There has been progress in bridging the gaps, for example, using “trait-based”
approaches to define and aggregate microbial functional groups (Lennon et al. 2012;
Krause et al. 2014; Malik et al. 2019). This approach was developed in plant
ecology, where to describe plant function at large scales, modelers have moved
away from using specific taxa in a model; rather plants are represented by traits
which can be quantified and modeled (e.g., Bonan et al. 2012). Those traits can then
be mapped onto either individual species of plants or onto growth forms or other
aggregated groups (Shipley et al. 2016). This approach may not be necessary in
low-diversity ecosystems where there are only a few key plant species (e.g., conifer
forests; Butler et al. 2017), but is key in more diverse communities (Asner et al.
2015) where taxa may share functional traits. Such a high-diversity condition
certainly describes soil communities.
4.3 Minerals
In the Democracy of Dirt, minerals comprise the “Silent Majority.” They create the
physical structure of the soil and regulate the accessibility of substrates to microbial
attack. It has become generally accepted that mineral-associated organic matter
(MAOM) comprises the more persistent components of SOM (Kleber et al. 2015;
Sokol et al. 2019), but this idea is not new. Concepts of “physical protection” date
back decades (e.g., Russel and McRuer 1927) and have remained a dominant theory
to explain how organic molecules that are readily metabolizable may persist for
centuries or even millennia in soil.
Soil texture regulates a soil’s organic matter content, with clay being seen as the
key to soil texture effects on SOM (Rasmussen et al. 2018). Clay’s high surface area
and charged surfaces (ion exchange capacity) can sorb organic molecules, while its
small particles allow clay to pack so tightly that pores may exclude microorganisms
from accessing trapped resources. This phenomenon led to “habitable pore space”
theory to explain soil foodweb structure (Elliott et al. 1980). Biogeochemical models
such as CENTURY (which simulates the long-term dynamics of carbon and nutrients in soil-plant systems) or its modern iteration DAYCENT (a more sophisticated
version that runs on a daily time step to model ecosystem fluxes and exchanges with
the atmosphere) may not require microbial community data as input variables, but
they do require knowledge of soil texture (Parton et al. 1987). Clay content is critical
to describe how active C partitions into slow and passive pools, and such models
predict ca. 50% higher C stocks in clay loams than in sandy soils.
Recent studies, however, have illustrated that “clay” on its own—encompassing
all mineral particles smaller than 2 μm—is inadequate to describe organic matter
stabilization. Rather, in neutral pH soils, where bulk clay mineralogy tends toward
phyllosilicates, SOM is sorbed primarily by short-range-order (SRO) mineral
phases—these comprise but a small, albeit chemically active, portion of the total
clays (Rasmussen et al. 2018). In contrast, alkaline soils are rich in base cations, and
so in these soils, SOM is stabilized by Ca-bridging where the divalent cations link
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J. Schimel
approaches to define and aggregate microbial functional groups (Lennon et al. 2012;
Krause et al. 2014; Malik et al. 2019). This approach was developed in plant
ecology, where to describe plant function at large scales, modelers have moved
away from using specific taxa in a model; rather plants are represented by traits
which can be quantified and modeled (e.g., Bonan et al. 2012). Those traits can then
be mapped onto either individual species of plants or onto growth forms or other
aggregated groups (Shipley et al. 2016). This approach may not be necessary in
low-diversity ecosystems where there are only a few key plant species (e.g., conifer
forests; Butler et al. 2017), but is key in more diverse communities (Asner et al.
2015) where taxa may share functional traits. Such a high-diversity condition
certainly describes soil communities.
4.3 Minerals
In the Democracy of Dirt, minerals comprise the “Silent Majority.” They create the
physical structure of the soil and regulate the accessibility of substrates to microbial
attack. It has become generally accepted that mineral-associated organic matter
(MAOM) comprises the more persistent components of SOM (Kleber et al. 2015;
Sokol et al. 2019), but this idea is not new. Concepts of “physical protection” date
back decades (e.g., Russel and McRuer 1927) and have remained a dominant theory
to explain how organic molecules that are readily metabolizable may persist for
centuries or even millennia in soil.
Soil texture regulates a soil’s organic matter content, with clay being seen as the
key to soil texture effects on SOM (Rasmussen et al. 2018). Clay’s high surface area
and charged surfaces (ion exchange capacity) can sorb organic molecules, while its
small particles allow clay to pack so tightly that pores may exclude microorganisms
from accessing trapped resources. This phenomenon led to “habitable pore space”
theory to explain soil foodweb structure (Elliott et al. 1980). Biogeochemical models
such as CENTURY (which simulates the long-term dynamics of carbon and nutrients in soil-plant systems) or its modern iteration DAYCENT (a more sophisticated
version that runs on a daily time step to model ecosystem fluxes and exchanges with
the atmosphere) may not require microbial community data as input variables, but
they do require knowledge of soil texture (Parton et al. 1987). Clay content is critical
to describe how active C partitions into slow and passive pools, and such models
predict ca. 50% higher C stocks in clay loams than in sandy soils.
Recent studies, however, have illustrated that “clay” on its own—encompassing
all mineral particles smaller than 2 μm—is inadequate to describe organic matter
stabilization. Rather, in neutral pH soils, where bulk clay mineralogy tends toward
phyllosilicates, SOM is sorbed primarily by short-range-order (SRO) mineral
phases—these comprise but a small, albeit chemically active, portion of the total
clays (Rasmussen et al. 2018). In contrast, alkaline soils are rich in base cations, and
so in these soils, SOM is stabilized by Ca-bridging where the divalent cations link
94
J. Schimel