i'm not sure u understand how speciation works. but if given enough time and different environmental constraints, why do u think they can't change into a new species?
actually, it doesnt even need that much time. all that's required is something to happen that makes it so that one group (say the bacteria in this case) can't reproduce with the other
it can be as simple as accidentally creating offspring with double the chromosomes which is what happened with american goatsbeard plant...which is a good example of observable speciation
or if plants arent enough for u, u can look at the apple maggot fly which has been observed to speciate. like i said, literally right in front of ur eyes