RESEARCH

A wide variety of microorganisms inhabit soil and the rhizosphere, playing a critical role in plant growth and health. Our group aims to diagnose soil health and reduce over 30% of chemical fertilizers in soybean cultivation by utilizing beneficial microbes. This initiative is based on the “AgriSoil Microbiome Atlas”, which we constructed by collecting and analyzing microbial genome data from diverse agricultural soils.
Soybean cultivation is conducted in fields and novel chambers using beneficial microbes and microbial materials selected from the Atlas. At Waseda University, we aim to improve the accuracy of soil diagnosis by comparing the predicted soil health with actual soybean growth. In parallel, we are expanding the Atlas by collecting biological data from soil and culturing soil microorganisms through a microdroplet-based cultivation system in collaboration with the National Institute of Advanced Industrial Science and Technology. Two types of microbial materials are applied: (1) a phosphorus recovery biofertilizer developed by Taiheiyo Cement Corporation, in which phosphate-solubilizing bacteria from Tokyo University of Agriculture and Technology are embedded, and (2) a functional biochar produced by TOWING Co., carrying beneficial microbes selected from the Atlas and capable of substituting for nitrogen, phosphorus, and potassium fertilizers.

Technological innovation has been demanded in order to achieve a sustainable crop production fed the growing human population without generating environmental burdens. The subgroup 5 aims to develop an “Agroecosystem engineering system” that simulate crop production in cyberspace utilizing integrated reduction models with large-scale digital data by field multiomics. The Agroecosystem engineering system integrates weather prediction and soil data to provide the best solution for the farming management practice. The system will allow farmers to produce crops with high yield and high quality without any empirical knowledge and minimize their environmental impacts.

In recent years, the environmental adaptability and long-term sustainability of agricultural production have emerged as critical priorities. To supply high-value agricultural products that remain resilient under diverse and shifting environmental conditions, we must accurately diagnose below-ground processes in each field and moment. Leveraging the extensive knowledge base curated in the Soil Microbe Atlas enables such site-, time-, and environment-specific assessments, allowing producers to implement the most appropriate agronomic strategies.
Our research group on farmland classification by greenhouse-gas (GHG) emissions and standardization of GHG measurement methods tackles this challenge by integrating two key innovations developed in earlier studies: (i) a next-generation cultivation platform capable of precisely controlling every environmental variable, and (ii) an in-situ soil GHG monitoring system. Operating the cultivation platform with intact field soils allows us to quantify GHG dynamics at high temporal resolution, thereby generating robust evidence to guide decisions on the sustainability and environmental compatibility of agricultural practices.
Building on these technical advances, we will collaborate with financial institutions to devise novel business models that harness our evidence-based guidelines, accelerating the adoption of truly sustainable agriculture.

Plants require the three major nutrients (nitrogen, phosphorus, and potassium) for growth, and a lack of these nutrients reduces crop productivity. Plants absorb these nutrients mainly as nitrate, phosphate, and potassium ions. On the other hand, it is well known that excessive fertilization causes eutrophication of water in the environmental. There is also a risk of causing health problems if high concentrations of potassium and nitrate ions remain in crops. Therefore, a simple method is required to measure nutrient ion concentrations in the culture medium and soil during cultivation, as well as nutrient concentrations in crops. Electrochemical measurement using an ion-selective electrode requires no pretreatment, allowing for rapid in-situ measurement and evaluation. Although sensors for nitrate and potassium ions in practical use have already been produced, there are still issues to be solved in terms of sensor strength and stability for continuous measurement in culture medium and soil. On the other hand, phosphate ion sensors have not yet been put to practical use and are still under new development. In the future, we aim to develop a method for measuring nutrient concentrations to make the electrodes stronger, smaller, and more stable over the long term.

The role of our group is to develop crops that can adapt environmental changes. For this objective we will cooperate with groups of soil microbe analysis and essential element utilization including phosphate.
We will propose cultivation conditions to optimize the plants’ abilities to uptake elements and nutrients from fertilizers, prevention from soil diseases, adaptation to environmental changes. We collaborate Waseda University on rhizosphere microbe analysis to identify microbes those affect soybean growth.
We will identify plant genes those are involving in plant-rhizobacteria interaction using soybean isoflavone mutants. By using them we aim to establish soybean with resistance to damage by repeated mono-cultivation and with high breeding value.
We also establish crop breeding foundation with Dr. Wada groups to prepare future environmental changes by using growth chambers with variable environmental conditions.