Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces

Abstract

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.

FIG. 1.

Genetic variability in the 16S rRNA gene, intergenic spacer region (ITS), and GSAT gene in sympatric Antarctic archaea. Asterisks represent a base substitution at residues where sequence variation was observed, relative to the 83A10 sequence. The plus sign indicates an insertion. Numbers at the right indicate the sequence positions (Escherichia coli numbering system) where variation was observed. Clone 19H8 is missing the GSAT gene because the recombinant DNA insert terminates in the ITS. Similarity tables for the 16S rRNA gene, ITS, and GSAT gene are shown at the far right. Fosmid 4B7 from deep temperate Pacific waters is included as an outgroup.

FIG. 2.

Nucleotide (A) and amino acid (B) sequence comparisons of the N terminus of the GSAT gene. The origin of the sequence is shown at the left. Triplets corresponding to amino acids are separated by spaces. Dashes indicate nucleotide residues identical to those of 15G10.

FIG. 2.

Nucleotide (A) and amino acid (B) sequence comparisons of the N terminus of the GSAT gene. The origin of the sequence is shown at the left. Triplets corresponding to amino acids are separated by spaces. Dashes indicate nucleotide residues identical to those of 15G10.

FIG. 3.

Genomic organization in planktonic marine crenarchaeotes. Gene maps for fosmids 4B7 (42) and 74A4 and C. symbiosum A (35) were aligned based on ribosomal 16S and 23S sequences. Homologous regions are connected with lines.