|MadSci Network: Biochemistry|
The basic idea behind biodegradation and/or bioremediation is to find bacteria that are capable of using the pollutant or contaminant as a food source (generally an energy source but it might also be a source of some essential compound like an ammonia compound (nitrogen in the form of NH3) and therefore they will use it up while growing on it. Let's take crude oil as an example. Crude oil is composed of a large number of different molecules. Many of the important ones are long chains of carbons, for example octane (a major component of gasoline) is an 8 carbon chain. Some are even longer. These long chains of carbon are energy sources, it takes much energy to make a long carbon chain and it would release much energy if you break it up. That is why burning gasoline can run a car, there is much energy released in its burning. This same energy can be used by biological systems. Sugars for example are also long carbon chains, generally of 4-6 carbons, and these are very important energy sources for living organisms. In addition to these long linear carbon chains, there are also many branched carbon chains, or even circularized molecules. These circularized ones are called aromatics. Some only contain carbon, others contain sulfur or nitrogen and these are among the leading sources of air pollution from burning gasoline or diesel oil when the sulfur or nitrogen is released. Besides burning these molecules, they could also be chopped up by enzymes and converted to simpler and more common molecules. Any organism needs to have the appropriate enzymes to break down whatever carbon chain it finds. Each enzyme is highly specific for a certain molecule. Virtually all living cells can degrade the sugar glucose, only some can degrade the sugar lactose, etc. Most organisms do not have enzymes can that degrade the longer chained molecules like those found in crude oil, or the aromatic circularized ones. However a few bacteria do have those enzymes. When they have those enzymes they can degrade the molecules found in crude oil by cutting them and converting them to simpler compounds. These are then cut again by other enzymes and eventually converted to a sugar or something similar and used by the bacteria to grow, as an energy source. Usually a number of enzymes (2- 10) are needed to degrade some compound to a simpler form that is considered a normal compound any bacteria could use (like a sugar). As an example, you can find the pathway for degradation of octane at this page: www.lab med.umn.edu/umbbd/oct/oct_image_map.html (In fact this page is found at a very interesting web site that describes in much detail the pathways for the biodegradation of more than 100 compounds www.labmed.umn.edu/umbbd/ After 4 enzymatic steps octane is converted to octanoyl CoA which can be readily used. n-Octane Pseudomonas oleovorans | | | alkane 1-monooxygenase | | v 1-Octanol | | | alcohol dehydrogenase | | v 1-Octanal | | | aldehyde dehydrogenase | | v Octanoate | | | acyl-CoA synthetase | | v Octanoyl-CoA | | | | | v Intermediary Metabolism (KEGG) Although bacteria that can do this are rare, they really aren't very hard to find. It is easy to get them to work in the laboratory. However these bacteria don't work that well in nature. There are a few reasons why. For example, we might isolate a bacteria that can degrade crude oil from a Texas oil well site, but if we try to use it and bioremediate an oil spill in Alaska it won't work because the environmental conditions (notably temperature) are so very different. Many bacteria are highly adapted for a specific environment. The second problem is that other nutrients may be limiting as well and if the bacteria don't grow well they aren't going to degrade things well. Recent advances have shown that adding "fertilizers" in the form of other molecules that allow the bacteria to grow efficiently will significantly improve their biodegradation ability.
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