Ruegeria arenilitoris sp. nov., isolated from the seashore sand around a seaweed farm

Abstract

A Gram-negative, motile and rod-shaped bacterial strain, G-M8T, which was isolated from seashore sand around a seaweed farm at Geoje island in South Korea, was characterized taxonomically. It grew optimally at 30–37 °C, at pH 7.0–8.0 and in presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain G-M8T joined the cluster comprising the type strains of Ruegeria atlantica and Ruegeria lacuscaerulensis, showing 97.5 % sequence similarity, by a bootstrap resampling value of 85.8 %. It exhibited 16S rRNA gene sequence similarity values of 95.4–96.7 % to the type strains of the other Ruegeria species. Strain G-M8T exhibited the highest gyrB sequence similarity value (88.5 %) to the type strain of R. lacuscaerulensis. Strain G-M8T contained Q-10 as the predominant ubiquinone and C18:1 ω7c as the predominant fatty acid. The polar lipid profile of strain G-M8T was similar to that of R. atlantica KCTC 12424T. The DNA G+C content of strain G-M8T was 64.6 mol% and its mean DNA–DNA relatedness values with R. atlantica KCTC 12424T and R. lacuscaerulensis KCTC 2953T were 18 ± 5.3 and 10 ± 3.6 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain G-M8T is distinguished from other Ruegeria species. On the basis of the data presented, strain G-M8T (=KCTC 23960T = CCUG 62412T) represents a novel species of the genus Ruegeria, for which the name Ruegeria arenilitoris sp. nov. is proposed.

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References

  1. Arahal DR, Macián MC, Garay E, Pujalte MJ (2005) Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int J Syst Evol Microbiol 55:2371–2376

    PubMed  Article  CAS  Google Scholar 

  2. Baumann P, Baumann L (1981) The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The Prokaryotes. Springer, Berlin, pp 1302–1331

    Google Scholar 

  3. Bruns A, Rohde M, Berthe-Corti L (2001) Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51:1997–2006

    PubMed  Article  CAS  Google Scholar 

  4. Cohen-Bazire G, Sistrom WR, Stanier RY (1957) Kinetic studies of pigment synthesis by nonsulfur purple bacteria. J Cell Comp Physiol 49:25–68

    Article  CAS  Google Scholar 

  5. Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London

    Google Scholar 

  6. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid–deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  7. González JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA (2003) Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol 53:1261–1269

    PubMed  Article  Google Scholar 

  8. Huo YY, Xu XW, Li X, Liu C, Cui HL, Wang CS, Wu M (2011) Ruegeria marina sp. nov., isolated from Marine Sediment. Int J Syst Evol Microbiol 61:347–350

    PubMed  Article  CAS  Google Scholar 

  9. Kim YO, Park S, Nam BH, Kang SJ, Hur YB, Lee SJ, Oh TK, Yoon JH (2012) Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi. Int J Syst Evol Microbiol 62:915–930

    Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Lai Q, Yuan J, Li F, Zheng T, Shao Z (2010) Ruegeria pelagia is a later heterotypic synonym of Ruegeria mobilis. Int J Syst Evol Microbiol 60:1918–1920

    PubMed  Article  Google Scholar 

  12. Lányí B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67

    Article  Google Scholar 

  13. Lee K, Choo YJ, Giovannoni SJ, Cho JC (2007) Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean. Int J Syst Evol Microbiol 57:1815–1818

    PubMed  Article  Google Scholar 

  14. Leifson E (1963) Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85:1183–1184

    PubMed  CAS  Google Scholar 

  15. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T (2006) Reclassification of Roseobacter gallaeciensis Ruiz- Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera. Int J Syst Evol Microbiol 56:1293–1304

    PubMed  Article  CAS  Google Scholar 

  16. 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

    Article  CAS  Google Scholar 

  17. 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

    Article  CAS  Google Scholar 

  18. 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

    PubMed  Article  CAS  Google Scholar 

  19. Oh KH, Jung YT, Oh TK, Yoon JH (2011) Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 61:1182–1188

    PubMed  Article  CAS  Google Scholar 

  20. Petursdottir SK, Kristjansson JK (1997) Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland. Extremophiles 1:94–99

    PubMed  Article  CAS  Google Scholar 

  21. Rüger HJ, Höfle MG (1992) Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev. Int J Syst Bacteriol 42:133–143

    PubMed  Article  Google Scholar 

  22. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. Microbial ID, Inc., Newark

  23. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

  24. Staley JT (1968) Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 95:1921–1942

    PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  26. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    PubMed  Article  CAS  Google Scholar 

  27. Uchino Y, Hirata A, Yokota A, Sugiyama J (1998) Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 44:201–210

    PubMed  Article  CAS  Google Scholar 

  28. Vandecandelaere I, 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

    PubMed  Article  CAS  Google Scholar 

  29. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  30. Yi H, Lim YW, Chun J (2007) Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int J Syst Evol Microbiol 57:815–819

    PubMed  Article  CAS  Google Scholar 

  31. Yoon JH, Kim H, Kim SB, Kim HJ, Kim WY, Lee ST, Goodfellow M, Park YH (1996) Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46:502–505

    Article  CAS  Google Scholar 

  32. Yoon JH, Lee ST, Park YH (1998) Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 48:187–194

    PubMed  Article  CAS  Google Scholar 

  33. Yoon JH, Kang KH, Park YH (2003) Psychrobacter jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 53:449–454

    PubMed  Article  CAS  Google Scholar 

  34. Yoon JH, Lee SY, Kang SJ, Lee CH, Oh TK (2007) Pseudoruegeria aquimaris gen. nov., sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbial 57:542–547

    Article  CAS  Google Scholar 

  35. Yoon JH, Kang SJ, Lee SY (2012) Salinimonas lutimais sp. nov., a polysaccharide-degrading bacterium isolated from a tidal flat. Antonie van Leeuwenhoek 101:803–810

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Acknowledgments

This work was supported by the Program for Collection, Management and Utilization of Biological Resources (grant M10867010003) and BK 21 program from the Ministry of Education, Science and Technology (MEST) of the Republic of Korea.

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Correspondence to Jung-Hoon Yoon.

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The GenBank/EMBL/DDBJ accession numbers of the 16S rRNA gene sequence and gyrB sequence of Ruegeria arenilitoris G-M8T are JQ807219 and JQ807221, respectively.

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Park, S., Yoon, JH. Ruegeria arenilitoris sp. nov., isolated from the seashore sand around a seaweed farm. Antonie van Leeuwenhoek 102, 581–589 (2012). https://doi.org/10.1007/s10482-012-9753-8

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Keywords

  • Ruegeria arenilitoris
  • Novel species
  • Polyphasic taxonomy
  • Seashore sand