Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Abstract

The phylogenetic diversity of a continental‐shelf picoplankton community was examined by analyzing 16S ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial‐specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, served as the source of bulk nucleic acids used in this study. A large proportion of the 169 rDNA clones recovered (33%) were related to plastid 16S rRNA genes, including plastids from both chromophyte and chlorophyte algae. Most bacterial gene clones (75% of bacterial clones, 50% of the total) were closely related to rRNA gene lineages that had been discovered previously in clone libraries from open‐ocean marine habitats, including the SAR86 cluster (γ‐Proteobacteria), SAR83, SAR11, and SAR116 clusters (all α‐Proteobaeteria), as well as the marine Gram‐positive cluster (high G+C Gram‐positive). Most of the remaining bacterial clones recovered were phylogenetically related to the γ and β subclasses of the Proteobacteria, including an rDNA lineage within the type 1 methylotroph clade of the β subclass. The abundance of plastid rDNAs and the lack of cyanobacterial‐related clones, as well as the presence of β‐Proteobacteria, are features of this coastal picoplankton gene clone library that distinguish it from similar studies of oligotrophic open‐ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open ocean, can account for most cells in this coastal marine bacterioplankton assemblage.