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While choosing a substrate for your aquariums, you have to keep in mind various things like water chemistry, well-being of the inhabitants and the aesthetic appeal of the reef tank, which varies accordingly.
It depends on the type of aquarium; you want to keep—fresh water or saline. The primary function of a substrate is to increase the good bacteria. However, they may also have direct affect on the water by releasing certain chemicals and absorbing some.
Aesthetically, the colour of substrates may also affect the over-all environment of your aquarium. Like the dark colour substrates looks good in contrast to the fish and also helps in keeping the fish timid.
Chemically, there are certain substrates which goes only with saltwater and some with fresh water. If you want to increase the pH or hardness of the water, you may use crushed corals or coral sand which contain calcium carbonate. And if you want to mimic soft water, you may use peat or decomposed plant matter. It suitable for demersal (bottom-dwelling) species such as Corydoras catfish. It softens water by acting as an ion changer. It is good for plants and for the reproductive health of fishes, and can even prevent algae growth and kill microorganisms. Peat often stains the water yellow or brown due to the leaching of tannins.
For fresh water tanks, gravel is the most common substrate. To prevent damage to fish, gravels should not be sharp. The size may differ from 1-2mm to a pea-sized. These come in different colours both natural and artificial. Sometimes, they have a polymer coating to prevent affecting water chemistry. These are generally composed of quartz or other lime-free materials.
Sand is often recommended for use with certain species, such as the river stingrays of family Potamotrygonidae, which bury themselves in the fine substrate. However, these species can be successfully kept with coarser substrates as well.
In some aquaria, different substrates are used in different parts of the tank. For example, peat can be used in one corner, while gravel in another portion allows rooted plants.
If you want to go for planted tanks, then go for loose substrates, which would allow the roots of the plants to penetrate deeper. It should be chemically inert and free of sharp edges. Like fine gravel (1-2mm) are preferred by aquarists as dirt tend to stick to the coarser materials which is difficult to clean. The substrate for planted aquariums should be at least 5 cms or 2 inches deep. If you want a lower layer in a smaller tank, it better to use clay, potting soil, peat, and vermiculate which are a source of iron and other elements beneficial for plants.
Another important criterion in planted tanks is Cation Exchange Capacity (CEC) which is the ability to absorb positively charged nutrient ions. So higher the CEC, it is better for the tank. This means the substrate would hold the nutrients and would make them available for the plants. For example Shell grit, crushed limestone, crushed marble, crushed coral skeletons, coral sand, and oolitic aragonite. Since calcium carbonate, the primary component of these substrates, increases water hardness and pH, these are used most often for hard water species.
In breeding tanks, you can use marble as the substrate which would protect the eggs which would fall between the marbles, hence could not be eaten by the parents.
However, quarantine tanks or hospital tanks do not use any substrate. These are kept clean to monitor fish excrements.