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A process-based soil microbial model to study the intricate interplay between moisture and carbon dynamics in soils
Year of publication: 2021
hydrologybiogeochemicalvadose-zone1Dsiteecologicalcritical zonerhizospherelab


Albert C Brangarí (University of Amsterdam), Stefano Manzoni (Stockholm University), Johannes Rousk (Lund University)



EcoSMMARTS is a process-based soil microbial model designed to simulate the intricate interplay between moisture and carbon dynamics in soils. The model consists of a set of mass-balance equations that describe the dynamics of various carbon compartments, including particulate organic carbon (POC), dissolved organic carbon (DOC), active microorganisms with different life strategies, dormant microorganisms, osmolytes, extracellular enzymes, and microbial residues (necromass). It accounts for processes/mechanisms such as the legacy of drought, different microbial life strategies (‘fast growers’ and ‘drought resistors’), adaptive allocation of carbon, osmoregulation and osmotic shock, extracellular mineralization by microbial residues, inactivation-reactivation of microorganisms, and disruption of soil aggregates. The model excels in characterizing the CO2 emissions and microbial biomass production dynamics amid soil drying and rewetting events, such as drought followed by rain. It has been instrumental in revealing how the legacy of drought can shape the structure and physiology of microbial communities, consequently determining their subsequent responses to drying-rewetting events. In general, microbial communities that have adapted to prolonged drought tend to exhibit a resilient response to future events; conversely, those inhabiting less harsh environments lack the mechanisms to endure stress and thus respond more sensitively. Future enhancements to the model will include incorporating the effects of temperature and developing a more nuanced organic carbon turnover model, furthering its utility in predicting and understanding the dynamics of carbon in soil ecosystems.


Scientific articles


  • Brangarí AC, Manzoni S, and Rousk J. A soil microbial model to analyze decoupled microbial growth and respiration during soil drying and rewetting, 2020. Soil Biology and Biochemistry, 148: 107871.
  • Brangarí AC, Manzoni S, and Rousk J. The mechanisms underpinning microbial resilience to drying and rewetting – A model analysis, 2021. Soil Biology and Biochemistry, 162: 108400.


Program and Technical information


Matlab scripts are available at

Operating system: All compatible with Matlab (Windows, MacOS, Linux)

Licence: Public domain

Output: soil respiration, microbial growth, organic matter decomposition, community composition, osmoregulation, osmolysis, enzyme production, dormancy, EPS production.

Export format: MAT files (built-in functions to export to Excel also available)

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