SGER: A Method to Genomic Sequence Uncultured Marine Phage

University Of California-San Diego Scripps Inst Of Oceanography, La Jolla CA

Investigators

Abstract

Our understanding of the marine environment was fundamentally changed when it was shown that marine phage (viruses that infect bacteria) are present in extraordinary numbers (ca.1010 per liter). Since this observation, marine microbial ecologists have attempted to incorporate phage into the microbial food web concepts. This work has shown that under various conditions phage account for 12-600% of all bacterial production via lysis. The high number of observable phage and their high production rates have called into question concepts of energy and nutrient cycles in the world's oceans. The observation of large numbers of phage in the ocean also raised two other extremely exciting questions: 1) What type of phage inhabit the marine environment?, and 2) How might phage affect genetic transfer (e.g., transduction or lysogenic conversion) in the marine environment?. Available evidence suggests that marine phage diversity is ten times as great as prokaryotic diversity and like their prokaryotic counterparts, it is believed that each phage will have a unique strategy for surviving and multiplying in the marine environment and these strategies will be reflected in the genes that each phage encodes. The life strategies adopted by phage will in turn help shape the MMFW and the biogeochemical processes of the ocean. Current methods of phage characterization rely on phage morphology, genome size, and host range. However, these approaches are extremely limited in their applicability to environmental samples, primarily because the majority of host are not culturable. Drs. Azam and Rohwer ill attempt to circumvent this problem by sequencing the genomes of uncultured phage. This will be accomplished in three steps. First, phage genomes will be separated from each other using pulse field gels. Second, randomly amplified shotgun libraries (RASLs) will be constructed from the bands isolated from the PF-gels. Finally, the shotgun libraries will be sequenced.