The subject invention provides systems and methods for classifying a microbiome at a geographic site where agricultural activity is, or will be, conducted in order to improve and/or promote agricultural productivity at the site. The subject invention utilizes a large sample set of diverse DNA sequencing input data collected from soil, plant, water and/or air samples, as well as environmental information, to determine relationships between environmental factors and the identities, quantities and distributions of microbial species, taxonomies, and/or groupings thereof, at a chosen site. Machine learning and/or artificial intelligence classifier tools use this information to generate various output data, such as, for example, recommendations for customized soil and/or crop treatment compositions, irrigation practices, and/or other agricultural activity, to enhance plant health and crop productivity at the site.