Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan

Daniel Evans-Yamamoto, Nao Takeuchi, Takahiro Masuda, Yumi Murai, Yasuhide Onuma, Hideto Mori, Nanami Masuyama, Soh Ishiguro, Nozomu Yachie, Kazuharu Arakawa
Frank J. Stewart, Editor
Daniel Evans-Yamamoto
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
cSynthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nao Takeuchi
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
dFaculty of Environment and Information Studies, Keio University, Fujisawa, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Takahiro Masuda
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yumi Murai
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
dFaculty of Environment and Information Studies, Keio University, Fujisawa, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yasuhide Onuma
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hideto Mori
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
cSynthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nanami Masuyama
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
cSynthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Soh Ishiguro
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
cSynthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nozomu Yachie
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
cSynthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
eDepartment of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
fPRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kazuharu Arakawa
aInstitute for Advanced Biosciences, Keio University, Tsuruoka, Japan
bSystems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
dFaculty of Environment and Information Studies, Keio University, Fujisawa, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kazuharu Arakawa
Frank J. Stewart
Georgia Institute of Technology
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00326-19
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Psychrobacter sp. strain KH172YL61 is a Gram-negative bacterium isolated from deep-sea sediment in the Nankai Trough in Japan. Here, we report the complete genome sequence of this strain, which has a genome size of 3.19 Mb, with a G+C content of 44.0%.

ANNOUNCEMENT

The genus Psychrobacter is a group of Gram-negative, psychrotolerant, aerobic, and nonmotile bacteria (1). They are able to grow below 5°C and have been isolated from various cold habitats. To date, strains of this genus have been isolated from low-temperature environments, including deep-sea sediments, Antarctic soil, and sea ice (2). Some Psychrobacter strains produce carbonic anhydrase enzymes, which suggests their potential for bioremediation through precipitation of heavy metals (3). Several Psychrobacter strains are reported to produce cold-adapted enzymes (4, 5). The diversity and high catalytic activity of strains as well as low energy consumption at low temperatures support great potential for further exploration of the genus.

Psychrobacter sp. strain KH172YL61 was isolated from deep-sea sediment collected 3,308 m below sea level in the Nankai Trough in Japan (33°27′005″N, 137°16′990″E). The taxonomy was assigned by Sanger sequencing of amplified 16S rRNA genes, for which BLAST search matched with 100% identity to many sequences from the Psychrobacter genus. A frozen sample was used to inoculate a modified seawater broth (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. A single colony was then used to inoculate an overnight culture in the modified artificial seawater broth (30°C with shaking at 160 rpm). The total genomic DNA was isolated using the Genomic-tip 20/G system (Qiagen). A genomic DNA library for sequencing was prepared using the rapid barcoding kit (SQK-RAB004) and sequenced on a GridION device with a FLO-MIN106 flow cell (Oxford Nanopore Technologies). Reads with at least 10,000 bp were used for the de novo assembly (86-fold coverage, 28,000 out of 111,000 reads) using Canu version 1.8.0 (6). Contigs obtained from the assembly were polished using Nanopolish version 0.10.1 (7). The resulting genome sequence was functionally annotated using DFAST version 1.0.2 (8). The assembled genome consists of one circular chromosome of 3,188,207 bp having 44.0% G+C content, including 4,129 coding sequences (CDSs), 50 tRNAs, and 15 rRNAs, respectively. Assessment of the genome completeness using gVolante version 1.2.0 (9) showed 85% BUSCO completeness, a quantitative assessment of assembly completeness based on the coverage of an evolutionarily conserved set of single-copy orthologs, indicating a certain amount of uncorrected indels. All software programs were used with the default settings.

According to the annotation results, the genome of Psychrobacter sp. KH172YL61 encodes genes involved in the production of cold shock proteins, namely cspA and cspV (10). Cold shock proteins are known to counteract cold stress conditions by serving as nucleic acid chaperons. The complete genome reported in this work may facilitate the understanding of mechanisms of cold stress response within psychrophiles.

Data availability.The chromosome sequence reported here was deposited in DDBJ/GenBank under accession number AP019516 and in the Sequence Read Archive (SRA) under accession number PRJNA521446.

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.

FOOTNOTES

    • Received 19 March 2019.
    • Accepted 25 March 2019.
    • Published 18 April 2019.
  • Copyright © 2019 Evans-Yamamoto et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Maruyama A,
    2. Honda D,
    3. Yamamoto H,
    4. Kitamura K,
    5. Higashihara T
    . 2000. Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. Int J Syst Evol Microbiol 50:835–846. doi:10.1099/00207713-50-2-835.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Bozal N,
    2. Montes MJ,
    3. Tudela E,
    4. Guinea J
    . 2003. Characterization of several Psychrobacter strains isolated from Antarctic environments and description of Psychrobacter luti sp. nov. and Psychrobacter fozii sp. nov. Int J Syst Evol Microbiol 53:1093–1100. doi:10.1099/ijs.0.02457-0.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Kumari D,
    2. Qian XY,
    3. Pan X,
    4. Achal V,
    5. Li Q,
    6. Gadd GM
    . 2016. Microbially-induced carbonate precipitation for immobilization of toxic metals. Adv Appl Microbiol 94:79–108. doi:10.1016/bs.aambs.2015.12.002.
    OpenUrlCrossRef
  4. 4.↵
    1. Chen R,
    2. Guo L,
    3. Dang H
    . 2011. Gene cloning, expression and characterization of a cold-adapted lipase from a psychrophilic deep-sea bacterium Psychrobacter sp. C18. World J Microbiol Biotechnol 27:431–441. doi:10.1007/s11274-010-0475-7.
    OpenUrlCrossRef
  5. 5.↵
    1. Wu G,
    2. Zhang S,
    3. Zhang H,
    4. Zhang S,
    5. Liu Z
    . 2013. A novel esterase from a psychrotrophic bacterium Psychrobacter celer 3Pb1 showed cold-adaptation and salt-tolerance. J Mol Catal B Enzym 98:119–126. doi:10.1016/j.molcatb.2013.10.012.
    OpenUrlCrossRef
  6. 6.↵
    1. Koren S,
    2. Walenz BP,
    3. Berlin K,
    4. Miller JR,
    5. Bergman NH,
    6. Phillippy AM
    . 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. doi:10.1101/gr.215087.116.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    1. Loman NJ,
    2. Quick J,
    3. Simpson JT
    . 2015. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12:733. doi:10.1038/nmeth.3444.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Tanizawa Y,
    2. Fujisawa T,
    3. Kaminuma E,
    4. Nakamura Y,
    5. Arita M
    . 2016. DFAST and Daga: Web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 35:173–184. doi:10.12938/bmfh.16-003.
    OpenUrlCrossRef
  9. 9.↵
    1. Nishimura O,
    2. Hara Y,
    3. Kuraku S
    . 2017. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 33:3635–3637. doi:10.1093/bioinformatics/btx445.
    OpenUrlCrossRef
  10. 10.↵
    1. Keto-Timonen R,
    2. Hietala N,
    3. Palonen E,
    4. Hakakorpi A,
    5. Lindström M,
    6. Korkeala H
    . 2016. Cold shock proteins: a minireview with special emphasis on Csp-family of enteropathogenic Yersinia. Front Microbiol 22:1151. doi:10.3389/fmicb.2016.01151.
    OpenUrlCrossRef
PreviousNext
Back to top
Download PDF
Citation Tools
Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan
Daniel Evans-Yamamoto, Nao Takeuchi, Takahiro Masuda, Yumi Murai, Yasuhide Onuma, Hideto Mori, Nanami Masuyama, Soh Ishiguro, Nozomu Yachie, Kazuharu Arakawa
Microbiology Resource Announcements Apr 2019, 8 (16) e00326-19; DOI: 10.1128/MRA.00326-19

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan
Daniel Evans-Yamamoto, Nao Takeuchi, Takahiro Masuda, Yumi Murai, Yasuhide Onuma, Hideto Mori, Nanami Masuyama, Soh Ishiguro, Nozomu Yachie, Kazuharu Arakawa
Microbiology Resource Announcements Apr 2019, 8 (16) e00326-19; DOI: 10.1128/MRA.00326-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X