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Anaerobic decomposition occurs naturally in swamps, bogs, stagnant ponds, deep bodies of water, and waterlogged soils. The bacteria in these places degrade organic matter to the simplest of compounds, which allows the nutrients to be recycled. For example, amino acids degrade to carbon dioxide (CO2), methane (CH4), hydrogen (H2), and small amounts of nitrogen and sulfur compounds.
Digestion of organic matter—in nature as well as in a digester—takes place in three stages. First, aerobic bacteria degrade complex compounds such as starches, proteins, and fibers into smaller carbohydrates or peptides. A second group of bacteria use these compounds as food and produce organic acids as end products of their enzyme reactions. The organic acids all have in common a carboxylic group as part of their structure (COOH). This section of the molecule contains a carbon that is linked both to an oxygen molecule and to an oxygen-hydrogen complex, called a hydroxyl group. Examples of the organic acids produced in this step are acetic acid (two total carbons), propionic acid (three carbons), and butyric acid (four carbons). As a third and final step, anaerobic bacteria use the acids for energy and produce methane, carbon dioxide, and a small amount of other gases (hydrogen, carbon monoxide, hydrogen sulfide, and nitrogen).
Methane cannot solve every environmental problem. For one thing, though methane can be used for making energy, it is also a predominant greenhouse gas that causes global warming. Sustainable wastewater treatment plants help reduce this problem by capturing all the methane emitted by a digester and using it, but methane come from additional sources in the world. Human activities that lead to methane production are waste treatment, biomass burning facilities, energy plants, and landfills. Methane also comes from natural sources: anaerobic soil and water bacteria, some vegetation, fossil fuel deposits such as coal mines and natural gas fields, and certain animals. Scientists have begun to realize in the past decade or so that the animal sources of methane contribute a significant amount of greenhouse gas to the atmosphere.

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