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

Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing

Daniel L. Vera, Arman Seuylemezian, Kyle S. Landry, Ryan Hendrickson
J. Cameron Thrash, Editor
Daniel L. Vera
bLiberty Biosecurity, Expeditionary and Special Programs Division, Worcester, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arman Seuylemezian
aJet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kyle S. Landry
bLiberty Biosecurity, Expeditionary and Special Programs Division, Worcester, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ryan Hendrickson
aJet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. Cameron Thrash
University of Southern California
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.01161-19
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Whole-genome sequencing and annotation have allowed planetary protection engineers to assess the functional capabilities of microorganisms isolated from spacecraft hardware and associated surfaces. Here, we report draft genomes of six strains isolated from the InSight mission, determined using Oxford Nanopore- and Illumina-based sequencing.

ANNOUNCEMENT

The Interior Exploration using Seismic Investigations, Geodesy, and Heat Transport (InSight) spacecraft was launched in May 2018 to explore the interior structure of Mars using the HP3 and SEIS instruments. Because it was classified as a planetary protection (PP) sensitive mission, microbial cleanliness requirements were imposed on the InSight mission, and PP sampling was performed using the NASA standard spore assay throughout the life cycle of the project leading up to launch on 5 May 2018 (1). The assay selects for hardy organisms capable of surviving heat shock at 80°C for 15 min and growing on Trypticase soy agar (TSA) incubated for 72 h at 32°C. Resulting colonies are subcultured and archived for long-term storage following previously established procedures (2). Flight hardware components were sampled during final closeout activities dictated by integration timelines. Isolates generated throughout the life cycle of the project were routinely identified with matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) using previously established procedures (2). Of particular interest were six strains isolated from various spacecraft surfaces and surfaces of cleanrooms where the spacecraft was assembled. These six strains originally were identified as belonging to the same species using MALDI-TOF MS and subsequently were subjected to whole-genome sequencing and functional annotation for further characterization.

Isolates were cultured on TSA plates and incubated for 24 h; once the purity of the culture was confirmed, DNA was extracted using phenol-chloroform extraction and ethanol precipitation (3). High-molecular-weight DNA (>20 kb) was isolated using a BluePippin system (Sage Science, Beverly, MA, USA) with a High Pass Plus cassette. Nanopore libraries were generated with the SQK-LSK109 1D genomic ligation kit (Oxford Nanopore Technologies, Oxford Science Park, UK). Reads were generated with an R9.4.1 flow cell using a 48-h script. Default parameters were used for all software tools unless otherwise noted. Reads were base called with Guppy v2.3.1+1b9405b6 (4), demultiplexed with Deepbinner v0.2.0 (5), trimmed of adapters with Porechop v0.2.4, and assembled with Canu v1.8 (6). For Illumina-based polishing, libraries were sequenced on a MiSeq platform with paired-end 300-bp v3 chemistry. Reads were trimmed and filtered using Cutadapt v2.5 (7). Reads were then aligned and used to polish the assemblies with NextPolish v1.1.0 using default parameters (8). The assembled draft genomes were submitted for annotation using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Assembly statistics for all six strains are provided in Table 1.

View this table:
  • View inline
  • View popup
  • Download powerpoint
TABLE 1

Genome statistics for six draft genomes of Bacillus megaterium strains isolated from the InSight spacecraft and associated surfaces

Taxonomic identification was performed using both average nucleotide identity (ANI) analysis using the Ortho-ANI algorithm (9) and pairwise comparisons of the 16S rRNA sequences extracted from whole-genome sequences against both the nonredundant/nucleotide and 16S rRNA type strain databases using BLASTn. Based on these techniques, all six strains belonged to Bacillus megaterium.

Several strains were annotated with putative genes that may have potential applications in the biotechnological or pharmaceutical industries. Strain IN_103 had a putative gene coding for a branched-chain amino acid (BCAA) aminotransferase, which catalyzes the formation of α-ketoacids and BCAAs (10). IN_903 had putative genes coding for 5-aminolevulinate synthase, which catalyzes the formation of tetrapyrroles (precursors to hemes); this enzyme has been utilized to biosynthetically produce tetrapyrrole compounds (11). Strain IN_866 had a putative gene coding for a flavin reductase, which has been utilized in gene-directed prodrug therapies to target tumor hypoxia (12).

Data availability.The draft genomes of all six strains have been deposited in DDBJ/EMBL/GenBank under the accession numbers provided in Table 1.

ACKNOWLEDGMENT

This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.

FOOTNOTES

    • Received 14 October 2019.
    • Accepted 15 April 2020.
    • Published 21 May 2020.
  • Copyright © 2020 Vera et al.

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

REFERENCES

  1. 1.↵
    National Aeronautics and Space Administration. 2010. Handbook for the microbial examination of space hardware. NASA-HDBK-6022. National Aeronautics and Space Administration, Washington, DC. https://explorers.larc.nasa.gov/2019APSMEX/SMEX/pdf_files/NASA-HDBK-6022b.pdf.
  2. 2.↵
    1. Seuylemezian A,
    2. Aronson HS,
    3. Tan J,
    4. Lin M,
    5. Schubert W,
    6. Vaishampayan P
    . 2018. Development of a custom MALDI-TOF MS database for species-level identification of bacterial isolates collected from spacecraft and associated surfaces. Front Microbiol 9:780. doi:10.3389/fmicb.2018.00780.
    OpenUrlCrossRef
  3. 3.↵
    1. Zumbo P
    . 1979. Phenol-chloroform extraction. Weill Cornell Medical College, New York, NY.
  4. 4.↵
    1. Wick RR,
    2. Judd LM,
    3. Holt KE
    . 2019. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 20:129. doi:10.1186/s13059-019-1727-y.
    OpenUrlCrossRef
  5. 5.↵
    1. Wick RR,
    2. Judd LM,
    3. Holt KE
    . 2018. Deepbinner: demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS Comput Biol 14:e1006583. doi:10.1371/journal.pcbi.1006583.
    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. Martin M
    . 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10. doi:10.14806/ej.17.1.200.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Hu J,
    2. Fan J,
    3. Sun Z,
    4. Liu S
    . 2020. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253–2255. doi:10.1093/bioinformatics/btz891.
    OpenUrlCrossRef
  9. 9.↵
    1. Yoon SH,
    2. Ha S,
    3. Lim J,
    4. Kwon S,
    5. Chun J
    . 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. doi:10.1007/s10482-017-0844-4.
    OpenUrlCrossRef
  10. 10.↵
    1. Bezsudnova EY,
    2. Boyko KM,
    3. Popov VO
    . 2017. Properties of bacterial and archaeal branched-chain amino acid aminotransferases. Biochemistry (Mosc) 82:1572–1591. doi:10.1134/S0006297917130028.
    OpenUrlCrossRef
  11. 11.↵
    1. Stojanovski BM,
    2. Hunter GA,
    3. Na I,
    4. Uversky VN,
    5. Jiang RHY,
    6. Ferreira GC
    . 2019. 5-Aminolevulinate synthase catalysis: the catcher in heme biosynthesis. Mol Genet Metab 128:178–189. doi:10.1016/j.ymgme.2019.06.003.
    OpenUrlCrossRef
  12. 12.↵
    1. Green LK,
    2. Storey MA,
    3. Williams EM,
    4. Patterson AV,
    5. Smaill JB,
    6. Copp JN,
    7. Ackerley DF
    . 2013. The flavin reductase MsuE is a novel nitroreductase that can efficiently activate two promising next-generation prodrugs for gene-directed enzyme prodrug therapy. Cancers (Basel) 5:985–997. doi:10.3390/cancers5030985.
    OpenUrlCrossRef
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing
Daniel L. Vera, Arman Seuylemezian, Kyle S. Landry, Ryan Hendrickson
Microbiology Resource Announcements May 2020, 9 (21) e01161-19; DOI: 10.1128/MRA.01161-19

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.
Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing
(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
Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing
Daniel L. Vera, Arman Seuylemezian, Kyle S. Landry, Ryan Hendrickson
Microbiology Resource Announcements May 2020, 9 (21) e01161-19; DOI: 10.1128/MRA.01161-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENT
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • 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