Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth

Abstract

Abstract. Despite the importance of fungi in soil ecosystem services, a theoretical framework that links soil management strategies with fungal ecology is still lacking. One of the key challenges is to understand how the complex geometrical shape of pores in soil affects fungal spread and species interaction. Progress in this area has long been hampered by a lack of experimental techniques for quantification. In this paper we use X-ray computed tomography to quantify and characterize the pore geometry at microscopic scales (30 µm) that are relevant for fungal spread in soil. We analysed the pore geometry for replicated samples with bulk-densities ranging from 1.2-1.6 g/cm 3 . The bulk-density of soils significantly affected the total volume, mean pore diameter and connectivity of the pore volume. A previously described fungal growth model comprising a minimal set of physiological processes required to produce a range of phenotypic responses was used to analyse the effect of these geometric descriptors on fungal invasion, and we showed that the degree and rate of fungal invasion was affected mainly by pore volume and pore connectivity. The presented experimental and theoretical framework is a significant first step towards understanding how environmental change and soil management impact on fungal diversity in soils.

The use of PET/CT scanning technique for 3D visualization and quantification of real-time soil/plant interactions

“…The main difference is that commercial units, unlike medical systems, feature static X-ray source and detector while sample is mounted on rotating turntable. They also offer a higher energy of X-ray source and higher spatial resolution down to the micrometer range (Pajor et al 2010). In this work, we used Nikon Metrology HMX 225 system, equipped in X-ray source with maximum energy of 225 kV, build in air-conditioning unit and flat panel detector Varian 2,520 allowing scanning samples sized 25×33 cm and maximum resolution of 3 μm for small samples.…”

Increasing soil carbon storage: mechanisms, effects of agricultural practices and proxies. A review

“…These models include an explicit 2D or 3D description of the pore network based on computer tomography images (Monga et al 2008(Monga et al , 2014Falconer et al 2007Falconer et al , 2015Pajor et al 2010;Resat et al 2012;Vogel et al 2015). They operate over short time scales and have been validated for simplified systems.…”

Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils

“…Evidence abounds (e.g., Moreau et al, 1999;Okabe and Blunt, 2004;Prado et al, 2009;Remeysen and Swennen, 2008;Thullner and Baveye, 2008;Van Geet et al, 2000) that many aspects of the behaviour of soils, including their transmission of liquid phases and solutes, can be described accurately only on the basis of 3-dimensional information, such as provided by Xray computed tomography, a technique that has experienced rapid development in recent years (Baveye et al, 2002Elliot and Heck, 2007;Iassonov et al, 2009;Iassonov and Tuller, 2010;Long et al, 2009;Taina et al, 2008;Yao et al, 2009). For example, the degree of connectivity or tortuosity of the pore space in 2-dimensional cuts through a soil is generally very different than in 3-dimensions, and only the full 3-D connectivity is relevant when one attempts to predict the hydraulic conductivity or dispersion coefficient of a given soil sample, or biomass spread (e.g., Pajor et al, 2010). In a similar way, in order to realistically describe how microscale heterogeneity affects processes that involve (bio)chemical reactions, 3-dimensional spatial data about the chemical make-up of soils, or at least about the distribution of targeted compounds, is necessary.…”