broadly distributed across microbial groups (Schimel 2001) and when organisms
have overlapping metabolic capacities; in this case much of the biodiversity can be
seen as “redundancy” (Allison and Martiny 2008).
Chemical kinetic theory states that the overall rate of a reaction sequence is
regulated by its slowest step—the “rate-limiting” or “rate-determining” step. That
slowest step defines a reaction’s kinetic rate equation.
Chemistry in soil occurs even in the absence of life, but life is the great “force
multiplier” for chemistry; it organizes enzyme systems and enables cells to link
energy-generating processes with energy-demanding ones to overcome activationenergy constrained or endergonic reactions.
Hence, the rate-limiting step in decomposition is rarely the physiological capacity
to process a molecule once it is within a cell’s membrane—most naturally occurring
molecules, once brought inside a cell, can be rapidly metabolized. Thus, to model the
kinetics of microbial processes, actual catabolism may be almost irrelevant in
defining the rate of the overall process. Rather, the challenge, more commonly, is
to mobilize molecules into a form a microbe can get across its membrane (Schimel
and Schaeffer 2012); hence, the critical, rate-controlling step is likely the process
that enables microbes to access a substrate molecule.
If, for example, substrate desorption from a mineral surface is substantially
slower than microbial uptake and metabolism, the approximate rate expression
would reflect the desorption rather than biochemistry (Scow 1993). An analogous
situation exists with polymer biodegradation. Microbes must excrete enzymes to
fragment plant polymers, which are generally too big for microbes to take up directly
(cellulose fibrils can be >10 μm long—longer than a bacterial cell; Taiz et al. 2015).
In such cases, the kinetic expression will reflect exoenzyme-driven depolymerization
(Schimel and Weintraub 2003) or enzyme diffusion to substrates rather than microbial uptake and metabolism (Manzoni et al. 2016).
More important for the long-term dynamics of organic substrates is what
microbes convert a substrate to—do they produce necromass or other constituents
that are readily stabilized? The importance of how microbes allocate organic substrates is reflected in the growing interest in carbon use efficiency (CUE), and the
closely related concept of microbial growth efficiency (MGE) which are vital in
carbon cycling models (Wieder et al. 2013; Todd-Brown et al. 2011; Hagerty et al.
2018), and in a growing focus on microbial anabolism—how microbes grow and
what they produce (Liang et al. 2017).
More sophisticated approaches to chemical reaction kinetics in complex systems,
such as flow-through reactor systems like soil, recognize that both the actual reaction
and the physical transport processes can be important. Hence approaches such as
reaction-diffusion models (Von Fischer et al. 2009) and reactive transport models
(Li et al. 2017) are becoming more common in ecological systems. Such models
integrate physical movement with chemical reactions and use transport to constrain
substrate and product concentrations at the point of reaction.
The second major challenge in using ‘omics tools to drive models of soil
biogeochemistry is the “simultaneous equation” problem: we may identify on the
order of 10,000 phylotypes of microorganisms in a soil sample, but the models we
92
J. Schimel
have overlapping metabolic capacities; in this case much of the biodiversity can be
seen as “redundancy” (Allison and Martiny 2008).
Chemical kinetic theory states that the overall rate of a reaction sequence is
regulated by its slowest step—the “rate-limiting” or “rate-determining” step. That
slowest step defines a reaction’s kinetic rate equation.
Chemistry in soil occurs even in the absence of life, but life is the great “force
multiplier” for chemistry; it organizes enzyme systems and enables cells to link
energy-generating processes with energy-demanding ones to overcome activationenergy constrained or endergonic reactions.
Hence, the rate-limiting step in decomposition is rarely the physiological capacity
to process a molecule once it is within a cell’s membrane—most naturally occurring
molecules, once brought inside a cell, can be rapidly metabolized. Thus, to model the
kinetics of microbial processes, actual catabolism may be almost irrelevant in
defining the rate of the overall process. Rather, the challenge, more commonly, is
to mobilize molecules into a form a microbe can get across its membrane (Schimel
and Schaeffer 2012); hence, the critical, rate-controlling step is likely the process
that enables microbes to access a substrate molecule.
If, for example, substrate desorption from a mineral surface is substantially
slower than microbial uptake and metabolism, the approximate rate expression
would reflect the desorption rather than biochemistry (Scow 1993). An analogous
situation exists with polymer biodegradation. Microbes must excrete enzymes to
fragment plant polymers, which are generally too big for microbes to take up directly
(cellulose fibrils can be >10 μm long—longer than a bacterial cell; Taiz et al. 2015).
In such cases, the kinetic expression will reflect exoenzyme-driven depolymerization
(Schimel and Weintraub 2003) or enzyme diffusion to substrates rather than microbial uptake and metabolism (Manzoni et al. 2016).
More important for the long-term dynamics of organic substrates is what
microbes convert a substrate to—do they produce necromass or other constituents
that are readily stabilized? The importance of how microbes allocate organic substrates is reflected in the growing interest in carbon use efficiency (CUE), and the
closely related concept of microbial growth efficiency (MGE) which are vital in
carbon cycling models (Wieder et al. 2013; Todd-Brown et al. 2011; Hagerty et al.
2018), and in a growing focus on microbial anabolism—how microbes grow and
what they produce (Liang et al. 2017).
More sophisticated approaches to chemical reaction kinetics in complex systems,
such as flow-through reactor systems like soil, recognize that both the actual reaction
and the physical transport processes can be important. Hence approaches such as
reaction-diffusion models (Von Fischer et al. 2009) and reactive transport models
(Li et al. 2017) are becoming more common in ecological systems. Such models
integrate physical movement with chemical reactions and use transport to constrain
substrate and product concentrations at the point of reaction.
The second major challenge in using ‘omics tools to drive models of soil
biogeochemistry is the “simultaneous equation” problem: we may identify on the
order of 10,000 phylotypes of microorganisms in a soil sample, but the models we
92
J. Schimel