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The soil microhabitat is a heterogeneous and complex environment where local variations can modulate phenomena observed at the plot scale. Most of the current methods used to describe soil functioning are bulk soil analyses which do not account for fine-scale spatial variability and cannot fully account for the processes that occur under the influence of the 3D organisation of soil. A good representation of spatial heterogeneities is necessary for the parametrisation of new models, which aim to represent pore-scale processes that affect microbial activity. The visualisation of soil at the scale of the microhabitat can be used to extract descriptors and reveal the nature of the relationships between the fine-scale organisation of soil's constituent parts and soil functioning. However, soil imaging techniques tend to be under-used, possibly due to a lack of awareness of the methods or due to a lack of access to the relevant instruments. In recent years, new methods have been developed, and continuously improved, offering new possibilities to decipher and describe soil physical, chemical and biological features of the soil microhabitat in evermore exquisite detail. This review is structured into several sections in which we consider first imaging methods that are useful for describing the distribution of microorganisms and identify them, second the methods for characterising the physical organisation and the chemical attributes of the microhabitat, including soil organic matter and, finally, methods for visualising in situ information on the activities of microorganisms are described. Special attention is given to the preparation steps that are required for the proper use of the methods, either alone or in combination. • Soil heterogeneity at the microscale can be approached with imaging methods. • Imaging methods have developed recently but are under-used for soil microorganisms. • We identified imaging methods suitable to characterise soil micro-habitats. • We addressed imaging limits and challenges raised for soils and microorganisms. • Imaging methods can allow to identify descriptors that account for soil functioning. [ABSTRACT FROM AUTHOR]

As a result of the heterogeneous spatial distribution of microorganisms and substrates in soil and their restricted accessibility, biodegradation occurs mainly in hotspots, such as in the detritusphere, induced by decomposing plant residues. Knowing the characteristics of the volume of soil involved in biodegradation of a given organic substrate will facilitate the understanding and prediction of biodegradation. Our objectives were (i) to identify the volume of soil involved in the biodegradation of plant residues and (ii) to determine to what extent this volume is affected by soil moisture under diffusive conditions by monitoring the mineralization and spatio-temporal evolution of residue C and microorganisms in soil at the microbial habitat scale. We incubated repacked soil cores with a central layer of 13C-labelled maize residues at three different matric potentials (−0.0031, −0.031 and −0.31 MPa). We monitored 13C and total C mineralization, and at different dates over 45 days of incubation, we separated soil slices with increasing distances from the residues and analysed 13C from the residues and the microbial community structure and its activity by PLFA and 13C-PLFA processing. Residue mineralization increased with increasing soil moisture. A detritusphere a few mm thick was rapidly established, with a decreasing gradient of 13C and total PLFAs and 13C-PLFAs away from the residue layer. Most 13C from the residues was located in the first 2 mm of the detritusphere and was not dependent on the matric potential. Residue mineralization seemed to take place mainly on the residues themselves, but increasing residue C was transferred to the surrounding soil with increasing soil moisture. Dry conditions slowed residue C transfer and favoured fungi, but residue mineralization was carried out by both bacteria and fungi. • The size of the maize residue detritusphere was a few millimetres. • Dry soil showed slower residue C transfer than wet soil. • Detritusphere size was hardly impacted by moisture content. • Residue C mineralization occurred mainly on residues rather than in adjacent soil. • Residue-degrading microorganisms in soil differed from total soil microorganisms. [ABSTRACT FROM AUTHOR]