GENOME ANNOUNCEMENT
Genome Sequence of the Halophilic Archaeon Halococcus hamelinensis Brendan P. Burns, Reema K. Gudhka, and Brett A. Neilan School of Biotechnology and Biomolecular Sciences and Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
Halococcus hamelinensis was isolated from hypersaline stromatolites in Shark Bay, Australia. Here we report the genome sequence (3,133,046 bp) of H. hamelinensis, which provides insights into the ecology, evolution, and adaptation of this novel microorganism.
H
alococcus hamelensis was first isolated from living stromatolites in the hypersaline waters of Shark Bay, Australia (5). These ecosystems are analogous to one of the earliest forms of life on Earth (15) and exhibit significant microbial diversity (1, 6, 9, 14). H. hamelinensis is the first archaeon isolated from stromatolites and displays a number of novel characteristics, including an oxidase-negative phenotype and lack of K⫹ uptake as a primary osmoprotective strategy (5, 7). Although several key genes (uvrABC) involved in the adaptive response to UV stress have been identified (10), what is lacking is a comprehensive whole genomic profile and related computational analyses of this organism, which would significantly enhance our understanding of its evolutionary and adaptive traits. Furthermore, although Halococcus members have been shown to exhibit diverse phenotypes (13), the present study reports the first genome sequenced for this genus. The genome sequence of H. hamelinensis was determined by the use of massively parallel pyrosequencing with a Roche 454 GS FLX sequencer. A total of 272,854 reads, counting up to 118,638,438 bases (a 32-fold coverage of the genome), were assembled using 454 Newbler GS de novo assembler software (version 2.0.01.12). A total of 223 contiguous sequence fragments that ranged from 500 to 105,929 bp were generated, with bases having quality scores of 40 and above. Sequencing output was uploaded onto two different autoannotation servers, the Rapid Annotation using Subsystem Technology (2) and Integrated Microbial Genomes/Expert Review (12) servers. Annotation was based on subsystems, and coding sequences were identified by using Glimmer software (3). tRNA genes were predicted by using tRNAScan-SE software (11), and rRNA genes were identified by using RNAmmer 1.2 (8). Functional annotation was performed by searching the NCBI Nonredundant Protein database and the Kyoto Encyclopedia of Genes and Genomes protein database, and Clusters of Orthologous Group (COG) analyses were undertaken using COG functions within IMG/ER. The genome of H. hamelinensis consists of 3,133,046 bp, with an average G⫹C content of 60.08%. The genome consists of 223 DNA scaffolds and 48 RNA genes, 45 of which are tRNA genes, and the remaining three are rRNA genes comprising a single rRNA operon (16S-23S-5S). Furthermore, the genome contains 3,150 predicted coding sequences or open reading frames, 2,196 (68.67%) of which are protein-coding genes with functional assignments and 954 (29.83%) of which are of unknown function. Codon prediction and frequency were calculated using programs from the EMBOSS package, and codon usage of the H. hamelinensis genome is consistent with a highly acidic proteome, a major adaptive mechanism for high salinity (4). The genome of H. hame-
2100
jb.asm.org
linensis also revealed various unique characteristics reflecting its ability to survive in the extreme environment in which it resides, including putative genes/pathways involved in osmoprotection (particularly glycine betaine accumulation), oxidative stress response, UV damage repair, heavy metal resistance, and antibiotic biosynthesis/degradation. Finally, genome analyses indicated the presence of six putative transposases as well as positive matches for genes of H. hamelinensis against various genomes of bacteria, archaea, and viruses, suggesting the potential for horizontal gene transfer. Nucleotide sequence accession number. The genome sequence of H. hamelinensis is accessible at GenBank under accession number PRJNA80845. ACKNOWLEDGMENTS This work was funded by the Australian Research Council. The genome of H. hamelinensis was sequenced by Jason Koval at The Clive and Vera Ramaciotti Centre, University of New South Wales.
REFERENCES 1. Allen MA, Goh F, Burns BP, Neilan BA. 2009. Bacterial, archaeal and eukaryotic diversity of microbial mat communities in the hypersaline lagoon of Shark Bay. Geobiology 7:82–96. 2. Aziz RK, et al. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. 3. Delcher AL, Bratke KA, Powers ECE, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673– 679. 4. Foster JW. 2000. Microbial responses to acid stress, p 99–115. In Storz G, Hengge-Aronis R (ed), Bacterial stress responses. ASM Press, Washington, DC. 5. Goh F, et al. 2006. Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia. Int. J. Syst. Evol. Microbiol. 56:1323–1329. 6. Goh F, et al. 2009. Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay. ISME J. 3:383–396. 7. Goh F, Jeon Y-J, Barrow KD, Neilan BA, Burns BP. 2011. Osmoadaptive strategies of the archaeon Halococcus hamelinensis isolated from a hypersaline stromatolite environment. Astrobiology 11:529 –536. 8. Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108. 9. Leuko S, et al. 2007. Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mat. Extremophiles 11:203–210.
Received 10 January 2012 Accepted 30 January 2012 Address correspondence to Brendan P. Burns,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.06599-11
0021-9193/12/$12.00
Journal of Bacteriology
p. 2100 –2101
Genome Announcement
10. Leuko S, Neilan BA, Burns BP, Walter MR, Rothschild LJ. 2011. Molecular assessment of UVC radiation-induced DNA damage repair in the stromatolitic halophilic archaeon, Halococcus hamelinensis. J. Photochem. Photobiol. B 102:140 –145. 11. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964. 12. Markowitz VM, et al. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34:D344 –D348.
April 2012 Volume 194 Number 8
13. Montero CG, Klenk HP, Nieto JJ, Ventosa A. 1993. DNA-rRNA hybridization studies on Halococcus saccharolyticus and other halobacteria. FEMS Microbiol. Lett. 111:69 –72. 14. Münchhoff J, Hirose H, Maruyama T, Burns BP, Neilan BA. 2007. Phylogeography of Prochloron and its didemnid ascidian host. Environ. Microbiol. 9:890 – 899. 15. Walter MR, Buick R, Dunlop JSR. 1980. Stromatolites 3,400 –3,500 Myr old from the North Pole area, Western Australia. Nature 284:443– 445.
jb.asm.org 2101
