Massively parallel single-cell genomics of microbiomes in rice paddies

Wataru Aoki*, Masato Kogawa, Shuhei Matsuda, Keisuke Matsubara, Shintaro Hirata, Yohei Nishikawa, Masahito Hosokawa, Haruko Takeyama*, Toru Matoh*, Mitsuyoshi Ueda*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant–microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.

Original languageEnglish
Article number1024640
JournalFrontiers in Microbiology
Publication statusPublished - 2022 Nov 3


  • bacterial community compositions
  • comparative genomics
  • massively parallel single-cell sequencing
  • microbiomes
  • rice paddies

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)


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