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.

Diversity of Bacterial Communities in Container Habitats of Mosquitoes

“…The Proteobacteria were the predominant group in our investigation, accounting for 45 (50%) of 90 sequences, consistent with other investigations reporting high prevalence (20-50%) of Proteobacteria in bacterial communities in aquatic habitats [2,3,18] such as seawater [15,33], decaying salt marsh grass [7], and wastewater [7]. In potable water distribution systems, many bacterial species, including members of the Proteobacteria, Actinobacteria, low-G+C-content gram-positive bacteria, and Cytophaga-Flavobacterium-Bacterioides group, readily adhere to surfaces to form multispecies biofilms [39].…”

Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids

“…Rappé et al, (1995) identified 16S ribosomal RNA (rRNA) genes derived from eukaryotic plastids in environmental clone libraries and found considerable diversity. Subsequently, a number of other studies have shown extensive diversity within marine eukaryotic phytoplankton communities using 16S rRNA gene clone libraries (Rappé et al, 1997;Brown and Bowman, 2001;Wilmotte et al, 2002;Fuller et al, 2006;Jardillier et al, 2010). These results indicate that there are also many as-of-yet uncultured phytoplankton taxa, similar to findings from environmental 18S rDNA clone libraries (Moon-van der Staay et al, 2001;Not et al, 2007;Viprey et al, 2008;Shi et al, 2009;Cuvelier et al, 2010).…”

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

“…Protein assimilation was identified in OM27 clade organisms (Supplementary Table S1), which are most closely related to the predatory deltaproteobacterial genus Bdellovibrio (Fuchs et al, 2005) and have a geographically wide distribution (for example, Rappe et al, 1997;Fuchs et al, 2005). The OM27 clade had the highest percentage of OTUs (21%) assimilating protein compared to all other groups in the 0.8-3 μm fraction suggesting their activity was relatively high in this size range (Table 1).…”