Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean

Abstract

We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to alpha-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to gamma-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria were characteristic of the halocline samples.

FIG. 1.

Location of Arctic Ocean stations where the samples used to generate clone libraries were obtained.

FIG. 2.

DGGE profiles of samples that were used to generate clone libraries. Bands indicated by small letters were assigned to cloned sequences by comparing mobility of PCR-DGGE fragments from clones with bands in the sample. The phylogenetic affiliations of these bands are given in Table 4. DNA from bands enclosed in boxes was sequenced by eluting the fragment and then sequencing it as described in the text.

FIG.3.

Neighbor-joining tree showing the correspondence between DGGE bands and phylogenetic relationships of SAR11 group sequences from the Arctic Ocean. Trees were constructed by using only the portion of cloned sequences interrogated by the primers used in our DGGE analysis (356f to 517r, including primer regions). The trees are unrooted, with E. coli as the out group. The bar indicates a Jukes-Cantor distance of 0.02.

FIG. 4.

Neighbor-joining trees showing phylogenetic relationships of 16S rDNA sequences cloned from Arctic Ocean samples to closely related sequences from GenBank. Clones from this study are indicated in boldface type. Bootstrap values of >50% (of 100 iterations) are shown. The trees are unrooted, with Halobacterium salinarum as the out group. Scale bars indicate Jukes-Cantor distances. (A) α-Proteobacteria; (B) γ-Proteobacteria; (C) all others.

FIG. 4.

Neighbor-joining trees showing phylogenetic relationships of 16S rDNA sequences cloned from Arctic Ocean samples to closely related sequences from GenBank. Clones from this study are indicated in boldface type. Bootstrap values of >50% (of 100 iterations) are shown. The trees are unrooted, with Halobacterium salinarum as the out group. Scale bars indicate Jukes-Cantor distances. (A) α-Proteobacteria; (B) γ-Proteobacteria; (C) all others.

FIG. 4.

Neighbor-joining trees showing phylogenetic relationships of 16S rDNA sequences cloned from Arctic Ocean samples to closely related sequences from GenBank. Clones from this study are indicated in boldface type. Bootstrap values of >50% (of 100 iterations) are shown. The trees are unrooted, with Halobacterium salinarum as the out group. Scale bars indicate Jukes-Cantor distances. (A) α-Proteobacteria; (B) γ-Proteobacteria; (C) all others.