Paradonghicola geojensis gen. nov., sp. nov., isolated from seawater, Geoje-si, South Korea

Abstract

A Gram-negative, non-motile, non-spore-forming and aerobic bacterium, designated FJ12T, was isolated from seawater, Geoje-si, South Korea. Strain FJ12T was catalase and oxidase positive. Growth of strain FJ12T was optimally observed at 30 °C and pH 6 and grew in the presence of 0–11 % (w/v) NaCl (optimum 2–3 % NaCl). The phylogenic analysis based on 16S rRNA gene sequence of strains FJ12T showed the highest sequence similarity to those of Doghicola eburneus KCTC 12735T (95.4 %), Aestuariihabitans beolgyonensis KTCT 32324T (95.3 %), Sulfitobacter pontiacus KCTC 32185T (94.9 %), Roseisalinus antarcticus DSM 11466T (94.8 %) and Loktanella soesokkaensis KCTC 32425T (94.7 %). The major polar lipids of FJ12T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid and unidentified lipids. It contained Q-10 as the predominant ubiquinone, and major fatty acid is C18:1 ω7c (51.7 %), C16:0 (24.0 %). The DNA G+C content of the strain FJ12T was 60 mol%. Based on physiological and chemotaxonomic characteristics, strain FJ12T should be regarded as the type species of a novel genus in the family Rhodobacteraceae for which the name Paradonghicola geojensis sp. nov. is proposed. The type strain FJ12T (=KEMB 3001-336T=JCM 30384T).

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References

  1. Buchan A, González JM, Moran MA (2005) Overview of the marine Roseobacter lineage. Appl Environ Microbiol 71:5665–5677

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Cappuccino JG, Sherman N (2010) Microbiology: a laboratory manual, 9th edn. Benjamin Cummings, San Francisco, pp 69–74, 161–164

  3. Dai X, Wang BJ, Yang QX, Jiao NZ, Liu SJ (2006) Yangia pacifica gen. nov., sp. nov., a novel member of the Roseobacter clade from coastal sediment of the East China Sea. Int J Syst Evol Microbiol 56:529–533

  4. Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GH (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, pp 21–33

    Google Scholar 

  5. Euzéby JP (1997) List of Bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592 (List of Prokaryotic names with standing in nomenclature. http://www.bacterio.ciet.fr/. Accessed 18 Jan 2013

  6. Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  7. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Fukui Y, Abe M, Kobayashi M, Shimada Y, Saito H, Oikawa H, Yano Y, Satomi M (2014) Sulfitobacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis. Int J Syst Evol Microbiol 64:438–443

  9. Garrity GM, Bell JA, Lilburn T (2005) Order III. Rhodobacterales ord. nov. In: Brenner DJ, Kreg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol. 2, Part C, 2nd edn. Springer, New York, p 161

  10. Garrity GM, Bell JA, Lilburn T (2006) Order III. Rhodobacterales ord. nov. In List of new names and new combinations previously effectively, but not validly, published, validation List no. 107. Int J Syst Evol Microbiol 56:1–6

    Article  Google Scholar 

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

    CAS  Google Scholar 

  12. Hammed A, Shahina M, Lin SY, Nakayan P, Liu YC, Lai WA, Hsu YH et al (2014) Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Doghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007. Int J Syst Evol Microbiol 64:2729–2737

    Article  Google Scholar 

  13. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469

    CAS  Article  Google Scholar 

  14. Hong Z, Lai Q, Luo Q, Jiang S, Zhu R, Liang J, Gao Y. (2015) Sulfitobacter pseudonitzschiae sp. nov., isolated from the toxic marine diatom Pseudo-nitzschia multiseries. Int J Syst Evol Microbiol 65:95–100

  15. Hosoya S, Yokota A (2007) Loktanella atrilutea sp. nov., isolated from seawater in Japan. Int J Syst Evol Microbiol 57:1966–1969

    CAS  Article  PubMed  Google Scholar 

  16. Ivanova EP, Zhukova NV, Lysenko AM, Gorshikova NM, Sergeev AF, Mikhailov VV, Bowman JP (2005) Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean. Int J Syst Evol Microbiol 55:2203–2207

    CAS  Article  PubMed  Google Scholar 

  17. Jung YT, Park SY, Park JM, Yoon JH (2014) Loktanella ponticola sp. nov., isolated from seawater. Int J Syst Evol Microbiol 64:3717–3723

    Article  PubMed  Google Scholar 

  18. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    CAS  Article  PubMed  Google Scholar 

  19. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Google Scholar 

  20. Komagata K, Suzuki K-I (1987) Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    CAS  Article  Google Scholar 

  21. Kuykendall LD, Roy MA, Oneill JJ, Devne TE (1988) Fatty acid, Antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38:358–361

    Article  Google Scholar 

  22. Kwak MJ, Lee JS, Lee KC, Kim KK, Eom MK, Kim BK, Kim JF (2014) Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacter noctilucicola sp. nov., isolated from coastal seawater. Int J Syst Bacteriol 67:3760–3767

  23. Labrenz M, Lawson PA, Tindall BJ, Collins MD, Hirsch P (2005) Roseisalinus antarcticus gen. nov., sp. nov., a novel aerobic bacteriochlorophyll α-producing α-proteobacterium isolated from hypersaline Ekho Lake, Antarctica. Int J Syst Evol Microbiol 55:41–47

    CAS  Article  PubMed  Google Scholar 

  24. Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Wu M, Wong PK, Qian PY (2004) Loktanella hongkongensis sp. nov., a novel member of the α-Proteobacteria originating from marine biofilms in Hong Kong waters. Int J Syst Evol Microbiol 54:2281–2284

    CAS  Article  PubMed  Google Scholar 

  25. Lee SD (2012) Loktanella tamlensis sp. nov., isolated from seawater. J Syst Evol Microbiol 62:586–590

    CAS  Article  Google Scholar 

  26. Liang J, Zhang Z, Liu Y, Wang M, Zhang XH (2015) Loktanella sediminum sp. nov., isolated from marine surface sediment. Int J Syst Evol Microbiol 65:686–691

    CAS  Article  PubMed  Google Scholar 

  27. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro organisms. J Mol Biol 3:208–218

    CAS  Article  Google Scholar 

  28. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  29. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117

  30. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  31. Moon YG, Seo SH, Lee SD, Heo MS (2010) Loktanella pyoseonensis sp. nov., isolated from beach sand, and emended description of the genus Loktanella. Int J Syst Evol Microbiol 60:785–789

    CAS  Article  PubMed  Google Scholar 

  32. Muramatsu Y, Uchino Y, Kasai H, Suzuki K, Nakagawa Y (2007) Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int J Syst Evol Microbiol 57:1304–1309

  33. Park S, Kang SJ SJ, Oh TK, Yoon JH (2010) Roseivivax lentus sp. nov., isolated from a tidal flat sediment, and emended description of the genus Roseivivax Suzuki et al. 1999. Int J Syst Evol Microbiol 60:1113–1117

  34. Park S, Lee JS, Lee KC, Yoon JH (2013a) Loktanella soesokkakensis sp. nov., isolated from the junction between the North Pacific Ocean and a freshwater spring. Antonie Van Leeuwenhoek 104:397–404

    CAS  Article  PubMed  Google Scholar 

  35. Park S, Jung YT, Yoon JH (2013b) Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 63:4118–4123

    CAS  Article  PubMed  Google Scholar 

  36. Park JM, Park S, Jung YT, Cho JY, Yoon JH (2014) Loktanella variabilis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 64:2579–2585

    CAS  Article  PubMed  Google Scholar 

  37. Rappé MS, Vergin K, Giovannoni SJ (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 33:219–232

  38. Romanenko LA, Tanaka N, Svetashev VL, Kainovskaya NL (2012) Poseidonocella pacifica gen. nov., sp. nov. and Poseidonocella sedimentorum sp. nov., novel alphaproteobacteria from the shallow sandy sediments of the Sea of Japan. Arch Microbiol 194:113–121

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

    CAS  PubMed  Google Scholar 

  40. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark

  41. Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128

    CAS  Article  Google Scholar 

  42. Tan T, Wang B, Shao Z (2009) Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China. Int J Syst Evol Microbiol 59:1143–1147

    CAS  Article  PubMed  Google Scholar 

  43. Tanaka N, Romanenko LA, Kurilenko VV, Svetashev VI, Kalinovskaya NI, Mikhailov VV (2014) Loktanella maritima sp. nov. isolated from shallow marine sediments. Int J Syst Evol Microbiol 64:2370–2375

    CAS  Article  PubMed  Google Scholar 

  44. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  45. Tsubouchi T, Shimane Y, Mori K, Miyazaki M, Tame A, Uematsu K, Maruyama T, Hatada Y (2013) Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus Loktanella. Int J Syst Evol Microbiol 63:1390–1395

    Article  PubMed  Google Scholar 

  46. Van Trappen S, Mergaert J, Swings J (2004) Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54:1263–1269

    Article  PubMed  Google Scholar 

  47. Vandecandelaere L, Nercessian O, Segaert E, Achouak W, Faimali M, Vandamme P (2008) Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm. Int J Syst Evol Microbiol 58:2726–2733

  48. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Weon HY, Kim BY, Yoo SH, Kim JS, Kwon SW, Go SJ, Stackebrandt E (2006) Loktanella koreensis sp. nov., isolated from sea sand in Korea. Int J Syst Evol Microbiol 56:2199–2202

    CAS  Article  PubMed  Google Scholar 

  50. Yoon JH, Kang SJ, Oh TK (2007a) Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 57:73–76

    CAS  Article  PubMed  Google Scholar 

  51. Yoon JH, Kang SJ, Lee SY, Oh TK (2007b) Loktanella maricola sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 57:1799–1802

    CAS  Article  PubMed  Google Scholar 

  52. Yoon JH, Jung YT, Lee JS (2013) Loktanella litorea sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63:175–180

    CAS  Article  PubMed  Google Scholar 

  53. Yurkov V, Stackebrandt E, Homes A, Fuerst JA, Hugenholtz P, Golecki J, Gad’on N, Gorlenko VM, Kompatseva EI, Drews G (1994) Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 44:427–434

    CAS  Article  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the National Research Foundation of Korea (NRF) (No. NRF-2013M3A2A1067498) and the Korea National Environmental Microorganisms Bank (2010-0007473).

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Correspondence to Sang-Seob Lee.

Additional information

The NCBI GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain FJ12T (=KEMB 3001-336T=JCM 30384T) is KR185328.

Communicated by Erko Stackebrandt.

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Supplement Fig. 1.

Phylogenetic tree of strains FJ12T and related other type strains based on 16S rRNA gene sequence comparisons. Distances were calculated, and clustering with the maximum-parsimony method was conducted by using the software MEGA5. Bootstrap values of > 50 % (percentages of 1,000 replications) are shown at branching points. The sequences used for the comparative study are included in parentheses (PPTX 115 kb)

Supplement Fig. 2.

Phylogenetic tree of strains FJ12T and related other type strains based on 16S rRNA gene sequence comparisons. Distances were calculated, and clustering with the maximum-likelihood method was conducted by using the software MEGA5. Bootstrap values of > 50 % (percentages of 1,000 replications) are shown at branching points. The sequences used for the comparative study are included in parentheses (PPTX 105 kb)

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Lee, K., Srinivasan, S. & Lee, SS. Paradonghicola geojensis gen. nov., sp. nov., isolated from seawater, Geoje-si, South Korea. Arch Microbiol 198, 501–507 (2016). https://doi.org/10.1007/s00203-015-1182-4

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Keywords

  • Paradonghicola geojensis
  • Taxonomy
  • Marine bacteria