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 r-RNA 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 r-RNA gene lineages that had been discovered previously in clone libraries from opcnocean marine habitats, including the SARI36 cluster (y-Proteobacteria), SAR83, SARll, and SAR116 clusters (all a-Proteobacteria), 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 y and /3 subclasses of the Proteobacteria, including an rDNA lineage within the type 1 methylotroph clade of the p subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of P-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. Information on marine microbial diversity has often been derived from enrichment culture studies (e.g. Baumann et al. 1972). In recognition of the biases implicit in microbiological cultivation techniques, there has been a marked shift to reliance on the cloning and sequencing of 16s ribosomal RNA genes directly from naturally occurring microbial assemblages as a means of assessing microbial diversity (Olsen et al. 1986; Ward et al. 1992; Giovannoni et al. 1995). Although biases associated with the molecular methods applied to microbial ecology are not yet well understood, they appear to be less limiting than those associated with culture-based methods (Ward et al. 1992; Giovannoni et al. 1995). Pelagic ocean habitats were among the first environments to be studied with rRNA gene cloning approaches. This choice was not surprising, since ocean systems are both biogeochemically significant and technically tractable for molecular studies (Giovannoni et al. 1990a; Schmidt et al. 1991). Most such studies have characterized bacterioplankton populations from oligotrophic regions of the open ocean, I Present address: Dept. Marine Sciences, Discovery Hall, Stony Brook, New York 11794-5000. 2 Corresponding author. Acknowledgments We are grateful to Kevin Vergin for comments regarding this manuscript and invaluable technical help. Let Kcrkoff provided us with the nucleic acid sample used in the construction of this clone library, and Doug Gordon aided in the design of probe SAR83R. We are indebted to Volker Huss and Linda Mcdlin for comparisons of our plastid clones to databases of unpublished plastid 16s rRNA gent sequences. WC also thank Terah Wright, Doug Gordon, Ena Urbach, Marcelino Suzuki, and Brian Lanoil for many useful comments. This work was supported by Department of Energy grant FG0693ER61697, a contract from Brookhaven National Laboratory, and the Oregon State Agricultural Experiment Station, of which this is technical paper No. 11,231. including samples from the surface of the Sargasso Sea in the Atlantic Ocean (Giovannoni et al. 1990a; Fuhrman et al. 1993), the surface of the central Pacific Ocean near Hawaii (Schmidt et al. 1991), and at depths of 100 and 500 m in the western California Current (Fuhrman et al. 1993). Additionally, PCR-amplified 16s rDNA were analyzed to compare marine snow-associated bacteria with free-living bacterioplankton collected in seawater from the Santa Barbara Channel off the California coast (DeLong et al. 1993). Two general conclusions have been drawn from these studies: the vast majority of 16s rDNAs retrieved from natural, mixedpopulation bacterioplankton samples do not correspond to the rRNA gene sequences obtained from cultured marine bacteria (Giovannoni et al. 1995); and although phylogenetically diverse, most rDNA clones obtained from oligotrophic open-ocean bacterioplankton communities fall into a few distinct phylogenetic groups (Fuhrman et al. 1993; Mullins et al. 1995; Giovannoni et al. 1996a). Current trends in oceanographic studies emphasize models that treat bacterioplankton as a compartment through which elements and energy flux (reviewed in Ducklow 1994). Typically, such studies measure bacterial processes as community averages, and do not characterize the physiological activity of individual species. These models have great utility and have served well the need to generally establish the relationship between bacterioplankton and other major elements in marine food webs. With the advent of molecular ecology, it has been recognized that bacterioplankton are dominated by a relatively limited subset of phylogenetic groups that are widely distributed and often exhibit clear trends in their vertical distributions in the water column (Mullins et al. 1995; Giovannoni et al. 19966; Gordon and Giovannoni 1996; Field et al. 1997). Data indicate that bacterioplankton communities are relatively structured, but the influence of community structure and dynamics on the re-

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@inproceedings{Rap1999PhylogeneticDO, title={Phylogenetic diversity of marine coastal picoplankton 16s rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina}, author={Michael S. Rap and Paul F. Kemp and Stephen J . Giovannoni}, year={1999} }