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Genome Analysis of Two Novel Lytic Vibrio maritimus Phages Isolated from the Coastal Surface Seawater of Qingdao, China

  • Yuye Han
  • Min Wang
  • Qian Liu
  • Yundan Liu
  • Qi Wang
  • Xueping Duan
  • Lu Liu
  • Yong Jiang
  • Hongbing Shao
  • Cui GuoEmail author
Article
  • 13 Downloads

Abstract

Two novel Vibrio phages, LP.1 and LP.2 that infected Vibrio maritimus R-40493, were isolated from surface seawater in Qingdao coastal area by the double-agar layer method. Morphological analysis by transmission electron microscope showed that the two phages displayed head–tail structures with icosahedral heads of 62.37 and 54.00 nm in diameter and long non-contractile tails of 119.00 and 105.20 nm in length, respectively, and can be grouped into the Siphoviridae family. Thermal and pH sensitivity tests exhibited that LP.1 was stable at temperature ranging from − 20 to 65 °C and at pH ranging from 5 to 12, and LP.2 showed vitality over a wider range of temperature (− 20–75 °C) and pH (3–12). Both LP.1 and LP.2 contained linear and double-stranded DNA genomes with a length of 46,791-bp and 37,128-bp, respectively. The genome of both phages can be classified into four functional groups, including DNA replication and regulation, phage packaging, phage structure, and additional function. The bioinformatic analysis demonstrated that the Vibrio phages LP.1 and LP.2 are novel phages. By conducting morphological, biochemical, and genomic analysis, our study provides useful information for further research on the interaction between Vibrio phages and their host.

Notes

Acknowledgements

The study was funded by National Key R&D Program of China (No. 2018YFC1406704); Open research fund of LMB (No. LMB20091001); the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (No. 2018SDKJ0406-6); Qingdao National Laboratory for Marine Science and Technology (No. 2016ASKJ14); The Fundamental Research Funds for the Central Universities (Nos. 201562018, 201812002, 201762017); State Oceanic Administration People’s republic of China (Nos. GASI-02-PAC-ST-MSwin, GASI-02-PAC-ST-MSaut); and Natural Science Foundation of China (Nos. 41076088, 41676178, 31500339).

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

References

  1. 1.
    Abedon ST, Hyman P, Thomas C (2003) Experimental examination of bacteriophage latent-period evolution as a response to bacterial availability. Appl Environ Microbiol 69(12):7499–7506.  https://doi.org/10.1128/AEM.69.12.7499-7506.2003 CrossRefGoogle Scholar
  2. 2.
    Baudoux AC, Hendrix RW, Lander GC, Bailly X, Podell S, Paillard C et al (2012) Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ Microbiol 14(8):2071–2086.  https://doi.org/10.1111/j.1462-2920.2011.02685.x CrossRefGoogle Scholar
  3. 3.
    Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A, Vos PD et al (2011) Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov. isolated from Palythoa caribaeorum. Int J Syst Evol Microbiol 61(12):3009.  https://doi.org/10.1099/ijs.0.026997-0 CrossRefGoogle Scholar
  4. 4.
    Danovaro R, Corinaldesi C, Dell’’nno A, Fuhrman JA, Middelburg JJ, Noble RT et al (2011) Marine viruses and global climate change. FEMS Microbiol Rev 35(6):993–1034.  https://doi.org/10.1111/j.1574-6976.2010.00258.x CrossRefGoogle Scholar
  5. 5.
    Dyson ZA, Brown TL, Farrar B, Doyle SR, Tucci J, Seviour RJ, Petrovski S (2016) Locating and activating molecular ‘Time Bombs’: induction of Mycolata prophages. PLoS ONE 11(8):e0159957.  https://doi.org/10.1371/journal.pone.0159957 CrossRefGoogle Scholar
  6. 6.
    Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399(6736):541–548.  https://doi.org/10.1038/21119 CrossRefGoogle Scholar
  7. 7.
    Gong Z, Wang M, Yang Q et al (2017) Isolation and complete genome sequence of a novel Pseudoalteromonas phage PH357 from the Yangtze River Estuary. Curr Microbiol 74:832.  https://doi.org/10.1007/s00284-017-1244-8 CrossRefGoogle Scholar
  8. 8.
    Grimes DJ, Johnson CN, Dillon KS, Flowers AR, Noriea NF, Berutti T (2009) What genomic sequence information has revealed about Vibrio ecology in the ocean-a review. Microb Ecol 58(3):447–460.  https://doi.org/10.1007/s00248-009-9578-9 CrossRefGoogle Scholar
  9. 9.
    Gupta A, Patil S, Vijayakumar R, Kondabagil K (2017) The polyphyletic origins of primase–helicase bifunctional proteins. J Mol Evol 85:188–204.  https://doi.org/10.1007/s00239-017-9816-6 CrossRefGoogle Scholar
  10. 10.
    Huang S, Wang K, Jiao N, Chen F (2012) Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage–host genetic exchanges. Environ Microbiol 14(2):540–558.  https://doi.org/10.1111/j.1462-2920.2011.02667.x CrossRefGoogle Scholar
  11. 11.
    Hyman P, Abedon ST (2010) Bacteriophage host range and bacterial resistance. Adv Appl Microbiol 70:217–248.  https://doi.org/10.1016/S0065-2164(10)70007-1 CrossRefGoogle Scholar
  12. 12.
    Kang I, Jang H, Cho JC (2015) Complete genome sequences of bacteriophages P12002L and P12002S, two lytic phages that infect a marine polaribacter strain. Stand Genomic Sci 10(1):82.  https://doi.org/10.1186/s40793-015-0076-z CrossRefGoogle Scholar
  13. 13.
    Kauffman KM, Hussain FA, Yang J, Arevalo P, Polz MF (2018) A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature 554:118–122.  https://doi.org/10.1038/nature25474 CrossRefGoogle Scholar
  14. 14.
    Lal TM, Sano M, Ransangan J (2017) Isolation and characterization of large marine bacteriophage (Myoviridae), VhKM4 infecting Vibrio harveyi. J Aquat Anim Health 29(1):26–30.  https://doi.org/10.1080/08997659.2016.1249578 CrossRefGoogle Scholar
  15. 15.
    Levasseur A, Bekliz M, Chabrière E, Pontarotti P, La Scola B, Raoult D (2016) MIMIVIRE is a defence system in mimivirus that confers resistance to virophage. Nature 531(7593):249.  https://doi.org/10.1038/nature17146 CrossRefGoogle Scholar
  16. 16.
    Li E, Wei X, Ma Y, Yin Z, Li H, Lin W et al (2017) Corrigendum: Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes. Sci Rep 7:46805.  https://doi.org/10.1038/srep28338 CrossRefGoogle Scholar
  17. 17.
    Li Y, Wang M, Liu Q, Song X, Wang D, Ma Y et al (2016) Complete genomic sequence of bacteriophage H188: a novel Vibrio kanaloae phage isolated from Yellow Sea. Curr Microbiol 72(5):628–633.  https://doi.org/10.1007/s00284-015-0984-6 CrossRefGoogle Scholar
  18. 18.
    Liu Z, Wang M, Meng X, Li Y, Wang D, Jiang Y et al (2017) Isolation and genome sequencing of a novel Pseudoalteromonas phage PH1. Curr Microbiol 74(2):212–218.  https://doi.org/10.1007/s00284-016-1175-9 CrossRefGoogle Scholar
  19. 19.
    Liu Z, Li H, Wang M, Jiang Y, Yang Q, Zhou X, Shao H (2018) Isolation, characterization and genome sequencing of the novel phage SL25 from the Yellow Sea, China. Mar Genomics 37:31–34.  https://doi.org/10.1016/j.margen.2017.09.008 CrossRefGoogle Scholar
  20. 20.
    Němeček D, Lander GC, Johnson JE, Casjens SR, Thomas GJ Jr (2008) Assembly architecture and DNA binding of the bacteriophage P22 terminase small subunit. J Mol Biol 383(3):494–501.  https://doi.org/10.1016/j.jmb.2008.08.050 CrossRefGoogle Scholar
  21. 21.
    Mateus L, Costa L, Silva YJ, Pereira C, Cunha A, Almeida A (2014) Efficiency of phage cocktails in the inactivation of Vibrio in aquaculture. Aquaculture 424:167–173.  https://doi.org/10.1016/j.aquaculture.2014.01.001 CrossRefGoogle Scholar
  22. 22.
    Meng X, Wang M, You S et al (2017) Characterization and complete genome sequence of a novel Siphoviridae bacteriophage BS5. Curr Microbiol 74(7):815–820.  https://doi.org/10.1007/s00284-017-1221-2 CrossRefGoogle Scholar
  23. 23.
    Moon K, Kang I, Kim S, Kim SJ, Cho JC (2018) Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium. Sci rep 8(1):7989.  https://doi.org/10.1038/s41598-018-26363-y CrossRefGoogle Scholar
  24. 24.
    Ramphul C, Casareto BE, Dohra H, Suzuki T, Yoshimatsu K, Yoshinaga K et al (2017) Genome analysis of three novel lytic, Vibrio coralliilyticus, phages isolated from seawater, Okinawa, Japan. Mar Genomics 35:69–75.  https://doi.org/10.1016/j.margen.2017.06.005 CrossRefGoogle Scholar
  25. 25.
    Stabili L, Giangrande A, Pizzolante G, Caruso G, Alifano P (2014) Characterization of vibrios diversity in the mucus of the polychaete Myxicola infundibulum (Annellida, Polichaeta). Microb Ecol 67:186.  https://doi.org/10.1007/s00248-013-0312-2 CrossRefGoogle Scholar
  26. 26.
    Suttle CA (2007) Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5(10):801–812.  https://doi.org/10.1038/nrmicro1750 CrossRefGoogle Scholar
  27. 27.
    Vezzulli L, Previati M, Pruzzo C et al (2012) Vibrio infections triggering mass mortality events in a warming Mediterranean Sea. Environ Microbiol 12(7):2007–2019.  https://doi.org/10.1111/j.1462-2920.2010.02209.x CrossRefGoogle Scholar
  28. 28.
    Vengadesh L, Kok-Gan C, Priyia P, Surasak S, Acharaporn D, Bey-Hing G et al (2016) Insights into bacteriophage application in controlling Vibrio species. Front Microbiol 7:1114.  https://doi.org/10.3389/fmicb.2016.01114 Google Scholar
  29. 29.
    Wang D, Li Y, Sun M et al (2016) Complete genome of a novel Pseudoalteromonas phage PHq0. Curr Microbiol 72:81.  https://doi.org/10.1007/s00284-015-0919-2 CrossRefGoogle Scholar
  30. 30.
    Yanai I, Wolf YI, Koonin EV (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol 3(5):1–13. https://hdl.handle.net/2144/2790
  31. 31.
    Yu YP, Gong T, Jost G, Liu WH, Ye DZ, Luo ZH (2013) Isolation and characterization of five lytic bacteriophages infecting a Vibrio strain closely related to Vibrio owensii. FEMS Microbiol Lett 348(2):112–119.  https://doi.org/10.1111/1574-6968.12277 CrossRefGoogle Scholar
  32. 32.
    Zhu M, Wang M, Jiang Y et al (2018) Isolation and complete genome sequence of a novel Marinobacter phage B23. Curr Microbiol 75(12):1619–1625.  https://doi.org/10.1007/s00284-018-1568-z CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Yuye Han
    • 1
  • Min Wang
    • 1
    • 2
    • 3
  • Qian Liu
    • 1
  • Yundan Liu
    • 1
  • Qi Wang
    • 1
  • Xueping Duan
    • 1
  • Lu Liu
    • 1
  • Yong Jiang
    • 1
    • 2
    • 3
  • Hongbing Shao
    • 1
  • Cui Guo
    • 1
    • 2
    • 3
    Email author
  1. 1.College of Marine Life SciencesOcean University of ChinaQingdaoChina
  2. 2.Institute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
  3. 3.Key Lab of Polar Oceanography and Global Ocean ChangeOcean University of ChinaQingdaoChina

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