EGU General Assembly 2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

Scaling up microbial dynamics for soil carbon cycling models

Stefano Manzoni1,2, Arjun Chakrawal1,2, and Naoise Nunan3
Stefano Manzoni et al.
  • 1Stockholm University, Department of Physical Geography, Stockholm, Sweden (
  • 2Bolin Centre for Climate Research, Stockholm, Sweden
  • 3Institute of Ecology and Environmental Sciences - Paris, Sorbonne Universités, Paris, France

Soils are heterogeneous at all scales and so are the biogeochemical reactions driving the cycling of carbon (C) and nutrients in soils. While the microbial processes involved in these reactions occur at the pore scale, what we observe at the soil core or pedon scale depends on how micro-scale processes are integrated in space (and time). This integration step requires accounting for the inherent patchiness of soils, but models used to describe element cycling in soils typically assume that conditions are well-mixed and that kinetics laws developed for laboratory conditions hold. Similarly, the response functions used in models to capture the effects of environmental conditions on C and nutrient fluxes neglect the contribution of spatial heterogeneities, which might alter their shape. There is therefore a need to re-evaluate model structures to test whether they can account for micro-scale heterogeneities. Alternatively, one can ask why some models are clearly successful in capturing observations despite neglecting soil heterogeneities. In this contribution, we present examples of how soil heterogeneities – in particular the spatial placement of soil microorganisms and their substrate – may affect decomposition kinetics and microbial responses to soil drying. We show that the kinetics laws used in current models are different from the kinetics obtained by integrating microbial dynamics at the micro-scale, and that respiration responses to soil drying may vary depending on soil heterogeneity. These results thus highlight structural uncertainties in current models that we propose can be assessed using existing ‘scale-aware’ methods to derive macro-scale model formulations. Model advances will need to be supported by empirical evidence bridging the gap between pore and core (or larger) scales, but can also provide new theory-based hypotheses for novel experiments.

How to cite: Manzoni, S., Chakrawal, A., and Nunan, N.: Scaling up microbial dynamics for soil carbon cycling models, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-3739,, 2020


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displays version 1 – uploaded on 29 Apr 2020
  • AC1: Display highlights, Stefano Manzoni, 29 Apr 2020
    • Micro-scale spatial heterogeneity affects C flow in soil by limiting contact between substrates and microbes.
    • Scale transition theory predicts that decomposition kinetics applied at the macro-scale should be modified to account for micro-scale spatial heterogeneity
    • The shape of the macro-scale decomposition kinetics is different from typical assumptions in soil C flow models because of spatial heterogeneity
    • Substrate-microbe separation in heterogeneous soils slows down decomposition (the opposite is true for co-location)