Phylogenetic diversity of Synechococcus in the Chesapeake Bay revealed by Ribulose-1,5- bisphosphate carboxylase-oxygenase (RuBisCO) large subunit gene (rbcL) sequences

In order to understand how Synechococcus in the estuarine environment (Chesapeake Bay) are phylogenetically related to other known marine Synechococcus, partial rbcL gene sequences from 25 strains of Synechococcus spp. isolated from estuarine, coastal and oceanic waters were sequenced. The rbcL gene phylogeny showed that Chesapeake Bay Synechococcus isolates together with other marine Synechococcus spp. formed a monophyletic group which belongs to the form IA RuBisCO. All the Chesapeake Bay Synechococcus were able to grow in a wide range of salinity (0 to 30‰), and most of them belong to the Marine Cluster B (MC-B). Interestingly, several phycoerythrin (PE)-containing Synechococcus isolated from the bay were clustered in the MC-B group, which had previously only contained the non-PE Synechococcus. A set of PCR primers was developed to specifically amplify the rbcL gene from natural marine Synechococcus populations. After screening 232 clones randomly selected from 5 clone libraries (built on 5 estuarine samples respectively), at least 7 different rbcL genotypes or the operational taxonomic units (OTUs) were identified. Despite the great genetic diversity among the OTU sequences, they were all clustered with 13 Chesapeake Bay isolates. The distribution frequency of these OTUs varied dramatically from the upper to lower bay. Our results suggest that the Chesapeake estuary provides an ideal environment for the MC-B type Synechococcus populations to thrive. Marine Synechococcus appear to adapt well to various ecological niches, and a clear boundary solely based on phenotypic features may not exist when more and more novel ecotypes and genotypes are unveiled with molecular tools.