This is an interesting observation and deserves a response. Let’s pretend there are no algae present, only bacteria. You are correct, there is a conflict going on between the aerobic bacteria (those that consume ammonia and nitrites and produce nitrates) and the heterotrophic bacteria (that consume nitrates and produce water and nitrogen gas. From Recirculating Aquaculture, Timmons & Eberling, 2007, the chemical equations for nitrification and denitrification by bacteria are as follows:
1) nitrificationNH4+ + 1.83 O2 + 1.97 HCO3- → 0.0244 C5H7O2N + 0.976 NO3- + 2.90 H2O + 1.86 CO2
2) denitrification0.2 NO3- + 1.2 H+ + e- → 0.1 N2 + 0.6 H2O
These formulas show the following reactants:
HCO3- demonstrates that nitrification removes alkalinity and will cause pH to fall over time;
C5H7O2N is the chemical equation for the bacteria biomass;
e- represents a source of carbon, typically fish feces, but a supplement such as methanol may be required.
It is worth noting that bioflocs (ZEAH systems) contain both types of bacteria, in the soup the shrimp live in. Algae are also present but are not managed in any engineering sense of that word.
Unfortunately, what equation 2) does not show is the intermediate product NH4+, ionized ammonia. This is precisely what equation 1) is trying to remove. So, clearly, the two processes are fighting each other, and since heterotrophic bacteria out-reproduce aerobic bacteria, the heterotrophs will win unless properly managed – preferably, in separate vessels.
Managing these populations so they are in balance is the point of using non-algae filtration methods to perform both of these processes. There are two differential equations (TBD) that define the physical manifestation of at least two filters, one aerobic, the other anoxic. That paper I posted that reports a partial nitrification-denitrification study in Iran successfully solved the problem using glucose as a carbon source in a small laboratory experiment. The challenge, at least for me, is to scale this model up to commercial size, or find someone, such as James Eberling at AST who can.
Now if anyone can design an algae scrubber of commercial scale that can perform both tasks simultaneously, you could go into business manufacturing them, make a fortune selling them to tilapia producers and compete with AST. Their PBF-25 Propeller Washed Bead Filter shown in the mixed-cell raceway plan-view I uploaded sells for a cool $12,578. Tilapia producers nothing; every city in the world with a wastewater treatment facility would be interested in such a filter. That plan, BTW, is for tilapia but is quite suitable for Pacific white shrimp, assuming nitrate can be managed, since nitrates in that plan are consumed by hydroponic lettuce.
Now amwassil, are you saying that you have discovered a species of algae that can directly metabolize ammonia, without any intermediate products? Please post links to papers? Even Dr. Adey in Dynamic Aquaria never made that assertion.