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Re: denitrification and nitrate reduction (technical)


I am a marine biologist, not a microbiologist, but I do have a lot of applicable
physiology and biochemistry.  I freely admit the following discussion is idle 
speculation on my part. :-)

Mark Fisher wrote:
>>> Just like oxygen respiration, denitrification and nitrate/nitrite 
>respiration allows for the complete oxidation of an organic molecule to CO2 and
>>> Whether or not ammonia or nitrogen gas is produced is dependent upon the 
>kinds of bacteria present in the substrate, not the amount of carbon (or 
>whether fertilizer is encased in clay). <<
>Ahh, I think I misunderstood what was told to me. But you are saying 
>that neither reduction process will occur without the presence of the 
>organic (carbon based) molecule? Therefore encasing the fertilizer in 
>clay should delay denitrification until the nitrate diffuses out, 

Perhaps.  But what is to prevent the bacteria from colonizing the 
outside of the clay ball, where they have access to both reduced carbon 
(food) and nitrate, as it slooowly leaches out?  Also, a penetrating 
plant root would just open the flood gates to internal colonization.

Paul Sears' comment about osmocote containing urea is a good one.  
However, I suppose it is also possible the ammonia cleaved from the urea 
could be easily converted to nitrite, where it could then enter into the 
usual denitrification pathway.  As I mentioned before, though, 
denitrification is strongly inhibited by oxygen, so a low-oxygen 
environment may lead to the accumulation of ammonia, in this case.
>I think we will find the production of both ammonia and nitrogen gas 
>occurring for several months in substrates containing organic matter or 
>nitrate fertilizer. My limited experience suggests that the ammonia 
>production occurs mainly in the first month whereas nitrogen gas is 
>produced for several months. Does this make sense? 

Yes, it makes a lot of sense.  Ammonia production yields only one ATP per 
nitrate molecule, while the production of N2 or N2O yields several ATP per 
nitrate.  Denitrification is a "better" long-term metabolic strategy than 
nitrate respiration, as it has a higher energy yield per unit input.  
Plus, as ammonia builds up in the substrate, it may favor the 
proliferation of bacteria who can convert the ammonia into nitrite, and 
into the denitrification pathway.
>You said the kinds of bacteria present determine which product is 
>released. What factors determine which bacterial colonies are favored? 
>Is it purely random?

Many genera of bacteria possess the ability to respire aerobically and 
anaerobically; some of the denitrifyers are quite common, like 
Bacillus, Pseudomonas, and Thiobacillus.  They are on your hands, your 
fish, the filter media, etc. (remember sneezing during your last water 
change?)  In the short-term, I suppose it depends on who gets there 
first (assuming your substrate was sterile to begin with), but in the 
long run, a real mixture could develop.  I also imagine the bacteria 
found at the bottom of the substrate would be quite different from 
those found nearer to the surface.

Fun, eh?