The chromobacterium violaceum that affected the child in the video actually is natural in many types of soil, not just lake beds. Infection from this bacteria is even rarer than the amoebic infections that has prompted Pete's concern about the lakes. But yes, it is pretty much all lakes, particularly in warm climates. For good or bad, you need to consider the relative risks for any activity. Certainly more children die each year from car accidents than from infections related to swimming in lakes, but choosing to never ride in a car is not really an option. For many people, lake activities (swimming, water skiing) is something that they choose to do and water skiing can't be done in a pool. If you choose to do these activities with full knowledge of the risks and using what you can to minimize the risk (nose plugs, etc.), that is a personal decision.
