TY - JOUR
T1 - Massively parallel single-cell genomics of microbiomes in rice paddies
AU - Aoki, Wataru
AU - Kogawa, Masato
AU - Matsuda, Shuhei
AU - Matsubara, Keisuke
AU - Hirata, Shintaro
AU - Nishikawa, Yohei
AU - Hosokawa, Masahito
AU - Takeyama, Haruko
AU - Matoh, Toru
AU - Ueda, Mitsuyoshi
N1 - Funding Information:
This research was supported by JST COI-NEXT (grant number JPMJPF2008), Japan.
Publisher Copyright:
Copyright © 2022 Aoki, Kogawa, Matsuda, Matsubara, Hirata, Nishikawa, Hosokawa, Takeyama, Matoh and Ueda.
PY - 2022/11/3
Y1 - 2022/11/3
N2 - 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.
AB - 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.
KW - bacterial community compositions
KW - comparative genomics
KW - massively parallel single-cell sequencing
KW - microbiomes
KW - rice paddies
UR - http://www.scopus.com/inward/record.url?scp=85142204686&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85142204686&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2022.1024640
DO - 10.3389/fmicb.2022.1024640
M3 - Article
AN - SCOPUS:85142204686
VL - 13
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
SN - 1664-302X
M1 - 1024640
ER -