Sorry, but you will have to excuse me...kinda new around here. But I was reef keeping before there was such a thing. Been out a few years and not paying attention to hobby reef keeping.
A lot has changed but a lot has remained the same, most of what worked 10 years ago still works today, with some added tweaks like organic carbon dosing to help proliferate bacteria, which in turn consumes nitrates and some phosphates.
Chasing nitrate with water changes got to be manageable. Manageable for the day, not under 1 mg/l like now.
This where controlled dosing of a carbon source has paid off, we can now easily manage nitrates to whatever level we want. I will add that many of us do not strive for natural reef water levels but have found better success with no3 of around 5.
So the questions. Are not nitrifying bacteria attached to a surface? Do they not consume one thing and release a waste product. I know harvesting algae removes DOM (dissolved organic matter). If we export bacteria are we just getting rid of a very small amount of biomass that could die and end up as DOM?
Yes
Isn't the skimmer to remove DOM before algae or bacteria can get it?
Yes and I guess you can consider a skimmer both a chemical and mechanical filter. I often find uneaten food in my skimmer, I suppose it took a ride up the bubble column.
What bacteria are we trying to export?
The above normal bacterial amount from dosing a carbon source
Is it the bacteria coming from out of those NO3/PO4 munching filters with the synthetic carbon beads that I saw someplace here on RC?
Yes, commonly referred to as bio-pellets, they are a solid carbon source which the bacteria feed on, it is the excess of these bacteria that skimming helps remove, which in turn is a nutrient export. In addition to the pellets people also use vinegar, vodka and at times sugar. Vinegar is probably the most widely used and the dosage is very easy to control.
I never really had yellow water way back when. I had a spot for it, but never really used carbon. I had no way of knowing but I was always afraid carbon would remove something I wanted. Wondered the same about skimmers, but still had to have it.
A big question... what beneficial things are removed with protein skimmers?
Some planktonic life and some trace elements and some salt are removed, with exception to the planktonic life, a simple water change replenishes and helps to correct the rest.
If not for removing beneficial compounds with a PS, would it be best to remove DOM with a skimmer and let the ATS grow as it could find nutrients? And then export algae.
An ATS is a good way to remove some of the buildup although neither the ATS or skimmer does much for buildup of metals that we introduce from feeding, water changes still rule for correcting the levels of metals. The ATS will consume a small percentage of the metals though but the more we feed the more we introduce. It is debatable how much actual toxicity can come from a buildup of trace metals, but I see no real reason to not do water changes.
--John