Multitrophic impact of viruses from different realms and hosts on rice health and growth

Rice is a major source of food for more than half of the world's population, especially in Asia, and is an important part of the agricultural economy in many countries, providing a source of income for farmers. Firstly, rice viral diseases can lead to a significant decrease in harvest yield. In severe cases, it may even result in total crop failure, posing a threat to global food security. Rice stripe virus (RSV) is transmitted by the small brown planthopper (SBPH, Laodelphax striatellus Fallen) in a persistent and propagative manner. In this study, RNA-Seq was used to analyze the transcriptomic differences between resistant and susceptible rice varieties at different times post RSV infection. Through Gene Ontology (GO) annotation, differentially expressed genes (DEGs) related to transcription factors, peroxidases, and kinases of 2 varieties at 3 time points were identified. Comparing these 2 varieties, the DEGs associated with these 3 GOs were numerically less in the resistant variety than in the susceptible variety. Eighty-seven DEGs involved in some pathways that have a contribution to disease resistance including plant hormone signal transduction and plant–pathogen interactions were identified. Resistance responses regulated by abscisic acid (ABA) and brassinosteroids (BR) were found to be similar for 2 varieties. Fifty-five DEGs in resistant and susceptible varieties at the 3 time points were identified in both PAMP-triggered immunity (PTI) and effector protein triggered immunity (ETI). These findings will provide valuable information for further research on the interactions between rice and RSV, particularly on molecular mechanisms of rice resistance to RSV infection. Secondly, phages that infect nitrogen-fixing bacteria can contribute to plant nutrition, thus impacting rice yield and quality. Phages act to regulate soil microbial community structure. Here, low relative abundance of nitrogen-fixing bacteria was found but Enterobacter-infecting phages were highly present in paddy soil where rice plants showed nitrogen deficiency. A novel virulent phage (named here Apdecimavirus NJ2) was identified infecting several species of Enterobacter. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on comparative genomics and phylogenetic analysis and ICTV demarcation criteria, Apdecimavirus NJ2 could be considered as a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural and sterilized field soil were inoculated with this phage, nitrogen-fixing bacteria and phage, respectively, soil nitrogen-fixation capacity and rice growth were impaired abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded natural soil control and sterilized soil added with nitrogen-fixing bacteria. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Leveraging phages in the soil could be a useful strategy for improving soil nitrogen fixation.