Aoki Wataru, Kogawa Masato, Matsuda Shuhei, Matsubara Keisuke, Hirata Shintaro, Nishikawa Yohei, Hosokawa Masahito, Takeyama Haruko, Matoh Toru, Ueda Mitsuyoshi
Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.
Front Microbiol. 2022 Nov 3;13:1024640. doi: 10.3389/fmicb.2022.1024640. eCollection 2022.
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.
促进植物生长的微生物（PGPMs）已引起越来越多的关注，因为它们可能有助于以低投入和可持续的方式提高作物产量，以确保粮食安全。以前的研究试图利用核糖体RNA测序、宏基因组测序和基因组解析宏基因组学来理解根际生态学以及植物与PGPMs之间相互作用的潜在原理；然而，这些方法无法为单个物种提供全面的基因组信息，也不利于对植物-微生物相互作用进行详细分析。在本研究中，我们开发了一种流程，以单细胞分辨率分析水稻根际微生物组的基因组多样性。我们从稻田土壤中分离出微生物细胞，并通过在微流控生成的凝胶胶囊中使用大规模平行全基因组扩增来确定它们的基因组序列。我们在一次实验中成功获得了3237个单扩增基因组，这些基因组序列为稻田生态系统中的微生物功能提供了见解。我们的方法为深入了解微生物在水稻根际微生物组中的作用以及开发用于改良和可持续水稻生产的微生物技术提供了一个有前景的平台。
