Complete Genome Sequence of Strain YCSC6, a Marine Bacterium Isolated from Saturated Saltpan with Activity Against Uronema marinum

  • Guang Xun Du
  • Ling Yun QuEmail author
  • Kun Shang
  • Ping Gao
  • De Wen Ding
  • Cheng Jun Sun


Salinivibrio proteolyticus strain YCSC6 was isolated from a saturated saltpan and demonstrated to have strong insecticidal activity against turbot’s pathogenic ciliate—Uronema marinum. In this study, we sequenced its complete genome. Results showed that it consists of two circular chromosomes: 2.49 Mbps and 0.74 Mbps, respectively. It encodes 3429 protein-coding sequences. Biosynthetic gene clusters predicted to synthesize bacteriocins and antimicrobial peptides were discovered, which might be the key factors to lyse and kill U. marinum. The complete genome sequence of strain YCSC6 provides insights into the fundamental genetic potential for elucidating its insecticidal mechanism against U. marinum.



This work was supported by the National Key R&D Program of China (2017YFC1404504); National Basic Research Program of China (2015CB755904); and the Youth Talent Program Supported by Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (2018-MFS-T16).

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no competing interests.

Research involving Human and Animal Participants

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


  1. 1.
    Mellado E, Moore ER, Nieto JJ, Ventosa A (1996) Analysis of 16S rRNA gene sequences of Vibrio costicola strains: description of Salinivibrio costicola gen. nov., comb. Nov. Int J Syst Bacteriol 46(3):817–821CrossRefGoogle Scholar
  2. 2.
    Amoozegar MA, Schumann P, Hajighasemi M, Fatemi AZ, Karbalaei-Heidari HR (2008) Salinivibrio proteolyticus sp. nov., a moderately halophilic and proteolytic species from a hypersaline lake in Iran. Int J Syst Evol Microbiol 58(5):1159–1163CrossRefGoogle Scholar
  3. 3.
    López-Hermoso C, de la Haba RR, Sánchez-Porro C, Ventosa A (2018) Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns. Syst Appl Microbiol 41(3):159–166CrossRefGoogle Scholar
  4. 4.
    Romano I, Orlando P, Gambacorta A, Nicolaus B, Dipasquale L, Pascual J, Giordano A, Lama L (2011) Salinivibrio sharmensis sp. nov., a novel haloalkaliphilic bacterium from a saline lake in Ras Mohammed Park (Egypt). Extremophiles 15(2):213–220CrossRefGoogle Scholar
  5. 5.
    Chamroensaksri N, Tanasupawat S, Akaracharanya A, Visessanguan W, Kudo T, Itoh T (2009) Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand. Int J Syst Evol Microbiol 59(4):880–885CrossRefGoogle Scholar
  6. 6.
    Gorriti MF, Dias GM, Chimetto LA, Trindade-Silva AE, Silva BS, Mesquita MM, Gregoracci GB, Farias ME, Thompson CC, Thompson FL (2014) Genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake. BMC Genomics 15(1):473–473CrossRefGoogle Scholar
  7. 7.
    Romano I, Gambacorta A, Lama L, Nicolaus B, Giordano A (2005) Salinivibrio costicola subsp. alcaliphilus subsp. nov., a haloalkaliphilic aerobe from Campania Region (Italy). Syst Appl Microbiol 28(1):34–42CrossRefGoogle Scholar
  8. 8.
    Huang CY, Garcia JL, Patel BK, Cayol JL, Baresi L, Mah RA (2000) Salinivibrio costicola subsp. vallismortis subsp. nov., a halotolerant facultative anaerobe from Death Valley, and emended description of Salinivibrio costicola. Int J Syst Evol Microbiol 50(2):615–622CrossRefGoogle Scholar
  9. 9.
    López-Hermoso C, Rr DLH, Sánchez-Porro C, Bayliss SC, Feil EJ, Ventosa A (2017) Draft genome sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 new isolates belonging to the genus Salinivibrio. Genome Announc 5(27):1–3CrossRefGoogle Scholar
  10. 10.
    Mohammad Ali A, Ensieh S, Khosro K, Mahbube K, Saied N (2010) Production of an extracellular thermohalophilic lipase from a moderately halophilic bacterium, Salinivibrio sp. strain SA-2. J Basic Microbiol 48(3):160–167Google Scholar
  11. 11.
    Amoozegar MA, Fatemi AZ, Karbalaei-Heidari HR, Razavi MR (2007) Production of an extracellular alkaline metalloprotease from a newly isolated, moderately halophile, Salinivibrio sp. strain AF-2004. Microbiol Res 162(4):369–377CrossRefGoogle Scholar
  12. 12.
    Du GX, Qu LY, Shang K, Wang C, Gao P (2017) Identification of marine bacterium YCSC6 and its insecticidal ability against Scuticociliate in vitro. Mar Science 41(8):24–31Google Scholar
  13. 13.
    Du GX, Qu LY, Shang K, Sun CJ, Wang C, Gao P (2019) Ciliate Uronema marinum is the causative agent of scuticociliatosis in farm raised turbot Scophthalmus maximus. J Oceanol Limnol 37(5):1726–1735CrossRefGoogle Scholar
  14. 14.
    Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46(5):2159–2168CrossRefGoogle Scholar
  15. 15.
    Reiner J, Pisani L, Qiao W, Singh R, Yang Y, Shi L, Khan WA, Sebra R, Cohen N, Babu A (2018) Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion. NPJ Genom Med 3(1):1–5CrossRefGoogle Scholar
  16. 16.
    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):2607–2618CrossRefGoogle Scholar
  17. 17.
    Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964CrossRefGoogle Scholar
  18. 18.
    Lagesen K, Hallin P, Rodland E, Staerfeldt H, Rognes T, Ussery D (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108CrossRefGoogle Scholar
  19. 19.
    Gardner PP, Jennifer D, Tate JG, Nawrocki EP, Kolbe DL, Stinus L, Wilkinson AC, Finn RD, Sam GJ, Eddy SR (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37(Database issue):136–140CrossRefGoogle Scholar
  20. 20.
    Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25(10):1335–1337CrossRefGoogle Scholar
  21. 21.
    William H, Ivan W, Jones SJ, Brinkman FSL (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19(3):418–420CrossRefGoogle Scholar
  22. 22.
    Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35(Web Server):W52–W57CrossRefGoogle Scholar
  23. 23.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25:25–29CrossRefGoogle Scholar
  24. 24.
    Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43(Database issue):261–269CrossRefGoogle Scholar
  25. 25.
    Minoru K, Susumu G, Masahiro H, Aoki-Kinoshita KF, Masumi I, Shuichi K, Toshiaki K, Michihiro A, Mika H (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(90001):D354–D357CrossRefGoogle Scholar
  26. 26.
    Minoru K, Susumu G, Shuichi K, Yasushi O, Masahiro H (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(90001):277–280CrossRefGoogle Scholar
  27. 27.
    Li W, Jaroszewski L, Godzik A (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18(1):77–82CrossRefGoogle Scholar
  28. 28.
    Medema MH, Kai B, Peter C, Victor DJ, Piotr Z, Fischbach MA, Tilmann W, Eriko T, Rainer B (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39(Web Server issue):W339–W346CrossRefGoogle Scholar
  29. 29.
    Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645CrossRefGoogle Scholar
  30. 30.
    Cotter PD, Hill C, Ross RP, (2005) Bacteriocins: developing innate immunity for food. Nat Rev Microbiol 3(10):777–788CrossRefGoogle Scholar
  31. 31.
    Shang-Te H, Eefjan B, Ben DK, Robert K, Bonvin AMJJ, Nuland NAJ, Van, (2002) Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles. Biochemistry 41(24):7670–7676CrossRefGoogle Scholar
  32. 32.
    Wiedemann I, Breukink E, Van Kraaij C, Kuipers OP, Bierbaum G, De Kruijff B, Sahl HG (2001) Specific binding of nisin to the peptidoglycan precursor lipid II combines pore formation and inhibition of cell wall biosynthesis for potent antibiotic activity. J Bio Chem 276(3):1772–1779CrossRefGoogle Scholar
  33. 33.
    Chan DI, Prenner EJ, Vogel HJ (2006) Tryptophan- and arginine-rich antimicrobial peptides: structures and mechanisms of action. BBA-Biomembranes 1758(9):1184–1202CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Guang Xun Du
    • 1
    • 2
  • Ling Yun Qu
    • 2
    • 3
    Email author
  • Kun Shang
    • 2
    • 4
  • Ping Gao
    • 2
  • De Wen Ding
    • 1
    • 2
  • Cheng Jun Sun
    • 2
  1. 1.School of Marine SciencesNingbo UniversityNingboPeople’s Republic of China
  2. 2.First Institute of Oceanography, MNRQingdaoPeople’s Republic of China
  3. 3.Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoPeople’s Republic of China
  4. 4.College of Fisheries and Life ScienceDalian Ocean UniversityDalianPeople’s Republic of China

Personalised recommendations