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Isolation and Complete Genome Sequence of a Novel Pseudoalteromonas Phage PH357 from the Yangtze River Estuary

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Abstract

Phage PH357, a novel lytic Pseudoalteromonas lipolytica phage belonging to the Myoviridae family was isolated from the Yangtze River estuary. The microbiological characterization demonstrated that phage PH357 is stable from −20 to 60 °C and the optimal pH 7. The one-step growth curve showed a latent period of 20 min, a rise period of 20 min, and the average burst size was about 85 virions per cell. Complete genome of phage PH357 was determined. Genome of phage PH357 consisted of a linear, double-stranded 136,203 bp DNA molecule with 34.58% G + C content, and 242 putative open reading frames (ORFs) without tRNA. All the predicted ORFs were classified into eight functional groups, including DNA replication, regulation and nucleotide metabolism, transcription, translation, phage packaging, phage structure, lysis, host or phage interactions, and hypothetical protein. A phylogenetic analysis showed that phage PH357 had similarity to the previously published Pseudoalteromonas phage PH101 and Vibrio phages. Furthermore, the study of phage PH357 genome will provide useful information for further research on the interaction between phages and their hosts.

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References

  1. Bai Q, Zhang W, Yang Y, Tang F, Nguyen X, Liu G, Lu C (2013) Characterization and genome sequencing of a novel bacteriophage infecting streptococcus agalactiae with high similarity to a phage from streptococcus pyogenes. Adv Virol 158(8):1733–1741

    CAS  Google Scholar 

  2. Boetzer M, Pirovano W (2012) Toward almost closed genomes with GapFiller. Genom Biol 13:R56

    Article  Google Scholar 

  3. Bowman JP (2007) Bioactive compound synthetic capacity and ecological significance of marine bacterial genus Pseudoalteromonas. Mar Drugs 5(4):220–241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cai L, Zhang R, He Y, Feng X, Jiao N (2016) Metagenomic analysis of Virioplankton of the subtropical Jiulong river estuary, China. Viruses 8(2):35

    Article  PubMed Central  Google Scholar 

  5. Capra ML, Quiberoni A, Reinheimer JA (2004) Thermal and chemical resistance of Lactobacillus casei and Lactobacillus paracasei bacteriophages. Lett Appl Microbiol 38(6):499–504

    Article  CAS  PubMed  Google Scholar 

  6. Colangelo-Lillis JR, Deming JW (2013) Genomic analysis of cold-active Colwelliaphage, 9A and psychrophilic phage–host interactions. Extremophiles 17(1):99–114

    Article  CAS  PubMed  Google Scholar 

  7. Duhaime MB, Wichels A, Waldmann J, Teeling H, Glöckner FO (2011) Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1. ISME J 5(1):107–121

    Article  CAS  PubMed  Google Scholar 

  8. Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399(6736):541–548

    Article  CAS  PubMed  Google Scholar 

  9. Goldsmith DB, Crosti G, Dwivedi B, Dwivedi B, McDaniel LD, Varsani A, Suttle CA, Weinbauer MG, Sandaa RA, Breitbart M (2011) Development of phoH as a novel signature gene for assessing marine phage diversity. Appl Environ Microbiol 77(21):7730–7739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Huang GT, Le S, Peng YZ, Zhao Y, Yin SP, Zhang L, Yao X, Tan Y, Li M, Hu FQ (2013) Characterization and genome sequencing of phage Abp1, a new phiKMV-like virus infecting multidrug-resistant Acinetobacter baumannii. Curr Microbiol 66:535–543

    Article  CAS  PubMed  Google Scholar 

  11. Hyman P, Abedon ST (2010) Bacteriophage host range and bacterial resistance. Adv Appl Microbiol 70:217–248

    Article  CAS  PubMed  Google Scholar 

  12. Kallies R, Kiesel B, Schmidt M, Kacza J, Ghanem N, Narr A, Zopfi J, Wick LY, Hackermüller J, Harms H, Chatzinotas A (2017) Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. Stand Genom Sci 12(1):20

    Article  Google Scholar 

  13. Kropinski AM, Waddell T, Meng J, Franklin K, Ackermann HW, Ahmed R, Mazzocco A, Yates J, Lingohr EJ, Johnson RP (2013) The host-range, genomics and proteomics of Escherichia coli, O157:H7 bacteriophage rV5. Virol J 10(1):1–12

    Article  Google Scholar 

  14. Li E, Xiao W, Ma Y, Zhe Y, Li H, Lin W, Wang X, Li C, Shen Z, Zhao R, Yang H, Jiang A, Yang W, Yuan J, Zhao X (2016) Isolation and characterization of a bacteriophage phieap-2 infecting multidrug resistant enterobacter aerogenes. Sci Rep 6:28338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Li P, Chen BB, Song Z, Song Y, Yang Y, Ma P, Wang H, Ying J, Ren P, Yang Y, Gao G, Jin S, Bao Q, Yang H (2012) Bioinformatic analysis of the Acinetobacter baumannii phage AB1 genome. Gene 507(2):125–134

    Article  CAS  PubMed  Google Scholar 

  16. Li Y, Wang M, Liu Q, Song X, Wang D, Ma Y, Jiang Y (2016) Complete genomic sequence of bacteriophage H188: a novel Vibrio kanaloae phage isolated from yellow sea. Curr Microbiol 72(5):628–633

    Article  CAS  PubMed  Google Scholar 

  17. Liu SB, Chen XL, He HL, Zhang XY, Xie BB, Yu Y, Zhang YZ (2013) Structure and ecological roles of a novel exopolysaccharide from the Arctic sea ice bacterium Pseudoalteromonas sp. strain SM20310. Appl Environ Microbiol 79(1):224–230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F, Rougemont J, Cole ST, Deplancke B (2010) Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods 7:6–485

    Article  Google Scholar 

  19. Middelboe M, Chan A, Bertelsen SK (2010) Isolation and life-cycle characterization of lytic viruses infecting heterotrophic bacteria and cyanobacteria. Man Aquat Viral Ecol 13:118–133

    Article  Google Scholar 

  20. Poli A, Anzelmo G, Nicolaus B (2010) Bacterial exopolysaccharides from extreme marine habitats: production, characterization and biological activities. Mar Drugs 8(6):1779–1802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang YZ (2011) Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. ISME J 5(2):274–284

    Article  PubMed  Google Scholar 

  22. Rao VB, Feiss M (2008) The bacteriophage DNA packaging motor. Annu Rev Genet 42:647–681

    Article  CAS  PubMed  Google Scholar 

  23. Saitou N, Nei M (1987) The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  24. Senčilo A, Luhtanen AM, Saarijärvi M, Bamford DH, Roine E (2015) Cold-active bacteriophages from the baltic sea ice have diverse genomes and virus–host interactions. Environ Microbiol 17(10):392–400

    Google Scholar 

  25. Suttle CA (2005) Viruses in the sea. Nature 437(7057):356–361

    Article  CAS  PubMed  Google Scholar 

  26. Wang DB, Sun MQ, Shao HB, Li Y, Meng X, Liu ZY, Wang M (2015) Characterization and genome sequencing of a novel bacteriophage PH101 infecting Pseudoalteromonas marina BH101 from the yellow sea of China. Curr Microbiol 71(5):594–600

    Article  CAS  PubMed  Google Scholar 

  27. Wang P, Yu Z, Li B, Cai X, Zeng Z, Chen X, Wang X (2015) Development of an efficient conjugation-based genetic manipulation system for Pseudoalteromonas. Microb Cell Fact 14(1):1

    Article  Google Scholar 

  28. Wang W, Li M, Lin H, Wang J, Mao X (2016) The Vibrio parahaemolyticus-infecting bacteriophage qdvp001: genome sequence and endolysin with a modular structure. Adv Virol 161(10):2645–2652

    CAS  Google Scholar 

  29. Wichels A, Biel SS, Gelderblom HR, Brinkhoff T, Muyzer G, Schütt C (1998) Bacteriophage diversity in the North Sea. Appl Environ Microbiol 64(11):4128–4133

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Xu J, Hendrix RW, Duda RL (2004) Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell 16:11–21

    Article  CAS  PubMed  Google Scholar 

  31. Xu XW, Wu YH, Wang CS, Gao XH, Wang XG, Wu M (2010) Pseudoalteromonas lipolytica sp. nov., isolated from the Yangtze River estuary. Int J Syst Evol Microbiol 60(9):2176–2181

    Article  CAS  PubMed  Google Scholar 

  32. Yu ZC, Chen XL, Shen QT, Zhao DL, Tang BL, Su HN, Wu ZY, Qin QL, Xie BB, Zhang XY, Yu Y (2015) Filamentous phages prevalent in Pseudoalteromonas spp. confer properties advantageous to host survival in Arctic sea ice. ISME J 9(4):871–881

    Article  CAS  PubMed  Google Scholar 

  33. Yuan L, Cui Z, Wang Y, Guo X, Zhao Y (2014) Complete genome sequence of virulent bacteriophage shou24, which infects foodborne pathogenic vibrio parahaemolyticus. Adv Virol 159(11):3089–3093

    CAS  Google Scholar 

  34. Zeng Z, Guo XP, Li B, Wang P, Cai X, Tian X, Wang X (2015) Characterization of self-generated variants in Pseudoalteromonas lipolytica biofilm with increased antifouling activities. Appl Microbiol Biotechnol 99(23):10127–10139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors greatly appreciate the officers, crew, and scientific staff onboard the research vessel Dong Fang Hong 2 for facilitating the collection of the seawater samples.

Funding

This work was supported by the National Natural Science Foundation of China (NSFC Grant Nos. 31500339, 41676178, 41076088), the National Key Basic Research Program of China (973Program, Grant No: 2013CB429704), China Postdoctoral Science Foundation (Grant Nos. 2015M570612 and 2016T90649), and Fundamental Research Funds for the Central University of Ocean University of China (Grant Nos. 201564010 and 201512008).

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Authors and Affiliations

  1. College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China

    Zheng Gong, Min Wang, Qingwei Yang, Zhongshi Li, Jun Xia, Yu Gao, Yong Jiang, Xue Meng, Zhaoyang Liu, Ding Yang, Fangfei Zhang, Hongbing Shao & Duobing Wang

  2. Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China

    Min Wang & Yong Jiang

  3. Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China

    Min Wang & Yong Jiang

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  1. Zheng Gong
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  2. Min Wang
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  3. Qingwei Yang
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  4. Zhongshi Li
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  5. Jun Xia
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  10. Ding Yang
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Correspondence to Min Wang or Yong Jiang.

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Gong, Z., Wang, M., Yang, Q. et al. Isolation and Complete Genome Sequence of a Novel Pseudoalteromonas Phage PH357 from the Yangtze River Estuary. Curr Microbiol 74, 832–839 (2017). https://doi.org/10.1007/s00284-017-1244-8

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  • DOI: https://doi.org/10.1007/s00284-017-1244-8

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