Picocyanobacteria of the Synechococcus genus are present in all marine environments. This ubiquity is partly explained by the large pigment diversity found within this genus, allowing them to efficiently capture photons over a broad spectral range. Most strains have a fixed pigmentation but some of them are able to match their pigmentation with the ambient light quality by a physiological process called type IV chromatic acclimation (CA4). An original targeted metagenomics approach, combining sophisticated techniques, was developed to study the diversity and distribution of pigment types of Synechococcus in situ. The interest of our approach has been demonstrated after specific optimizations. Availability of 25 new genomes of Synechococcus has allowed us to make significant advances in the understanding of molecular mechanism of CA4. A cluster of 4 to 6 genes, encoding a phycobilin lyase and several transcriptional regulators, is consistently present in all strains capable of this phenotypic plasticity. Two distinct configurations of this cluster, named CA4-A and CA4-B, have been discovered and were found in different Synechococcus lineages. These two types of clusters have undergone distinct evolutionary processes. In addition, some phenotypic peculiarities between strains having these two types of genomic clusters have been demonstrated. This thesis raises new hypotheses about the regulation of this phenotypic plasticity as well as the biochemical mechanisms involved. Keywords : Synechococcus, pigment diversity, genetic diversity, targeted metagenomics, chromatic acclimation
