My narration in this video might have been a little more accurate, so I'll clarify here:
Essentially we are trying to make a protein in B. megaterium fluoresce with GFP, green fluorescent protein. We are doing so by transforming it with a plasmid that gives resistance to Tetracycline, an antibiotic, as well as the desired characteristic. I've noticed that every time I streak out a new plate of this stuff (including the example above) the morphology changes noticably. The bacterial strain of B. megaterium that we are using is very mucoid in a liquid broth, so it seems likely that the non-uniform colonies are due to the bacterium's ability to change it's mucus production in relation to its environment.
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Coming to you from the University of Maryland, College Park.