1887

Abstract

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25–30 °C, at pH 6.5–8.5 and with 0–4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568 was a member of the genus with high similarity to JCM 30852 (97.7 %), KACC 17089 (97.3 %) and LMG F28894 (97.3 %). The predominant cellular fatty acids were C, summed feature 3 (C 6 and/or C 7) and summed feature 8 (C 7 and/or C 6), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568 was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568 as representing a novel species, for which the name sp. nov. is proposed. The type strain of this novel species is CAU 1568 (=KCTC 82404=MCCC 1K05668).

Funding
This study was supported by the:
  • Chung-Ang University (Award 2020)
    • Principle Award Recipient: WonyongKim
  • Ministry of Environment (MOE) of the Republic of Korea (Award NIBR201902203)
    • Principle Award Recipient: WonyongKim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005034
2021-10-04
2024-03-28
Loading full text...

Full text loading...

References

  1. Beijerinck MW. Le photobacterium luminosum, Bactérie lumineuse de la Mer du Nord. Arch Neerl Sci 1889; 23:401–427
    [Google Scholar]
  2. Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E. Photobacterium halotolerans sp. nov., isolated from Lake Martel in Spain. Int J Syst Evol Microbiol 2006; 56:1067–1071 [View Article] [PubMed]
    [Google Scholar]
  3. Park Y-D, Baik K-S, Seong C-N, Bae KS, Kim S et al. Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water. Int J Syst Evol Microbiol 2006; 56:745–749 [View Article] [PubMed]
    [Google Scholar]
  4. Yoshizawa S, Wada M, Kita-Tsukamoto K, Yokota A, Kogure K. Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2009; 59:1438–1442 [View Article] [PubMed]
    [Google Scholar]
  5. Lucena T, Ruvira MA, Pascual J, Garay E, Macian MC et al. Photobacterium aphoticum sp. nov., isolated from coastal water. Int J Syst Evol Microbiol 2011; 61:1579–1584 [View Article] [PubMed]
    [Google Scholar]
  6. Wang X, Wang Y, Yang X, Sun H, Li B et al. Photobacterium alginatilyticum sp. nov., a marine bacterium isolated from bottom seawater. Int J Syst Evol Microbiol 2017; 67:1912–1917 [View Article] [PubMed]
    [Google Scholar]
  7. Wang X, Li Y, Xue CX, Li B, Zhou S et al. Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea. Int J Syst Evol Microbiol 2019; 69:1477–1483 [View Article] [PubMed]
    [Google Scholar]
  8. Jung SY, Jung YT, Oh TK, Yoon JH. Photobacterium lutimaris sp. nov., isolated from a tidal flat sediment in Korea. Int J Syst Evol Microbiol 2007; 57:332–336 [View Article] [PubMed]
    [Google Scholar]
  9. Kim YO, Kim KK, Park S, Kang SJ, Lee JH et al. Photobacterium gaetbulicola sp. nov., a lipolytic bacterium isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2010; 60:2587–2591 [View Article] [PubMed]
    [Google Scholar]
  10. Lo N, Jin HM, Jeon CO. Photobacterium aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2014; 64:625–630 [View Article] [PubMed]
    [Google Scholar]
  11. Yoon JH, Lee JK, Kim YO, Oh TK. Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:335–339 [View Article] [PubMed]
    [Google Scholar]
  12. Nogi Y, Masui N, Kato C. Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment. Extremophiles 1998; 2:1–7 [View Article] [PubMed]
    [Google Scholar]
  13. Li Y, Zhou M, Wang F, Wang ET, Du Z et al. Photobacterium proteolyticum sp. nov., a protease-producing bacterium isolated from ocean sediments of Laizhou Bay. Int J Syst Evol Microbiol 2017; 67:1835–1840 [View Article] [PubMed]
    [Google Scholar]
  14. Seo HJ, Bae SS, Lee JH, Kim SJ. Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount. Int J Syst Evol Microbiol 2005; 55:1661–1666 [View Article] [PubMed]
    [Google Scholar]
  15. Seo HJ, Bae SS, Yang SH, Lee JH, Kim SJ. Photobacterium aplysiae sp. nov., a lipolytic marine bacterium isolated from eggs of the sea hare Aplysia kurodai. Int J Syst Evol Microbiol 2005; 55:2293–2296 [View Article] [PubMed]
    [Google Scholar]
  16. Thompson FL, Thompson CC, Naser S, Hoste B, Vandemeulebroecke K et al. Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching. Int J Syst Evol Microbiol 2005; 55:913–917 [View Article] [PubMed]
    [Google Scholar]
  17. Ast JC, Cleenwerck I, Engelbeen K, Urbanczyk H, Thompson FL et al. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes. Int J Syst Evol Microbiol 2007; 57:2073–2078 [View Article] [PubMed]
    [Google Scholar]
  18. Chimetto LA, Cleenwerck I, Thompson CC, Brocchi M, Willems A et al. Photobacterium jeanii sp. nov., isolated from corals and zoanthids. Int J Syst Evol Microbiol 2010; 60:2843–2848 [View Article] [PubMed]
    [Google Scholar]
  19. Gomez-Gil B, Roque A, Rotllant G, Peinado L, Romalde JL et al. Photobacterium swingsii sp. nov., isolated from marine organisms. Int J Syst Evol Microbiol 2011; 61:315–319 [View Article] [PubMed]
    [Google Scholar]
  20. Deep K, Poddar A, Das SK. Photobacterium panuliri sp. nov., an alkalitolerant marine bacterium isolated from eggs of spiny lobster, Panulirus penicillatus from Andaman Sea. Curr Microbiol 2014; 69:660–668 [View Article] [PubMed]
    [Google Scholar]
  21. Machado H, Giubergia S, Mateiu RV, Gram L. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea. Int J Syst Evol Microbiol 2015; 65:4503–4507 [View Article] [PubMed]
    [Google Scholar]
  22. Gomez-Gil B, Roque A, Rotllant G, Romalde JL, Doce A et al. Photobacterium sanguinicancri sp. nov. isolated from marine animals. Antonie Van Leeuwenhoek 2016; 109:817–825 [View Article] [PubMed]
    [Google Scholar]
  23. Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G et al. Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod. Syst Appl Microbiol 2014; 37:329–335 [View Article] [PubMed]
    [Google Scholar]
  24. Labella AM, Arahal DR, Lucena T, Manchado M, Castro D. Photobacterium toruni sp. nov., a bacterium isolated from diseased farmed fish. Int J Syst Evol Microbiol 2017; 67:4518–4525 [View Article] [PubMed]
    [Google Scholar]
  25. Smith SK, Sutton DC, Fuerst JA, Reichelt JL. Evaluation of the genus Listonella and reassignment of Listonella damsela (Love et al.) MacDonell and Colwell to the genus Photobacterium as Photobacterium damsela comb. nov. with an emended description. Int J Syst Bacteriol 1991; 41:529–534 [View Article] [PubMed]
    [Google Scholar]
  26. Urakawa H, Kita-Tsukamoto K, Ohwada K. Reassessment of the taxonomic position of Vibrio iliopiscarius (Onarheim et al. 1994) and proposal for Photobacterium iliopiscarium comb. nov. Int J Syst Bacteriol 1999; 49:257–260 [View Article] [PubMed]
    [Google Scholar]
  27. Boisvert H, Chatelain R, Bassot JM. Study on a Photobacterium isolated from the light organ of the Leiognathidae fish. Ann Inst Pasteur 1967; 112:521–525 [PubMed]
    [Google Scholar]
  28. Enciso-Ibarra J, Gonzalez-Castillo A, Soto-Rodriguez SA, Enciso-Ibarra K, Bolan-Mejia C et al. Photobacterium lucens sp. nov., isolated from a cultured shrimp Penaeus vannamei. Curr Microbiol 2020; 77:1111–1116 [View Article] [PubMed]
    [Google Scholar]
  29. Moreira APB, Duytschaever G, Chimetto Tonon LA, Fróes AM, de Oliveira LS et al. Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. PeerJ 2014; 2:e427 [View Article] [PubMed]
    [Google Scholar]
  30. Labella AM, Arahal DR, Lucena T, Manchado M, Castro D et al. Photobacterium toruni sp. nov., a bacterium isolated from diseased farmed fish. Int J Syst Evol Microbiol 2017; 67:4518–4525 [View Article] [PubMed]
    [Google Scholar]
  31. Nam SW, Kim W, Chun J, Goodfellow M. Tsukamurella pseudospumae sp. nov., a novel actinomycete isolated from activated sludge foam. Int J Syst Evol Microbiol 2004; 54:1209–1212 [View Article] [PubMed]
    [Google Scholar]
  32. Lane DJ. 16S/23S RNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics 1991 pp 115–175
    [Google Scholar]
  33. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Micobiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  34. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
    [Google Scholar]
  35. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  36. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  37. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evolution 1987; 17:368–376
    [Google Scholar]
  38. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  39. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian Protein Metabolism 1969; 3:21–132 [View Article]
    [Google Scholar]
  40. Felsenstein J. Confidence limits on phylogenies, an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  41. Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  42. Auch AF, Von Jan M, Klenk HP, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  43. 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 [View Article]
    [Google Scholar]
  44. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. AntiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
    [Google Scholar]
  45. Na S-. I, Kim YO, Yoon S-. H, Ha S-. M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  46. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article]
    [Google Scholar]
  47. Imchang L, Mauricio C, Sung-Min H, Seong-In N, Seok-Hwan Y. ContEst16S: an algorithm that identifiles contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
    [Google Scholar]
  48. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  49. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
    [Google Scholar]
  50. Li M, Kong D, Wang Y, Ma Q, Han X. Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil. Int J Syst Evol Microbiol 2019; 69:3910–3916 [View Article] [PubMed]
    [Google Scholar]
  51. Smibert RM, Krieg NR. Phenotypic characterization. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General and Molecular Bacteriology Washington, DC; USA: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  52. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67 [View Article]
    [Google Scholar]
  53. 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 [View Article]
    [Google Scholar]
  54. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  55. Embley TM, Wait R. Structural lipids of eubacteria. Goodfellow M. eds In Chemical Methods in Prokaryotic Systematics New York, USA: Chichester, John Wiley and Sons; 1994 pp 121–161
    [Google Scholar]
  56. Kim JH, Ward Alan C, Kim W. Kagiella chungangensis sp. nov. isolated from marine sand. Antonie van Leeuwenhoek 2015; 107:1291–1298 [View Article]
    [Google Scholar]
  57. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl esters (GC-FAME). Technical Note 101 Newark, DE, USA: Microbial ID Inc; 2006
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005034
Loading
/content/journal/ijsem/10.1099/ijsem.0.005034
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error