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Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008

Authors:
Madhvi Joshi at Gujarat Biotechnology Research Centre
Madhvi Joshi
  • Gujarat Biotechnology Research Centre
Aanal S Pandit at Gujarat State Biotechnology Mission
Aanal S Pandit
A. Sharma
A. Sharma
A. Sharma
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Rohan Pandya at Atmiya University
Rohan Pandya
  • Atmiya University
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Abstract

The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production.
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Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp.
Strain BAB-2008
M. N. Joshi, A. S. Pandit, A. Sharma, R. V. Pandya, A. K. Saxena, S. B. Bagatharia
Gujarat State Biotechnology Mission, Department of Science & Technology, Gujarat, India
The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-
producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome
sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production.
Received 18 December 2012 Accepted 31 December 2012 Published 21 February 2013
Citation Joshi MN, Pandit AS, Sharma A, Pandya RV, Saxena AK, Bagatharia SB. 2013. Draft genome sequence of the halophilic bacterium Halobacillus sp. strain BAB-2008.
Genome Announc. 1(1):e00222-12. doi:10.1128/genomeA.00222-12.
Copyright © 2013 Joshi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to S. B. Bagatharia, snehalbagatharia@hotmail.com.
The genus Halobacillus was identified by Spring et al. (1) and
comprises 18 species with validly published names: H. halo-
philus,H. litoralis, and H. trueperi (1), H. salinus (2), H. karajensis
(3), H. locisalis (4), H. aidingensis and H. dabanensis (5), H. yeom-
jeoni (6), H. campisalis (7), H. profundi and H. kuroshimensis (8),
H. faecis (9), H. mangrovei (10), H. alkaliphilus (11), H. nao-
zhouensis (12), H. salsuginis (13), and H. seohaensis (14). The Ha-
lobacillus genus comprises moderate halophiles which can grow
and produce enzymes over a very wide range of salinities, making
them very attractive for research and for screening of novel en-
zymes with unusual properties (15). Many moderate halophiles
produce carotenoids as a protective mechanism against photooxi-
dation processes. Carotenoids have major applications in the food
industry as food-coloring agents and as additives in health food
products (16). The halophilic aspect of these bacteria has exciting
potential, for instance, in their possible application in agriculture
to construct salt-resistant plants carrying prokaryotic genes en-
coding enzymes for the synthesis of osmoprotective compounds
(17).
The halophilic bacterium Halobacillus sp. strain BAB-2008 was
isolated from a soil sample near Zazam-Solar Park Road, District
Patan (23°55=782⬙N, 71°18=480⬙E), Gujarat, India, by using the
traditional dilution-plating method. Preliminary characterization
revealed that Halobacillus sp. BAB-2008 is Gram positive, orange
pigmented, and halophilic (can grow at up to 15% NaCl).
Whole-genome sequencing of the strain was done with a high-
throughput Ion Torrent Personal Genome Machine with an Ion
Torrent Server (Torrent suite version 3.2). Following the manu-
facturer’s protocol, 22.11⫻coverage data and a total of 1,078,490
mate-paired reads (shortest read with 91 bp and longest read with
176 bp) were obtained. De novo assembly was performed using the
MIRA-3 assembler (version 3.1.0). The automatic annotation of
the genome was performed using the NCBI Prokaryotic Genomes
Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm
.nih.gov/genomes/static/Pipeline.html), which utilizes GeneMark
(18), Glimmer (19), and tRNAscan-SE searches (20), and using
the RAST server (21) with the SEED database (22). Functional
annotation of genes was performed using the KEGG Automatic
Annotation Server (23).
The total length of the genome was found to be 3,784,751 bp,
which was distributed in 137 contigs (scaffold N
50
⫽51,319 bp).
The G⫹C content was 46.83%. The Halobacillus sp. BAB-2008
harbored 410 subsystems, having 3,935 protein-coding genes, 60
tRNAs, and 9 rRNAs. Carotenoid biosynthesis genes (crtN,crtP,
crtB, and crtM) present on the chromosome of Halobacillus sp.
BAB-2008 indicate that this species might have possible applica-
tions in carotenoid production. Genes encoding serine protein-
ases, amylases, nucleases, esterases, and lipases were also identified
on the chromosome.
Thus, the ability to grow under halophilic conditions, the pres-
ence of a clearly defined carotenoid biosynthetic pathway, and the
probable potential toward enzyme production make Halobacillus
sp. BAB-2008 an organism of industrial importance. Moreover,
this bacterium may be used as a model organism for molecular
study of the osmoregulatory mechanisms which help moderate
halophiles grow over a wide range of salt concentrations.
Nucleotide sequence accession number. The draft genome se-
quence of Halobacillus sp. BAB-2008 has been deposited at
GenBank under the accession number ANPF00000000.
ACKNOWLEDGMENTS
This work was supported by the Department of Science & Technology,
Government of Gujarat, under Project-151, a joint initiative of the Guja-
rat Biodiversity Gene Bank, the Gujarat Genomics Initiative, and the Vir-
tual Institute of Bioinformatics.
REFERENCES
1. Spring S, Ludwig W, Marquez MC, Ventosa A, Schleifer KH. 1996.
Halobacillus gen. nov., with descriptions of Halobacillus litoralis sp. nov,
and Halobacillus trueperi sp. nov, and transfer of Sporosarcina halophila
to Halobacillus halophilus comb. Int. J. Syst. Bacteriol. 46:492– 496.
2. Yoon JH, Kang KH, Park YH. 2003. Halobacillus salinus sp. nov., Iso-
lated from a salt lake on the coast of the East Sea in Korea. Int. J. Syst. Evol.
Microbiol. 53:687– 693.
3. Amoozegar MA, Malekzadeh F, Malik KA, Schumann P, Spröer C.
2003. Halobacillus karajensis sp. nov., A novel moderate halophile. Int. J.
Syst. Evol. Microbiol. 53:1059 –1063.
Genome AnnouncementsJanuary/February 2013 Volume 1 Issue 1 e00222-12 genomea.asm.org 1
4. Yoon JH, Kang KH, Oh TK, Park YH. 2004. Halobacillus locisalis sp.
nov., A halophilic bacterium isolated from a marine solar saltern of the
Yellow Sea in Korea. Extremophiles 8:23–28.
5. Liu WY, Zeng J, Wang L, Dou YT, Yang SS. 2005. Halobacillus da-
banensis sp. nov. and Halobacillus aidingensis sp. nov., isolated from salt
lakes in Xinjiang, China. Int. J. Syst. Evol. Microbiol. 55:1991–1996.
6.Yoon JH, Kang SJ, Lee CH, Oh HW, Oh TK. 2005. Halobacillus
yeomjeoni sp. nov., Isolated from a marine solar saltern in Korea. Int. J.
Syst. Evol. Microbiol. 55:2413–2417.
7. Yoon JH, Kang SJ, Jung YT, Oh TK. 2007. Halobacillus campisalis sp.
nov., Containing meso-diaminopimelic acid in the cell-wall peptidogly-
can, and emended description of the genus Halobacillus. Int. J. Syst. Evol.
Microbiol. 57:2021–2025.
8. Hua NP, Kanekiyo A, Fujikura K, Yasuda H, Naganuma T. 2007.
Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.,
moderately halophilic bacteria isolated from a deep-sea methane cold
seep. Int. J. Syst. Evol. Microbiol. 57:1243–1249.
9. An SY, Kanoh K, Kasai H, Goto K, Yokota A. 2007. Halobacillus faecis
sp. nov. in a spore-forming bacterium isolated from a mangrove area on
Ishigaki Island, Japan. Int. J. Syst. Evol. Microbiol. 57:2476 –2479.
10. Soto-Ramírez N, Sánchez-Porro C, Rosas-Padilla S, Almodóvar K,
Jiménez G, Machado-Rodríguez M, Zapata M, Ventosa A, Montalvo-
Rodríguez R. 2008. Halobacillus mangrovi sp. nov., A moderately halo-
philic bacterium isolated from the black mangrove Avicennia germinans.
Int. J. Syst. Evol. Microbiol. 58:125–130.
11. Romano I, Finore I, Nicolaus G, Huertas FJ, Lama L, Nicolaus B, Poli
A. 2008. Halobacillus alkaliphilus sp. nov., A halophilic bacterium isolated
from a salt lake in Fuente de Piedra, southern Spain. Int. J. Syst. Evol.
Microbiol. 58:886 – 890.
12. Chen YG, Liu ZX, Zhang YQ, Zhang YX, Tang SK, Borrathybay E, Li
WJ, Cui XL. 2012. Halobacillus naozhouensis sp. nov., a moderately
halophilic bacterium isolated from a sea anemone. Antonie Van Leeuwen-
hoek 96:99 –107.
13. Chen YG, Zhang YQ, Liu ZX, Zhuang DC, Klenk HP, Tang SK, Cui XL,
Li WJ. 2009. Halobacillus salsuginis sp. nov., a moderately halophilic
bacterium from a subterranean brine. Int. J. Syst. Evol. Microbiol. 59:
2505–2509.
14. Yoon JH, Kang SJ, Oh TK. 2008. Halobacillus seohaensis sp. nov., iso-
lated from a marine solar saltern in Korea. Int. J. Syst. Evol. Microbiol.
58:622– 627.
15. Kushner DJ. 1986. Molecular adaptation of enzymes, metabolic systems
and transport systems in halophilic bacteria. FEMS Microbiol. Rev. 39:
121–127.
16. Köcher S, Jurgen B, Müller V, Sandmann G. 2009. Structure, function
and biosynthesis of carotenoids in the moderately halophilic bacterium
Halobacillus halophilus. Arch. Microbiol. 191:95–104.
17. Ventosa A, Nieto JJ, Oren A. 1998. Biology of moderately halophilic
bacteria. Microbiol. Mol. Biol. Rev. 62:504 –544.
18. Borodovsky M, McIninch J. 1993. GeneMark: parallel gene recognition
for both DNA strands. Comput. Chem. 17:123–133.
19. Delcher AL, Hormon D, Kasif S, White O, Salzberg SL. 1999. Improved
microbial gene identification with GLIMMER. Nucleic Acids Res. 27:
4636 – 4641.
20. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-
tion of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:
955–964.
21. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,
Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson
R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,
Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,
Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using
subsystems technology. BMC Genomics 9:75.
22. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens
R, Edwards RA. 2010. Accessing the SEED genome databases via Web
services API: tools for programmers. BMC Bioinformatics 11:319.
23. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS:
an automatic genome annotation and pathway reconstruction server. Nu-
cleic Acids Res. 35:W182–W185.
Joshi et al.
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