Obtaining information on genetic capabilities and phylogenetic
affinities of individual prokaryotic cells within natural communities is a
high priority in the fields of microbial ecology, microbial biogeochemistry,
and applied microbiology, among others.  A method is presented here for
prokaryotic in situ PCR (PI-PCR), a technique which will allow single
cells within complex mixtures to be identified and characterized
genetically.  The method involves amplification of specific nucleic acid
sequences inside intact prokaryotic cells, followed by color or fluorescence
detection of the localized PCR product via brightfield or epifluorescence
microscopy.  Prokaryotic DNA and mRNA were both used successfully as targets
for PI-PCR.  We demonstrate the use of PI-PCR to identify nahA
positive cells in mixtures of bacterial isolates and in model marine
bacterial communities.