One of the main differences between soil exposed to chronic use of chemical fertilizers and natural soil is the amount of microorganisms. Previously on farmland, organic matter such as fallen leaves and manure from animals was decomposed into non-organic matter by microorganisms in the soil, and using these natural fertilizers, agricultural produce could be grown. However, chemical fertilizers do not decompose, and are directly absorbed by plants—and without the food provided by organic matter, microorganisms die off. According to Kubo's research, there are quite a few farmlands in Japan where the number of microorganisms is so close to zero to be measured. In soils without microorganisms, plant pathogens and pests breed easily, resulting in a vicious cycle in which more and more pesticide is needed.

For the sake of food safety, it would be ideal to grow healthy vegetables without any chemical fertilizers or pesticides. But if growers begin haphazardly practicing organic agriculture on farmland where such substances have been used for many years, produce will not immediately grow. “To recover material circulation in the soil, it is necessary to increase the number of microorganisms to function as an engine,” says Kubo, who is trying to encourage a recovery in Japanese organic agriculture by applying science with the keyword, microorganisms. Developed by Kubo as an index of fertility in soil is the Soil Fertility Index (SOFIX) which will function as a guide.

To judge the fertility of soil, SOFIX measures the amount of microorganisms and the conditions that facilitate their activity. Kubo first extracted and analyzed environmental DNA (eDNA) from soil and developed a unique technology to quickly and accurately measure the amount of bacteria. This was followed by a study of soil conditions which allow microorganisms to be easily activated. “What is most important for the activity of microorganisms is a balance between carbon and nitrogen which function as their nutrients,” Kubo says. Because microorganisms do not propagate when carbon and nitrogen are input at random, he identified the optimal ratios of carbon to nitrogen. Based on these studies, he developed biological indices to track factors such as the circulation of nitrogen and phosphorus. He then went on to establish a total of 19 indices by combining his biological indices with chemical and physical indices based on conventional analysis. The results of measurements based on these indices are represented in graphs, diagrams, and scores, thereby providing a mechanism for instantaneously diagnosing the level of soil fertility.

Furthermore, Kubo says, “However good organic vegetables are in terms of their health properties, the business model is not sustainable if it increases the burden on farmers,” emphasizing the necessity for business models that involve profitable organic agriculture. He demonstrates that with organic agriculture based on SOFIX, not only will the yield increase, but material costs such as manure can be drastically reduced in comparison to using chemical fertilizers. He also calculates that producers can earn higher profits compared to conventional agricultural methods using chemical fertilizers by selling added-value “Safe and high nutrient” vegetables at higher prices.

To realize this goal, Kubo is currently working on establishing a “SOFIX soil fertility certification” as a means to certify quality agricultural land based on SOFIX. In addition, he is considering developing “Soil consultants”—experts who can analyze the figures obtained from SOFIX and provide advice on improving soil—and establishing a certification system for this purpose.

A major supermarket chain in Shiga Prefecture has started to sell “SOFIX vegetables” grown using SOFIX-based organic agriculture in their stores. The time when “SOFIX vegetables” become popular all over Japan as a safe and secure brand of vegetables is coming closer.