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Gravel
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Gravel works best for most aquariums. Pea-sized gravel has a larger surface-area-to-volume ratio than marbles. This matters because beneficial bacteria, which help break down fish waste, need lots of surface area to colonize. Smaller gravel or sand tends to get impacted and create dead spaces where less useful bacteria thrive. Pea gravel seems just the right size for most aquarium setups -- not too big and not too small.
Drawbacks of Marbles
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Marbles have two major drawbacks over pea gravel. Marbles have a smaller surface-area-to-volume ratio. This means that they have less surface area for beneficial bacteria to colonize, reducing biological filtration. Additionally, larger particles, like marbles, tend to create gaps where food can get stuck beyond the reach of fish. Uneaten food will rot and foul the aquarium water. You can mix a few marbles in with aquarium gravel, but using them as your only substrate does not work as well as gravel in most situations.
When to Use Marbles
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Marbles do work better than gravel for certain fish-breeding endeavors. Some fish, called egg-scatterers, lay their eggs in open water and allow the eggs to sink to the bottom with no further parental care. In an aquarium with gravel, the adults will usually eat most of their eggs. However, marbles are just the right size to allow gaps to hide the eggs. These gaps keep eggs safe, preventing parents from getting at them. Many small minnows, like the zebra danio, spawn in this fashion.
How Much Substrate
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In addition to selecting your substrate, you also have to know how much to use. In general, you will want 1 to 2 inches of substrate for tanks up to 55 gallons. In larger tanks, you should shoot for 3 to 4 inches of substrate. If you use about 1 1/2 pounds of gravel per gallon, this will give you roughly enough substrate, depending on the shape of your aquarium.
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Marbles vs. Gravel in an Aquarium
You have several options competing to be your aquarium substrate. Gravel and marbles each have specific applications in the home aquarium, and each works best in different situations. In most cases, you'll want to use pea-sized gravel, except in very specific fish tanks.