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William J Riley - One of the best experts on this subject based on the ideXlab platform.
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a theory of effective microbial substrate affinity parameters in variably saturated soils and an Example Application to aerobic soil heterotrophic respiration
Journal of Geophysical Research, 2019Co-Authors: Jinyun Tang, William J RileyAbstract:Author(s): Tang, J; Riley, WJ | Abstract: ©2019. The Authors. Affinity parameters are essential for substrate kinetics-based modeling of soil biogeochemistry. These parameters were originally defined for well-mixed aqueous solutions to represent enzyme substrate binding. For variably saturated soils, they are often calibrated and highly uncertain. Here we develop a predictive theory of effective substrate affinity parameters to account for other processes that affect microbial substrate acquisition, so that the substrate kinetics for well-mixed aqueous solutions can be similarly applied to variably saturated soils. The theory is based on an analytical approximation of how diffusive substrates are intercepted by soil microbial cells and integrates microbial characteristics, microsite structure, and soil physical properties. The predicted effective substrate affinity thus closely integrates the physical substrate limitation in soils with the intrinsic substrate affinity parameter. The theory predicts that, as moisture changes, the effective diffusive substrate delivery rates vary by orders of magnitude, resulting in highly variable effective affinity parameters for substrates like oxygen, methane, and nonvolatile solutes. As an Example, we apply the theory with three substrate kinetics to aerobic soil incubations. Our models accurately reproduced observations of 32 soil incubations in four soil classes, demonstrating that the soil moisture versus respiration relationship varies with maximum respiration rate, soil texture, soil carbon content, and microbial biomass. This Example suggests that the traditional use of a single static multiplicative function to parameterize how soil respiration depends on moisture is inappropriate. Because of its capability to integrate microbial traits and soil physical properties, our theory will help develop more robust soil biogeochemistry models.
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supeca kinetics for scaling redox reactions in networks of mixed substrates and consumers and an Example Application to aerobic soil respiration
Geoscientific Model Development, 2017Co-Authors: Jinyun Tang, William J RileyAbstract:Abstract. Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A + BE → products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistry problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with the equilibrium chemistry solution for some simple problems and found SUPECA outperformed SU kinetics. As an Example Application, we show that a steady-state SUPECA-based approach predicted an aerobic soil respiration moisture response function that agreed well with laboratory observations. We conclude that, as an extension to SU and ECA kinetics, SUPECA provides a robust mathematical representation of complex soil substrate–consumer interactions and can be applied to improve Earth system model (ESM) land models.
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a total quasi steady state formulation of substrate uptake kinetics in complex networks and an Example Application to microbial litter decomposition
Biogeosciences, 2013Co-Authors: Jinyun Tang, William J RileyAbstract:We demonstrate that substrate uptake kinetics in any consumer–substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis–Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple substrates. We then applied the EC and ECA kinetics to a guild based C-only microbial litter decomposition model and found that both approaches successfully simulated the commonly observed (i) two-phase temporal evolution of the decomposition dynamics; (ii) final asymptotic convergence of the lignocellulose index to a constant that depends on initial litter chemistry and microbial community structure; and (iii) microbial biomass proportion of total organic biomass (litter plus microbes). In contrast, the MM kinetics failed to realistically predict these metrics. We therefore conclude that the ECA kinetics are more robust than the MM kinetics in representing complex microbial, C substrate, and mineral surface interactions. Finally, we discuss how these concepts can be applied to other consumer–substrate networks.
Jinyun Tang - One of the best experts on this subject based on the ideXlab platform.
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a theory of effective microbial substrate affinity parameters in variably saturated soils and an Example Application to aerobic soil heterotrophic respiration
Journal of Geophysical Research, 2019Co-Authors: Jinyun Tang, William J RileyAbstract:Author(s): Tang, J; Riley, WJ | Abstract: ©2019. The Authors. Affinity parameters are essential for substrate kinetics-based modeling of soil biogeochemistry. These parameters were originally defined for well-mixed aqueous solutions to represent enzyme substrate binding. For variably saturated soils, they are often calibrated and highly uncertain. Here we develop a predictive theory of effective substrate affinity parameters to account for other processes that affect microbial substrate acquisition, so that the substrate kinetics for well-mixed aqueous solutions can be similarly applied to variably saturated soils. The theory is based on an analytical approximation of how diffusive substrates are intercepted by soil microbial cells and integrates microbial characteristics, microsite structure, and soil physical properties. The predicted effective substrate affinity thus closely integrates the physical substrate limitation in soils with the intrinsic substrate affinity parameter. The theory predicts that, as moisture changes, the effective diffusive substrate delivery rates vary by orders of magnitude, resulting in highly variable effective affinity parameters for substrates like oxygen, methane, and nonvolatile solutes. As an Example, we apply the theory with three substrate kinetics to aerobic soil incubations. Our models accurately reproduced observations of 32 soil incubations in four soil classes, demonstrating that the soil moisture versus respiration relationship varies with maximum respiration rate, soil texture, soil carbon content, and microbial biomass. This Example suggests that the traditional use of a single static multiplicative function to parameterize how soil respiration depends on moisture is inappropriate. Because of its capability to integrate microbial traits and soil physical properties, our theory will help develop more robust soil biogeochemistry models.
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supeca kinetics for scaling redox reactions in networks of mixed substrates and consumers and an Example Application to aerobic soil respiration
Geoscientific Model Development, 2017Co-Authors: Jinyun Tang, William J RileyAbstract:Abstract. Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A + BE → products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistry problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with the equilibrium chemistry solution for some simple problems and found SUPECA outperformed SU kinetics. As an Example Application, we show that a steady-state SUPECA-based approach predicted an aerobic soil respiration moisture response function that agreed well with laboratory observations. We conclude that, as an extension to SU and ECA kinetics, SUPECA provides a robust mathematical representation of complex soil substrate–consumer interactions and can be applied to improve Earth system model (ESM) land models.
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a total quasi steady state formulation of substrate uptake kinetics in complex networks and an Example Application to microbial litter decomposition
Biogeosciences, 2013Co-Authors: Jinyun Tang, William J RileyAbstract:We demonstrate that substrate uptake kinetics in any consumer–substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis–Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple substrates. We then applied the EC and ECA kinetics to a guild based C-only microbial litter decomposition model and found that both approaches successfully simulated the commonly observed (i) two-phase temporal evolution of the decomposition dynamics; (ii) final asymptotic convergence of the lignocellulose index to a constant that depends on initial litter chemistry and microbial community structure; and (iii) microbial biomass proportion of total organic biomass (litter plus microbes). In contrast, the MM kinetics failed to realistically predict these metrics. We therefore conclude that the ECA kinetics are more robust than the MM kinetics in representing complex microbial, C substrate, and mineral surface interactions. Finally, we discuss how these concepts can be applied to other consumer–substrate networks.
Diego Melgar - One of the best experts on this subject based on the ideXlab platform.
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a global database of strong motion displacement gnss recordings and an Example Application to pgd scaling
Seismological Research Letters, 2019Co-Authors: C J Ruhl, Diego Melgar, Jianghui Geng, Dara E Goldberg, Brendan W Crowell, Richard M Allen, Yehuda Bock, Sergio Barrientos, Sebastian RiquelmeAbstract:Displacement waveforms derived from Global Navigation Satellite System (GNSS) data have become more commonly used by seismologists in the past 15 yrs. Unlike strong‐motion accelerometer recordings that are affected by baseline offsets during very strong shaking, GNSS data record displacement with fidelity down to 0 Hz. Unfortunately, fully processed GNSS waveform data are still scarce because of limited public availability and the highly technical nature of GNSS processing. In an effort to further the use and adoption of high‐rate (HR) GNSS for earthquake seismology, ground‐motion studies, and structural monitoring Applications, we describe and make available a database of fully curated HR‐GNSS displacement waveforms for significant earthquakes. We include data from HR‐GNSS networks at near‐source to regional distances (1–1000 km) for 29 earthquakes between M_w 6.0 and 9.0 worldwide. As a demonstration of the utility of this dataset, we model the magnitude scaling properties of peak ground displacements (PGDs) for these events. In addition to tripling the number of earthquakes used in previous PGD scaling studies, the number of data points over a range of distances and magnitudes is dramatically increased. The data are made available as a compressed archive with the article.
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kinematic rupture scenarios and synthetic displacement data an Example Application to the cascadia subduction zone
Journal of Geophysical Research, 2016Co-Authors: Diego Melgar, Randall J Leveque, Douglas S Dreger, Richard M AllenAbstract:Scenario ruptures and ground motion simulation are important tools for studies of expected earthquake and tsunami hazards during future events. This is particularly important for large (Mw8+) and very large (Mw8.5+) events for which observations are still limited. In particular, synthetic waveforms are important to test the response of earthquake and tsunami warning systems to large events. These systems are not often exercised in this manner. We will show an Application of the Karhunen-Loeve (KL) expansion to generate stochastic slip distributions of large events with an Example Application to the Cascadia subduction zone. We will discuss how to extend the static slip distributions obtained from the K-L expansion to produce kinematic rupture models and generate synthetic long-period displacement data at the sampling rates of traditional GNSS stations. We will validate the waveforms produced by this method by comparison to a displacement based ground motion prediction equation (GMPE) obtained from GNSS measurements of large earthquakes worldwide.
Richard M Allen - One of the best experts on this subject based on the ideXlab platform.
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a global database of strong motion displacement gnss recordings and an Example Application to pgd scaling
Seismological Research Letters, 2019Co-Authors: C J Ruhl, Diego Melgar, Jianghui Geng, Dara E Goldberg, Brendan W Crowell, Richard M Allen, Yehuda Bock, Sergio Barrientos, Sebastian RiquelmeAbstract:Displacement waveforms derived from Global Navigation Satellite System (GNSS) data have become more commonly used by seismologists in the past 15 yrs. Unlike strong‐motion accelerometer recordings that are affected by baseline offsets during very strong shaking, GNSS data record displacement with fidelity down to 0 Hz. Unfortunately, fully processed GNSS waveform data are still scarce because of limited public availability and the highly technical nature of GNSS processing. In an effort to further the use and adoption of high‐rate (HR) GNSS for earthquake seismology, ground‐motion studies, and structural monitoring Applications, we describe and make available a database of fully curated HR‐GNSS displacement waveforms for significant earthquakes. We include data from HR‐GNSS networks at near‐source to regional distances (1–1000 km) for 29 earthquakes between M_w 6.0 and 9.0 worldwide. As a demonstration of the utility of this dataset, we model the magnitude scaling properties of peak ground displacements (PGDs) for these events. In addition to tripling the number of earthquakes used in previous PGD scaling studies, the number of data points over a range of distances and magnitudes is dramatically increased. The data are made available as a compressed archive with the article.
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kinematic rupture scenarios and synthetic displacement data an Example Application to the cascadia subduction zone
Journal of Geophysical Research, 2016Co-Authors: Diego Melgar, Randall J Leveque, Douglas S Dreger, Richard M AllenAbstract:Scenario ruptures and ground motion simulation are important tools for studies of expected earthquake and tsunami hazards during future events. This is particularly important for large (Mw8+) and very large (Mw8.5+) events for which observations are still limited. In particular, synthetic waveforms are important to test the response of earthquake and tsunami warning systems to large events. These systems are not often exercised in this manner. We will show an Application of the Karhunen-Loeve (KL) expansion to generate stochastic slip distributions of large events with an Example Application to the Cascadia subduction zone. We will discuss how to extend the static slip distributions obtained from the K-L expansion to produce kinematic rupture models and generate synthetic long-period displacement data at the sampling rates of traditional GNSS stations. We will validate the waveforms produced by this method by comparison to a displacement based ground motion prediction equation (GMPE) obtained from GNSS measurements of large earthquakes worldwide.
Paul L G Vlek - One of the best experts on this subject based on the ideXlab platform.
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a landscape planning and management tool for land and water resources management an Example Application in northern ethiopia
Water Resources Management, 2014Co-Authors: Lulseged Tamene, Paul L G VlekAbstract:Land and water degradation due to on-site soil/nutrient loss and off-site pollution/sedimentation are serious environmental problems. Landscape planning and management tools are essential to implement best management practices targeted at locations where they are needed most. Although many soil/water-landscape studies have been published in the last 2 decades, progress in developing operational tools for supporting landscape planning to minimize land and water degradation in developing regions is still modest. Some of the existing tools are data demanding and/or complicated to be useful to data scarce regions. Some require detailed understanding of the hydrological and modelling processes and thus less applicable to local stakeholders involved in land use planning and management. A user-friendly LAndscape Planning and MAnagement Tool (LAPMAT) developed to facilitate land management decision-making. LAPMAT is a menu-oriented interactive graphical user interface that can aid decision makers identify hotspot areas of soil erosion and evaluate the effects of alternative land use management practices at a catchment scale. The modelling framework and its interfaces are designed to guide the user through a series of menus that: 1) allow input model parameters, adjusting coefficients, visualizing input parameters and executing the model; 2) enable changing land use and management practices and re-evaluating potential consequences; 3) allow viewing results in tabular, graphical or map form side-by-side; and 4) (re)-evaluating the respective impacts of management/conservation options. The framework has been applied to assess the severity of soil erosion and simulate the impact of different land management practices using the Revised Universal Soil Loss Equation (RUSLE) adjusted for sediment delivery ratio in an Example catchment of northern Ethiopia. The results showed average sediment yield rate of 55 t ha −1 y −1 . Conservation measures targeted at high soil loss areas and gullies gave the maximum reduction in sediment yield by about 80 %. Since LAPMAT allows users handle the selection of management/planning options and provide fast and responsive outputs, it can assist in effective multi-stakeholder negotiations over land-use planning where the minimization of land/water degradation is the ultimate goal. Copyright Springer Science+Business Media Dordrecht 2014
