NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

First author: Jingying Zhang; Affiliations: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (中科院遗传学与发育生物学研究所): Beijing, China

Corresponding author: Yang Bai 

Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.

籼稻（indica）品种的氮利用效率要比粳稻（japonica）品种更高。作者通过16S rRNA测序研究了68个籼稻和27个粳稻品种大田条件下的根际微生物情况。作者发现籼稻和粳稻会招募不同的微生物群落。有趣的是，相比于粳稻来说，籼稻根际富集的细菌种类更加多样化，包含更多具有氮代谢功能的细菌种类。利用遗传学的方法，作者的研究显示水稻氮转运和感知基因NRT1.1B与籼稻根际富集细菌的招募相关。代谢组测序显示nrt1.1b突变体根基微生物的氨化过程比野生型少得多。作者从籼稻和粳稻的根上分离纯化到了1079个分离菌株，并人工构建了合成群落（synthetic communities, SynCom）。在籼稻品种IR24上的接种试验显示，相比于粳稻富集的SynCom，接种籼稻富集的SynCom能够在有机氮条件下提升水稻的生长。该研究所建立的植物表型与根际微生物组成之间的关联将有利于未来有关增加作物氮利用的育种策略的制定。

p.s. 拓展阅读：Variation in NRT1.1Bcontributes to nitrate-use divergence between rice subspecies. (Nature Genetics)

通讯：白洋（http://sourcedb.genetics.cas.cn/zw/zjrck/201603/t20160314_4549299.html）

个人简介：2005年，武汉大学，学士；2007年，武汉大学，植物发育生物学硕士；2010年，德国科隆大学，植物发育生物学博士；2011-2015年，德国马克斯普朗克植物育种研究所，博士后，方向：植物根系微生物组学。

研究方向：根系微生物群体在植物抗病，营养吸收，生长发育等过程中的功能和分子机理。

doi: https://doi.org/10.1038/s41587-019-0104-4

Journal: Nature Biotechnology

Published date: April 29, 2019