Methods and systems for generating and applying agronomic indices from microbiome-derived parameters

A method for generating agronomic indices and executing one or more actions in response to said agronomic indices at an agriculture site, the method comprising:

• receiving a set of samples associated with the agriculture site;
• generating a sample dataset upon processing the set of samples with a set of sample processing operations comprising spiking the set of samples with a synthetic construct comprising a structure of:
• [16S Forward Primer][ITS Forward Primer][Random Sequence comprising a 16S sequence and an ITS sequence][16S Reverse Complement Primer][ITS Reverse Complement Primer];
• generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset, wherein the set of microbiome-associated features comprises a first subset of taxonomic annotations, a second subset of functional annotations and a third subset of ecological indices, wherein generating the set of microbiome-associated features comprises simultaneously generating absolute concentrations of each bacterial organism and each fungal organism represented in the set of samples, based upon a copy number of the synthetic construct;
• generating values of a set of agronomic indices based upon the set of microbiome-associated features;
• and
• executing an action for improving fertility at the agriculture site, based upon the set of agronomic indices.