The biology and ecology of Synechococcus and their viruses in open oceans have been studied extensively in the past decade. However, little is known about these virus-host systems in the estuarine environment. In this study, Synechococcus spp. isolated from the Chesapeake Bay were characterized in terms of their RuBisCO gene and ITS sequences. Chesapeake Bay harbors unique and diverse Synechococcus spp., which belong to a poorly defined cluster, named marine cluster B (MC-B) Synechococcus. This finding revived the phylogenetic position of MC-B cluster of marine Synechococcus. The estuarine Synechococcus strains can tolerate a much broader range of salinity compared to oceanic Synechococcus spp., suggesting the adaptation of Synechococcus to the dynamic estuarine ecosystem.

Seven cyanophages isolated from four MC-B Synechococcus strains were characterized in terms of their phenotypic and genetic traits. Among the seven MC-B Synechococcus phages, three are podoviruses, three are siphoviruses and one is a myovirus. Six of seven phage isolates did not cross infect any other closely related MC-B Synechococcus strains, indicating the prevalence of highly specific cyanophages for MC-B strains. The podoviruses have significantly shorter latent periods compared to the myo- and siphoviruses. For the first time, photosynthetic gene (psbA) was found in the podoviruses infecting marine Synechococcus. DNA polymerase gene (pol) sequences were obtained from three MC-B Synechococcus podoviruses, and they cluster with all the known podoviruses of marine picocyanobacteria. Viral capsid assembly gene (g20) was found to be conserved among cyanomyoviruses for marine picocyanobacteria.

Synechococcus abundance often exceeded 10 sup 6cells ml sup-1 in summer, and sometimes contributed more than 50% of total phytoplankton biomass and primary production in the Chesapeake Bay. Cyanophage titer ranged from undetectable to over 10 sup 5 MPN ml sup -1 in the Bay. Both Synechococcus abundance and their phage titers varied dramatically in different seasons, and the two co-varied on temporal and spatial scales. No synchronized seasonal succession was seen for population compositions of Synechococcus and cyanomyovirus, suggesting that "kill the winner" module may not apply to polyvalent cyanomyoviruses. Synechococcus and their viruses living in the Chesapeake Bay may develop an ecological strategy different from their oceanic counterparts.