Articles | Volume 10, issue 12
https://doi.org/10.5194/bg-10-8329-2013
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-10-8329-2013
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition
J. Y. Tang
Earth Science Division, Lawrence Berkeley National Laboratory (LBL), Berkeley, CA, USA
W. J. Riley
Earth Science Division, Lawrence Berkeley National Laboratory (LBL), Berkeley, CA, USA
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Cited
72 citations as recorded by crossref.
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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 J. Tang & W. Riley 10.1029/2018JG004779
- Improved modelling of soil nitrogen losses Q. Zhu & W. Riley 10.1038/nclimate2696
- Temperature sensitivity of ecoenzyme kinetics driving litter decomposition: The effects of nitrogen enrichment, litter chemistry, and decomposer community X. Tan et al. 10.1016/j.soilbio.2020.107878
- Emergent properties of organic matter decomposition by soil enzymes B. Wang & S. Allison 10.1016/j.soilbio.2019.107522
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- Modeling coupled enzymatic and solute transport controls on decomposition in drying soils S. Manzoni et al. 10.1016/j.soilbio.2016.01.006
- Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model G. Marschmann et al. 10.1038/s41564-023-01582-w
- Microbial Controls on the Biogeochemical Dynamics in the Subsurface M. Thullner & P. Regnier 10.2138/rmg.2019.85.9
- Combination of energy limitation and sorption capacity explains 14C depth gradients B. Ahrens et al. 10.1016/j.soilbio.2020.107912
- Improved global-scale predictions of soil carbon stocks with Millennial Version 2 R. Abramoff et al. 10.1016/j.soilbio.2021.108466
- Developing systems theory in soil agroecology: incorporating heterogeneity and dynamic instability N. Medina & J. Vandermeer 10.3389/fenvs.2023.1171194
- Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests Q. Zhu et al. 10.5194/bg-13-341-2016
- A chemical kinetics theory for interpreting the non-monotonic temperature dependence of enzymatic reactions J. Tang & W. Riley 10.5194/bg-21-1061-2024
- Multiple models and experiments underscore large uncertainty in soil carbon dynamics B. Sulman et al. 10.1007/s10533-018-0509-z
- Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle T. Barnum et al. 10.1038/s41396-020-0599-1
- Expanding the role of reactive transport models in critical zone processes L. Li et al. 10.1016/j.earscirev.2016.09.001
- Observed variation in soil properties can drive large variation in modelled forest functioning and composition during tropical forest secondary succession D. Medvigy et al. 10.1111/nph.15848
- Chemodiversity controls microbial assimilation of soil organic carbon: A theoretical model J. Weverka et al. 10.1016/j.soilbio.2023.109161
- Global patterns and substrate‐based mechanisms of the terrestrial nitrogen cycle S. Niu et al. 10.1111/ele.12591
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- Competitor and substrate sizes and diffusion together define enzymatic depolymerization and microbial substrate uptake rates J. Tang & W. Riley 10.1016/j.soilbio.2019.107624
- ORCHIMIC (v1.0), a microbe-mediated model for soil organic matter decomposition Y. Huang et al. 10.5194/gmd-11-2111-2018
- Dynamic upscaling of decomposition kinetics for carbon cycling models A. Chakrawal et al. 10.5194/gmd-13-1399-2020
- A new theory of plant–microbe nutrient competition resolves inconsistencies between observations and model predictions Q. Zhu et al. 10.1002/eap.1490
- Root traits explain observed tundra vegetation nitrogen uptake patterns: Implications for trait‐based land models Q. Zhu et al. 10.1002/2016JG003554
- Comparison With Global Soil Radiocarbon Observations Indicates Needed Carbon Cycle Improvements in the E3SM Land Model J. Chen et al. 10.1029/2018JG004795
- Supporting hierarchical soil biogeochemical modeling: version 2 of the Biogeochemical Transport and Reaction model (BeTR-v2) J. Tang et al. 10.5194/gmd-15-1619-2022
- The effect of temperature on the rate, affinity, and 15N fractionation of NO3 − during biological denitrification in soils F. Maggi & W. Riley 10.1007/s10533-015-0095-2
- Representing leaf and root physiological traits in CLM improves global carbon and nitrogen cycling predictions B. Ghimire et al. 10.1002/2015MS000538
- SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration J. Tang & W. Riley 10.5194/gmd-10-3277-2017
- Abiotic and Biotic Controls on Soil Organo–Mineral Interactions: Developing Model Structures to Analyze Why Soil Organic Matter Persists D. Dwivedi et al. 10.2138/rmg.2019.85.11
- Merging a mechanistic enzymatic model of soil heterotrophic respiration into an ecosystem model in two AmeriFlux sites of northeastern USA D. Sihi et al. 10.1016/j.agrformet.2018.01.026
- Microbial community-level regulation explains soil carbon responses to long-term litter manipulations K. Georgiou et al. 10.1038/s41467-017-01116-z
- Revising the dynamic energy budget theory with a new reserve mobilization rule and three example applications to bacterial growth J. Tang & W. Riley 10.1016/j.soilbio.2023.108954
- Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process H. Song et al. 10.3389/fmicb.2017.01866
- Linear two-pool models are insufficient to infer soil organic matter decomposition temperature sensitivity from incubations J. Tang & W. Riley 10.1007/s10533-020-00678-3
- Relationship between enzyme concentration and Michaelis constant in enzyme assays K. Yun & T. Han 10.1016/j.biochi.2020.06.002
- Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency K. Cyle et al. 10.1128/AEM.01851-20
- Representing Nitrogen, Phosphorus, and Carbon Interactions in the E3SM Land Model: Development and Global Benchmarking Q. Zhu et al. 10.1029/2018MS001571
- Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems X. Xu et al. 10.5194/bg-13-3735-2016
- When and why microbial-explicit soil organic carbon models can be unstable E. Schwarz et al. 10.5194/bg-21-3441-2024
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- Redox and temperature-sensitive changes in microbial communities and soil chemistry dictate greenhouse gas loss from thawed permafrost J. Ernakovich et al. 10.1007/s10533-017-0354-5
- Equifinality, sloppiness, and emergent structures of mechanistic soil biogeochemical models G. Marschmann et al. 10.1016/j.envsoft.2019.104518
- On the role of soil water retention characteristic on aerobic microbial respiration T. Ghezzehei et al. 10.5194/bg-16-1187-2019
- Model exploration of interactions between algal functional diversity and productivity in chemostats to represent open ponds systems across climate gradients Y. Cheng et al. 10.1016/j.ecolmodel.2019.05.007
- Competitive effects in bacterial mRNA decay T. Etienne et al. 10.1016/j.jtbi.2020.110333
- Near Activation and Differential Activation in Enzymatic Reactions F. Maggi & W. Riley 10.1002/kin.21076
- Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient K. Cyle et al. 10.1111/jam.15652
- Jena Soil Model (JSM v1.0; revision 1934): a microbial soil organic carbon model integrated with nitrogen and phosphorus processes L. Yu et al. 10.5194/gmd-13-783-2020
- The Central Amazon Biomass Sink Under Current and Future Atmospheric CO2: Predictions From Big‐Leaf and Demographic Vegetation Models J. Holm et al. 10.1029/2019JG005500
- Decomposition rate as an emergent property of optimal microbial foraging S. Manzoni et al. 10.3389/fevo.2023.1094269
- On the modeling paradigm of plant root nutrient acquisition J. Tang & W. Riley 10.1007/s11104-020-04798-5
- Microbial Models for Simulating Soil Carbon Dynamics: A Review A. Chandel et al. 10.1029/2023JG007436
- Mathematical Reconstruction of Land Carbon Models From Their Numerical Output: Computing Soil Radiocarbon From C Dynamics H. Metzler et al. 10.1029/2019MS001776
- Weaker land–climate feedbacks from nutrient uptake during photosynthesis-inactive periods W. Riley et al. 10.1038/s41558-018-0325-4
- Global Simulation and Evaluation of Soil Organic Matter and Microbial Carbon and Nitrogen Stocks Using the Microbial Decomposition Model ORCHIMIC v2.0 Y. Huang et al. 10.1029/2020GB006836
- Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis E. Schwarz et al. 10.1021/acs.est.2c03397
- Microbial dormancy improves development and experimental validation of ecosystem model G. Wang et al. 10.1038/ismej.2014.120
- Future challenges in coupled C–N–P cycle models for terrestrial ecosystems under global change: a review D. Achat et al. 10.1007/s10533-016-0274-9
- Finding Liebig’s law of the minimum J. Tang & W. Riley 10.1002/eap.2458
- Understanding the joint impacts of soil architecture and microbial dynamics on soil functions: Insights derived from microscale models V. Pot et al. 10.1111/ejss.13256
- Soil Organic Matter Temperature Sensitivity Cannot be Directly Inferred From Spatial Gradients R. Abramoff et al. 10.1029/2018GB006001
- Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy J. Tang et al. 10.1029/2021MS002469
- On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics J. Tang 10.5194/gmd-8-3823-2015
- The evolution and application of the reverse Michaelis-Menten equation D. Moorhead & M. Weintraub 10.1016/j.soilbio.2018.07.021
- Quantifying the contribution of mass flow to nitrogen acquisition by an individual plant root R. McMurtrie & T. Näsholm 10.1111/nph.14927
- Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling J. Soong et al. 10.1111/gcb.14962
- Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics W. Riley et al. 10.5194/gmd-7-1335-2014
- Permafrost microbial community traits and functional diversity indicate low activity at in situ thaw temperatures J. Ernakovich & M. Wallenstein 10.1016/j.soilbio.2015.04.009
71 citations as recorded by crossref.
- Meta-analysis of high-latitude nitrogen-addition and warming studies implies ecological mechanisms overlooked by land models N. Bouskill et al. 10.5194/bg-11-6969-2014
- A Theory of Effective Microbial Substrate Affinity Parameters in Variably Saturated Soils and an Example Application to Aerobic Soil Heterotrophic Respiration J. Tang & W. Riley 10.1029/2018JG004779
- Improved modelling of soil nitrogen losses Q. Zhu & W. Riley 10.1038/nclimate2696
- Temperature sensitivity of ecoenzyme kinetics driving litter decomposition: The effects of nitrogen enrichment, litter chemistry, and decomposer community X. Tan et al. 10.1016/j.soilbio.2020.107878
- Emergent properties of organic matter decomposition by soil enzymes B. Wang & S. Allison 10.1016/j.soilbio.2019.107522
- Reviews and syntheses: Ironing out wrinkles in the soil phosphorus cycling paradigm C. McConnell et al. 10.5194/bg-17-5309-2020
- Nitrification, denitrification, and competition for soilN: Evaluation of twoEarth System Modelsagainst observations C. Nevison et al. 10.1002/eap.2528
- Modeling coupled enzymatic and solute transport controls on decomposition in drying soils S. Manzoni et al. 10.1016/j.soilbio.2016.01.006
- Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model G. Marschmann et al. 10.1038/s41564-023-01582-w
- Microbial Controls on the Biogeochemical Dynamics in the Subsurface M. Thullner & P. Regnier 10.2138/rmg.2019.85.9
- Combination of energy limitation and sorption capacity explains 14C depth gradients B. Ahrens et al. 10.1016/j.soilbio.2020.107912
- Improved global-scale predictions of soil carbon stocks with Millennial Version 2 R. Abramoff et al. 10.1016/j.soilbio.2021.108466
- Developing systems theory in soil agroecology: incorporating heterogeneity and dynamic instability N. Medina & J. Vandermeer 10.3389/fenvs.2023.1171194
- Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests Q. Zhu et al. 10.5194/bg-13-341-2016
- A chemical kinetics theory for interpreting the non-monotonic temperature dependence of enzymatic reactions J. Tang & W. Riley 10.5194/bg-21-1061-2024
- Multiple models and experiments underscore large uncertainty in soil carbon dynamics B. Sulman et al. 10.1007/s10533-018-0509-z
- Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle T. Barnum et al. 10.1038/s41396-020-0599-1
- Expanding the role of reactive transport models in critical zone processes L. Li et al. 10.1016/j.earscirev.2016.09.001
- Observed variation in soil properties can drive large variation in modelled forest functioning and composition during tropical forest secondary succession D. Medvigy et al. 10.1111/nph.15848
- Chemodiversity controls microbial assimilation of soil organic carbon: A theoretical model J. Weverka et al. 10.1016/j.soilbio.2023.109161
- Global patterns and substrate‐based mechanisms of the terrestrial nitrogen cycle S. Niu et al. 10.1111/ele.12591
- Earth System Model Needs for Including the Interactive Representation of Nitrogen Deposition and Drought Effects on Forested Ecosystems B. Drewniak & M. Gonzalez-Meler 10.3390/f8080267
- Competitor and substrate sizes and diffusion together define enzymatic depolymerization and microbial substrate uptake rates J. Tang & W. Riley 10.1016/j.soilbio.2019.107624
- ORCHIMIC (v1.0), a microbe-mediated model for soil organic matter decomposition Y. Huang et al. 10.5194/gmd-11-2111-2018
- Dynamic upscaling of decomposition kinetics for carbon cycling models A. Chakrawal et al. 10.5194/gmd-13-1399-2020
- A new theory of plant–microbe nutrient competition resolves inconsistencies between observations and model predictions Q. Zhu et al. 10.1002/eap.1490
- Root traits explain observed tundra vegetation nitrogen uptake patterns: Implications for trait‐based land models Q. Zhu et al. 10.1002/2016JG003554
- Comparison With Global Soil Radiocarbon Observations Indicates Needed Carbon Cycle Improvements in the E3SM Land Model J. Chen et al. 10.1029/2018JG004795
- Supporting hierarchical soil biogeochemical modeling: version 2 of the Biogeochemical Transport and Reaction model (BeTR-v2) J. Tang et al. 10.5194/gmd-15-1619-2022
- The effect of temperature on the rate, affinity, and 15N fractionation of NO3 − during biological denitrification in soils F. Maggi & W. Riley 10.1007/s10533-015-0095-2
- Representing leaf and root physiological traits in CLM improves global carbon and nitrogen cycling predictions B. Ghimire et al. 10.1002/2015MS000538
- SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration J. Tang & W. Riley 10.5194/gmd-10-3277-2017
- Abiotic and Biotic Controls on Soil Organo–Mineral Interactions: Developing Model Structures to Analyze Why Soil Organic Matter Persists D. Dwivedi et al. 10.2138/rmg.2019.85.11
- Merging a mechanistic enzymatic model of soil heterotrophic respiration into an ecosystem model in two AmeriFlux sites of northeastern USA D. Sihi et al. 10.1016/j.agrformet.2018.01.026
- Microbial community-level regulation explains soil carbon responses to long-term litter manipulations K. Georgiou et al. 10.1038/s41467-017-01116-z
- Revising the dynamic energy budget theory with a new reserve mobilization rule and three example applications to bacterial growth J. Tang & W. Riley 10.1016/j.soilbio.2023.108954
- Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process H. Song et al. 10.3389/fmicb.2017.01866
- Linear two-pool models are insufficient to infer soil organic matter decomposition temperature sensitivity from incubations J. Tang & W. Riley 10.1007/s10533-020-00678-3
- Relationship between enzyme concentration and Michaelis constant in enzyme assays K. Yun & T. Han 10.1016/j.biochi.2020.06.002
- Ecophysiological Study ofParaburkholderiasp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency K. Cyle et al. 10.1128/AEM.01851-20
- Representing Nitrogen, Phosphorus, and Carbon Interactions in the E3SM Land Model: Development and Global Benchmarking Q. Zhu et al. 10.1029/2018MS001571
- Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems X. Xu et al. 10.5194/bg-13-3735-2016
- When and why microbial-explicit soil organic carbon models can be unstable E. Schwarz et al. 10.5194/bg-21-3441-2024
- Weaker soil carbon–climate feedbacks resulting from microbial and abiotic interactions J. Tang & W. Riley 10.1038/nclimate2438
- Redox and temperature-sensitive changes in microbial communities and soil chemistry dictate greenhouse gas loss from thawed permafrost J. Ernakovich et al. 10.1007/s10533-017-0354-5
- Equifinality, sloppiness, and emergent structures of mechanistic soil biogeochemical models G. Marschmann et al. 10.1016/j.envsoft.2019.104518
- On the role of soil water retention characteristic on aerobic microbial respiration T. Ghezzehei et al. 10.5194/bg-16-1187-2019
- Model exploration of interactions between algal functional diversity and productivity in chemostats to represent open ponds systems across climate gradients Y. Cheng et al. 10.1016/j.ecolmodel.2019.05.007
- Competitive effects in bacterial mRNA decay T. Etienne et al. 10.1016/j.jtbi.2020.110333
- Near Activation and Differential Activation in Enzymatic Reactions F. Maggi & W. Riley 10.1002/kin.21076
- Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient K. Cyle et al. 10.1111/jam.15652
- Jena Soil Model (JSM v1.0; revision 1934): a microbial soil organic carbon model integrated with nitrogen and phosphorus processes L. Yu et al. 10.5194/gmd-13-783-2020
- The Central Amazon Biomass Sink Under Current and Future Atmospheric CO2: Predictions From Big‐Leaf and Demographic Vegetation Models J. Holm et al. 10.1029/2019JG005500
- Decomposition rate as an emergent property of optimal microbial foraging S. Manzoni et al. 10.3389/fevo.2023.1094269
- On the modeling paradigm of plant root nutrient acquisition J. Tang & W. Riley 10.1007/s11104-020-04798-5
- Microbial Models for Simulating Soil Carbon Dynamics: A Review A. Chandel et al. 10.1029/2023JG007436
- Mathematical Reconstruction of Land Carbon Models From Their Numerical Output: Computing Soil Radiocarbon From C Dynamics H. Metzler et al. 10.1029/2019MS001776
- Weaker land–climate feedbacks from nutrient uptake during photosynthesis-inactive periods W. Riley et al. 10.1038/s41558-018-0325-4
- Global Simulation and Evaluation of Soil Organic Matter and Microbial Carbon and Nitrogen Stocks Using the Microbial Decomposition Model ORCHIMIC v2.0 Y. Huang et al. 10.1029/2020GB006836
- Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis E. Schwarz et al. 10.1021/acs.est.2c03397
- Microbial dormancy improves development and experimental validation of ecosystem model G. Wang et al. 10.1038/ismej.2014.120
- Future challenges in coupled C–N–P cycle models for terrestrial ecosystems under global change: a review D. Achat et al. 10.1007/s10533-016-0274-9
- Finding Liebig’s law of the minimum J. Tang & W. Riley 10.1002/eap.2458
- Understanding the joint impacts of soil architecture and microbial dynamics on soil functions: Insights derived from microscale models V. Pot et al. 10.1111/ejss.13256
- Soil Organic Matter Temperature Sensitivity Cannot be Directly Inferred From Spatial Gradients R. Abramoff et al. 10.1029/2018GB006001
- Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy J. Tang et al. 10.1029/2021MS002469
- On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics J. Tang 10.5194/gmd-8-3823-2015
- The evolution and application of the reverse Michaelis-Menten equation D. Moorhead & M. Weintraub 10.1016/j.soilbio.2018.07.021
- Quantifying the contribution of mass flow to nitrogen acquisition by an individual plant root R. McMurtrie & T. Näsholm 10.1111/nph.14927
- Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling J. Soong et al. 10.1111/gcb.14962
- Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics W. Riley et al. 10.5194/gmd-7-1335-2014
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