Some info from a good man T. Wilson reference Growing with Organics and why it will always win for me is in the unknown consequences of synthetics. Note this debate clearly follows the principles of the Microbial Loop theory, but in doing so, also shows the limitation of MLT with regards a whole answer.
the difference between nutrient processing and utilization from a chemical and natural (or organic) standpoint (for want of a better word). The following information and opinion is stated by me and is derived from the citations and links provided. I use the words ‘apparently’ and ‘appears’ because I believe knowledge and science is fluid. I also don’t pretend to understand everything perfectly and may need correcting. Just because we know the Earth is not flat does not mean we know everything about it.
To simplify things I’ll restrict the discussion to the plant’s use of nitrogen (N). The forms of N which plant roots are able to uptake are in ionic form or soluble. These soluble forms of N are ammonium (NH4+) and nitrate (NO3-). Very simply stated these soluble forms of N are instantly available in chemical N and there is no need for any bacterial/archaeal (B/A) mineralization to make them available to the roots of plants. There is some indication that some soluble ammonium is utilized by B/A and mineralized into nitrates, however this appears (to me) somewhat an opportunistic occurrence (from the B/A perspective). So yes we can concur that B/A eats and thrives on some chemically provided ions but this action is not a necessary one for the plant to uptake exactly the same ions as are being consumed by the B/A. In certain circumstances the B/A will be in competition with the plant for these nutrients. So it appears that plants can grow in this fashion without interaction by mineralizing B/A. It appears that the chemically provided ions (soluble N) completely bypass the microbial nutrient cycle.
With natural or organic growing, N ( R-NH2 ) for the plant is contained (sequestered) in a non-soluble (non-ionic) form in organic matter (or in the case of the gardener; compost and other soil foods). It is true that there are certain known bacteria (and now some archaea) which directly fix and supply ionic forms of N to the roots of plants and this is an area where ‘we’ are still learning so all is not known by any stretch. However soil scientists have discovered and it is common knowledge (as knowledge goes) that the bulk of NH4+ and NO3- are delivered to the roots of plants by protozoa (flagellates, amoebae and ciliates). This occurs in a complex network ostensibly, controlled in large degree by the plant. The plant releases compounds from the roots which feed B/A, thereby increasing the B/A population. The B/A consumes/processes forms of R-NH2 or forms which are pre-degraded by fungi and or other B/A. The B/A further multiply with a good supply of food and their large population encourages the excysting (hatching from cysts) and dividing of protozoa. The protozoa prey upon the B/A and in an approximate 30 minute period complete the excretion of NH4+ and/or NO3- available to the roots of the plants. Apparently protozoa only utilize 30 to 40 percent of the nutrient consumed making 60 to 70% available to plants and many have a division cycle of 2 hours so the efficiency of this nutrient delivery system is considerable. Just as it began, the microbial N cycle can be rapidly shut down by chemical emissions from the plant. It is apparent that the nutrient needs of the plant can change within short periods (perhaps in hours). There is much yet unknown, however I hypothesize that even disease control may be effected by a sudden reduction of N in the rhizosphere. This is certainly something which cannot be effectively manipulated by chemical N applications.
My goal in writing this was to illustrate the stark differences between the use by a plant of chemically provided ions and those derived through the microbial nutrient cycle. I believe I have succeeded. There are other ways which plants obtain N, such as through fungal interactions but that is nature; always have a back up.
I did fail to find information detailing the effects of chemical soluble N on protozoa populations. Although we humans have great confidence in our ability to mimic natural molecules sometimes we discover it is the subtle variances going unnoticed which end up having the greatest effects.