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(1) State analysis of an ecosystem


We perform field research in the target farm or forest land to collect samples. The samples are subjected to high-throughput DNA sequencing to obtain a vast amount of information on the diversity of species. We then mine the datasets by integrating ecology, genomics, informatics, and microbiology and then diagnose the state of an ecosystem and propose appropriate management protocols.

(2) The analysis of the core of an ecosystem


By applying the analytical technologies developed on the basis of network science and machine learning (artificial intelligence) to the above-mentioned ecosystem information, we identify "core species" that play pivotal roles within the target ecosystem. By uncovering the complex interactions among species, we explore the keys to put into practical use a recycling-oriented production system with highly-efficient use of resources.

(3) Identification and utilization as resources of beneficial organisms


We search for biological resources based on the big data of biodiversity and ecosystems. After analyzing a target ecosystem to identify species usable as a biological resource, we find out the optimal conditions for isolation and cultivation of the species on the basis of our accumulated microbiological know-how. Through the development of new biological resources applicable in the fields of agriculture, forestry, fisheries, environment, industry, and drug discovery, we will contribute to the creation of new businesses in line with the SDGs.

Examples of technological application in agriculture and forestry

Healthy soil is necessary for the healthy growth of crops. Conventionally, soil condition has been diagnosed on the basis of analyses of the soil’s chemical or physical properties. However, a more comprehensive assessment system on soil functions is needed to monitor the complex processes occurring in farmland soil and to create a more sustainable food production system.

Here, what plays a key role is information about the myriad of microbial species that inhabit the soil. By analyzing the structure of microbiomes, we can directly assess the soil's state for organisms. At least several thousand species of microorganisms inhabit the soil of a farm. Thus, A DNA analysis of the entire ecosystem provides information on the state of the farmland as if it were being determined by several thousands of sensors or devices.

We have developed a fast and low-cost method for DNA-based profiling of ecosystems, organized databases of soil biomes, and invented advanced diagnostic technology for ecosystems. Through the application of these technologies to agricultural fields, we propose systems for sustainable agriculture, which need minimal amounts of fertilizers, pesticides, and management costs

Kyoto University basic technology example; the analysis of plant-fungus belowground symbiotic networks

Toju et al.(2018) Microbiome 6:116

Plants began to expand on land 400 million years ago. Since then, they have been dependent on symbiotic fungi for the acquisition of water and soil nutrients. Plant roots are inhabited by a variety of mycorrhizal and endophytic fungi, which not only functions as an infrastructure to supply water and phosphorus but also protects the plants from pests and environmental stresses. Evaluating the state of such belowground symbiotic systems enables us to diagnose the health of the soil and to take appropriate countermeasures against possible risks.

Examples of technology applications in aquaculture and aquatic environment

As the demand for protein grows rapidly around the world, there is concern about the depletion of marine resources. Aquaculture is attracting significant attention as a protein production system with high efficiency of resource utilization. In aquaculture, technology of monitoring aquatic ecosystems is expected to play a key role for the stable management of aquaculture systems.

Within an aquaculture system, there exist microorganisms that decompose fish waste and purify water, and microorganisms that live symbiotically in the intestinal tract of fish and play a major role in immunity and acquisition of nutrients including vitamins of the fish. On the basis of high-throughput DNA sequencing, the dynamics and potential functions of the microbiomes can be diagnosed and monitored. The analyses are expected to enable aquaculture systems to be managed efficiently and stably.

Such ecosystem analyses of aquatic environments can be applied to the management of environments such as in lakes, rivers, tidal flats, and inner bays. The state of the aquatic environment is comprehensively diagnosed by analyzing the DNA of fish and plankton as well as that of microorganisms. Depending on the biome states, specific solutions or protocols for environmental restoration and management can be proposed.

Kyoto University basic technology example; analysis of microbiome dynamics in aquaculture tanks

Yajima et al.(2023) Microbiome 11:53

In land aquaculture systems, microorganisms are thought to play an important role not only in water purification, but also in fish growth and disease prevention. The analysis based on a DNA metabarcoding has revealed dramatic shifts in microbiome structure within aquaculture systems. It has also become clear that the structure of the microbiomes significantly affects the activity of the fish being farmed. The technology to integrate information on microbiomes is expected to play a key role in the stable management of aquatic environments.

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