In natural soil, plant roots provide an ecological niche for multiple soil microorganisms known as the root microbiota. These microbes develop an intimate association with plants, enhancing plants nutrient uptake, growth and tolerance to pathogens. Indica and japonica are the two major subspecies of cultivated rice (Oryza sativa L.). Indica varieties show a better nitrogen-use efficiency (NUE) compared with japonica varieties in the field, which was contributed by the natural variation of rice NRT1.1B. However, the variations of root microbiota involved in NUE variation between indica and japonica varieties are not yet clear.
Recently, a collaborated team led by Prof. BAI Yang and Prof. CHU Chengcai in the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), examined the variation in the root microbiota within 68 indica and 27 japonica varieties grown in field conditions, and uncovered that indica and japonica varieties recruited distinct root microbiota.
They established a model using a random-forest machine-learning approach, and found that this model can accurately predict indica and japonica varieties in the tested fields, suggesting that the root microbes can serve as a biomarker to distinguish indica and japonica varieties.
It is interesting that indica enriched more bacteria annotated with the function of nitrogen metabolism compared with japonica varieties, indicating that nitrogen transformation is more active in the root environment of indica than japonica varieties.
By comparing root-associated microbiota of wild-type and the nrt1.1b mutant, they found that NRT1.1B was associated with the recruitment of approximate half of indica-enriched bacterial taxa. Notably, the relative abundance of root bacteria that harbor key genes in the ammonification process was defective in root microbiome of the nrt1.1b mutant, indicating that these root microbes may catalyse the formation of ammonium in the root environment.
Using the improved high-throughput protocol to cultivate and identify bacteria, the researchers successfully cultivated more than 70 percent of bacterial species that were reproducibly detectable in rice roots, and established the first systematic rice root bacterial culture collections. Then, they used the gnotobiotic experimental systems with the reconstructed synthetic community (SynCom) and found that indica-enriched SynCom showed a stronger ability to promote rice growth under the supply of organic nitrogen than japonica-enriched SynCom, further suggesting that indica-enriched bacteria may contribute to higher nitrogen-use efficiency in indica rice.
These results not only reveal the relationship between root microbiome and nitrogen use efficiency in rice subspecies, but demonstrate the role of NRT1.1B in establishment of root microbiota. The bacterial culture collections provide a resource for functional research of root microbiota. The research on the interaction between root microbes and rice has laid an important foundation for the application of beneficial microbes in the process of nitrogen utilization and provides a theoretical basis on reducing nitrogen fertilizer in sustainable agriculture.
This study entitled “
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice” has been published online in
Nature Biotechnology on April 29, 2019 (
DOI: 10.1038/s41587-019-0104-4).
This research is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences, the Key Research Program of Frontier Sciences of the Chinese Academy of Science and the National Natural Science Foundation of China.
Contact:
Mr. QI Lei
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
