Re: How does biodegration and bioremediation work?

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.