Analysis of Cyanophage Diversity in the Marine Environment Using Denaturing Gradient Gel Electrophoresis

Abstract

Cyanophages (viruses that infect cyanobacteria) are abundant in the marine environment and are thought to be a significant factor in determining the population dynamics of members of the unicellular phycoerythrin-containing cyanobacteria of the genus Synechococcus. In an effort to use molecular techniques to characterise cyanophage populations, a conserved region from the cyanophage genome was identified in 3 genetically distinct marine cyanomyoviruses and sequence analysis revealed that they exhibited significant similarity to a gene encoding a capsid assembly protein (gp20) from the enteric coliphage T4. Comparison of these sequences permitted the design of PCR primers which specifically amplified a region of 165 bp from cyanomyovirus isolates tested. Denaturing gradient gel electrophoresis (DGGE) was then used to separate 165 bp DNA fragments from a range of different cyanomyovirus isolates which had been PCR-amplified together. DGGE was subsequently used to investigate the population structure of cyanophages during the course of a south-north transect of the Atlantic ocean in April/May 1996. Cyanophage population structure changed dramatically in the surface (7 m) waters across the transect. It was also noted that some DNA fragments in the DGGE analysis were common throughout the transect suggesting that some genetically identical cyanophages have ubiquitous distribution in the surface ocean. DGGE analysis also revealed a high cyanophage diversity through all the depth profiles and changes in population structure were observed with depth. Maximum diversity was invariably correlated to maximum Synechococcus spp. abundances. In some stations where there was a deep mixed layer, cyanophage population structure was similar throughout the water column. In contrast, changes were observed in cyanophage population structure when water column stratification occurred. Environmental factors which shape cyanophage population structure such as nutrient availability, fluctuating light and changing physical conditions are discussed; all of which were measured on the south-north transect of the Atlantic ocean.