Nitrogen Cycle

Ammonia (NH3) is not available to plants, but ammonium (NH4+) ion is. To get from ammonia (NH3) to ammonium (NH4+), ammonia (NH3) would need to be transformed (in the 2nd step of aminization process) to NH4+ ion. After NH4+ ion is formed (by aminization) it can either be: (i) taken up by plants or (ii) taken up by soil organisms (eg bacteria), or (iii) adsorbed on exchange complex (ie by negatively charged soil particles), or (iv) transformed back to ammonia (NH3).
Inorganic (or mineral) forms of N are NH4+ and NO3-, while organic forms are various organic compounds that contain N.

In my notes, aminization is the process of protein transforming to R-NH2, and ammonia volatilization is the process of transformation between NH3 and NH4+. But you just mentioned that NH3 transform to NH4+ through aminization. I am a bit confused about these processes. Also, NH3 is not inorganic forms of N?

Ammonia volatilization is the conversion of NH4 to NH3 gas, which is lost to the atmosphere. So it holds that NH3 becomes NH4 via aminization.

Be careful gentlemen. See lecture #25, slide #5 the steps in N mineralization: aminization, ammonification and nitrification. The gaseous loss of NH₃⁺ is volatilization - lecture #26, slide #13.

Another question is one of the bacteria's roles is to decompose organic matter by participation in nitrification process. I don't understand how decomposition of SOM and nitrification are related? Thanks!

or (v) the Ammonium can undergo nitrification to become Nitrate which is the other plant-available form of N

YuhaoZhou, regarding bacteria and nitrification, my understanding is that various types of bacteria play different roles in nitrification:

1) Certain types of decomposing bacteria (and actinomycetes) decompose detritus which contains organic N, storing the N in their bodies (pretty sure as NH2¹). This is aminization.
2) Next, the decomposing bacteria are eaten by protozoa and nematodes, which have lower N requirements than most bacteria, and they excrete the excess N as ammonia (inorganic N), as explained here.
3) Next, this ammonia reacts with H+ or H2O to form NH4 (ammonium). This took me a lot of digging to figure out, I hope it's right.
4) Finally, other types of bacteria (and actinomycetes), called nitrifying bacteria, convert this ammonium to nitrite, then nitrate.

¹Somewhere along the way the NH2 becomes NH3, and according to this page that process is part of ammonification (so is step 3). I'm not sure whether it's within the decomposing bacteria, or within the protozoa and nematodes after they eat the bacteria.

See lecture #25 slide 5 and 6. What we are asking you to understand is the major roles of soil organisms. With respect to bacteria, Mitchell is correct that they are a diverse group of organisms and play a range of roles including decomposition of SOM.

If you are interested in knowing more, you may wish to consider APBI 342 / FRST 310 Soil Biology next year.

Thx! Your answer is so clear!