title: Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.
abstract: Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, and ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although they were syntenic, overlapping a- and b-type ribotype genomes harbored significant variability. A single tiling path comprising the dominant a-type genotype was assembled and used to explore the genomic properties of C. symbiosum and its planktonic relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from previously sequenced genomes. The remaining genes partitioned between functional RNAs (2.4%) and hypotheticals (42%) with limited homology to known functional genes. The latter category included some genes likely involved in the archaeal-sponge symbiotic association. Conversely, 525 C. symbiosum ORFs were most highly similar to sequences from marine environmental genomic surveys, and they apparently represent orthologous genes from free-living planktonic Crenarchaeota. In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives.
authors.affiliation: Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.forename: Konstantinos T
authors.initials: KT
authors.lastname: Konstantinidis
authors.forename: Nik
authors.initials: N
authors.lastname: Putnam
authors.forename: Christa
authors.initials: C
authors.lastname: Schleper
authors.forename: Yoh-ichi
authors.initials: Y
authors.lastname: Watanabe
authors.forename: Junichi
authors.initials: J
authors.lastname: Sugahara
authors.forename: Christina
authors.initials: C
authors.lastname: Preston
authors.forename: José
authors.initials: J
authors.lastname: de la Torre
authors.forename: Paul M
authors.initials: PM
authors.lastname: Richardson
authors.forename: Edward F
authors.initials: EF
authors.lastname: DeLong
mesh_terms: D019615:Crenarchaeota / Q000235:genetics* / Q000378:metabolism; D020745:Genome, Archaeal / Q000235:genetics*; D008969:Molecular Sequence Data; D009792:Oceans and Seas; D010802:Phylogeny