A korarchaeal genome reveals insights into the evolution of the Archaea

Abstract

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, "Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.

Fig. 1.

Microscopy of Ca. K. cryptofilum. (A) FISH analysis with Korarchaeota-specific Cy3-labeled oligonucleotide probes KR515R/KR565R. The undulated cell shape results from drying of the specimen on gelatin coated slides before hybridization. (Scale bar, 5 μm.) (B) Phase-contrast image of korarchaeal filaments after physical enrichment. (Scale bar, 5 μm.) (C) Scanning electron micrograph of purified cells. (D) Transmission electron micrograph after negative staining with uranyl acetate displaying the paracrystalline S layer. Cells are flattened, which increases their apparent thickness.

Fig. 2.

Phylogenetic analysis of Ca. K cryptofilum. (A) Maximum-likelihood phylogenetic tree of combined (SSU + LSU) rRNAs rooted with corresponding bacterial sequences. Numbers at the nodes indicate bootstrap support. (B) Archaeal phylogeny based on translation EF2 proteins rooted with bacterial homologs. The numbers indicate bootstrap support for PhyML/consensus posterior probability (Phyloblast), an asterisk indicates <50 support. Where both values were <50, the branch was collapsed. Also see Fig. S6. (C) Maximum-likelihood tree made from aligned sequences of 33 universally conserved ribosomal proteins and the three largest RNA polymerase subunits, RpoA, RpoB, and RpoD. Bootstrap support numbers are given at the nodes as a percentage (n = 10,000). (Scale bars represent the average number of substitutions per residue.)