1887

Abstract

A novel orange to pink coloured bacterial strain designated as CT19 was isolated from the gastrointestinal tract of mirror carp, var. (Lacepède, 1803) collected from the Gobind Sagar reservoir at village Lathiani, Una, Himachal Pradesh, India. Cells of the strain were found to be aerobic, Gram-stain-positive, non-motile and non-spore-forming coccoids. Based on the 16S rRNA gene sequence, the strain was closely related to J-82 (=DSM 5352; 97.4 %), followed by CC-SPL15-2 (=DSM 23267; 96.4 %), JC304 (=KCTC 33661; 95.6 %) and DSM 5351 (95.4 %). Identity with all other members of the genus were <94.5 %. The draft genome of strain CT19 was assembled to 2.4 Mbp with a G+C content of 47.9 mol%. Average nucleotide identity and digital DNA–DNA hybridization values between strain CT19 and J-82 were found to be 85.9 and 31.3% respectively which is far below the threshold for species delineation. Iso-C, anteiso-C, iso-C, C and anteiso-C were the major cellular fatty acids of strain CT19. Major polar lipids were diphosphatidylglycerol, phosphatidylgylcerol and an unidentified glycolipid. Respiratory quinone system was composed of menaquinone-6 and major cell wall amino acid was -lysine. Based on phylogenomic, physiological and biochemical characteristics, strain CT19 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is CT19 (=KCTC 43022 =CCM 8886=MCC 3834).

Keyword(s): Salinicoccus , taxo-genomics and taxonomy
Funding
This study was supported by the:
  • Ram Krishan Negi , National Bureau of Agriculturally Important Microorganisms , (Award NBAIM/AMAAS/2017-20/GF/1a)
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/content/journal/ijsem/10.1099/ijsem.0.004247
2020-06-15
2021-02-26
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References

  1. Ventosa A, Márquez MC, Ruiz-Berraquero F, Kocur M. Salinicoccus roseus gen. nov., sp. nov., a new moderately halophilic Gram-positive coccus. Syst Appl Microbiol 1990; 13:29–33 [CrossRef]
    [Google Scholar]
  2. Marquez MC, Ventosa A, Ruiz-Berraquero F. Marinococcus hispanicus, a new species of moderately halophilic gram-positive cocci. Int J Syst Bacteriol 1990; 40:165–169 [CrossRef]
    [Google Scholar]
  3. Ventosa A, Marquez MC, Weiss N, Tindall BJ. Transfer of Marinococcus hispanicus to the genus Salinicoccus as Salinicoccus hispanicus comb. nov. Syst Appl Microbiol 1992; 15:530–534 [CrossRef]
    [Google Scholar]
  4. Zhang W, Xue Y, Ma Y, Zhou P, Ventosa A et al. Salinicoccus alkaliphilus sp. nov., a novel alkaliphile and moderate halophile from Baer Soda Lake in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 2002; 52:789–793 [CrossRef][PubMed]
    [Google Scholar]
  5. França L, Rainey FA, Nobre MF, da Costa MS. Salinicoccus salsiraiae sp. nov.: a new moderately halophilic Gram-positive bacterium isolated from salted skate. Extremophiles 2006; 10:531–536 [CrossRef][PubMed]
    [Google Scholar]
  6. Aslam Z, Lim JH, Im W-T, Yasir M, Chung YR et al. Salinicoccus jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2007; 57:633–638 [CrossRef][PubMed]
    [Google Scholar]
  7. Chen Y-G, Cui X-L, Pukall R, Li H-M, Yang Y-L et al. Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 2007; 57:2327–2332 [CrossRef][PubMed]
    [Google Scholar]
  8. Zhang Y-Q, Yu L-Y, Liu H-Y, Zhang Y-Q, Xu L-H et al. Salinicoccus luteus sp. nov., isolated from a desert soil. Int J Syst Evol Microbiol 2007; 57:1901–1905 [CrossRef][PubMed]
    [Google Scholar]
  9. Pakdeeto A, Tanasupawat S, Thawai C, Moonmangmee S, Kudo T et al. Salinicoccus siamensis sp. nov., isolated from fermented shrimp paste in Thailand. Int J Syst Evol Microbiol 2007; 57:2004–2008 [CrossRef][PubMed]
    [Google Scholar]
  10. Amoozegar MA, Schumann P, Hajighasemi M, Ashengroph M, Razavi MR. Salinicoccus iranensis sp. nov., a novel moderate halophile. Int J Syst Evol Microbiol 2008; 58:178–183 [CrossRef][PubMed]
    [Google Scholar]
  11. Wang X, Xue Y, Yuan S, Zhou C, Ma Y. Salinicoccus halodurans sp. nov., a moderate halophile from saline soil in China. Int J Syst Evol Microbiol 2008; 58:1537–1541 [CrossRef][PubMed]
    [Google Scholar]
  12. Chen Y-G, Cui X-L, Wang Y-X, Zhang Y-Q, Li Q-Y et al. Salinicoccus albus sp. nov., a halophilic bacterium from a salt mine. Int J Syst Evol Microbiol 2009; 59:874–879 [CrossRef][PubMed]
    [Google Scholar]
  13. Jung M-J, Kim M-S, Roh SW, Shin K-S, Bae J-W. Salinicoccus carnicancri sp. nov., a halophilic bacterium isolated from a Korean fermented seafood. Int J Syst Evol Microbiol 2010; 60:653–658 [CrossRef][PubMed]
    [Google Scholar]
  14. Kämpfer P, Arun AB, Busse H-J, Young C-C, Lai W-A et al. Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum . Int J Syst Evol Microbiol 2011; 61:2348–2352 [CrossRef][PubMed]
    [Google Scholar]
  15. Qu Z, Li Z, Zhang X, Zhang X-H. Salinicoccus qingdaonensis sp. nov., isolated from coastal seawater during a Bloom of green algae. Int J Syst Evol Microbiol 2012; 62:545–549 [CrossRef][PubMed]
    [Google Scholar]
  16. Ramana CV, Srinivas A, Subhash Y, Tushar L, Mukherjee T et al. Salinicoccus halitifaciens sp. nov., a novel bacterium participating in halite formation. Antonie Van Leeuwenhoek 2013; 103:885–898 [CrossRef][PubMed]
    [Google Scholar]
  17. Kumar RM, Kaur G, Kumar N, Kumar A, Singh NK et al. Taxonomic description and genome sequence of Salinicoccus sediminis sp. nov., a halotolerant bacterium isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:3794–3799 [CrossRef][PubMed]
    [Google Scholar]
  18. Srinivas A, Divyasree B, Tushar L, Suresh G, Sasikala C et al. Salinicoccus amylolyticus sp. nov., isolated from a saltern. Int J Syst Evol Microbiol 2016; 66:3814–3820 [CrossRef][PubMed]
    [Google Scholar]
  19. Chen Y-G, Cui X-L, Li W-J, Xu L-H, Wen M-L et al. Salinicoccus salitudinis sp. nov., a new moderately halophilic bacterium isolated from a saline soil sample. Extremophiles 2008; 12:197–203 [CrossRef][PubMed]
    [Google Scholar]
  20. Gao M, Wang L, Chen S-feng, Zhou Y-guang, Liu H-can. Salinicoccus kekensis sp. nov., a novel alkaliphile and moderate halophile isolated from Keke salt lake in Qinghai, China. Antonie van Leeuwenhoek 2010; 98:351–357 [CrossRef][PubMed]
    [Google Scholar]
  21. Talwar C, Nagar S, Lal R, Negi RK. Fish gut microbiome: current approaches and future perspectives. Indian J Microbiol 2018; 58:397–414 [CrossRef][PubMed]
    [Google Scholar]
  22. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K et al. Polyphasic taxonomy, a consensus approach to bacterial Systematics. Microbiol Rev 1996; 60:407–438 [CrossRef][PubMed]
    [Google Scholar]
  23. Mahato NK, Gupta V, Singh P, Kumari R, Verma H et al. Microbial taxonomy in the era of omics: application of DNA sequences, computational tools and techniques. Antonie Van Leeuwenhoek 2017; 110:1357–1371 [CrossRef][PubMed]
    [Google Scholar]
  24. Sambrook J, Russell DW. Molecular Cloning: a Laboratory Manual, 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2000
    [Google Scholar]
  25. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [CrossRef][PubMed]
    [Google Scholar]
  26. Pantos O, Cooney RP, Le Tissier MDA, Barer MR, O'Donnell AG et al. The bacterial ecology of a plague-like disease affecting the Caribbean coral Montastrea annularis . Environ Microbiol 2003; 5:370–382 [CrossRef][PubMed]
    [Google Scholar]
  27. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  28. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  29. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  30. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  31. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  33. Chen Y, Chen Y, Shi C, Huang Z, Zhang Y et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 2018; 7:1–6 [CrossRef][PubMed]
    [Google Scholar]
  34. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  35. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  36. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  37. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004; 32:11–16 [CrossRef][PubMed]
    [Google Scholar]
  38. Grant JR, Stothard P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008; 36:W181–W184 [CrossRef][PubMed]
    [Google Scholar]
  39. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [CrossRef][PubMed]
    [Google Scholar]
  40. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [CrossRef][PubMed]
    [Google Scholar]
  41. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  42. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  43. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  44. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  45. Bowman JP, Nichols CM, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 2003; 53:1343–1355 [CrossRef][PubMed]
    [Google Scholar]
  46. Jones MP, McCarthy AJ, Cross T. Taxonomic and serologic studies on Micropolyspora faeni and Micropolyspora strains from soil bearing the specific epithet rectivirgula. J Gen Microbiol 1979; 115:343–354 [CrossRef][PubMed]
    [Google Scholar]
  47. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  48. Maczulak AE, Dawson KA, Baker JP. Nitrogen utilization in bacterial isolates from the equine cecum. Appl Environ Microbiol 1985; 50:1439–1443 [CrossRef][PubMed]
    [Google Scholar]
  49. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [CrossRef][PubMed]
    [Google Scholar]
  50. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  51. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  52. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 1980; 48:277–282 [CrossRef][PubMed]
    [Google Scholar]
  53. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
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