Combined metabolomic and genomic analyses reveal phage-specific and infection stage-specific alterations to marine <i>Roseobacter</i> metabolism

Phages can reshape the metabolic network of hosts to support specific requirements for replication during infection. However, metabolomic profiling of phage-elicited host global metabolic alterations and the linkage of phage-encoded auxiliary metabolic genes to these alterations are understudied. In this study, the dynamics of intracellular metabolites of <i>Dinoroseobacter shibae</i> DFL12, a member of marine environmentally and biogeochemically relevant <i>Roseobacter</i> clade, in response to four distinct lytic roseophage infections were investigated. Metabolomic profiling indicated that roseophage infections significantly altered host metabolism in a phage-specific manner. Pathway enrichment analyses showed that the central carbon pathway and DNA, amino acid, and coenzyme metabolism were commonly altered by roseophages, revealing a central role of these pathways in phage replication. Furthermore, clear infection stage-specific host responses were observed, corresponding to different metabolic demands of phage replication in the early and late infection stages. Interestingly, the content of host vitamin B₁, which is the essential nutrient provided by <i>D. shibae</i> to its symbiotic microalgae, increased in the early infection stage for most roseophages, implying that phage infection may impact the symbiosis of <i>D. shibae</i> with microalgae. Finally, combined metabolomic and phage genomics analyses showed that roseophages adopt different strategies to expand the host pyrimidine pool (recycling or <i>de novo</i> synthesis of pyrimidine nucleotides), and this difference was likely related to variation in the GC content between phage and host genomes. Collectively, these results highlight the potential importance of phage-specific and infection stage-specific host metabolic reprogramming in marine phage-host interactions, bacteria-microalgae symbiosis, and biogeochemical cycles.