Fluorescence in situ hybridization (FISH) detection of nitrite reductase transcripts (nirS mRNA) in Pseudomonas stutzeri biofilms relative to a microscale oxygen gradient

Microsensor measurements of oxygen were combined with mRNA-targeted fluorescence in situ hybridization (FISH) to relate the expression of nitrite reductase (nirS) to oxygen concentrations in artificial biofilms of the denitrifier Pseudomonas stutzeri. A distinct zone of nirS transcript-containing cells was detected at the oxic–anoxic transition zone, below an oxygen threshold concentration of 0.7–2.5 μM, depending on incubation conditions. Although not a routine technique yet, the possibility of coupling microsensor and mRNA-targeted FISH analyses described here opens for studies addressing microenvironment, identity, and actual activity of microbes in stratified environments at single cell resolution.