Synchronization primarily acts on gene expression, as evidenced first by studies focusing on individual cell cycle (e.g. dnaA, ftsZ) and photosynthesis related genes (e.g. pcbA, psbA) [12, 13], then more recently at the whole transcriptome level . Under optimal growth conditions, generation times of Prochlorococcus populations are generally around 24 h, though faster growth rates have sometimes been reported . The DNA replication period is usually restricted to the late afternoon and dusk period and cytokinesis occurs during the night [6, 7, 13]. Studying the interplay between energy #Selleckchem Trichostatin A randurls[1|1|,|CHEM1|]# source fluctuations (i.e. changes
in light quantities and/or spectral composition) and cell cycle dynamics of Prochlorococcus is of special interest as it lays the foundation for designing PF01367338 reliable population growth models for this key organism, considered to be the most abundant free-living photosynthetic organism on Earth . As early as 1995, Vaulot and coworkers  noticed that in field populations of Prochlorococcus, the timing of DNA replication varied with depth, with the initiation
of DNA synthesis occurring about 3 h earlier below the thermocline than in the upper mixed layer. At that time, these authors interpreted this delay as a possible protective mechanism to prevent exposure of replicating DNA to the high midday irradiances and especially UV. Since then, a number of studies have shown that Prochlorococcus populations are in fact composed of several genetically distinct aminophylline ecotypes adapted to
different light niches in the water column [16–18]. The upper mixed layer is dominated by the so-called high light adapted (HL) ecotypes (HLI and HLII, also called eMED4 and eMIT9312, respectively), whereas low light adapted (LL) ecotypes (such as LLII and LLIV, also called eSS120 and eMIT9313, respectively) are restricted to the bottom of the euphotic zone [19–22]. These studies also showed that a third ecotype (eNATL), initially classified as a LL clade (LLI), preferentially lived at intermediate depth, reaching maximal concentrations in the vicinity of the thermocline. Comparative genomics revealed that these various ecotypes display a number of genomic differences, including distinct sets of genes involved in DNA repair pathways [3, 23, 24]. For instance, genes encoding DNA photolyases, which are involved in the repair of thymidine dimers, are found in HL and eNATL ecotypes, but not in “”true”" LL strains (i.e., LLII-IV clades). Besides this light niche specialization, a dramatic genome reduction has affected all Prochlorococcus lineages except the LLIV clade, situated at the base of the Prochlorococcus radiation.