induce even the simplest of metabolic capabilities would cost a cell an absolute
minimum of the equivalent of 60–70 glucose molecules if the needed amino acids
are available, to well over 300 if those amino acids are not. And, of course, the costs
rise proportionally if several different enzymes are required. That investment must
pay off.
That idea that synthesizing enzymes is energetically expensive has been incorporated into models of exoenzyme production and kinetics, because those enzymes
are excreted and so don’t contribute to cell biomass (Schimel and Weintraub 2003).
Investment energetics has only recently begun to be explored in thinking about SOM
dynamics more broadly or why simple molecules may persist for extended periods
(Lehmann et al. 2020).
For a cell living in an environment where there is a lot of just a few dominant
substrate types, those costs are not a problem. Consider a litter degrader on the soil
surface which attacks primarily cellulose and hemicellulose. These are polymers
composed of simple sugars such as glucose, arabinose, xylose, mannose, and
galactose that are readily assimilated into core metabolic pathways (via glycolysis,
pentose shunt, TCA, etc.) and hence readily catabolized to generate energy or used
as carbon skeletons in anabolism.
Consider, instead, a microbe living deeper in the soil profile in a micropore or on
the surface of a clay mineral. There is no fresh plant material; instead, the mineralassociated OM is a diverse mix of molecules, some of which may be plant-derived,
but many may be from dead soil microbes (Kleber et al. 2007; Liang et al. 2017). No
single molecule type is likely to be available in large quantities. Yet to metabolize
any one of them, the acquired molecule must be shunted into core metabolism,
which may require synthesizing new enzymes. If there is not enough of a potential
substrate molecule to pay the energetic costs to make the enzyme(s) needed to
metabolize it, then it would be detrimental for a cell to use that substrate—the
investment might never pay off; there would be a negative energy yield. Essentially
by “eating” this compound, a microbe would only starve faster. I might call this the
“celery effect” after the well-known myth that celery has negative calories; i.e., it
takes more energy to digest than you get from eating it.
Given enough time, it is possible that a microbe might eventually get enough of a
substrate to pay off the costs of synthesizing the needed enzymes, but enzymes are
not “immortal” in microbial cells—turning over proteins is a substantial fraction of
overall cell maintenance costs (Kempes et al. 2017). A cell must take up enough of a
particular substrate molecule over the life of the required enzymes to make using the
substrate energetically and “economically” viable. A microbe might well have the
genes for the necessary enzymes and even have access to some of that substrate, yet
still leave it untouched.
This “celery effect” would become more likely to limit microbial activity with
increased depth in a soil, as total organic matter levels decline, molecules are more
tightly tied up with the mineral phase, and the diversity of organic structures that
microbes have access to may increase (Lehmann et al. 2020). Despite having the
genetic potential to use every substrate present, a microbe might starve.
4 The Democracy of Dirt: Relating Micro-Scale Dynamics to Macro-Scale Ecosystem. . .
97
minimum of the equivalent of 60–70 glucose molecules if the needed amino acids
are available, to well over 300 if those amino acids are not. And, of course, the costs
rise proportionally if several different enzymes are required. That investment must
pay off.
That idea that synthesizing enzymes is energetically expensive has been incorporated into models of exoenzyme production and kinetics, because those enzymes
are excreted and so don’t contribute to cell biomass (Schimel and Weintraub 2003).
Investment energetics has only recently begun to be explored in thinking about SOM
dynamics more broadly or why simple molecules may persist for extended periods
(Lehmann et al. 2020).
For a cell living in an environment where there is a lot of just a few dominant
substrate types, those costs are not a problem. Consider a litter degrader on the soil
surface which attacks primarily cellulose and hemicellulose. These are polymers
composed of simple sugars such as glucose, arabinose, xylose, mannose, and
galactose that are readily assimilated into core metabolic pathways (via glycolysis,
pentose shunt, TCA, etc.) and hence readily catabolized to generate energy or used
as carbon skeletons in anabolism.
Consider, instead, a microbe living deeper in the soil profile in a micropore or on
the surface of a clay mineral. There is no fresh plant material; instead, the mineralassociated OM is a diverse mix of molecules, some of which may be plant-derived,
but many may be from dead soil microbes (Kleber et al. 2007; Liang et al. 2017). No
single molecule type is likely to be available in large quantities. Yet to metabolize
any one of them, the acquired molecule must be shunted into core metabolism,
which may require synthesizing new enzymes. If there is not enough of a potential
substrate molecule to pay the energetic costs to make the enzyme(s) needed to
metabolize it, then it would be detrimental for a cell to use that substrate—the
investment might never pay off; there would be a negative energy yield. Essentially
by “eating” this compound, a microbe would only starve faster. I might call this the
“celery effect” after the well-known myth that celery has negative calories; i.e., it
takes more energy to digest than you get from eating it.
Given enough time, it is possible that a microbe might eventually get enough of a
substrate to pay off the costs of synthesizing the needed enzymes, but enzymes are
not “immortal” in microbial cells—turning over proteins is a substantial fraction of
overall cell maintenance costs (Kempes et al. 2017). A cell must take up enough of a
particular substrate molecule over the life of the required enzymes to make using the
substrate energetically and “economically” viable. A microbe might well have the
genes for the necessary enzymes and even have access to some of that substrate, yet
still leave it untouched.
This “celery effect” would become more likely to limit microbial activity with
increased depth in a soil, as total organic matter levels decline, molecules are more
tightly tied up with the mineral phase, and the diversity of organic structures that
microbes have access to may increase (Lehmann et al. 2020). Despite having the
genetic potential to use every substrate present, a microbe might starve.
4 The Democracy of Dirt: Relating Micro-Scale Dynamics to Macro-Scale Ecosystem. . .
97