Diversity of the O-chain biosynthetic cluster in the Pelagibacterales

In this study, we have used single-amplified genomes (SAGs) and long-read metagenomics to examine the intrapopulation diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order. OBCs are notorious for their diversity and have been used to type strains in pathogens and saprophytes, but their patterns of variation in free-living bacteria are little known. We found that, for these major photoheterotrophic bacteria, the diversity is comparable to that of saprophytes, such as Enterobacteriales i.e. nearly each strain carries a different OBC involved in its synthesis. Therefore, different OBCs had completely different gene complements, as they had few ortholog genes. However, although OBC inheritance was largely vertical, the existence of some shared clusters allowed a comparative analysis that showed that the cluster diverges along with the genome, indicative of old horizontal gene transfer (HGT). Only 14 cases of recent HGT were detected and they happened independently of taxonomy or location. Although the O-chain is a major phage receptor in Gram-negative bacteria, the exchange of the complete cluster seems to play a minor role in arms-race evolution. However, dN/dS was significantly larger for the genes in the OBC than for the whole genome so OBC genes appear to be more variable. By long-read metagenomics, we could detect 380 different OBCs in a single sampling site in the Mediterranean. A single population (single species and sample) of the endemic Ia.3/VII genomospecies had a set of 158 OBCs of which 130 were different.