Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

Journal Article · Sat Jun 24 04:00:00 EDT 2006 · Proceedings of the National Academy ofSciences

OSTI ID:927384

Hallam, Steven J; Konstantinidis, Konstantinos T; Brochier, Celine; Putnam, Nik; Schleper, Christa; Watanabe, Yoh-ichi; Sugahara, Junichi; Preston, Christina; de la Torre, Jose; Richardson, Paul M; DeLong, Edward F

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, 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 synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as a basal crenarchaeon, sharing specific genomic features in common with either Crenarchaea, Euryarchaea, or both. The genome sequence of C. symbiosum reflect a unique and unusual evolutionary, physiological, and ecological history, one remarkably distinct from that of any other previously known microbial lineage.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 927384
• Report Number(s): LBNL--62943; BnR: KP1103010
• Journal Information: Proceedings of the National Academy ofSciences, Journal Name: Proceedings of the National Academy ofSciences Journal Issue: 48 Vol. 103
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BACTERIA
FUNCTIONALS
GENES
GENETIC VARIABILITY
GENOTYPE
LAKES
RIBOSOMAL RNA
SEDIMENTS
SOILS
SYMBIOSIS
VIRUSES