Soil health indicators using microbial functional genes

Abstract

In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines 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. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.

1 .(canceled) 
     
     
         2 . A method comprising:
 determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location;   determining a set of measures of a plurality of metabolic pathways of microorganisms present in the soil sample by processing the nucleic acid sequence reads;   determining a plurality of soil health indicators using the set of measures of the plurality of metabolic pathways of microorganisms;   determining oxygen availability at the geographical location as a function of the plurality of soil health indicators;   determining an agricultural intervention for soil at the geographical location based on the oxygen availability; and   providing the agricultural intervention for presentation to a user.   
     
     
         3 . The method of  claim 2 , wherein determining the set of measures of the plurality of metabolic pathways of microorganisms present in the soil sample comprises:
 determining a first measure of aerobic respiration; and   determining a second measure of anaerobic respiration.   
     
     
         4 . The method of  claim 3 , wherein the second measure of anaerobic respiration is associated with denitrification, iron reduction, sulfate reduction, or methanogenesis. 
     
     
         5 . The method of  claim 3 , wherein determining the plurality of soil health indicators comprises:
 determining a ratio of the first measure of aerobic respiration to the second measure of anaerobic respiration.   
     
     
         6 . The method of  claim 2 , wherein determining the plurality of soil health indicators comprises:
 determining a weighted sum of gene counts of the plurality of metabolic pathways.   
     
     
         7 . The method of  claim 2 , wherein each of the plurality of soil health indicators is associated with a different level of soil drainage at the geographical location. 
     
     
         8 . The method of  claim 2 , further comprising:
 determining that the oxygen availability at the geographical location is inversely related to soil clay content of the soil at the geographical location.   
     
     
         9 . The method of  claim 2 , wherein the plurality of metabolic pathways of microorganisms is associated with a plurality of different electron acceptors. 
     
     
         10 . The method of  claim 2 , wherein the agricultural intervention includes one or more of: altered tillage, addition of mineral or organic materials, drainage ditches, tile drainage, and altered irrigation. 
     
     
         11 . 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:
 determine a set of measures of a plurality of metabolic pathways of microorganisms present in the soil sample by processing the nucleic acid sequence reads; 
 determine a plurality of soil health indicators using the set of measures of the plurality of metabolic pathways of microorganisms; 
 determine oxygen availability at the geographical location as a function of the plurality of soil health indicators; 
 determine an agricultural intervention for soil at the geographical location based on the oxygen availability; and 
 provide the agricultural intervention for presentation to a user. 
   
     
     
         12 . The system of  claim 11 , wherein determine the set of measures of the plurality of metabolic pathways of microorganisms present in the soil sample comprises:
 determine a first measure of aerobic respiration; and   determine a second measure of anaerobic respiration.   
     
     
         13 . The system of  claim 12 , wherein the second measure of anaerobic respiration is associated with denitrification, iron reduction, sulfate reduction, or methanogenesis. 
     
     
         14 . The method of  claim 12 , wherein determine the plurality of soil health indicators comprises:
 determine a ratio of the first measure of aerobic respiration to the second measure of anaerobic respiration.   
     
     
         15 . The system of  claim 11 , wherein determine the plurality of soil health indicators comprises:
 determine a weighted sum of gene counts of the plurality of metabolic pathways.   
     
     
         16 . The system of  claim 11 , wherein each of the plurality of soil health indicators is associated with a different level of soil drainage at the geographical location. 
     
     
         17 . The system of  claim 11 , wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
 determine that the oxygen availability at the geographical location is inversely related to soil clay content of the soil at the geographical location.   
     
     
         18 . The system of  claim 11 , wherein the plurality of metabolic pathways of microorganisms is associated with a plurality of different electron acceptors. 
     
     
         19 . The system of  claim 11 , wherein the agricultural intervention includes one or more of: altered tillage, addition of mineral or organic materials, drainage ditches, tile drainage, and altered irrigation.