Newer models have mapped SOM into more readily measurable and identifiable
materials rather than relying upon “conceptual pools.” An example of this approach
is the “Millenial” model (which defines C and nutrients as low-molecular-weight
(i.e., soluble), microbial biomass, particulate, mineral-associated, and aggregateprotected; Abramoff et al. 2017). Developing such models recognizes that, ultimately, our theories need to link more concretely with actual physical materials and
the real chemistry and physics through which they interact. Such models recognize
that microbes don’t, in fact, metabolize “organic matter”; rather, they metabolize
specific organic molecules that have to move to a microbial cell.
For a microbe to access a substrate, either the substrate must already be small
enough to diffuse to the cell, or the microbe must fragment the substrate extracellularly by excreting an enzyme that can break the polymer into monomers or
oligomers—molecules small enough that they can diffuse to the cell (Schimel and
Schaeffer 2012).
Outside of a living cell’s controlled environment, enzymes are limited in the
chemistry they are capable of carrying out. Many extracellular enzymes catalyze
simple
hydrolytic
reactions
(e.g.,
glucosidase,
cellobiohydrolase,
N-acetylglucosaminidase, etc.). Others (e.g., peroxidase, phenol oxidase) oxidize
substrates by what I describe as “shotgun metabolism”; these enzymes are
non-specific in how they transfer an electron from a substrate to a metal ion, either
in the enzyme itself or as a free intermediate (e.g., Mn
3+ in the case of manganese
peroxidase; Conesa et al. 2002). This process can almost randomly knock fragments
off macromolecules, fragments that can then recondense via abiotic chemistry or that
can be taken up and metabolized by microbes. Such shotgun metabolism allows
oxidative enzymes to be very non-specific (Ruiz-Dueñas and Martínez 2009).
However, once a microbe takes up a molecule, it requires specific enzymes to
convert that molecule into an intermediate of the central metabolic pathways that
cells use to generate energy and provide C-skeletons for biosynthesis (e.g., glycolysis and the tricarboxylic acid cycle). Some enzymes are produced constitutively;
hence, the substrates for those enzymes can always be metabolized. For other
substrates, however, inducing their synthesis may invoke a high investment in C,
N, and energy—possibly expenditures that can never be recouped.
Kaleta et al. (2013) calculated that to synthesize a protein costs 4.2 ATP per
residue to polymerize amino acids. That calculation, however, assumes an average
of 30 protein copies are made from each mRNA. For the first copy of a protein
(hence, the minimum possible cost to induce a metabolic capability), the cost is
10 ATP per residue (6 ATP for each coding triplet in mRNA plus 4 to charge the
tRNA and attach the amino acid to the forming polymer). For a small protein with
250 amino acids, the cost just to transcribe and translate a gene to produce one copy
of a new protein (from existing amino acids) would therefore be 2500 ATP.
When a bacterium completely respires a glucose molecule, it can generate
38 ATP, so it would have to respire >65 glucose molecules to provide the energy
to synthesize the needed ATP to assemble that new protein. There are additional
costs associated with taking up the glucose and NH 4
+
, plus those associated with
synthesizing the needed amino acids. Accounting for all the costs means that to
96
J. Schimel
materials rather than relying upon “conceptual pools.” An example of this approach
is the “Millenial” model (which defines C and nutrients as low-molecular-weight
(i.e., soluble), microbial biomass, particulate, mineral-associated, and aggregateprotected; Abramoff et al. 2017). Developing such models recognizes that, ultimately, our theories need to link more concretely with actual physical materials and
the real chemistry and physics through which they interact. Such models recognize
that microbes don’t, in fact, metabolize “organic matter”; rather, they metabolize
specific organic molecules that have to move to a microbial cell.
For a microbe to access a substrate, either the substrate must already be small
enough to diffuse to the cell, or the microbe must fragment the substrate extracellularly by excreting an enzyme that can break the polymer into monomers or
oligomers—molecules small enough that they can diffuse to the cell (Schimel and
Schaeffer 2012).
Outside of a living cell’s controlled environment, enzymes are limited in the
chemistry they are capable of carrying out. Many extracellular enzymes catalyze
simple
hydrolytic
reactions
(e.g.,
glucosidase,
cellobiohydrolase,
N-acetylglucosaminidase, etc.). Others (e.g., peroxidase, phenol oxidase) oxidize
substrates by what I describe as “shotgun metabolism”; these enzymes are
non-specific in how they transfer an electron from a substrate to a metal ion, either
in the enzyme itself or as a free intermediate (e.g., Mn
3+ in the case of manganese
peroxidase; Conesa et al. 2002). This process can almost randomly knock fragments
off macromolecules, fragments that can then recondense via abiotic chemistry or that
can be taken up and metabolized by microbes. Such shotgun metabolism allows
oxidative enzymes to be very non-specific (Ruiz-Dueñas and Martínez 2009).
However, once a microbe takes up a molecule, it requires specific enzymes to
convert that molecule into an intermediate of the central metabolic pathways that
cells use to generate energy and provide C-skeletons for biosynthesis (e.g., glycolysis and the tricarboxylic acid cycle). Some enzymes are produced constitutively;
hence, the substrates for those enzymes can always be metabolized. For other
substrates, however, inducing their synthesis may invoke a high investment in C,
N, and energy—possibly expenditures that can never be recouped.
Kaleta et al. (2013) calculated that to synthesize a protein costs 4.2 ATP per
residue to polymerize amino acids. That calculation, however, assumes an average
of 30 protein copies are made from each mRNA. For the first copy of a protein
(hence, the minimum possible cost to induce a metabolic capability), the cost is
10 ATP per residue (6 ATP for each coding triplet in mRNA plus 4 to charge the
tRNA and attach the amino acid to the forming polymer). For a small protein with
250 amino acids, the cost just to transcribe and translate a gene to produce one copy
of a new protein (from existing amino acids) would therefore be 2500 ATP.
When a bacterium completely respires a glucose molecule, it can generate
38 ATP, so it would have to respire >65 glucose molecules to provide the energy
to synthesize the needed ATP to assemble that new protein. There are additional
costs associated with taking up the glucose and NH 4
+
, plus those associated with
synthesizing the needed amino acids. Accounting for all the costs means that to
96
J. Schimel