Characterizing soil microhabitats
Soil exhibits heterogeneity at a range of spatial scales. The extreme heterogeneity and interconnectivity of the 3D pore space within soil makes it a unique habitat for the diverse microbial population and has a pivotal role in microbial interactions. Our research focuses on the development of novel techniques to characterize soil at spatial scales that are relevant for micro-organisms.
Fungal hyphae spreading through soil.The physical, chemical and biological heterogeneity of soils is enormous even over small spatial and temporal scales. The soil architecture is generally considered key to soil functioning, yet despite years of research we are still not much closer to linking the soil architecture to function. The opacity of soils has hampered quantification of soil architecture and resulted in a range of destructive techniques to determine average soil properties. At the same time there is increasing evidence that knowledge of the micro-environment of soils holds the key to a more precise prediction of soil ecosystem functioning.
Internal pore network in soilAt the SIMBIOS Centre we address the question what is the effect of soil architecture on the physical, biological and chemical processes?. Our research is at the forefront of the development of X-ray micro-tomography to look inside soils. This technology enables us to quantify pore geometries of undisturbed soil samples, and to asses the effect of soil management on the physical environment at scales that matter to micro-organisms. This offers unrivalled new insights that differ substantially from the approaches to date that treated soils either as a black box within which homogeneity is implicitly assumed, a bundle of capillary tubes with a range of diameters, or a collection of aggregates of different sizes. Our work in this area focuses on further improvements of the technology to obtain higher spatial and temporal resolutions, on the development of protocols to visualize water and organic matter in soils, and to derive rigorous criteria for segmentation of pores space in tomography data.
Current advances in chemical (e.g. micro-focus XRF or NANO-SIMS) and microbiological (e.g. FISH) sciences also offer rich opportunities towards an integrative understanding of soil systems. However, the development of these modern techniques has evolved within separate disciplines. This hampers a holistic approach to the soil system which requires a full integration of physical, biological and chemical methodologies. Perhaps more important, opportunities to apply these techniques simultaneously or combine them with the help of mathematical modelling and statistical techniques are being overlooked. At SIMBIOS we work on novel methodologies to characterise the physical, chemical and biological properties of soil micro-habitats. This includes the development of statistical methods to link 3D non-invasive X-ray CT with 2D destructive techniques such as SEM-EDX (to characterise the chemical environment) or biological thin sections (visualizing microbial distributions within soil microstructures). We will develop these techniques to look at the distribution of carbon in soil. In addition we currently investigate in collaboration with SKYSCAN if novel X-ray CT/ micro XRF scanners can quantify non-destructively the spatial distribution of chemical elements in soil.
Soil Fly Through: Data captured from the CT@SIMBIOS tomography system; scanned at 60 μm resolution. Watch Video
Thresholding tomography data is a major challenge: Download Paper
Microbial distributions in soil: Download Paper