Cyanophage host‐derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific

Summary Cyanophages encode host‐derived genes that may increase their fitness. We examined the relative abundance of 18 host‐derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to light and phosphate stress ( psbA , psbD and pstS in T4‐like and psbA in T7‐like), but the proportion of cyanophage with these genes decreased with depth. The proportion of cyanophage with purine biosynthesis genes increased with depth in T4‐like, but not T7‐like cyanophages. No additional host‐derived genes were found in deep T7‐like cyanophages, suggesting that T4‐like and T7‐like cyanophages have different host‐derived gene acquisition strategies, possibly linked to their different genome packaging mechanisms. In contrast to the ETNP, in the oxic North Atlantic T4‐like cyanophages encoded psbA and pstS throughout the euphotic zone. Differences in pstS between the ETNP and the North Atlantic stations were consistent with differences in phosphate concentrations in those regimes. We suggest that the low proportion of cyanophage with psbA within the ODZ reflects the stably stratified low‐light conditions occupied by their hosts, a Prochlorococcus ecotype endemic to ODZs.