There's not enough natural means to control the population outbreak. They are doomed sooner or later when the ecosystem (read: aquarium) can't support them anymore.
Would be nice if at least there's some kind of poison that can make older yukkuri die "naturally". It would help to keep the population in check, although it won't be enough if they still grow by the logarithmic scale.
Should be possible. Factory operates on convenient science after all.