The geographic impact on genomic divergence as revealed by comparison of nine Citromicrobial genomes

Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus Citromicrobium , widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine Citromicrobium strains isolated from the South China Sea, the Mediterranean Sea or the tropical South Atlantic were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs), involved mainly in type IV secretion systems, flagellar biosynthesis, prophage and integrative conjugative elements, were identified by a fine scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the co-existence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for Citromicrobium members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, ANI, SNPs and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea vs Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences, and allow microbes to evolve through local adaptation. Three Citromicrobium strains isolated from the Mediterranean Sea diverged millions of years ago from other strains, and evolved into a novel group.