1. Opportunities and limits in imaging microorganisms and their activities in soil microhabitats
- Author
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Védère, Charlotte, Vieublé-Gonod, L., Nunan, Naoise, Chenu, Claire, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), This work was supported by a grant from the French Agence National de la Recherche, ANR, to project Soilμ-3D (ANR-15-CE01-0006)., and ANR-15-CE01-0006,Soilµ-3D,Propriétés émergentes des fonctions microbiennes dans les sols : Identification de descripteurs spatiaux de la structure du sol à partir de modélisations 3D à l'échelle des habitats microbiens(2015)
- Subjects
soil organic matter ,microhabitat ,microscale ,[SDE]Environmental Sciences ,Soil Science ,microorganisms ,soil characterisation ,Microbiology ,Imaging - Abstract
International audience; 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 visualization 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. 1 This review is structured into several parts in which first imaging methods that are useful for describing the distribution of microorganisms and microbial activities, followed by methods for characterising the physical organisation of the microhabitat and, finally, methods for characterising the distribution of soil chemical features, including soil organic matter, 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.
- Published
- 2022