Inventions provided are designed to improve states of agriculture sites and crops, in relation to agricultural inputs and management practices. Some inventions covered are able to generate agronomic indices and execute actions in response to agronomic indices at an agriculture site. An example method includes receiving samples associated with the agriculture site; generating a sample dataset upon processing the samples with a set of sample processing operations; 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 taxonomic annotations, functional annotations and ecological indices; generating values of a set of agronomic indices based upon the set of microbiome-associated features; and executing an action for producing a desired outcome at the agriculture site, based upon the set of agronomic indices.

Methods and systems 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; 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; generating values of a set of agronomic indices based upon the set of microbiome-associated features; and executing an action for producing a desired outcome at the agriculture site, based upon the set of agronomic indices.