Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal


A new species of Vibrio (annotated as SBOTS_Iso1) was isolated in August 2014 from the Stn1 located in Chemaguri creek of Sundarbans mangrove ecoregion and taxonomically characterized using a polyphasic approach. Phenotypic analysis including biochemical tests and growth across a wide range of salinities indicated the typical estuarine characteristics of this new species. The bacterium was Gram negative, rod-shaped, oxidase and catalase negative and grows in the presence of NaCl. FAME analysis indicated 31.7% of the cellular fatty acids to be made up of 16:1 ω7c/16:1 ω6c. Amplification and sequencing of 16S rRNA and multilocus sequence analysis of four loci (2040 bp; rpoA, topA, mreB, pyrH) and additional sequence data of ftsZ, atpD, ompW and rpoB genes showed this isolate to be a member of Harveyi clade of the genus Vibrio. The closest phylogenetic neighbour was Vibrio alginolyticus ATCC 17749T with 96.8% similarity. Whole-genome sequence data indicates the presence of ~ 5 Mbp genome. GGDC, orthoANIu and AAI indicated 45%, 92% and 0.962 identity respectively with genome of Vibrio alginolyticus ATCC 17749T. The isolate SBOTS_Iso1 has been named Vibrio chemaguriensis sp. nov. on the name of the site from where it was first isolated.

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Accession number of 16S rRNA sequence


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  1. 1.

    Lee K-H, Ruby EG (1994) Effect of the squid host on the abundance and distribution of symbiotic Vibrio fischeri in nature. Appl Environ Microbiol 60:1565–1571

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Nyholm S, Nishiguchi M (2008) The evolutionary ecology of a sepiolid squid-Vibrio association: from cell to environment. Vie Milieu Paris 58:175–184

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Eiler A, Johansson M, Bertilsson S (2006) Environmental influences on Vibrio populations in northern temperate and boreal coastal waters (Baltic and Skagerrak Seas). Appl Environ Microbiol 72:6004–6011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Hasan NA, Grim CJ, Lipp EK, Rivera IN, Chun J, Haley BJ et al (2015) Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species. Proc Natl Acad Sci USA 112:E2813–E2819.

    Article  CAS  PubMed  Google Scholar 

  5. 5.

    Thompson JR, Polz MF (2006) Dynamics of Vibrio populations and their role in environmental nutrient cycling. In: Thompson FL, Austin B, Swings J (eds) The Biology of Vibrios. ASM Press, Washington, DC, pp 190–203

    Google Scholar 

  6. 6.

    Urdaci MC, Stal LJ, Marchand M (1988) Occurrence of nitrogen fixation among Vibrio spp. Arch Microbiol 150:224–229

    Article  CAS  Google Scholar 

  7. 7.

    Austin B, Austin DA (1999) Bacterial fish pathogens: disease of farmed and wild fish, 3rd edn. Springer, Berlin

    Google Scholar 

  8. 8.

    Cano-Gómez A, Goulden EF, Owens L, Høj L (2010) Vibrio owensii sp. nov., isolated from cultured crustaceans in Australia. FEMS Microbiol Lett 302:175–181

    Article  CAS  Google Scholar 

  9. 9.

    Hoffmann M, Monday SR, Fischer M, Brown EW (2012) Genetic and phylogenetic evidence for misidentification of Vibrio species within the Harveyi clade. Lett Appl Microbiol 54:160–165

    Article  CAS  PubMed  Google Scholar 

  10. 10.

    Sawabe T, Kita-Tsukamoto K, Thompson FL (2007) Inferring the evolutionary history of Vibrios by means of multilocus sequence analysis. J Bacteriol 189:7932–7936

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Yoshizawa S, Tsuruya Y, Fukui Y, Sawabe T, Yokota A, Kogure K, Higgins M, Carson J, Thompson FL (2012) Vibrio jasicida sp. nov., a member of the Harveyi clade, isolated from marine animals (packhorse lobster, abalone and Atlantic salmon). Int J Syst Evolut Microbiol 62:1864–1870

    Article  CAS  Google Scholar 

  12. 12.

    Fukui Y, Sawabe T (2007) Improved one step colony PCR detection of Vibrio harveyi. Microbes Environ 22:1–10

    Article  Google Scholar 

  13. 13.

    Thompson FL, Gomez-Gil B, Vasconcelos ATR, Sawabe T (2007) Multilocus sequence analysis reveals that Vibrio harveyi and V. campbellii form distinct species. Appl Environ Microbiol 73:4279–4285.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Liu PC, Lee KK, Tu CC, Chen SN (1997) Purification and characterization of a cysteine protease produced by pathogenic luminous Vibrio harveyi. Curr Microbiol 35:32–39.

    Article  CAS  PubMed  Google Scholar 

  15. 15.

    Liu PC, Lee KK (1999) Cysteine protease is a major exotoxin of pathogenic luminous Vibrio harveyi in the tiger prawn, Penaeus monodon. Lett Appl Microbiol 28:428–430.

    Article  CAS  PubMed  Google Scholar 

  16. 16.

    McCall JO, Sizemore RK (1979) Description of a bacteriocinogenic plasmid in Beneckea harveyi. Appl Environ Microbiol 38:974–979

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Svitil AL, Chadhain S, Moore J, Kirchman DL (1997) Chitin degradation proteins produced by the marine bacterium Vibrio harveyi growing on different forms of chitin. Appl Environ Microbiol 63:408–413

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Dunlap PV (2009) Bioluminescence, microbial. In: Schaechter M (ed) Encyclopedia of microbiology, 3rd edn. Elsevier, Oxford, pp 45–61

    Google Scholar 

  19. 19.

    Henke JM, Bassler BL (2004) Quorum sensing regulates type III secretion in Vibrio harveyi and Vibrio parahaemolyticus. J Bacteriol 186:3794–3805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Yildiz FH, Visick KL (2009) Vibrio biofilms: so much the same yet so different. Trends Microbiol 17:109–118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Thompson FL, Iida T, Swings J (2004) Biodiversity of Vibrios. Microbiol Mol Biol Rev 68:403–431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Ushijima B, Smith A, Aeby GS, Callahan SM (2012) Vibrio owensii induces the tissue loss disease Montipora white syndrome in the Hawaiian reef coral Montipora capitata. PLoS ONE 7:e46717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102(7):2567–2572

    Article  CAS  Google Scholar 

  24. 24.

    Medlar AJ, Törönen P, Holm L (2018) AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 46(W1):W479–W485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106(45):19126–19131

    Article  Google Scholar 

  26. 26.

    Costa RA, Silva GC, Peixoto JRO, Vieira GHF, Vieira HSF (2010) Quantification and distribution of Vibrio species in water from an estuary in Ceará-Brazil impacted by shrimp farming. Braz J Oceanogr 58(3):183–188

    Article  Google Scholar 

  27. 27.

    Feldman KA, Buck JD (1984) Distribution and characterization of luminescent bacteria in a temperature estuary. Estuaries 7(1):93–97

    Article  Google Scholar 

  28. 28.

    Ghosh A, Bhadury P (2017) Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem. Environ Sci Pollut Res 25(3):15.

    CAS  Article  Google Scholar 

  29. 29.

    Zhou J, Fang W, Yang X, Zhou S, Hu L, Li X et al (2012) A nonluminescent and highly virulent Vibrio harveyi strain is associated with “bacterial white tail disease” of Litopenaeus vannamei shrimp. PLoS ONE 7(2):e29961.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Ghosh A, Bhadury P (2016) Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: a comparative analysis. Genom Data 11:39–42.

    Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703

    Article  CAS  Google Scholar 

  32. 32.

    Reiner, K. (2010). Catalase test protocol.

  33. 33.

    Sasser M (1990) Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME). Technical Note #101.

  34. 34.

    Bostrӧm KH, Simu K, Hagstrӧm A, Riemann L (2004) Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnol Oceanogr Methods 2:365–373.

    Article  Google Scholar 

  35. 35.

    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  36. 36.

    Braker G, Fesefeldt A, Witzel K-P (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64(10):3769–3775

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66(8):3376–3380

    Article  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Dybvig K, Hollingshead SK, Heath DG, Clewell DB, Sun F, Woodard A (1992) Degenerate oligonucleotide primers for enzymatic amplification of recA sequences from gram-positive bacteria and mycoplasmas. J Bacteriol 174(8):2729–2732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Gaunt MW, Turner SL, Rigottier-Gois L, Lloyd-Macqilp SA, Young JP (2001) Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evolut Microbiol 51(Pt 6):2037–2048

    Article  CAS  Google Scholar 

  40. 40.

    Goel AK, Ponmariappan S, Kamboj DV, Singh L (2007) Single multiplex polymerase chain reaction for environmental surveillance of toxigenic-pathogenic O1 and non-O1 Vibrio cholerae. Folia Microbiol (Praha) 52:81–85.

    Article  CAS  Google Scholar 

  41. 41.

    Nandi B, Nandy RK, Mukhopadhyay S, Nair GB, Shimada T, Ghose AC (2000) Rapid method for species-specific identification of Vibrio cholerae using primers targeted to the gene of outer membrane protein OmpW. J Clin Microbiol 38(11):4145–4151

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S, Hoste B et al (2005) Phylogeny and molecular identification of Vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 71:5107–5115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Weigel LM, Steward CD, Tenover FC (1998) gyrA mutations associated with fluoroquinolone resistance in eight species of Enterobacteriaceae. Antimicrob Agents Chemother 42(10):2661–2667

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Hall TA (1999) BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98.

    CAS  Google Scholar 

  45. 45.

    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948

    Article  CAS  Google Scholar 

  47. 47.

    Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. J EMBnet. 17(1):10–12

    Article  Google Scholar 

  48. 48.

    Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6):e1005595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL (2017) IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45(W1):W30–W35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Yoon SH, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evolut Microbiol 67(5):1613–1617

    Article  CAS  Google Scholar 

  52. 52.

    Kolthoff-Meier JP, Auch AD, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  53. 53.

    Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC (2016) From genomes to phenotypes: traitar, the microbial trait analyzer. mSystems 1(6):e00101–e00116

    Article  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain loss and rearrangement. PLoS ONE 5(6):e11147.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Grant JR, Stothard P (2008) The CGView Server:a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181–W184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539

    Article  CAS  PubMed  Google Scholar 

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Anwesha Ghosh is the recipient of IISER Kolkata Integrated Ph.D. Fellowship. This work is partly supported by grants from IISER Kolkata as well as from WWF-India awarded to Punyasloke Bhadury.

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Supplementary material 1 (DOCX 26 kb)

Supplementary material 2 Fig. S1 The top left panel indicated the cell size and shape as observed under 100× magnification using a light microscope. The top right panel shows DAPI stained image from binding of the dye to the nuclei acid of SBOTS_Iso1 as observed under fluorescent microscopy. The lower left panel shows single cells of SBOTS_Iso1 as observed under FESEM. The lower right panel shows TEM image. The scale bar and magnification is indicated in each image (JPEG 3932 kb)

Supplementary material 3 Fig. S2 The OD (600 nm) versus time (h) values obtained during the growth curve experiment performed at different salinities. Growth of the isolate at salinity 11.5, temperature 32 °C and pH 8 indicated the in situ conditions of the study site during sampling (TIFF 2607 kb)

Supplementary material 4 Fig. S3 The OD (600 nm) versus media pH shows growth of the isolate at different media pH levels at salinity 11.5 and incubation at 32 °C (TIFF 11 kb)

Supplementary material 5 Fig. S4 Circular genome of the SBOTS_Iso1 (TIFF 234 kb)

Supplementary material 6 Fig. S5a Alignment between genomes of V. alginolyticus ATCC17749T and SBOTS_Iso1 (TIFF 254 kb)

Supplementary material 7 Fig. S5b Circular genome map indicating ORFs, GC content, GC skew and alignment genome7 (TIFF 1695 kb)

Supplementary material 8 Fig. S6 Genome map showing the position of genomic islands (typically > 8 kb) as seen against V. alginolyticus ATCC17749T reference genome. Genes within these genomic islands might be linked to antibiotic resistance or virulence (TIFF 130 kb)

Supplementary material 9 Fig. S7 Results indicating in silico phenotyping obtained from genome sequence of SBOTS_Iso1 (TIFF 1801 kb)

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Ghosh, A., Bhadury, P. Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal. Curr Microbiol 76, 1118–1127 (2019).

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