Air-drying is sufficient pre-treatment for in situ visualization of microbes on minerals with scanning electron microscopy

Scanning electron microscopy (SEM) is a powerful tool for observing microbe-mineral interactions in situ. Despite its wide usage in geomicrobiology there is no consensus on how the samples should be handled before visualizing in SEM. We compared response of artificial laboratory-grown bacterial community and natural in situ microbes on terrestrial basalt to different sample pre-treatment methods with the aim to preserve microbe-mineral interaction interface. Air-drying was the only method that maintained the location of loosely attached bacteria on a mineral surface, whereas chemical fixation and drying dislocated the cells. On the contrary, chemical fixation preserved the cellular morphology while air-drying caused the collapse of most of the laboratory-grown cells. Natural microbial communities on dry terrestrial basalt were composed of desiccation resistant microbes which remained attached to the surface and partially maintained their morphology regardless of the sample pre-treatment method. None of the tested methods allowed visualization of microbe-mineral interface in a biofilm. We suggest air-drying as a main sample pre-treatment method for visualizing microbes on mineral surfaces when loss of morphology is secondary to potentially dislocated cells and to potential chemical changes in the sample caused by the chemical fixation reagents.