Use of soil and other environmental data to recommend customized agronomic programs

A method for promoting agricultural productivity at a geographic site using a computer system, the method comprising:

• obtaining a Training Data Set comprising DNA sequencing data derived from soil, plant, water and/or air samples taken from a plurality of geographic sites, wherein said DNA sequencing data provides relative frequencies of taxonomic-indicating and/or function-indicating microbial gene markers in the samples;
• inputting the Training Data Set into an Algorithm Development (AD) module, wherein the AD module comprises an Unsupervised Machine Learning Classifier (UMLC);
• using the UMLC, developing a microbiome classifier model that assigns a microbiome classification to each sample based upon similarities between the relative frequencies of taxonomic-indicating and/or function-indicating microbial gene markers in each sample;
• using the UMLC, assigning a microbiome classification to each sample;
• inputting environmental training data from the samples and microbial test training data from the samples into the AD module;
• using a Supervised Machine Learning Classifier (SMLC), developing a predictive classifier model based on relationships between the assigned microbiome classifications, the environmental training data and the microbial test training data from the samples;
• inputting site-specific prediction data from a specific geographic site into the SMLC and using the SMLC to predict a soil, plant, water and/or air microbiome classification for the specific geographic site, wherein the site-specific prediction data is site-specific environmental data and site-specific microbial test data from the specific geographic site;
• and
• using a Recommendation Engine, correlating the predicted microbiome classification for the specific geographic site, and optionally, additional site-specific environmental data, with an optimal agronomic program for the specific geographic site,
• wherein the optimal agronomic program comprises a list and/or schedule of agricultural activities to conduct, and/or a customized formulation for a soil and/or crop treatment composition to apply, at the specific geographic site, in order to promote agricultural activity at the site.