Soil Organic Matter Dynamics and Structure

  • Nikolaos P. Nikolaidis
  • G. Bidoglio
Part of the Sustainable Agriculture Reviews book series (SARV, volume 12)


Soil ecosystem functions have significantly deteriorated due to agricultural intensification with dramatic consequences on carbon loss, loss of soil biodiversity, erosion, compaction as well as unsustainable use of water and mineral resources. Sustainable agricultural practices are necessary if we are to face the challenge of food security while preserving the integrity of soil and aquatic ecosystems. Conservation agriculture, which is comprised of zero or minimum tillage, carbon amendments and crop rotations, holds great promise in delivering higher yields, using water and soil resources in a sustainable manner and increasing soil biodiversity. This article presents a synthesis of current knowledge on soil ecosystem processes and modeling with a focus on carbon and nitrogen dynamics and their link to soil structure, and proposes a conceptual framework for model parameterization capable of predicting critical soil functions and potential shifts.

We reviewed the dynamics of carbon, nitrogen and soil structure with an emphasis in elucidating predominant state variables and the interaction with plants and food web dynamics. Existing models that simulate the dynamics of organic matter and structure in soils at various scales were evaluated for their ability to simulate the functions of soil ecosystem. Current modeling approaches treat carbon, nitrogen and soil structure for the most part separately without incorporating feedback mechanisms. The synergistic and antagonistic processes between bacteria and plants and fungi and plants are partially understood and more importantly the community lacks the knowledge to predict if and when these processes fail and any related potential ecosystem shift. A conceptual modeling framework is proposed, developed along the following three axes: incorporate emerging ecosystem state variables, account for the ecology of life in soils, and model processes from first principles. A synthesis of the carbon and nitrogen cycles is suggested in which the dynamics of the two cycles are interlinked. State variables in soil ecosystem models that link carbon and nitrogen dynamics with soil structure and the biological community are recommended. Plant feedback mechanisms with the physical, biochemical and biotic soil components and the symbiotic relationship between bacteria, fungi, and plants should be modeled using principles from the ecological succession theory that would relate the taxonomic structure with function and nutrient fluxes. A conceptual model of soil structure and soil stability is suggested that links the soil organic matter sub-model to an aggregation sub-model and a dynamic soil structure sub-model. The development of new generation soil ecosystem models is a necessary step to better quantify soil functions, assess possible soil tipping points, and develop methods to restore soil functions.


Soil carbon Soil nitrogen Soil structure Model Feedback mechanisms 



Particulate Organic Matter


Soil Organic Matter



Funding for this work was provided by the EU FP7-ENV-2009 Project SoilTrEC “Soil Transformations in European Catchments” (Grant #244118). This work was conducted at the Institute for Environment and Sustainability of the Joint Research Centre (JRC) of the European Commission. Professor Nikolaidis is grateful for the Technical University of Crete financial support of his sabbatical leave at the JRC.


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© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Department of Environmental EngineeringTechnical University of CreteChaniaGreece
  2. 2.Institute for Environment and Sustainability, Joint Research CentreEuropean CommissionISPRAItaly

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