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Biophysics and soil structure

This working group on biophysics and soil structure aims to bring together international experts working on biophysics and soil structure



Andrea Carminati

ETH Zürich

Department of Environmental Systems Science


Hans-Jörg Vogel

UFZ Leipzig

Soil System Science


Tentative list of Participants

will come soon

General starting point 

Soil structure drives soil biology, and soil biology drives soil structure, with disruptions to either having huge implications to the way soils work and their sustainability.  The advent of various extremely powerful tools to visualize and quantify soil structure has increased the understanding of these interactions considerably, but the vast array of data generated from multiple approaches can be difficult to interpret. Soil pore structure can be measured at micron resolution in 3D with X-ray tomography. Chemical structure can be analyzed at very high spatial resolution using tools for chemical mapping (NanoSims, XEDX, ….). Even the spatial distribution of bacteria and fungi can be visualized to some extent. Coupled with imaging approaches are new physical tests that disentangle mechanical and hydrological impacts of soil biology, and a range of modelling approaches that can describe and predict behaviour.

We identified four main research themes to be addressed. All four are (of course) highly connected:

1. Structure dynamics driven by interactions of physical and biological processes 

Far too little is known on the temporal dynamics of soil structure brought about by physical (swelling/shrinking, freezing/thawing) and biological (microbial growth and decay, bioturbation) processes.  We are well aware about the importance of soil structure dynamics to the formation of aggregates, the mixing of mineral and organic matter, and the stability of the soil pore system, but we have no clear idea on characteristic time scales for structure dynamics (or turnover). Macroscopic properties such as porosity, pore connectivity, water retention characteristic of conductivity may not change at all while internally the microscopic neighborhood relations may change constantly. This is critical for the generation of spatial heterogeneity, local gradients, the exploration of the soil volume by soil biota including plants and the turnover of soil organic matter. It is a formidable challenge to focus more research on this aspect.

2. Soil structure as biological habitat

Soil structure forms the habitat of soil organisms and, thus, it is an obvious assumption that soil structure forms variably connected pore spaces and separated niches (i.e. habitats) that are of critical importance for the diversity of soil biota. This affects not only the genetic diversity of individual species, but more importantly the functional diversity within biological communities. Soil biology may also drive soil structure, possibly building favourable properties. The quantitative description of these interactions is weak, but a huge potential exists to learn more by exploiting new technologies and modelling.  A more profound understanding would open new avenues to increase the stability and resilience of soil system in response to external perturbations by putting soil structural properties in the focus of soil management.

3. Soil structure impacts on biological processes – element cycling, carbon sequestration

Today, it is widely accepted that stabilization of soil organic matter is controlled by spatial accessibility for degraders rather than chemical structure of the organic molecules. Hence, the same is true for nutrient cycling in general. However, there is dispute about how organic matter and mineral particles arrange themselves through aggregation in order to form zones of different accessibility. The importance of diffusion of gases and dissolved organic matter,  of bioturbation and of microbial mobility and flexibility is often neglected, and the impacts of soil structure dynamics are rarely considered.

4. Biological impacts on soil physical processes – transport, retention, mechanics

The impact of biological activity on physical processes and properties is mainly brought about by the structure forming activity of soil biota and the excretion of organic substances changing physico-chemical properties of internal surfaces. The most prominent effects are the generation of preferential flow along macro-pores generated by earthworms and roots, the increasing stability of the organo-mineral soil matrix caused by biological exudates, reinforcement at larger scale by fungal hyphae and plant roots, and the change in wettability induced by biological compounds.  While the mechanisms have received considerable research interest, implementing these process in today’s model approaches remains at the level of empirical parametrizations which typically need to be calibrated to experimental observation. Hence, a mechanistic approach required for predictive modelling is still missing. Recent modelling of plant exudation effects on rhizosphere physics and bioturbation impacts of roots and earthworms is moving the right direction, providing outputs directly relevant to soil sustainability and water use.

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