Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE PAGES

Graham, Emily B.; Stegen, James C.

2017-11-01

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

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

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

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

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different frommore » that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.« less

Temporal dynamics of biogeochemical processes at the Norman Landfill site

USGS Publications Warehouse

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

2013-01-01

The temporal variability observed in redox sensitive species in groundwater can be attributed to coupled hydrological, geochemical, and microbial processes. These controlling processes are typically nonstationary, and distributed across various time scales. Therefore, the purpose of this study is to investigate biogeochemical data sets from a municipal landfill site to identify the dominant modes of variation and determine the physical controls that become significant at different time scales. Data on hydraulic head, specific conductance, δ2H, chloride, sulfate, nitrate, and nonvolatile dissolved organic carbon were collected between 1998 and 2000 at three wells at the Norman Landfill site in Norman, OK. Wavelet analysis on this geochemical data set indicates that variations in concentrations of reactive and conservative solutes are strongly coupled to hydrologic variability (water table elevation and precipitation) at 8 month scales, and to individual eco-hydrogeologic framework (such as seasonality of vegetation, surface-groundwater dynamics) at 16 month scales. Apart from hydrologic variations, temporal variability in sulfate concentrations can be associated with different sources (FeS cycling, recharge events) and sinks (uptake by vegetation) depending on the well location and proximity to the leachate plume. Results suggest that nitrate concentrations show multiscale behavior across temporal scales for different well locations, and dominant variability in dissolved organic carbon for a closed municipal landfill can be larger than 2 years due to its decomposition and changing content. A conceptual framework that explains the variability in chemical concentrations at different time scales as a function of hydrologic processes, site-specific interactions, and/or coupled biogeochemical effects is also presented.

Biogeochemical regions of the Mediterranean Sea: An objective multidimensional and multivariate environmental approach

NASA Astrophysics Data System (ADS)

Reygondeau, Gabriel; Guieu, Cécile; Benedetti, Fabio; Irisson, Jean-Olivier; Ayata, Sakina-Dorothée; Gasparini, Stéphane; Koubbi, Philippe

2017-02-01

When dividing the ocean, the aim is generally to summarise a complex system into a representative number of units, each representing a specific environment, a biological community or a socio-economical specificity. Recently, several geographical partitions of the global ocean have been proposed using statistical approaches applied to remote sensing or observations gathered during oceanographic cruises. Such geographical frameworks defined at a macroscale appear hardly applicable to characterise the biogeochemical features of semi-enclosed seas that are driven by smaller-scale chemical and physical processes. Following the Longhurst's biogeochemical partitioning of the pelagic realm, this study investigates the environmental divisions of the Mediterranean Sea using a large set of environmental parameters. These parameters were informed in the horizontal and the vertical dimensions to provide a 3D spatial framework for environmental management (12 regions found for the epipelagic, 12 for the mesopelagic, 13 for the bathypelagic and 26 for the seafloor). We show that: (1) the contribution of the longitudinal environmental gradient to the biogeochemical partitions decreases with depth; (2) the partition of the surface layer cannot be extrapolated to other vertical layers as the partition is driven by a different set of environmental variables. This new partitioning of the Mediterranean Sea has strong implications for conservation as it highlights that management must account for the differences in zoning with depth at a regional scale.

Modeling and Assimilating Ocean Color Radiances

NASA Technical Reports Server (NTRS)

Gregg, Watson

2012-01-01

Radiances are the source of information from ocean color sensors to produce estimates of biological and geochemical constituents. They potentially provide information on various other aspects of global biological and chemical systems, and there is considerable work involved in deriving new information from these signals. Each derived product, however, contains errors that are derived from the application of the radiances, above and beyond the radiance errors. A global biogeochemical model with an explicit spectral radiative transfer model is used to investigate the potential of assimilating radiances. The results indicate gaps in our understanding of radiative processes in the oceans and their relationships with biogeochemical variables. Most important, detritus optical properties are not well characterized and produce important effects of the simulated radiances. Specifically, there does not appear to be a relationship between detrital biomass and its optical properties, as there is for chlorophyll. Approximations are necessary to get beyond this problem. In this reprt we will discuss the challenges in modeling and assimilation water-leaving radiances and the prospects for improving our understanding of biogeochemical process by utilizing these signals.

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

PubMed

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

2018-03-09

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

Compound-specific isotopic analyses: a novel tool for reconstruction of ancient biogeochemical processes

NASA Technical Reports Server (NTRS)

Hayes, J. M.; Freeman, K. H.; Popp, B. N.; Hoham, C. H.

1990-01-01

Patterns of isotopic fractionation in biogeochemical processes are reviewed and it is suggested that isotopic fractionations will be small when substrates are large. If so, isotopic compositions of biomarkers will reflect those of their biosynthetic precursors. This prediction is tested by consideration of results of analyses of geoporphyrins and geolipids from the Greenhorn Formation (Cretaceous, Western Interior Seaway of North America) and the Messel Shale (Eocene, lacustrine, southern Germany). It is shown (i) that isotopic compositions of porphyrins that are related to a common source, but which have been altered structurally, cluster tightly and (ii) that isotopic differences between geolipids and porphyrins related to a common source are equal to those observed in modern biosynthetic products. Both of these observations are consistent with preservation of biologically controlled isotopic compositions during diagenesis. Isotopic compositions of individual compounds can thus be interpreted in terms of biogeochemical processes in ancient depositional environments. In the Cretaceous samples, isotopic compositions of n-alkanes are covariant with those of total organic carbon, while delta values for pristane and phytane are covariant with those of porphyrins. In this unit representing an open marine environment, the preserved acyclic polyisoprenoids apparently derive mainly from primary material, while the extractable, n-alkanes derive mainly from lower levels of the food chain. In the Messel Shale, isotopic compositions of individual biomarkers range from -20.9 to -73.4% vs PDB. Isotopic compositions of specific compounds can be interpreted in terms of origin from methylotrophic, chemautotrophic, and chemolithotrophic microorganisms as well as from primary producers that lived in the water column and sediments of this ancient lake.

Projecting changes in Everglades soil biogeochemistry for carbon and other key elements, to possible 2060 climate and hydrologic scenarios.

PubMed

Orem, William; Newman, Susan; Osborne, Todd Z; Reddy, K Ramesh

2015-04-01

Based on previously published studies of elemental cycling in Everglades soils, we projected how soil biogeochemistry, specifically carbon, nitrogen, phosphorus, sulfur, and mercury might respond to climate change scenarios projected for 2060 by the South Florida Water Management Model. Water budgets and stage hydrographs from this model with future scenarios of a 10% increased or decreased rainfall, a 1.5 °C rise in temperature and associated increase in evapotranspiration (ET) and a 0.5 m rise in sea level were used to predict resulting effects on soil biogeochemistry. Precipitation is a much stronger driver of soil biogeochemical processes than temperature, because of links among water cover, redox conditions, and organic carbon accumulation in soils. Under the 10% reduced rainfall scenario, large portions of the Everglades will experience dry down, organic soil oxidation, and shifts in soil redox that may dramatically alter biogeochemical processes. Lowering organic soil surface elevation may make portions of the Everglades more vulnerable to sea level rise. The 10% increased rainfall scenario, while potentially increasing phosphorus, sulfur, and mercury loading to the ecosystem, would maintain organic soil integrity and redox conditions conducive to normal wetland biogeochemical element cycling. Effects of increased ET will be similar to those of decreased precipitation. Temperature increases would have the effect of increasing microbial processes driving biogeochemical element cycling, but the effect would be much less than that of precipitation. The combined effects of decreased rainfall and increased ET suggest catastrophic losses in carbon- and organic-associated elements throughout the peat-based Everglades.

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

PubMed

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

2016-08-01

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

Development of a 3D coupled physical-biogeochemical model for the Marseille coastal area (NW Mediterranean Sea): what complexity is required in the coastal zone?

PubMed

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

2013-01-01

Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period of 5 years (2007-2011). The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model.

Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone?

PubMed Central

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

2013-01-01

Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period of 5 years (2007–2011). The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model. PMID:24324589

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

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

RoyChowdhury, Taniya; Bramer, Lisa; Hoyt, David W.

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedent moisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. The objective was tomore » understand shifts in biogeochemical processes in response to changing soil moisture, based on soil respiration and methane production rates, and to elucidate such responses based on the observed electron acceptor and metabolite profiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidence that soil redox was the principal factor driving metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of their concentrations in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction compared to carbon loss due to methanogenesis. These results show that extended and short-term saturation created conditions conducive to increasing metabolite availability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast, extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.« less

The environmental controls that govern the end product of bacterial nitrate respiration

DOE PAGES

Kraft, Beate; Tegetmeyer, Halina E.; Sharma, Ritin; ...

2014-08-08

In the biogeochemical nitrogen cycle, microbial respiration processes compete for nitrate as an electron acceptor. Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium, which is directly reusable by primary producers. In this paper, we combined multiple parallel long-term incubations of marine microbial nitrate-respiring communities with isotope labeling and metagenomics to unravel how specific environmental conditions select for either process. Microbial generation time, supply of nitrite relative to nitrate, and the carbon/nitrogen ratio were identified as key environmental controls that determine whether nitrite will be reduced to nitrogenous gasmore » or ammonium. Finally, our results define the microbial ecophysiology of a biogeochemical feedback loop that is key to global change, eutrophication, and wastewater treatment.« less

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...

Biogeochemical Processes Regulating the Mobility of Uranium in Sediments

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

Belli, Keaton M.; Taillefert, Martial

This book chapters reviews the latest knowledge on the biogeochemical processes regulating the mobility of uranium in sediments. It contains both data from the literature and new data from the authors.

Quantifying Hydro-biogeochemical Model Sensitivity in Assessment of Climate Change Effect on Hyporheic Zone Processes

NASA Astrophysics Data System (ADS)

Song, X.; Chen, X.; Dai, H.; Hammond, G. E.; Song, H. S.; Stegen, J.

2016-12-01

The hyporheic zone is an active region for biogeochemical processes such as carbon and nitrogen cycling, where the groundwater and surface water mix and interact with each other with distinct biogeochemical and thermal properties. The biogeochemical dynamics within the hyporheic zone are driven by both river water and groundwater hydraulic dynamics, which are directly affected by climate change scenarios. Besides that, the hydraulic and thermal properties of local sediments and microbial and chemical processes also play important roles in biogeochemical dynamics. Thus for a comprehensive understanding of the biogeochemical processes in the hyporheic zone, a coupled thermo-hydro-biogeochemical model is needed. As multiple uncertainty sources are involved in the integrated model, it is important to identify its key modules/parameters through sensitivity analysis. In this study, we develop a 2D cross-section model in the hyporheic zone at the DOE Hanford site adjacent to Columbia River and use this model to quantify module and parametric sensitivity on assessment of climate change. To achieve this purpose, We 1) develop a facies-based groundwater flow and heat transfer model that incorporates facies geometry and heterogeneity characterized from a field data set, 2) derive multiple reaction networks/pathways from batch experiments with in-situ samples and integrate temperate dependent reactive transport modules to the flow model, 3) assign multiple climate change scenarios to the coupled model by analyzing historical river stage data, 4) apply a variance-based global sensitivity analysis to quantify scenario/module/parameter uncertainty in hierarchy level. The objectives of the research include: 1) identifing the key control factors of the coupled thermo-hydro-biogeochemical model in the assessment of climate change, and 2) quantify the carbon consumption in different climate change scenarios in the hyporheic zone.

Biogeochemical Factors Influencing the Transport and Fate of Colloids and Colloid-Associated Contaminants in the Vadose Zone

NASA Astrophysics Data System (ADS)

Bradford, S. A.

2016-12-01

The vadose zone exhibits large spatial and temporal variability in many physical, chemical, and biological factors that strongly influence the transport and fate of colloids (e.g., microbes, nanoparticles, clays, and dissolved organic matter) and colloid-associated contaminants (e.g., heavy metals, radionuclides, pesticides, and antibiotics). This presentation highlights our research activities to better understand and predict the influence of specific biogeochemical processes on colloid and colloid-facilitated transport. Results demonstrate the sensitivity of colloid transport, retention, release, and clogging to transients in solution chemistry (e.g., ionic strength, pH, cation and anion type, and surfactants), water velocity and saturation, and preferential flow. Mathematical modeling at interface-, pore-, and continuum-scales is shown to be a critical tool to quantify the relative importance and coupling of these biogeochemical factors on colloid and contaminant transport and fate, which otherwise might be experimentally intractable. Existing gaps in knowledge and model limitations are identified.

Disturbance decouples biogeochemical cycles across forests of the southeastern US

Treesearch

Ashley D. Keiser; Jennifer D. Knoepp; Mark A. Bradford

2016-01-01

Biogeochemical cycles are inherently linked through the stoichiometric demands of the organisms that cycle the elements. Landscape disturbance can alter element availability and thus the rates of biogeochemical cycling. Nitrification is a fundamental biogeochemical process positively related to plant productivity and nitrogen loss from soils to aquatic systems, and the...

Biogeochemical cycles of Chernobyl-born radionuclides in the contaminated forest ecosystems: long-term dynamics of the migration processes

NASA Astrophysics Data System (ADS)

Shcheglov, Alexey; Tsvetnova, Ol'ga; Klyashtorin, Alexey

2013-04-01

Biogeochemical migration is a dominant factor of the radionuclide transport through the biosphere. In the early XX century, V.I. Vernadskii, a Russian scientist known, noted about a special role living things play in transport and accumulation of natural radionuclide in various environments. The role of biogeochemical processes in migration and redistribution of technogenic radionuclides is not less important. In Russia, V. M. Klechkovskii and N.V. Timofeev-Ressovskii showed some important biogeochemical aspects of radionuclide migration by the example of global fallout and Kyshtym accident. Their followers, R.M. Alexakhin, M.A. Naryshkin, N.V. Kulikov, F.A. Tikhomirov, E.B. Tyuryukanova, and others also contributed a lot to biogeochemistry of radionuclides. In the post-Chernobyl period, this area of knowledge received a lot of data that allowed building the radioactive element balance and flux estimation in various biogeochemical cycles [Shcheglov et al., 1999]. Regrettably, many of recent radioecological studies are only focused on specific radionuclide fluxes or pursue some applied tasks, missing the holistic approach. Most of the studies consider biogeochemical fluxes of radioactive isotopes in terms of either dose estimation or radionuclide migration rates in various food chains. However, to get a comprehensive picture and develop a reliable forecast of environmental, ecological, and social consequences of radioactive pollution in a vast contaminated area, it is necessary to investigate all the radionuclide fluxes associated with the biogeochemical cycles in affected ecosystems. We believe such an integrated approach would be useful to study long-term environmental consequences of the Fukushima accident as well. In our long-term research, we tried to characterize the flux dynamics of the Chernobyl-born radionuclides in the contaminated forest ecosystems and landscapes as a part of the integrated biogeochemical process. Our field studies were started in June of 1986 (less than two months after the accident) and have been continued up to now, focused on the most common forest ecosystems scattered over the contaminated areas of Russian Federation and Ukraine. A comprehensive analysis of the 137Cs and 90Sr biogeochemical fluxes shows that downward radionuclide fluxes (those directed from tree crowns to the soil) dominated over the upward fluxes (from the soil to forest vegetation) in the first years after the accident. Currently, the biological cycle in the contaminated ecosystems is a main factor impeding further vertical migration of long-lived radionuclides from upper soil layers to the ground water. The role of biota as a retardation factor depends on landscape type as well. In accumulative landscapes (with positive material balance), biota plays leading role in radionuclide retardation, while in eluvial landscapes (with the negative balance) soil absorbing complex serves as the dominant barrier for radionuclides leaching down the soil profile. The manifestation of both soil- and biota-driven factors depends on the radionuclide chemical speciation in the initial fallout. The latter factor is most important for 137Cs, yet less manifested for 90Sr. Among the biota components, fungi and forest vegetation are of particular importance for 137Cs and 90Sr accumulation, respectively. In summary, biogeochemical cycles of 137Cs and 90Sr in the investigated forest ecosystems serve as main factors impeding the radionuclide migration from the fallout to ground water. Larger-scale landscape factors determine the radionuclide flux intensity in the biogeochemical cycles and affect the radionuclide spatial variability in the contaminated biota components.

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

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

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

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

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

EPA Science Inventory

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

Recent directions taken in water, energy, and biogeochemical budgets research

USGS Publications Warehouse

Lins, Harry F.

1994-01-01

Understanding and predicting global change is a major scientific focus of the late 20th century. Although atmospheric scientists have made substantial progress in developing models that account for many components of the climate system, significant progress is needed in understanding processes associated with the exchange of water, energy, and carbon between terrestrial systems and the atmosphere.To strengthen terrestrial process research, especially research associated with the interactions of water, energy, gases, nutrients, and vegetation, the U.S. Geological Survey initiated an intensive study of Water, Energy, and Biogeochemical Budgets (WEBB). WEBB is aimed at improving understanding of processes controlling terrestrial water, energy, and biogeochemical fluxes, their interactions, and their relations to climatic variables; and the ability to predict continental water, energy, and biogeochemical budgets over a range of spatial and temporal scales.

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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...

Linking Seasonal Variations in the Spectral Slope of Chromophoric Dissolved Organic Matter (CDOM) with Apparent Oxygen Utilization and Excess Nitrogen (DINxs) in the North Atlantic Subtropical Gyre

NASA Astrophysics Data System (ADS)

McDonald, N.; Barnes, R.; Nelson, N. B.

2016-02-01

The optically active or chromophoric fraction of dissolved organic matter (CDOM) is a topic of much interest to researchers due to its role in many biogeochemical processes in the global oceans. As CDOM effectively regulates the underwater light field, its influences on photosynthesis and primary productivity are significant. Despite recognition of its importance in biogeochemical cycles in natural waters, its chemical composition remains nebulous, due to photochemical processes, as well as spatial and temporal variations in composition. Understanding of CDOM composition and links to ocean processes is especially complex in pelagic, oligotrophic waters such as the North Atlantic Subtropical Gyre. In this region, minimum CDOM concentrations have been observed and it is decoupled from both dissolved organic carbon (DOC) and from net primary production (NPP). As CDOM absorbance has been shown to influence estimates of NPP from remote sensing models in the subtropical gyres, and as it has the potential to serve as an invaluable tracer of ocean DOM cycling, a better understanding of links between the optical properties of CDOM and biogeochemical processes in the subtropical gyres is crucial. In this study, monthly depth profiles of CDOM absorbance (between 1m and 3000m) were measured for a period of five years at the Bermuda Atlantic Timeseries Site (BATS) in the North Atlantic Subtropical Gyre to investigate seasonal variations and periodicity in CDOM optical properties. From this data, the spectral slope ratio (Sr) was calculated according to Helms et. al, 2008. Sr can be a useful tool in eliciting information about molecular weight, diagenetic state and microbial processes affecting CDOM composition, especially when coupled with other diagnostic parameters. In this study multivariate analysis techniques were utilized to examine links between Sr and ancillary parameters including apparent oxygen utilization (AOU) and excess nitrogen (DINxs) both of which can be a useful indicator of specific biogeochemical processes in the ocean. Results showed distinct seasonality in CDOM optical properties in conjunction with biological parameters and provide preliminary evidence that CDOM could be used as a proxy for organic carbon removal through the microbial loop.

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...

Temporal dynamics of CO 2 and CH 4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils

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

RoyChowdhury, Taniya; Bramer, Lisa; Hoyt, David W.

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedent moisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. The objective was tomore » understand shifts in biogeochemical processes in response to changing soil moisture, based on soil respiration and methane production rates, and to elucidate such responses based on the observed electron acceptor and metabolite profiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidence that soil redox was the principal factor driving metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of their concentrations in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction compared to carbon loss due to methanogenesis. These results show that extended and short-term saturation created conditions conducive to increasing metabolite availability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast, extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.« less

Temporal dynamics of CO 2 and CH 4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils

DOE PAGES

RoyChowdhury, Taniya; Bramer, Lisa; Hoyt, David W.; ...

2017-06-27

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedent moisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. The objective was tomore » understand shifts in biogeochemical processes in response to changing soil moisture, based on soil respiration and methane production rates, and to elucidate such responses based on the observed electron acceptor and metabolite profiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidence that soil redox was the principal factor driving metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of their concentrations in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction compared to carbon loss due to methanogenesis. These results show that extended and short-term saturation created conditions conducive to increasing metabolite availability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast, extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.« less

EFFECT OF NUTRIENT LOADING ON BIOGEOCHEMICAL AND MICROBIAL PROCESSES IN A NEW ENGLAND HIGH SALT MARSH, SPARTINA PATNES, (AITON MUHL)

EPA Science Inventory

Coastal marshes represent an important transitional zone between uplands and estuaries and can assimilate nutrient inputs from uplands. We examined the effects of nitrogen (N) and phosphorus (P) fertilization on biogeochemical and microbial processes during the summer growing sea...

Characterization of Thermal Refugia and Biogeochemical Hotspots at Sleepers River Watershed, VT

NASA Astrophysics Data System (ADS)

Hwang, K.; Chandler, D. G.; Kelleher, C.; Shanley, J. B.; Shaw, S. B.

2017-12-01

During low flow, changes in the extent of the channel network in headwater catchments depend on groundwater-surface water interactions, and dictate thermal and biogeochemical heterogeneities. Channel reaches with low temperature may act as refugia for valued species such as brook trout, and warmer reaches with high dissolved organic matter may act as biogeochemical hotspots. Prior studies have found uniform scaling of hydrologic and biogeochemical processes above certain spatial thresholds but sizable heterogeneities in these processes below the threshold. We utilize high resolution measurements of water quality parameters including stream temperature, conductivity and fluorescent dissolved organic matter (fDOM) at tributaries in two catchments of Sleepers River Watershed, Vermont to investigate seasonal and spatial variation of water quality and scaling of stream chemistry within the intensive study area and the larger Sleepers River Watershed. This study leverages findings from various small scale regional studies to identify differences in headwater channel reach behavior in a similar climate across some dissimilar geomorphic units, to inform the identification of thermal refugia and biogeochemical hotspots.

Lipids as paleomarkers to constrain the marine nitrogen cycle.

PubMed

Rush, Darci; Sinninghe Damsté, Jaap S

2017-06-01

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction-oxidation transformations of bio-available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio-available nitrogen species. As most microorganisms are soft-bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically-important cycle, and provides examples of biomarker applications in the geological past. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Ocean Carbon and Biogeochemistry Scoping Workshop on Terrestrial and Coastal Carbon Fluxes in the Gulf of Mexico, St. Petersburg, FL

NASA Technical Reports Server (NTRS)

Robbins, L. L.; Coble, P. G.; Clayton, T. D.; Cai, W. J.

2008-01-01

Despite their relatively small surface area, ocean margins may have a significant impact on global biogeochemical cycles and, potentially, the global air-sea fluxes of carbon dioxide. Margins are characterized by intense geochemical and biological processing of carbon and other elements and exchange large amounts of matter and energy with the open ocean. The area-specific rates of productivity, biogeochemical cycling, and organic/inorganic matter sequestration are high in coastal margins, with as much as half of the global integrated new production occurring over the continental shelves and slopes (Walsh, 1991; Doney and Hood, 2002; Jahnke, in press). However, the current lack of knowledge and understanding of biogeochemical processes occurring at the ocean margins has left them largely ignored in most of the previous global assessments of the oceanic carbon cycle (Doney and Hood, 2002). A major source of North American and global uncertainty is the Gulf of Mexico, a large semi-enclosed subtropical basin bordered by the United States, Mexico, and Cuba. Like many of the marginal oceans worldwide, the Gulf of Mexico remains largely unsampled and poorly characterized in terms of its air-sea exchange of carbon dioxide and other carbon fluxes. The goal of the workshop was to bring together researchers from multiple disciplines studying terrestrial, aquatic, and marine ecosystems to discuss the state of knowledge in carbon fluxes in the Gulf of Mexico, data gaps, and overarching questions in the Gulf of Mexico system. The discussions at the workshop were intended to stimulate integrated studies of marine and terrestrial biogeochemical cycles and associated ecosystems that will help to establish the role of the Gulf of Mexico in the carbon cycle and how it might evolve in the face of environmental change.

Regulation of pesticide degradation in the detritusphere

NASA Astrophysics Data System (ADS)

Pagel, Holger; Poll, Christian; Ingwersen, Joachim; Ditterich, Franziska; Gebala, Aurelia; Kandeler, Ellen; Streck, Thilo

2015-04-01

The detritusphere is a microbial hot spot of C turnover and degradation of pesticides in soils. We aimed at an improved understanding of the regulation mechanisms, which are responsible for stimulated degradation of the herbicide MCPA (2-Methyl-4-chlorophenoxyacetic acid) in response to increased C availability in the detritusphere. We combined a microcosm experiment with biogeochemical modeling and linked genetic information on abundances of total bacteria, fungi and specific pesticide degraders in soil to the coupled biogeochemical dynamics of C and MCPA. As a result of diffusive and convective C transport from litter into the adjacent soil we found increased dissolved organic C (DOC) in soil up to a 6 mm distance to litter (detritusphere). In the detritusphere, we observed increased microbial C and accelerated MCPA degradation. These dynamics were accurately reproduced by the model. Whereas the observed increase of bacteria and pesticide degrader populations in the detritusphere was simulated satisfactorily, the model could not reproduce the steep increase of fungi indicated by the fungal marker gene. Our simulations suggest that bacterial MCPA degraders mostly benefited from high-quality DOC, whereas fungal activity and growth were specifically stimulated by low-quality DOC. According to the simulations, MCPA was predominantly degraded via fungal co-metabolism. Our study demonstrates that biogeochemical processes in soil hotspots are regulated by the interaction of transport processes and microbial dynamics. It further reveals that mathematical modelling is as powerful tool to gain comprehensive insight into the microbial regulation of matter cycling in soil. Genetic information has a high potential to parameterize and evaluate complex mechanistic models, but model approaches must be improved based on extended information on gene dynamics at the cellular level.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

PubMed

Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure. Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Program of mineralization and cycling in marine systems: Organic geochemistry of particulates and sediments (CaBS): Progress report, November 15, 1987--November 14, 1988

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

Venkatesan, M.I.; Kaplan, I.R.

1988-11-01

The biogeochemical processes and the dynamics involved in the cycling and transport of organic carbon can be elucidated only by determining distributions of specific organic compounds associated with the particles. At UCLA, the quantitative data of the various organic compounds in the sediment cores and trap particulates from various depths of water column are gathered in order to construct a dynamic model of the biogeochemical cycling and processes occurring in the water and sedimentary columns. The sources of organic carbon in southern California Bight derive from both terrestrial and marine regimes. The varied organic carbon sources can be reasonably delineatedmore » within limits by the organic geochemical approach of determining various characteristic biomarkers, as well as a variety of pollution indicators. The distributions of organic biomarker compounds are characteristic of marine algae, terrestrial vascular plants, bacteria, etc. Presence of specific biomarkers also indicate the occurrence of specific species (e.g., dinosterol specific of dinoflagellates). There are some pollution indicators which one can look for in the marine environment to trace their origin to terrestrial inputs, i.e., polycyclic aromatic hydrocarbons from petroleum and combustion, coprostanol from sewage, etc. We study the distribution of many of these compounds and from a correlation of their relative abundance, an attempt is made to delineate marine vs terrestrial influx to the organic carbon in the study area. 18 refs., 1 fig., 4 tabs.« less

A Hybrid Multiscale Framework for Subsurface Flow and Transport Simulations

DOE PAGES

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

2015-06-01

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

The Bermuda BioOptics Project (BBOP) Years 9-11

NASA Technical Reports Server (NTRS)

Nelson, Norm

2003-01-01

The Bermuda BioOptics Project (BBOP) is a collaborative effort between the Institute for Computational Earth System Science (ICESS) at the University of California at Santa Barbara (UCSB) and the Bermuda Biological Station for Research (BBSR). This research program is designed to characterize light availability and utilization in the Sargasso Sea, and to provide an optical link by which biogeochemical observations may be used to evaluate bio-optical models for pigment concentration, primary production, and sinking particle fluxes from satellite-based ocean color sensors. The BBOP time-series was initiated in 1992, and is carried out in conjunction with the U.S. JGOFS Bermuda Atlantic Time-series Study (BATS) at the Bermuda Biological Station for Research. The BATS program itself has been observing biogeochemical processes (primary productivity, particle flux and elemental cycles) in the mesotrophic waters of the Sargasso Sea since 1988. Closely affiliated with BBOP and BATS is a separate NASA-funded study of the spatial variability of biogeochemical processes in the Sargasso Sea using high-resolution AVHRR and SeaWiFS data collected at Bermuda. The collaboration between BATS and BBOP measurements has resulted in a unique data set that addresses not only the SIMBIOS goals but also the broader issues of important factors controlling the carbon cycle. This final report addresses specific research activities, research results, and lists of presentations and papers submitted for publication.

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

Hammond, Glenn Edward; Yang, Xiaofan; Song, Xuehang

The groundwater-surface water interaction zone (GSIZ) plays an important role in riverine and watershed ecosystems as the exchange of waters of variable composition and temperature (hydrologic exchange flows) stimulate microbial activity and associated biogeochemical reactions. Variable temporal and spatial scales of hydrologic exchange flows, heterogeneity of the subsurface environment, and complexity of biogeochemical reaction networks in the GSIZ present challenges to incorporation of fundamental process representations and model parameterization across a range of spatial scales (e.g. from pore-scale to field scale). This paper presents a novel hybrid multiscale simulation approach that couples hydrologic-biogeochemical (HBGC) processes between two distinct length scalesmore » of interest.« less

Biogeochemistry Science and Education. Part One: Using Non-Traditional Stable Isotopes as Environmental Tracers. Part Two: Identifying and Measuring Undergraduate Misconceptions in Biogeochemistry

ERIC Educational Resources Information Center

Mead, Chris

2014-01-01

This dissertation is presented in two sections. First, I explore two methods of using stable isotope analysis to trace environmental and biogeochemical processes. Second, I present two related studies investigating student understanding of the biogeochemical concepts that underlie part one. Fe and Hg are each biogeochemically important elements in…

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Understanding dynamic pattern and process across spatial scales in river systems using simultaneous deployments of in situ sensors

NASA Astrophysics Data System (ADS)

Wollheim, W. M.; Mulukutla, G.; Cook, C.; Carey, R. O.

2014-12-01

Biogeochemical conditions throughout aquatic landscapes are spatially varied and temporally dynamic due to interactions of upstream land use, climate, hydrologic responses, and internal aquatic processes. One of the key goals in aquatic ecosystem ecology is to parse the upstream influences of terrestrial and aquatic processes on local conditions, which becomes progressively more difficult as watershed size increases and as processes are altered by diverse human activities. Simultaneous deployments of high frequency, in situ aquatic sensors for multiple constituents (e.g. NO3-N, CDOM, turbidity, conductivity, D.O., water temperature, along with flow) offer a new approach for understanding patterns along the aquatic continuum. For this talk, we explore strategies for deployments within single watersheds to improve understanding of terrestrial and aquatic processes. We address applications regarding mobilization of non-point nutrient sources across temporal scales, interactions with land use and watershed size, and the importance of aquatic processes. We also explore ways in which simultaneous sensor deployments can be designed to improve parameterization and testing of river network biogeochemical models. We will provide several specific examples using conductivity, nitrate and carbon from ongoing sensor deployments in New England, USA. We expect that improved deployments of sensors and sensor networks will benefit the management of critical freshwater resources.

Dimensionless Numbers For Morphological, Thermal And Biogeochemical Controls Of Hyporheic Processes

NASA Astrophysics Data System (ADS)

Bellin, Alberto; Marzadri, Alessandra; Tonina, Daniele

2013-04-01

Transport of solutes and heat within the hyporheic zone are interface processes that gained growing attention in the last decade, when several modelling strategies have been proposed, mainly at the local or reach scale. We propose to upscale local hyporheic biogeochemical processes to reach and network scales by means of a Lagrangian modelling framework, which allows to consider the impact of the flow structure on the processes modelled. This analysis shows that geochemical processes can be parametrized through two new Damköhler numbers, DaO, and DaT. DaO = ?up,50-?lim is defined as the ratio between the median hyporheic residence time, ?up,50 and the time of consuming dissolved oxygen to a prescribed threshold concentration, ?lim, below which reductive reactions are activated. It quantifies the biogeochemical status of the hyporheic zone and could be a metric for upscaling local hyporheic biogeochemical processes to reach and river-network scale processes. In addition, ?up,50 is the time scale of hyporheic advection; while ?lim is the representative time scale of biogeochemical reactions and indicates the distance along the streamline, measured as the time needed to travel that distance, that a particle of water travels before the dissolved oxygen concentration declines to [DO]lim, the value at which denitrification is activated. We show that DaO is representative of the redox status and indicates whether the hyporheic zone is a source or a sink of nitrate. Values of DaO larger than 1 indicate prevailing anaerobic conditions, whereas values smaller than 1 prevailing aerobic conditions. Similarly, DaT quantifies the importance of the temperature daily oscillations of the stream water on the hyporheic environment. It is defined as the ratio between ?up,50, and the time limit at which the ratio between the amplitude of the temperature oscillation within the hyporheic zone (evaluated along the streamline) and in the stream water is smaller than e-1. We show that values of DaT > 1 indicate a thermally stable hyporheic zone, where organism metabolism is not influenced by surface water thermal oscillations and biogeochemical reaction rates depend on the mean daily stream water temperature. Values smaller than 1 suggest that organisms need to adapt to the daily thermal variations and biogeochemical reaction rates will depend on the daily fluctuations induced by stream water.

Ocean Carbon States: Data Mining in Observations and Numerical Simulations Results

NASA Astrophysics Data System (ADS)

Latto, R.; Romanou, A.

2017-12-01

Advanced data mining techniques are rapidly becoming widely used in Climate and Earth Sciences with the purpose of extracting new meaningful information from increasingly larger and more complex datasets. This is particularly important in studies of the global carbon cycle, where any lack of understanding of its combined physical and biogeochemical drivers is detrimental to our ability to accurately describe, understand, and predict CO2 concentrations and their changes in the major carbon reservoirs. The analysis presented here evaluates the use of cluster analysis as a means of identifying and comparing spatial and temporal patterns extracted from observational and model datasets. As the observational data is organized into various regimes, which we will call "ocean carbon states", we gain insight into the physical and/or biogeochemical processes controlling the ocean carbon cycle as well as how well these processes are simulated by a state-of-the-art climate model. We find that cluster analysis effectively produces realistic, dynamic regimes that can be associated with specific processes at different temporal scales for both observations and the model. In addition, we show how these regimes can be used to illustrate and characterize the model biases in the model air-sea flux of CO2. These biases are attributed to biases in salinity, sea surface temperature, wind speed, and nitrate, which are then used to identify the physical processes that are inaccurately reproduced by the model. In this presentation, we provide a proof-of-concept application using simple datasets, and we expand to more complex ones, using several physical and biogeochemical variable pairs, thus providing considerable insight into the mechanisms and phases of the ocean carbon cycle over different temporal and spatial scales.

Ecophysiological parameters for Pacific Northwest trees.

Treesearch

Amy E. Hessl; Cristina Milesi; Michael A. White; David L. Peterson; Robert E. Keane

2004-01-01

We developed a species- and location-specific database of published ecophysiological variables typically used as input parameters for biogeochemical models of coniferous and deciduous forested ecosystems in the Western United States. Parameters are based on the requirements of Biome-BGC, a widely used biogeochemical model that was originally parameterized for the...

Metagenomic insights into zooplankton‐associated bacterial communities

PubMed Central

Srivastava, Abhishek; Koski, Marja; Garcia, Juan Antonio L.; Takaki, Yoshihiro; Yokokawa, Taichi; Nunoura, Takuro; Elisabeth, Nathalie H.; Sintes, Eva; Herndl, Gerhard J.

2017-01-01

Summary Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. PMID:28967193

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

USGS Publications Warehouse

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

2015-01-01

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

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

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

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

2015-03-15

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

Marine Biogeochemistry Under The Influence of Fish And Fisheries: An Ecosystem Modeling Study

NASA Astrophysics Data System (ADS)

Disa, Deniz; Akoglu, Ekin; Salihoglu, Baris

2017-04-01

The ocean and the marine ecosystems are important controllers of the global carbon cycle. They play a pivotal role in capturing atmospheric carbon into the ocean body, transforming it into organic carbon through photosynthesis and transporting it to the depths of the ocean. Fish, which has a significant role in the marine food webs, is thought to have a considerable impact on carbon export. More specifically, fish has a control on plankton dynamics as a predator, it provides nutrient to the ecosystem by its metabolic activities and it has the ability of moving actively and transporting materials. Fishing is also expected to impact carbon cycle because it directly changes the fish biomasses. However, how fish impacts the biogeochemistry of marine ecosystems is not studied extensively. The aim of this study is to analyze the impact of fish and fisheries on marine biogeochemical processes by setting up an end-to-end model, which simulates lower and higher tropic levels of marine ecosystems simultaneously. For this purpose, a one dimensional biogeochemical model simulating lower tropic level dynamics (e.g. carbon export, nutrient cycles) and an food web model simulating fisheries exploitation and higher tropic level dynamics were online and two-way coupled. Representing the marine ecosystem from one end to the other, the coupled model served as a tool for the analysis of fishing impacts on marine biogeochemical dynamics. Results obtained after incorporation of higher trophic level model changed the plankton compositions and enhanced detritus pools and increased carbon export. Additionally, our model showed that active movement of fish contributed to transport of carbon from surface to the deeper parts of the ocean. Moreover, results after applying different fishing intensities indicated that changes in fisheries exploitation levels directly influence the marine nutrient cycles and hence, the carbon export. Depending on the target and the intensity of fisheries, considerable changes in the biogeochemical responses observed. In conclusion, unlike the models that do not represent the fish explicitly, we demonstrate how marine biogeochemical processes are impacted by the activity of fish assemblages and fisheries exploitation.

Cost of riparian buffer zones: A comparison of hydrologically adapted site-specific riparian buffers with traditional fixed widths

NASA Astrophysics Data System (ADS)

Tiwari, T.; Lundström, J.; Kuglerová, L.; Laudon, H.; Öhman, K.; Ågren, A. M.

2016-02-01

Traditional approaches aiming at protecting surface waters from the negative impacts of forestry often focus on retaining fixed width buffer zones around waterways. While this method is relatively simple to design and implement, it has been criticized for ignoring the spatial heterogeneity of biogeochemical processes and biodiversity in the riparian zone. Alternatively, a variable width buffer zone adapted to site-specific hydrological conditions has been suggested to improve the protection of biogeochemical and ecological functions of the riparian zone. However, little is known about the monetary value of maintaining hydrologically adapted buffer zones compared to the traditionally used fixed width ones. In this study, we created a hydrologically adapted buffer zone by identifying wet areas and groundwater discharge hotspots in the riparian zone. The opportunity cost of the hydrologically adapted riparian buffer zones was then compared to that of the fixed width zones in a meso-scale boreal catchment to determine the most economical option of designing riparian buffers. The results show that hydrologically adapted buffer zones were cheaper per hectare than the fixed width ones when comparing the total cost. This was because the hydrologically adapted buffers included more wetlands and low productive forest areas than the fixed widths. As such, the hydrologically adapted buffer zones allows more effective protection of the parts of the riparian zones that are ecologically and biogeochemically important and more sensitive to disturbances without forest landowners incurring any additional cost than fixed width buffers.

Surface Ocean-Lower Atmosphere Studies: SOLAS

NASA Astrophysics Data System (ADS)

Wanninkhof, R.; Dickerson, R.; Barber, R.; Capone, D. G.; Duce, R.; Erickson, D.; Keene, W. C.; Lenschow, D.; Matrai, P. A.; McGillis, W.; McGillicuddy, D.; Penner, J.; Pszenny, A.

2002-05-01

The US Surface Ocean - Lower Atmosphere Study (US SOLAS) is a component of an international program (SOLAS) with an overall goal: to achieve a quantitative understanding of the key biogeochemical-physical interactions between the ocean and atmosphere, and of how this coupled system affects and is affected by climateand environmental change. There is increasing evidence that the biogeochemical cycles containing the building blocks of life such as carbon, nitrogen, and sulfur have been perturbed. These changes result in appreciable impacts and feedbacks in the SOLA region. The exact nature of the impacts and feedbacks are poorly constrained because of sparse observations, in particular relating to the connectivity and interrelationships between the major biogeochemical cycles and their interaction with physical forcing. It is in these areas that the research and the interdisciplinary research approaches advocated in US SOLAS will provide high returns. The research in US SOLAS will be heavily focused on process studies of the natural variability of key processes, anthropogenic perturbation of the processes, and the positive and negative feedbacks the processes will have on the biogeochemical cycles in the SOLA region. A major objective is to integrate the process study findings with the results from large-scale observations and with small and large- scale modeling and remote sensing efforts to improve our mechanistic understanding of large scale biogeochemical and physical phenomena and feedbacks. US SOLAS held an open workshop in May 2001 to lay the groundwork for the SOLAS program in the United States. Resulting highlights and issues will be summarized around 4 major themes: (1) Boundary-layer Physics, (2) Dynamics of long-lived climate relevant compounds, (3) Dynamics of short-lived climate relevant compounds, and (4) Atmospheric effects on marine biogeochemical processes. Comprehensive reports from the working groups of U.S. SOLAS, and the international science plan which served as overall guidance, can be found at We will explore possible dedicated, interdisciplinary ocean-atmosphere projects as examples of the critical interconnectivity of atmospheric, interfacial, and upper ocean processes to study phenomena of critical importance in understanding the earth's system.

Effects of hydrologic conditions on biogeochemical processes and organic pollutant degradation in salt marsh sediments

Treesearch

W. James Catallo

2000-01-01

This work addressed the influence of tidal vs. static hydrologic conditions on biogeochemical processes and the transformation of pollutant organic chemicals (eight representative N-, O-, and S-heterocycles (NOSHs) from coal chemicals, crude oils, and pyrogenic mixtures) in salt marsh sediments. The goals were to: (1) determine the effects of static (flooded, drained)...

Advances in the application of amino acid nitrogen isotopic analysis in ecological and biogeochemical studies

USDA-ARS?s Scientific Manuscript database

Compound-specific isotopic analysis of amino acids (CSIA-AA) has emerged in the last decade as a powerful approach for tracing the origins and fate of nitrogen in ecological and biogeochemical studies. This approach is based on the empirical knowledge that source AAs (i.e., phenylalanine), fractiona...

Polychlorinated Biphenyls as Probes of Biogeochemical Processes in Rivers

USGS Publications Warehouse

Fitzgerald, S.A.; Steuer, J.J.

1997-01-01

A field study was conducted to investigate the use of PCB (polychlorinated biphenyl) congener and homolog assemblages as tracers of biogeochemical processes in the Milwaukee and Manitowoc Rivers in southeastern Wisconsin from 1993 to 1995. PCB congeners in the dissolved and suspended particle phases, along with various algal indicators (algal carbon and pigments), were quantitated in the water seasonally. In addition, PCB congener assemblages were determined seasonally in surficial bed sediments. Biogeochemical processes investigated included: determination of the source of suspended particles and bottom sediments by comparison with known Aroclor mixtures, water-solid partitioning, and algal uptake of PCBs. Seasonal differences among the PCB assemblages were observed mainly in the dissolved phase, somewhat less in the suspended particulate phase, and not at all in the bed sediments.

Temporal dynamics of CO 2 and CH 4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils

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

RoyChowdhury, Taniya; Bramer, Lisa; Hoyt, David W.

tEarth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alterthe nature and rate of biogeochemical transformations and significantly impact the carbon balance ofthe ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedentmoisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidalfreshwater wetland system in the lower Columbia River, WA, USA. Our objective was to understand shiftsin biogeochemical processesmore » in response to changing soil moisture, based on soil respiration and methaneproduction rates, and to elucidate such responses based on the observed electron acceptor and metaboliteprofiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidencethat soil redox was the principal factor driving metabolic function. Fluctuating redox conditions alteredterminal electron acceptor and donor availability and recovery strengths of their concentrations in soilsuch that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradationprocesses like sulfate and iron reduction compared to carbon loss due to methanogenesis. Our resultsshow that extended and short-term saturation created conditions conducive to increasing metaboliteavailability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast,extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.« less

Temporal dynamics of CO2and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils

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

Roy Chowdhury, Taniya; Bramer, Lisa M.; Hoyt, Davi

2018-04-15

tEarth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alterthe nature and rate of biogeochemical transformations and significantly impact the carbon balance ofthe ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedentmoisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidalfreshwater wetland system in the lower Columbia River, WA, USA. Our objective was to understand shiftsin biogeochemical processesmore » in response to changing soil moisture, based on soil respiration and methaneproduction rates, and to elucidate such responses based on the observed electron acceptor and metaboliteprofiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidencethat soil redox was the principal factor driving metabolic function. Fluctuating redox conditions alteredterminal electron acceptor and donor availability and recovery strengths of their concentrations in soilsuch that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradationprocesses like sulfate and iron reduction compared to carbon loss due to methanogenesis. Our resultsshow that extended and short-term saturation created conditions conducive to increasing metaboliteavailability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast,extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.« less

Sorption of organic chemicals at biogeochemical interfaces - calorimetric measurements

NASA Astrophysics Data System (ADS)

Krüger, J.; Lang, F.; Siemens, J.; Kaupenjohann, M.

2009-04-01

Biogeochemical interfaces in soil act as sorbents for organic chemicals, thereby controlling the degradation and mobility of these substances in terrestrial environments. Physicochemical properties of the organic chemicals and the sorbent determine sorptive interactions. We hypothesize that the sorption of hydrophobic organic chemicals ("R-determined" chemicals) is an entropy-driven partitioning process between the bulk aqueous phase and biogeochemical interface and that the attachment of more polar organic chemicals ("F-determined" chemicals) to mineral surfaces is due to electrostatic interactions and ligand exchange involving functional groups. In order to determine thermodynamic parameters of sorbate/sorbent interactions calorimetric titration experiments have been conducted at 20˚ C using a Nanocalorimeter (TAM III, Thermometric). Solutions of different organic substances ("R-determined" chemicals: phenanthrene, bisphenol A, "F-determined" chemicals: MCPA, bentazone) with concentrations of 100 mol l-1 were added to suspensions of pure minerals (goethite, muscovite, and kaolinite and to polygalacturonic acid (PGA) as model substance for biofilms in soil. Specific surface, porosity, N and C content, particle size and point of zero charge of the mineral were analyzed to characterize the sorbents. The obtained heat quantities for the initial injection of the organic chemicals to the goethite were 55 and 71 J for bisphenol A and phenanthrene ("R-determined representatives") and 92 and 105 J for MCPA and bentazone ("F-determined" representatives). Further experiments with muscovite, kaolinite and PGA are in progress to determine G and H of the adsorption process.

Spatial Distribution of Small Water Body Types in Indiana Ecoregions

EPA Science Inventory

Due to their large numbers and biogeochemical activity, small water bodies (SWBs), such as ponds and wetlands, can have substantial cumulative effects on hydrologic and biogeochemical processes. Using updated National Wetland Inventory data, we describe the spatial distribution o...

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Biogeochemical Processes in Microbial Ecosystems

NASA Technical Reports Server (NTRS)

DesMarais, David J.

2001-01-01

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

NIGHTHAWK - A Program for Modeling Saturated Batch and Column Experiments Incorporating Equilibrium and Kinetic Biogeochemistry

EPA Science Inventory

NIGHTHAWK simulates the fate and transport of biogeochemically reactive contaminants in the saturated subsurface. Version 1.2 supports batch and one- dimensional advective-dispersive-reactive transport involving a number of biogeochemical processes, including: microbially-mediate...

Spatial Distribution of Small Water Body Types across Indiana Ecoregions

EPA Science Inventory

Due to their large numbers and biogeochemical activity, small water bodies (SWB), such as ponds and wetlands, can have substantial cumulative effects on hydrologic, biogeochemical, and biological processes; yet the spatial distributions of various SWB types are often unknown. Usi...

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

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

Hu, Ping; Tom, Lauren; Singh, Andrea

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to bemore » the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of theAcetothermia(OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylumParcubacteria(OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, includingMicrogenomates(OP11),Atribacteria(OP9), candidate phyla TA06 and WS6, andMarinimicrobia(SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. In conclusion, we show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.« less

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs.

PubMed

Hu, Ping; Tom, Lauren; Singh, Andrea; Thomas, Brian C; Baker, Brett J; Piceno, Yvette M; Andersen, Gary L; Banfield, Jillian F

2016-01-19

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. We show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes. Copyright © 2016 Hu et al.

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

DOE PAGES

Hu, Ping; Tom, Lauren; Singh, Andrea; ...

2016-01-19

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to bemore » the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of theAcetothermia(OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylumParcubacteria(OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, includingMicrogenomates(OP11),Atribacteria(OP9), candidate phyla TA06 and WS6, andMarinimicrobia(SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. In conclusion, we show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.« less

15N indicates an active N-cycling microbial community in low carbon, freshwater sediments.

NASA Astrophysics Data System (ADS)

Sheik, C.

2017-12-01

Earth's large lakes are unique aquatic ecosystems, but we know little of the microbial life driving sedimentary biogeochemical cycles and ultimately the isotopic record. In several of these large lakes, water column productivity is constrained by element limitation, such as phosphorus and iron, creating oligotrophic water column conditions that drive low organic matter content in sediments. Yet, these sediments are biogeochemically active and have been shown to have oxygen consumption rates akin to pelagic ocean sediments and complex sulfur cycling dynamics. Thus, large oligotrophic lakes provide unique and interesting biogeochemical contrast to highly productive freshwater and coastal marine systems. Using Lake Superior as our study site, we found microbial community structure followed patterns in bulk sediment carbon and nitrogen concentrations. These observed patterns were loosely driven by land proximity, as some stations are more coastal and have higher rates of sedimentation, allochthonous carbon inputs and productivity than pelagic sites. Interestingly, upper sediment carbon and nitrogen stable isotopes were quite different from water column. Sediment carbon and nitrogen isotopes correlated significantly with microbial community structure. However, 15N showed much stronger correlation than 13C, and became heavier with core depth. Coinciding with the increase in 15N values, we see evidence of both denitrification and anammox processes in 16S rRNA gene libraries and metagenome assembled genomes. Given that microorganisms prefer light isotopes and that these N-cycling processes both contribute to N2 production and efflux from the sediment, the increase in 15N with sediment depth suggests microbial turnover. Abundance of these genomes also varies with depth suggesting these novel microorganisms are partitioning into specific sediment geochemical zones. Additionally, several of these genomes contain genes involved in sulphur cycling, suggesting a dual biogeochemical role and potential for a cryptic sulfur cycle. Together, Lake Superior sediments offer a glimpse into microbial metabolism in carbon limited environments. Further the pervasiveness of co-metabolic pathways suggests interpretation of isotopic records may be messier than previously thought.

Engineering Pseudomonas stutzeri as a biogeochemical biosensor

NASA Astrophysics Data System (ADS)

Boynton, L.; Cheng, H. Y.; Del Valle, I.; Masiello, C. A.; Silberg, J. J.

2016-12-01

Biogeochemical cycles are being drastically altered as a result of anthropogenic activities, such as the burning of fossil fuels and the industrial production of ammonia. We know microbes play a major part in these cycles, but the extent of their biogeochemical roles remains largely uncharacterized due to inadequacies with culturing and measurement. While metagenomics and other -omics methods offer ways to reconstruct microbial communities, these approaches can only give an indication of the functional roles of microbes in a community. These -omics approaches are rapidly being expanded to the point of outpacing our knowledge of functional genes, which highlights an inherent need for analytical methods that non-invasively monitor Earth's processes in real time. Here we aim to exploit synthetic biology methods in order to engineer a ubiquitous denitrifying microbe, Pseudomonas stutzeri that can act as a biosensor in soil and marine environments. By using an easily cultivated microbe that is also common in many environments, we hope to develop a tool that allows us to zoom in on specific aspects of the nitrogen cycle. In order to monitor processes occurring at the genetic level in environments that cannot be resolved with fluorescence-based methods, such as soils, we have developed a system that instead relies on gas production by engineered microbial biosensors. P. stutzeri has been successfully engineered to release a gas, methyl bromide, which can continuously and non-invasively be measured by GC-MS. Similar to using Green Fluorescent Protein, GFP, in the biological sciences, the gene controlling gas production can be linked to those involved in denitrification, thereby creating a quantifiable gas signal that is correlated with microbial activity in the soil. Synthetically engineered microbial biosensors could reveal key aspects of metabolism in soil systems and offer a tool for characterizing the scope and degree of microbial impact on major biogeochemical cycles.

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...

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...

Reappraisal of soil C storage processes. The controversy on structural diversity of humic substances as biogeochemical driver for soil C fluxes

NASA Astrophysics Data System (ADS)

Almendros, Gonzalo; Gonzalez-Vila, Francisco J.; Gonzalez-Perez, Jose Antonio; Knicker, Heike

2016-04-01

The functional relationships between the macromolecular structure of the humic substances (HS) and a series of biogeochemical processes related with the C sequestration performance in soils have been recently questioned. In this communication we collect recent data from a wide array of different ecosystems where the C storage in soils has been studied and explained as a possible cause-to-effect relationship or has been found significantly correlated (multivariate statistical models) with a series of structural characteristics of humic materials. The study of humic materials has methodological analytical limitations that are derived from its complex, chaotic and not completely understood structure, that reflects its manifold precursors as well as the local impact of environmental/depositional factors. In this work we attempt to design an exploratory, multiomic approach based on the information provided by the molecular characterization of the soil organic matter (SOM). Massive data harvesting was carried out of statistical variables, to infer biogeochemical proxies (spectroscopic, chromatographic, mass spectrometric quantitative descriptors). The experimental data were acquired from advanced instrumental methodologies, viz, analytical pyrolysis, compound-specific stable isotope analysis (CSIA), derivative infrared (FTIR) spectroscopy, solid-state C-13 and N-15 nuclear magnetic resonance (NMR) and mass spectrometry (MS) data after direct injection (thermoevaporation), previous pyrolysis, or ion averaging of specific m/z ranges from classical GC/MS chromatograms. In the transversal exploratory analysis of the multianalytical information, the data were coded for on-line processing in a stage in which there is no need for interpretation, in molecular or structural terms, of the quantitative data consisting of e.g., peak intensities, signal areas, chromatographic (GC) total abundances, etc. A series of forecasting chemometric approaches (aiming to express SOM biodegradability, or soil C resilience as a function of intrinsic molecular characteristics of the SOM) were especially successful in the case of: a) linear multiple regression models (LMR) with automatic backward variable selection, b) supervised removal of internal redundancy of the variables based on multidimensional scaling (MDS), and c) partial least squares (PLS) regression to obtain the variable importance for projection (VIP) which is useful to identify new environmental proxies. At least the results obtained from differing continental Mediterranean soils showed that a large influence of local (soil-dependant) abiotic factors in the final variance (of the total soil C quality and quantity) was explained by the SOM molecular structure. This conclusion is relevant as regards the recent (in our opinion hermeneutic and speculative) controversy disregarding the importance of the structural features of HS in biogeochemical and environmental processes controlling C sequestration in soils.

Preface [to special section on recent Loch Vale Watershed research

USGS Publications Warehouse

Baron, Jill S.; Williams, Mark W.

2000-01-01

Catchment-scale intensive and extensive research conducted over the last decade shows that our understanding of the biogeochemical and hydrologic processes in subalpine and alpine basins is not yet sufficiently mature to model and predict how biogeochemical transformations and surface water quality will change in response to climatic or human-driven changes in energy, water, and chemicals. A better understanding of these processes is needed for input to decision-making regulatory agencies and federal land managers. In recognition of this problem the National Research Council [1998] has identified as a critical research need an improved understanding of how global change will affect biogeochemical interactions with the hydrologic cycle and biogeochemical controls over the transport of water, nutrients, and materials from land to freshwater ecosystems. Improved knowledge of alpine and subalpine ecosystems is particularly important since high-elevation catchments are very sensitive to small changes in the flux of energy, chemicals, and water. Furthermore, alpine ecosystems may act as early warning indicators for ecosystem changes at lower elevations.

Assessment of the GHG Reduction Potential from Energy Crops Using a Combined LCA and Biogeochemical Process Models: A Review

PubMed Central

Jiang, Dong; Hao, Mengmeng; Wang, Qiao; Huang, Yaohuan; Fu, Xinyu

2014-01-01

The main purpose for developing biofuel is to reduce GHG (greenhouse gas) emissions, but the comprehensive environmental impact of such fuels is not clear. Life cycle analysis (LCA), as a complete comprehensive analysis method, has been widely used in bioenergy assessment studies. Great efforts have been directed toward establishing an efficient method for comprehensively estimating the greenhouse gas (GHG) emission reduction potential from the large-scale cultivation of energy plants by combining LCA with ecosystem/biogeochemical process models. LCA presents a general framework for evaluating the energy consumption and GHG emission from energy crop planting, yield acquisition, production, product use, and postprocessing. Meanwhile, ecosystem/biogeochemical process models are adopted to simulate the fluxes and storage of energy, water, carbon, and nitrogen in the soil-plant (energy crops) soil continuum. Although clear progress has been made in recent years, some problems still exist in current studies and should be addressed. This paper reviews the state-of-the-art method for estimating GHG emission reduction through developing energy crops and introduces in detail a new approach for assessing GHG emission reduction by combining LCA with biogeochemical process models. The main achievements of this study along with the problems in current studies are described and discussed. PMID:25045736

AUV based study on physical and ecological processes at fronts

NASA Astrophysics Data System (ADS)

Tippenhauer, Sandra; Wulff, Thorben; Von Appen, Wilken-Jon

2017-04-01

Small-scale processes and their effects get more and more attention when it comes to understanding processes and changes in the (Arctic) ocean. Here we present a study on physical processes and ecological responses at submesoscale frontal systems in the Fram Strait investigated using an autonomous underwater vehicle (AUV). The AUV is equipped with physical and biogeochemical sensors such as an acoustic Doppler current profiler, a turbulence probe, a conductivity-temperature-depth probe, and sensors for Oxygen, Nitrate, Chlorophyll a, and photosynthetically active radiation (PAR). The study is designed such that the AUV covers tracks of several kilometers length in cross-frontal direction with the front roughly located in the middle of the track. On its way, the AUV records high-resolution vertical or zigzag profiles of the physical and biogeochemical properties in the upper 50 m which includes the euphotic zone. In both, physical and biogeochemical terms, the measurements revealed a complex structure of the water column. At the fronts the distribution of phytoplankton and nutrients was highly inhomogeneous, possibly due to wind-driven frontogenesis or the growth of mixed layer eddies. To set the observations into a larger context we also examine ship-based and satellite data. We investigate how the observed patterns of the potential vorticity and the biogeochemical properties may be formed and which processes could lead to a smoothing of the observed gradients.

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

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

Helton, Ashley; Poole, Geoffrey C.; Meyer, Judy

2011-01-01

Agricultural and urban development alters nitrogen and other biogeochemical cycles in rivers worldwide. Because such biogeochemical processes cannot be measured empirically across whole river networks, simulation models are critical tools for understanding river-network biogeochemistry. However, limitations inherent in current models restrict our ability to simulate biogeochemical dynamics among diverse river networks. We illustrate these limitations using a river-network model to scale up in situ measures of nitrogen cycling in eight catchments spanning various geophysical and land-use conditions. Our model results provide evidence that catchment characteristics typically excluded from models may control river-network biogeochemistry. Based on our findings, we identify importantmore » components of a revised strategy for simulating biogeochemical dynamics in river networks, including approaches to modeling terrestrial-aquatic linkages, hydrologic exchanges between the channel, floodplain/riparian complex, and subsurface waters, and interactions between coupled biogeochemical cycles.« less

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

The biogeochemical structuring role of horizontal stirring: Lagrangian perspectives on iron delivery downstream of the Kerguelen Plateau

NASA Astrophysics Data System (ADS)

d'Ovidio, F.; Della Penna, A.; Trull, T. W.; Nencioli, F.; Pujol, M.-I.; Rio, M.-H.; Park, Y.-H.; Cotté, C.; Zhou, M.; Blain, S.

2015-10-01

Field campaigns are instrumental in providing ground truth for understanding and modeling global ocean biogeochemical budgets. A survey however can only inspect a fraction of the global oceans, typically a region hundreds of kilometers wide for a temporal window of the order of (at most) several weeks. This spatiotemporal domain is also the one in which the mesoscale activity induces through horizontal stirring a strong variability in the biogeochemical tracers, with ephemeral, local contrasts which can easily mask the regional and seasonal gradients. Therefore, whenever local in situ measures are used to infer larger-scale budgets, one faces the challenge of identifying the mesoscale structuring effect, if not simply to filter it out. In the case of the KEOPS2 investigation of biogeochemical responses to natural iron fertilization, this problem was tackled by designing an adaptive sampling strategy based on regionally optimized multisatellite products analyzed in real time by specifically designed Lagrangian diagnostics. This strategy identified the different mesoscale and stirring structures present in the region and tracked the dynamical frontiers among them. It also enabled back trajectories for the ship-sampled stations to be estimated, providing important insights into the timing and pathways of iron supply, which were explored further using a model based on first-order iron removal. This context was essential for the interpretation of the field results. The mesoscale circulation-based strategy was also validated post-cruise by comparing the Lagrangian maps derived from satellites with the patterns of more than one hundred drifters, including some adaptively released during KEOPS2 and a subsequent research voyage. The KEOPS2 strategy was adapted to the specific biogeochemical characteristics of the region, but its principles are general and will be useful for future in situ biogeochemical surveys.

The biogeochemical structuring role of horizontal stirring: Lagrangian perspectives on iron delivery downstream of the Kerguelen plateau

NASA Astrophysics Data System (ADS)

d'Ovidio, F.; Della Penna, A.; Trull, T. W.; Nencioli, F.; Pujol, I.; Rio, M. H.; Park, Y.-H.; Cotté, C.; Zhou, M.; Blain, S.

2015-01-01

Field campaigns are instrumental in providing ground truth for understanding and modelling global ocean biogeochemical budgets. A survey however can only inspect a fraction of the global oceans, typically a region 100s km wide for a temporal window of the order of (at most) several weeks. This spatiotemporal domain is also the one in which the mesoscale activity induces through horizontal stirring a strong variability in the biogeochemical tracers, with ephemeral, local contrasts which can easily mask the regional and seasonal gradients. Therefore, whenever local in-situ measures are used to infer larger scale budgets one faces the challenge of identifying the mesoscale structuring effect, if not simply to filter it out. In the case of the KEOPS2 investigation of biogeochemical responses to natural iron fertilization, this problem was tackled by designing an adaptive sampling strategy based on regionally-optimized multisatellite products analyzed in real time by specifically designed Lagrangian diagnostics. This strategy identified the different mesoscale and stirring structures present in the region and tracked the dynamical frontiers among them. It also enabled back-trajectories for the ship sampled stations to be estimated, providing important insights into the timing and pathways of iron supply, which were explored further using model based on first order iron removal. This context was essential for the interpretation of the field results. The mesoscale circulation based strategy was also validated post-cruise by comparing the Lagrangian maps derived from satellite with the patterns of more than one hundred drifters adaptively released during KEOPS2 and a subsequent research voyage. The KEOPS2 strategy was adapted to the specific biogeochemical characteristics of the region, but its principles are general and will be useful for future in-situ biogeochemical surveys.

Microbial Surface Colonization and Biofilm Development in Marine Environments

PubMed Central

2015-01-01

SUMMARY Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. PMID:26700108

Microbial Surface Colonization and Biofilm Development in Marine Environments.

PubMed

Dang, Hongyue; Lovell, Charles R

2016-03-01

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Biogeochemical Coupling between Ocean and Sea Ice

NASA Astrophysics Data System (ADS)

Wang, S.; Jeffery, N.; Maltrud, M. E.; Elliott, S.; Wolfe, J.

2016-12-01

Biogeochemical processes in ocean and sea ice are tightly coupled at high latitudes. Ongoing changes in Arctic and Antarctic sea ice domain likely influence the coupled system, not only through physical fields but also biogeochemical properties. Investigating the system and its changes requires representation of ocean and sea ice biogeochemical cycles, as well as their coupling in Earth System Models. Our work is based on ACME-HiLAT, a new offshoot of the Community Earth System Model (CESM), including a comprehensive representation of marine ecosystems in the form of the Biogeochemical Elemental Cycling Module (BEC). A full vertical column sea ice biogeochemical module has recently been incorporated into the sea ice component. We have further introduced code modifications to couple key growth-limiting nutrients (N, Si, Fe), dissolved and particulate organic matter, and phytoplankton classes that are important in polar regions between ocean and sea ice. The coupling of ocean and sea ice biology-chemistry will enable representation of key processes such as the release of important climate active constituents or seeding algae from melting sea ice into surface waters. Sensitivity tests suggest sea ice and ocean biogeochemical coupling influences phytoplankton competition, biological production, and the CO2 flux. Sea ice algal seeding plays an important role in determining phytoplankton composition of Arctic early spring blooms, since different groups show various responses to the seeding biomass. Iron coupling leads to increased phytoplankton biomass in the Southern Ocean, which also affects carbon uptake via the biological pump. The coupling of macronutrients and organic matter may have weaker influences on the marine ecosystem. Our developments will allow climate scientists to investigate the fully coupled responses of the sea ice-ocean BGC system to physical changes in polar climate.

Biogeochemical metabolic modeling of methanogenesis by Methanosarcina barkeri

NASA Astrophysics Data System (ADS)

Jensvold, Z. D.; Jin, Q.

2015-12-01

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

The genetic potential for key biogeochemical processes in Arctic frost flowers and young sea ice revealed by metagenomic analysis.

PubMed

Bowman, Jeff S; Berthiaume, Chris T; Armbrust, E Virginia; Deming, Jody W

2014-08-01

Newly formed sea ice is a vast and biogeochemically active environment. Recently, we reported an unusual microbial community dominated by members of the Rhizobiales in frost flowers at the surface of Arctic young sea ice based on the presence of 16S gene sequences related to these strains. Here, we use metagenomic analysis of two samples, from a field of frost flowers and the underlying young sea ice, to explore the metabolic potential of this surface ice community. The analysis links genes for key biogeochemical processes to the Rhizobiales, including dimethylsulfide uptake, betaine glycine turnover, and halocarbon production. Nodulation and nitrogen fixation genes characteristic of terrestrial root-nodulating Rhizobiales were generally lacking from these metagenomes. Non-Rhizobiales clades at the ice surface had genes that would enable additional biogeochemical processes, including mercury reduction and dimethylsulfoniopropionate catabolism. Although the ultimate source of the observed microbial community is not known, considerations of the possible role of eolian deposition or transport with particles entrained during ice formation favor a suspended particle source for this microbial community. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

INTERACTIONS OF CHANGING CLIMATE AND ULTRAVIOLET RADIATION IN AQUATIC AND TERRESTRIAL BIOGEOCHEMICAL CYCLES

EPA Science Inventory

During the past decade interest has developed in the interactive effects of climate change and UV radiation on aquatic and terrestrial biogeochemical cycles. This talk used selected case studies to illustrate approaches that are being used to investigate these intriguing processe...

Restoration effects on N cycling pools and processes

Treesearch

James M. Vose; Chris Geron; John Walker; Karsten Raulund-Rasmussen

2005-01-01

Over the past several years, there has been an acceleration of restoration efforts to mitigate the consequences (i.e., ground and surface water chemical pollutants, erosion, etc.) of degraded ecosystems and enhance structural and functional components of watershed ecosystems that regulate biogeochemical cycling and associated aquatic components. Biogeochemical...

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

Treesearch

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

2011-01-01

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

Biogeochemical research priorities for sustainable biofuel and bioenergy feedstock production in the Americas

USDA-ARS?s Scientific Manuscript database

Rapid expansion in biomass production for biofuels and bioenergy in the Americas is increasing demands on the ecosystem resources required to sustain soil and site productivity. We review the current state of knowledge and highlight gaps in research on biogeochemical processes and ecosystem sustaina...

Wetland eco-engineering: measuring and modeling feedbacks of oxidation processes between plants and clay-rich material

NASA Astrophysics Data System (ADS)

Saaltink, Rémon; Dekker, Stefan C.; Griffioen, Jasper; Wassen, Martin J.

2016-09-01

Interest is growing in using soft sediment as a foundation in eco-engineering projects. Wetland construction in the Dutch lake Markermeer is an example: here, dredging some of the clay-rich lake-bed sediment and using it to construct wetland will soon begin. Natural processes will be utilized during and after construction to accelerate ecosystem development. Knowing that plants can eco-engineer their environment via positive or negative biogeochemical plant-soil feedbacks, we conducted a 6-month greenhouse experiment to identify the key biogeochemical processes in the mud when Phragmites australis is used as an eco-engineering species. We applied inverse biogeochemical modeling to link observed changes in pore water composition to biogeochemical processes. Two months after transplantation we observed reduced plant growth and shriveling and yellowing of foliage. The N : P ratios of the plant tissue were low, and these were affected not by hampered uptake of N but by enhanced uptake of P. Subsequent analyses revealed high Fe concentrations in the leaves and roots. Sulfate concentrations rose drastically in our experiment due to pyrite oxidation; as reduction of sulfate will decouple Fe-P in reducing conditions, we argue that plant-induced iron toxicity hampered plant growth, forming a negative feedback loop, while simultaneously there was a positive feedback loop, as iron toxicity promotes P mobilization as a result of reduced conditions through root death, thereby stimulating plant growth and regeneration. Given these two feedback mechanisms, we propose the use of Fe-tolerant species rather than species that thrive in N-limited conditions. The results presented in this study demonstrate the importance of studying the biogeochemical properties of the situated sediment and the feedback mechanisms between plant and soil prior to finalizing the design of the eco-engineering project.

Biogeochemical zonation of sulfur during the discharge of groundwater to lake in desert plateau (Dakebo Lake, NW China).

PubMed

Su, Xiaosi; Cui, Geng; Wang, Huang; Dai, Zhenxue; Woo, Nam-Chil; Yuan, Wenzhen

2018-06-01

As one of the important elements of controlling the redox system within the hyporheic and hypolentic zone, sulfur is involved in a series of complex biogeochemical processes such as carbon cycle, water acidification, formation of iron and manganese minerals, redox processes of trace metal elements and a series of important ecological processes. Previous studies on biogeochemistry of the hyporheic and hypolentic zones mostly concentrated on nutrients of nitrogen and phosphorus, heavy metals and other pollutants. Systematic study of biogeochemical behavior of sulfur and its main controlling factors within the lake hypolentic zone is very urgent and important. In this paper, a typical desert plateau lake, Dakebo Lake in northwestern China, was taken for example within which redox zonation and biogeochemical characteristics of sulfur affected by hydrodynamic conditions were studied based on not only traditional hydrochemical analysis, but also environmental isotope evidence. In the lake hypolentic zone of the study area, due to the different hydrodynamic conditions, vertical profile of sulfur species and environmental parameters differ at the two sites of the lake (western side and center). Reduction of sulfate, deposition and oxidation of sulfide, dissolution and precipitation of sulfur-bearing minerals occurred are responded well to Eh, dissolved oxygen, pH, organic carbon and microorganism according to which the lake hypolentic zone can be divided into reduced zone containing H 2 S, reduced zone containing no H 2 S, transition zone and oxidized zone. The results of this study provide valuable insights for understanding sulfur conversion processes and sulfur biogeochemical zonation within a lake hypolentic zone in an extreme plateau arid environment and for protecting the lake-wetland ecosystem in arid and semiarid regions.

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

PubMed Central

Hawley, Alyse K.; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P.; Kheirandish, Sam; Michiels, Céline C.; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A.; Hallam, Steven J.

2016-01-01

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales. PMID:27655888

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

PubMed

Louca, Stilianos; Hawley, Alyse K; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P; Kheirandish, Sam; Michiels, Céline C; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A; Hallam, Steven J

2016-10-04

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.

BIO ARGO floats: tools for operational monitoring of the Black Sea

NASA Astrophysics Data System (ADS)

Palazov, Atanas; Slabakova, Violeta; Peneva, Elisaveta; Stanev, Emil

2014-05-01

The assessment of ecological status in the context of the Water Framework Directive (WFD) and Marine Strategy Framework Directive (MSFD) requires comprehensive knowledge and understanding of the physical and biogeochemical processes that determine the functioning of marine ecosystems. One of the main challenges however is the need of data with frequency relevant to the spatial and temporal scales of the ecological processes. The majority of in situ observations that are commonly used for ecological monitoring of the Black Sea are generally based on near-shore monitoring programs or irregular oceanographic cruises that provide either non-synoptic, coarse resolution realizations of large scale processes or detailed, but time and site specific snapshots of local features. These gaps can be filled by two independent sources: satellite observation and profiling floats. In fact satellite ocean color sensors allows for determination at synoptic scale of water quality parameters through its absorption properties. However the satellite ocean color methods have a number of limitations such as: measurements can only be made during daylight hours; require cloud-free conditions and are sensitive to atmospheric aerosols; provide information only for the upper layer of the ocean (approximately the depth of 10% incident light); algorithms developed for global applications are a source of large uncertainties in the marginal seas and costal areas. These constrains of the optical remote sensing observations can be avoided by using miniature biogeochemical sensors and autonomous platforms that offer remarkable perspectives for observing the "biological" ocean, notably at critical spatiotemporal scales which have been out of reach until recently (Claustre et al., 2010). In the frame of "E-AIMS: Euro-Argo Improvements for the GMES marine Service" 7 EC FP project two Bio Argo floats were deployed in the Black Sea. Beside the traditionally CTD the floats were equipped with biogeochemical sensors (oxygen, irradiance, chl-a and backscattering). The selection of the deployment locations was limited only to the Bulgarian Black Sea waters, so that the optimal deployment strategy that has been chosen was the floats to be deployed in the maximum distant positions from each other along the Black Sea geostrophic current at depth ~ 1800 m. Coincident biogeochemical and in-water radiometric measurements were collected at the time of each float deployment to ensure intercalibration of the instruments mounted on the floats and as well as to find empirical relationship between optical data and biogeochemical variables. The data obtained form Bio floats will be used to: investigate the seasonal evolution of oxygen in the upper layers, including the subsurface oxygen maximum; study the seasonal and inter annual dynamics of phytoplankton blooms in the deeper Black Sea; cross validation of satellite derived Chl-a and backscattering. References: Claustre et al. (2010). Bio-optical profiling floats as new observational tools for biogeochemical and ecosystem studies: potential synergies with ocean color remote sensing. Proceedings of the "OceanObs'09: Sustained Ocean Observations and Information for Society" Conference, Venice/Italy.

Natural attenuation of chlorinated solvents at Area 6, Dover Air Force Base: Groundwater biogeochemistry

USGS Publications Warehouse

Witt, M.E.; Klecka, G.M.; Lutz, E.J.; Ei, T.A.; Grosso, N.R.; Chapelle, F.H.

2002-01-01

Monitored natural attenuation (MNA) has recently emerged as a viable groundwater remediation technology in the United States. Area 6 at Dover Air Force Base (Dover, DE) was chosen as a test site to examine the potential for MNA of tetrachloroethene (PCE) and trichloroethene (TCE) in groundwater and aquifer sediments. A "lines of evidence" approach was used to document the occurrence of natural attenuation. Chlorinated hydrocarbon and biogeochemical data were used to develop a site-specific conceptual model where both anaerobic and aerobic biological processes are responsible for the destruction of PCE, TCE, and daughter metabolites. An examination of groundwater biogeochemical data showed a region of depleted dissolved oxygen with elevated dissolved methane and hydrogen concentrations. Reductive dechlorination likely dominated in the anaerobic portion of the aquifer where PCE and TCE levels were observed to decrease with a simultaneous increase in cis-1,2-dichloroethene (cis-DCE), vinyl chloride (VC), ethene, and dissolved chloride. Near the anaerobic/aerobic interface, concentrations of cis-DCE and VC decreased to below detection limits, presumably due to aerobic biotransformation processes. Therefore, the contaminant and daughter product plumes present at the site appear to have been naturally attenuated by a combination of active anaerobic and aerobic biotransformation processes. ?? 2002 Elsevier Science B.V. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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

Quantification of terrestrial ecosystem carbon dynamics in the conterminous United States combining a process-based biogeochemical model and MODIS and AmeriFlux data

USDA-ARS?s Scientific Manuscript database

Satellite remote sensing provides continuous temporal and spatial information of terrestrial ecosystems. Using these remote sensing data and eddy flux measurements and biogeochemical models, such as the Terrestrial Ecosystem Model (TEM), should provide a more adequate quantification of carbon dynami...

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

USGS Publications Warehouse

Wetzel, P.R.; Sklar, Fred 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

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.

Use of slow filtration columns to assess oxygen respiration, consumption of dissolved organic carbon, nitrogen transformations, and microbial parameters in hyporheic sediments.

PubMed

Mermillod-Blondin, F; Mauclaire, L; Montuelle, B

2005-05-01

Biogeochemical processes mediated by microorganisms in river sediments (hyporheic sediments) play a key role in river metabolism. Because biogeochemical reactions in the hyporheic zone are often limited to the top few decimetres of sediments below the water-sediment interface, slow filtration columns were used in the present study to quantify biogeochemical processes (uptakes of O2, DOC, and nitrate) and the associated microbial compartment (biomass, respiratory activity, and hydrolytic activity) at a centimetre scale in heterogeneous (gravel and sand) sediments. The results indicated that slow filtration columns recreated properly the aerobic-anaerobic gradient classically observed in the hyporheic zone. O2 and NO3- consumptions (256 +/- 13 microg of O2 per hour and 14.6 +/- 6.1 microg of N-NO3- per hour) measured in columns were in the range of values measured in different river sediments. Slow filtration columns also reproduced the high heterogeneity of the hyporheic zone with the presence of anaerobic pockets in sediments where denitrification and fermentation processes occurred. The respiratory and hydrolytic activities of bacteria were strongly linked with the O2 consumption in the experimental system, highlighting the dominance of aerobic processes in our river sediments. In comparison with these activities, the bacterial biomass (protein content) integrated both aerobic and anaerobic processes and could be used as a global microbial indicator in our system. Finally, slow filtration columns are an appropriate tool to quantify in situ rates of biogeochemical processes and to determine the relationship between the microbial compartment and the physico-chemical environment in coarse river sediments.

Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions

PubMed Central

Lamba, Sanjay; Bera, Soumen; Rashid, Mubasher; Medvinsky, Alexander B.; Acquisti, Claudia; Li, Bai-Lian

2017-01-01

Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics. We show that alternative biochemical pathways play a key role in keeping nitrogen conversion and conservation properties invariant in fluctuating environments. Our results indicate that the biochemical network holds inherent adaptive capacity to stabilize ammonium and nitrate availability, and that the bistability in the formation of ammonium is linked to the transient upregulation of the amo-hao mediated nitrification pathway. The bistability is maintained by a pair of complementary subsystems acting as either source or sink type systems in response to soil redox fluctuations. It is further shown how elevated anthropogenic pressure has the potential to break down the stability of the system, altering substantially ammonium and nitrate availability in the soil, with dramatic effects on biodiversity. PMID:28280580

Biogeochemical Mg cycle in the Barton Peninsula, King George Island, West Antarctica

NASA Astrophysics Data System (ADS)

Choi, H. B.; Ryu, J. S.; Lee, J.; Lim, H. S.; Yoon, H.

2016-12-01

Understanding of biogeochemical Mg cycle is important in terms of plant growth as well as global climate because Mg participates in numerous biogeochemical processes. Here, we collected rock, soil, water and moss samples in the Barton peninsula, King George Island, West Antarctica, and measured their elemental and Mg isotope compositions in order to quantify and understand the biogeochemical processes of the Mg cycle. Elemental results show that the input of seawater derived Mg mainly controls dissolved Mg in meltwater. Mg isotope compositions in rocks and soils are consistent within the error, -0.03 ± 0.15‰ (n=6) and +0.03 ± 0.07‰ (n=8), respectively. However, δ26Mg values of meltwater and moss are -0.69 ± 0.09‰ (n=34) and -0.46 ± 0.19‰ (n=16), respectively, indicating that mosses display higher δ26Mg values compared to meltwater they uptake. This implies an isotope fractionation in favor of heavy isotopes during moss growth. The apparent Mg isotope fractionation between moss and meltwater (Δ26Mgmoss-meltwater) ranges from 0.02‰ to 0.55‰, with an average of +0.29‰ (n=6), which is within the range previously reported during higher plant growth. Our finding suggests that enhanced plant growth in Arctic and Antarctica due to climate change and global warming may play an important role in the biogeochemical Mg cycle globally.

Scientific Discovery through Advanced Computing (SciDAC-3) Partnership Project Annual Report

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

Hoffman, Forest M.; Bochev, Pavel B.; Cameron-Smith, Philip J..

The Applying Computationally Efficient Schemes for BioGeochemical Cycles ACES4BGC Project is advancing the predictive capabilities of Earth System Models (ESMs) by reducing two of the largest sources of uncertainty, aerosols and biospheric feedbacks, with a highly efficient computational approach. In particular, this project is implementing and optimizing new computationally efficient tracer advection algorithms for large numbers of tracer species; adding important biogeochemical interactions between the atmosphere, land, and ocean models; and applying uncertainty quanti cation (UQ) techniques to constrain process parameters and evaluate uncertainties in feedbacks between biogeochemical cycles and the climate system.

Benthic boundary layer processes in the Lower Florida Keys

USGS Publications Warehouse

Lavoie, D.L.; Richardson, M.D.; Holmes, C.

1997-01-01

This special issue of Geo-Marine Letters, "Benthic Boundary Layer Processes in the Lower Florida Keys," includes 12 papers that present preliminary results from the Key West Campaign. The Dry Tortugas and Marquesas Keys test sites were selected by a group of 115 scientists and technicians to study benthic boundary layer processes in a carbonate environment controlled by bioturbation and biogeochemical processes. Major activities included remote sediment classification; high-frequency acoustic scattering experiments; sediment sampling for radiological, geotechnical, biological, biogeochemical, physical, and geoacoustic studies; and hydrodynamic studies using an instrumented tetrapod. All these data are being used to improve our understanding of the effects of environmental processes on sediment structure and behavior.

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

USGS Publications Warehouse

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

2011-01-01

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

Biogeochemical research priorities for sustainable biofuel and bioenergy feedstock production in the Americas

Treesearch

Hero T. Gollany; Brian D. Titus; D. Andrew Scott; Heidi Asbjornsen; Sigrid C. Resh; Rodney A. Chimner; Donald J. Kaczmarek; Luiz F.C. Leite; Ana C.C. Ferreira; Kenton A. Rod; Jorge Hilbert; Marcelo V. Galdos; Michelle E. Cisz

2015-01-01

Rapid expansion in biomass production for biofuels and bioenergy in the Americas is increasing demand on the ecosystem resources required to sustain soil and site productivity. We review the current state of knowledge and highlight gaps in research on biogeochemical processes and ecosystem sustainability related to biomass production. Biomass production systems...

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

Treesearch

Jianbo Cui; Changsheng Li; Carl Trettin

2005-01-01

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

A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

NASA Astrophysics Data System (ADS)

Shapiro, B.; Jin, Q.

2015-12-01

Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

Understanding the Day Cent model: Calibration, sensitivity, and identifiability through inverse modeling

USGS Publications Warehouse

Necpálová, Magdalena; Anex, Robert P.; Fienen, Michael N.; Del Grosso, Stephen J.; Castellano, Michael J.; Sawyer, John E.; Iqbal, Javed; Pantoja, Jose L.; Barker, Daniel W.

2015-01-01

The ability of biogeochemical ecosystem models to represent agro-ecosystems depends on their correct integration with field observations. We report simultaneous calibration of 67 DayCent model parameters using multiple observation types through inverse modeling using the PEST parameter estimation software. Parameter estimation reduced the total sum of weighted squared residuals by 56% and improved model fit to crop productivity, soil carbon, volumetric soil water content, soil temperature, N2O, and soil3NO− compared to the default simulation. Inverse modeling substantially reduced predictive model error relative to the default model for all model predictions, except for soil 3NO− and 4NH+. Post-processing analyses provided insights into parameter–observation relationships based on parameter correlations, sensitivity and identifiability. Inverse modeling tools are shown to be a powerful way to systematize and accelerate the process of biogeochemical model interrogation, improving our understanding of model function and the underlying ecosystem biogeochemical processes that they represent.

Biogeochemical Processes in Microbial Ecosystems

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Water, Carbon, and Nutrient Cycling Following Insect-induced Tree Mortality: How Well Do Plot-scale Observations Predict Ecosystem-Scale Response?

NASA Astrophysics Data System (ADS)

Brooks, P. D.; Barnard, H. R.; Biederman, J. A.; Borkhuu, B.; Edburg, S. L.; Ewers, B. E.; Gochis, D. J.; Gutmann, E. D.; Harpold, A. A.; Hicke, J. A.; Pendall, E.; Reed, D. E.; Somor, A. J.; Troch, P. A.

2011-12-01

Widespread tree mortality caused by insect infestations and drought has impacted millions of hectares across western North America in recent years. Although previous work on post-disturbance responses (e.g. experimental manipulations, fire, and logging) provides insight into how water and biogeochemical cycles may respond to insect infestations and drought, we find that the unique nature of these drivers of tree mortality complicates extrapolation to larger scales. Building from previous work on forest disturbance, we present a conceptual model of how temporal changes in forest structure impact the individual components of energy balance, hydrologic partitioning, and biogeochemical cycling and the interactions among them. We evaluate and refine this model using integrated observations and process modeling on multiple scales including plot, stand, flux tower footprint, hillslope, and catchment to identify scaling relationships and emergent patterns in hydrological and biogeochemical responses. Our initial results suggest that changes in forest structure at point or plot scales largely have predictable effects on energy, water, and biogeochemical cycles that are well captured by land surface, hydrological, and biogeochemical models. However, observations from flux towers and nested catchments suggest that both the hydrological and biogeochemical effects observed at tree and plot scales may be attenuated or exacerbated at larger scales. Compensatory processes are associated with attenuation (e.g. as transpiration decreases, evaporation and sublimation increase), whereas both attenuation and exacerbation may result from nonlinear scaling behavior across transitions in topography and ecosystem structure that affect the redistribution of energy, water, and solutes. Consequently, the effects of widespread tree mortality on ecosystem services of water supply and carbon sequestration will likely depend on how spatial patterns in mortality severity across the landscape affect large-scale hydrological partitioning.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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

PubMed

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

2017-08-01

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

Seasonal and event-scale controls on dissolved organic carbon and nitrate flushing from catchments

NASA Astrophysics Data System (ADS)

Sebestyen, S. D.; Boyer, E. W.; Shanley, J. B.; Doctor, D. H.

2005-05-01

To explore terrestrial and aquatic linkages controlling nutrient dynamics in forested catchments, we collected high-frequency samples from 2002 to 2004 at the Sleepers River Research Watershed in northeastern Vermont USA. We measured DOC (dissolved organic carbon), SUVA (specific UV absorbance), nitrate, and major ion concentrations over a wide range of flow conditions. In addition, weekly samples since 1991 provide a longer term record of stream nutrient fluxes. During events, DOC concentrations increased with flow consistent with the flushing of a large reservoir of mobile organic carbon from forest soils. Higher concentrations of DOC and SUVA in the growing versus dormant season illustrated seasonal variation in sources, characteristics (i.e. reactivity), availability, and controls on the flushing response of organic matter from the landscape to streams. In contrast, stream nitrate concentrations increased with flow but only when catchments "wetted-up" after baseflow periods. Growing season stream nitrate responses were dependent on short-term antecedent moisture conditions indicating rapid depletion of the soil nitrate reservoir when source areas became hydrologically connected to streams. While the different response patterns emphasized variable source and biogeochemical controls in relation to flow patterns, coupled carbon and nitrogen biogeochemical processes were also important controls on stream nutrient fluxes. In particular, leaf fall was a critical time when reactive DOC from freshly decomposing litter fueled in-stream consumption of nitrate leading to sharp declines of stream nitrate concentrations. Our measurements highlight the importance of "hot spots" and "hot moments" of biogeochemical and hydrological processes that control stream responses. Furthermore, our work illustrates how carbon, nitrogen, and water cycles are coupled in catchments, and provides a conceptual model for future work aimed at modeling forest stream hydrochemistry at the catchment scale.

Development of Advanced Eco-hydrologic and Biogeochemical Coupling Model to Constrain Missing Role of Inland Waters on Boundless Biogeochemical Cycle

NASA Astrophysics Data System (ADS)

Nakayama, T.; Maksyutov, S. S.

2016-12-01

Inland waters including rivers, lakes, and groundwater are suggested to act as a transport pathway for water and dissolved substances, and play some role in continental biogeochemical cycling (Cole et al., 2007; Battin et al., 2009). The authors have developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (Nakayama, 2014, 2015, etc.), which includes feedback between hydrologic-geomorphic-ecological processes. In this study, NICE was further developed to couple with various biogeochemical cycle models in biosphere, those for water quality in aquatic ecosystems, and those for carbon weathering, etc. (NICE-BGC) (Nakayama, accepted). The new model incorporates connectivity of the biogeochemical cycle accompanied by hydrologic cycle between surface water and groundwater, hillslopes and river networks, and other intermediate regions. The model also includes reaction between inorganic and organic carbons, and its relation to nitrogen and phosphorus in terrestrial-aquatic continuum. The model results of CO2 evasion to the atmosphere, sediment storage, and carbon transport to the ocean (DOC, POC, and DIC flux) were reasonably in good agreement with previous compiled data. The model also showed carbon budget in major river basins and in each continent in global scale. In order to decrease uncertainty about carbon cycle, it became clear the previous empirical estimation by compiled data should be extended to this process-oriented model and higher resolution data to further clarify mechanistic interplay between inorganic and organic carbon and its relationship to nitrogen and phosphorus in terrestrial-aquatic linkages. NICE-BGC would play important role to re-evaluate greenhouse gas budget of the biosphere, and to bridge gap between top-down and bottom-up approaches (Battin et al., 2009; Regnier et al., 2013).

What can high frequency data tell us about hydrological and biogeochemical processes in a permafrost-underlain watershed that we do not already know?

NASA Astrophysics Data System (ADS)

Carey, S. K.; Shatilla, N. J.; Tang, W.

2017-12-01

Permafrost and frozen ground play a key role in the delivery of water and solutes from the landscape to the stream, and in biogeochemical cycling by acting as a cold season or semi-permanent aquitard. Conceptual models of permafrost hydrology have been well defined for over 40 years, yet renewed interest in the face of global climate change and rapid degradation of frozen ground has provided an opportunity to revisit previous paradigms. At the same time, new instruments and techniques to understand coupled hydrological and biogeochemical processes have emerged, providing a more nuanced view of northern systems. High-frequency sub-hourly measures of flows, water quality and biogeochemical parameters such as salinity and chromophoric dissolved organic matter (CDOM), along with eddy covariance systems provide considerable data, yet using this data to reveal new process information remains challenging. In this presentation, multi-year high frequency data sets of water, solute and carbon fluxes from Granger Creek, an instrumented alpine watershed with discontinuous permafrost within the Wolf Creek Research Basin, Yukon Territory, Canada, will be shown. While several decades of hydrometric and geochemical data exist for Granger Creek, inter-annual variability is considerable and makes evaluating long-term trends difficult. Insights derived from high-frequency sub-hourly salinity, CDOM and flow over recent years reveal that hysteresis loops among variables can be used to assess changing connectivity and flow paths as both magnitude and direction of loops can be used to infer landscape-scale linkages. These patterns highlight spatial connections among landscape units not previously observed, and identify periods when hydrological and biogeochemical cycles are coupled. Evaluation of these patterns at the headwater scale provides alternate hypotheses for how permafrost landscapes will respond to a changing climate.

Depth-Resolved Quantification of Anaerobic Toluene Degraders and Aquifer Microbial Community Patterns in Distinct Redox Zones of a Tar Oil Contaminant Plume▿

PubMed Central

Winderl, Christian; Anneser, Bettina; Griebler, Christian; Meckenstock, Rainer U.; Lueders, Tillmann

2008-01-01

Microbial degradation is the only sustainable component of natural attenuation in contaminated groundwater environments, yet its controls, especially in anaerobic aquifers, are still poorly understood. Hence, putative spatial correlations between specific populations of key microbial players and the occurrence of respective degradation processes remain to be unraveled. We therefore characterized microbial community distribution across a high-resolution depth profile of a tar oil-impacted aquifer where benzene, toluene, ethylbenzene, and xylene (BTEX) degradation depends mainly on sulfate reduction. We conducted depth-resolved terminal restriction fragment length polymorphism fingerprinting and quantitative PCR of bacterial 16S rRNA and benzylsuccinate synthase genes (bssA) to quantify the distribution of total microbiota and specific anaerobic toluene degraders. We show that a highly specialized degrader community of microbes related to known deltaproteobacterial iron and sulfate reducers (Geobacter and Desulfocapsa spp.), as well as clostridial fermenters (Sedimentibacter spp.), resides within the biogeochemical gradient zone underneath the highly contaminated plume core. This zone, where BTEX compounds and sulfate—an important electron acceptor—meet, also harbors a surprisingly high abundance of the yet-unidentified anaerobic toluene degraders carrying the previously detected F1-cluster bssA genes (C. Winderl, S. Schaefer, and T. Lueders, Environ. Microbiol. 9:1035-1046, 2007). Our data suggest that this biogeochemical gradient zone is a hot spot of anaerobic toluene degradation. These findings show that the distribution of specific aquifer microbiota and degradation processes in contaminated aquifers are tightly coupled, which may be of value for the assessment and prediction of natural attenuation based on intrinsic aquifer microbiota. PMID:18083871

Metabolite recycling and bidirectional C fluxes: Revolutionizing our view on microbial C cycling in soils

NASA Astrophysics Data System (ADS)

Dippold, M. A.; Apostel, C.; Kuzyakov, Y.

2016-12-01

Biogeochemists' view on microbial C transformation in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the anabolism. However, life in a C limited environment as challenging as soil requires microbial adaptation strategies at all levels of metabolism. By coupling of position-specific labeling of core metabolites with compound-specific isotope analysis we demonstrated that catabolic oxidation of these metabolites exists in parallel to reductive, energy consuming pathways, reducing them for anabolic purposes. Up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in the citric acid cycle. Furthermore, position-specific labeling of rather `cost-intensive' biomass compounds such as fatty acids revealed that intact recycling of metabolites is a crucial microbial adaptation to C scarcity in soils. Both processes are unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. To understand how microorganisms catalyze the biogeochemical fluxes in soil, a profound understanding of their metabolic adaptation strategies such as recycling or switching between bidirectional fluxes is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the underlying microbial processes.

Biogeochemical redox processes and their impact on contaminant dynamics

USGS Publications Warehouse

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

2010-01-01

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.

Incorporating microbes into large-scale biogeochemical models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Martiny, J. B.

2008-12-01

Micro-organisms, including Bacteria, Archaea, and Fungi, control major processes throughout the Earth system. Recent advances in microbial ecology and microbiology have revealed an astounding level of genetic and metabolic diversity in microbial communities. However, a framework for interpreting the meaning of this diversity has lagged behind the initial discoveries. Microbial communities have yet to be included explicitly in any major biogeochemical models in terrestrial ecosystems, and have only recently broken into ocean models. Although simplification of microbial communities is essential in complex systems, omission of community parameters may seriously compromise model predictions of biogeochemical processes. Two key questions arise from this tradeoff: 1) When and where must microbial community parameters be included in biogeochemical models? 2) If microbial communities are important, how should they be simplified, aggregated, and parameterized in models? To address these questions, we conducted a meta-analysis to determine if microbial communities are sensitive to four environmental disturbances that are associated with global change. In all cases, we found that community composition changed significantly following disturbance. However, the implications for ecosystem function were unclear in most of the published studies. Therefore, we developed a simple model framework to illustrate the situations in which microbial community changes would affect rates of biogeochemical processes. We found that these scenarios could be quite common, but powerful predictive models cannot be developed without much more information on the functions and disturbance responses of microbial taxa. Small-scale models that explicitly incorporate microbial communities also suggest that process rates strongly depend on microbial interactions and disturbance responses. The challenge is to scale up these models to make predictions at the ecosystem and global scales based on measurable parameters. We argue that meeting this challenge will require a coordinated effort to develop a series of nested models at scales ranging from the micron to the globe in order to optimize the tradeoff between model realism and feasibility.

Constructing wetlands: measuring and modeling feedbacks of oxidation processes between plants and clay-rich material

NASA Astrophysics Data System (ADS)

Saaltink, Rémon; Dekker, Stefan C.; Griffioen, Jasper; Wassen, Martin J.

2016-04-01

Interest is growing in using soft sediment as a building material in eco-engineering projects. Wetland construction in the Dutch lake Markermeer is an example: here the option of dredging some of the clay-rich lake-bed sediment and using it to construct 10.000 ha of wetland will soon go under construction. Natural processes will be utilized during and after construction to accelerate ecosystem development. Knowing that plants can eco-engineer their environment via positive or negative biogeochemical plant-soil feedbacks, we conducted a six-month greenhouse experiment to identify the key biogeochemical processes in the mud when Phragmites australis is used as an eco-engineering species. We applied inverse biogeochemical modeling to link observed changes in pore water composition to biogeochemical processes. Two months after transplantation we observed reduced plant growth and shriveling as well as yellowing of foliage. The N:P ratios of plant tissue were low and were affected not by hampered uptake of N but by enhanced uptake of P. Plant analyses revealed high Fe concentrations in the leaves and roots. Sulfate concentrations rose drastically in our experiment due to pyrite oxidation; as reduction of sulfate will decouple Fe-P in reducing conditions, we argue that plant-induced iron toxicity hampered plant growth, forming a negative feedback loop, while simultaneously there was a positive feedback loop, as iron toxicity promotes P mobilization as a result of reduced conditions through root death, thereby stimulating plant growth and regeneration. Given these two feedback mechanisms, we propose that when building wetlands from these mud deposits Fe-tolerant species are used rather than species that thrive in N-limited conditions. The results presented in this study demonstrate the importance of studying the biogeochemical properties of the building material and the feedback mechanisms between plant and soil prior to finalizing the design of the eco-engineering project.

Impact of phenanthrene on the properties of biogeochemical interfaces in soil: A two-layer column study

NASA Astrophysics Data System (ADS)

Reichel, Katharina; Totsche, Kai Uwe

2013-04-01

Biogeochemical interfaces in soils (Totsche et al. 2010) are the "hot spots" of microbial activity and the processing of organic compounds in soils. The production and relocation of mobile organic matter (MOM) and biocolloids like microorganisms are key processes for the formation and depth propagation of biogeochemical interfaces in soils (BGI). Phenanthrene (PHE) has been shown to affect microbial communities in soils (Ding et al. 2012) and may induce shifts in MOM quantity and quality (amount, type and properties of MOM). We hypothesize that the properties of BGI in soil change significantly due to the presence of PHE. The objectives of this study are (i) to evaluate the effect of PHE on soil microbial communities and on MOM quantity and quality under flow conditions with single- and two-layer column experiments and (ii) to assess the role of these processes for the physicochemical, mechanical and sorptive properties of BGI in soils. The soil columns were operated under water-unsaturated conditions. The top layer (source layer, SL, 2 cm) is made of sieved soil material (Luvisol, Scheyern, Germany) spiked with PHE (0.2 mg/g). The bottom layer (reception layer, RL, 10 cm) comprised the same soil without PHE. PHE-free columns were conducted in parallel as reference. Release and transport of MOM in mature soil of a single-layer column experiment was found to depend on the transport regime. The release of larger sized MOM (>0.45 µm) was restricted to an increased residence time during flow interruptions. Steady flow conditions favor the release of smaller MOM (<0.45 µm). Compared to the reference, in the two-layer column experiments higher OC concentrations were detected in the effluent from PHE spiked columns after enhanced flow interruptions (26d, 52d). That indicated the PHE influenced production or mobilization of MOM. Parallel factor analysis of fluorescence excitation and emission matrices revealed the presence of a constant DOM background and two new unknown components in the effluent, probably PHE metabolites. The emergence of new components emphasizes the role of metabolization processes in the release of MOM. The identification of key microbial actors and communities are currently in progress. Totsche, K.U. et al. (2010): Biogeochemical interfaces in soil: The interdisciplinary challenge for soil science. J. Plant Nutr. Soil Sci., 173(1), 88-99 Ding, G.-C., Heuer, H. & Smalla, K. (2012): Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. Front Microbio 10.3389/fmicb.2012.00290.

The influence of tides on biogeochemical dynamics at the mouth of the Amazon River

NASA Astrophysics Data System (ADS)

Ward, N. D.; Sawakuchi, H. O.; Neu, V.; de Matos Valerio, A.; Less, D.; Guedes, V.; Wood, J.; Brito, D. C.; Cunha, A. C.; Kampel, M.; Richey, J. E.

2017-12-01

A major barrier to computing the flux of constituents from the world's largest rivers to the ocean is understanding the dynamic processes that occur along tidally-influenced river reaches. Here, we examine the response of a suite of biogeochemical parameters to tide-induced flow reversals at the mouth of the Amazon River. Continuous measurements of pCO2, pCH4, dissolved O2, pH, turbidity, and fluorescent dissolved organic matter (FDOM) were made throughout tidal cycles while held stationary in the center of the river and during hourly transects for ADCP discharge measurements. Samples were collected hourly from the surface and 50% depth during stationary samplings and from the surface during ADCP transects for analysis of suspended sediment concentrations along with other parameters such as nutrient and mercury concentrations. Suspended sediment and specific components of the suspended phase, such as particulate mercury, concentrations were positively correlated to mean river velocity during both high and low water periods with a more pronounced response at 50% depth than the surface. Tidal variations also influenced the concentration of O2 and CO2 by altering the dynamic balance between photosynthesis, respiration, and gas transfer. CO2 was positively correlated and O2 and pH were negatively correlated with river velocity. The concentration of methane generally increased during low tide (i.e. when river water level was lowest) both in the mainstem and in small side channels. In side channels concentrations increased by several orders of magnitude during low tide with visible bubbling from the sediment, presumably due to a release of hydrostatic pressure. These results suggest that biogeochemical processes are highly dynamic in tidal rivers, and these dynamic variations need to be quantified to better constrain global and regional scale budgets. Understanding these rapid processes may also provide insight into the long-term response of aquatic systems to change.

In Situ Stoichiometry in a Large River: Continuous Measurement of Doc, NO3 and PO4 in the Sacramento River

NASA Astrophysics Data System (ADS)

Downing, B. D.; Pellerin, B. A.; Bergamaschi, B. A.; Saraceno, J.

2011-12-01

Studying controls on geochemical processes in rivers and streams is difficult because concentration and composition often changes rapidly in response to physical and biological forcings. Understanding biogeochemical dynamics in rivers will improve current understanding of the role of watershed sources to carbon cycling, river and stream ecology, and loads to estuaries and oceans. Continuous measurements of dissolved organic carbon (DOC), nitrate (NO3-) and soluble reactive phosphate (SRP) concentrations are now possible, along with some information about DOC composition. In situ sensors designed to measure these constituents provide high frequency, real-time data that can elucidate hydrologic and biogeochemical controls which are difficult to detect using more traditional sampling approaches. Here we present a coupled approach, using in situ optical instrumentation with discharge measurements to provide quantitative estimates of constituent loads to investigate C, NO3- and SRP sources and processing in the Sacramento River, CA, USA. Continuous measurement of DOC concentration was conducted by use of a miniature in situ fluorometer (Turner Designs Cyclops) designed to measure chromophoric dissolved organic matter fluorescence (FDOM) over the course of an entire year. Nitrate was measured concurrently using a Satlantic SUNA and phosphate was measured using a WETLabs model Cycle-P instrument for a two week period in July 2011. Continuous measurement from these instruments paired with continuous measurement of physical water quality variables such as temperature, pH, specific conductance, dissolved oxygen, and turbidity, were used to investigate physical and chemical dynamics of DOC, NO3-, SRP over varying time scales. Deploying these instruments at pre-existing USGS discharge gages allowed for calculation of instantaneous and integrated constituent fluxes, as well as filling in gaps in our understanding biogeochemical processes and transport. Results from the study show that diurnal, event driven and seasonal changes are key to calculating accurate watershed fluxes and detecting transient sources of DOC, NO3- and SRP.

Benthic exchange and biogeochemical cycling in permeable sediments.

PubMed

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

2014-01-01

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.

Simulation Based Exploration of Critical Zone Dynamics in Intensively Managed Landscapes

NASA Astrophysics Data System (ADS)

Kumar, P.

2017-12-01

The advent of high-resolution measurements of topographic and (vertical) vegetation features using areal LiDAR are enabling us to resolve micro-scale ( 1m) landscape structural characteristics over large areas. Availability of hyperspectral measurements is further augmenting these LiDAR data by enabling the biogeochemical characterization of vegetation and soils at unprecedented spatial resolutions ( 1-10m). Such data have opened up novel opportunities for modeling Critical Zone processes and exploring questions that were not possible before. We show how an integrated 3-D model at 1m grid resolution can enable us to resolve micro-topographic and ecological dynamics and their control on hydrologic and biogeochemical processes over large areas. We address the computational challenge of such detailed modeling by exploiting hybrid CPU and GPU computing technologies. We show results of moisture, biogeochemical, and vegetation dynamics from studies in the Critical Zone Observatory for Intensively managed Landscapes (IMLCZO) in the Midwestern United States.

Hidden biosphere in an oxygen-deficient Atlantic open ocean eddy: future implications of ocean deoxygenation on primary production in the eastern tropical North Atlantic

NASA Astrophysics Data System (ADS)

Loescher, Carolin; Fischer, Martin; Neulinger, Sven; Fiedler, Björn; Philippi, Miriam; Schütte, Florian; Singh, Arvind; Hauss, Helena; Karstensen, Johannes; Körtzinger, Arne; Schmitz, Ruth

2016-04-01

The eastern tropical North Atlantic (ETNA) is characterized by a highly productive coastal upwelling system and a moderate oxygen minimum zone with lowest open ocean oxygen (O2) concentrations of approximately 40 μmol kg-1. The recent discovery of re-occurring mesoscale eddies with close to anoxic O2 concentrations (<1 μmol kg-1) located just below the mixed layer has challenged our understanding of O2 distribution and biogeochemical processes in this area. Here, we present the first microbial community study from a deoxygenated anticyclonic modewater eddy in the open waters of the ETNA. In the eddy, we observed significantly lower bacterial diversity compared to surrounding waters, along with a significant community shift. We detected enhanced primary productivity in the surface layer of the eddy indicated by elevated chlorophyll concentrations and carbon uptake rates of up to three times as high as in surrounding waters. Carbon uptake rates below the euphotic zone correlated to the presence of a specific high-light ecotype of Prochlorococcus, which is usually underrepresented in the ETNA. Our data indicate that high primary production in the eddy fuels export production and supports enhanced respiration in a specific microbial community at shallow depths, below the mixed layer base. The O2-depleted core waters eddy promoted transcription of the key gene for denitrification, nirS. This process is usually absent from the open ETNA waters. In light of future projected ocean deoxygenation, our results show that even distinct events of anoxia have the potential to alter microbial community structure with critical impacts on primary productivity and biogeochemical processes of oceanic water bodies.

Hidden biosphere in an oxygen-deficient Atlantic open ocean eddy: future implications of ocean deoxygenation on primary production in the eastern tropical North Atlantic

NASA Astrophysics Data System (ADS)

Löscher, C. R.; Fischer, M. A.; Neulinger, S. C.; Fiedler, B.; Philippi, M.; Schütte, F.; Singh, A.; Hauss, H.; Karstensen, J.; Körtzinger, A.; Künzel, S.; Schmitz, R. A.

2015-08-01

The eastern tropical North Atlantic (ETNA) is characterized by a highly productive coastal upwelling system and a moderate oxygen minimum zone with lowest open ocean oxygen (O2) concentrations of around 40 μmol kg-1. Only recently, the discovery of re-occurring mesoscale eddies with sometimes close to anoxic O2 concentrations (<1 μmol kg-1) and located just below the mixed layer challenged our understanding of O2 distribution and biogeochemical processes in this area. Here, we present the first metagenomic dataset from a deoxygenated anticyclonic modewater eddy in the open waters of the ETNA. In the eddy, we observed a significantly lower bacterial diversity compared to surrounding waters, along with a significant community shift. We detected enhanced primary productivity in the surface layer of the eddy indicated by elevated chlorophyll concentrations and increased carbon uptake rates up to three times as high as in surrounding waters. Carbon uptake below the euphotic zone correlated to the presence of a specific high-light ecotype of Prochlorococcus, which is usually underrepresented in the ETNA. Our combined data indicate that high primary production in the eddy fuels export production and the presence of a specific microbial community responsible for enhanced respiration at shallow depths, below the mixed layer base. Progressively decreasing O2 concentrations in the eddy were found to promote transcription of the key gene for denitrification, nirS, in the O2-depleted core waters. This process is usually absent from the open ETNA waters. In the light of future ocean deoxygenation our results show exemplarily that even distinct events of anoxia have the potential to alter microbial community structures and with that critically impact primary productivity and biogeochemical processes of oceanic water bodies.

Hidden biosphere in an oxygen-deficient Atlantic open-ocean eddy: future implications of ocean deoxygenation on primary production in the eastern tropical North Atlantic

NASA Astrophysics Data System (ADS)

Löscher, C. R.; Fischer, M. A.; Neulinger, S. C.; Fiedler, B.; Philippi, M.; Schütte, F.; Singh, A.; Hauss, H.; Karstensen, J.; Körtzinger, A.; Künzel, S.; Schmitz, R. A.

2015-12-01

The eastern tropical North Atlantic (ETNA) is characterized by a highly productive coastal upwelling system and a moderate oxygen minimum zone with lowest open-ocean oxygen (O2) concentrations of approximately 40 μmol kg-1. The recent discovery of re-occurring mesoscale eddies with close to anoxic O2 concentrations (< 1 μmol kg-1) located just below the mixed layer has challenged our understanding of O2 distribution and biogeochemical processes in this area. Here, we present the first microbial community study from a deoxygenated anticyclonic modewater eddy in the open waters of the ETNA. In the eddy, we observed significantly lower bacterial diversity compared to surrounding waters, along with a significant community shift. We detected enhanced primary productivity in the surface layer of the eddy indicated by elevated chlorophyll concentrations and carbon uptake rates of up to three times as high as in surrounding waters. Carbon uptake rates below the euphotic zone correlated to the presence of a specific high-light ecotype of Prochlorococcus, which is usually underrepresented in the ETNA. Our data indicate that high primary production in the eddy fuels export production and supports enhanced respiration in a specific microbial community at shallow depths, below the mixed-layer base. The transcription of the key functional marker gene for dentrification, nirS, further indicated a potential for nitrogen loss processes in O2-depleted core waters of the eddy. Dentrification is usually absent from the open ETNA waters. In light of future projected ocean deoxygenation, our results show that even distinct events of anoxia have the potential to alter microbial community structure with critical impacts on primary productivity and biogeochemical processes of oceanic water bodies.

Technical Note: A generic law-of-the-minimum flux limiter for simulating substrate limitation in biogeochemical models

DOE PAGES

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

2016-02-05

We present a generic flux limiter to account for mass limitations from an arbitrary number of substrates in a biogeochemical reaction network. The flux limiter is based on the observation that substrate (e.g., nitrogen, phosphorus) limitation in biogeochemical models can be represented as to ensure mass conservative and non-negative numerical solutions to the governing ordinary differential equations. Application of the flux limiter includes two steps: (1) formulation of the biogeochemical processes with a matrix of stoichiometric coefficients and (2) application of Liebig's law of the minimum using the dynamic stoichiometric relationship of the reactants. This approach contrasts with the ad hoc down-regulationmore » approaches that are implemented in many existing models (such as CLM4.5 and the ACME (Accelerated Climate Modeling for Energy) Land Model (ALM)) of carbon and nutrient interactions, which are error prone when adding new processes, even for experienced modelers. Through an example implementation with a CENTURY-like decomposition model that includes carbon, nitrogen, and phosphorus, we show that our approach (1) produced almost identical results to that from the ad hoc down-regulation approaches under non-limiting nutrient conditions, (2) properly resolved the negative solutions under substrate-limited conditions where the simple clipping approach failed, (3) successfully avoided the potential conceptual ambiguities that are implied by those ad hoc down-regulation approaches. We expect our approach will make future biogeochemical models easier to improve and more robust.« less

Patterns of deoxygenation: sensitivity to natural and anthropogenic drivers

NASA Astrophysics Data System (ADS)

Oschlies, Andreas; Duteil, Olaf; Getzlaff, Julia; Koeve, Wolfgang; Landolfi, Angela; Schmidtko, Sunke

2017-08-01

Observational estimates and numerical models both indicate a significant overall decline in marine oxygen levels over the past few decades. Spatial patterns of oxygen change, however, differ considerably between observed and modelled estimates. Particularly in the tropical thermocline that hosts open-ocean oxygen minimum zones, observations indicate a general oxygen decline, whereas most of the state-of-the-art models simulate increasing oxygen levels. Possible reasons for the apparent model-data discrepancies are examined. In order to attribute observed historical variations in oxygen levels, we here study mechanisms of changes in oxygen supply and consumption with sensitivity model simulations. Specifically, the role of equatorial jets, of lateral and diapycnal mixing processes, of changes in the wind-driven circulation and atmospheric nutrient supply, and of some poorly constrained biogeochemical processes are investigated. Predominantly wind-driven changes in the low-latitude oceanic ventilation are identified as a possible factor contributing to observed oxygen changes in the low-latitude thermocline during the past decades, while the potential role of biogeochemical processes remains difficult to constrain. We discuss implications for the attribution of observed oxygen changes to anthropogenic impacts and research priorities that may help to improve our mechanistic understanding of oxygen changes and the quality of projections into a changing future. This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

[Ammonia-oxidizing archaea and their important roles in nitrogen biogeochemical cycling: a review].

PubMed

Liu, Jing-Jing; Wu, Wei-Xiang; Ding, Ying; Shi, De-Zhi; Chen, Ying-Xu

2010-08-01

As the first step of nitrification, ammonia oxidation is the key process in global nitrogen biogeochemical cycling. So far, the autotrophic ammonia-oxidizing bacteria (AOB) in the beta- and gamma-subgroups of proteobacteria have been considered as the most important contributors to ammonia oxidation, but the recent researches indicated that ammonia-oxidizing archaea (AOA) are widely distributed in various kinds of ecosystems and quantitatively predominant, playing important roles in the global nitrogen biogeochemical cycling. This paper reviewed the morphological, physiological, and ecological characteristics and the molecular phylogenies of AOA, and compared and analyzed the differences and similarities of the ammonia monooxygenase (AMO) and its encoding genes between AOA and AOB. In addition, the potential significant roles of AOA in nitrogen biogeochemical cycling in aquatic and terrestrial ecosystems were summarized, and the future research directions of AOA in applied ecology and environmental protection were put forward.

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

NASA Astrophysics Data System (ADS)

Nordsiek, Sven; Gilfedder, Ben; Frei, Sven

2017-04-01

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

Ecohydrological interfaces as hot spots of ecosystem processes

NASA Astrophysics Data System (ADS)

Krause, Stefan; Lewandowski, Jörg; Grimm, Nancy B.; Hannah, David M.; Pinay, Gilles; McDonald, Karlie; Martí, Eugènia; Argerich, Alba; Pfister, Laurent; Klaus, Julian; Battin, Tom; Larned, Scott T.; Schelker, Jacob; Fleckenstein, Jan; Schmidt, Christian; Rivett, Michael O.; Watts, Glenn; Sabater, Francesc; Sorolla, Albert; Turk, Valentina

2017-08-01

The movement of water, matter, organisms, and energy can be altered substantially at ecohydrological interfaces, the dynamic transition zones that often develop within ecotones or boundaries between adjacent ecosystems. Interdisciplinary research over the last two decades has indicated that ecohydrological interfaces are often "hot spots" of ecological, biogeochemical, and hydrological processes and may provide refuge for biota during extreme events. Ecohydrological interfaces can have significant impact on global hydrological and biogeochemical cycles, biodiversity, pollutant removal, and ecosystem resilience to disturbance. The organizational principles (i.e., the drivers and controls) of spatially and temporally variable processes at ecohydrological interfaces are poorly understood and require the integrated analysis of hydrological, biogeochemical, and ecological processes. Our rudimentary understanding of the interactions between different drivers and controls critically limits our ability to predict complex system responses to change. In this paper, we explore similarities and contrasts in the functioning of diverse freshwater ecohydrological interfaces across spatial and temporal scales. We use this comparison to develop an integrated, interdisciplinary framework, including a roadmap for analyzing ecohydrological processes and their interactions in ecosystems. We argue that, in order to fully account for their nonlinear process dynamics, ecohydrological interfaces need to be conceptualized as unique, spatially and temporally dynamic entities, which represents a step change from their current representation as boundary conditions at investigated ecosystems.

Green Infrastructure Increases Biogeochemical Responsiveness, Vegetation Growth and Decreases Runoff in a Semi-Arid City, Tucson, AZ, USA

NASA Astrophysics Data System (ADS)

Meixner, T.; Papuga, S. A.; Luketich, A. M.; Rockhill, T.; Gallo, E. L.; Anderson, J.; Salgado, L.; Pope, K.; Gupta, N.; Korgaonkar, Y.; Guertin, D. P.

2017-12-01

Green Infrastructure (GI) is often viewed as a mechanism to minimize the effects of urbanization on hydrology, water quality, and other ecosystem services (including the urban heat island). Quantifying the effects of GI requires field measurements of the dimensions of biogeochemical, ecosystem, and hydrologic function that we expect GI to impact. Here we investigated the effect of GI features in Tucson, Arizona which has a low intensity winter precipitation regime and a high intensity summer regime. We focused on understanding the effect of GI on soil hydraulic and biogeochemical properties as well as the effect on vegetation and canopy temperature. Our results demonstrate profound changes in biogeochemical and hydrologic properties and vegetation growth between GI systems and nearby control sites. In terms of hydrologic properties GI soils had increased water holding capacity and hydraulic conductivity. GI soils also have higher total carbon, total nitrogen, and organic matter in general than control soils. Furthermore, we tested the sampled soils (control and GI) for differences in biogeochemical response upon wetting. GI soils had larger respiration responses indicating greater biogeochemical activity overall. Long-term Lidar surveys were used to investigate the differential canopy growth of GI systems versus control sites. The results of this analysis indicate that while a significant amount of time is needed to observe differences in canopy growth GI features due increase tree size and thus likely impact street scale ambient temperatures. Additionally monitoring of transpiration, soil moisture, and canopy temperature demonstrates that GI features increase vegetation growth and transpiration and reduce canopy temperatures. These biogeochemical and ecohydrologic results indicate that GI can increase the biogeochemical processing of soils and increase tree growth and thus reduce urban ambient temperatures.

Stream biogeochemical resilience in the age of Anthropocene

NASA Astrophysics Data System (ADS)

Dong, H.; Creed, I. F.

2017-12-01

Recent evidence indicates that biogeochemical cycles are being pushed beyond the tolerance limits of the earth system in the age of the Anthropocene placing terrestrial and aquatic ecosystems at risk. Here, we explored the question: Is there empirical evidence of global atmospheric changes driving losses in stream biogeochemical resilience towards a new normal? Stream biogeochemical resilience is the process of returning to equilibrium conditions after a disturbance and can be measured using three metrics: reactivity (the highest initial response after a disturbance), return rate (the rate of return to equilibrium condition after reactive changes), and variance of the stationary distribution (the signal to noise ratio). Multivariate autoregressive models were used to derive the three metrics for streams along a disturbance gradient - from natural systems where global drivers would dominate, to relatively managed or modified systems where global and local drivers would interact. We observed a loss of biogeochemical resilience in all streams. The key biogeochemical constituent(s) that may be driving loss of biogeochemical resilience were identified from the time series of the stream biogeochemical constituents. Non-stationary trends (detected by Mann-Kendall analysis) and stationary cycles (revealed through Morlet wavelet analysis) were removed, and the standard deviation (SD) of the remaining residuals were analyzed to determine if there was an increase in SD over time that would indicate a pending shift towards a new normal. We observed that nitrate-N and total phosphorus showed behaviours indicative of a pending shift in natural and managed forest systems, but not in agricultural systems. This study provides empirical support that stream ecosystems are showing signs of exceeding planetary boundary tolerance levels and shifting towards a "new normal" in response to global changes, which can be exacerbated by local management activities. Future work will consider the potential for cascading effects on downstream systems.

The interplay between estuarine transport and biogeochemical processes in determining the nutrient conditions in bottom layers of non-tidal Gulf of Finland

NASA Astrophysics Data System (ADS)

Kõuts, Mariliis; Raudsepp, Urmas; Maljutenko, Ilja

2017-04-01

In coastal areas, especially estuaries, spatial distribution and seasonal cycling of chemical and biological variables is largely determined by local biogeochemical processes and water transport of different properties. In tidal estuaries, however, biogeochemical processes are affected by tides as frequent water exchange alters nutrient and oxygen concentrations. In wide and deep non-tidal estuary-type marginal seas spatial distribution and seasonal cycling are determined by the mixture of water transport and local biogeochemistry. The Baltic Sea is a stratified water basin where halocline divides the water column into two parts: upper layer, which is horizontally uniform in terms of distribution of chemical and biological parameters, and has clear seasonal cycle; and bottom part, where nutrient and oxygen dynamics is more complex. There water transport and sediment-water interface fluxes play a major role. Our prime focus is the Gulf of Finland in the Baltic Sea. It is a wide, non-tidal and stratified sub-basin known for its high nutrient concentrations and severe oxygen deficiency in summer. We modelled the Baltic Sea (including Gulf of Finland) using ERGOM, a biogeochemical model coupled with circulation model GETM. Seasonal cycling and water circulation were observed with a 40-year simulation from 1966 to 2006. Our results show that in shallow areas above halocline the seasonal cycle of phytoplankton, nutrients and oxygen concentrations is uniform in space. Water circulation does not create inhomogeneous distribution pattern of biogeochemical parameters and their seasonal cycle. The circulation in the Gulf of Finland is strongly modulated by the seasonality of estuarine transport. Below the halocline saline low-oxygen and nutrient-rich water is transported from the open Baltic Proper to the Gulf of Finland in spring and early summer. This results in the highest nutrient concentrations and the poorest oxygen conditions by the end of August. In the shallow area nutrients have high concentrations in March-April before the spring bloom of diatoms starts. Low oxygen and nutrient concentrations are observed at the end of August. There is a qualitative difference of nutrient dynamics between shallow and deep layers but quantification of the role of transport and local biogeochemical processes is still challenging.

The GRASP project - a multidisciplinary study of hydrology and biogeochemistry in a periglacial catchment area

NASA Astrophysics Data System (ADS)

Johansson, Emma; Lindborg, Tobias

2017-04-01

The Arctic region is sensitive to global warming, and permafrost thaw and release of old carbon are examples of processes that may have a positive feedback effect to the global climate system. Quantification and assumptions on future change are often based on model predictions. Such models require cross-disciplinary data of high quality that often is lacking. Biogeochemical processes in the landscape are highly influenced by the hydrology, which in turn is intimately related to permafrost processes. Thus, a multidisciplinary approach is needed when collecting data and setting up field experiments aiming at increase the understanding of these processes. Here we summarize and present data collected in the GRASP, Greenland Analogue Surface Project. GRASP is a catchment-scale field study of the periglacial area in the Kangerlussuaq region, West Greenland, focusing on hydrological and biogeochemical processes in the landscape. The site investigations were initiated in 2010 and have since then resulted in three separate data sets published in ESSD (Earth system and Science Data) each one focusing on i) meteorological data and hydrology, ii) biogeochemistry and iii) geometries of sediments and the active layer. The three data-sets, which are freely available via the PANGAEA data base, enable conceptual and coupled numerical modeling of hydrological and biogeochemical processes. An important strength with the GRASP data is that all data is collected within the same, relatively small, catchment area. This implies that measurements are more easily linked to the right source area or process. Despite the small catchment area it includes the major units of the periglacial hydrological system; a lake, a talik, a supra- and subpermafrost aquifer and, consequently, biogeochemical processes in each of these units may be studied. The new data from GRASP is both used with the aim to increase the knowledge of present day periglacial hydrology and biogeochemistry but also in order to predict consequences within these subjects of future climate change.

Climate Regulation Services of Natural and Managed Ecosystems of the Americas

NASA Astrophysics Data System (ADS)

Anderson-Teixeira, K. J.; Snyder, P. K.; Twine, T. E.; Costa, M. H.; Cuadra, S.; DeLucia, E. H.

2011-12-01

Terrestrial ecosystems regulate climate through both biogeochemical mechanisms (greenhouse gas regulation) and biophysical mechanisms (regulation of water and energy). Land management therefore provides some of the most effective strategies for climate change mitigation. However, most policies aimed at climate protection through land management, including UNFCCC mechanisms and bioenergy sustainability standards, account only for biogeochemical climate services. By ignoring biophysical climate regulation services that in some cases offset the biogeochemical regulation services, these policies run the risk of failing to advance the best climate solutions. Quantifying the combined value of biogeochemical and biophysical climate regulation services remains an important challenge. Here, we use a combination of data synthesis and modeling to quantify how biogeochemical and biophysical effects combine to shape the climate regulation value (CRV) of 18 natural and managed ecosystem types across the Western Hemisphere. Natural ecosystems generally had higher CRVs than agroecosystems, largely driven by differences in biogeochemical services. Biophysical contributions ranged from minimal to dominant. They were highly variable in space and across ecosystem types, and their relative importance varied strongly with the spatio-temporal scale of analysis. Our findings pertain to current efforts to protect climate through land management. Specifically, they reinforce the importance of protecting tropical forests and recent findings that the climatic effects of bioenergy production may be somewhat more positive than previously estimated. Given that biophysical effects in some cases dominate, ensuring effective climate protection through land management requires consideration of combined biogeochemical and biophysical climate regulation services. While quantification of ecosystem climate services is necessarily complex, our CRV index serves as one potential approach to measure the full climate services of terrestrial ecosystems.

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

Treesearch

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

2010-01-01

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

Influence of harvesting on biogeochemical exchange in sheetflow and soil processes in a eutrophic floodplain forest

Treesearch

B.G. Lockaby; R.G. Clawson; K. Flynn; Robert Rummer; S. Meadows; B Stokes; John A. Stanturf

1997-01-01

Floodplain forests contribute to the maintenance of water quality as a result of various biogeochemical transformations which occur within them. In particular, they can serve as sinks for nutrient run-off from adjacent uplands or as nutrient transformers as water moves downstream. However, little is known about the potential that land management activities may have for...

The role of experimental forests and ranges in the development of ecosystem science and biogeochemical cycling research

Treesearch

James M. Vose; Wayne T. Swank; Mary Beth Adams; Devendra Amatya; John Campbell; Sherri Johnson; Frederick J. Swanson; Randy Kolka; Ariel E. Lugo; Robert Musselman; Charles Rhoades

2014-01-01

Forest Service watershed-based Experimental Forests and Ranges (EFRs) have significantly advanced scientific knowledge on ecosystem structure and function through long-term monitoring and experimental research on hydrologic and biogeochemical cycling processes. Research conducted in the 1940s and 1950s began as “classic” paired watershed studies. The emergence of the...

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

Treesearch

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

2014-01-01

Autumn is a season of dynamic change in forest streams of the northeastern United States due to effects of leaf fall on both hydrology and biogeochemistry. Few studies have explored how interactions of biogeochemical transformations, various nitrogen sources, and catchment flow paths affect stream nitrogen variation during autumn. To provide more information on this...

Exploring Fingerprints of the Extreme Thermoacidophile Metallosphaera sedula Grown on Synthetic Martian Regolith Materials as the Sole Energy Sources.

PubMed

Kölbl, Denise; Pignitter, Marc; Somoza, Veronika; Schimak, Mario P; Strbak, Oliver; Blazevic, Amir; Milojevic, Tetyana

2017-01-01

The biology of metal transforming microorganisms is of a fundamental and applied importance for our understanding of past and present biogeochemical processes on Earth and in the Universe. The extreme thermoacidophile Metallosphaera sedula is a metal mobilizing archaeon, which thrives in hot acid environments (optimal growth at 74°C and pH 2.0) and utilizes energy from the oxidation of reduced metal inorganic sources. These characteristics of M. sedula make it an ideal organism to further our knowledge of the biogeochemical processes of possible life on extraterrestrial planetary bodies. Exploring the viability and metal extraction capacity of M. sedula living on and interacting with synthetic extraterrestrial minerals, we show that M. sedula utilizes metals trapped in the Martian regolith simulants (JSC Mars 1A; P-MRS; S-MRS; MRS07/52) as the sole energy sources. The obtained set of microbiological and mineralogical data suggests that M. sedula actively colonizes synthetic Martian regolith materials and releases free soluble metals. The surface of bioprocessed Martian regolith simulants is analyzed for specific mineralogical fingerprints left upon M. sedula growth. The obtained results provide insights of biomining of extraterrestrial material as well as of the detection of biosignatures implementing in life search missions.

Oceanic biogeochemical controls on global dynamics of persistent organic pollutants.

PubMed

Dachs, Jordi; Lohmann, Rainer; Ockenden, Wendy A; Méjanelle, Laurence; Eisenreich, Steven J; Jones, Kevin C

2002-10-15

Understanding and quantifying the global dynamics and sinks of persistent organic pollutants (POPs) is important to assess their environmental impact and fate. Air-surface exchange processes, where temperature plays a central role in controlling volatilization and deposition, are of key importance in controlling global POP dynamics. The present study is an assessment of the role of oceanic biogeochemical processes, notably phytoplankton uptake and vertical fluxes of particles, on the global dynamics of POPs. Field measurements of atmospheric polychlorinated biphenyls (PCBs), polychlorinated dibenzodioxins (PCDDs), and furans (PCDFs) are combined with remote sensing estimations of oceanic temperature, wind speed, and chlorophyll, to model the interactions between air-water exchange, phytoplankton uptake, and export of organic matter and POPs out of the mixed surface ocean layer. Deposition is enhanced in the mid-high latitudes and is driven by sinking marine particulate matter, rather than by a cold condensation effect. However, the relative contribution of the biological pump is a function of the physical-chemical properties of POPs. It is concluded that oceanic biogeochemical processes play a critical role in controlling the global dynamics and the ultimate sink of POPs.

Linking Chaotic Advection with Subsurface Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Mays, D. C.; Freedman, V. L.; White, S. K.; Fang, Y.; Neupauer, R.

2017-12-01

This work investigates the extent to which groundwater flow kinematics drive subsurface biogeochemical processes. In terms of groundwater flow kinematics, we consider chaotic advection, whose essential ingredient is stretching and folding of plumes. Chaotic advection is appealing within the context of groundwater remediation because it has been shown to optimize plume spreading in the laminar flows characteristic of aquifers. In terms of subsurface biogeochemical processes, we consider an existing model for microbially-mediated reduction of relatively mobile uranium(VI) to relatively immobile uranium(IV) following injection of acetate into a floodplain aquifer beneath a former uranium mill in Rifle, Colorado. This model has been implemented in the reactive transport code eSTOMP, the massively parallel version of STOMP (Subsurface Transport Over Multiple Phases). This presentation will report preliminary numerical simulations in which the hydraulic boundary conditions in the eSTOMP model are manipulated to simulate chaotic advection resulting from engineered injection and extraction of water through a manifold of wells surrounding the plume of injected acetate. This approach provides an avenue to simulate the impact of chaotic advection within the existing framework of the eSTOMP code.

Biogeochemical Cycles of Carbon and Sulfur

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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

NASA Astrophysics Data System (ADS)

Ulmer, K. M.; Taylor, C.

2010-12-01

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

A molecular dawn for biogeochemistry

USGS Publications Warehouse

Zak, D.R.; Blackwood, C.B.; Waldrop, M.P.

2006-01-01

Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes. ?? 2006 Elsevier Ltd. All rights reserved.

Downstream approaches to phosphorus management in agricultural landscapes: regional applicability and use.

PubMed

Kröger, R; Dunne, E J; Novak, J; King, K W; McLellan, E; Smith, D R; Strock, J; Boomer, K; Tomer, M; Noe, G B

2013-01-01

This review provides a critical overview of conservation practices that are aimed at improving water quality by retaining phosphorus (P) downstream of runoff genesis. The review is structured around specific downstream practices that are prevalent in various parts of the United States. Specific practices that we discuss include the use of controlled drainage, chemical treatment of waters and soils, receiving ditch management, and wetlands. The review also focuses on the specific hydrology and biogeochemistry associated with each of those practices. The practices are structured sequentially along flowpaths as you move through the landscape, from the edge-of-field, to adjacent aquatic systems, and ultimately to downstream P retention. Often practices are region specific based on geology, cropping practices, and specific P related problems and thus require a right practice, and right place mentality to management. Each practice has fundamental P transport and retention processes by systems that can be optimized by management with the goal of reducing downstream P loading after P has left agricultural fields. The management of P requires a system-wide assessment of the stability of P in different biogeochemical forms (particulate vs. dissolved, organic vs. inorganic), in different storage pools (soil, sediment, streams etc.), and under varying biogeochemical and hydrological conditions that act to convert P from one form to another and promote its retention in or transport out of different landscape components. There is significant potential of hierarchically placing practices in the agricultural landscape and enhancing the associated P mitigation. But an understanding is needed of short- and long-term P retention mechanisms within a certain practice and incorporating maintenance schedules if necessary to improve P retention times and minimize exceeding retention capacity. Copyright © 2012 Elsevier B.V. All rights reserved.

Demonstrating the Value of Fine-resolution Optical Data for Minimising Aliasing Impacts on Biogeochemical Models of Surface Waters

NASA Astrophysics Data System (ADS)

Chappell, N. A.; Jones, T.; Young, P.; Krishnaswamy, J.

2015-12-01

There is increasing awareness that under-sampling may have resulted in the omission of important physicochemical information present in water quality signatures of surface waters - thereby affecting interpretation of biogeochemical processes. For dissolved organic carbon (DOC) and nitrogen this under-sampling can now be avoided using UV-visible spectroscopy measured in-situ and continuously at a fine-resolution e.g. 15 minutes ("real time"). Few methods are available to extract biogeochemical process information directly from such high-frequency data. Jones, Chappell & Tych (2014 Environ Sci Technol: 13289-97) developed one such method using optically-derived DOC data based upon a sophisticated time-series modelling tool. Within this presentation we extend the methodology to quantify the minimum sampling interval required to avoid distortion of model structures and parameters that describe fundamental biogeochemical processes. This shifting of parameters which results from under-sampling is called "aliasing". We demonstrate that storm dynamics at a variety of sites dominate over diurnal and seasonal changes and that these must be characterised by sampling that may be sub-hourly to avoid aliasing. This is considerably shorter than that used by other water quality studies examining aliasing (e.g. Kirchner 2005 Phys Rev: 069902). The modelling approach presented is being developed into a generic tool to calculate the minimum sampling for water quality monitoring in systems driven primarily by hydrology. This is illustrated with fine-resolution, optical data from watersheds in temperate Europe through to the humid tropics.

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes.

PubMed

Kumar, Amit; Ng, Daphne H P; Wu, Yichao; Cao, Bin

2018-05-28

Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.

The role of experimental forests and ranges in the development of ecosystem science and biogeochemical cycling research [Chapter 17

Treesearch

James M. Vose; Wayne T. Swank; Mary Beth Adams; Devendra Amatya; John Campbell; Sherri Johnson; Frederick J. Swanson; Randy Kolka; Ariel E. Lugo; Robert Musselman; Charles Rhoades

2014-01-01

Forest Service watershed-based Experimental Forests and Ranges (EFRs) have significantly advanced scientific knowledge on ecosystem structure and function through long-term monitoring and experimental research on hydrologic and biogeochemical cycling processes. Research conducted in the 1940s and 1950s began as “classic” paired watershed studies. The emergence of the...

Native Mussels Alter Nutrient Availability and Reduce Blue ...

EPA Pesticide Factsheets

Nutrient cycling is a key process that ties all organisms together. This is especially apparent in stream environments in which nutrients are taken up readily and cycled through the system in a downstream trajectory. Ecological stoichiometry predicts that biogeochemical cycles of different elements are interdependent because the organisms that drive these cycles require fixed ratios of nutrients. There is growing recognition that animals play an important role in biogeochemical cycling across ecosystems. In particular, dense aggregations of consumers can create biogeochemical hotspots in aquatic ecosystems via nutrient translocation. We predicted that filter-feeding freshwater mussels, which occur as speciose, high biomass aggregates, would create biogeochemical hotspots in streams by altering nutrient limitation and algal dynamics. In a field study, we manipulated nitrogen and phosphorus using nutrient-diffusing substrates in areas with high and low mussel abundance, recorded algal growth and community composition, and determined in situ mussel excretion stoichiometry at 18 sites in 3 rivers (Kiamichi, Little, and Mt. Fork rivers, southcentral U.S.). Our results indicate that mussels greatly influence ecosystem processes by modifying the nutrients that limit primary productivity. Sites without mussels were N-limited with ~26% higher abundances of N-fixing blue-green algae, while sites with high mussel densities were co-limited (N and P) and dominated by diatoms

Global Analysis, Interpretation and Modelling: An Earth Systems Modelling Program

NASA Technical Reports Server (NTRS)

Moore, Berrien, III; Sahagian, Dork

1997-01-01

The Goal of the GAIM is: To advance the study of the coupled dynamics of the Earth system using as tools both data and models; to develop a strategy for the rapid development, evaluation, and application of comprehensive prognostic models of the Global Biogeochemical Subsystem which could eventually be linked with models of the Physical-Climate Subsystem; to propose, promote, and facilitate experiments with existing models or by linking subcomponent models, especially those associated with IGBP Core Projects and with WCRP efforts. Such experiments would be focused upon resolving interface issues and questions associated with developing an understanding of the prognostic behavior of key processes; to clarify key scientific issues facing the development of Global Biogeochemical Models and the coupling of these models to General Circulation Models; to assist the Intergovernmental Panel on Climate Change (IPCC) process by conducting timely studies that focus upon elucidating important unresolved scientific issues associated with the changing biogeochemical cycles of the planet and upon the role of the biosphere in the physical-climate subsystem, particularly its role in the global hydrological cycle; and to advise the SC-IGBP on progress in developing comprehensive Global Biogeochemical Models and to maintain scientific liaison with the WCRP Steering Group on Global Climate Modelling.

Overview of the 1988 GCE/CASE/WATOX Studies of biogeochemical cycles in the North Atlantic region

NASA Astrophysics Data System (ADS)

Pszenny, Alexander A. P.; Galloway, James N.; Artz, Richard S.; Boatman, Joseph F.

1990-06-01

The 1988 Global Change Expedition/Coordinated Air-Sea Experiment/Western Atlantic Ocean Experiment (GCE/CASE/WATOX) was a multifaceted research program designed to study atmospheric and oceanic processes affecting the biogeochemical cycles of carbon, nitrogen, sulfur, and trace metals in the North Atlantic Ocean region. Field work included (1) a 49-day research cruise aboard NOAA ship Mt. Mitchell (Global Change Expedition) from Norfolk, Virginia, to Bermuda, Iceland, the Azores, and Barbados, (2) eight flights of the NOAA King Air research aircraft, four off the Virginia Capes and four near Bermuda (CASE/WATOX), and (3) a research cruise aboard the yacht Fleurtie near Bermuda (WATOX). Objectives of GCE/CASE/WATOX were (1) to examine processes controlling the mesoscale distributions of productivity, chlorophyll, and phytoplankton growth rates in Atlantic surface waters, (2) to identify factors controlling the distribution of ozone in the North Atlantic marine boundary layer, and (3) to estimate the contributions of sources on surrounding continents to the biogeochemical cycles of sulfur, nitrogen, and trace metals over the North Atlantic region during the boreal summer season. The individual papers in this and the next two issues of Global Biogeochemical Cycles provide details on the results and analyses of the individual measurement efforts. This paper provides a brief overview of GCE/CASE/WATOX.

Hyporheic zone as a bioreactor: sediment heterogeneity influencing biogeochemical processes

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

A biogeochemical model was developed, coupling a physically based water temperature model (T-NET) with a semi-mechanistic biogeochemical model (RIVE, used in ProSe and Riverstrahler models) in order to assess at a fine temporal and spatial resolution the biogeochemical processes in the eutrophic Middle Loire hydrosystem (≈10 000 km², 3361 river segments). The code itself allows parallelized computing, which decreased greatly the calculation time (5 hours for simulating 3 years hourly). We conducted a daily survey during the period 2012-2014 at 2 sampling stations located in the Middle Loire of nutrients, chlorophyll pigments, phytoplankton and physic-chemical variables. This database was used as both input data (upstream Loire boundary) and validation data of the model (basin outlet). Diffuse and non-point sources were assessed based on a land cover analysis and WWTP datasets. The results appeared very sensible to the coefficients governing the dynamic of suspended solids and of phosphorus (sorption/desorption processes) within the model and some parameters needed to be estimated numerically. Both the Lagrangian point of view and fluxes budgets at the seasonal and event-based scale evidenced the biogeochemical functioning of the Loire River. Low discharge levels set up favorable physical conditions for phytoplankton growth (long water travel time, limited water depth, suspended particles sedimentation). Conversely, higher discharge levels highly limited the phytoplankton biomass (dilution of the colony, washing-out, limited travel time, remobilization of suspended sediments increasing turbidity), and most biogeochemical species were basically transferred downstream. When hydrological conditions remained favorable for phytoplankton development, P-availability was the critical factor. However, the model evidenced that most of the P in summer was recycled within the water body: on one hand it was assimilated by the algae biomass, and on the other hand it was released by mineralization of the dead cells. The high resolution of the model allowed understanding some fine temporal scale events, especially during some minor flood events occurring in summer. Paradoxically such events played two opposite roles: first it was disturbing the phytoplankton by diluting the biomass and remobilizing suspended sediments; then, it indirectly re-supplied the system with more available phosphorus, mainly because the washed-out phytoplankton could not assimilate the P available upstream. The model also pointed out the significant role played by Corbicula invasive clams in the river biogeochemical functioning, substantially reducing the phytoplankton biomass, and thus impacting the nutrients, oxygen and carbon cycles. However, the temporal and spatial distribution of Corbicula was questioned, and highlighted the need for data collection on this topic.

The two-layer geochemical structure of modern biogeochemical provinces and its significance for spatially adequate ecological evaluations and decisions

NASA Astrophysics Data System (ADS)

Korobova, Elena; Romanov, Sergey

2014-05-01

Contamination of the environment has reached such a scale that ecogeochemical situation in any area can be interpreted now as a result of the combined effect of natural and anthropogenic factors. The areas that appear uncomfortable for a long stay can have natural and anthropogenic genesis, but the spatial structure of such biogeochemical provinces is in any case formed of a combination of natural and technogenic fields of chemical elements. Features of structural organization and the difference in factors and specific time of their formation allow their separation on one hand and help in identification of areas with different ecological risks due to overlay of the two structures on the other. Geochemistry of soil cover reflects the long-term result of the naturally balanced biogeochemical cycles, therefore the soil geochemical maps of the undisturbed areas may serve the basis for evaluation of the natural geochemical background with due regard to the main factors of geochemical differentiation in biosphere. Purposeful and incidental technogenic concentrations and dispersions of chemical elements of specific (mainly mono- or polycentric) structure are also fixed in soils that serve as secondary sources of contamination of the vegetation cover and local food chains. Overlay of the two structures forms specific heterogeneity of modern biogeochemical provinces with different risk for particular groups of people, animals and plants adapted to specific natural geochemical background within particular concentration interval. The developed approach is believed to be helpful for biogeochemical regionalizing of modern biosphere (noosphere) and for spatially adequate ecogeochemical evaluation of the environment and landuse decisions. It allows production of a set of applied geochemical maps such as: 1) health risk due to chemical elements deficiency and technogenic contamination accounting of possible additive effects; 2) adequate soil fertilization and melioration with due regard to secondary redistribution of chemical elements; 3) selection of areas adequate for the short- and long-term ecogeochemical monitoring; 4) selection of areas as global and regional biogeochemical standards. The approach was used to evaluate contribution of stable iodine deficiency and radioactive iodine fallout to distribution of thyroid diseases among population of the Bryansk region [1], to evaluate natural transformation of the initially uniform spatial structure of N, P, K in agricultural fields [2] and radiocesium in forest and flood plain landscapes [3]. The work has been partly supported by the Russian Foundation for Basic Research (grants 07-05-00912; 10-05-01148; 13-05-00823). References Korobova E.M., S.L. Romanov, A.I. Kuvylin, E.I. Chesalova, V.Yu. Beriozkin, I.V. Kurnosova. Modern natural and technogenic iodine biogeochemical provinces: spatial structure and health effects. Goldschmidt 2011, Prague, August 14-19, 2011. Mineralogical Magazine, 75, 3, June 2011, Goldschmidt abstracts 2011, www.minersoc.org, 1224. Romanov S.L. Patterns of the structure of nitrogen, phosphorous and potassium fields in landscape systems of Belorussia. Thesis. Moscow, Moscow State University, 1991, 20 p. Korobova E.M., Romanov S.L., 2009. A Chernobyl 137Cs contamination study as an example for the spatial structure of geochemical fields and modeling of the geochemical field structure. Chemometrics and Intelligent Laboratory Systems 99, 1-8.

Emergent Archetype Hydrological-Biogeochemical Response Patterns in Heterogeneous Catchments

NASA Astrophysics Data System (ADS)

Jawitz, J. W.; Gall, H. E.; Rao, P.

2013-12-01

What can spatiotemporally integrated patterns observed in stream hydrologic and biogeochemical signals generated in response to transient hydro-climatic and anthropogenic forcing tell us about the interactions between spatially heterogeneous soil-mediated hydrological and biogeochemical processes? We seek to understand how the spatial structure of solute sources coupled with hydrologic responses affect observed concentration-discharge (C-Q) patterns. These patterns are expressions of the spatiotemporal structure of solute loads exported from managed catchments, and their likely ecological consequences manifested in receiving water bodies (e.g., wetlands, rivers, lakes, and coastal waters). We investigated the following broad questions: (1) How does the correlation between flow-generating areas and biogeochemical source areas across a catchment evolve under stochastic hydro-climatic forcing? (2) What are the feasible hydrologic and biogeochemical responses that lead to the emergence of the observed archetype C-Q patterns? and; (3) What implications do these coupled dynamics have for catchment monitoring and implementation of management practices? We categorize the observed temporal signals into three archetypical C-Q patterns: dilution; accretion, and constant concentration. We introduce a parsimonious stochastic model of heterogeneous catchments, which act as hydrologic and biogeochemical filters, to examine the relationship between spatial heterogeneity and temporal history of solute export signals. The core concept of the modeling framework is considering the types and degree of spatial correlation between solute source zones and flow generating zones, and activation of different portions of the catchments during rainfall events. Our overarching hypothesis is that each of the archetype C-Q patterns can be generated by explicitly linking landscape-scale hydrologic responses and spatial distributions of solute source properties within a catchment. The model simulations reproduce the three major C-Q patterns observed in published data, offering valuable insight into coupled catchment processes. The findings have important implications for effective catchment management for water quality improvement, and stream monitoring strategies.

Investigating the organic carbon cycle and the anaerobic oxidation of methane in the Guaymas Basin: a biogeochemical approach

NASA Astrophysics Data System (ADS)

Cathalot, C.; Decker, C.; Caprais, J.; Ruffine, L.; Le Bruchec, J.; Olu, K.

2013-12-01

The Guaymas Basin is a pretty unique environment located in the Gulf of California and characterized by the emanation of fluids enriched in hydrocarbon, mainly methane, and sulfides. In this peculiar environment, both cold seeps and hydrothermal vents co-exist very closely, and are separated only by a few kilometers. In addition, highly productive surface waters and strong terrestrial inputs are responsible for strong sedimentation rates in this area. This special geological system allows for the development of various and complex macrofaunal and/or bacterial assemblages, based on chemosynthetic activity. These sea-bottom communities have been previously described [1,2] and several studies have demonstrated the occurrence of Anaerobic Oxidation of Methane (AOM) in the shallow sediment layers. Nevertheless, the quantification of the biogeochemical processes (e.g. rates, relative proportions) involved in both ecosystems in relation with the associated communities, and their role in the local organic carbon (OC) cycle is still lacking. Using a diagenetic modeling approach, this study aims at studying the OC production and recycling processes by describing the biogeochemical pathways and their associated rates in the ecosystems from the Guaymas Basin. Twelve stations presenting distinct biological assemblages (microbial mats, vesicomyids and bare sediment) were selected among both cold-seeps and hydrothermal vents sites from the Guaymas basin. A transport-reaction model including respiration, sulfate reduction, methanogenesis and AOM was developed and applied to each station. To constrain the model, at each station, cores were sampled using an ROV and the pore-waters extracted using Rhizon syringes. Pore-water concentrations of CH4, SO42-, Cl- and H2S were then measured. In addition, ex situ O2 microprofiles equipped with microsensors and in situ incubations using benthic chambers were performed to estimate the sediment uptake rates (O2, H2S, CH4). The overall dataset was used to feed the model. The preliminary results indicate 1) significant differences of biogeochemical processes between the different biological assemblages and 2) between the cold seeps and hydrothermal vents sites. Model outputs show the occurrence of AOM and sulfate reduction at all sites except the reference (i.e. bare sediment) confirming hence the chemosynthetic activity (OC production) within the specific biological assemblages (mats and Vesicomyid). AOM in bacterial mats was more active in hydrothermal vents than in cold-seeps. In addition, the results indicate strong sulfate reduction rates in Vesicomyids assemblages but with a clear mismatch between modeled and measured H2S concentrations in the sediment: such differences reflect the symbiosis chemosynthetic activity (i.e. the H2S consumption) within the organisms. This integrated model-data approach proves hence to be useful to infer the biogeochemical functioning of biological ecosystems. [1] Kallmeyer, J. & Boetius, A (2004): Applied and Environmental Microbiology, 70, 2, 1231-1233. [2] Biddle J. F. et al. (2012). ISME J. 6 1018-1031

Impacts of Suspended Sediment and Estuarine - Shelf Exchange Pathways on Shelf Ecosystem Dynamics in the Northern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Wiggert, J. D.; Pan, C.; Dinniman, M. S.; Lau, Y.; Fitzpatrick, P. J.; O'Brien, S. J.; Bouchard, C.; Quas, L. M.; Miles, T. N.; Cambazoglu, M. K.; Dykstra, S. L.; Dzwonkowski, B.; Jacobs, G. A.; Church, I.; Hofmann, E. E.

2017-12-01

A circulation model based on the Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System, with coupled biogeochemical and sediment transport modules, has been implemented for Mississippi Sound and the adjacent continental shelf region. The model has 400-m horizontal resolution, 24 vertical layers, and includes wetting/drying capability to resolve shallow inshore regions. The circulation model was spun-up using oceanographic initial and lateral boundary conditions provided by a 1-km resolution regional implementation of the Navy Coastal Ocean Model (NCOM) in the Gulf of Mexico. The biogeochemical module includes multiple size classes of phytoplankton, zooplankton and detritus, a fish larvae compartment, and explicitly tracks dissolved oxygen with benthic cycling interaction. The sediment transport model is implemented based on benthic mapping data that provides bottom sediment type distributions and spatio-temporal validation. A regionally specific atmospheric forcing product that provides improved spatial and temporal resolution, including diurnal sea breeze impacts, has been developed and applied. Model experiments focus on periods when comprehensive ship-based sampling was deployed by the CONCORDE (Consortium for Coastal River-Dominated Ecosystems) research program, which was established to investigate the complex fine-scale biological, chemical and physical interactions in a marine system controlled by pulsed-river plume dynamics. Biophysical interactions and biogeochemical variability associated with estuarine - shelf exchanges between nearshore lagoonal estuarine waters and the continental shelf revealed by the model provide new insight into how seasonal variation of hydrological forcing conditions influence ecological and biogeochemical processes in the highly productive Northern Gulf region. Application of the COAWST-based model system with and without inclusion of the sediment transport module demonstrates how suspended sediment in the nearshore waters influences inner shelf ecosystem function through impacts exerted on the in situ light environment and particle aggregation-mediated organic matter fluxes.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

USGS Publications Warehouse

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

2012-01-01

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

Diurnal variability in carbon and nitrogen pools within Chesapeake Bay and northern Gulf of Mexico: implications for future ocean color satellite sensors

NASA Astrophysics Data System (ADS)

Mannino, A.; Novak, M. G.; Tzortziou, M.; Salisbury, J.

2016-02-01

Relative to their areal extent, estuaries and coastal ocean ecosystems contribute disproportionately more to global biogeochemical cycling of carbon, nitrogen and other elements compared to the open ocean. Applying ocean color satellite data to study biological and biogeochemical processes within coastal ecosystems is challenging due to the complex mixtures of aquatic constituents derived from terrestrial, anthropogenic, and marine sources, human-impacted atmospheric properties, presence of clouds during satellite overpass, fine-scale spatial gradients, and time-varying processes on diurnal scales that cannot be resolved with current sensors. On diurnal scales, biological, photochemical, and biogeochemical processes are regulated by the variation in solar radiation. Other physical factors, such as tides, river discharge, estuarine and coastal ocean circulation, wind-driven mixing, etc., impart further variability on biological and biogeochemical processes on diurnal to multi-day time scales. Efforts to determine the temporal frequency required from a NASA GEO-CAPE ocean color satellite sensor to discern diurnal variability C and N stocks, fluxes and productivity culminated in field campaigns in the Chesapeake Bay and northern Gulf of Mexico. Near-surface drogues were released and tracked in quasi-lagrangian space to monitor hourly changes in community production, C and N stocks, and optical properties. While only small diurnal changes were observed in dissolved organic carbon (DOC) and colored dissolved organic matter (CDOM) absorption in Chesapeake Bay, substantial variation in particulate organic carbon (POC) and nitrogen (PN), chlorophyll-a, and inorganic nitrogen (DIN) were measured. Similar or greater diurnal changes in POC, PN, chlorophyll-a and DIN were found in Gulf of Mexico nearshore and offshore sites. These results suggest that satellite observations at hourly frequency are desirable to capture diurnal variability in carbon and nitrogen stocks, fluxes and productivity within coastal ecosystems.

Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

NASA Astrophysics Data System (ADS)

Chen, M.; Kocar, B. D.

2016-12-01

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

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

NASA Astrophysics Data System (ADS)

Romaniello, Stephen J.; Derry, Louis A.

2010-08-01

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

Grand challenges in understanding the interplay of climate and land changes

USGS Publications Warehouse

Liu, Shuguang; Bond-Lamberty, Ben; Boysen, Lena R.; Ford, James D.; Fox, Andrew; Gallo, Kevin; Hatfield, Jerry L.; Henebry, Geoffrey M.; Huntington, Thomas G.; Liu, Zhihua; Loveland, Thomas R.; Norby, Richard J.; Sohl, Terry L.; Steiner, Allison L.; Yuan, Wenping; Zhang, Zhao; Zhao, Shuqing

2017-01-01

Half of Earth’s land surface has been altered by human activities, creating various consequences on the climate and weather systems at local to global scales, which in turn affect a myriad of land surface processes and the adaptation behaviors. This study reviews the status and major knowledge gaps in the interactions of land and atmospheric changes and present 11 grand challenge areas for the scientific research and adaptation community in the coming decade. These land-cover and land-use change (LCLUC)-related areas include 1) impacts on weather and climate, 2) carbon and other biogeochemical cycles, 3) biospheric emissions, 4) the water cycle, 5) agriculture, 6) urbanization, 7) acclimation of biogeochemical processes to climate change, 8) plant migration, 9) land-use projections, 10) model and data uncertainties, and, finally, 11) adaptation strategies. Numerous studies have demonstrated the effects of LCLUC on local to global climate and weather systems, but these putative effects vary greatly in magnitude and even sign across space, time, and scale and thus remain highly uncertain. At the same time, many challenges exist toward improved understanding of the consequences of atmospheric and climate change on land process dynamics and services. Future effort must improve the understanding of the scale-dependent, multifaceted perturbations and feedbacks between land and climate changes in both reality and models. To this end, one critical cross-disciplinary need is to systematically quantify and better understand measurement and model uncertainties. Finally, LCLUC mitigation and adaptation assessments must be strengthened to identify implementation barriers, evaluate and prioritize opportunities, and examine how decision-making processes work in specific contexts.

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Genome-to-Watershed Predictive Understanding of Terrestrial Environments

NASA Astrophysics Data System (ADS)

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

2014-12-01

Although terrestrial environments play a critical role in cycling water, greenhouse gasses, and other life-critical elements, the complexity of interactions among component microbes, plants, minerals, migrating fluids and dissolved constituents hinders predictive understanding of system behavior. The 'Sustainable Systems 2.0' project is developing genome-to-watershed scale predictive capabilities to quantify how the microbiome affects biogeochemical watershed functioning, how watershed-scale hydro-biogeochemical processes affect microbial functioning, and how these interactions co-evolve with climate and land-use changes. Development of such predictive capabilities is critical for guiding the optimal management of water resources, contaminant remediation, carbon stabilization, and agricultural sustainability - now and with global change. Initial investigations are focused on floodplains in the Colorado River Basin, and include iterative model development, experiments and observations with an early emphasis on subsurface aspects. Field experiments include local-scale experiments at Rifle CO to quantify spatiotemporal metabolic and geochemical responses to O2and nitrate amendments as well as floodplain-scale monitoring to quantify genomic and biogeochemical response to natural hydrological perturbations. Information obtained from such experiments are represented within GEWaSC, a Genome-Enabled Watershed Simulation Capability, which is being developed to allow mechanistic interrogation of how genomic information stored in a subsurface microbiome affects biogeochemical cycling. This presentation will describe the genome-to-watershed scale approach as well as early highlights associated with the project. Highlights include: first insights into the diversity of the subsurface microbiome and metabolic roles of organisms involved in subsurface nitrogen, sulfur and hydrogen and carbon cycling; the extreme variability of subsurface DOC and hydrological controls on carbon and nitrogen cycling; geophysical identification of floodplain hotspots that are useful for model parameterization; and GEWaSC demonstration of how incorporation of identified microbial metabolic processes improves prediction of the larger system biogeochemical behavior.

Using NEON Data to Test and Refine Conceptual and Numerical Models of Soil Biogeochemical and Microbial Dynamics

NASA Astrophysics Data System (ADS)

Weintraub, S. R.; Stanish, L.; Ayers, E.

2017-12-01

Recent conceptual and numerical models have proposed new mechanisms that underpin key biogeochemical phenomena, including soil organic matter storage and ecosystem response to nitrogen deposition. These models seek to explicitly capture the ecological links among biota, especially microbes, and their physical and chemical environment to represent belowground pools and fluxes and how they respond to perturbation. While these models put forth exciting new concepts, their broad predictive abilities are unclear as some have been developed and tested against only small or regional datasets. The National Ecological Observatory Network (NEON) presents new opportunities to test and validate these models with multi-site data that span wide climatic, edaphic, and ecological gradients. NEON is measuring surface soil biogeochemical pools and fluxes along with diversity, abundance, and functional potential of soil microbiota at 47 sites distributed across the United States. This includes co-located measurements of soil carbon and nitrogen concentrations and stable isotopes, net nitrogen mineralization and nitrification rates, soil moisture, pH, microbial biomass, and community composition via 16S and ITS rRNA sequencing and shotgun metagenomic analyses. Early NEON data demonstrates that these wide edaphic and climatic gradients are related to changes in microbial community structure and functional potential, as well as element pools and process rates. Going forward, NEON's suite of standardized soil data has the potential to advance our understanding of soil communities and processes by allowing us to test the predictions of new soil biogeochemical frameworks and models. Here, we highlight several recently developed models that are ripe for this kind of data validation, and discuss key insights that may result. Further, we explore synergies with other networks, such as (i)LTER and (i)CZO, which may increase our ability to advance the frontiers of soil biogeochemical modeling.

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

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

Pelagic functional group modeling: Progress, challenges and prospects

NASA Astrophysics Data System (ADS)

Hood, Raleigh R.; Laws, Edward A.; Armstrong, Robert A.; Bates, Nicholas R.; Brown, Christopher W.; Carlson, Craig A.; Chai, Fei; Doney, Scott C.; Falkowski, Paul G.; Feely, Richard A.; Friedrichs, Marjorie A. M.; Landry, Michael R.; Keith Moore, J.; Nelson, David M.; Richardson, Tammi L.; Salihoglu, Baris; Schartau, Markus; Toole, Dierdre A.; Wiggert, Jerry D.

2006-03-01

In this paper, we review the state of the art and major challenges in current efforts to incorporate biogeochemical functional groups into models that can be applied on basin-wide and global scales, with an emphasis on models that might ultimately be used to predict how biogeochemical cycles in the ocean will respond to global warming. We define the term "biogeochemical functional group" to refer to groups of organisms that mediate specific chemical reactions in the ocean. Thus, according to this definition, "functional groups" have no phylogenetic meaning—these are composed of many different species with common biogeochemical functions. Substantial progress has been made in the last decade toward quantifying the rates of these various functions and understanding the factors that control them. For some of these groups, we have developed fairly sophisticated models that incorporate this understanding, e.g. for diazotrophs (e.g. Trichodesmium), silica producers (diatoms) and calcifiers (e.g. coccolithophorids and specifically Emiliania huxleyi). However, current representations of nitrogen fixation and calcification are incomplete, i.e., based primarily upon models of Trichodesmium and E. huxleyi, respectively, and many important functional groups have not yet been considered in open-ocean biogeochemical models. Progress has been made over the last decade in efforts to simulate dimethylsulfide (DMS) production and cycling (i.e., by dinoflagellates and prymnesiophytes) and denitrification, but these efforts are still in their infancy, and many significant problems remain. One obvious gap is that virtually all functional group modeling efforts have focused on autotrophic microbes, while higher trophic levels have been completely ignored. It appears that in some cases (e.g., calcification), incorporating higher trophic levels may be essential not only for representing a particular biogeochemical reaction, but also for modeling export. Another serious problem is our tendency to model the organisms for which we have the most validation data (e.g., E. huxleyi and Trichodesmium) even when they may represent only a fraction of the biogeochemical functional group we are trying to represent. When we step back and look at the paleo-oceanographic record, it suggests that oxygen concentrations have played a central role in the evolution and emergence of many of the key functional groups that influence biogeochemical cycles in the present-day ocean. However, more subtle effects are likely to be important over the next century like changes in silicate supply or turbulence that can influence the relative success of diatoms versus dinoflagellates, coccolithophorids and diazotrophs. In general, inferences drawn from the paleo-oceanographic record and theoretical work suggest that global warming will tend to favor the latter because it will give rise to increased stratification. However, decreases in pH and Fe supply could adversely impact coccolithophorids and diazotrophs in the future. It may be necessary to include explicit dynamic representations of nitrogen fixation, denitrification, silicification and calcification in our models if our goal is predicting the oceanic carbon cycle in the future, because these processes appear to play a very significant role in the carbon cycle of the present-day ocean and they are sensitive to climate change. Observations and models suggest that it may also be necessary to include the DMS cycle to predict future climate, though the effects are still highly uncertain. We have learned a tremendous amount about the distributions and biogeochemical impact of bacteria in the ocean in recent years, yet this improved understanding has not yet been incorporated into many of our models. All of these considerations lead us toward the development of increasingly complex models. However, recent quantitative model intercomparison studies suggest that continuing to add complexity and more functional groups to our ecosystem models may lead to decreases in predictive ability if the models are not properly constrained with available data. We also caution that capturing the present-day variability tells us little about how well a particular model can predict the future. If our goal is to develop models that can be used to predict how the oceans will respond to global warming, then we need to make more rigorous assessments of predictive skill using the available data.

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

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

We present a generic flux limiter to account for mass limitations from an arbitrary number of substrates in a biogeochemical reaction network. The flux limiter is based on the observation that substrate (e.g., nitrogen, phosphorus) limitation in biogeochemical models can be represented as to ensure mass conservative and non-negative numerical solutions to the governing ordinary differential equations. Application of the flux limiter includes two steps: (1) formulation of the biogeochemical processes with a matrix of stoichiometric coefficients and (2) application of Liebig's law of the minimum using the dynamic stoichiometric relationship of the reactants. This approach contrasts with the ad hoc down-regulationmore » approaches that are implemented in many existing models (such as CLM4.5 and the ACME (Accelerated Climate Modeling for Energy) Land Model (ALM)) of carbon and nutrient interactions, which are error prone when adding new processes, even for experienced modelers. Through an example implementation with a CENTURY-like decomposition model that includes carbon, nitrogen, and phosphorus, we show that our approach (1) produced almost identical results to that from the ad hoc down-regulation approaches under non-limiting nutrient conditions, (2) properly resolved the negative solutions under substrate-limited conditions where the simple clipping approach failed, (3) successfully avoided the potential conceptual ambiguities that are implied by those ad hoc down-regulation approaches. We expect our approach will make future biogeochemical models easier to improve and more robust.« less

Tidal Marsh Outwelling of Dissolved Organic Matter and Resulting Temporal Variability in Coastal Water Optical and Biogeochemical Properties

NASA Technical Reports Server (NTRS)

Tzortziou, Maria; Neale, Patrick J.; Megonigal, J. Patrick; Butterworth, Megan; Jaffe, Rudolf; Yamashita, Youhei

2010-01-01

Coastal wetlands are highly dynamic environments at the land-ocean interface where human activities, short-term physical forcings and intense episodic events result in high biological and chemical variability. Long being recognized as among the most productive ecosystems in the world, tidally-influenced coastal marshes are hot spots of biogeochemical transformation and exchange. High temporal resolution observations that we performed in several marsh-estuarine systems of the Chesapeake Bay revealed significant variability in water optical and biogeochemical characteristics at hourly time scales, associated with tidally-driven hydrology. Water in the tidal creek draining each marsh was sampled every hour during several semi-diurnal tidal cycles using ISCO automated samplers. Measurements showed that water leaving the marsh during ebbing tide was consistently enriched in dissolved organic carbon (DOC), frequently by more than a factor of two, compared to water entering the marsh during flooding tide. Estimates of DOC fluxes showed a net DOC export from the marsh to the estuary during seasons of both low and high biomass of marsh vegetation. Chlorophyll amounts were typically lower in the water draining the marsh, compared to that entering the marsh during flooding tide, suggesting that marshes act as transformers of particulate to dissolved organic matter. Moreover, detailed optical and compositional analyses demonstrated that marshes are important sources of optically and chemically distinctive, relatively complex, high molecular weight, aromatic-rich and highly colored dissolved organic compounds. Compared to adjacent estuarine waters, marsh-exported colored dissolved organic matter (CDOM) was characterized by considerably stronger absorption (more than a factor of three in some cases), larger DOC-specific absorption, lower exponential spectral slope, larger fluorescence signal, lower fluorescence per unit absorbance, and higher fluorescence at visible wavelengths. Observed patterns in water optical and biogeochemical variables were very consistent among different marsh systems and throughout the year, despite continued tidal exchange, implying rapid transformation of marsh DOM in the estuary through both photochemical and microbial processes. These findings illustrate the importance of tidal marsh ecosystems as sources, sinks and/or transformers of biologically important nutrients, carbon and colored dissolved organic compounds, and their influence on short-term biological, optical and biogeochemical variability in coastal waters.

Understanding the Spatial and Temporal Variations in Hormone Transport within the Stream Ecosystem

NASA Astrophysics Data System (ADS)

Mallakpour, I.; Ward, A. S.; Basu, N. B.

2012-12-01

Agricultural, urban, and industrial activities, including land application of manures and discharge of municipal and industrial wastewater, act as point and nonpoint sources for steroid hormones in soils, water, and sediments. Hormones are endocrine disruptors, and their occurrence in stream ecosystems has been implicated in the decline of certain species and change of sex in fish. Laboratory studies indicate that steroid hormones tend to have moderately large sorption coefficients and relatively short half-lives, from a few hours to a few days, suggesting that their persistence and subsequent leaching from soils will be limited. However, these chemicals continue to be detected in streams, indicating that laboratory studies may not capture the coupled hydrologic and biogeochemical dynamics occurring at the field or stream-reach scale. Understanding the spatial and temporal persistence of these chemicals downstream of a confined animal feeding operation (CAFO) or wastewater treatment plant (WWTP) requires a coupled hydrologic and biogeochemical model that takes into account multiple interacting species, sediment processes, and different aerobic and anaerobic reaction pathways and rates. In this study, we focus on two hormones, estrone (E1) and 17β-estradiol (E2), with redox dynamics controlling the conversion between E1 and E2. A 1D stream-reach model with a main-channel and a hyporheic zone was developed similar to the commonly used OTIS model. Processes such as photolysis, decay, and sorption to sediments were included in the model framework. The inclusion of coupled reactions, with specific reaction rates and pathways driven by different reaction pathway, that in turn can be dynamic during a storm event (for example, increasing discharge might lead to more aerobic conditions), was the novelty of the approach. The modeling framework was then used to quantify the relative importance of the different reaction pathways under varying flow conditions, and evaluate the persistence of these chemicals as a function of hydrologic and biogeochemical controls.

Examining the diversity and distribution of microbial communities from newly discovered methane seeps along the Cascadia Margin

NASA Astrophysics Data System (ADS)

Seabrook, S.; Thurber, A. R.; Embley, R. W.; Raineault, N.; Baumberger, T.; Merle, S. G.

2016-12-01

Methane seeps provide biogeochemical and microbial heterogeneity in deep-sea habitats. In June of 2016 the E/V Nautilus, exploring for methane seeps along the Cascadia continental margin, discovered over 450 bubble streams, indicative of active seepage, and collected biological samples at 6 of the resulting newly discovered seeps. These seeps covered a range of depths, latitudes, habitat types and biogeochemical environments and included: Juan de Fuca (150m), Astoria canyon (800m and 500m), Nehalem Bank (185m), Heceta SW (1200m), SW Coquille Bank (600m), and Klamath Knoll seep (700m). Geologic environment types included continental shelf, canyons and slopes, and these sites spanned the zone of hydrate stability and the Oxygen Minimum Zone. A range of seep-specific habitat were found and sampled including: reduced sediments, microbial mats, methane hydrates, clam beds (Calyptogena spp.), Siboglinidae tubeworm assemblages and sparse assemblages of stalked barnacles. Here, we present an initial characterization of the microbial communities collected via push cores by a remotely operated vehicle (ROV) at the six aforementioned sites. With high throughput amplicon sequencing of the V4-V5 region of the 16S rRNA gene, we characterize the diversity and microbial composition of the seep sites sampled. This characterization is furthered with digital drop PCR of the pmoA gene (involved with aerobic methanotrophy) to allow for a comparison of the community composition with functional gene abundance of critical microbial processes. These data will be placed in the greater biogeochemical context of the region, including direct comparison with paired gas-tight sampling at key locations. The results of these analyses will provide the first microbial description of this broad range of seep ecosystems along the Cascadia Margin adding to our overall understanding of microbial diversity, the dominant physiological processes at seep ecosystems, and the connection between community structure, function and biogeochemistry in habitats which we are just starting to appreciate for their ubiquity in marine environments.

Thresholds of understanding: Exploring assumptions of scale invariance vs. scale dependence in global biogeochemical models

NASA Astrophysics Data System (ADS)

Wieder, W. R.; Bradford, M.; Koven, C.; Talbot, J. M.; Wood, S.; Chadwick, O.

2016-12-01

High uncertainty and low confidence in terrestrial carbon (C) cycle projections reflect the incomplete understanding of how best to represent biologically-driven C cycle processes at global scales. Ecosystem theories, and consequently biogeochemical models, are based on the assumption that different belowground communities function similarly and interact with the abiotic environment in consistent ways. This assumption of "Scale Invariance" posits that environmental conditions will change the rate of ecosystem processes, but the biotic response will be consistent across sites. Indeed, cross-site comparisons and global-scale analyses suggest that climate strongly controls rates of litter mass loss and soil organic matter turnover. Alternatively, activities of belowground communities are shaped by particular local environmental conditions, such as climate and edaphic conditions. Under this assumption of "Scale Dependence", relationships generated by evolutionary trade-offs in acquiring resources and withstanding environmental stress dictate the activities of belowground communities and their functional response to environmental change. Similarly, local edaphic conditions (e.g. permafrost soils or reactive minerals that physicochemically stabilize soil organic matter on mineral surfaces) may strongly constrain the availability of substrates that biota decompose—altering the trajectory of soil biogeochemical response to perturbations. Identifying when scale invariant assumptions hold vs. where local variation in biotic communities or edaphic conditions must be considered is critical to advancing our understanding and representation of belowground processes in the face of environmental change. Here we introduce data sets that support assumptions of scale invariance and scale dependent processes and discuss their application in global-scale biogeochemical models. We identify particular domains over which assumptions of scale invariance may be appropriate and potential thresholds where shifts in ecosystem function may be expected. Finally, we discuss the mechanistic insight that can be applied in process-based models and datasets that can evaluate models across spatial and temporal scales.

Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies.

PubMed

Taubert, Martin; Grob, Carolina; Howat, Alexandra M; Burns, Oliver J; Chen, Yin; Neufeld, Josh D; Murrell, J Colin

2016-01-01

Methylotrophs are microorganisms ubiquitous in the environment that can metabolize one-carbon (C1) compounds as carbon and/or energy sources. The activity of these prokaryotes impacts biogeochemical cycles within their respective habitats and can determine whether these habitats act as sources or sinks of C1 compounds. Due to the high importance of C1 compounds, not only in biogeochemical cycles, but also for climatic processes, it is vital to understand the contributions of these microorganisms to carbon cycling in different environments. One of the most challenging questions when investigating methylotrophs, but also in environmental microbiology in general, is which species contribute to the environmental processes of interest, or "who does what, where and when?" Metabolic labeling with C1 compounds substituted with (13)C, a technique called stable isotope probing, is a key method to trace carbon fluxes within methylotrophic communities. The incorporation of (13)C into the biomass of active methylotrophs leads to an increase in the molecular mass of their biomolecules. For DNA-based stable isotope probing (DNA-SIP), labeled and unlabeled DNA is separated by isopycnic ultracentrifugation. The ability to specifically analyze DNA of active methylotrophs from a complex background community by high-throughput sequencing techniques, i.e. targeted metagenomics, is the hallmark strength of DNA-SIP for elucidating ecosystem functioning, and a protocol is detailed in this chapter.

Microbe-Mineral Interactions Along Biogeochemical Gradients in Bahamian Stromatolites: Key to Lithification and Preservation

NASA Astrophysics Data System (ADS)

Andres, M. S.; Sumner, D. Y.; Visscher, P. T.; Swart, P. K.; Reid, R. P.

2005-12-01

Understanding on how modern stromatolites form and lithify is critical to properly interpreting the origins of ancient stromatolites and the early evolution of life. Lithification in Bahamian stromatolites is tied to specific, 20-60-micron thick horizons characterized by laterally continuous sheets of microcrystalline carbonate (aragonite). Microbial processes associated with these horizons are 1) photosynthetic production by cyanobacteria and 2) heterotrophic respiration by bacteria as well as the production of extrapolymeric substances (EPS). The aim of this study is to better understand the coupling of microstructure and microbial processes. The competing influences of photosynthetic CO2 uptake, sulfate reduction, and degradation of Ca-binding EPS influence both carbonate saturation states and the isotopic composition of dissolved inorganic carbon (DIC). In Bahamian stromatolites, photosynthesis and sulfate reduction are associated with specific microbial mat types creating distinctive chemical gradients that can be preserved in authigenic carbonate. Aragonite that precipitated within stromatolites is > 1 per mill depleted in 13C relative to aragonite precipitated in equilibrium with local seawater. These data suggest that more aragonite precipitates when and where respiration, rather than photosynthesis, influences local DIC, which is consistent with sulfate reduction promoting carbonate precipitation and calcium release during decay of exopolymeric substances. Biogeochemical gradients vary on a temporal and spatial scale as indicated by in-situ pH measurements across a the living mat. Highest pH correlates to maximum photosynthesis signal in the early afternoon while the lowest pH to that of maximum respiration just before sunrise. Corresponding carbon isotope analysis of authigenic carbonate precipitate will determine when microscale biological activity is captured in the mineral phase and potentially preserved.

Land-use/land-cover drives variation in the specific inherent optical properties of estuaries

EPA Science Inventory

Changes in land-use/land-cover (LULC) can impact the exports of optically and biogeochemically active constituents to estuaries. Specific inherent optical properties (SIOPs) of estuarine optically active constituents (OACs) are directly related to the composition of the OACs, and...

From Position-Specific Labeling to Environmental Fluxomics: Elucidating Biogeochemical Cycles from the Metabolic Perspective (BG Division Outstanding ECS Award Lecture)

NASA Astrophysics Data System (ADS)

Dippold, Michaela; Apostel, Carolin; Dijkstra, Paul; Kuzyakov, Yakov

2017-04-01

Understanding soil and sedimentary organic matter (SOM) dynamics is one of the most important challenges in biogeoscience. To disentangle the fluxes and transformations of C in soils a detailed knowledge on the biochemical pathways and its controlling factors is required. Biogeochemists' view on the C transformation of microorganisms in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the microbial anabolism. Biochemists, however, thoroughly identified in the past decades the individual reactions of glycolysis, pentose-phosphate pathway and citric acid cycle underlying the microbial catabolism. At various points within that metabolic network the anabolic fluxes feeding biomass formation branch off. Recent studies on metabolic flux tracing by position-specific isotope labeling allowed tracing these C transformations in soils in situ, an approach which is qunatitatively complemented by metabolic flux modeling. This approach has reached new impact by the cutting-edge combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites which allows 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. Thus, the combination of position-specific labeling, compound-specific isotope incorporation in biomarkers and quantitative metabolic flux modelling provide the toolbox for quantitative soil fluxomics. Our studies combining position-specific labeled glucose with amino sugar 13C analysis showed that up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in citric acid cycle. Thus, oxidizing catabolic pathways and anabolic pathways, i.e. building-up new cellular compounds, occurred in soils simultaneously, a combination unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. Coupling these results with the position-specific fingerprint of microbial biomarkers revealed that microbial groups show deviating adaptation strategies and that they react on environmental changes by activation or deactivation of specific metabolic pathways such as anaplerotic fluxes. To understand how microorganisms catalyze the biogeochemical fluxes in soil a profound understanding of their metabolic adaptation strategies such as recycling or switching between pathways is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the underlying microbial processes.

Belowground Carbon Cycling Processes at the Molecular Scale: An EMSL Science Theme Advisory Panel Workshop

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

Hess, Nancy J.; Brown, Gordon E.; Plata, Charity

2014-02-21

As part of the Belowground Carbon Cycling Processes at the Molecular Scale workshop, an EMSL Science Theme Advisory Panel meeting held in February 2013, attendees discussed critical biogeochemical processes that regulate carbon cycling in soil. The meeting attendees determined that as a national scientific user facility, EMSL can provide the tools and expertise needed to elucidate the molecular foundation that underlies mechanistic descriptions of biogeochemical processes that control carbon allocation and fluxes at the terrestrial/atmospheric interface in landscape and regional climate models. Consequently, the workshop's goal was to identify the science gaps that hinder either development of mechanistic description ofmore » critical processes or their accurate representation in climate models. In part, this report offers recommendations for future EMSL activities in this research area. The workshop was co-chaired by Dr. Nancy Hess (EMSL) and Dr. Gordon Brown (Stanford University).« less

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

PubMed Central

Nazaries, Loïc; Pan, Yao; Bodrossy, Levente; Baggs, Elizabeth M.; Millard, Peter; Murrell, J. Colin

2013-01-01

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles. PMID:23624469

2010 MARINE MICROBES GORDON RESEARCH CONFERENCE (JULY 4-9, 2010 - TILTON SCHOOL, TILTON NH)

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

David Kirchman

Marine microbes include representatives from all three kingdoms of life and collectively carry out virtually all forms of metabolisms found on the planet. Because of this metabolic and genetic diversity, these microbes mediate many of the reactions making up global biogeochemical cycles which govern the flow of energy and material in the biosphere. The goal of this conference is to bring together approaches and concepts from studies of microbial evolution, genomics, ecology, and oceanography in order to gain new insights into marine microbes and their biogeochemical functions. The integration of scales, from genes to global cycles, will result in amore » better understanding of marine microbes and of their contribution to the carbon cycle and other biogeochemical processes.« less

Impacts of mesoscale eddies in the South China Sea on biogeochemical cycles

NASA Astrophysics Data System (ADS)

Guo, Mingxian; Chai, Fei; Xiu, Peng; Li, Shiyu; Rao, Shivanesh

2015-09-01

Biogeochemical cycles associated with mesoscale eddies in the South China Sea (SCS) were investigated. The study was based on a coupled physical-biogeochemical Pacific Ocean model (Regional Ocean Model System-Carbon, Silicate, and Nitrogen Ecosystem, ROMS-CoSiNE) simulation for the period from 1991 to 2008. A total of 568 mesoscale eddies with lifetime longer than 30 days were used in the analysis. Composite analysis revealed that the cyclonic eddies were associated with abundance of nutrients, phytoplankton, and zooplankton while the anticyclonic eddies depressed biogeochemical cycles, which are generally controlled by the eddy pumping mechanism. In addition, diatoms were dominant in phytoplankton species due to the abundance of silicate. Dipole structures of vertical fluxes with net upward motion in cyclonic eddies and net downward motion in anticyclonic eddies were revealed. During the lifetime of an eddy, the evolutions of physical, biological, and chemical structures were not linearly coupled at the eddy core where plankton grew, and composition of the community depended not only on the physical and chemical processes but also on the adjustments by the predator-prey relationship.

Potential for real-time understanding of coupled hydrologic and biogeochemical processes in stream ecosystems: Future integration of telemetered data with process models for glacial meltwater streams

NASA Astrophysics Data System (ADS)

McKnight, Diane M.; Cozzetto, Karen; Cullis, James D. S.; Gooseff, Michael N.; Jaros, Christopher; Koch, Joshua C.; Lyons, W. Berry; Neupauer, Roseanna; Wlostowski, Adam

2015-08-01

While continuous monitoring of streamflow and temperature has been common for some time, there is great potential to expand continuous monitoring to include water quality parameters such as nutrients, turbidity, oxygen, and dissolved organic material. In many systems, distinguishing between watershed and stream ecosystem controls can be challenging. The usefulness of such monitoring can be enhanced by the application of quantitative models to interpret observed patterns in real time. Examples are discussed primarily from the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. Although the Dry Valley landscape is barren of plants, many streams harbor thriving cyanobacterial mats. Whereas a daily cycle of streamflow is controlled by the surface energy balance on the glaciers and the temporal pattern of solar exposure, the daily signal for biogeochemical processes controlling water quality is generated along the stream. These features result in an excellent outdoor laboratory for investigating fundamental ecosystem process and the development and validation of process-based models. As part of the McMurdo Dry Valleys Long-Term Ecological Research project, we have conducted field experiments and developed coupled biogeochemical transport models for the role of hyporheic exchange in controlling weathering reactions, microbial nitrogen cycling, and stream temperature regulation. We have adapted modeling approaches from sediment transport to understand mobilization of stream biomass with increasing flows. These models help to elucidate the role of in-stream processes in systems where watershed processes also contribute to observed patterns, and may serve as a test case for applying real-time stream ecosystem models.

Reimplementation of the Biome-BGC model to simulate successional change.

PubMed

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

2005-04-01

Biogeochemical process models are increasingly employed to simulate current and future forest dynamics, but most simulate only a single canopy type. This limitation means that mixed stands, canopy succession and understory dynamics cannot be modeled, severe handicaps in many forests. The goals of this study were to develop a version of Biome-BGC that supported multiple, interacting vegetation types, and to assess its performance and limitations by comparing modeled results to published data from a 150-year boreal black spruce (Picea mariana (Mill.) BSP) chronosequence in northern Manitoba, Canada. Model data structures and logic were modified to support an arbitrary number of interacting vegetation types; an explicit height calculation was necessary to prioritize radiation and precipitation interception. Two vegetation types, evergreen needle-leaf and deciduous broadleaf, were modeled based on site-specific meteorological and physiological data. The new version of Biome-BGC reliably simulated observed changes in leaf area, net primary production and carbon stocks, and should be useful for modeling the dynamics of mixed-species stands and ecological succession. We discuss the strengths and limitations of Biome-BGC for this application, and note areas in which further work is necessary for reliable simulation of boreal biogeochemical cycling at a landscape scale.

Field-Integrated Studies of Long-Term Sustainability of Chromium Bioreduction at Hanford 100H Site

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

Long, Philip E.

2006-06-01

The objectives of the project are to investigate coupled hydraulic, geochemical, and microbial conditions, and to determine the critical biogeochemical parameters necessary to maximize the extent of Cr(VI) bioreduction and minimize Cr(III) reoxidation in groundwater. Specific goals of the project are as follows: (1) Field testing and monitoring of Cr(VI) bioreduction in ground water and its transformation into insoluble species of Cr(III) at the Hanford 100H site, to develop the optimal strategy of water sampling for chemical, microbial, stable isotope analyses, and noninvasive geophysical monitoring; (2) Bench-scale flow and transport investigations using columns of undisturbed sediments to obtain diffusion andmore » kinetic parameters needed for the development of a numerical model, predictions of Cr(VI) bioreduction, and potential of Cr(III) reoxidation; and (3) Development of a multiphase, multi-component 3D reactive transport model and a code, TOUGHREACT-BIO, to predict coupled biogeochemical-hydrological processes associated with bioremediation, and to calibrate and validate the developed code based on the results of bench-scale and field-scale Cr(VI) biostimulation experiments in ground water at the Hanford Site.« less

Fate of microbial metabolites of hydrocarbons in a coastal plain aquifer: The role of electron acceptors

USGS Publications Warehouse

Cozzarelli, I.M.; Herman, J.S.; Baedecker, M. Jo

1995-01-01

A combined field and laboratory study was undertaken to understand the distribution and geochemical conditions that influence the prevalence of low molecular weight organic acids in groundwater of a shallow aquifer contaminated with gasoline. Aromatic hydrocarbons from gasoline were degraded by microbially mediated oxidation-reduction reactions, including reduction of nitrate, sulfate, and Fe(III). The biogeochemical reactions changed overtime in response to changes in the hydrogeochemical conditions in the aquifer. Aliphatic and aromatic organic acids were associated with hydrocarbon degradation in anoxic zones of the aquifer. Laboratory microcosms demonstrated that the biogeochemical fate of specific organic acids observed in groundwater varied with the structure of the acid and the availability of electron acceptors. Benzoic and phenylacetic acid were degraded by indigenous aquifer microorganisms when nitrate was supplied as an electron acceptor. Aromatic acids with two or more methyl substituants on the benzene ring persisted under nitrate-reducing conditions. Although iron reduction and sulfate reduction were important processes in situ and occurred in the microcosms, these reactions were not coupled to the biological oxidation of aromatic organic acids that were added to the microcosms as electron donors. ?? 1995 American Chemical Society.

SUSPENDED AND BENTHIC SEDIMENT RELATIONSHIPS IN THE YAQUINA ESTUARY, OREGON: NUTRIENT PROCESSING

EPA Science Inventory

Measurements of nutrient loading and subsequent nutrient processing are fundamental for determining biogeochemical processes in rivers and estuaries. In Oregon coastal watersheds, nutrient transport is strongly seasonal with up to 94% of the riverine dissolved nitrate and silic...

Carbon and nitrogen biogeochemistry in the ocean: A study using stable isotope natural abundance

NASA Technical Reports Server (NTRS)

Rau, G. H.; Desmarais, David J.

1985-01-01

Determining the biogeochemical pathways traveled by carbon and nitrogen in the ocean is fundamental to the understanding of how the ocean participates in the cycling of these elements within the biosphere. Because biological production, metabolism, and respiration can significantly alter the natural abundance of C-13 and N-15, these abundances can provide important information about the nature of these biological processes and their variability in the marine environment. The research initially seeks to characterize the spatial and temporal patterns of stable isotope abundances in organic matter, and to relate these abundances to C and N biogeochemical processes within selected areas of the northeastern Pacific Ocean.

Carbohydrates as indicators of biogeochemical processes

NASA Astrophysics Data System (ADS)

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

2012-05-01

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.

Combined effects of hydrologic alteration and cyprinid fish in mediating biogeochemical processes in a Mediterranean stream.

PubMed

Rubio-Gracia, Francesc; Almeida, David; Bonet, Berta; Casals, Frederic; Espinosa, Carmen; Flecker, Alexander S; García-Berthou, Emili; Martí, Eugènia; Tuulaikhuu, Baigal-Amar; Vila-Gispert, Anna; Zamora, Lluis; Guasch, Helena

2017-12-01

Flow regimes are important drivers of both stream community and biogeochemical processes. However, the interplay between community and biogeochemical responses under different flow regimes in streams is less understood. In this study, we investigated the structural and functional responses of periphyton and macroinvertebrates to different densities of the Mediterranean barbel (Barbus meridionalis, Cyprinidae) in two stream reaches differing in flow regime. The study was conducted in Llémena Stream, a small calcareous Mediterranean stream with high nutrient levels. We selected a reach with permanent flow (permanent reach) and another subjected to flow regulation (regulated reach) with periods of flow intermittency. At each reach, we used in situ cages to generate 3 levels of fish density. Cages with 10 barbels were used to simulate high fish density (>7indm -2 ); cages with open sides were used as controls (i.e. exposed to actual fish densities of each stream reach) thus having low fish density; and those with no fish were used to simulate the disappearance of fish that occurs with stream drying. Differences in fish density did not cause significant changes in periphyton biomass and macroinvertebrate density. However, phosphate uptake by periphyton was enhanced in treatments lacking fish in the regulated reach with intermittent flow but not in the permanent reach, suggesting that hydrologic alteration hampers the ability of biotic communities to compensate for the absence of fish. This study indicates that fish density can mediate the effects of anthropogenic alterations such as flow intermittence derived from hydrologic regulation on stream benthic communities and associated biogeochemical processes, at least in eutrophic streams. Copyright © 2017. Published by Elsevier B.V.

Biogeochemistry of natural ponds in agricultural landscape: Lessons learned from modeling a kettle hole in Northeast Germany.

PubMed

Onandia, Gabriela; Lischeid, Gunnar; Kalettka, Thomas; Kleeberg, Andreas; Omari, Mohamed; Premke, Katrin; Arhonditsis, George B

2018-09-01

Kettle holes, small shallow ponds of glacial origin, represent hotspots for biodiversity and biogeochemical cycling. They abound in the young moraine landscape of Northeast Germany, potentially modulating element fluxes in a region where intensive agriculture prevails. The Rittgarten kettle hole, with semi-permanent hydroperiod and a surrounding reed belt, can be considered as a representative case study for such systems. Aiming to provide insights into the biogeochemical processes driving nutrient and primary producer dynamics in the Rittgarten kettle hole, we developed a mechanistic model that simulates the carbon, nitrogen, phosphorus and oxygen, phytoplankton, and free-floating macrophyte biomass dynamics. After model calibration and sensitivity analysis, our modeling exercise quantified the simulated nutrient fluxes associated with all the major biogeochemical processes considered by the model. Seasonality of nutrient concentrations, magnitude of primary productivity rates, and biogeochemical process characterization in the pond were reasonably reproduced by the model from July 2013 to July 2014. Our results suggest that the establishment of a phytoplankton community well-adapted to low light availability, together with the differential use of N and P from free-floating macrophytes and phytoplankton can explain their coexistence in kettle holes. Sediment nutrient release along with decomposition of decaying submerged macrophyte are essential drivers of internal nutrient cycling in kettle holes. Our results also suggest that the Rittgarten kettle hole act as a net source of CO 2 to the atmosphere on an annual scale, which offers a testable hypothesis for kettle holes with structural and functional similarities. We conclude by discussing the need to shed light on the effects of water level fluctuations on nutrient dynamics and biological succession patterns, as well as the relative importance of external sources and internal nutrient recycling mechanisms. Copyright © 2018 Elsevier B.V. All rights reserved.

Authigenic Carbonate Formation on the Peru Margin; New Insights from IODP Site 1230

NASA Astrophysics Data System (ADS)

Abdullajintakam, S.; Naehr, T. H.

2015-12-01

Fluid seepage of reduced organic compounds such as methane impacts the geology and biology of the seabed by inducing complex, microbially mediated biogeochemical processes. Authigenic carbonates serve as one of the few permanent records of these of dynamic biogeochemical interactions that involve methanogenesis, methanotrophy, sulfate reduction and carbonate precipitation. Meister et al. (2007) investigated deep-sea dolomite formation at Sites 1227-1229 on the Peru margin, where dolomite precipitation occurs in association with organic carbon-rich continental margin sediments. Geochemical and petrographic studies indicated episodic dolomite precipitation at a dynamic sulfate methane transition zone (SMTZ). Variations in δ13C values of these dolomites between +15‰ and -15‰ were attributed to non-steady state conditions as a result of the upward and downward migration of the SMTZ. Our study aims to better understand the biogeochemical processes associated with authigenic carbonate precipitation in this dynamic deep-sea setting. We focused our efforts on IODP Site 1230, which is a gas-hydrate-bearing site that shows sulphate consumption within the uppermost 10 m below the seafloor as well as high methane production. Using a multi proxy approach, we combined X-ray diffraction, stable isotope geochemistry, and trace metal analysis of authigenic carbonates to elucidate conditions for authigenic carbonate formation. Results from Site 1230 are compared to Sites 1227 and 1229, which lacks gas hydrates and is characterized by high pore water sulfate and low methane concentrations. This study contributes to a more comprehensive understanding of authigenic carbonate formation and associated biogeochemical processes in continental margin sediments. Meister, P., Mckenzie, J. A., Vasconcelos, C., Bernasconi, S., Frank, M., Gutjhar, M. and SCHRAG, D. P. (2007), Dolomite formation in the dynamic deep biosphere: results from the Peru Margin. Sedimentology, 54: 1007-1032.

Impacts of Bottom Fishing on Sediment Biogeochemical and Biological Parameters in Cohesive and Non-cohesive Sediments

NASA Astrophysics Data System (ADS)

Sciberras, M.; Hiddink, J. G.; Powell, C.; Parker, R.; Krӧger, S.; Bolam, S. G.; Robertson, C.

2016-02-01

Sediment resuspension and bed reworking by tides, waves and biological activity are frequent in the energetic coastal environments. Sediment mixing by tides and waves are generally more important in regulating sediment processes in advection-dominated system such as sandy sediments, whereas sediment reworking by bioturbation is more important in diffusion-dominated systems such as muddy sediments. Bottom fishing constitutes an additional significant impact on benthic communities and sediment biogeochemical processes in coastal areas through physical changes in sediment resuspension and mixing and changes to bioturbating fauna. This study examined the biological (macro-infaunal) and biogeochemical responses to fishing at a muddy and sandy site in the Irish Sea that were predominantly impacted by otter trawls and scallop dredges, respectively. The sandy habitat (>90% sand) was typical of a hydrodynamic environment characterized by a diverse array of small infaunal species, low organic carbon levels and fast remineralisation of organic matter in the sediment. The muddier habitat (>65% fines) was dominated by fewer but larger bioturbating species compared to sand, and illustrated highly diffusional solute transport, higher organic carbon content and a shallower oxygen penetration depth. Generally there appeared to be no clear statistically significant changes in the biogeochemistry of the sandy or muddy habitat that could be attributed to different intensities of fishing. However, pore-water nutrient profiles of ammonium, phosphate and silicate provided clear evidence of organic matter burial and/or mixing as a result of trawling at the muddy site. The biogeochemistry at the sandy site appeared to remain dominated by the natural physical environment, so impact of fishing disturbance was less evident. These results suggest that fishing does not have comparable effects on the biology and biogeochemical processes in all benthic habitats.

Seasonal Dynamics of Biogeochemical Processes in the Water Column of the Northeastern Black Sea

NASA Astrophysics Data System (ADS)

Rusanov, I. I.; Lein, A. Yu.; Makkaveev, P. N.; Klyuvitkin, A. A.; Kravchishina, M. D.; Ivanov, M. V.; Flint, M. V.

2018-01-01

Integrated studies on the hydrochemistry and water column rates of microbial processes in the eastern sector of the Black Sea along a standard 100-miles transect off Gelendzhik from the coast to the central part of the sea at water depths of 100-2170 m show that a series of warm winters and the absence of intense convective winter mixing resulted in a relatively low content of suspended particulate matter (SPM), particulate organic carbon (POC), and nutrients in the water column in March 2009. The relatively high SPM concentrations and the presence of isotopically light POC at the offshore station are indicative of the supply of terrigenous material from land and low contributions of phytoplanktonic organic matter to the composition of SPM. This may explain the low rates of biogeochemical processes in the water column near the coast. The surface layer at deep-water stations is dominated by isotopically heavy phytoplanktonic organic matter. This suggests that the supply of terrigenous material from land was insufficient in offshore deep-water areas. Therefore, warm winters and insufficient nutrient supply do not prevent photosynthesis in the photic layer of the deep-water zone, which generates organic substrates for heterotrophic aquatic communities. The results of isotopic analysis of POC, measurements of the rates biogeochemical processes, and the hydrochemical characteristics of the water column can be used to determine the nature and seasonal variability of the POC composition.

Evaluating the fate of six common pharmaceuticals using a reactive transport model: insights from a stream tracer test.

PubMed

Riml, Joakim; Wörman, Anders; Kunkel, Uwe; Radke, Michael

2013-08-01

Quantitative information regarding the capacity of rivers to self-purify pharmaceutical residues is limited. To bridge this knowledge gap, we present a methodology for quantifying the governing processes affecting the fate of pharmaceuticals in streaming waters and, especially, to evaluate their relative significance for tracer observations. A tracer test in Säva Brook, Sweden was evaluated using a coupled physical-biogeochemical model framework containing surface water transport together with a representation of transient storage in slow/immobile zones of the stream, which are presumably important for the retention and attenuation of pharmaceuticals. To assess the key processes affecting the environmental fate of the compounds, we linked the uncertainty estimates of the reaction rate coefficients to the relative influence of transformation and sorption that occurred in different stream environments. The hydrological and biogeochemical contributions to the fate of the pharmaceuticals were decoupled, and the results indicate a moderate hydrological retention in the hyporheic zone as well as in the densely vegetated parts of the stream. Biogeochemical reactions in these transient storage zones further affected the fate of the pharmaceuticals, and we found that sorption was the key process for bezafibrate, metoprolol, and naproxen, while primary transformation was the most important process for clofibric acid and ibuprofen. Conversely, diclofenac was not affected by sorption or transformation. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling hyporheic zone processes

USGS Publications Warehouse

Runkel, Robert L.; McKnight, Diane M.; Rajaram, Harihar

2003-01-01

Stream biogeochemistry is influenced by the physical and chemical processes that occur in the surrounding watershed. These processes include the mass loading of solutes from terrestrial and atmospheric sources, the physical transport of solutes within the watershed, and the transformation of solutes due to biogeochemical reactions. Research over the last two decades has identified the hyporheic zone as an important part of the stream system in which these processes occur. The hyporheic zone may be loosely defined as the porous areas of the stream bed and stream bank in which stream water mixes with shallow groundwater. Exchange of water and solutes between the stream proper and the hyporheic zone has many biogeochemical implications, due to differences in the chemical composition of surface and groundwater. For example, surface waters are typically oxidized environments with relatively high dissolved oxygen concentrations. In contrast, reducing conditions are often present in groundwater systems leading to low dissolved oxygen concentrations. Further, microbial oxidation of organic materials in groundwater leads to supersaturated concentrations of dissolved carbon dioxide relative to the atmosphere. Differences in surface and groundwater pH and temperature are also common. The hyporheic zone is therefore a mixing zone in which there are gradients in the concentrations of dissolved gasses, the concentrations of oxidized and reduced species, pH, and temperature. These gradients lead to biogeochemical reactions that ultimately affect stream water quality. Due to the complexity of these natural systems, modeling techniques are frequently employed to quantify process dynamics.

The Value of Long-Term Research at the Five USGS WEBB Catchments

NASA Astrophysics Data System (ADS)

Shanley, J. B.; Murphy, S. F.; Scholl, M. A.; Wickland, K.; Aulenbach, B. T.; Hunt, R.; Clow, D. W.

2017-12-01

Long-term catchment studies are sentinel sites for detecting, documenting, and understanding ecosystem processes and environmental change. The small catchment approach fosters in-depth site-based hydrological, biogeochemical, and ecological process understanding, while a collective network of catchment observatories offers a broader context to synthesize understanding across a range of climates and geologies. The USGS Water, Energy, and Biogeochemical Budgets (WEBB) program is a network of five sites established in 1991 to assess the impact of climate and environmental change on hydrology and biogeochemistry. Like other networks, such as the USDA - Forest Service Experimental Forests and the Czech Geomon network, WEBB exploits gradients of climate, geology, and topography to understand controls on biogeochemical processes. We present examples from each site and some cross-site syntheses to demonstrate how WEBB has advanced catchment science and informed resource management and policy. WEBB has relied on strong academic partnerships, providing long-term continuity for shorter-term academic grants, which have offered rich graduate educational opportunities. Like other sites and networks, the long-term datasets and process understanding of WEBB provide context to detect and interpret change. Without this backdrop, we have no baseline to quantify effects of droughts, floods, and extreme events, and no test sites to validate process-based models. In an era of lean budgets for science funding, the long-term continuity of WEBB and other catchment networks is in jeopardy, as is the critical scientific value and societal benefits they embody.

The Origin of Carbon-Bearing Volatiles in a Continental Hydrothermal System in the Great Basin: Water Chemistry and Isotope Characterizations

NASA Technical Reports Server (NTRS)

Fu, Qi; Socki, Richard A.; Niles, Paul B.; Romanek, Christopher; Datta, Saugata; Darnell, Mike

2012-01-01

Hydrothermal systems on Earth are active centers in the crust where organic molecules can be synthesized biotically or abiotically under a wide range of physical and chemical conditions [1-3]. Not only are volatile species (CO, CO2, H2, and hydrocarbons) a reflection of deep-seated hydrothermal alteration processes, but they also form an important component of biological systems. Studying carbon-bearing fluids from hydrothermal systems is of specific importance to understanding (bio-)geochemical processes within these systems. With recent detection of methane in the martian atmosphere [4-7] and the possibility of its hydrothermal origin [8, 9], understanding the formation mechanisms of methane may provide constraints on the history of the martian aqueous environments and climate.

Isotope biogeochemical assessment of natural biodegradation processes in open cast pit mining landscapes

NASA Astrophysics Data System (ADS)

Jeschke, Christina; Knöller, Kay; Koschorreck, Matthias; Ussath, Maria; Hoth, Nils

2014-05-01

In Germany, a major share of the energy production is based on the burning of lignite from open cast pit mines. The remediation and re-cultivation of the former mining areas in the Lusatian and Central German lignite mining district is an enormous technical and economical challenge. After mine closures, the surrounding landscapes are threatened by acid mine drainage (AMD), i.e. the acidification and mineralization of rising groundwater with metals and inorganic contaminants. The high content of sulfur (sulfuric acid, sulfate), nitrogen (ammonium) and iron compounds (iron-hydroxides) deteriorates the groundwater quality and decelerates sustainable development of tourism in (former) mining landscapes. Natural biodegradation or attenuation (NA) processes of inorganic contaminants are considered to be a technically low impact and an economically beneficial solution. The investigations of the stable isotope compositions of compounds involved in NA processes helps clarify the dynamics of natural degradation and provides specific informations on retention processes of sulfate and nitrogen-compounds in mine dump water, mine dump sediment, and residual pit lakes. In an active mine dump we investigated zones where the process of bacterial sulfate reduction, as one very important NA process, takes place and how NA can be enhanced by injecting reactive substrates. Stable isotopes signatures of sulfur and nitrogen components were examined and evaluated in concert with hydrogeochemical data. In addition, we delineated the sources of ammonium pollution in mine dump sediments and investigated nitrification by 15N-labeling techniques to calculate the limit of the conversion of harmful ammonium to nitrate in residual mining lakes. Ultimately, we provided an isotope biogeochemical assessment of natural attenuation of sulfate and ammonium at mine dump sites and mining lakes. Also, we estimated the risk potential for water in different compartments of the hydrological system. In laboratory experiments, we tested reactive materials that may speed up the process of bacterial sulfate reduction. In in-situ experiments, we quantified nitrification rates. Based on the results, we are able to suggest promising technical measures that enhance natural attenuation processes at mine dump site and in mining lakes. The natural water cycle in lignite mining landscapes is heavily impacted by human activities. Basically, nature is capable of cleaning itself to a certain extent after mining activities stopped. However, it is our responsibility to support biogeochemical processes to make them more efficient and more sustainable. Isotopic monitoring proved to be an excellent tool for assessing the relevance and performance of different re-cultivation measures for a positive long-term development of the water quality in large-scale aquatic systems affected by the impact of lignite mining.

The Biogeochemical Response to Inter-decadal Atmospheric Forcing Across Watershed Scales in Canada's Subarctic

NASA Astrophysics Data System (ADS)

Spence, C.

2016-12-01

Rapid landscape changes in the circumpolar north have been documented, including degradation of permafrost and alteration of vegetation communities. These are widely expected to have profound impacts on the freshwater fluxes of solutes, carbon and nitrogen across the Arctic domain. However, there have been few attempts to document trends across the diversity of landscapes in the circumpolar north, mostly due to a dearth of long term data. Some of the fastest rates of warming over the last thirty years have occurred in Canada's Northwest Territories, so this region should already exhibit changes in aquatic chemistry. Observations of chemical loads in streams draining the ice-poor discontinuous permafrost subarctic Canadian Shield region were analyzed with the goal of determining how basins across scales have responded to changes in atmospheric forcing. Smaller streams, with much closer linkages to terrestrial processes, experienced a synchrony among hydrological and biogeochemical processes that enhanced chemical flux above that in their larger counterparts. This demonstrates that there are differences in resiliency and resistance across scales to climate change. These results highlight the importance of biogeochemical process understanding to properly explain and predict how chemical loading scales from headwaters to river mouths. This is important information if society is to properly adapt policies for effluent discharge, nearshore marine management, among others.

Long-term impact of hydrological regime on structure and functions of microbial communities in riverine wetland sediments.

PubMed

Foulquier, Arnaud; Volat, Bernadette; Neyra, Marc; Bornette, Gudrun; Montuelle, Bernard

2013-08-01

In a context of global change, alterations in the water cycle may impact the structure and function of terrestrial and aquatic ecosystems. Wetlands are particularly at risk because hydrological regime has a major influence on microbially mediated biogeochemical processes in sediments. While the influence of water availability on wetland biogeochemical processes has been comprehensively studied, the influence of hydrological regime on microbial community structure has been overlooked. We tested for the effect of hydrological regime on the structure and functions of microbial communities by comparing sediments collected at multiple sites in the Ain département (Eastern France). Each site consisted of two plots, one permanently and one seasonally inundated. At the time of sampling, all plots were continuously inundated for more than 6 months but still harboured distinct bacterial communities. This change in community structure was not associated with marked modifications in the rates of microbial activities involved in the C and N cycles. These results suggest that the observed structural change could be related to bacterial taxa responding to the environmental variations associated with different hydrological regimes, but not strongly associated with the biogeochemical processes monitored here. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Impacts of mesoscale eddies on biogeochemical cycles in the South China Sea

NASA Astrophysics Data System (ADS)

Xiu, P.; Chai, F.; Guo, M.

2016-02-01

Biogeochemical cycles associated with mesoscale eddies in the South China Sea (SCS) are investigated by using satellite surface chlorophyll concentration, altimeter data, satellite sea surface temperature, and a coupled physical-biogeochemical Pacific Ocean model (ROMS-CoSiNE) simulation for the period from 1991 to 2007. Considering the annual mean, composite analysis reveals that cyclonic eddies are associated with higher concentrations of nutrients, phytoplankton and zooplankton while the anticyclonic eddies are with lower concentrations compared with surrounding waters, which is generally controlled by the eddy pumping mechanism. Dipole structures of vertical fluxes with net upward motion in cyclonic eddies and net downward motion in anticyclonic eddies are also revealed. During the lifetime of an eddy, the evolutions of physical, biological, and chemical structures are not linearly coupled at the eddy core where plankton grow and composition of the community depend not only on the physical and chemical processes but also on the adjustments by the predator-prey relationship. Considering the seasonal variability, we find eddy pumping mechanisms are generally dominant in winter and eddy advection effects are dominant in summer. Over the space, variability of chlorophyll to the west of Luzon Strait and off northwest of Luzon Island are mainly controlled by eddy pumping mechanism. In regions off the Vietnam coast, chlorophyll distributions are generally associated with horizontal eddy advection. This research highlights different mesoscale mechanisms affecting biological structures that can potentially disturb ocean biogeochemical cycling processes in the South China Sea.

Biogeochemical Modeling of Ureolytically-Driven Calcium Carbonate Precipitation for Contaminant Immobilization

NASA Astrophysics Data System (ADS)

Smith, R. W.; Fujita, Y.; Taylor, J. L.

2008-12-01

Radionuclide and metal contaminants such as strontium-90 are present beneath U.S. Department of Energy (DOE) lands in both the groundwater (e.g., 100-N area at Hanford, WA) and vadose zone (e.g., Idaho Nuclear Technology and Engineering Center at the Idaho National Laboratory [INL]). Manipulation of in situ biogeochemical conditions to induce immobilization of these contaminants is a promising remediation approach that could yield significant risk and cost benefits to DOE. However, the effective design and interpretation of such field remediation activities requires the availability of numerical tools to model the biogeochemical processes underlying the remediation strategy. We are evaluating the use of microbial urea hydrolysis coupled to calcite precipitation as a means for the cost effective in situ stabilization of trace inorganic contaminants in groundwater and vadose zone systems. The approach relies upon the activity of indigenous ureolytic bacteria to hydrolyze introduced urea and causing an increase in pH and alkalinity, thereby accelerating calcium carbonate precipitation. The precipitation reaction results in the co- precipitation of trace metals and is sustained by the release of cations (both calcium and trace metals) from the aquifer matrix via exchange reactions involving the ammonium ions produced by urea hydrolysis. We have developed and parameterized a mixed kinetic-equilibrium reaction model using the Geochemist's Workbench computer code. Simulation results based on laboratory- and field-scale studies demonstrate the importance of transient events in systems with geochemical fluxes as well as of the coupling of biogeochemical processes.

Transitions in Arctic ecosystems: Ecological implications of a changing hydrological regime

NASA Astrophysics Data System (ADS)

Wrona, Frederick J.; Johansson, Margareta; Culp, Joseph M.; Jenkins, Alan; Mârd, Johanna; Myers-Smith, Isla H.; Prowse, Terry D.; Vincent, Warwick F.; Wookey, Philip A.

2016-03-01

Numerous international scientific assessments and related articles have, during the last decade, described the observed and potential impacts of climate change as well as other related environmental stressors on Arctic ecosystems. There is increasing recognition that observed and projected changes in freshwater sources, fluxes, and storage will have profound implications for the physical, biogeochemical, biological, and ecological processes and properties of Arctic terrestrial and freshwater ecosystems. However, a significant level of uncertainty remains in relation to forecasting the impacts of an intensified hydrological regime and related cryospheric change on ecosystem structure and function. As the terrestrial and freshwater ecology component of the Arctic Freshwater Synthesis, we review these uncertainties and recommend enhanced coordinated circumpolar research and monitoring efforts to improve quantification and prediction of how an altered hydrological regime influences local, regional, and circumpolar-level responses in terrestrial and freshwater systems. Specifically, we evaluate (i) changes in ecosystem productivity; (ii) alterations in ecosystem-level biogeochemical cycling and chemical transport; (iii) altered landscapes, successional trajectories, and creation of new habitats; (iv) altered seasonality and phenological mismatches; and (v) gains or losses of species and associated trophic interactions. We emphasize the need for developing a process-based understanding of interecosystem interactions, along with improved predictive models. We recommend enhanced use of the catchment scale as an integrated unit of study, thereby more explicitly considering the physical, chemical, and ecological processes and fluxes across a full freshwater continuum in a geographic region and spatial range of hydroecological units (e.g., stream-pond-lake-river-near shore marine environments).

Improving Coastal Ocean Color Validation Capabilities through Application of Inherent Optical Properties (IOPs)

NASA Technical Reports Server (NTRS)

Mannino, Antonio

2008-01-01

Understanding how the different components of seawater alter the path of incident sunlight through scattering and absorption is essential to using remotely sensed ocean color observations effectively. This is particularly apropos in coastal waters where the different optically significant components (phytoplankton, detrital material, inorganic minerals, etc.) vary widely in concentration, often independently from one another. Inherent Optical Properties (IOPs) form the link between these biogeochemical constituents and the Apparent Optical Properties (AOPs). understanding this interrelationship is at the heart of successfully carrying out inversions of satellite-measured radiance to biogeochemical properties. While sufficient covariation of seawater constituents in case I waters typically allows empirical algorithms connecting AOPs and biogeochemical parameters to behave well, these empirical algorithms normally do not hold for case I1 regimes (Carder et al. 2003). Validation in the context of ocean color remote sensing refers to in-situ measurements used to verify or characterize algorithm products or any assumption used as input to an algorithm. In this project, validation capabilities are considered those measurement capabilities, techniques, methods, models, etc. that allow effective validation. Enhancing current validation capabilities by incorporating state-of-the-art IOP measurements and optical models is the purpose of this work. Involved in this pursuit is improving core IOP measurement capabilities (spectral, angular, spatio-temporal resolutions), improving our understanding of the behavior of analytical AOP-IOP approximations in complex coastal waters, and improving the spatial and temporal resolution of biogeochemical data for validation by applying biogeochemical-IOP inversion models so that these parameters can be computed from real-time IOP sensors with high sampling rates. Research cruises supported by this project provides for collection and processing of seawater samples for biogeochemical (pigments, DOC and POC) and optical (CDOM and POM absorption coefficients) analyses to enhance our understanding of the linkages between in-water optical measurements (IOPs and AOPs) and biogeochemical constituents and to provide a more comprehensive suite of validation products.

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

PubMed

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

2017-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Using continuous underway isotope measurements to map water residence time in hydrodynamically complex tidal environments

USGS Publications Warehouse

Downing, Bryan D.; Bergamaschi, Brian; Kendall, Carol; Kraus, Tamara; Dennis, Kate J.; Carter, Jeffery A.; von Dessonneck, Travis

2016-01-01

Stable isotopes present in water (δ2H, δ18O) have been used extensively to evaluate hydrological processes on the basis of parameters such as evaporation, precipitation, mixing, and residence time. In estuarine aquatic habitats, residence time (τ) is a major driver of biogeochemical processes, affecting trophic subsidies and conditions in fish-spawning habitats. But τ is highly variable in estuaries, owing to constant changes in river inflows, tides, wind, and water height, all of which combine to affect τ in unpredictable ways. It recently became feasible to measure δ2H and δ18O continuously, at a high sampling frequency (1 Hz), using diffusion sample introduction into a cavity ring-down spectrometer. To better understand the relationship of τ to biogeochemical processes in a dynamic estuarine system, we continuously measured δ2H and δ18O, nitrate and water quality parameters, on board a small, high-speed boat (5 to >10 m s–1) fitted with a hull-mounted underwater intake. We then calculated τ as is classically done using the isotopic signals of evaporation. The result was high-resolution (∼10 m) maps of residence time, nitrate, and other parameters that showed strong spatial gradients corresponding to geomorphic attributes of the different channels in the area. The mean measured value of τ was 30.5 d, with a range of 0–50 d. We used the measured spatial gradients in both τ and nitrate to calculate whole-ecosystem uptake rates, and the values ranged from 0.006 to 0.039 d–1. The capability to measure residence time over single tidal cycles in estuaries will be useful for evaluating and further understanding drivers of phytoplankton abundance, resolving differences attributable to mixing and water sources, explicitly calculating biogeochemical rates, and exploring the complex linkages among time-dependent biogeochemical processes in hydrodynamically complex environments such as estuaries.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2011-03-01

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

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

PubMed

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

2013-10-01

With a pace of about twice the observed rate of global warming, the temperature on the Qinghai-Tibetan Plateau (Earth's 'third pole') has increased by 0.2 °C per decade over the past 50 years, which results in significant permafrost thawing and glacier retreat. Our review suggested that warming enhanced net primary production and soil respiration, decreased methane (CH(4)) emissions from wetlands and increased CH(4) consumption of meadows, but might increase CH(4) emissions from lakes. Warming-induced permafrost thawing and glaciers melting would also result in substantial emission of old carbon dioxide (CO(2)) and CH(4). Nitrous oxide (N(2)O) emission was not stimulated by warming itself, but might be slightly enhanced by wetting. However, there are many uncertainties in such biogeochemical cycles under climate change. Human activities (e.g. grazing, land cover changes) further modified the biogeochemical cycles and amplified such uncertainties on the plateau. If the projected warming and wetting continues, the future biogeochemical cycles will be more complicated. So facing research in this field is an ongoing challenge of integrating field observations with process-based ecosystem models to predict the impacts of future climate change and human activities at various temporal and spatial scales. To reduce the uncertainties and to improve the precision of the predictions of the impacts of climate change and human activities on biogeochemical cycles, efforts should focus on conducting more field observation studies, integrating data within improved models, and developing new knowledge about coupling among carbon, nitrogen, and phosphorus biogeochemical cycles as well as about the role of microbes in these cycles. © 2013 John Wiley & Sons Ltd.

Contribution of natural terrestrial sources to the atmospheric chloroform budget

NASA Astrophysics Data System (ADS)

Rhew, R. C.; Abel, T.; Pan, D.; Whelan, M.

2008-12-01

Chloroform (trichloromethane, CHCl3) is the second largest carrier of natural chlorine in the troposphere after methyl chloride, contributing to the reactive chlorine burden in the troposphere and to ozone destruction in the stratosphere. Our understanding of the biogeochemical cycling of atmospheric CHCl3 has undergone major adjustments recently, including the quantification of the total atmospheric burden of this compound, the estimated global source and sink strengths, and the relative contributions of anthropogenic versus natural contributions. Numerous natural terrestrial sources have been identified, including temperate peatlands, Arctic tundra, termite mounds, salt marshes, grasslands, forests and woodlands. However, the wide variability of fluxes within each ecosystem has complicated efforts to quantify the overall terrestrial source. In addition, the environmental and biogeochemical controls remain largely unknown. We shall present a comparison of recent CHCl3 flux measurements that cover a range of biome types and climatic conditions. To address within-biome variability, flux measurements from the Arctic tundra and temperate grasslands will be compared to common environmental parameters (e.g., temperature, soil moisture, solar insolation) and other trace gas fluxes (CH3Cl, CH4, CCl4). The generally poor correlations demonstrate that the variability of CHCl3 emissions may be affected by site-specific parameters that are not currently measured or by drastic changes in hydrologic conditions. Similar patterns are observed in laboratory incubations of tundra peat and grassland soils. We explore the possibility that the humification of plant material, which has been shown to produce organochlorine compounds through the chlorination of organic matter, may contribute to CHCl3 emissions. If this link exists, then CHCl3 production could potentially act as a proxy for organic matter degradation and carbon sequestration, essential biogeochemical and ecosystem processes.

Ocean Carbon Flux, Transport, and Burial Within the Western and Eastern US Coastal Zones

NASA Technical Reports Server (NTRS)

McWilliams, James C.; Moisan, John R.; Haidvogel, Dale B.; Miller, Arthur J.; Cornuelle, Bruce; Stolzenbach, Keith D.

2004-01-01

This project has been to develop and apply a regional. eddy-resolving circulation and biogeochemistry model of both the western and eastern U.S. coastal regions, capable of simulating the processes that control the carbon cycle. Validation has been by statistical comparison with analyses from various satellite measurements, including those from EOS sensors, as well as from in situ measurements. Sensitivity studies were carried out to investigate how the coastal ecosystem and biogeochemical cycles respond to changes in climate, large-scale eutrophication from indus- trial pollution, and other anthropogenic induced changes. The research has been conducted in collaboration with research groups at UCLA. NASA/GSFC (Wallops), Rutgers, and SIO. Overall. the project was focused on several key modeling issues, each of which tie back into completing the primary task of developing a coastal carbon model for both the eastern and western US. coasts. Individual groups within the entire program are still collaborating to address these specific tasks. These include: implementation of the coupled circulation/biogeochemical model within the U.S. West Coast. including high-resolution, embedded subdomains for the Southern California Bight and Monterey Bay region; development of a biogeochemical model with resolved carbon, nitrogen and oxygen cycles; development of data assimilation techniques for use of satellite data sets; reconfiguration of the model domain to U.S. East Coast; development of coastal forcing fields: development of methods to compare the model against remotely sensed data; and, the test of model sensitivity to environmental conditions. Below, we present a summary of the progress made toward achieving these soak. Because this has been a multi-institutional, collaborative effort, we note the groups involved with particular activities.

Aerosols in atmospheric chemistry and biogeochemical cycles of nutrients

NASA Astrophysics Data System (ADS)

Kanakidou, Maria; Myriokefalitakis, Stelios; Tsigaridis, Kostas

2018-06-01

Atmospheric aerosols have complex and variable compositions and properties. While scientific interest is centered on the health and climatic effects of atmospheric aerosols, insufficient attention is given to their involvement in multiphase chemistry that alters their contribution as carriers of nutrients in ecosystems. However, there is experimental proof that the nutrient equilibria of both land and marine ecosystems have been disturbed during the Anthropocene period. This review study first summarizes our current understanding of aerosol chemical processing in the atmosphere as relevant to biogeochemical cycles. Then it binds together results of recent modeling studies based on laboratory and field experiments, focusing on the organic and dust components of aerosols that account for multiphase chemistry, aerosol ageing in the atmosphere, nutrient (N, P, Fe) emissions, atmospheric transport, transformation and deposition. The human-driven contribution to atmospheric deposition of these nutrients, derived by global simulations using past and future anthropogenic emissions of pollutants, is put into perspective with regard to potential changes in nutrient limitations and biodiversity. Atmospheric deposition of nutrients has been suggested to result in human-induced ecosystem limitations with regard to specific nutrients. Such modifications favor the development of certain species against others and affect the overall functioning of ecosystems. Organic forms of nutrients are found to contribute to the atmospheric deposition of the nutrients N, P and Fe by 20%–40%, 35%–45% and 7%–18%, respectively. These have the potential to be key components of the biogeochemical cycles since there is initial proof of their bioavailability to ecosystems. Bioaerosols have been found to make a significant contribution to atmospheric sources of N and P, indicating potentially significant interactions between terrestrial and marine ecosystems. These results deserve further experimental and modeling studies to reduce uncertainties and understand the feedbacks induced by atmospheric deposition of nutrients to ecosystems.

Genome Informed Trait-Based Models

NASA Astrophysics Data System (ADS)

Karaoz, U.; Cheng, Y.; Bouskill, N.; Tang, J.; Beller, H. R.; Brodie, E.; Riley, W. J.

2013-12-01

Trait-based approaches are powerful tools for representing microbial communities across both spatial and temporal scales within ecosystem models. Trait-based models (TBMs) represent the diversity of microbial taxa as stochastic assemblages with a distribution of traits constrained by trade-offs between these traits. Such representation with its built-in stochasticity allows the elucidation of the interactions between the microbes and their environment by reducing the complexity of microbial community diversity into a limited number of functional ';guilds' and letting them emerge across spatio-temporal scales. From the biogeochemical/ecosystem modeling perspective, the emergent properties of the microbial community could be directly translated into predictions of biogeochemical reaction rates and microbial biomass. The accuracy of TBMs depends on the identification of key traits of the microbial community members and on the parameterization of these traits. Current approaches to inform TBM parameterization are empirical (i.e., based on literature surveys). Advances in omic technologies (such as genomics, metagenomics, metatranscriptomics, and metaproteomics) pave the way to better-initialize models that can be constrained in a generic or site-specific fashion. Here we describe the coupling of metagenomic data to the development of a TBM representing the dynamics of metabolic guilds from an organic carbon stimulated groundwater microbial community. Illumina paired-end metagenomic data were collected from the community as it transitioned successively through electron-accepting conditions (nitrate-, sulfate-, and Fe(III)-reducing), and used to inform estimates of growth rates and the distribution of metabolic pathways (i.e., aerobic and anaerobic oxidation, fermentation) across a spatially resolved TBM. We use this model to evaluate the emergence of different metabolisms and predict rates of biogeochemical processes over time. We compare our results to observational outputs.

Scaling Hydrologic Exchange Flows and Biogeochemical Reactions from Bedforms to Basins

NASA Astrophysics Data System (ADS)

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

2015-12-01

River water moves in and out of the main channel along pathways that are perpendicular to the channel's main axis that flow across or beneath the ground surface. These hydrologic exchange flows (HEFs) are difficult to measure, yet no less important than a river's downstream flow, or exchanges with the atmosphere and deeper groundwater (Harvey and Gooseff, 2015, WRR). There are very few comprehensive investigations of exchange fluxes to understand patterns with river size and relative importance of specific types of exchanges. We used the physically based model NEXSS to simulate multiple scales of hyporheic flow and their cumulative effects on solute reaction in large basins (on the order of Chesapeake Bay basin or larger). Our goal was to explain where and when particular types of hyporheic flow are important in enhancing key biogeochemical reactions, such as organic carbon respiration and denitrification. Results demonstrate that hyporheic flux (expressed per unit area of streambed) varies surprisingly little across the continuum of first-order streams to eighth-order rivers, and vertical exchange beneath small bedforms dominates in comparison with lateral flow beneath gravel bars and meanders. Also, the river's entire volume is exchanged many times with hyporheic flow within a basin, and the turnover length (after one entire river volume is exchanged) is strongly influenced by hydrogeomorphic differences between physiographic regions as well as by river size. The cumulative effects on biogeochemical reactions were assessed using a the reaction significance factor, RSF, which computes the cumulative potential for hyporheic reactions using a dimensionless index that balances reaction progress in a single hyporheic flow path against overall processing efficiency of river turnover through hyporheic flow paths of that type. Reaction significance appears to be strongly dominated by hydrologic factors rather than biogeochemical factors, and seems to be dominated by vertical exchange beneath small bedforms throughout river networks. Future implementations of NEXSS will expand the model to consider flow variation and to consider HEFs beyond hyporheic flow to include exchange with marginal surface waters such as riparian wetlands, floodplains, and ponded water.

Investigating the Role of Hydrologic Residence Time in Nitrogen Transformations at the Sediment-Water Interface using Controlled Variable Head Experiments

NASA Astrophysics Data System (ADS)

Hampton, T. B.; Zarnetske, J. P.; Briggs, M. A.; Singha, K.; Day-Lewis, F. D.

2017-12-01

Many important biogeochemical processes governing both carbon and nitrogen dynamics in streams take place at the sediment-water interface (SWI). This interface is highly variable in biogeochemical function, with stream stage often influencing the magnitude and direction of water and solute exchange through the SWI. It is well known that the SWI can be an important location for carbon and nitrogen transformations, including denitrification and greenhouse gas production. The degree of mixing of carbon and nitrate, along with oxygen from surface waters, is strongly influenced by hydrologic exchange at the SWI. We hypothesize that hydrologic residence time, which is also determined by the magnitude of exchange, is a key control on the fate of nitrate at the SWI and on the end products of denitrification. Previous studies in the headwaters of the Ipswich River in MA as part of the Lotic Intersite Nitrogen Experiments (LINX II) and other long-term monitoring suggest that the Ipswich River SWI represents an important source of nitrous oxide, a potent greenhouse gas. Using a novel constant-head infiltrometer ring embedded in the stream sediments, we created four unique controlled down-welling (i.e., recharge) conditions, and tested how varying this hydrologic flux and thus the residence time distribution influenced biogeochemical function of the Ipswich River SWI. Specifically, we added isotopically-labelled 15N-nitrate to stream water during each controlled hydrologic flux experiment to quantify nitrate transformation rates, including denitrification end products, under the different hydrologic conditions. We also measured a suite of carbon and nitrogen solutes, along with dissolved oxygen conditions throughout each experiment to characterize the broader residence timescale and biogeochemical responses to the hydrologic manipulations. Initial results show that the oxic conditions of the SWI were strongly responsive to changes in hydrologic flux rates, thereby changing the redox conditions and likely the fate of the nitrate through the infiltrometer. The forthcoming 15N data will quantify the nitrate response. Overall, this study will help demonstrate how the SWI of this historically important research river transforms nitrate under variable hydrologic conditions.

Development of a multi-data assimilation scheme to integrate Bio-Argo floats data with ocean colour satellite data into the CMEMS MFC-Biogeochemistry

NASA Astrophysics Data System (ADS)

Cossarini, Gianpiero; D'Ortenzio, Fabrizio; Mariotti, Laura; Mignot, Alexandre; Salon, Stefano

2017-04-01

The Mediterranean Sea is a very promising site to develop and test the assimilation of Bio-Argo data since 1) the Bio-Argo network is one of the densest of the global ocean, and 2) a consolidate data assimilation framework of biogeochemical variables (3DVAR-BIO, presently based on assimilation of satellite-estimated surface chlorophyll data) already exists within the CMEMS biogeochemical model system for Mediterranean Sea. The MASSIMILI project, granted by the CMEMS Service Evolution initiative, is aimed to develop the assimilation of Bio-Argo Floats data into the CMEMS biogeochemical model system of the Mediterranean Sea, by means of an upgrade of the 3DVAR-BIO scheme. Specific developments of the 3DVAR-BIO scheme focus on the estimate of new operators of the variational decomposition of the background error covariance matrix and on the implementation of the new observation operator specifically for the Bio-Argo float vertical profile data. In particular, a new horizontal covariance operator for chlorophyll, nitrate and oxygen is based on 3D fields of horizontal correlation radius calculated from a long-term reanalysis simulation. A new vertical covariance operator is built on monthly and spatial varying EOF decomposition to account for the spatiotemporal variability of vertical structure of the three variables error covariance. Further, the observation error covariance is a key factor for an effective assimilation of the Bio-Argo data into the model dynamics. The sensitivities of assimilation to the different factors are estimated. First results of the implementation of the new 3DVAR-BIO scheme show the impact of Bio-Argo data on the 3D fields of chlorophyll, nitrate and oxygen. Tuning the length scale factors of horizontal covariance, analysing the sensitivity of the observation error covariance, introducing non-diagonal biogeochemical covariance operator and non-diagonal multi-platform operator (i.e. Bio-Argo and satellite) are crucial future steps for the success of the MASSIMILI project. In our contribute, we will discuss the recent and promising advancements this strategic project has been having in the past year and its potential for the whole operational biogeochemical modelling community.

The roles of resuspension, diffusion and biogeochemical processes on oxygen dynamics offshore of the Rhône River, France: a numerical modeling study

NASA Astrophysics Data System (ADS)

Moriarty, Julia M.; Harris, Courtney K.; Fennel, Katja; Friedrichs, Marjorie A. M.; Xu, Kehui; Rabouille, Christophe

2017-04-01

Observations indicate that resuspension and associated fluxes of organic material and porewater between the seabed and overlying water can alter biogeochemical dynamics in some environments, but measuring the role of sediment processes on oxygen and nutrient dynamics is challenging. A modeling approach offers a means of quantifying these fluxes for a range of conditions, but models have typically relied on simplifying assumptions regarding seabed-water-column interactions. Thus, to evaluate the role of resuspension on biogeochemical dynamics, we developed a coupled hydrodynamic, sediment transport, and biogeochemical model (HydroBioSed) within the Regional Ocean Modeling System (ROMS). This coupled model accounts for processes including the storage of particulate organic matter (POM) and dissolved nutrients within the seabed; fluxes of this material between the seabed and the water column via erosion, deposition, and diffusion at the sediment-water interface; and biogeochemical reactions within the seabed. A one-dimensional version of HydroBioSed was then implemented for the Rhône subaqueous delta in France. To isolate the role of resuspension on biogeochemical dynamics, this model implementation was run for a 2-month period that included three resuspension events; also, the supply of organic matter, oxygen, and nutrients to the model was held constant in time. Consistent with time series observations from the Rhône Delta, model results showed that erosion increased the diffusive flux of oxygen into the seabed by increasing the vertical gradient of oxygen at the seabed-water interface. This enhanced supply of oxygen to the seabed, as well as resuspension-induced increases in ammonium availability in surficial sediments, allowed seabed oxygen consumption to increase via nitrification. This increase in nitrification compensated for the decrease in seabed oxygen consumption due to aerobic remineralization that occurred as organic matter was entrained into the water column. Additionally, entrainment of POM into the water column during resuspension events, and the associated increase in remineralization there, also increased oxygen consumption in the region of the water column below the pycnocline. During these resuspension events, modeled rates of oxygen consumption increased by factors of up to ˜ 2 and ˜ 8 in the seabed and below the pycnocline, respectively. When averaged over 2 months, the intermittent cycles of erosion and deposition led to a ˜ 16 % increase of oxygen consumption in the seabed, as well as a larger increase of ˜ 140 % below the pycnocline. These results imply that observations collected during quiescent periods, and biogeochemical models that neglect resuspension or use typical parameterizations for resuspension, may underestimate net oxygen consumption at sites like the Rhône Delta. Local resuspension likely has the most pronounced effect on oxygen dynamics at study sites with a high oxygen concentration in bottom waters, only a thin seabed oxic layer, and abundant labile organic matter.

Chromium speciation, bioavailability, uptake, toxicity and detoxification in soil-plant system: A review.

PubMed

Shahid, Muhammad; Shamshad, Saliha; Rafiq, Marina; Khalid, Sana; Bibi, Irshad; Niazi, Nabeel Khan; Dumat, Camille; Rashid, Muhammad Imtiaz

2017-07-01

Chromium (Cr) is a potentially toxic heavy metal which does not have any essential metabolic function in plants. Various past and recent studies highlight the biogeochemistry of Cr in the soil-plant system. This review traces a plausible link among Cr speciation, bioavailability, phytouptake, phytotoxicity and detoxification based on available data, especially published from 2010 to 2016. Chromium occurs in different chemical forms (primarily as chromite (Cr(III)) and chromate (Cr(VI)) in soil which vary markedly in term of their biogeochemical behavior. Chromium behavior in soil, its soil-plant transfer and accumulation in different plant parts vary with its chemical form, plant type and soil physico-chemical properties. Soil microbial community plays a key role in governing Cr speciation and behavior in soil. Chromium does not have any specific transporter for its uptake by plants and it primarily enters the plants through specific and non-specific channels of essential ions. Chromium accumulates predominantly in plant root tissues with very limited translocation to shoots. Inside plants, Cr provokes numerous deleterious effects to several physiological, morphological, and biochemical processes. Chromium induces phytotoxicity by interfering plant growth, nutrient uptake and photosynthesis, inducing enhanced generation of reactive oxygen species, causing lipid peroxidation and altering the antioxidant activities. Plants tolerate Cr toxicity via various defense mechanisms such as complexation by organic ligands, compartmentation into the vacuole, and scavenging ROS via antioxidative enzymes. Consumption of Cr-contaminated-food can cause human health risks by inducing severe clinical conditions. Therefore, there is a dire need to monitor biogeochemical behavior of Cr in soil-plant system. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

NASA Technical Reports Server (NTRS)

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

1985-01-01

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

Effects of stratospheric ozone depletion, solar UV radiation, and climate change on biogeochemical cycling: interactions and feedbacks

DOE PAGES

Erickson III, David J.; Sulzberger, Barbara; Zepp, Richard G.; ...

2014-11-07

Climate change modulates the effects of solar UV radiation on biogeochemical cycles in terrestrial and aquatic ecosystems, particularly for carbon cycling, resulting in UV-mediated positive or negative feedbacks on climate. Possible positive feedbacks discussed in this assessment include: (i) enhanced UV-induced mineralisation of above ground litter due to aridification; (ii) enhanced UV-induced mineralisation of photoreactive dissolved organic matter (DOM) in aquatic ecosystems due to changes in continental runoff and ice melting; (iii) reduced efficiency of the biological pump due to UV-induced bleaching of coloured dissolved organic matter (CDOM) in stratified aquatic ecosystems, where CDOM protects phytoplankton from the damaging solarmore » UV-B radiation. Mineralisation of organic matter results in the production and release of CO 2, whereas the biological pump is the main biological process for CO 2 removal by aquatic ecosystems. This research also assesses the interactive effects of solar UV radiation and climate change on the biogeochemical cycling of aerosols and trace gases other than CO 2, as well as of chemical and biological contaminants. Lastly,, interacting effects of solar UV radiation and climate change on biogeochemical cycles are particularly pronounced at terrestrial-aquatic interfaces.« less

Biogeochemical carbon coupling influences global precipitation in geoengineering experiments

NASA Astrophysics Data System (ADS)

Fyfe, J. C.; Cole, J. N. S.; Arora, V. K.; Scinocca, J. F.

2013-02-01