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.