In my opinion there is direct correlation b/w microbial population and crop productivity. Increase in bacterial no. occurs due to decomposition of organic matter. Faster the decomposition, more multiplication of microbes and thus more availability of nutrients and thus benefitting crops.
It is possible that crop yield decline with increasing soil microbial organism. If such trend become progressive at certain stage of crop or growing seasons then need to quantifying the microbial status through molecular sequencing analysis eg, 454-pyrosequencing, Illumina Miseq. particular residue addition in soil can induce or suppress the particular microbial class. Generally C-rich and N-rich residue addition for long term amendment deferentially influence the below ground microbiota, however their magnitude effect can vary with particular microbial taxa. Its better to find the relationship what specific identified taxon directly corroborate with yield response. As my perception, yield reduction with increasing microbial status could be due to suppressing or eliminating the beneficial microbes through alter in their community diversities and taxa abundances, or induction of certain pathogenic genera as common phenomena in soil wild exercise, eg. mono-cropping system . Proliferation or suppression of certain soil microbs under such conditions could directly associate with final harvest output. specific taxa to crop productivity disturbances have not been explored well.