FIGURES AND TABLES

Figure 1.

Phylogenetic analysis of representative 16S rRNA gene nucleotide sequences from the Gammaproteobacteria clone libraries prepared from samples from mesocosm (coastal) and Northern Atlantic Gyre (open ocean) samples and representative sequences from the NCBI and ARB sequence database. The tree was calculated from a nucleotide alignment of 16S rRNA gene fragments (356 bases) using the neighbour-joining method within ARB, with Jukes–Cantor corrections and a maximum frequency filter (Ludwig et al., 2004). Escherichia coli (accession J01859) was used as outgroup. The confidence of branch points was determined by three separate analyses (maximum likelihood, neighbour-joining, maximum parsimony), with multifurcations indicating branch points that were collapsed using a strict consensus rule until supported in all three analyses. Values of 100 bootstrap replicates (calculated using the neighbour-joining method) are given as numbers at branching points, but those <70 are omitted. Clade OM182 is split into two on this tree (a and b) as the two subclades grouped differently in one of the three methods used, and therefore the branching was collapsed to represent the most stringent consensus branching. The strains that are grouped together in the two OM182 clades are also grouped together into subclades in the phylogenetic analysis of Cho and Giovannoni (2004). Filled triangles indicate clades containing formally described species, and filled circles indicate clades or subclades for which no formally described species is available.

Figure 2.

Denaturing gradient gel electrophoresis (DGGE) analyses of 16S rRNA gene fragments amplified from DNA samples from the Northern Atlantic Gyre and the mesocosm experiments. Details on the primers used for the two- or three-step nested PCR approach are outlined in the text. The sequence identity of the numbered bands is given in the Supplementary data. The abbreviations indicate the target group of the corresponding primers: alpha, Alphaproteobacteria; beta, Betaproteobacteria; gamma, Gammaproteobacteria; Firm, Firmicutes; Plancto, Planctomycetes; Bacter, Bacteroidetes; Cyano, Cyanobacteria; Bac, Bacteria.

Table 1 - Summary of group-specific 16S rRNA gene PCR primers, their specificity towards taxonomic groups as revealed by in silico analysis and the annealing temperatures used in the PCR reactions.

Table 2 - Nested PCR approach with DGGE primers.

Table 3 - Comparison of 16S rRNA gene group-specific primers developed in this study with those used in previous studies by Blackwood et al. (2005) and Nübel et al. (1997) .