Soil health indicators using microbial functional genes

A system comprising:

• a sampling container for obtaining a soil sample from a geographical location;
• a sequencer for determining nucleic acid sequence reads of genetic material in the soil sample from the geographical location, wherein the soil sample is prepared for sequencing of microbes in the soil sample;
• and
• one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
• receive the nucleic acid sequence reads of genetic material in the soil sample from the geographical location from the sequencer;
• identify alignments between reference genes and the nucleic acid sequence reads;
• determine, by processing the alignments between the reference genes and the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
• determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
• determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
• determine measures of a plurality of agronomic attributes of the soil at the geographical location as a function of the first, second, and third sets of measures;
• and
• transmit the measures of the plurality of agronomic attributes for display on a client device.