Abstract
We describe here the draft genome sequence of Sporosarcina pasteurii, a urease-producing bacterium with potential applications in biocement production.
GENOME ANNOUNCEMENT
The use of microbes in biomineralization has been an active area in research worldwide (1, 2). One of the major microorganisms studied for its biomineralization capacity has been the urease-producing species Sporosarcina pasteurii, which has the potential to precipitate calcium carbonate and thus aid in the production of biocement (3, 4). The organism produces a significantly high amount of urease without the requirement for additional methods of concentration (3, 4). S. pasteurii releases carbonate ions, which in a calcium-rich environment and under adequate conditions can precipitate hard calcium carbonate or calcite (5). A recent crystallographic study on the citrate-bound urease enzyme complex shed light on the mechanisms of action of this enzyme (6). The organism has an additional advantage in that it tolerates a highly alkaline environment, which is required for biomineralization (7). The microorganism has also gained interest and applications in a wide variety of areas, including the restoration of structures and mining (8), and it may have biomedical applications. The microorganism also provides an ecofriendly alternative to traditional cement production systems.
The strain was procured from the National Collection of Industrial Microorganisms (NCIM) maintained at the CSIR National Chemical Laboratory, Pune, India (NCIM ID, 2477). DNA was isolated from the culture, which was revived from the freeze-dried samples. The raw sequence data were generated after library preparation on an Illumina HiSeq 2500 platform as per the manufacturer’s protocols. A total of >11.5 million single-end reads of 101 bases were generated. The draft genome was assembled de novo using the CLC Genomics Workbench 6.0.5. The assembly resulted in 38 contigs with an N50 value of 232,940 bp and a total assembly of 4,040,808 bp. Further, automated gene prediction on the draft genomes was performed using RAST server (9). The analysis revealed 4,259 genes, including 46 RNA genes.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AYOX00000000. The version described in this paper is version AYOX00000000.1.
ACKNOWLEDGMENTS
We acknowledge Anupam Kumar Mondal for his technical help and Mitali Mukerji for her discussions. We acknowledge the National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, India, for the resource material.
The sequencing was performed as part of the Undergraduate exploratory Sequencing Project (USP) as part of the coursework of AcSIR at CSIR-IGIB. This work was funded by the Council of Scientific and Industrial Research (CSIR), India. P.K.T. and K.J. acknowledge fellowships from DBT-BINC-JRF and V.B. acknowledges a fellowship from CSIR-NET-JRF.
Footnotes
Citation Tiwari PK, Joshi K, Rehman R, Bhardwaj V, Shamsudheen KV, Sivasubbu S, Scaria V. 2014. Draft genome sequence of urease-producing Sporosarcina pasteurii with potential application in biocement production. Genome Announc. 2(1):e01256-13. doi:10.1128/genomeA.01256-13.
REFERENCES
- 1. Sarikaya M. 1999. Biomimetics: materials fabrication through biology. Proc. Natl. Acad. Sci. U. S. A. 96:14183–14185. 10.1073/pnas.96.25.14183 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Cantaert B, Beniash E, Meldrum FC. 2013. Nanoscale confinement controls the crystallization of calcium phosphate: relevance to bone formation. Chemistry 19:14918–14924. 10.1002/chem.201302835 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Lauchnor EG, Schultz LN, Bugni S, Mitchell AC, Cunningham AB, Gerlach R. 2013. Bacterially induced calcium carbonate precipitation and strontium coprecipitation in a porous media flow system. Environ. Sci. Technol. 47:1557–1564. 10.1021/es304240y [DOI] [PubMed] [Google Scholar]
- 4. Rodriguez DE, Thula-Mata T, Toro EJ, Yeh YW, Holt C, Holliday LS, Gower LB. 2014. Multifunctional role of osteopontin in directing intrafibrillar mineralization of collagen and activation of osteoclasts. Acta. Biomater. 10:494–507. 10.1016/j.actbio.2013.10.010 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Bang SS, Galinat JK, Ramakrishnan V. 2001. Calcite precipitation induced by polyurethane-immobilized Bacillus pasteurii. Enzyme Microb. Technol. 28:404–409. 10.1016/S0141-0229(00)00348-3 [DOI] [PubMed] [Google Scholar]
- 6. Benini S, Kosikowska P, Cianci M, Mazzei L, Vara A, Berlicki Ł, Ciurli S. 2013. The crystal structure of Sporosarcina pasteurii urease in a complex with citrate provides new hints for inhibitor design. J. Biol. Inorg. Chem. 18:391–399. 10.1007/s00775-013-0983-7 [DOI] [PubMed] [Google Scholar]
- 7. Wiley WR, Stokes JL. 1962. Requirement of an alkaline pH and ammonia for substrate oxidation by Bacillus pasteurii. J. Bacteriol. 84:730–734 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Raut SH, Sarode DD, Lele SS. 2014. Biocalcification using B. pasteurii for strengthening brick masonry civil engineering structures. World J. Microbiol. Biotechnol. 30:191–200. 10.1007/s11274-013-1439-5 [DOI] [PubMed] [Google Scholar]
- 9. 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. 10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]