That a scientific model is an idealized vision of something is well reflected by
another use of the word “model”—I don’t think I’ve ever seen a real person who
looks like the pictures on the covers of fashion magazines! We may be surrounded
by such images, but they are distinctly idealized. Models of soil function are equally
idealized (though hopefully not photoshopped to hide flaws), as well as being
simplified. I can’t comprehend the full complexity of soils, so a model that captured
every aspect of soil function would be equally beyond my comprehension and so
would not be useful. Instead, we represent our conceptual framing of processes and
mechanisms in simplified forms, first as concepts and then in equations that we can
incorporate into a mathematical architecture that allows us to put pieces together and
quantitatively explore their interactions and outcomes (Blankinship et al. 2018).
4.2 Microbes and Metabolism
“Is soil alive?” Hans Jenny asked me that when I was a new Ph.D. student and I’m
still not sure I have a good answer. But, unquestionably, soil is structured by life.
Plants create organic matter, microbes rework it into new forms, and soil animals
tunnel and mix. Without life, there’s just rock and dust, not soil.
Soil is the most complex habitat on Earth, contributing to the vast diversity of
microorganisms and microfauna that exist within the soil. Analyses of the diversity
of microorganisms in soil typically identify on the order of ~10,000 phylotypes of
microorganisms. But even before DNA sequence-based methods showed the full
sweep of life in soil, researchers had recognized that soil contained vast biodiversity;
for example, nearly a century ago, Waksman had noted “It is almost impossible at
present to make a complete study of the various types of bacteria occurring in the
soil, due both to the great variety of forms and to the lack of sufficient knowledge
concerning many of them” (Waksman 1927).
Since that time, our ability to analyze the composition of the microbial community in soil has been vastly expanded by the development of DNA- and RNA-based
molecular tools. ‘Omic analyses have identified new microbial lineages and new
biochemical pathways that had not been observed using previous culture-based
approaches; they also have allowed exploration of how microbial communities are
structured in complex environments and how communities respond to environmental perturbations (Jansson and Hofmockel 2020). The depth of information and
understanding these tools give us about microbial communities is phenomenal.
Yet, the significance of that diversity in the functioning of the soil system remains
a subject of debate (Schimel and Schaeffer 2012; Sokol et al. 2019; Jansson and
Hofmockel 2020; Reed and Martiny 2007; Fierer 2017). There also remain challenges in applying purely biological tools to understanding the rates and pathways of
soil processes (Baveye et al. 2016). Challenges come from both chemical kinetic
theory and biogeochemical modeling.
Even when only a limited group of organisms carry out a process, it can be
difficult to link population sizes to process rates. This is harder for processes that are
4 The Democracy of Dirt: Relating Micro-Scale Dynamics to Macro-Scale Ecosystem. . .
91
another use of the word “model”—I don’t think I’ve ever seen a real person who
looks like the pictures on the covers of fashion magazines! We may be surrounded
by such images, but they are distinctly idealized. Models of soil function are equally
idealized (though hopefully not photoshopped to hide flaws), as well as being
simplified. I can’t comprehend the full complexity of soils, so a model that captured
every aspect of soil function would be equally beyond my comprehension and so
would not be useful. Instead, we represent our conceptual framing of processes and
mechanisms in simplified forms, first as concepts and then in equations that we can
incorporate into a mathematical architecture that allows us to put pieces together and
quantitatively explore their interactions and outcomes (Blankinship et al. 2018).
4.2 Microbes and Metabolism
“Is soil alive?” Hans Jenny asked me that when I was a new Ph.D. student and I’m
still not sure I have a good answer. But, unquestionably, soil is structured by life.
Plants create organic matter, microbes rework it into new forms, and soil animals
tunnel and mix. Without life, there’s just rock and dust, not soil.
Soil is the most complex habitat on Earth, contributing to the vast diversity of
microorganisms and microfauna that exist within the soil. Analyses of the diversity
of microorganisms in soil typically identify on the order of ~10,000 phylotypes of
microorganisms. But even before DNA sequence-based methods showed the full
sweep of life in soil, researchers had recognized that soil contained vast biodiversity;
for example, nearly a century ago, Waksman had noted “It is almost impossible at
present to make a complete study of the various types of bacteria occurring in the
soil, due both to the great variety of forms and to the lack of sufficient knowledge
concerning many of them” (Waksman 1927).
Since that time, our ability to analyze the composition of the microbial community in soil has been vastly expanded by the development of DNA- and RNA-based
molecular tools. ‘Omic analyses have identified new microbial lineages and new
biochemical pathways that had not been observed using previous culture-based
approaches; they also have allowed exploration of how microbial communities are
structured in complex environments and how communities respond to environmental perturbations (Jansson and Hofmockel 2020). The depth of information and
understanding these tools give us about microbial communities is phenomenal.
Yet, the significance of that diversity in the functioning of the soil system remains
a subject of debate (Schimel and Schaeffer 2012; Sokol et al. 2019; Jansson and
Hofmockel 2020; Reed and Martiny 2007; Fierer 2017). There also remain challenges in applying purely biological tools to understanding the rates and pathways of
soil processes (Baveye et al. 2016). Challenges come from both chemical kinetic
theory and biogeochemical modeling.
Even when only a limited group of organisms carry out a process, it can be
difficult to link population sizes to process rates. This is harder for processes that are
4 The Democracy of Dirt: Relating Micro-Scale Dynamics to Macro-Scale Ecosystem. . .
91