1. Establishment of N₂O detoxification
with root nodule symbiosis
with root nodule symbiosis
2. Detoxification and recycling
of N₂O in upland and paddy soil
of N₂O in upland and paddy soil
3. Construction of the rhizosphere cultivation system for designing and evaluating the soil ecosystem for N₂O recycling
Root nodule symbiosis between rhizobia and legumes can fix atmospheric nitrogen, but it is also known to release N₂O during the late growth stages of legumes. In this project, we will establish symbiosis systems in which N₂O-reducing rhizobia preferentially infect the host leguminous plants, by (i) searching for rhizobia with higher activities of N₂O reduction and establishing new technology to improve their N₂O-reducing activities, and (ii) optimizing host plants that preferentially accommodate N₂O-reducing rhizobia.

Ⅱ-1-b: Optimizing of symbiotic interactions for successful rhizobial inoculation.
Since a wide variety of rhizobia exist in the soil, even if useful N₂O-reducing rhizobia are inoculated, about 80% of the nodules formed on soybean root are occupied by indigenous rhizobia that do not have N₂O-reducing activity. To maximize the N₂O reducing ability of N₂O-reducing bacteria, it is necessary to develop technology to improve the infection prevalence of N₂O-reducing bacteria.
Infectivity of rhizobia is based on "compatibility" between rhizobia and host plants. It is controlled by "effector proteins" that rhizobia inject into host plant cell during infection, and "incompatibility genes" of host plants that recognize specific effectors. Therefore, our group has been studying
1) Breeding soybean cultivars with high compatibility for N₂O-reducing bacteria by searching for and integrating various incompatibility genes of soybean.
2) Selection of strains of N₂O-reducing bacteria with high compatibility to the soybean cultivars described in 1) based on the mechanism of incompatibility system.
The goal of this project is to establish a soybean/rhizobia symbiosis system in which N₂O-reducing bacteria preferentially coexist and express high N₂O-reducing activity.

Ⅱ-1-a: N₂O reduction by strains with higher N₂O reducing activity.
N₂O is generated from agricultural land due to nitrogen fertilization and crop residues, causing global warming. However, N₂O generated from agricultural land can be reduced by inoculating microorganisms such as rhizobia that are able to reduce N₂O. Therefore, we will search for rhizobia with higher N₂O-reducing ability and investigate their behavior in soil.
1) Search for Bradyrhizobium root nodule bacteria with higher N₂O reducing activity.
We are exploring bacterial strains possessing N₂O reductase gene (nos) and high N₂O reducing activity in various soil ecosystems (nodules, soil, rhizosphere, roots).
2) Behavior of N₂O reducing rhizobia in soil.
N₂O is generated from agricultural land due to nitrogen fertilization and crop residues, causing global warming. However, N₂O generated from agricultural land can be reduced by inoculating microorganisms such as rhizobia that are able to reduce N₂O. Therefore, we will search for rhizobia with higher N₂O-reducing ability and investigate their behavior in soil.
1) Search for Bradyrhizobium root nodule bacteria with higher N₂O reducing activity.
We are exploring bacterial strains possessing N₂O reductase gene (nos) and high N₂O reducing activity in various soil ecosystems (nodules, soil, rhizosphere, roots).
2) Behavior of N₂O reducing rhizobia in soil.
Little is known about the behavior of rhizobial survivability in soil when inoculated. Therefore, we are analyzing the dynamics of rhizobia in soil microcosm experiments, and clarify the environmental factors and microbial factors that affect the survivability of inoculated microorganisms. In addition, we will assess the impact of microbial inoculation on soil biodiversity.

Ⅱ-1-b: Optimizing of symbiotic interactions for successful rhizobial inoculation.
Since a wide variety of rhizobia exist in the soil, even if useful N₂O-reducing rhizobia are inoculated, about 80% of the nodules formed on soybean root are occupied by indigenous rhizobia that do not have N₂O-reducing activity. To maximize the N₂O reducing ability of N₂O-reducing bacteria, it is necessary to develop technology to improve the infection prevalence of N₂O-reducing bacteria.
Infectivity of rhizobia is based on "compatibility" between rhizobia and host plants. It is controlled by "effector proteins" that rhizobia inject into host plant cell during infection, and "incompatibility genes" of host plants that recognize specific effectors. Therefore, our group has been studying
1) Breeding soybean cultivars with high compatibility for N₂O-reducing bacteria by searching for and integrating various incompatibility genes of soybean.
2) Selection of strains of N₂O-reducing bacteria with high compatibility to the soybean cultivars described in 1) based on the mechanism of incompatibility system.
The goal of this project is to establish a soybean/rhizobia symbiosis system in which N₂O-reducing bacteria preferentially coexist and express high N₂O-reducing activity.
2021年度
Haruko Imaizumi-Anraku
National Agriculture and Food Research Organization, NARO
Group Leader
⦾ Field of research
Plant-Microbe interactions
⦾ Key Words
Root nodule symbiosis
⦾ Achievements
MINAMISAWA Kiwamu
⦾ Project manager
Tohoku University
Specially-appointed Professor
⦾ Field of research
Soil Microbiology, Plant Microbiology
⦾ Key Words
Bradyrhizobium, Denitrification, Nitrogen fixation
Yasuyuki Kawaharada
Iwate University
Assistant Professor
⦾ Field of research
Plant Microbe Interaction
⦾ Key Words
symbiotic nodulation
Feng Li
National Agriculture and Food Research Organization, NARO
Senior researcher
⦾ Field of research
Plant Breeding and Genetics
⦾ Key Words
NGS analysis, Mutagenesis, QTL analysis, GWAS, Population genetic analysis
⦾ Achievements
Arthur Fernandes Siqueira
Tohoku University
Project Assistant Professor
⦾ Field of research
Environmental Plant Microbiology
⦾ Key Words
Microorganism, Denitrification, Rhizobia
Shin Okazaki
Tokyo University of Agriculture and Technology
Professor
⦾ Field of research
Plant Microbiology
⦾ Key Words
Plant-Microbe Symbiosis, Rhizobia, Soybean, Biofertilizer
⦾ Achievements
Masayuki Sugawara
Obihiro University of Agriculture and Veterinary Medicine
Associate Professor
⦾ Field of research
Applied Microbiology
⦾ Key Words
Plant-microbe interactions, rhizobia
Manabu Itakura
Tohoku University
Project Assistant Professor
⦾ Field of research
Environmental Microbiology
⦾ Key Words
Bradyrhizobium, Denitrification
⦾ Achievements
Kengo Kubota
Tohoku University
Associate Professor
⦾ Field of research
Environmental Bioengineering and Biotechnology
⦾ Key Words
Environmental microorganisms, Wastewater treatment
⦾ Achievements
Ayumi Matsuo
Tohoku University
Assistant professor
⦾ Field of research
Molecular Ecology
⦾ Key Words
Community structure and diversity
⦾ Achievements
Yuichi Aoki
Tohoku University
Assistant Professor
⦾ Field of research
Genome Science、Plant physiology、Bioinformatics
⦾ Key Words
Biological Interaction、Network Biology、Environmental Adaptation
Satoshi Ohkubo
Tohoku University
Project Assistant Professor
⦾ Field of research
Soil Microbiology
⦾ Key Words
Microbial Ecology
⦾ Achievements
Masato Araragi
Iwate University
Project Researcher
⦾ Field of research
Plant molecular biology
⦾ Key Words
Samanthi Wathsala Pelpolage
Obihiro University of Agriculture and Veterinary Medicine
Faculty of Life and Food Science
Postdoc
⦾ Field of research
Applied Microbiology
⦾ Key Words
Rhizobium, Soy bean, Symbiotic incompatibility
Sawa Hara
National Agriculture and Food Research Organization, NARO
Research Fellow
⦾ Field of research
Plant-microbe symbiosis
⦾ Key Words
Microbial Ecology
⦾ Achievements
Hanna Nishida
National Agriculture and Food Research Organization, NARO
Researcher
⦾ Field of research
Plant-microbe symbiosis
⦾ Key Words
Root nodule symbiosis
⦾ Achievements
Hiromi Kato
Tohoku University
Graduate School of Life Sciences
Assistant professor
⦾ Field of research
soil microbiology, microbial ecology
⦾ Key Words
Soil microbiome, Bradyrhizobium, Metagenome
⦾ Achievements
Yoshihisa Suyama
Tohoku University
Professor
⦾ Field of research
Forest Molecular Ecology
⦾ Key Words
Population genetics, Conservation genetics, Genetic diversity
Shota Teramoto
National Agriculture and Food Research Organization, NARO
Researcher
⦾ Field of research
Breeding Science
⦾ Key Words
Root system measurement
⦾ Achievements
Safirah Tasa Nerves Ratu
Tokyo University of Agriculture and Technology
GIR Specially Appointed Assistant Professor
⦾ Field of research
Plant Microbiology
⦾ Key Words
Plant-Microbe Interaction, Rhizobia
To establish the N₂O detoxifying/recycling/absorbing upland and paddy field technology, (i) isolation and characterization of N₂O detoxifying/recycling microorganisms and (ii) functional analysis of N₂O-transforming soil microbial community will be performed.

Ⅱ-2: Detoxification of N₂O by rhizospheric/endohytic microorganisms
Since the Industrial Revolution, atmospheric CO₂ level has raised to 410 ppm, which has induced approximately 1.09 ℃ increasing in the global surface temperature. An environmental-friendly agronomy using the combination of cover crop and no-tillage managements results in a massive CO₂ capture and storage into the soil carbon pools, therefore, it has been expected to mitigate the global warming and climate change. However, the increased soil organic carbon enhances the N₂O emission from soil. Our study is aimed to 1) unveil the microbial process involved in the nitrogen cycle in the field soil managed with the long-term cover crop and no-tillage treatments; 2) obtain high-affinity N₂O-reducing microbes and develop their application in the sustainable crop cultivation.
Endophytic bacteria are derived from diverse soil bacteria, but which are limited to specific bacteria by strong effects of plant such as supply of specific substances from plant and protective responses of plant. Therefore, it is expected that endophytic bacteria with high N₂O detoxification ability can be used sustainably and effectively to N₂O detoxification in crops. In this study, we are searching for endophytic bacteria with high N₂O detoxification ability from the forage crop.

Ⅱ-3: N₂O recycling by N₂O fixing bacteria and iron-reducing bacteria
Recently, we isolated the iron-reducing bacteria from paddy soil, which harbors the potential not only to reduce N₂O but also to convert into organic nitrogen, i.e., to fix N₂O. In this project, we verify the N₂O fixation activity of iron-reducing bacteria and develop basic technology to enhance their N₂O activity in soils. In addition, we work on researches to elucidate the dynamics of N₂O-fixing iron-reducing bacteria in soils based on microcosmic experiments and global trends for diversity of N₂O-fixing microbiome in soils by analyzing soil metagenomic data around the world.

Ⅱ-2: Detoxification of N₂O by rhizospheric/endohytic microorganisms
Since the Industrial Revolution, atmospheric CO₂ level has raised to 410 ppm, which has induced approximately 1.09 ℃ increasing in the global surface temperature. An environmental-friendly agronomy using the combination of cover crop and no-tillage managements results in a massive CO₂ capture and storage into the soil carbon pools, therefore, it has been expected to mitigate the global warming and climate change. However, the increased soil organic carbon enhances the N₂O emission from soil. Our study is aimed to 1) unveil the microbial process involved in the nitrogen cycle in the field soil managed with the long-term cover crop and no-tillage treatments; 2) obtain high-affinity N₂O-reducing microbes and develop their application in the sustainable crop cultivation.
Endophytic bacteria are derived from diverse soil bacteria, but which are limited to specific bacteria by strong effects of plant such as supply of specific substances from plant and protective responses of plant. Therefore, it is expected that endophytic bacteria with high N₂O detoxification ability can be used sustainably and effectively to N₂O detoxification in crops. In this study, we are searching for endophytic bacteria with high N₂O detoxification ability from the forage crop.

Ⅱ-3: N₂O recycling by N₂O fixing bacteria and iron-reducing bacteria
Recently, we isolated the iron-reducing bacteria from paddy soil, which harbors the potential not only to reduce N₂O but also to convert into organic nitrogen, i.e., to fix N₂O. In this project, we verify the N₂O fixation activity of iron-reducing bacteria and develop basic technology to enhance their N₂O activity in soils. In addition, we work on researches to elucidate the dynamics of N₂O-fixing iron-reducing bacteria in soils based on microcosmic experiments and global trends for diversity of N₂O-fixing microbiome in soils by analyzing soil metagenomic data around the world.
2021年度
⦾ Field of research
Soil Science
⦾ Key Words
soil microorganisms, nitrogen cycle, paddy soil, upland soil
Reiko Sameshima-Saito
Shizuoka University
Associate Professor
⦾ Field of research
Soil Microbiology
⦾ Key Words
Denitrification, Microbial community structure, Rhizobia
⦾ Achievements
Tomoyasu Nishizawa
Associate Professor
⦾ Field of research
⦾ Key Words
Soil Nitrogen Cycle, Soil Microbial Analysis、
⦾ Achievements
Yoko Masuda
The University of Tokyo
Postdoctoral fellow
⦾ Field of research
Soil Microbiology
⦾ Key Words
Metagenome/Metatranscriptome/Nitrogen cycle/Iron reducing bacteria
⦾ Achievements
Hideomi Itoh
National Institute of Advanced Industrial Science and Technology
Senior researcher
⦾ Field of research
Soil microbiology
⦾ Key Words
soil microbes, nitrogen fixation, Acidobacteria, animals
⦾ Achievements
Zhenxing Xu
The University of Tokyo
Postdoctoral Fellow
⦾ Field of research
Soil microbiology
⦾ Key Words
anaerobic bacteria, Fe(III) reduction, nitrogen cycle, bacterial taxonomy
⦾ Achievements
Yong Guo
Ibaraki University
College of Agriculture
Researcher
⦾ Field of research
Microbiology
⦾ Key Words
Microbial ecology, Genomics, Microbial interaction
Kazumori Mise
National Institute of Advanced Industrial Science and Technology
Postdoctoral Fellow
⦾ Field of research
Bioinformatics
⦾ Key Words
Soil Microbiology, Metagenomics, Microbial Genomics, Community Ecology
Takashi Narihiro
National Institute of Advanced Industrial Science and Technology (AIST)
Group Leader
⦾ Field of research
Environmental Microbiology
⦾ Key Words
Microbial Ecology, Biological wastewater treatment process
When we encounter something unknown, we try to “observe” it carefully. The well-known phrase “seeing is believing” is undoubtedly applicable to biology. Recent advances in various microscopic imaging techniques using state-of-the-art instruments have enabled novel insights into a wide range of biological processes. In our project aiming at “Cool Earth via Microbes in Agriculture”, there still exist many fundamental questions, for instance, where the N₂O-/CH₄-detoxifying microbes actually reside in the soil structure and how they colonize rhizosphere of plant roots. Revealing these key points under natural conditions should accelerate our project as well as the practical application of these microbes, and microscopy can help it a lot.
In the subject II-4, we will construct a rhizosphere environmental chamber system for in situ imaging analyses of plant-microbe interactions in the soil. The system that is able to reconstitute adequately natural soil ecosystems will be used to investigate, evaluate and optimize greenhouse gas mitigation by synthetic soil-microbe-plant interactions. “Seeing is believing, but sometimes the most real things in the world are the things we can't see (Chris Van Allsburg, The Polar Express)” UNDER THE DARK SOIL. We will make it VISIBLE!
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2021年度
⦾ Field of research
Plant-microbe interaction
⦾ Key Words
Plant immunity, Microbial ecology, Imaging
⦾ Achievements
Atsushi J. Nagano
Ryukoku University
Associate Professor
⦾ Field of research
Transcriptomics
⦾ Key Words
RNA-Seq, Plant, Meteorology
⦾ Achievements
Yasuyuki Nomura
Ryukoku University
Postdoctoral researcher
⦾ Field of research
Ecology
⦾ Key Words
Hybridization
⦾ Achievements
Kazuya Takeda
Research Institute for Food and Agriculture, Ryukoku University
Postdoctoral Researcher
⦾ Field of research
Plant Ecology
⦾ Key Words
Biological Interaction
⦾ Achievements