A flow cell simulating a subsurface rock fracture for investigations of groundwater-derived biofilms

Laboratory scale continuous-flow-through chambers (flow cells) facilitate the observation of microbes in a controlled, fully hydrated environment, although these systems often do not simulate the environmental conditions under which microorganisms are found. We developed a flow cell that mimics a subsurface groundwater-saturated rock fracture and is amenable to confocal laser scanning microscopy while allowing for the simple removal of the attached biomass. This flow cell was used to investigate the effect of toluene, a representative contaminant for non-aqueous phase liquids, on groundwater-derived biofilms. Reduced average biofilm biomass and thickness, and diminished diversity of amplifiable 16S rRNA sequences were observed for biofilms that developed in the presence of toluene, compared to the biofilms grown in the absence of toluene. The flow cell also allowed the detection of fluorescent protein-labelled cells.