The marine cyanobacterium Prochlorococcus is the most abundant photosynthetic 
organism in oligotrophic regions of the oceans. The inability to assimilate 
nitrate is considered an important factor underlying the distribution of 
Prochlorococcus, and thought to explain, in part, low abundance of 
Prochlorococcus in coastal, temperate, and upwelling zones. Here, we describe 
the widespread occurrence of a genomic island containing nitrite and nitrate 
assimilation genes in uncultured Prochlorococcus cells from marine surface 
waters. These genes are characterized by low GC content, form a separate 
phylogenetic clade most closely related to marine Synechococcus, and are located 
in a different genomic region compared with an orthologous cluster found in 
marine Synechococcus strains. This sequence distinction suggests that these 
genes were not transferred recently from Synechococcus. We demonstrate that the 
nitrogen assimilation genes encode functional proteins and are expressed in the 
ocean. Also, we find that their relative occurrence is higher in the Caribbean 
Sea and Indian Ocean compared with the Sargasso Sea and Eastern Pacific Ocean, 
which may be related to the nitrogen availability in each region. Our data 
suggest that the ability to assimilate nitrite and nitrate is associated with 
microdiverse lineages within high- and low-light (LL) adapted Prochlorococcus 
ecotypes. It challenges 2 long-held assumptions that (i) Prochlorococcus cannot 
assimilate nitrate, and (ii) only LL adapted ecotypes can use nitrite. The 
potential for previously unrecognized productivity by Prochlorococcus in the 
presence of oxidized nitrogen species has implications for understanding the 
biogeography of Prochlorococcus and its role in the oceanic carbon and nitrogen 
cycles.