Abstract
The high-altitude Andean lakes (HAAL) in the Argentinean Puna-high Andes region represent an almost unexplored ecosystem exposed to extreme conditions (high UV irradiation, hypersalinity, drastic temperature changes, desiccation, and high pH). Here we present the first genome sequence, a Sphingomonas sp., isolated from this extreme environment.
GENOME ANNOUNCEMENT
Sphingomonas sp. S17 was isolated from a modern stromatolite community in Socompa Lake (3,800-m altitude), placed near the active volcano Socompa in northwest Argentina. The environmental conditions of these lakes include a pH of 9, a salinity of 22%, and an arsenic content of 32 mg/liter (2, 3, 4, 5, 11).
The genome sequence was obtained using a whole-genome shotgun (WGS) strategy with a 454 GS Titanium pyrosequencer at INDEAR, Argentina. Assembly was done using 454 Newbler, version 2.5.3, using the –urt option with 63× genome coverage. This assembly generated 62 large contigs. The draft genome was 4,268,406 bases in length, with a mean GC content of 65.74%.
Genome annotation was done using the standard operating procedures (SOPs) for prokaryotic annotation from ISGA (7) and from the RAST annotation server (1). A total of 3,892 coding sequences (CDS) and 52 structural RNAs (49 tRNAs) were predicted. Annotation covered 340 RAST subsystems (43%) with 1,650 CDS, while 1,251 CDS (32%) were classified as hypothetical proteins. The complete 16S rRNA gene presented a maximum identity of 95% with that of Sphingomonas wittichii (10).
Consistent with the extreme environment and high UV irradiation, Sphingomonas sp. S17 presented a complete DNA repair system, including a photolyase gene and a SOS regulatory system, with the umuCD operon harbored for translesion synthesis. Neither of these CDS was found in the reference genome of Sphingomonas wittichii RW1 (10). Accordingly, this bacterial genome also presented 24 genes devoted to sulfur metabolism, compared with only 4 such genes in S. wittichii. A set of 95 genes was present in the subsystem for resistance to antibiotics and toxic compounds, compared with only 41 such genes in S. wittichii. The majority of these genes are devoted to the resistance of arsenic, chromium, and fluoroquinolones, with 18 genes devoted to multidrug resistance efflux pumps. The genome also contained two copies of a NhaA-type CDS for the Na+/H+ antiporter (12) and six subunits of the multisubunit cation antiporter (Na+/H+), compatible with its alkaline and hypersaline environment.
As in other Sphingomonas genomes, a rich set of genes (47 CDS) for metabolism of aromatic compounds was present in the subsystem. It is interesting to note two other features absent from the S. wittichii genome: (i) the presence of 5 CDS related to the prokaryotic immune system CRISPR (one Cas1, one Cas2, two Cas3, and one Csn1 CDS), with seven associated direct repeats of 36 bases separated by spacers of 31 bases (8), and (ii) the presence of the operon containing the LodA and LodB CDS for the production of marinocine, a broad-spectrum antibacterial protein (9).
Finally, Sphingomonas sp. S17 contains at least one megaplasmid of the IncF type, with a complete set of mobilization proteins (variant 1 in the conjugative transfer subsystem; RAST annotation) (6). The megaplasmid contains several resolvase/integrase proteins (8 CDS) and transposases (5 CDS). Interestingly, it also harbors the umuCD operon.
This represents the first genome sequence reported from the unexplored extreme high-altitude Andean lake (HAAL) ecosystem.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number AFGG00000000. The version described in this paper is the first version, accession number AFGG01000000.
Acknowledgments
We thank other members of LIMLA for helpful discussions during the sequencing and analysis of this project.
This work was supported by grants PICT-1707, PICT-1221, and PICT2007-0043 from ANPCyT-MINCyT, Argentina.
Footnotes
Published ahead of print on 20 May 2011.
REFERENCES
- 1. Aziz R. K., et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Dib J. R., et al. 2009. Isolation of bacteria from remote high altitude Andean wetlands able to grow in the presence of antibiotics. Recent Pat. Antiinfect. Drug Discov. 4:66–76 [DOI] [PubMed] [Google Scholar]
- 3. Dib J. R., Fenandez Zenoff V., Motok J., Ordoñez O. F., Farías M. E. 2008. Occurrence of resistance to antibiotics, UV-B and arsenic in bacteria isolated from extreme environment in high altitude Andean wetlands (4,560 m and 4,400 m altitude). Curr. Microbiol. 56:510–517 [DOI] [PubMed] [Google Scholar]
- 4. Fernandez Zenoff V., Siñeriz F., Farías M. E. 2006. Bacteria isolated from Andean high altitude lakes display diverse responses to UV-B radiation and repair mechanisms. Appl. Environ. Microbiol. 72:7857–7863 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Flores M. R., Ordoñez O. F., Farías M. E. 2009. Isolation of UV-B resistant bacteria from two Andean wetlands (4,400 m) with saline and hypersaline conditions. J. Gen. Appl. Microbiol. 55:447–458 [DOI] [PubMed] [Google Scholar]
- 6. Frost L. S., Koraimann G. 2010. Regulation of bacterial conjugation: balancing opportunity with adversity. Future Microbiol. 5:1057–1071 [DOI] [PubMed] [Google Scholar]
- 7. Hemmerich C., Buechlein A., Podicheti R., Revanna K. V., Dong Q. 2010. An Ergatis-based prokaryotic genome annotation web server. Bioinformatics 26:1122–1124 [DOI] [PubMed] [Google Scholar]
- 8. Horvath P., Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170 [DOI] [PubMed] [Google Scholar]
- 9. Lucas-Elio P., Hernandez P., Sanchez-Amat A., Solano F. 2005. Purification and partial characterization of marinocine, a new broad-spectrum antibacterial protein produced by Marinomonas mediterranea. Biochim. Biophys. Acta 1721:193–203 [DOI] [PubMed] [Google Scholar]
- 10. Miller T. R., et al. 2010. Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J. Bacteriol. 192:6101–6102 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Ordoñez O. F., Flores M. R., Dib J. R., Paz A., Farías M. E. 2009. Extremophile culture collection from Andean lakes: extreme pristine environments that host a wide diversity of microorganisms with tolerance to UV radiation. Microb. Ecol. 58:461–473 [DOI] [PubMed] [Google Scholar]
- 12. Padan E., et al. 2004. NhaA of Escherichia coli, as a model of a pH-regulated Na+/H+ antiporter. Biochim. Biophys. Acta 1658:2–13 [DOI] [PubMed] [Google Scholar]