I think there are two issues: 1) how to get the bacteria necessary to convert ammonia into nitrite, nitrite into nitrate and then potentially even eliminating nitrate (I think maybe in some low oxygen zones); and 2) how to get the variety of really small living things found in a 'normal' reef environment?
With respect to #1, the bacteria is essentially everywhere so, in a tank with organics to process, the bacteria population will grow over time to handle the load. This is what's typically referred to as a tank 'cycling'. The process can be sped up by using bacteria in a bottle or possibly 'seeding' the tank with sand/rock/other things from another tank, but, this gets us to point two.
One of the reasons people like reef tanks is the remarkable biodiversity possible, including organisms you can and cannot see, pods, worms, feather dusters, sponges, etc., etc.. The frustration is that sometimes you're inadvertently adding things you don't want, bubble algae, aiptasia, gorilla crabs, etc., etc. when you're trying to make your tank more 'diverse'.
I'm not sure there is a perfect solution. Adding biodiversity may carry an inherent risk that you'll add some bad with the good. The safest bet may be to find someone with a well established tank that appears to have been free of the most troublesome pests for an extended period of time and ask them for a little rock/sand to seed your tank. Even if no bubble algae or aiptasia have been spotted for years in their tank, it may pop up in your tank because the original tank may have offered it less favorable conditions to thrive, enough to keep it alive but out of sight.
Every time you put something living (or coming from a living environment) in your tank, you may be unknowingly adding new and different critters to your tank, pleasant and unpleasant surprises alike. How much risk you're will to tolerate to try to establish a 'diverse' tank is ultimately up to you.
I think the consensus is that the best way to reduce risk is to quarantine everything, if at all possible. Some living things are far more than an annoyance and can quickly wipe out various fish, corals, invertebrates. Many people do not but, they are accepting a larger risk of problems as a result.
Sorry for the rambling.............
Matt