Under the microscope: microbial life at pore scale under extreme deep-environment conditions.

Microcapillaries are shown to be cheap but attractive alternatives to custom micromodels for the investigation of extremophile motility and tropism under reconstituted in situ conditions. We discuss practicalities and pitfalls of their use in anoxic sample preparation and observation. Widefield transmission and fluorescence microscopy, combined with a simple particle tracking algorithm provide insights into motility and tropism. As an example, mono and co-cultures of Thermodesulfatator atlanticus and Methanocaldococcus villosus are examined at 70 °C and 100 bar under H2:CO2 :: 4:1 (v:v), diluted here in 99 parts N2 to reproduce the standard headspace mixture for culture of methanogens. Surprisingly, despite 36 h incubation under these expected favourable conditions, we observe general mortality of both species, except for vigourous population growth of T. atlanticus at a point a few millimetres from the interface with the headspace. The space-time development of the concentrations of dissolved gases and of the pH are modelled in a numerical solution of the diffusion equations. It predicts quasi-stationary conditions at that particular point during the first ≈ 1/2h of incubation.