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Draft Genome Sequences of Two Ureolytic Bacteria Isolated from Concrete Block Waste Hongjae Park,a Byeonghyeok Park,a Hyun Jung Kim,b Woojun Park,b In-Geol Choia Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, South Koreaa; Department of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, South Koreab H.P. and B.P. contributed equally to this work.
We sequenced genomes of two ureolytic bacteria, Bacillus sp. JH7 and Sporosarcina sp. HYO08, which were isolated from concrete waste and have a potential for biocementation applications. Received 7 June 2016 Accepted 10 June 2016 Published 4 August 2016 Citation Park H, Park B, Kim HJ, Park W, Choi I-G. 2016. Draft genome sequences of two ureolytic bacteria isolated from concrete block waste. Genome Announc 4(4):e00762-16. doi:10.1128/genomeA.00762-16. Copyright © 2016 Park et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to In-Geol Choi, [email protected], or Woojun Park, [email protected].
M
icrobiologically induced calcite precipitation (MICP) is a natural biogeochemical process in which microbial ureases often intervene (1). The biomediated production of calcite crystals has been regarded as a biocementation process that can be utilized for self-healing of concrete cracks in buildings (2). Seeking candidate microbes for biocementation, we isolated two MICP-capable bacteria, Bacillus sp. JH7 and Sporosarcina sp. HYO08, from concrete block waste collected from two deserted construction sites in South Korea (3). The genome sequencing was carried out by the Illumina MiSeq platform using paired-end libraries with an average insert size of 500 bp. We obtained 1.46 million paired-end reads (total 851 Mbp; 152-fold coverage) and 1.94 million paired-end reads (total 1,090 Mbp; 352-fold coverage) from the JH7 and HYO08 strains, respectively. Low-quality (Q ⬍ 30) reads were eliminated by the HTQC program (4). The filtered reads were assembled using the SPAdes program (5). The final assembly was 5,547,983 bp with 36 scaffolds for JH7 and 3,051,793 bp with 32 scaffolds for HYO08. The N50 values for the two assemblies were 3,345,253 bp for JH7 and 413,117 bp for HYO08. Annotation of genomic sequences was performed using the NCBI Prokaryotic Genome Annotation Pipeline. A total of 5,404 and 2,891 protein-coding genes, 38 and 27 rRNA coding sequences, and 91 and 81 tRNA coding sequences for JH7 and HYO08, respectively, were identified. Nucleotide sequence accession numbers. The nucleotide sequences have been deposited in GenBank under the accession
July/August 2016 Volume 4 Issue 4 e00762-16
numbers LPUS00000000 for Bacillus sp. JH7 and LPUT00000000 for Sporosarcina sp. HYO08. ACKNOWLEDGMENTS This work was supported by the Korea University. We thank Wook Kim and Namhyun Chung for their advice.
FUNDING INFORMATION This work, including the efforts of In-Geol Choi, was funded by Korea University (KU).
REFERENCES 1. Bachmeier KL, Williams AE, Warmington JR, Bang SS. 2002. Urease activity in microbiologically-induced calcite precipitation. J Biotechnol 93: 171–181. http://dx.doi.org/10.1016/S0168-1656(01)00393-5. 2. Seifan M, Samani AK, Berenjian A. 2016. Bioconcrete: next generation of self-healing concrete. Appl Microbiol Biotechnol 100:2591–2602. http:// dx.doi.org/10.1007/s00253-016-7316-z. 3. Kim HJ, Eom HJ, Park C, Jung J, Shin B, Kim W, Chung N, Choi IG, Park W. 2016. Calcium carbonate precipitation by Bacillus and Sporosarcina strains isolated from concrete and analysis of the bacterial community of concrete. J Microbiol Biotechnol 26:540 –548. http://dx.doi.org/10.4014/ jmb.1511.11008. 4. Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F, Zhu B. 2013. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics 14:33. http://dx.doi.org/10.1186/1471-2105-14-33. 5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.
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Draft Genome Sequences of Two Ureolytic Bacteria Isolated from Concrete Block Waste Hongjae Park,a Byeonghyeok Park,a Hyun Jung Kim,b Woojun Park,b In-Geol Choia Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, South Koreaa; Department of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, South Koreab H.P. and B.P. contributed equally to this work.
We sequenced genomes of two ureolytic bacteria, Bacillus sp. JH7 and Sporosarcina sp. HYO08, which were isolated from concrete waste and have a potential for biocementation applications. Received 7 June 2016 Accepted 10 June 2016 Published 4 August 2016 Citation Park H, Park B, Kim HJ, Park W, Choi I-G. 2016. Draft genome sequences of two ureolytic bacteria isolated from concrete block waste. Genome Announc 4(4):e00762-16. doi:10.1128/genomeA.00762-16. Copyright © 2016 Park et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to In-Geol Choi, [email protected], or Woojun Park, [email protected].
M
icrobiologically induced calcite precipitation (MICP) is a natural biogeochemical process in which microbial ureases often intervene (1). The biomediated production of calcite crystals has been regarded as a biocementation process that can be utilized for self-healing of concrete cracks in buildings (2). Seeking candidate microbes for biocementation, we isolated two MICP-capable bacteria, Bacillus sp. JH7 and Sporosarcina sp. HYO08, from concrete block waste collected from two deserted construction sites in South Korea (3). The genome sequencing was carried out by the Illumina MiSeq platform using paired-end libraries with an average insert size of 500 bp. We obtained 1.46 million paired-end reads (total 851 Mbp; 152-fold coverage) and 1.94 million paired-end reads (total 1,090 Mbp; 352-fold coverage) from the JH7 and HYO08 strains, respectively. Low-quality (Q ⬍ 30) reads were eliminated by the HTQC program (4). The filtered reads were assembled using the SPAdes program (5). The final assembly was 5,547,983 bp with 36 scaffolds for JH7 and 3,051,793 bp with 32 scaffolds for HYO08. The N50 values for the two assemblies were 3,345,253 bp for JH7 and 413,117 bp for HYO08. Annotation of genomic sequences was performed using the NCBI Prokaryotic Genome Annotation Pipeline. A total of 5,404 and 2,891 protein-coding genes, 38 and 27 rRNA coding sequences, and 91 and 81 tRNA coding sequences for JH7 and HYO08, respectively, were identified. Nucleotide sequence accession numbers. The nucleotide sequences have been deposited in GenBank under the accession
July/August 2016 Volume 4 Issue 4 e00762-16
numbers LPUS00000000 for Bacillus sp. JH7 and LPUT00000000 for Sporosarcina sp. HYO08. ACKNOWLEDGMENTS This work was supported by the Korea University. We thank Wook Kim and Namhyun Chung for their advice.
FUNDING INFORMATION This work, including the efforts of In-Geol Choi, was funded by Korea University (KU).
REFERENCES 1. Bachmeier KL, Williams AE, Warmington JR, Bang SS. 2002. Urease activity in microbiologically-induced calcite precipitation. J Biotechnol 93: 171–181. http://dx.doi.org/10.1016/S0168-1656(01)00393-5. 2. Seifan M, Samani AK, Berenjian A. 2016. Bioconcrete: next generation of self-healing concrete. Appl Microbiol Biotechnol 100:2591–2602. http:// dx.doi.org/10.1007/s00253-016-7316-z. 3. Kim HJ, Eom HJ, Park C, Jung J, Shin B, Kim W, Chung N, Choi IG, Park W. 2016. Calcium carbonate precipitation by Bacillus and Sporosarcina strains isolated from concrete and analysis of the bacterial community of concrete. J Microbiol Biotechnol 26:540 –548. http://dx.doi.org/10.4014/ jmb.1511.11008. 4. Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F, Zhu B. 2013. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics 14:33. http://dx.doi.org/10.1186/1471-2105-14-33. 5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.
Genome Announcements
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