Open access
Announcement
16 April 2020

Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment

ABSTRACT

Bacillus sp. strain KH172YL63 is a Gram-positive bacterium isolated from the deep-sea floor surface sediment at 3,308 m below sea level in the Nankai Trough in Japan. Here, we report the complete genome sequence of Bacillus sp. strain KH172YL63, which has a genome size of 4,251,700 bp and a G+C content of 44.8%.

ANNOUNCEMENT

In the past few decades, there has been an increasing interest in marine organisms as possible sources of bioactive compounds, e.g., proteases (1) and alkaline cellulases (2). Bacillus species have been isolated from a huge variety of environments, both terrestrial and aquatic, including the model species Bacillus subtilis. Bacillus sp. strain KH172YL63 (phylum Firmicutes, class Bacilli, order Bacillales, family Bacillaceae) is a moderately psychrotrophic bacterium isolated from seawater of deep-sea sediment 3,308 m below sea level in the Nankai Trough in Japan (33°27′005ʺN, 137°16′990ʺE). Sediments from the sea bed were collected using a multiple corer, which collects sediments 0 to 1 m below the sea floor. We resuspended 100 mg of the dissolved mud samples in 3 ml of artificial seawater, plated dilution series onto modified seawater medium plates (360.75 mM NaCl, 7.5 mM KCl, 8.25 mM CaCl2 · 2H2O, 18 mM MgCl2 · 6H2O, 0.75 mM NaHCO3, 10.5 mM MgSO4 · 7H2O, 5.0% [wt/vol] Bacto peptone, 3.0% [wt/vol] yeast extract, and 1.5% Bacto agar), and incubated them at 20°C for single colony isolation. Colonies were obtained from samples collected 0 m below the sea floor.
Bacillus sp. KH172YL63 was inoculated onto a modified seawater medium (360.75 mM NaCl, 7.5 mM KCl, 8.25 mM CaCl2 · 2H2O, 18 mM MgCl2 · 6H2O, 0.75 mM NaHCO3, 10.5 mM MgSO4 · 7H2O, 5.0% [wt/vol] Bacto peptone, 3.0% [wt/vol] yeast extract, and 1.5% Bacto agar) plate for the isolation of single colonies. Taxonomic identification was performed using Sanger sequencing of amplified 16S rRNA genes, and a BLAST search matched with 99.93% identity to Bacillus sp. strain CNJ817 PL04. Genomic DNA was extracted using a Genomic-tip 20/G kit (Qiagen), and extracted DNA was used for both Nanopore and Illumina sequencing. The long reads for Bacillus sp. KH172YL63 were generated with GridION sequencing (Oxford Nanopore Technologies), where the sequencing library was prepared using the rapid barcoding kit (SQK-RBK004) and was run in a FLO-MIN106 flow cell. For Illumina sequencing, a library of fragmented genomic DNA was prepared using a HyperPlus library preparation kit (KAPA Biosystems) and sequenced on a NextSeq 500 sequencer with high-output mode and 75 cycles (Illumina). A total of 251,000 (N50 value, 19 kbp; maximum length, 183 kbp) and 79.7 million reads were obtained for the Nanopore and Illumina sequencing, respectively.
The genome sequence was obtained by de novo assembly using raw Nanopore reads with default settings of the Canu assembler v1.8.0 (3). An improved consensus sequence for the draft assembly was obtained with raw Illumina reads and the Pilon software v1.23 using default parameters (4). The assembly resulted in a single contig spanning the entire chromosome, with a total length of 4,251,700 bp and a G+C content of 44.8%. Automatic genome annotation was performed with DFAST (DDBJ Fast Annotation and Submission Tool) (5). We identified 4,243 coding sequences (CDSs), 108 tRNAs, and 33 rRNAs. The assembly completeness was assessed with BUSCO v1 (6) on the gVolante server (7), resulting in 100% completeness.
Bacillus sp. KH172YL63 has several proteases, such as germination protease, an ATP-dependent Clp protease, and the ATP-binding subunits ClpE and ClpX. These proteases may be applied in industrial processes (8). The complete genome sequence of Bacillus sp. KH172YL63 reported here may facilitate proteases studies.

Data availability.

The complete genome sequence of Bacillus sp. KH172YL63 has been deposited in DDBJ/GenBank under the accession number AP022842. The assembly and raw reads are collected together under BioProject number PRJNA606022.

ACKNOWLEDGMENTS

The samples were obtained as part of the joint-use research voyage KH-17-2. We thank Juichiro Ashi of the Atmosphere and Ocean Research Institute of the University of Tokyo for leading this voyage. We thank Yuki Yoshida and Yuki Takai for technical assistance. The sequencing and assembly were conducted in the Genome Engineering Workshop course of the Systems Biology Program, Graduate School of Media and Governance, Keio University.
This work was supported, in part, by research funds from the Yamagata prefectural government and Tsuruoka City, Japan.

REFERENCES

1.
Phelan RW, O’Halloran JA, Kennedy J, Morrissey JP, Dobson ADW, O’Gara F, Barbosa TM. 2012. Diversity and bioactive potential of endospore-forming bacteria cultured from the marine sponge Haliclona simulans. J Appl Microbiol 112:65–78.
2.
Trivedi N, Gupta V, Kumar M, Kumari P, Reddy CR, Jha B. 2011. Solvent tolerant marine bacterium Bacillus aquimaris secreting organic solvent stable alkaline cellulase. Chemosphere 83:706–712.
3.
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736.
4.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963.
5.
Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. 2016. DFAST and DAGA: Web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 35:173–184.
6.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212.
7.
Nishimura O, Hara Y, Kuraku S. 2017. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 33:3635–3637.
8.
Contesini FJ, Melo RR, Sato HH. 2018. An overview of Bacillus proteases: from production to application. Crit Rev Biotechnol 38:321–334.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 9Number 1616 April 2020
eLocator: 10.1128/mra.00291-20
Editor: Simon Roux, DOE Joint Genome Institute

History

Received: 17 March 2020
Accepted: 25 March 2020
Published online: 16 April 2020

Contributors

Authors

Yumi Murai
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Takahiro Masuda
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Yasuhide Onuma
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Daniel Evans-Yamamoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
Nao Takeuchi
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Hideto Mori
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
Nanami Masuyama
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
Soh Ishiguro
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
Nozomu Yachie
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
PRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan

Editor

Simon Roux
Editor
DOE Joint Genome Institute

Notes

Address correspondence to Kazuharu Arakawa, [email protected].

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy