Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell–mineral interface using FIB and TEM

Focused ion beam (FIB) sample preparation in combination with subsequent transmission electron microscopy (TEM) analysis are powerful tools for nanometre-scale examination of the cell–mineral interface in bio-geological samples. In this study, we used FIB-TEM to investigate the interaction between a cyanobacterium (Hassallia byssoidea) and a common sheet silicate mineral (biotite) following a laboratory-based bioweathering, incubation experiment. We discuss the FIB preparation of cross-sections of the cell mineral interface for TEM investigation. We also establish an electron fluence threshold (at 200 keV) in biotite for the transition from scanning (S)TEM electron beam induced contamination build up on the surface of biotite thin sections to mass loss, or hole-drilling within the sections. Working below this threshold fluence nanometre-scale structural and elemental information has been obtained from biotite directly underneath cyanobacterial cells incubated on the biotite for 3 months. No physical alteration of the biotite was detected by TEM imaging and diffraction with little or no elemental alteration detected by STEM–energy dispersive X-ray (EDX) elemental line-scanning or by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of H. byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after 3 months of incubation on its surface.

► Cyanobacteria were incubated on biotite for 3 months in a laboratory.
► TEM cross-sections from the cyanobacteria–biotite interface were prepared using FIB.
► TEM analysis showed no modification of the biotite in these experiments.
► A maximum electron fluence for damage-free focussed probe analysis of biotite was established.