SEM techniques for the bio- and organo-mineral interface characterisation in environmental science

International audienceBacteria, both as planktonic cells or biofilms (group of microorganisms embedded in an exopolymeric matrix in which cells interact with each other) are involved in numerous processes interacting with geological materials, i.e. rocks, soils, minerals… This has led scientists to focus on the effects of such interactions on soils, rocks (for example, biomineralization i.e. synthesis of a mineral by micro-organisms), and their potential applications for industry or environment such as biolixiviation or bioremediation. Microbial-mineral interactions are also now strongly involved in bio-remediation processes. Bioremediation is the decontamination of polluted environments by techniques involving biochemical activity or properties of living organisms. As an example, the ability of biofilms to interact with pollutants or to catch them in their spatial structure can be used for remediation. But in some cases, biofilms can have a negative impact on the bioremediation process (mainly biofouling that inhibits water purification). In this context, part of this work is the evaluation of the interactions of multi-species biofilms with metals (presently iron nanoparticles) and sand, and its impact on depollution processes.The microbial-mineral interface usually requires micrometric or nanometric scale observations; electron microscopy is thus an observation and analysis technique perfectly suited for that. However electron microscopy applied to living samples is faced by numerous technical challenges including the hydrated state of the initial sample, degradation of the sample during drying, freezing... and finally a high sensitivity to electron beam. Thus specific techniques are required for maintaining water or removing it with adapted protocols. We applied conventional, low vacuum and cryo-SEM, STEM-in SEM and TEM techniques for the observation of biofilms involved in bio-remediation processes in interaction with mineral and metallic materials. For this, appropriate procedures and protocols were applied or adapted to address the different problems caused by these specific samples made of a mixture of “soft” hydrated biological samples and “high hardness” mineral particles. These observations enabled to understand the behavior and the internal structure of biofilms in contact with mineral or metallic particles, and the ability of biofilms to fix iron nanoparticles or to bind to sand particles