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Title: SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

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 +  B E  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 incorporatemore » 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.« less

Authors:
 [1];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences Area
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1378394
Alternate Identifier(s):
OSTI ID: 1408471
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Geoscientific Model Development (Online)
Additional Journal Information:
Journal Name: Geoscientific Model Development (Online); Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 1991-9603
Publisher:
European Geosciences Union
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Tang, Jin-Yun, and Riley, William J. SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration. United States: N. p., 2017. Web. doi:10.5194/gmd-10-3277-2017.
Tang, Jin-Yun, & Riley, William J. SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration. United States. doi:10.5194/gmd-10-3277-2017.
Tang, Jin-Yun, and Riley, William J. Tue . "SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration". United States. doi:10.5194/gmd-10-3277-2017.
@article{osti_1378394,
title = {SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration},
author = {Tang, Jin-Yun and Riley, William J.},
abstractNote = {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.},
doi = {10.5194/gmd-10-3277-2017},
journal = {Geoscientific Model Development (Online)},
number = 9,
volume = 10,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
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DOI: 10.5194/gmd-10-3277-2017

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