Check out Trace Genomics [1] for a new company at QB3 that is taking a stab at quantifying what organisms are part of a particular farm's microbiome. They sequence the DNA of everything in a given soil sample, then figure out who's DNA is who's - providing a snapshot of what life is living in that soil. And with enough snapshots, a farmer can actually start to develop a quantitative picture of the web of inhabitants in a given parcel of land. And then act on that information.

[1] https://www.tracegenomics.com