink terms in its simulation; CLM3 uses saturation and capillary pressure profiles, calculated by TOUGH2, as state variables in its simulation. This new model, CLMT2, preserves the best aspects of both submodels: the state-of-the-art modeling capability of surface energy and hydrologic processes (including snow, runoff, freezing/melting, evapotranspiration, radiation, and biophysiological processes) from CLM3 and the more realistic physical-process-based modeling capability of subsurface hydrologic processes (including heterogeneity, three-dimensional flow, seamless combining of unsaturated and saturated zone, and water table) from TOUGH2. The preliminary simulation results show that the coupled model greatly improved the predictions of the groundwater table, evapotranspiration, and surface temperature at a real watershed, as evaluated using 18 years of observed data. The new model is also ready to be coupled with an atmospheric simulation model, to form one of the first top of the atmosphere to deep groundwater atmosphere-land-surface-subsurface models.

Pan, Lehua; Jin, Jiming; Miller, Norman; Wu, Yu-Shu; Bodvarsson,Gudmundur

2006-05-19

282

Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes  

SciTech Connect

Many subsurface flow and transport problems of importance today involve coupled non-linear flow, transport, and reactions in media exhibiting complex heterogeneity. In particular, problems involving biological mediation of reactions fall into this class of problems. Recent experimental research has revealed important details about the physical, chemical, and biological mechanisms involved in these processes at a variety of scales ranging from molecular to laboratory scales. We are developing a hybrid multiscale modeling framework that combines discrete pore-scale models (which explicitly represent the geometry of grains and pores at a local scale) with continuum field-scale models (which conceptualize flow and transport in a porous medium without explicit pores and grains). At the pore scale, we have implemented a parallel three-dimensional Lagrangian model of flow and transport using the Smoothed Particle Hydrodynamics (SPH) method and performed test simulations using millions of computational particles on the supercomputer at the Environmental Molecular Sciences Laboratory (EMSL). We have also developed methods for gridding arbitrarily complex pore geometries and solution of pore-scale flow and transport using parallel implementations of grid-based computational fluid dynamics (CFD) methods. Within the multiscale hybrid framework, we have coupled pore- and continuum-scale models to simulate coupled diffusive mixing, reaction, and mineral precipitation, and compared the results with conventional continuum-only simulations. The hybrid multiscale modeling framework is being developed using a number of SciDAC enabling technologies including the Common Component Architecture (CCA), advanced solvers, grid technologies, scientific workflow tools, and visualization technologies.

Scheibe, Timothy D.; Tartakovsky, Alexandre M.; Tartakovsky, Daniel M.; Redden, George D.; Meakin, Paul; Palmer, Bruce J.; Schuchardt, Karen L.

2008-08-18

283

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

EPA Science Inventory

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

284

INTERACTIVE EFFECTS OF OZONE DEPLETION AND CLIMATE CHANGE ON BIOGEOCHEMICAL CYCLES  

EPA Science Inventory

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

285

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

EPA Science Inventory

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

286

Biogeochemical marine ecosystem models II: the effect of physiological detail on model performance  

Microsoft Academic Search

The level of detail required to efficiently capture system dynamics in ecosystem models has not been well defined. To this end an ecosystem model of a generalised temperate bay, Bay Model 2 (BM2), was constructed. It is a trophically diverse biogeochemical model built using the functional groups from another ecosystem model, the Integrated Generic Bay Ecosystem Model (IGBEM) and the

Elizabeth A. Fulton; John S. Parslow; Anthony D. M. Smitha; Craig R. Johnson

2004-01-01

287

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

Microsoft Academic Search

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

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

2001-01-01

288

Distribution of barium in the Weddell Gyre: Impact of circulation and biogeochemical processes  

E-print Network

of barium in the Weddell Gyre: Impact of circulation and biogeochemical processes M. Hoppemaa,1 , F Institute for Polar and Marine Research, Climate Sciences Department, Postfach 120161, D-27515 Bremerhaven layer as compared to the adjacent waters north (Antarctic Circumpolar Current) and east (Antarctic Zone

Paris-Sud XI, Université de

289

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

EPA Science Inventory

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

290

Biogeochemical changes at early stage after the closure of radioactive waste geological repository in South Korea  

E-print Network

Biogeochemical changes at early stage after the closure of radioactive waste geological repository e Korea Radioactive Waste Agency (KORAD), 111, Daedeok-daero 989 beon-gil, Yuseong-gu, Daejeon 305 Organic waste a b s t r a c t Permanent disposal of low- and intermediate-level radioactive wastes

Ohta, Shigemi

291

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

USGS Publications Warehouse

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

Campbell, W.L.

1986-01-01

292

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

Microsoft Academic Search

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

Jörg M Lobbes; Hans Peter Fitznar; Gerhard Kattner

2000-01-01

293

Locally enhanced or decreased microbially driven biogeochemical activity can often be identified in space  

E-print Network

process rates (reaction rates; e.g.,temperature, redox potential, pH, moisture). Changes in any or all affecting resources and abiotic reaction conditions (Atlas and Bartha 1986). However,there is also engineers can affect the occurrence or rates of biogeochemical processes. To do so, we first discuss two

Berkowitz, Alan R.

294

SWS4180: Earth System Analysis Catalogue Description: Analysis of global-scale interdependences between climate, biogeochemical  

E-print Network

the physical climate ­ i.e. the circulation of the atmosphere and ocean, the marine and terrestrial life course reserves) Optional Text Jacobson M.C. et al., 2000, Earth System Science from Biogeochemical Ocean-atmosphere carbon balance Chapter 8 Gruber and Sarmiento (available in course reserves

Ma, Lena

295

Sulphur speciation and biogeochemical cycling in long-term arable cropping of subtropical soils: evidence  

E-print Network

of arable cropping of the native grassland soils. Hence, there was a shift in oxidation state towardsSulphur speciation and biogeochemical cycling in long-term arable cropping of subtropical soils b , C. E. MARTINEZ c , S. TVEITNES d , C. C. DU PREEZ e & W. AMELUNG b a Department of Crop and Soil

Lehmann, Johannes

296

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...

297

[10-384] Improved Cold Region Hydrology Process Representation as a Cornerstone of Arctic Biogeochemical Modeling  

E-print Network

Biogeochemical Modeling [10-384] PI Co PIs Collaborating Institutions Andrew G. Slater* U. Colorado* David a holistic study of the Arctic permafrost carbon problem. To address this limitation, we propose a targeted, we will pursue robust and reliable simulation of river hydrographs, inundated area distribution

298

Deepened snow increases late thaw biogeochemical pulses in mesic low arctic tundra  

E-print Network

Deepened snow increases late thaw biogeochemical pulses in mesic low arctic tundra Kate M of plant-available nutrients to the soil solution are expected to occur during the dynamic winter­spring transition in arctic tundra. Our aims were to quantify the magnitude of these potential nutrient pulses

Grogan, Paul

299

Author's personal copy A biogeochemical study of sediments from the eutrophic Lake Lugano  

E-print Network

Author's personal copy A biogeochemical study of sediments from the eutrophic Lake Lugano) and carbonate from sediment cores from the oligotrophic Lake Brienz and the eutrophic Lake Lugano (both. Eutrophic conditions at Lake Lugano are reflected in elevated total organic carbon (TOC) content

Wehrli, Bernhard

300

Simulated biogeochemical responses to iron enrichments in three high nutrient, low chlorophyll (HNLC) regions  

E-print Network

Simulated biogeochemical responses to iron enrichments in three high nutrient, low chlorophyll nutrient low chlorophyll (HNLC) regions; Algal bloom; Limiting factors; Water temperature; Reminer;1. Introduction The North Pacific, the Southern Ocean and the Equatorial Pacific are known as major high-nutrient

Maine, University of

301

On the biogeochemical signature of the Lena River from its headwaters to the Arctic Ocean  

Microsoft Academic Search

The Lena River integrates biogeochemical signals from its vast drainage basin and its signal reaches far out over the Arctic Ocean. Transformation of riverine organic carbon into mineral carbon, and mineral carbon into the organic form in the Lena River watershed, can be considered a quasi-equilibrated processes. Increasing the Lena discharge causes opposite effects on total organic (TOC) and inorganic

I. P. Semiletov; I. I. Pipko; N. E. Shakhova; O. V. Dudarev; S. P. Pugach; A. N. Charkin; C. P. McRoy; D. Kosmach; O. Gustafsson

2011-01-01

302

Biogeochemical Characteristics of the Lower Mississippi River, USA, During June 2003  

E-print Network

Biogeochemical Characteristics of the Lower Mississippi River, USA, During June 2003 M. J. DAGG1, a period of mid level discharge (17,400 m23 s21 ), a parcel of water in the lower Mississippi River indicate there was little autotrophic or heterotrophic activity in the lower Mississippi River at this time

Breed, Greg A.

303

Global Warming: A Consequence of Human Activities Rivaling Earth's Biogeochemical Processes  

Microsoft Academic Search

The planet is growing warmer because of a massive disruption in global biogeochemical cycles. We are burning our reserves of fossil fuels, which formed over a period of 300 million years, in the blink of an eye in geologic time. One manifestation of our addiction to fossil fuels is a dramatic change in the composition of the atmosphere and its

Jerald L. Schnoor

2005-01-01

304

Tracing the Sources and Biogeochemical Cycling of Phosphorus in Aquatic Systems Using  

E-print Network

Chapter 21 Tracing the Sources and Biogeochemical Cycling of Phosphorus in Aquatic Systems Using to oxygen (O), which has three stable isotopes, providing a system to track phosphorus cycling to understand phosphorous dynamics in many environments. 21.1 Introduction Phosphorus (P, atomic number 15

Paytan, Adina

305

Winter flooding in Dutch stream valley floodplains: biogeochemical effects and vegetation consequences  

Microsoft Academic Search

Winter flooding in Dutch stream valley floodplains: biogeochemical effects and vegetation consequences Victor Beumer Climatic change has great impacts on stream catchments and their ecology. Expectations are that more extreme climate events will result in undesired flooding in stream catchments. In the Netherlands, former floodplains with a history of agricultural or semi natural land use are put into use again

V. Beumer

2009-01-01

306

Potential impacts of emerald ash borer invasion on biogeochemical and water cycling in residential  

E-print Network

services in cities, yet the vulnerability of the urban forest to massive tree losses from pest outbreaks currently underneath ash tree canopies. Overall, the percentage change in biogeochemical and hydrological fluxes corresponded closely with the percent of the total urban tree population that was represented

Weiblen, George D

307

Interannual variability of oceanic CO and biogeochemical properties in the Western North Atlantic subtropical gyre  

Microsoft Academic Search

Understanding the relationship between Earth's climate and the oceanic carbon cycle requires an understanding of the time-variations of CO in the ocean, it's exchange with the atmosphere, and the rate of uptake of anthropogenic CO by the ocean. Since 1988, hydrographic and biogeochemical data have been collected at the Bermuda Atlantic Time-Series Study (BATS) site in the Sargasso Sea, located

Nicholas R. Bates

308

The effect of surface flooding on the physical-biogeochemical dynamics of a warm  

E-print Network

The effect of surface flooding on the physical-biogeochemical dynamics of a warm core eddy off;1 Introduction Mesoscale eddies are a common feature in the open ocean and in particular in boundary currents-clockwise rotation (Bakun, 2006). A simple conceptual model of the biological dynamics of a WCE considers the warm

Baird, Mark

309

Geomorphodynamic Modulation of Biogeochemical Fluxes and Basin Stratigraphy of the Fly River  

Microsoft Academic Search

The focus of this recently awarded project is a multidisciplinary investigation of the processes responsible for the transport and sequestration of organic carbon by the Fly River and the associated floodplain. Our research team will investigate the role that sediment exchange processes between channels and floodplains play in modulating biogeochemical fluxes and how these processes affect the composition, source, age

M. Goni; J. W. Lauer; W. Dietrich; A. Aufdenkampe; R. Aalto

310

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

NASA Astrophysics Data System (ADS)

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

Ford, David; Barciela, Rosa

2013-04-01

311

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

312

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

313

The Influence of Groundwater Seepage on Lakeshore Biogeochemical Processes and Fluxes of Solutes Within Watersheds.  

NASA Astrophysics Data System (ADS)

Biogeochemical transformations occur at key interface zones within the landscape and dramatically alter water chemistry along hydrologic flowpaths. Past research has demonstrated that transformations at sediment and water interfaces are particularly important to changes of surface water chemistry within watersheds. However, past studies have rarely explored biogeochemical transformations associated with seepage, the advective flux of water through sediments. Changes of the direction and magnitude of seepage influence the transport of gases, ions, and compounds through shoreline sediment profiles. Seepage could influence the availability and cycling of elements within lakeshore ecosystems because groundwater flowpaths converge at lake shorelines. Biogeochemical transformations associated with seepage interfaces may be particularly important in the Adirondack Mountains region of New York, USA, where lakes are an important landscape feature and surface water has historically been influenced by atmospheric deposition. We investigated the influence of seepage on pore water biogeochemistry along three Adirondack lakeshores. Seepage meters were intensively monitored and pore water samples were collected over two summers and through spring snowmelt. The data indicated that the direction, magnitude, and variability of seepage fluxes influenced the fluxes and biogeochemical cycling of base cations and trace metals (particularly zinc and iron) in pore waters. Seepage fluxes were temporally and spatially variable, but sites that had highly variable seepage fluxes disproportionately contributed to the flux of solutes both to and from the lakes. In contrast, biogeochemical transformations at low flow areas altered pore water chemistry as seepage water passed through the sediment profile. Our findings suggest that temporal as well as spatial heterogeneity of seepage fluxes along lake shorelines must be quantified to understand the extent of chemical transformations that occur along groundwater flowpaths.

SEBESTYEN, S. D.; SCHNEIDER, R. L.

2001-05-01

314

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

SciTech Connect

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

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

2008-11-01

315

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

NASA Astrophysics Data System (ADS)

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

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

2003-04-01

316

A model of biogeochemical cycles of carbon, nitrogen, and phosphorus including symbiotic nitrogen fixation and phosphatase production  

NASA Astrophysics Data System (ADS)

Global climate models have not yet considered the effects of nutrient cycles and limitation when forecasting carbon uptake by the terrestrial biosphere into the future. Using the principle of resource optimization, we here develop a new theory by which C, N, and P cycles interact. Our model is able to replicate the observed responses of net primary production to nutrient additions in N-limited, N- and P-colimited, and P-limited terrestrial environments. Our framework identifies a new pathway by which N2 fixers can alter P availability: By investing in N-rich, phosphorus liberation enzymes (phosphatases), fixers can greatly accelerate soil P availability and P cycling rates. This interaction is critical for the successful invasion and establishment of N2 fixers in an N-limited environment. We conclude that our model can be used to examine nutrient limitation broadly, and thus offers promise for coupling the biogeochemical system of C, N, and P to broader climate-system models.

Wang, Y.-P.; Houlton, B. Z.; Field, C. B.

2007-03-01

317

Eastern Mediterranean biogeochemical flux model: simulations of the pelagic ecosystem  

NASA Astrophysics Data System (ADS)

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

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

2006-08-01

318

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

USGS Publications Warehouse

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

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

2010-01-01

319

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

PubMed

Gaseous nitrous acid (HONO), the protonated form of nitrite, contributes up to ?60% to the primary formation of hydroxyl radical (OH), which is a key oxidant in the degradation of most air pollutants. Field measurements and modeling studies indicate a large unknown source of HONO during daytime. Here, we developed a new tracer method based on gas-phase stripping-derivatization coupled to liquid chromatography-mass spectrometry (LC-MS) to measure the 15N relative exceedance, ?(15N), of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye, purified by solid phase extraction (SPE), and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). In the optimal working range of ?(15N)=0.2-0.5, the relative standard deviation of ?(15N) is <4%. The optimum pH and solvents for extraction by SPE and potential interferences are discussed. The method was applied to measure HO15NO emissions from soil in a dynamic chamber with and without spiking 15) labeled urea. The identification of HO15NO from soil with 15N urea addition confirmed biogenic emissions of HONO from soil. The method enables a new approach of studying the formation pathways of HONO and its role for atmospheric chemistry (e.g., ozone formation) and environmental tracer studies on the formation and conversion of gaseous HONO or aqueous NO2- as part of the biogeochemical nitrogen cycle, e.g., in the investigation of fertilization effects on soil HONO emissions and microbiological conversion of NO2- in the hydrosphere. PMID:24954648

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

2014-07-15

320

Hybrid Numerical Methods for Multiscale Simulations of Subsurface Biogeochemical Processes  

SciTech Connect

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

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

2007-08-01

321

Dynamics of sinuosity-driven hyporheic zones: the effects of hydraulic and biogeochemical timescales  

NASA Astrophysics Data System (ADS)

Groundwater-surface water interactions take place across a range of spatio-temporal scales. Sinuosity-driven hyporheic exchange, a ubiquitous example of these interactions, occurs over spatial scales of the order of 1-1000 m and over time scales from hours to years. This exchange is modulated by event, diurnal, and seasonal dynamic forcing that modifies the hyporheic zone's geometry, flow field, and residence time distributions (RTDs), and, at the same time, influences timing-sensitive biogeochemical reactions. This work explores the role of dynamic forcing on the flow field and RTDs for the case of channel sinuousity-driven lateral hyporheic exchange. A two-dimensional, transient, numerical flow and transport model is used to illustrate the effect that dynamics, caused by deterministically and stochastically generated flood events, has on flow fields and RTDs, and therefore on the character of the hyporheic zone as a biogeochemical reactor. In particular, the characteristic hydraulic time scale, expressed as a function of sediment hydraulic diffusivity and the system geometry, plays a key role in determining the memory that the hyporheic zone has of previous flood events. For example, the rising limb of flood events causes accumulation of fresh water into the system and diminishes the flux of hyporheic water with long RTs into the stream. Water with longer RTD is then released during the falling limb at time scales dictated by the hydraulic characteristic time of the system; however, if the characteristic hydraulic time scale is of the order of the time between flood events, long-RT water is accumulated, increasing the water RTs inside the system. Additionally, a simple analytical model is used to estimate the characteristic biogeochemical time scales associated to the degradation of dissolved organic carbon in these hydrologic systems, which are compared to numerically-modeled RTDs and used to estimate the biogeochemical zonation within the HZ and its net biogeochemical response. This parsimonious approach can be used as a predictive tool to quantify the potential of meanders as biogeochemical reactors at the watershed scale with the aid of historic discharge data, remote sensing data, and GIS processing techniques.

Gomez, J. D.; Wilson, J. L.; Cardenas, M. B.

2012-12-01

322

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

323

Global response of the terrestrial biosphere to CO2 and climate change using a coupled climate-carbon cycle model  

E-print Network

feedback in the climate-carbon cycle system. INDEX TERMS: 0315 Atmospheric Composition and Structure: Impact phenomena; KEYWORDS: climate change impact, terrestrial carbon cycle Citation: Berthelot, M., P of the terrestrial biosphere to CO2 and climate change using a coupled climate-carbon cycle model, Global Biogeochem

Dufresne, Jean-Louis

324

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

SciTech Connect

The objective of this research program was to take a highly multidisciplinary approach to define the biogeochemical factors that control technetium (Tc) mobility in FRC sediments. The aim was to use batch and column studies to probe the biogeochemical conditions that control the mobility of Tc at the FRC. Background sediment samples from Area 2 (pH 6.5, low nitrate, low {sup 99}Tc) and Area 3 (pH 3.5, high nitrate, relatively high {sup 99}Tc) of the FRC were selected (http://www.esd.ornl.gov/nabirfrc). For the batch experiments, sediments were mixed with simulated groundwater, modeled on chemical constituents of FRC waters and supplemented with {sup 99}Tc(VII), both with and without added electron donor (acetate). The solubility of the Tc was monitored, alongside other biogeochemical markers (nitrate, nitrite, Fe(II), sulfate, acetate, pH, Eh) as the 'microcosms' aged. At key points, the microbial communities were also profiled using both cultivation-dependent and molecular techniques, and results correlated with the geochemical conditions in the sediments. The mineral phases present in the sediments were also characterized, and the solid phase associations of the Tc determined using sequential extraction and synchrotron techniques. In addition to the batch sediment experiments, where discrete microbial communities with the potential to reduce and precipitate {sup 99}Tc will be separated in time, we also developed column experiments where biogeochemical processes were spatially separated. Experiments were conducted both with and without amendments proposed to stimulate radionuclide immobilization (e.g. the addition of acetate as an electron donor for metal reduction), and were also planned with and without competing anions at high concentration (e.g. nitrate, with columns containing Area 3 sediments). When the columns had stabilized, as determined by chemical analysis of the effluents, we used a spike of the short-lived gamma emitter {sup 99m}Tc (50-200 MBq; half life 6 hours) and its mobility was monitored using a {gamma}-camera. Incorporation of low concentrations of the long-lived 99Tc gave a tracer that can be followed by scintillation counting, should the metastable form of the radionuclide decay to below detection limits before the end of the experiment (complete immobilization or loss of the Tc from the column). After the Tc was reduced and immobilized, or passed through the system, the columns were dismantled carefully in an anaerobic cabinet and the pore water geochemistry and mineralogy of the columns profiled. Microbial community analysis was determined, again using molecular and culture-dependent techniques. Experimental results were also modeled using an established coupled speciation and transport code, to develop a predictive tool for the mobility of Tc in FRC sediments. From this multidisciplinary approach, we hoped to obtain detailed information on the microorganisms that control the biogeochemical cycling of key elements at the FRC, and we would also be able to determine the key factors that control the mobility of Tc at environmentally relevant concentrations at this site.

Jonathan R. Lloyd

2009-02-03

325

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

USGS Publications Warehouse

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

Callender, E.; Granina, L.

1997-01-01

326

Dissolved Organic Matter and Biogeochemical Hotspots in a Northern Peatland Catchment  

NASA Astrophysics Data System (ADS)

Research on peatland catchments at the Marcell Experimental Forest in northern Minnesota, USA demonstrates the importance of dissolved organic matter (DOM) as a control on ecosystem processes. DOM is linked to biogeochemical cycles, especially in areas of the landscape where upland soils interface with organic soils of peatlands. At those interface areas, we investigate data from long-term (30+ years) and short-term studies for relationships between DOM (constituent concentrations and compositional measures) and phosphorus, mercury (total and methyl), and other trace metals. At the catchment scale, decades of stream chemistry monitoring show changes in the forms and concentrations of the constituents of DOM in response to forest management and other environmental change. Together, these data help to show how DOM from various source areas in the landscape is linked to hotspots of biogeochemical transformations and why these small areas of the landscape are important controls on solute yields at larger spatial scales.

Sebestyen, S. D.; Kolka, R. K.; Jacobson, M.; Tsui, M. T.; Cotner, J. B.; Finlay, J. C.; Jeremiason, J.; Mitchell, C. P.; Watson, K. A.; Carlos, B.

2010-12-01

327

A bottom-up approach: using residence time distributions and characteristic biogeochemical timescales to upscale multiphysics models of hyporheic exchange  

NASA Astrophysics Data System (ADS)

Residence time distributions (RTDs) and characteristic biogeochemical time scales (CBTSs) are integrated metrics that can be used to describe the biogeochemical evolution of water within hydrologic systems. RTDs describe the time that water and solutes are in contact with the system and strongly depend on the forcing and geomorphic features driving exchange and the system's hydraulic properties. On the other hand, CBTSs describe the time necessary for a biogeochemical transformation to take place and depend on the reaction type, solute concentrations entering the system, and chemical kinetics (or thermodynamics). Comparing RTDs and CBTSs allow us to evaluate the potential for transformation within the hydrologic system. In this work, we illustrate this approach with sinuosity-driven hyporheic zones; however, these concepts can be applied to other hydrologic systems. A two-dimensional, transient, numerical flow and transport model is used to illustrate the effect that dynamics, caused by deterministically generated flood events, has on flow fields and RTDs, and therefore on the character of the hyporheic zone as a biogeochemical reactor. A simple analytical model is used to estimate the CBTSs associated to the degradation of dissolved organic carbon in these hydrologic systems, which are compared to numerically-modeled RTDs and used to estimate the biogeochemical zonation within the HZ and its net biogeochemical response. Additionally, we use a multispecies, reactive transport model to assess this approach, paying special attention to those portions of the system with intermittent hyporheic contributions. In particular, transient flow results in time-varying hot-spot for biogeochemical reactions and induces the emergence of new modes on the dynamic RTDs, which are observed within the system and at the outlet. This parsimonious approach can be used as a predictive tool to quantify the potential of meanders as biogeochemical reactors at the watershed scale with the aid of historic discharge data, remote sensing data, and GIS processing techniques.

Gomez, Jesus D.; Wilson, John L.

2013-04-01

328

A biogeochemical study of the coccolithophore, Emiliania huxleyi, in the North Atlantic  

Microsoft Academic Search

The biogeochemical properties of an extensive bloom (~250,000 km2) of the coccolithophore, EMiliania huxleyi, in the north east Atlantic Ocean were investigated in June 1991. Satellite (NOAA-AVHRR) imagery showed that the bloom was centered initially at 60°-63°N by 13°-28°W and lasted approximately 3 weeks. Spatial variations in satellite-measured reflectance were well correlated with surface measurements of the beam attenuation coefficient,

Patrick M. Holligan; Emilio Fernández; James Aiken; William M. Balch; Philip Boyd; Peter H. Burkill; Miles Finch; Stephen B. Groom; Gillian Malin; Kerstin Muller; Charles C. Trees; Suzanne M. Turner; Paul van der Wal

1993-01-01

329

Toward a dynamic biogeochemical division of the Mediterranean Sea in a context of global climate change  

NASA Astrophysics Data System (ADS)

In recent decades, it has been found useful to ecoregionalise the pelagic environment assuming that within each partition environmental conditions are distinguishable and unique. Indeed, each partition of the ocean that is proposed aimed to delineate the main oceanographical and ecological patterns to provide a geographical framework of marine ecosystems for ecological studies and management purposes. The aim of the present work is to integrate and process existing data on the pelagic environment of the Mediterranean Sea in order to define biogeochemical regions. Open access databases including remote sensing observations, oceanographic campaign data and physical modeling simulations are used. These various dataset allow the multidisciplinary view required to understand the interactions between climate and Mediterranean marine ecosystems. The first step of our study has consisted in a statistical selection of a set of crucial environmental factors to propose the most parsimonious biogeographical approach that allows detecting the main oceanographic structure of the Mediterranean Sea. Second, based on the identified set of environmental parameters, both non-hierarchical and hierarchical clustering algorithms have been tested. Outputs from each methodology are then inter-compared to propose a robust map of the biotopes (unique range of environmental parameters) of the area. Each biotope was then modeled using a non parametric environmental niche method to infer a dynamic biogeochemical partition. Last, the seasonal, inter annual and long term spatial changes of each biogeochemical regions were investigated. The future of this work will be to perform a second partition to subdivide the biogeochemical regions according to biotic features of the Mediterranean Sea (ecoregions). This second level of division will thus be used as a geographical framework to identify ecosystems that have been altered by human activities (i.e. pollution, fishery, invasive species) for the European project PERSEUS (Protecting EuRopean Seas and borders through the intelligence US of surveillance) and the French program MERMEX (Marine Ecosystems Response in the Mediterranean Experiment).

Reygondeau, Gabriel; Olivier Irisson, Jean; Guieu, Cecile; Gasparini, Stephane; Ayata, Sakina; Koubbi, Philippe

2013-04-01

330

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

SciTech Connect

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

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

2009-04-15

331

Small Players, Large Role: Microbial Influence on Biogeochemical Processes in Pelagic Aquatic Ecosystems  

Microsoft Academic Search

Although prokaryotes are small in size, they are a significant biomass component in aquatic planktonic ecosystems and play\\u000a a major role in biogeochemical processes. A review of the recent literature shows that the relative importance of prokaryotes\\u000a to material and energy fluxes is maximized in low-productivity (oligotrophic) ecosystems and decreases in high-productivity\\u000a (eutrophic) ecosystems. We conclude that competition with eukaryotic

James B. Cotner; Bopaiah A. Biddanda

2002-01-01

332

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

NSDL National Science Digital Library

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

Lixin Jin

333

How to `Elk-test' biogeochemical models in a data rich world? (Invited)  

Microsoft Academic Search

Process-oriented biogeochemical models are a primary tool that has been used to project future states of climate and ecosystems in the earth system in response to anthropogenic and other forcing, and receive tremendous attention also in the context us the planned assessment report AR5 by the IPCC. However, model intercomparison and data-model comparison studies indicate large uncertainties regarding predictions of

M. Reichstein; P. Ciais; S. I. Seneviratne; N. Carvalhais; D. Dalmonech; M. Jung; Y. Luo; M. D. Mahecha; A. M. Moffat; E. Tomelleri; S. Zaehle

2010-01-01

334

Defining Mediterranean and Black Sea biogeochemical subprovinces and synthetic ocean indicators using mesoscale oceanographic features.  

PubMed

The Mediterranean and Black Seas are semi-enclosed basins characterized by high environmental variability and growing anthropogenic pressure. This has led to an increasing need for a bioregionalization of the oceanic environment at local and regional scales that can be used for managerial applications as a geographical reference. We aim to identify biogeochemical subprovinces within this domain, and develop synthetic indices of the key oceanographic dynamics of each subprovince to quantify baselines from which to assess variability and change. To do this, we compile a data set of 101 months (2002-2010) of a variety of both "classical" (i.e., sea surface temperature, surface chlorophyll-a, and bathymetry) and "mesoscale" (i.e., eddy kinetic energy, finite-size Lyapunov exponents, and surface frontal gradients) ocean features that we use to characterize the surface ocean variability. We employ a k-means clustering algorithm to objectively define biogeochemical subprovinces based on classical features, and, for the first time, on mesoscale features, and on a combination of both classical and mesoscale features. Principal components analysis is then performed on the oceanographic variables to define integrative indices to monitor the environmental changes within each resultant subprovince at monthly resolutions. Using both the classical and mesoscale features, we find five biogeochemical subprovinces for the Mediterranean and Black Seas. Interestingly, the use of mesoscale variables contributes highly in the delineation of the open ocean. The first axis of the principal component analysis is explained primarily by classical ocean features and the second axis is explained by mesoscale features. Biogeochemical subprovinces identified by the present study can be useful within the European management framework as an objective geographical framework of the Mediterranean and Black Seas, and the synthetic ocean indicators developed here can be used to monitor variability and long-term change. PMID:25360783

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

2014-01-01

335

Biogeochemical and environmental study of the chromite-rich ultramafic terrain of Malakand area, Pakistan  

Microsoft Academic Search

The biogeochemical distribution of enzyme-bound metals in the plants and soil of the chromite-rich mineralized area of Malakand Agency and the non-mineralized area of Mardan (N.W.F.P., Pakistan) has been studied in regard to mineral prospecting and environmental pollution. Samples of lower plants accompanied with their associated soil samples were collected and analysed for copper, lead, zinc, nickel, chromium and cobalt.

Q. Kfayatullah; M. Tahir Shah; M. Arfan

2001-01-01

336

Biogeochemical regimes, net community production and carbon export in the Ross Sea, Antarctica  

Microsoft Academic Search

The net community production (NCP) of the Ross Sea, from the early austral spring (mid-October) to the austral summer (mid-February), has been estimated from the seasonal drawdown of CO2 concentrations integrated over the top 100m of the water column. The deficits in nutrients and CO2 indicate three distinct biogeochemical regimes. The regime in the southwestern Ross Sea (Region I) had

Colm Sweeney; Dennis A. Hansell; Craig A. Carlson; L. A. Codispoti; Louis I. Gordon; John Marra; Frank J. Millero; Walker O. Smith; Taro Takahashi

2000-01-01

337

Investigation of biogeochemical functional proxies in headwater streams across a range of channel and catchment alterations.  

PubMed

Historically, headwater streams received limited protection and were subjected to extensive alteration from logging, farming, mining, and development activities. Despite these alterations, headwater streams provide essential ecological functions. This study examines proxy measures of biogeochemical function across a range of catchment alterations by tracking nutrient cycling (i.e., inputs, processing, and stream loading) with leaf litter fall, leaf litter decomposition, and water quality parameters. Nutrient input and processing remained highest in second growth forests (the least altered areas within the region), while recently altered locations transported higher loads of nutrients, sediments, and conductivity. Biogeochemical functional proxies of C and N input and processing significantly, positively correlated with rapid assessment results (Pearson coefficient = 0.67-0.81; P = 0.002-0.016). Additionally, stream loading equations demonstrate that N and P transport, sediment, and specific conductivity negatively correlated with rapid assessment scores (Pearson coefficient = 0.56-0.81; P = 0.002-0.048). The observed increase in stream loading with lower rapid assessment scores indicates that catchment alterations impact stream chemistry and that rapid assessments provide useful proxy measures of function in headwater ecosystems. Significant differences in nutrient processing, stream loading, water quality, and rapid assessment results were also observed between recently altered (e.g., mined) headwater streams and older forested catchments (Mann-Whitney U = 24; P = 0.01-0.024). Findings demonstrate that biogeochemical function is reduced in altered catchments, and rapid assessment scores respond to a combination of alteration type and recovery time. An analysis examining time and economic requirements of proxy measurements highlights the benefits of rapid assessment methods in evaluating biogeochemical functions. PMID:24310643

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

2014-03-01

338

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

339

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

Microsoft Academic Search

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

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

1997-01-01

340

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

PubMed Central

The Mediterranean and Black Seas are semi-enclosed basins characterized by high environmental variability and growing anthropogenic pressure. This has led to an increasing need for a bioregionalization of the oceanic environment at local and regional scales that can be used for managerial applications as a geographical reference. We aim to identify biogeochemical subprovinces within this domain, and develop synthetic indices of the key oceanographic dynamics of each subprovince to quantify baselines from which to assess variability and change. To do this, we compile a data set of 101 months (2002–2010) of a variety of both “classical” (i.e., sea surface temperature, surface chlorophyll-a, and bathymetry) and “mesoscale” (i.e., eddy kinetic energy, finite-size Lyapunov exponents, and surface frontal gradients) ocean features that we use to characterize the surface ocean variability. We employ a k-means clustering algorithm to objectively define biogeochemical subprovinces based on classical features, and, for the first time, on mesoscale features, and on a combination of both classical and mesoscale features. Principal components analysis is then performed on the oceanographic variables to define integrative indices to monitor the environmental changes within each resultant subprovince at monthly resolutions. Using both the classical and mesoscale features, we find five biogeochemical subprovinces for the Mediterranean and Black Seas. Interestingly, the use of mesoscale variables contributes highly in the delineation of the open ocean. The first axis of the principal component analysis is explained primarily by classical ocean features and the second axis is explained by mesoscale features. Biogeochemical subprovinces identified by the present study can be useful within the European management framework as an objective geographical framework of the Mediterranean and Black Seas, and the synthetic ocean indicators developed here can be used to monitor variability and long-term change. PMID:25360783

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

2014-01-01

341

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

Microsoft Academic Search

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

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

1999-01-01

342

Environmental and biogeochemical process of accumulation of iron-phosphorus in marine sediments  

Microsoft Academic Search

This paper discusses the environmental and biogeochemical process of accumulation of iron-phosphorus in marine sediments for\\u000a the north aktian of the South China Sea and analyzes the relationships between the contents of iron, phosphorus and calcium\\u000a carbonate as well as their existent characteristics. The results show that the variances of phosphorus and calcium carbonate\\u000a contents with depths are opposite and

Huanxin Weng; Xingmao Zhang; Nengyou Wu; Lihong Chen; Jingfeng Chen; Ying Wang; Yachao Qin; Rongxiang Tian

2004-01-01

343

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

344

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

345

Invasive Fishes Generate Biogeochemical Hotspots in a Nutrient-Limited System  

PubMed Central

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

Capps, Krista A.; Flecker, Alexander S.

2013-01-01

346

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

NASA Astrophysics Data System (ADS)

Representation of gaseous diffusion in variably saturated near-surface soils is becoming more common in land biogeochemical models, yet the formulations and numerical solution algorithms applied vary widely. We present three different but equivalent formulations of the dual-phase (gaseous and aqueous) tracer diffusion transport problem that is relevant to a wide class of volatile tracers in land biogeochemical models. Of these three formulations (i.e., the gas-primary, aqueous-primary, and bulk-tracer-based formulations), we contend that the gas-primary formulation is the most convenient for modeling tracer dynamics in biogeochemical models. We then provide finite volume approximation to the gas-primary equation and evaluate its accuracy against three analytical models: one for steady-state soil CO2 dynamics, one for steady-state soil CH4 dynamics, and one for transient tracer diffusion from a constant point source into two different sequentially aligned medias. All evaluations demonstrated good accuracy of the numerical approximation. We expect our result will standardize an efficient mechanistic numerical method for solving relatively simple, multi-phase, one-dimensional diffusion problems in land models.

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

2014-07-01

347

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

NASA Astrophysics Data System (ADS)

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

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

2005-12-01

348

Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach  

NASA Astrophysics Data System (ADS)

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

2013-12-01

349

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

USGS Publications Warehouse

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

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

2011-01-01

350

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

351

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

NASA Astrophysics Data System (ADS)

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.

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

2004-12-01

352

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

USGS Publications Warehouse

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.

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

2008-01-01

353

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

NASA Astrophysics Data System (ADS)

In order to assess the intrinsic heterogeneity of paddy soils, a set of biogeochemical soil parameters was investigated in five field replicates of seven paddy fields (50, 100, 300, 500, 700, 1000, and 2000 yr of wetland rice cultivation), one flooded paddy nursery, one tidal wetland (TW), and one freshwater site (FW) from a coastal area at Hangzhou Bay, Zhejiang Province, China. All soils evolved from a marine tidal flat substrate due to land reclamation. The biogeochemical parameters based on their properties were differentiated into (i) a group behaving conservatively (TC, TOC, TN, TS, magnetic susceptibility, soil lightness and colour parameters, ?13C, ?15N, lipids and n-alkanes) and (ii) one encompassing more labile properties or fast cycling components (Nmic, Cmic, nitrate, ammonium, DON and DOC). The macroscale heterogeneity in paddy soils was assessed by evaluating intra- versus inter-site spatial variability of biogeochemical properties using statistical data analysis (descriptive, explorative and non-parametric). Results show that the intrinsic heterogeneity of paddy soil organic and minerogenic components per field is smaller than between study sites. The coefficient of variation (CV) values of conservative parameters varied in a low range (10% to 20%), decreasing from younger towards older paddy soils. This indicates a declining variability of soil biogeochemical properties in longer used cropping sites according to progress in soil evolution. A generally higher variation of CV values (>20-40%) observed for labile parameters implies a need for substantially higher sampling frequency when investigating these as compared to more conservative parameters. Since the representativeness of the sampling strategy could be sufficiently demonstrated, an investigation of long-term carbon accumulation/sequestration trends in topsoils of the 2000 yr paddy chronosequence under wetland rice cultivation restricted was conducted. Observations cannot be extrapolated to global scale but with coastal paddy fields developed on marine tidal flat substrates after land reclamation in the Zhejiang Province represent a small fraction (<1%) of the total rice cropping area. The evolutionary trend showed that the biogeochemical signatures characteristic for paddy soils were fully developed in less than 300 yr since onset of wetland rice cultivation. A six-fold increase of topsoil TOC suggests a substantial gain in CO2 sequestration potential when marine tidal wetland substrate developed to 2000 yr old paddy soil.

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

2012-03-01

354

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

NASA Astrophysics Data System (ADS)

In order to assess the intrinsic heterogeneity of paddy soils, a set of biogeochemical soil parameters was investigated in five field replicates of seven paddy fields (50, 100, 300, 500, 700, 1000, and 2000 yr of wetland rice cultivation), one flooded paddy nursery, one tidal wetland (TW), and one freshwater site (FW) from a coastal area at Hangzhou Bay, Zhejiang Province, China. All soils evolved from a marine tidal flat substrate due to land reclamation. The biogeochemical parameters based on their properties were differentiated into (i) a group behaving conservatively (TC, TOC, TN, TS, magnetic susceptibility, soil lightness and colour parameters, ?13C, ?15N, lipids and n-alkanes) and (ii) one encompassing more labile properties or fast cycling components (Nmic, Cmic, nitrate, ammonium, DON and DOC). The macroscale heterogeneity in paddy soils was assessed by evaluating intra- versus inter-site spatial variability of biogeochemical properties using statistical data analysis (descriptive, explorative and non-parametric). Results show that the intrinsic heterogeneity of paddy soil organic and minerogenic components per field is smaller than between study sites. The coefficient of variation (CV) values of conservative parameters varied in a low range (10 % to 20 %), decreasing from younger towards older paddy soils. This indicates a declining variability of soil biogeochemical properties in longer used cropping sites according to progress in soil evolution. A generally higher variation of CV values (>20-40 %) observed for labile parameters implies a need for substantially higher sampling frequency when investigating these as compared to more conservative parameters. Since the representativeness of the sampling strategy could be sufficiently demonstrated, an investigation of long-term carbon accumulation/sequestration trends in topsoils of the 2000 year paddy chronosequence under wetland rice cultivation was conducted. The evolutionary trend showed that the biogeochemical signatures characteristic for paddy soils were fully developed in less than 300 yr since onset of wetland rice cultivation. A six-fold increase of topsoil TOC suggests a substantial gain in CO2 sequestration potential when marine tidal wetland substrate developed to 2000 year old paddy soil.

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

2011-10-01

355

Nitrogen biogeochemical cycling in the northwestern Indian Ocean  

NASA Astrophysics Data System (ADS)

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

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

356

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

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

357

Chemosynthetic communities and biogeochemical energy pathways along the Mid-Atlantic Ridge: The case of Bathymodiolus azoricus  

NASA Astrophysics Data System (ADS)

Hydrothermal vents fields from the Mid-Atlantic Ridge (MAR) are hosted in diverse geological contexts, resulting in contrasted end-member fluids. Despite this variability, the same animal species dominate the chemosynthetic fauna at almost all sites. Among these organisms, two Bathymodiolus mussel species occur. Both harbor similar sulfide- and methane-oxidizing endosymbionts in their gills. This dual symbiosis is thought to allow mussels to adapt to the different types of fluids encountered along the MAR. Distribution, abundances, and nutritional role of the two symbiont types tend to be correlated with end-member composition, but their variability cannot be fully explained without considering local influences. In this paper, the processes governing the environment of mussel aggregates in terms of available electron donors and energy sources are discussed. The properties of mixed fluids surrounding animals depart from those predicted from end-member conservative dilution. Both subsurface transformations and the influence of mussels on their own environment can significantly modify the relative availability of electron donors. Recent observations about mussel dual symbioses are summarized, leading to the assumption that flexible response of symbiont populations may be a key adaptation allowing mussels to colonize the diversified MAR vent habitats. As illustrated here, tools are becoming available to investigate both environment and symbiosis in detail. We advocate for a more integrative study of the biogeochemical couplings between fluids and chemosynthetic species at hydrothermal vents, using combined interdisciplinary approaches at the scale of organisms. Bathymodiolus azoricus from contrasted chemical environments appear as particularly relevant models for such studies.

Le Bris, N.; Duperron, S.

358

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

USGS Publications Warehouse

DayCent is a biogeochemical model of intermediate complexity widely used to simulate greenhouse gases (GHG), soil organic carbon and nutrients in crop, grassland, forest and savannah ecosystems. Although this model has been applied to a wide range of ecosystems, it is still typically parameterized through a traditional “trial and error” approach and has not been calibrated using statistical inverse modelling (i.e. algorithmic parameter estimation). The aim of this study is to establish and demonstrate a procedure for calibration of DayCent to improve estimation of GHG emissions. We coupled DayCent with the parameter estimation (PEST) software for inverse modelling. The PEST software can be used for calibration through regularized inversion as well as model sensitivity and uncertainty analysis. The DayCent model was analysed and calibrated using N2O flux data collected over 2 years at the Iowa State University Agronomy and Agricultural Engineering Research Farms, Boone, IA. Crop year 2003 data were used for model calibration and 2004 data were used for validation. The optimization of DayCent model parameters using PEST significantly reduced model residuals relative to the default DayCent parameter values. Parameter estimation improved the model performance by reducing the sum of weighted squared residual difference between measured and modelled outputs by up to 67 %. For the calibration period, simulation with the default model parameter values underestimated mean daily N2O flux by 98 %. After parameter estimation, the model underestimated the mean daily fluxes by 35 %. During the validation period, the calibrated model reduced sum of weighted squared residuals by 20 % relative to the default simulation. Sensitivity analysis performed provides important insights into the model structure providing guidance for model improvement.

Rafique, Rashad; Fienen, Michael N.; Parkin, Timothy B.; Anex, Robert P.

2013-01-01

359

Helix coupling  

DOEpatents

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

Ginell, W.S.

1982-03-17

360

Helix coupling  

DOEpatents

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

Ginell, W.S.

1989-04-25

361

Afforestation alters the composition of functional genes in soil and biogeochemical processes in South American grasslands  

SciTech Connect

Soil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacent Eucalyptus plantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, we analyzed functional genes using the GeoChip 2.0 microarray, which simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grassland differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Most grassland profiles were similar, but plantation profiles generally differed from those of grasslands due to differences in functional gene abundance across diverse taxa. Eucalypts decreased ammonification and N fixation functional genes by 11% and 7.9% (P < 0.01), which correlated with decreased microbial biomass N and more NH{sub 4}{sup +} in plantation soils. Chitinase abundance decreased 7.8% in plantations compared to levels in grassland (P = 0.017), and C polymer-degrading genes decreased by 1.5% overall (P < 0.05), which likely contributed to 54% (P < 0.05) more C in undecomposed extractable soil pools and 27% less microbial C (P < 0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes, corresponding with changes in soil biogeochemistry, in part through altered abundance of overall functional gene types rather than simply through changes in specific taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.

Berthrong, Sean T [ORNL; Schadt, Christopher Warren [ORNL; Pineiro, Gervasio [Duke University; Jackson, Robert B [Duke University

2009-01-01

362

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

363

Morphological, hydrological, biogeochemical and ecological changes and challenges in river restoration - the Thur River case study  

NASA Astrophysics Data System (ADS)

River restoration can enhance river dynamics, environmental heterogeneity and biodiversity, but the underlying processes governing the dynamic changes need to be understood to ensure that restoration projects meet their goals, and adverse effects are prevented. In particular, we need to comprehend how hydromorphological variability quantitatively relates to ecosystem functioning and services, biodiversity as well as ground- and surface water quality in restored river corridors. This involves (i) physical processes and structural properties, determining erosion and sedimentation, as well as solute and heat transport behavior in surface water and within the subsurface; (ii) biogeochemical processes and characteristics, including the turnover of nutrients and natural water constituents; and (iii) ecological processes and indicators related to biodiversity and ecological functioning. All these aspects are interlinked, requiring an interdisciplinary investigation approach. Here, we present an overview of the recently completed RECORD (REstored CORridor Dynamics) project in which we combined physical, chemical, and biological observations with modeling at a restored river corridor of the perialpine Thur River in Switzerland. Our results show that river restoration, beyond inducing morphologic changes that reshape the river bed and banks, triggered complex spatial patterns of bank infiltration, and affected habitat type, biotic communities and biogeochemical processes. We adopted an interdisciplinary approach of monitoring the continuing changes due to restoration measures to address the following questions: How stable is the morphological variability established by restoration? Does morphological variability guarantee an improvement in biodiversity? How does morphological variability affect biogeochemical transformations in the river corridor? What are some potential adverse effects of river restoration? How is river restoration influenced by catchment-scale hydraulics and which feedbacks exist on the large scale? Beyond summarizing the major results of individual studies within the project, we show that these overarching questions could only be addressed in an interdisciplinary framework.

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

2014-06-01

364

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

PubMed

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

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

2013-10-01

365

A new implementation of the Biogeochemical Flux Model in sea ice  

NASA Astrophysics Data System (ADS)

The Biogeochemical Flux Model (BFM) is a direct descendent of the European Regional Seas Ecosystem Model (ERSEM) and it has been widely used and validated among the scientific community. The BFM view of the of the marine ecosystem is based upon the recognition that the major ecological functions of producers, decomposers and consumers and their specific trophic interactions can be expressed in terms of material flows of basic elements. The concentration and characteristics of organic and inorganic compounds are thus seen under a stoichiometrical perspective. This functional approach brings to the definition of Chemical Functional Families (CFF) and Living Functional Groups (LFG). The BFM is thus a set of biogeochemical equations describing the cycling of carbon, the macro-nutrients and oxygen through the lower trophic levels of marine ecosystems. A Sea-Ice system has now been implemented in the BFM and the new BFM-SI consists of three new LFG (sea ice algae, heterotrophic zooplankton, bacterioplankton), one new non-living organic functional group (sea ice DOM and POM) and two new inorganic functional groups: dissolved gases (sea ice CO2 and O2) and four nutrients (sea ice PO4, NH3, NO3 and SiO4). The innovative approach consists in simulating the biogeochemistry of the sea ice Biologically-Active-Layer (BAL), where the majority of the biomass (bottom communities) concentrates. The BFM-SI requires the physical properties of the BAL in order to be able to simulate the physiological and ecological response of the biological community to the physical environment. This is currently done by using an Enhanced 1-D thermo-halodynamic Sea Ice Model (ESIM2), developed to be suitable for biogeochemical studies. Since the biogeochemistry of sea ice is largely unknown, the BFM-SI is a useful tool that allow us to test hypotheses on the functioning of the sea ice ecosystem. By initially setting the sea ice community as having the same characteristics than the pelagic community, it is possible to change many parametrizations of the model, such as the adaptation to the different environmental conditions (light, temperature and salinity) but also nutrient utilization and carbon-chlorophyll ratio. Elected experiments will be shown to elucidate some dynamics of sea ice ecosystems. Once biogeochemical dynamics have been studied in local process studies, it will be possible to apply the new implementation of the model both regionally and globally in order to give a wider picture of the role and importance of the sea ice biogeochemistry in the global carbon cycle, also in view of climate change scenarios.

Tedesco, L.; Vichi, M.

2009-04-01

366

BIOGEOCHEMICAL CYCLING AND ENVIRONMENTAL STABILITY OF PLUTONIUM RELEVANT TO LONG-TERM STEWARDSHIP OF DOE SITES.  

SciTech Connect

Pu is generally considered to be relatively immobile in the terrestrial environment, with the exception of transport via airborne and erosion mechanisms. More recently the transport of colloidal forms of Pu is being studied as a mobilization pathway from subsurface contaminated soils and sediments. The overall objective of this research is to understand the biogeochemical cycling of Pu in environments of interest to long-term DOE stewardship issues. Microbial processes are central to the immobilization of Pu species, through the metabolism