I want to grow some bacteria in soft agar then collect the bacteria (a lot of it, not just a single colony). This has been done with phage but does anybody know how to do it with bacteria?
It can definitely be done similarly to phages. Just cut out a small agar plug, add some buffer or media, vortex for about a minute, and grow the bacteria overnight in conditions that fit your strain.
But have you thought about just picking a single colony? You’d get the same number of cells either way. The difference is that starting with a single colony gives you a more homogeneous population, which can be useful for some experiments. With a stub, you’ll probably have more variability but mayne that's what you're after.
Is there a reason you can't do this experiment in broth culture instead?
You could consider just spreading the cells instead of using soft agar, then you can easily scrape them off. You are also going to have more equal growth of colonies because in soft agar there will be some variability due to distance from the surface (and oxygen access).
Having said that, you can still just add some buffer and scrape the soft agar and collect it, just as you would with phage. Put in a tube and you might want to let the agar settle down for an hour or so and collect some of the more liquid phase at the top. Most likely you will only need a tiny amount to represent the entire repertoire of colonies that were on the plate (less than 100ul).
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