Skip to main content
SpringerLink
Log in

Complete genome sequence of a novel Bacillus phage, P59, that infects Bacillus oceanisediminis

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

P59, a virulent phage of Bacillus oceanisediminis, was isolated from the sediment of Weiming Lake at Peking University (Beijing, China). P59 showed the typical morphology of myovirids. The complete genome sequence of P59 is 159,363 bp in length with a G+C content of 42.34%. The genome sequence has very low similarity to the other phage genome sequences in the GenBank database, suggesting that P59 is a new phage. A total of 261 open reading frames and 15 tRNA genes were predicted. Based on its morphological and genetic traits, we propose phage P59 to be a new member of the family Herelleviridae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Dion MB, Oechslin F, Moineau S (2020) Phage diversity, genomics and phylogeny. Nat Rev Microbiol 18(3):125–138. https://doi.org/10.1038/s41579-019-0311-5

    Article  CAS  PubMed  Google Scholar 

  2. Salmond GP, Fineran PC (2015) A century of the phage: past, present and future. Nat Rev Microbiol 13(12):777–786. https://doi.org/10.1038/nrmicro3564

    Article  CAS  PubMed  Google Scholar 

  3. Hernandez-Gonzalez IL, Moreno-Hagelsieb G, Olmedo-Alvarez G (2018) Environmentally-driven gene content convergence and the Bacillus phylogeny. BMC Evol Biol 18(1):148. https://doi.org/10.1186/s12862-018-1261-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ (2020) Bacillus species in soil as a natural resource for plant health and nutrition. J Appl Microbiol 128(6):1583–1594. https://doi.org/10.1111/jam.14506

    Article  CAS  PubMed  Google Scholar 

  5. Dunne M, Hupfeld M, Klumpp J, Loessner MJ (2018) Molecular basis of bacterial host interactions by gram-positive targeting bacteriophages. Viruses 10(8):397. https://doi.org/10.3390/v10080397

    Article  CAS  PubMed Central  Google Scholar 

  6. Krasowska A, Biegalska A, Augustyniak D, Los M, Richert M, Lukaszewicz M (2015) Isolation and characterization of phages infecting Bacillus subtilis. Biomed Res Int 2015:179597. https://doi.org/10.1155/2015/179597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Fu Y, Deng S, Liang L, Wu Y, Gao M (2019) Complete genome sequence of the novel phage vB_BthS-HD29phi infecting Bacillus thuringiensis. Arch Virol 164(12):3089–3093. https://doi.org/10.1007/s00705-019-04416-5

    Article  CAS  PubMed  Google Scholar 

  8. Kong L, Ding Y, Wu Q, Wang J, Zhang J, Li H, Yu S, Yu P, Gao T, Zeng H, Yang M, Liang Y, Wang Z, Xie Z, Wang Q (2019) Genome sequencing and characterization of three Bacillus cereus-specific phages, DK1, DK2, and DK3. Arch Virol 164(7):1927–1929. https://doi.org/10.1007/s00705-019-04258-1

    Article  CAS  PubMed  Google Scholar 

  9. Zhang J, Wang J, Fang C, Song F, Xin Y, Qu L, Ding K (2010) Bacillus oceanisediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 60(12):2924–2929. https://doi.org/10.1099/ijs.0.019851-0

    Article  CAS  PubMed  Google Scholar 

  10. Lee YJ, Lee SJ, Jeong H, Kim HJ, Ryu N, Kim BC, Lee HS, Lee DW, Lee SJ (2012) Draft genome sequence of Bacillus oceanisediminis 2691. J Bacteriol 194(22):6351–6352. https://doi.org/10.1128/JB.01643-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Peng F, Mi Z, Huang Y, Yuan X, Niu W, Wang Y, Hua Y, Fan H, Bai C, Tong Y (2014) Characterization, sequencing and comparative genomic analysis of vB_AbaM-IME-AB2, a novel lytic bacteriophage that infects multidrug-resistant Acinetobacter baumannii clinical isolates. BMC Microbiol 14:181. https://doi.org/10.1186/1471-2180-14-181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wang R, Xing S, Zhao F, Li P, Mi Z, Shi T, Liu H, Tong Y (2018) Characterization and genome analysis of novel phage vB_EfaP_IME195 infecting Enterococcus faecalis. Virus Genes 54(6):804–811. https://doi.org/10.1007/s11262-018-1608-6

    Article  CAS  PubMed  Google Scholar 

  13. Zhang W, Mi Z, Yin X, Fan H, An X, Zhang Z, Chen J, Tong Y (2013) Characterization of Enterococcus faecalis phage IME-EF1 and its endolysin. PLoS ONE 8(11):e80435. https://doi.org/10.1371/journal.pone.0080435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wang H, Guo Z, Feng H, Chen Y, Chen X, Li Z, Hernandez-Ascencio W, Dai X, Zhang Z, Zheng X, Mora-Lopez M, Fu Y, Zhang C, Zhu P, Huang L (2018) Novel Sulfolobus virus with an exceptional capsid architecture. J Virol 92(5):e01727–e1817. https://doi.org/10.1128/JVI.01727-17

    Article  PubMed  PubMed Central  Google Scholar 

  15. Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31(4):587–589. https://doi.org/10.1093/bioinformatics/btu661

    Article  CAS  PubMed  Google Scholar 

  16. 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(5):455–477. https://doi.org/10.1089/cmb.2012.0021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29(12):2607–2618. https://doi.org/10.1093/nar/29.12.2607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44(W1):W54–57. https://doi.org/10.1093/nar/gkw413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Barylski J, Enault F, Dutilh BE, Schuller MB, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Jang HB, Simmonds P, Aiewsakun P, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM (2020) Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages. Syst Biol 69(1):110–123. https://doi.org/10.1093/sysbio/syz036

    Article  CAS  PubMed  Google Scholar 

  20. Barylski J, Kropinski AM, Alikhan NF, Adriaenssens EM, Consortium IR (2020) ICTV virus taxonomy profile: Herelleviridae. J Gen Virol 101(4):362–363. https://doi.org/10.1099/jgv.0.001392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhao X, Shen M, Jiang X, Shen W, Zhong Q, Yang Y, Tan Y, Agnello M, He X, Hu F, Le S (2017) Transcriptomic and metabolomics profiling of phage-host interactions between phage PaP1 and Pseudomonas aeruginosa. Front Microbiol 8:548. https://doi.org/10.3389/fmicb.2017.00548

    Article  PubMed  PubMed Central  Google Scholar 

  22. Gao EB, Huang Y, Ning D (2016) Metabolic genes within cyanophage genomes: implications for diversity and evolution. Genes (Basel) 7(10):80. https://doi.org/10.3390/genes7100080

    Article  CAS  Google Scholar 

  23. Dwivedi B, Xue B, Lundin D, Edwards RA, Breitbart M (2013) A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol 13:33. https://doi.org/10.1186/1471-2148-13-33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Morgado S, Vicente AC (2019) Global in-silico scenario of tRNA genes and their organization in virus genomes. Viruses 11(2):180. https://doi.org/10.3390/v11020180

    Article  CAS  PubMed Central  Google Scholar 

  25. Bailly-Bechet M, Vergassola M, Rocha E (2007) Causes for the intriguing presence of tRNAs in phages. Genome Res 17(10):1486–1495. https://doi.org/10.1101/gr.6649807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Delesalle VA, Tanke NT, Vill AC, Krukonis GP (2016) Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes. Bacteriophage 6(3):e1219441. https://doi.org/10.1080/21597081.2016.1219441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Xu YL, Zhang R, Wang NN, Cai LL, Tong YG, Sun Q, Chen F, Jiao NZ (2018) Novel phage-host interactions and evolution as revealed by a cyanomyovirus isolated from an estuarine environment. Environ Microbiol 20(8):2974–2989. https://doi.org/10.1111/1462-2920.14326

    Article  CAS  PubMed  Google Scholar 

  28. Lancaster JC, Hodde MK, Hernandez AC, Kuty Everett GF (2015) Complete genome sequence of Bacillus megaterium myophage mater. Genome Announc 3(1):e01424–e1514. https://doi.org/10.1128/genomeA.01424-14

    Article  PubMed  PubMed Central  Google Scholar 

  29. Miller SY, Colquhoun JM, Perl AL, Chamakura KR, Kuty Everett GF (2013) Complete genome of Bacillus subtilis myophage grass. Genome Announc 1(6):e00857–e913. https://doi.org/10.1128/genomeA.00857-13

    Article  PubMed  PubMed Central  Google Scholar 

  30. Cadungog JN, Khatemi BE, Hernandez AC, Kuty Everett GF (2015) Complete genome sequence of Bacillus megaterium myophage moonbeam. Genome Announc 3(1):e01428–e1514. https://doi.org/10.1128/genomeA.01428-14

    Article  PubMed  PubMed Central  Google Scholar 

  31. Burton BM, Marquis KA, Sullivan NL, Rapoport TA, Rudner DZ (2007) The ATPase SpoIIIE transports DNA across fused septal membranes during sporulation in Bacillus subtilis. Cell 131(7):1301–1312. https://doi.org/10.1016/j.cell.2007.11.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27(7):1009–1010. https://doi.org/10.1093/bioinformatics/btr039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Liu GY, Lin X, Xu SY, Liu G, Liu F, Mu W (2020) Screening, identification and application of soil bacteria with nematicidal activity against root-knot nematode (Meloidogyne incognita) on tomato. Pest Manag Sci 76(6):2217–2224. https://doi.org/10.1002/ps.5759

    Article  CAS  PubMed  Google Scholar 

  35. Boucherba N, Gagaoua M, Bouanane-Darenfed A, Bouiche C, Bouacem K, Kerbous MY, Maafa Y, Benallaoua S (2017) Biochemical properties of a new thermo- and solvent-stable xylanase recovered using three phase partitioning from the extract of Bacillus oceanisediminis strain SJ3. Bioresour Bioprocess 4(1):29. https://doi.org/10.1186/s40643-017-0161-9

    Article  PubMed  PubMed Central  Google Scholar 

  36. Jung J, Jeong H, Kim HJ, Lee DW, Lee SJ (2016) Complete genome sequence of Bacillus oceanisediminis 2691, a reservoir of heavy-metal resistance genes. Mar Genom 30:73–76. https://doi.org/10.1016/j.margen.2016.07.002

    Article  Google Scholar 

Download references

Acknowledgements

The authors want to express their many thanks to Prof. Yigang Tong from Beijing University of Chemical Technology and Prof. Xiangyu Fan from Jinan University for valuable discussions. This work was supported by the National Key R&D Program of China (2018YFA0902100 and 2018YFA0902103) and the National Natural Science Foundation of China (31761133006 to XLW).

Funding

This work was supported by the National Key R&D Program of China (2018YFA0902100 and 2018YFA0902103) and the National Natural Science Foundation of China (31761133006 to XLW).

Author information

Authors and Affiliations

  1. College of Engineering, Peking University, Beijing, 100871, China

    Zhou Feng, Xinwu Liu, Yong Nie & Xiaolei Wu

  2. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China

    Wang Liu

  3. Institute of Ocean Research, Peking University, Beijing, 100871, China

    Xiaolei Wu

Authors
  1. Zhou Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xinwu Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yong Nie
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiaolei Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yong Nie or Xiaolei Wu.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Availability of data and material

The nucleotide sequence data reported here are available in the GenBank database under the accession number MT151604.

Additional information

Handling Editor: T. K. Frey.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 1011 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Feng, Z., Liu, X., Liu, W. et al. Complete genome sequence of a novel Bacillus phage, P59, that infects Bacillus oceanisediminis. Arch Virol 165, 2679–2683 (2020). https://doi.org/10.1007/s00705-020-04761-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-020-04761-w

Search

Navigation