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Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile

ABSTRACT

In this report, we present a draft genome of 2,886,173 bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named “Salar del Huasco” in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.

Keywords:
Alkaline; Arsenic; Heavy metals; Pigments

The Exiguobacterium genus is comprised of 17 species, including several strains that come from extreme habitat.11 Vishnivetskaya TA, Kathariou S, Tiedje JM. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles. 2009;13:541-555.

2 Vishnivetskaya TA, Chauhan A, Layton AC, et al. Draft genome sequences of 10 strains of the genus Exiguobacterium. Genome Announc. 2014;2:e01058-e1114.

3 Zhang DC, Liu YX, Huo YY, Xu XW, Li XZ. Draft genome sequence of thermophilic Exiguobacterium sp. strain JLM-2, isolated from deep-sea ferromanganese nodules. Genome Announc. 2015;3:e00794-e815.

4 Rout SP, Rai A, Humphreys PN. Draft genome sequence of alkaliphilic Exiguobacterium sp. strain HUD, isolated from a polymicrobial consortia. Genome Announc. 2015;3:e01451-e1514.
-55 Cabria GLB, Argayosa VB, Lazaro JEH, Argayosa AM, Arcilla CA. Draft genome sequence of haloalkaliphilic Exiguobacterium sp. strain AB2 from Manleluag Ophiolitic Spring, Philippines. Genome Announc. 2014;2(4):e00840-e914. The “Salar del Huasco” is a saline pond located at an altitude of 3778 m in the Andes Mountains of northern Chile. The average temperature of this pond is 5 °C with high UV irradiation (>1100 W m2), alkaline pH (8-10) and sediments with high Arsenic and Boron concentrations.66 Risacher F, Alonso H, Salazar C. Geoquímica de aguas en cuencas cerradas: I, II y III regiones - Chile. vol. 1. Santiago, Chile: Ministerio de Obras Públicas, Dirección General de Aguas; 1999. Available at: http://documentos.dga.cl/CQA1921v1.pdf.
http://documentos.dga.cl/CQA1921v1.pdf...
,77 Risacher F, Alonso H, Salazar C. Geoquímica de aguas en cuencas cerradas: I, II y III regiones - Chile. vol. 2. Santiago, Chile: Ministerio de Obras Públicas, Dirección General de Aguas; 1999. Available at: http://documentos.dga.cl/CQA1921v1.pdf.
http://documentos.dga.cl/CQA1921v1.pdf...
In this extreme environment, a rich community of microorganisms, including the Exiguobacterium genus have been described.88 Dorador C, Meneses D, Urtuvia V, et al. Diversity of Bacteroidetes in high-altitude saline evaporitic basins in northern Chile. J Geophys Res. 2009;114:G00D05.

9 Dorador C, Vila I, Remonsellez F, Imhoff JF, Witzel KP. Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano. FEMS Microbiol Ecol. 2010;73:291-302.

10 Demergasso C, Dorador C, Meneses D, et al. Prokaryotic diversity pattern in high-altitude ecosystems of the Chilean Altiplano. J Geophys Res. 2010;115:G00D09.
-1111 Scott S, Dorador C, Oyanedel JP, et al. Diversidad microbiana y componentes tróficos de dos humedales de altura del altiplano chileno. Gayana (Concepción). 2015;79:45-56. To understand the bacterial mechanism involved in this natural adaptation, the Exiguobacterium aurantiacum strain PN47 was isolated (20°19'29.69″S, 68°51'8.85″O), and its genome was sequenced and analyzed.

The PN47 strain is a Gram-positive, non-spore forming bacteria with orange colony on Luria-Bertani agar plate and capability of growth at alkaline pH in the presence of heavy metals and saline conditions. Whole-genome sequencing was performed using 300 bp pair-end reads on the Illumina MiSeq platform. A total of 14.2 million reads were obtained with an average length of 178 nucleotides. Reads were filtered by quality (at least 20) and assembled using A5 pipeline (2015 version 2015 year for linux).1212 Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE. 2012;7:e42304. Open reading frame prediction and annotation was performed using Prokka software version 1.11.1313 Seemann T. Prokka: Prokaryotic Genome Annotation System; 2012. Available at: http://vicbioinformatics.com/.
http://vicbioinformatics.com/...

The PN47 strain exhibits 83% homology with the genome of E. aurantiacum DSM 6208 (accession number JNIQ00000000), covering 91% of the genome according to BLAST microbe analysis (National Center for Biotechnology Information). In addition, 16S rRNA genes comparison showed a 99% identity match with E. aurantiacum strain Q20 (accession number KU933354.1), thereby confirming species identity. Using the RNAmmer Prediction Server (Technical University of Denmark) and tRNA analysis by ARAGORN,1414 Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32:11-16. 10 copies of 5S rRNA, a single copy of 16S and 23S rRNA gene, and a total of 65 tRNAs sequences were identified.

Using the RAST-NMPDR server,1515 Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:1. the genome was observed to include 2927 coding sequence (CDS) spread in 392 subsystems, including lipid, fatty acid and isoprenoid metabolism pathways probably related with the synthesis of the orange pigment. In addition, PN47 strain has genes related with hot and cold temperature stress in accordance with atmospheric temperature changes commonly described in this area (22 to -8 °C). The presence of ars operon and arsenite oxidase genes are probably associated with an arsenic resistance mechanism, but the classical atr1, van1 or bor genes described for boron resistance mechanisms were absent. One possibility is that a putative cross-stress resistance mechanism produces boron tolerance,1616 Sen M, Yılmaz Ü, Baysal A, Akman S, Çakar ZP. In vivo evolutionary engineering of a boron-resistant bacterium: Bacillus boroniphilus. Antonie Van Leeuwenhoek. 2011;99:825-835. through their own copper and salt stress response genes. Among salt resistance genes, several proton/anti-porters were found, which along with genes of choline-glycine betaine transport and synthesis, could contribute to salt tolerance and facilitate growth in alkaline conditions.1717 Mirete S, Morgante V, González-Pastor JE. Functional metagenomics of extreme environments. Curr Opin Biotechnol. 2016;38:143-149.

18 Robert H, Le Marrec C, Blanco C, Jebbar M. Glycine betaine, carnitine, and choline enhance salinity tolerance and prevent the accumulation of sodium to a level inhibiting growth of Tetragenococcus halophila. Appl Environ Microbiol. 2000;66:509-517.
-1919 Padan E, Bibi E, Ito M, Krulwich TA. Alkaline pH homeostasis in bacteria: new insights. BBA Biomembranes. 2005;1717:67-88.

In light of this report, future genomic comparisons will contribute to understanding the flexibility of E. aurantiacum species to survive in diverse environmental conditions. Strains of PN47 that more closely match the genome described in this study are those that come from potato processing factories (E. aurantiacum DSM 6208)2020 Collins MD, Lund BM, Farrow JAE, Schleifer KH. Chemotaxonomic study of an alkalophilic bacterium, Exiguobacterium aurantiacum gen. nov., sp. nov.. Microbiology. 1983;129:2037-2042. and petroleum contaminated soil (Q20 strain).

Regarding nucleotide sequence accession numbers, this Whole Genome Shotgun project has been deposited at DDBJ/ENA/Embank under the accession MKXO00000000. The version described in this paper is version MKXO01000000.

Acknowledgments

This work was supported by the Academic Vice Rectory of Arturo Prat University, project DE1549 and by the Vice Rectory of Research Innovation and Postgrade of Arturo Prat University, project VRIIP0220-15, VRIIP0218-15, and the program of InnovaChile CORFO for Attraction of International Centers of Excellence (FCR-CSB 09CEII-6991).

References

  • 1
    Vishnivetskaya TA, Kathariou S, Tiedje JM. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 2009;13:541-555.
  • 2
    Vishnivetskaya TA, Chauhan A, Layton AC, et al. Draft genome sequences of 10 strains of the genus Exiguobacterium Genome Announc 2014;2:e01058-e1114.
  • 3
    Zhang DC, Liu YX, Huo YY, Xu XW, Li XZ. Draft genome sequence of thermophilic Exiguobacterium sp. strain JLM-2, isolated from deep-sea ferromanganese nodules. Genome Announc 2015;3:e00794-e815.
  • 4
    Rout SP, Rai A, Humphreys PN. Draft genome sequence of alkaliphilic Exiguobacterium sp. strain HUD, isolated from a polymicrobial consortia. Genome Announc 2015;3:e01451-e1514.
  • 5
    Cabria GLB, Argayosa VB, Lazaro JEH, Argayosa AM, Arcilla CA. Draft genome sequence of haloalkaliphilic Exiguobacterium sp. strain AB2 from Manleluag Ophiolitic Spring, Philippines. Genome Announc 2014;2(4):e00840-e914.
  • 6
    Risacher F, Alonso H, Salazar C. Geoquímica de aguas en cuencas cerradas: I, II y III regiones - Chile vol. 1. Santiago, Chile: Ministerio de Obras Públicas, Dirección General de Aguas; 1999. Available at: http://documentos.dga.cl/CQA1921v1.pdf
    » http://documentos.dga.cl/CQA1921v1.pdf
  • 7
    Risacher F, Alonso H, Salazar C. Geoquímica de aguas en cuencas cerradas: I, II y III regiones - Chile vol. 2. Santiago, Chile: Ministerio de Obras Públicas, Dirección General de Aguas; 1999. Available at: http://documentos.dga.cl/CQA1921v1.pdf
    » http://documentos.dga.cl/CQA1921v1.pdf
  • 8
    Dorador C, Meneses D, Urtuvia V, et al. Diversity of Bacteroidetes in high-altitude saline evaporitic basins in northern Chile. J Geophys Res 2009;114:G00D05.
  • 9
    Dorador C, Vila I, Remonsellez F, Imhoff JF, Witzel KP. Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano. FEMS Microbiol Ecol 2010;73:291-302.
  • 10
    Demergasso C, Dorador C, Meneses D, et al. Prokaryotic diversity pattern in high-altitude ecosystems of the Chilean Altiplano. J Geophys Res 2010;115:G00D09.
  • 11
    Scott S, Dorador C, Oyanedel JP, et al. Diversidad microbiana y componentes tróficos de dos humedales de altura del altiplano chileno. Gayana (Concepción) 2015;79:45-56.
  • 12
    Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS ONE 2012;7:e42304.
  • 13
    Seemann T. Prokka: Prokaryotic Genome Annotation System; 2012. Available at: http://vicbioinformatics.com/
    » http://vicbioinformatics.com/
  • 14
    Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004;32:11-16.
  • 15
    Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:1.
  • 16
    Sen M, Yılmaz Ü, Baysal A, Akman S, Çakar ZP. In vivo evolutionary engineering of a boron-resistant bacterium: Bacillus boroniphilus Antonie Van Leeuwenhoek 2011;99:825-835.
  • 17
    Mirete S, Morgante V, González-Pastor JE. Functional metagenomics of extreme environments. Curr Opin Biotechnol 2016;38:143-149.
  • 18
    Robert H, Le Marrec C, Blanco C, Jebbar M. Glycine betaine, carnitine, and choline enhance salinity tolerance and prevent the accumulation of sodium to a level inhibiting growth of Tetragenococcus halophila Appl Environ Microbiol 2000;66:509-517.
  • 19
    Padan E, Bibi E, Ito M, Krulwich TA. Alkaline pH homeostasis in bacteria: new insights. BBA Biomembranes 2005;1717:67-88.
  • 20
    Collins MD, Lund BM, Farrow JAE, Schleifer KH. Chemotaxonomic study of an alkalophilic bacterium, Exiguobacterium aurantiacum gen. nov., sp. nov.. Microbiology 1983;129:2037-2042.

Edited by

Associate Editor: John McCulloch

Publication Dates

  • Publication in this collection
    Jan-Mar 2018

History

  • Received
    3 Nov 2016
  • Accepted
    10 Mar 2017
Sociedade Brasileira de Microbiologia USP - ICB III - Dep. de Microbiologia, Sociedade Brasileira de Microbiologia, Av. Prof. Lineu Prestes, 2415, Cidade Universitária, 05508-900 São Paulo, SP - Brasil, Ramal USP 7979, Tel. / Fax: (55 11) 3813-9647 ou 3037-7095 - São Paulo - SP - Brazil
E-mail: bjm@sbmicrobiologia.org.br