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This idea has popped up a couple of times which makes me think I've miscommunicated something. Usually when multiple people have the same mistaken idea it means I have misspokenif indeed the proportions in the water are the same, for example as on rock or in the sump vs the tank, etc.
I'm not suggesting that the quantities of biofilm bacteria are the same in the water as in the biofilm. Or that their ratios are even the same. I expect that each microhabitat has its own, characteristic microbiome, based on what we see in marine microbial ecology.
Fortunately, our goals don't rely on inferring those levels. We're using the water + biofilm data themselves to compare tanks, not trying to infer the levels in other parts of these tanks. I think of this like sampling the blood to learn about the liver. Sure you could take a liver biopsy, but it would be costly and difficult while blood chemistry is relatively easy; draw blood and send it off to the lab.
Does that make any more sense?