How do you interpret this microbiology/ bacteriology research figure?
The short answer is that it looks like the colors are meant to represent different, partial copies of the bacterial genome in the process of being synthesized.

When bacteria replicate, they initiate replication at the origins of their chromosomes.  In fact, these origins can be replicated multiple times before it gets to the "end" of the bacterial chromosome (terminus). Looks like the stacking on the right figure shows this, with the colors just aiding in differentiating the partially replicated chromosomes. The coverage plot on the left shows how this might look based on read coverage from deep sequencing (again the colors just show different, partially replicated, chromosomes).