Suttle, C.A., F. Chen and M.T. Cottrell. 1995. DNA polymerase genes as probes of the diversity and phylogeny of marine microbial populations (invited). Keystone Symposium on Molecular Approaches to Marine Ecology and Evolution, Santa Fe, NM, March 1995; Journal of Cellular Biochemistry 19B (suppl.): 334.
Marine viruses are possibly the most abundant biological entities on earth while bacteria constitute the greatest biomass in the oceans. Despite the ecological importance of marine bacteria and viruses to marine ecosystems and the biosphere, we have only begun to scratch the surface in terms of the structure, diversity and evolutionary relationships among these components. One approach for trying to measure diversity and genetic relatedness among components in marine microbial communities is by sequence analysis of DNA polymerase genes. DNA polymerase genes are excellent candidates for examining genetic and phyletic relationships because they possess highly conserved and variable domains, and occur in all living organisms as well as in many types of viruses. A significant concern when estimating genetic relatedness based on sequence analysis is that differences inferred from a single gene may not accurately reflect the genetic distance among entire genomes. We have examined this question using total genomic DNA hybridization and sequence analysis of DNA polymerase genes to compare genetic similarities among viruses (MpV) which infect a marine photosynthetic flagellate, Micromonas pusilla. These are large double-stranded DNA viruses that are ubiquitous in distribution and which can occur at abundances of >105 ml-1 in natural waters. We examined 8 clonal isolates of MpV obtained from widely separated geographic locations, including the coastal waters of New York, Texas, California and British Columbia, and the central Gulf of Mexico. Restriction fragment digests indicated that each of these clones was genetically different (1). Analysis of genetic relatedness among these viruses using either hybridization of total genomic DNA or sequence analysis of DNA polymerase genes demonstrated that the isolates belonged to a group of closely related viruses, and that the genetic variation among MpV isolated from the same water sample can be as large as the variation among viruses isolated from different oceans. Moreover, sequence analysis showed that viruses which infect M. pusilla are related to morphologically similar viruses which infect other photosynthetic microalgae, namely, Chrysochromulina spp. and Chlorella spp. The hybridization and sequencing methods resulted in similarities between all pair-wise combinations that were well correlated (r = 0.90). These results indicate that DNA polymerase genes provide a good basis for examining the genetic structure and diversity of marine microbial populations. The approach should also be suitable for examining populations of marine bacteria and other organisms.