The last such report I saw pinned lower micronutrient density not on the quality of soils, but on higher atmospheric CO2 concentrations, leading to quicker growth of the plants. Plants in lower concentrations grew more slowly but had relatively more micronutrients for the same mass.
And, for example, there are many trace elements which are not replenished with standard fertilizer.
Selenium is an example here, I think it is the Danish?, which have a law now, forcing it to be added to fertilizer.
Bacteria don't make elements.... although I suppose they could free them from rocks...