How can gravel be both good and bad?
Deciding whether you want gravel or not :Some things to consider:
Anaerobic bacteria living deep under gravel breathe/respirate gases like nitrates, sulfate, and carbon dioxide in an electron transport chain process, and these gases build up over time. These gases collect under all (deeper than 2cm) gravel. Anaerobic bacteria lack the enzyme to convert oxygen into a viable form so they hate the higher level, oxygenated places. When we disturb the gravel these gases that they are using are released back into the aquarium. This is one possibility for gravel disturbance followed by sudden floaty fish. Anaerobic bacteria that live under gravel hate oxygen, they literally live in fear of it because it causes their death. By churning the gravel vigorously we expose many of these bacteria to oxygen and they die. They release gases as they die too. These are the twin processes of sulfate reduction and bacterial fermentation. While alive these bacteria can however play a small role in absorbing nitrates and nitric compounds. The surface of gravel also houses aerobic beneficial bacteria who attach to the surface stones and assist with the nitrogen cycle by converting ammonia and nitrites to nitrates.
About Anaerobic bacteria:
1. Hundreds of thousands of bacteria live in a space the size of the period at the end of this sentence .
2. Bacteria have an average life span of only 20 minutes. This means that during this time every single bacterium must replicate/reproduce every minute. In that gravel there are probably trillions of millions of billions. Each one reproducing by cell transfer and binary fission- trillions and millions more every second.
3. When they reproduce, each one reproduces the amount of bacteria the size of a sugar lump.
Some of them are motile, they move up through the water. Most like the dark recesses of deep gravel. Its ideal for breeding. Dark, wet and undisturbed.
Beneficial aerobic bacteria live in the very top 2cms of the gravel bed.. the maximum amount of gravel that can hold beneficial bacteria is 1/4 of an inch. As said above, these gravel surface bacteria assist with the nitrogen cycle by converting harmful ammonia and nitrite to nitrate. The bacteria deeper down then utilize the end product nitrates. EVERY bacterium and larval parasitic form beneath that top layer is potentially a bad one. Bacteria that cause ulcer disease for example and parasites like flukes that sink in under stones and can stay encysted for some time completely untouched by meds under gravel.
What happens when they run out of their supply of respiratory gases?
It sometimes happens that the anaerobic bacteria's supply of gases is used up. The fish have not been fed for some time. Or perhaps there is an algae crash etc. At this time you will smell a rotten egg smell in the tank which is the sulfate reduction process- a sort of decomposition or fermentation of the bacteria. There can even be a sprinkling of black dust visible at this point.
Brown rust or "algae"...is zinc oxide a derivative of iron in the water. It isn't dangerous- just unsightly.As the water settles some of the trace elements are leached out of the water - they are then processed and can be re-assimilated by any plant or algae life. When you have gravel for the first few months you may see these deposits coloring your gravel. White gravel may look soiled. These oxides compete for oxygen with green algae and so must be removed to promote green algae (which takes about 4-6months under average lighting).
Iron, manganese and some other of the trace elements are only water soluble for a short time. They oxidise in the presence of oxygen, then precipitate and are assimilated via plant matter. A perfectly balanced water will also hold the elements longer and you will rarely see zinc oxide in a well established tank that has a perfect water balance. You should find that as your water stabilises the zinc oxide will decrease. Some will be re-assimilated. Light (turning the gravel regularly) and oxygen will help your gravel stay white.
In the end, choosing to have gravel or not should be a personal aesthetic and informed choice. On the one hand while anaerobic bacteria can be an endless source of worry and disease in some tanks where aeration is low and gravel deep, for people whose source water has a low kH/gH, gravel it can be useful. It can be mixed for example with coral which releases minerals into the water that stabilize pH. The top surface area of gravel can also house quite a number of good cycling bacteria. And fish do get some exercise and fun from turning and sniffing at gravel perhaps. It also looks pretty when kept well.