Different transcriptional impacts of prophage within the rhizobia-legume symbiosis

Abstract Prophages – viruses that infect and integrate into bacteria - have important effects for their bacterial hosts. These include fitness benefits, for example, through carrying adaptive traits or killing competitors, and costs due to regulatory disruption and cell lysis. Such effects can be dramatic, particularly when the bacterial hosts play key ecological roles, for instance, in pathogens where prophages can drive virulence and rapid adaptation. However, their role in non-pathogens, such as symbiotic bacteria where subtle changes may have outsized effects, has been overlooked. Here, we investigate the impact of carrying a prophage on the nitrogen-fixing symbiont, rhizobia. Rhizobia form symbioses with legumes in the form of root nodules. Their nitrogen-fixing ability has an important role in the transition to sustainable agriculture, potentially reducing the use of inorganic fertilisers. In this study, we show that prophage, vTRX32-1, has different effects on gene expression across two Rhizobium strains while in symbiosis with clover. While in one strain, the phage has no measurable impact whatsoever, in another strain, prophage carriage is associated with significant downregulation of many rhizobial genes, including those involved in nitrogen fixation. Moreover, phage presence has a positive effect on plant biomass at 4 weeks, which decreased slightly after 8 weeks. However, since these results were non-significant, they suggest that phage presence does not significantly affect the performance of the rhizobia-legume symbiosis. This implies that the rhizobia-legume system can be robust even in the face of prophage-induced disruption to cellular regulation.