1887

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Volume 69, Issue 9

sp. nov., isolated from marine sediment, Masan Bay, South Korea Free

Abstract

A Gram-stain-negative, non-motile, mesophilic, short rod-shaped, aerobic bacterium designated as 318-1 was isolated from a marine sediment collected from Masan Bay, South Korea. Strain 318-1 grew optimally at pH 6–7, at 30 °C and in the presence of 2–3 % (w/v) NaCl, tolerant of up to 8 % (w/v) NaCl, and accumulated poly--hydroxybutyrate (PHB). A comparative analysis of 16S rRNA gene sequences revealed that strain 318-1 formed a distinct phyletic lineage in the genus (family , class ) and showed high sequence similarity to DSM 27839 (96.5 %) and DSM 28453 (96.3 %). Comparing the genome sequence of 318-1 with those of the type strains of seven species of the genus and two species of the genus the values obtained were below the thresholds with analysis of average nucleotide identities (ANI, 71.6–76.8 %) and DNA–DNA hybridisation, Genome-to-Genome Distance Calculator (GGDC, 18.5–20.6 %). The DNA GC content was 65.75 mol%. Chemotaxonomic data [predominant quinone ubiquinone Q10; polar lipid profile consisting of major compounds phosphatidylcholine (PC), phosphatidylglycerol (PG), an unidentified aminolipid and an unidentified lipid; major fatty acids summed feature 8 (Cω and/or Cω)] supported the affiliation of strain 318-1 to the genus . Genomic, chemotaxonomic, and phenotypic differentiation of strain 318-1 from the members of the genus support it as a novel species. On the basis of the results in this study, a novel species, sp. nov., is proposed. The type strain is 318-1 (=JCM 30927=KEMB 7306-525=KCTC 72105).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alphaproteobacteria , marine bacteria , PHB , Rhodobacteraceae , Ruegeria and slime
© 2019 The Authors
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2019-09-01
2024-04-25
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References

  1. Uchino Y, Hirata A, Yokota A, Sugiyama J. 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 1998; 44:201–210 [View Article][PubMed]
     [Google Scholar]
  2. Arahal DR, Macián MC, Garay E, Pujalte MJ. Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int J Syst Evol Microbiol 2005; 55:2371–2376 [View Article][PubMed]
     [Google Scholar]
  3. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ et al. 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 2006; 56:1293–1304 [View Article][PubMed]
     [Google Scholar]
  4. Petursdottir SK, Kristjansson JK. Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland. Extremophiles 1997; 1:94–99 [View Article][PubMed]
     [Google Scholar]
  5. González JM, Covert JS, Whitman WB, Henriksen JR, Mayer F et al. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol 2003; 53:1261–1269 [View Article][PubMed]
     [Google Scholar]
  6. Yi H, Lim YW, Chun J. 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 2007; 57:815–819 [View Article][PubMed]
     [Google Scholar]
  7. Lee K, Choo YJ, Giovannoni SJ, Cho JC. Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean. Int J Syst Evol Microbiol 2007; 57:1815–1818 [View Article][PubMed]
     [Google Scholar]
  8. Lai Q, Yuan J, Li F, Zheng T, Shao Z. Ruegeria pelagia is a later heterotypic synonym of Ruegeria mobilis . Int J Syst Evol Microbiol 2010; 60:1918–1920 [View Article][PubMed]
     [Google Scholar]
  9. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article][PubMed]
     [Google Scholar]
  10. Muramatsu Y, Uchino Y, Kasai H, Suzuki K, Nakagawa Y. Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int J Syst Evol Microbiol 2007; 57:1304–1309 [View Article][PubMed]
     [Google Scholar]
  11. Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Faimali M et al. Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm. Int J Syst Evol Microbiol 2008; 58:2726–2733 [View Article][PubMed]
     [Google Scholar]
  12. Park S, Yoon JH. Ruegeria arenilitoris sp. nov., isolated from the seashore sand around a seaweed farm. Antonie van Leeuwenhoek 2012; 102:581–589 [View Article][PubMed]
     [Google Scholar]
  13. Lee J, Whon TW, Shin NR, Roh SW, Kim J et al. Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii. Int J Syst Evol Microbiol 2012; 62:2851–2857 [View Article][PubMed]
     [Google Scholar]
  14. Arahal DR, Lucena T, Rodrigo-Torres L, Pujalte MJ. Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis. Int J Syst Evol Microbiol 2018; 68:2515–2522 [View Article][PubMed]
     [Google Scholar]
  15. Jung YT, Yoon JH. Jannaschia faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:945–951 [View Article][PubMed]
     [Google Scholar]
  16. Kim YO, Park S, Nam BH, Kang SJ, Hur YB et al. Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi . Int J Syst Evol Microbiol 2012; 62:925–930 [View Article][PubMed]
     [Google Scholar]
  17. Kämpfer P, Arun AB, Rekha PD, Busse HJ, Young CC et al. Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. Int J Syst Evol Microbiol 2013; 63:2538–2544 [View Article][PubMed]
     [Google Scholar]
  18. Zhang L, Wang KL, Yin Q, Liang JY, Xu Y. Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel. Int J Syst Evol Microbiol 2018; 68:2653–2658 [View Article][PubMed]
     [Google Scholar]
  19. Lucena T, Ruvira MA, Macián MC, Pujalte MJ, Arahal DR. Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov. Syst Appl Microbiol 2013; 36:325–329 [View Article][PubMed]
     [Google Scholar]
  20. Huo YY, Xu XW, Li X, Liu C, Cui HL et al. Ruegeria marina sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:347–350 [View Article][PubMed]
     [Google Scholar]
  21. Zhang G, Haroon MF, Zhang R, Dong X, Wang D et al. Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea. Int J Syst Evol Microbiol 2017; 67:4624–4631 [View Article][PubMed]
     [Google Scholar]
  22. Kim YO, Park S, Nam BH, Jung YT, Kim DG et al. Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi . Antonie van Leeuwenhoek 2014; 105:551–558 [View Article][PubMed]
     [Google Scholar]
  23. Rüger HJ, Höfle MG. 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 1992; 42:133–143 [View Article][PubMed]
     [Google Scholar]
  24. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
     [Google Scholar]
  25. Kim J, Srinivasan S, You T, Bang JJ, Park S et al. Brevibacterium ammoniilyticum sp. nov., an ammonia-degrading bacterium isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2013; 63:1111–1118 [View Article][PubMed]
     [Google Scholar]
  26. 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 Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  27. Phillips JL, Gnanakaran S. A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps. Proteins 2015; 83:46–65 [View Article][PubMed]
     [Google Scholar]
  28. 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][PubMed]
     [Google Scholar]
  29. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. Chow GC. Maximum-likelihood estimation of misspecified models. Econ Model 1984; 1:134–138 [View Article]
     [Google Scholar]
  32. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  33. 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]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  35. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article][PubMed]
     [Google Scholar]
  36. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
     [Google Scholar]
  37. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
     [Google Scholar]
  38. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  39. Lee I, Ouk Kim Y, 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]
  40. Jg C, Sherman N. Microbiology: A Laboratory Manual, 6th ed. San Francisco, CA: Benjamin Cummings; 2002
     [Google Scholar]
  41. Hayat MA, Miller SE. Negative Staining: Applications and Methods New York, NY: McGraw-Hill; 1990
     [Google Scholar]
  42. Spiekermann P, Rehm BH, Kalscheuer R, Baumeister D, Steinbüchel A. A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 1999; 171:73–80 [View Article][PubMed]
     [Google Scholar]
  43. Bozzola JJ, Russell LD. Electron Microscopy: Principles and Techniques for Biologists Sudbury, MA: Jones & Bartlett; 1999 pp. 17–47
     [Google Scholar]
  44. Corazza M, Simonsen SB, Gnaegi H, Thydén KTS, Krebs FC et al. Comparison of ultramicrotomy and focused-ion-beam for the preparation of TEM and STEM cross section of organic solar cells. Appl Surf Sci 2016; 389:462–468 [View Article]
     [Google Scholar]
  45. Brown A. Benson's Microbiological Applications: Laboratory Manual in General Microbiology New York, NY: McGraw-Hill; 2005
     [Google Scholar]
  46. Hyun DW, Kim MS, Shin NR, Kim JY, Kim PS et al. Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai . Int J Syst Evol Microbiol 2013; 63:4248–4253 [View Article][PubMed]
     [Google Scholar]
  47. Choi DH, Cho BC. Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. Int J Syst Evol Microbiol 2006; 56:1869–1873 [View Article][PubMed]
     [Google Scholar]
  48. Xie BS, Lv XL, Cai M, Tang YQ, Wang YN et al. Seohaeicola nanhaiensis sp. nov., a moderately halophilic bacterium isolated from the benthic sediment of South China Sea. Curr Microbiol 2014; 69:802–808 [View Article][PubMed]
     [Google Scholar]
  49. Kunitsky C, Osterhout G, Sasser M. Identification of microorganisms using fatty acid methyl ester (FAME) analysis and the MIDI Sherlock Microbial Identification System. Encycl Rapid Microbiol Methods 2006; 3:1–18
     [Google Scholar]
  50. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  51. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
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Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea
Int J Syst Evol Microbiol 69, 2854 (2019); https://doi.org/10.1099/ijsem.0.003568
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