Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages

Abstract

Archaea assemblages from the Arctic Ocean and Antarctic waters were compared by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified using the Archaea-specific primers 344f and 517r. Inspection of the DGGE fingerprints of 33 samples from the Arctic Ocean (from SCICEX submarine cruises in 1995, 1996, and 1997) and 7 Antarctic samples from Gerlache Strait and Dallman Bay revealed that the richness of Archaea assemblages was greater in samples from deep water than in those from the upper water column in both polar oceans. DGGE banding patterns suggested that most of the Archaea ribotypes were common to both the Arctic Ocean and the Antarctic Ocean. However, some of the Euryarchaeota ribotypes were unique to each system. Cluster analysis of DGGE fingerprints revealed no seasonal variation but supported depth-related differences in the composition of the Arctic Ocean Archaea assemblage. The phylogenetic composition of the Archaea assemblage was determined by cloning and then sequencing amplicons obtained from the Archaea-specific primers 21f and 958r. Sequences of 198 clones from nine samples covering three seasons and all depths grouped with marine group I Crenarchaeota (111 clones), marine group II Euryarchaeota (86 clones), and group IV Euryarchaeota (1 clone). A sequence obtained only from a DGGE band was similar to those of the marine group III Euryarchaeota:

FIG. 1.

Locations of Arctic Ocean stations where the samples used in this study were collected. The locations of samples used to generate clone libraries are shown in boldface and larger.

FIG. 2.

DGGE fingerprints of Archaea amplicons. Clone libraries were constructed from the samples marked by arrows and from two other SCICEX 97 samples; however, these samples were not analyzed by DGGE. The numbered boxes indicate bands that were excised for sequencing.

FIG. 3.

Denaturing gradient gel comparing antarctic and arctic samples. The numbered boxes indicate bands that were excised for sequencing.

FIG. 4.

Dendrogram showing similarities of DGGE banding patterns for Arctic Ocean samples shown in Fig. 2. Std, standards.

FIG. 5.

Neighbor-joining trees showing phylogenetic affiliations of representative partial 16S rRNA gene sequences retrieved from Arctic Ocean samples to closely related database sequences. Only one representative from each clone library of sequences that are ≥99% similar is shown; the total number of clones represented by a sequence is given in parentheses. Clones from this study are indicated in boldface. Bootstrap values higher than 50% are shown. The tree is unrooted, and the bar indicates a Jukes-Cantor distance of 0.1. (A) Marine group I Crenarchaeota (positions 536 to 941); clone SB95-72 is used as an outgroup; clusters are named as in reference . (B) Marine group II and IV Euryarchaeota (positions 512 to 937); clone SB95-57 is used as an outgroup.

FIG. 5.

Neighbor-joining trees showing phylogenetic affiliations of representative partial 16S rRNA gene sequences retrieved from Arctic Ocean samples to closely related database sequences. Only one representative from each clone library of sequences that are ≥99% similar is shown; the total number of clones represented by a sequence is given in parentheses. Clones from this study are indicated in boldface. Bootstrap values higher than 50% are shown. The tree is unrooted, and the bar indicates a Jukes-Cantor distance of 0.1. (A) Marine group I Crenarchaeota (positions 536 to 941); clone SB95-72 is used as an outgroup; clusters are named as in reference . (B) Marine group II and IV Euryarchaeota (positions 512 to 937); clone SB95-57 is used as an outgroup.