Long-read metagenomics uncovering the molecular basis underlying plant symbiotic microbiomes

March 27, 2024

Genome sequences of novel microbes have been revealed successively

A joint research group of the RIKEN CSRS, the RIKEN Center for Integrative Medical Sciences, and the University of Tokyo investigated the whole genomic information of plant symbiotic microbiomes using long-read metagenomic sequencing and revealed its molecular basis.

Plants host many symbiotic microbes, some of which are known to be crucial role for plant growth, including those that provide nitrogen and phosphorus to plants and those that inhibit the growth of plant pathogens. However, the microbes’ genetic information essential to exerting these functions is limited. In this study, the research group used a long-read sequencer to perform a metagenomic analysis of symbiotic microbiomes of the rice phyllosphere. About three-quarters of the resulting 16S rRNA gene sequences were from new species. Some sequences were from novel complete chromosome, plasmids, and bacteriophages. The researchers found the Type 4 Secretion System associated with plant-microbiome interactions on the novel plasmids. They also obtained the complete chromosome of a difficult-to-culture bacterium, which elucidated the molecular basis of plant symbiotic microbiomes.

These findings would lead to isolating novel, valuable microorganisms using genome information.

Original article

Communications Biology doi: 10.1038/s42003-024-05998-w

S. Masuda, P. Gan, Y. Kiguchi, M. Anda, K. Sasaki, A. Shibata, W. Iwasaki, W. Suda, K. Shirasu,

"Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing".

Contact

Ken Shirasu; Group Director
Sachiko Masuda; Research Scientist
Plant Immunity Research Group