The largest concern that arises from nitrate and phosphate bottoming out is the reduction in the size of bacterial colonies both within the water column and on the rock and substrate itself. When both nitrate and phosphate hit zero, purely photosynthetic organisms that can survive (and indeed thrive) without nitrate and phosphate (such as dinoflagellates or cyanobacteria) will start to take over as the bacterial colonies die off due to starvation, leaving them an easy life with no competition. This will cause a negative feedback loop, where more bacteria die off as the dinos or cyano start to replicate and take over, less bacteria will reduce the amount of natural food corals have available to consume so will reduce their growth (or even starve them), as well as make the tank look very unsightly. This process can be difficult to get under control if not caught early. Dinos in particular (more so than cyano) are a nightmare, and in some cases people have ended up restarting their entire tank to eradicate the problem, or left the hobby altogether due to frustration.
I experienced this first hand when I first got into saltwater tanks, and made the mistake of letting my tank bottom out on nitrate and phosphate. Dinos took over very badly and in a short space of time, and it was a serious battle to get things back under control, but I won the battle by doing this:
- Use Fauna Marin DinoX to eradicate the existing dinos in the tank, and reset to a fresh slate
- Once DinoX treatment complete, and remaining dinos had died, heavily dose bottled bacteria daily to outcompete any new dinos trying to regrow
- Dose nitrate to at least 10ppm and phosphate to at least 0.1ppm to feed the bottled bacteria (water was cloudy due to such an enormous bacterial bloom)
- After a few weeks, slowly stop dosing bacteria and allow the excess bacteria to start naturally die off, ensuring that nitrate was kept to at least 5ppm and phosphate 0.05ppm going forwards to keep the colonies fed
The dinos have since (touch wood!) not reared their ugly head again
I still have to dose my tank with bottled nitrate and phosphate to this day to ensure the levels don't bottom out, and don't see an issue with this. Letting nutrients bottom out, or just get close to 0 without very careful supervision is not a good idea in my opinion.