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Recent analysis of the bioweathering of minerals has highlighted the challenges for investigating the interface between fungi or bacteria and the surface of the mineral that they live on. Transmission electron microscopy (TEM) with its ability to gather imaging information and collect elemental data at high spatial resolution is the ideal technique to analyse such interfaces. Further to this, a dual beam scanning electron and focused ion beam (FIB) microscope is an ideal instrument to prepare specimens for TEM because of its ability to simultaneously cut through hard and soft materials from specific sites of interest. There are however precautions that must be taken when analysing such mineral systems. The electron beam sensitive nature of most sheet silicate minerals means that consideration has to be made as to whether the structure and/or chemistry of the material is being altered during (S)TEM analysis. Here, results from a study of cyanobacteria grown on the surface of biotite are discussed. Particular reference is given to the methods used to determine an electron beam intensity threshold, below which STEM-EDX analysis could be performed without detrimental alteration to the mineral.

Studying the interface between cyanobacteria and biotite mineral surfaces using FIB and TEM