The rhizosphere microbiome of rice

In a field investigation, we found rice plants showing typical symptoms of nitrogen deficiency in a field in Nanjing, Jiangsu Province, China. We collected soil samples in the field for metagenomic sequencing, which showed low relative abundance of nitrogen-fixing bacteria and high relative abundance of phages infecting Enterobacter spp. Then, we isolated and identified a novel virulent phage (named as Apdecimavirus NJ2) in the same field that infects various Enterobacter species. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil by 16S rRNA sequencing.

本研究通过田间调查，在中国江苏省南京市的一处稻田中发现了表现出典型缺氮症状的水稻植株。我们采集该稻田的土壤样本进行宏基因组测序（metagenomic sequencing），结果显示固氮菌（nitrogen-fixing bacteria）的相对丰度较低，而感染肠杆菌属（Enterobacter spp.）的噬菌体相对丰度较高。随后，我们从同一块稻田中分离并鉴定出一株新型烈性噬菌体（novel virulent phage），命名为Apdecimavirus NJ2，该噬菌体可感染多种肠杆菌属物种。将天然田间土壤与灭菌后的田间土壤分别装盆并接种该噬菌体后，与未添加噬菌体的对照稻田土壤相比，土壤固氮能力与水稻生长均受到抑制，肠杆菌属丰度降低，且通过16S rRNA测序分析可知，细菌群落组成与生物多样性均发生改变。