Methods and systems for evaluating ecological disturbance of an agricultural microbiome based upon network properties of organism communities

A method for characterization and improvement of an agricultural site, the method comprising:

• receiving a set of agriculture samples from an agriculture site, in association with a perturbation to the agriculture site;
• generating a sample dataset upon processing the set of agriculture samples with a set of sample processing operations that characterize microbial composition of said set of agriculture samples, wherein the set of sample processing operations comprises processing Bayes factors associated with connections between at least one of multiple operational taxonomic units (OTUs) and multiple amplicon sequence variants (ASVs) represented in sequenced nucleic acids from the set of agriculture samples, for use as edge-weights for weighted directed networks;
• generating a set of features upon performing a set of transformation operations upon the sample dataset, wherein the set of features is associated with a set of network properties of organisms of the set of agriculture samples;
• returning an analysis characterizing a status of the agriculture site in relation to the perturbation, upon processing the set of features;
• and
• executing an action for at least one of maintaining and improving the status of the agriculture site, based upon the analysis.