Kateri asks: How did organic matter become fossil fuels? As the covering materials pressed down on the carbon-rich organic matter, it was ultimately changed into one of the fossil fuels. The proteins and cellulose break down soon, leaving only “one fraction of organic matter . Natural gas can also be formed biogenically, when special microorganisms, called methanogens, chemically break down organic matter, producing methane. When producing useful natural gas, these methanogens are found in places without oxygen yet near the surface of the earth.