Hi James,

Yes, you could use a confocal microscope and the live/dead stains and see what proportion of the cells stain one way or the other. In fact, it doesn't need to be a confocal in particular. I've used a traditional epifluorescent scope with a 100x oil immersion objective and could see how the cells stain. What I've noticed is some cells stain with PI even when they are alive, but that's usually when I incubate them with the dye for too long. You might have some issues because your population will be quite mixed.

Have you considered alternative approaches to determining if the bacteria are live/dead? Yes, most of the bacteria can't be cultured, but quite a number will be on different medias. It's not an ideal experiment, but maybe you could do an in vitro experiment on a mono-culture +/- high pressure, pure oxygen, etc.

Thanks for the reply, Kyler.  I think that the nature of the wastewater being a mixed culture might make it difficult to assess using media but I will look more in to that.  I had considering running a side experiment on a single strain of bacteria in order to confirm my results.  This might be easier to do using standard plate culturing.  

The crux of the whole problem though with the mixed culture is I still want to make sure that the sample viewed in the confocal/light microscope is representative of the whole.