Opportunities and limits in imaging microorganisms and their activities in soil microhabitats

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.