Re: significance of nitrifying bacteria

Hi Shourya!

Great questions... I love plants and the nitrogen cycle.
OK, the first point of confusion that needs to be cleared up concerns the
form of nitrogen assimilated by plants. Plants absorb nitrogen from the
soil in two inorganic forms: ammonium (NH4+) AND nitrate (NO3-). Ammonium
is the preferred form because, as you note, plants use the ammonium ions
directly for the synthesis of amino acids and proteins. However, when
plants absorb nitrate, they must convert the nitrate into ammonium within
the plant cell before it can be used to synthesis amino acids (nitrate is
converted into nitrite within the cytoplasm, and then the nitrite enters
the plastid where it is converted into ammonium, which is then assimilated
to amino acids). So, plants can live happily with either ammonium or
nitrate as their sole source of nitrogen. However, plants compete for
ammonium with certain abundant soil bacteria (Nitrosomonas and Nitrobacter)
that use ammonium in their own metabolism. These bacteria are called
nitrifying bacteria because they convert ammonium to nitrites
(Nitrosomonas) and nitrates (Nitrobacter). This means that, in the soil,
there is often more nitrate than ammonium available for plants. The
nitrification link, I think, is where most of your confusion rests...
plants are not needlessly converting ammonium to nitrate; rather, they have
adapted to be able to utilize the “waste” by-products of ubiquitous soil
bacteria to meet their nitrogen demands. As I said, the plant itself will
only convert nitrates into ammonium ions within the plant body, not within
the soil... they will not convert ammonium into nitrate! So, it seems like
there is probably some misleading information on this website!! Plants can
absorb nitrates, but it needs to be converted to ammonium to be used in
amino acids and protein synthesis. 

Regarding nitrogen turnover in the soil, nitrogen will be returned to the
soil through the decomposing activities of bacteria AND FUNGI. Fungi are
actually chiefly responsible for the decomposition of most plant material,
breaking down tough plant cell walls and releasing the stored nitrogenous
components back into the soil (which is then absorbed by plants, fungi and
bacteria, or transformed by nitrifying bacteria). Certain types of fungi
(the white-rot fungi) are the only organisms on earth that can degrade
lignin, the polymer that makes wood hard.

Lastly, yes, ammonium ions can cause nitrogen toxicity in soils. In
agriculture, ammonium fertilizer is supplied to plants in the form of urea,
and too much urea can be toxic to many organisms. 

I hope this helps resolve some of your confusion!