PHYLOGENETIC DIVERSITY OF SUBSURFACE MARINE MICROBIAL COMMUNITIES FROM THE ATLANTIC AND PACIFIC OCEANS

The extent of the diversity of marine prokaryotes is not well known, p rimarily because of poor cultivability. However, new techniques permit the characterization of such organisms without culturing, via 16S rRN A sequences obtained directly from biomass. We performed such an analy sis by polymerase chain reaction amplification with universal primers on five oligotrophic open-ocean samples: from 100-m (three samples) an d 500-m depths in the western California Current (Pacific Ocean) and f rom a 10-m depth in the Atlantic Ocean near Bermuda. Of 61 clones, 90% were in clusters of two or more related marine clones obtained by our selves or others. We report 15 clones related to clone SAR 11 found ea rlier near Bermuda (S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, an d K. G. Field, Nature [London] 345:60-63, 1990), 11 related to marine cyanobacteria, 9 clustered in a group affiliated with gram-positive ba cteria, 9 in an archaeal cluster we recently described (mostly from th e 500-m sample), 4 in a novel gamma-proteobacterial cluster, and 6 in three two-membered clusters (including other archaea). One clone was r elated to flavobacteria. Only the cyanobacteria plus one other clone, related to Roseobacter denitrificans (formerly Erythrobacter longus Oc h114), were within 10% sequence identity to any previously sequenced c ultured organism in a major data base. We never found more than two oc currences of the same sequence in a sample, although four times we fou nd identical sequences between samples, two of which were between ocea ns; one of these sequences was also identical to SAR 11. Overall, the results point to broadly diverse microbial assemblages, with the commo n presence of heretofore phylogenetically undescribed groups.