I have potting soil with a small covering of play sand and flourite (1 year old). I made a stupid mistake and made the substrate too deep, so it's anaerobic in quite a few places. I know this because methane bubbles come out periodically. From what I've read and experienced, these bubbles are harmless. I've lost no fish to them and the bubbling doesn't happen often.
However, I think this needs to be corrected. I'm having a serious algae issue and I haven't been able to balance the tank for a while now.
It's a heavily planted 65g. It's been going for a year now. Fairly heavily stocked, CO2 injected, Finnex Finnray2 (actually 2, but I don't turn the second one on), RO water, Sunsun 302 with inline atomizer.
It's a marginally dirty tank and I believe that the substrate is making it worse. Between the organics and the substrate, I believe I have a nutrient sink. Nitrates stay at a fairly solid 5-10 ppm. If things were moving correctly, I should be adding nitrates.
Should I correct the substrate? If so, I'm tempted to do very small sections at a time. Leave the fish, remove the plants from a small section, scrape the top of the substrate, replace plants. Its the most stress free way for the fish but the danger is allowing the tank to get overwhelmed by organics that will be released. The second method is do it all at once, remove the fish, the plants, scrape, replace the plants and put the fish back in when things have stabilized.