High resolution genetic diversity studies of marine Synechococcus isolates using rpoC1-based restriction fragment length polymorphism

Synechococcus-specific polymerase chain reaction (PCR) primers were developed and used to amplify fragments of the RNA polymerase core subunit gene rpoC1 of a set of 23 marine isolates from different oceanographic locations. Restriction fragment length polymorphism (RFLP) analysis of the PCR products differentiated between most strains and all phylogenetic clades, thus allowing the screening of large sample sets at high genetic resolution. The method was used to analyse changes in the genetic diversity of marine Synechococcus strains through an annual cycle at 100 m depth in the Gulf of Aqaba, Red Sea, and along the depth profile of a sample from June 1999. RFLP analysis of 36 clones of each of the 8 rpoC1 clone libraries screened showed that the Synechococcus population during summer and autumn was dominated by 1 to 3 genetically different clones, while maximum genetic richness was found during spring and winter. Analysis of the depth profile during the period of stratification revealed differences in relative abundance of particular RFLP types among depths (10, 30, 100 m), although the same genotypes dominated the assemblage throughout. Multivariate analysis of environmental variables and Synechococcus assemblage composition showed that Synechococcus genetic diversity was most closely, and significantly, correlated to a combination of temperature and NO3- (P = 0.645, p = 0.038). Phylogenetic analysis of the marine rpoC1 nucleotide sequences of the 40 different RFLP types identified in this study, and all Synechococcus rpoC1 sequences in the databases, demonstrates that the new PCR primers amplify rpoC1 gene fragments from all MC-A and some Cyanobium lineages of marine Synechococcus strains and are also useful for the identification of potentially novel lineages.