I was told that the use of synthetic ferts will kill microbes, but it will kill them by starving them of organics.
I expect that's largely true--but I think ultimately this has a lot to do with the ionic strength of that solution you're providing. It has to do with how localized all of the nutrients are. Instead of applying something which, through a series of processes and reactions at or near the root, maintains an optimal or near-optimal balance of the proper ionic species for the plant, you are attempting to apply that same "ideal" concentration throughout the entire soil.
A problem with this is that the bacteria's job is to produce these "nutrients" (for the plant) as waste products. As with any organism, a waste product is a waste product for one reason. It is harmful to the organism. There is no nutritive value in it. As you increase the concentration of waste products you are in effect suppressing the metabolism of the bacteria and you are also, for all intents and purposes, bathing it in a sea of it's own shit.
When you think of it from that nuts and bolts physical perspective it's easy to see why this might not be an ideal environment.
Bacteria are the most hardy organism in the world. They live in the salty ocean where hot magma spews from the earth.
That is certainly true of bacteria as a whole, but organism to organism they can be quite frail. Microbiological life in soil strikes a very delicate balance in nature, it is not all that difficult to throw off from the ideal. Humans have been doing it for centuries now.
Edited to add a lot:
I mean just go water some table salt into your lillies for a month and then come back and tell me what the soil analysis looks like in terms of what microbiology is there. The before and after would be striking. At the smallest levels of biological machinery a lot of what is being employed for energy is maintaining a charge differential across membranes.
If one side of a membrane has a higher concentration of cations (+ charge) versus the other side's population of anions (- charge), it can pump cations across that membrane to equalize the charge. The pump itself acts as a motor, (a lot like a hydroelectric power plant actually) which can be turned by the pumping action--imparting some chemical energy so that a molecule of ATP or other such energy rich molecule can be made. Furthermore, many proteins are held together by ionic bridges. These are only stable in solutions of proper ionic strength. This is why it is possible to purify some proteins by a process called "salting out".
At the organic scale (bonding between atoms to form molecules), the whole thing is basically about following the charge. So introducing positive and negative charges has an effect on that, especially if they are being preferentially taken up on one side of the equation (plants mostly gobble up cations).
When you amplify that up to the next level of complexity in unicellular life--it's obvious there is going to be an effect.
