title: Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.
abstract: Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Reema K
authors.initials: RK
authors.lastname: Gudhka
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia ; Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Brett A
authors.initials: BA
authors.lastname: Neilan
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia ; Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Brendan P
authors.initials: BP
authors.lastname: Burns
mesh_terms: D000220:Adaptation, Biological; D001482:Base Composition; D000458:Cyanobacteria / Q000254:growth & development; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D019625:Halococcus / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D017422:Sequence Analysis, DNA
chemical_list: D019641:DNA, Archaeal