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Front. Environ. Sci. | doi: 10.3389/fenvs.2018.00106

Soil microstructures examined through transmission electron microscopy reveal soil-microorganisms interactions

 Francoise Watteau1* and Geneviève Villemin1
  • 1Université de Lorraine, France

Research over the last few decades has shown that the characterization of microaggregates at the micrometer scale using Transmission Electron Microscopy (TEM) provides useful information on the influence of microorganisms on soil functioning. By taking soil heterogeneity into account, TEM provides qualitative information about the state of bacteria and fungi (e.g., intact state of living organisms, spores, residues) at the sampling date within organo-mineral associations, from the soil-root interface to the bulk soil, and in biogenic structures such as casts. The degree of degradation of organic matter can be related to the visualized enzymatic potential of microorganisms that degrade them, thus indicating organic matter dynamics within soil aggregates. In addition, analytical TEM characterization of microaggregates by EELS (Electron Energy Loss Spectroscopy) or EDX (Energy Dispersive X-rays spectroscopy) provides in situ identification of microbial involvement in the biogeochemical cycles of elements. Furthermore, micrometer characterization associated with other methodologies such as Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) or soil fractionation, enables monitoring both incorporation of biodegraded litter within soil aggregates and impacts of microbial dynamics on soil aggregation, particularly due to production of extracellular polymeric substances. The present focused review suggests that such an approach using micrometer characterization of soil microhabitats provides relevant qualitative and quantitative information when monitoring and modelling microbial processes in dynamics of organo-mineral associations.

Keywords: Bacteria, Microhabitats, in situ localization, soil fractionation, micro-analyses, hotspots of biological activity, EPS

Received: 28 Feb 2018; Accepted: 30 Aug 2018.

Edited by:

Philippe C. Baveye, AgroParisTech Institut des Sciences et Industries du Vivant et de L'environnement, France

Reviewed by:

Hannes Schmidt, Universität Wien, Austria
Kai U. Totsche, Friedrich-Schiller-Universität Jena, Germany  

Copyright: © 2018 Watteau and Villemin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Francoise Watteau, Université de Lorraine, Nancy, 54505, France,