Citreibacter salsisoli gen. nov., sp. nov., a bacterium isolated from marine soil

Abstract

A Gram-stain-negative, strictly aerobic, yellow-colored, rod-shaped, chemoheterotrophic bacterium, designated SNA426T, was isolated from marine soil in the Republic of Korea. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel marine isolate was affiliated with the family Flavobacteriaceae of phylum Bacteroidetes and that it shared the highest (96.2%) sequence similarity with Gillisia mitskevichiae KMM 6034T. The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. The major fatty acids of strain SNA426T were iso-C15:0, C16:1 ω7c and/or C16:1 ω6c and iso-C17:0 3-OH. The DNA G+C content of the strain was 39.6 mol% and the major respiratory quinone was menaquinone 6 (MK-6). Strain SNA426T had phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids and nine unidentified lipids as polar lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Citreibacter gen. nov. is proposed. The type species is Citreibacter salsisoli sp. nov., with the type strain SNA426T (= KCCM 90269T = CGMCC 1.16129T).

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References

  1. Abell GC, Bowman JP (2005) Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51:265–277

    CAS  Article  PubMed  Google Scholar 

  2. Alonso C, Warnecke F, Amann R, Pernthaler J (2007) High local and global diversity of Flavobacteria in marine plankton. Environ Microbiol 9:1253–1266

    CAS  Article  PubMed  Google Scholar 

  3. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Bernardet JF, Bowman JP (2006) The genus Flavobacterium. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria, vol 7, 3rd edn. Springer, New York, pp 481–531

    Google Scholar 

  5. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148

    Article  Google Scholar 

  6. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    CAS  PubMed  Google Scholar 

  7. Bowman JP, Nichols DS (2005) Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol 55:1471–1486

    CAS  Article  PubMed  Google Scholar 

  8. Collins MD, Jones D (1981) A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 51:129–134

    CAS  Article  PubMed  Google Scholar 

  9. Colwell RR (1970) Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104:410–433

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Cottrell MT, Kirchman DL (2000) Natural assemblages of marine proteobacteria and members of the CytophagaFlavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 66:1692–1697

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Dobson SJ, Colwell RR, McMeekin TA, Franzmann PD (1993) Direct sequencing of the polymerase chain reaction-amplified 16S rRNA gene of Flavobacterium gondwanense sp. nov. and Flavobacterium salegens sp. nov., two new species from a hypersaline Antarctic lake. Int J Syst Bacteriol 43:77–83

    CAS  Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  13. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  14. Garrity GM, Holt JG (2001) The road map to the manual. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn. Springer, New York, pp 119–166

    Google Scholar 

  15. Glöckner FO, Fuchs BM, Amann R (1999) Bacterioplankton composition of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65:3721–3726

    PubMed  PubMed Central  Google Scholar 

  16. Hansen GH, Sørheim R (1991) Improved method for phenotypical characterization of marine bacteria. J Microbiol Method 13:231–241

    Article  Google Scholar 

  17. Ivanova EP, Bowman JP, Christen R, Zhukova NV, Lysenko AM, Gorshkova NM, Mitik-Dineva N, Sergeev AF, Mikhailov VV (2006) Salegentibacter flavus sp. nov. Int J Syst Evol Microbiol 56:583–586

    CAS  Article  PubMed  Google Scholar 

  18. Jooste PJ (1985) The taxonomy and significance of FlavobacteriumCytophaga strains from dairy sources. PhD thesis, University of the Orange Free State, South Africa

  19. Kim JH, Yoon JH, Kim W (2016) Salinimicrobium soli sp. nov., isolated from soil of reclaimed land. Int J Syst Evol Microbiol 66:462–467

    CAS  Article  PubMed  Google Scholar 

  20. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through the comparative studies of sequence evolution. J Mol Evol 16:111–120

    CAS  Article  PubMed  Google Scholar 

  21. Kirchman DL (2002) The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91–100

    CAS  PubMed  Google Scholar 

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

    CAS  Article  Google Scholar 

  23. Lee OO, Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S, Wu MC, Wong PK, Qian PY (2006) Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge Myxilla incrustans. Int J Syst Evol Microbiol 56:1795–1799

    CAS  Article  PubMed  Google Scholar 

  24. Lee SY, Park S, Oh TK, Yoon JH (2012) Salinimicrobium gaetbulicola sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 62:1027–1031

    CAS  Article  PubMed  Google Scholar 

  25. Lewin RA, Lounsbery DM (1969) Isolation, cultivation and characterization of flexibacteria. J Gen Microbiol 58:145–170

    CAS  Article  PubMed  Google Scholar 

  26. Lim JM, Jeon CO, Lee SS, Park DJ, Xu LH, Jiang CL, Kim CJ (2008) Reclassification of Salegentibacter catena Ying et al. 2007 as Salinimicrobium catena gen. nov., comb. nov. and description of Salinimicrobium xinjiangense sp. nov., a halophilic bacterium isolated from Xinjiang province in China. Int J Syst Evol Microbiol 58:438–442

    CAS  Article  PubMed  Google Scholar 

  27. McCammon SA, Bowman JP (2000) Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int J Syst Evol Microbiol 50:1055–1063

    CAS  Article  PubMed  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, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinines and polar lipids. J Microbiol Method 2:233–241

    CAS  Article  Google Scholar 

  30. Nedashkovskaya OI, Kim SB, Lee KH, Mikhailov VV, Bae KS (2005) Gillisia mitskevichiae sp. nov., a novel bacterium of the family Flavobacteriaceae, isolated from sea water. Int J Syst Evol Microbiol 55:321–323

    CAS  Article  PubMed  Google Scholar 

  31. Nedashkovskaya OI, Kim SB, Vancanneyt M, Shin DS, Lysenko AM, Shevchenko LS, Krasokhin VB, Mikhailov VV, Swings J, Bae KS (2006) Salegentibacter agarivorans sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the sponge Artemisina sp. Int J Syst Evol Microbiol 56:883–887

    CAS  Article  PubMed  Google Scholar 

  32. Nedashkovskaya OI, Vancanneyt M, Kim SB, Han J, Zhukova NV, Shevchenko LS (2010) Salinimicrobium marinum sp. nov., a halophilic bacterium of the family Flavobacteriaceae, and emended descriptions of the genus Salinimicrobium and Salinimicrobium catena. Int J Syst Evol Microbiol 60:2303–2306

    CAS  Article  PubMed  Google Scholar 

  33. Power DA, Johnson JA (2009) Difco™ and BBL™ manual: manual of microbiological culture media, 2nd edn. Becton Dickinson and Company, Sparks, pp 359–360

    Google Scholar 

  34. Reichenbach H (1992) Flavobacteriaceae fam. nov. in validation of the publication of new names and new combinations previously effectively published outside the IJSB, list no. 41. Int J Syst Bacteriol 42:327–329

    Article  Google Scholar 

  35. Roh SW, Lee M, Lee HW, Yim KJ, Heo SY, Kim KN, Yoon C, Nam YD, Kim JY, Hyun DW, Bae JW, Jeong JB, Kang H, Kim D (2013) Gillisia marina sp. nov., from seashore sand, and emended description of the genus Gillisia. Int J Syst Evol Microbiol 63:3640–3645

    CAS  Article  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  38. Siamphan C, Kim W (2014) Salegentibacter chungangensis sp. nov., isolated from a sea sand and emended description of the genus Salegentibacter. Int J Syst Evol Microbiol 64:1514–1519

    CAS  Article  PubMed  Google Scholar 

  39. Subhash Y, Sasikala Ch, Ramana ChV (2014) Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment. Int J Syst Evol Microbiol 64:984–988

    CAS  Article  PubMed  Google Scholar 

  40. Tamura K, Peterson D, Petersen N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 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 Acid Res 25:4876–4882

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Van Trappen S, Vandecandelaere I, Mergaert J, Swings J (2004) Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. Int J Syst Evol Microbiol 54:445–448

    Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. Worliczek HL, Kämpfer P, Rosengarten R, Tindall RBJ, Busse HJ (2007) Polar lipid and fatty acid profiles-re-vitalizing old approaches as a modern tool for the classification of mycoplasmas? Syst Appl Microbiol 30:355–370

    CAS  Article  PubMed  Google Scholar 

  45. Xia HF, Li XL, Liu QQ, Miao TT, Du ZJ, Chen GJ (2013) Salegentibacter echinorum sp. nov., isolated from the sea urchin Hemicentrotus pulcherrimus. Antonie Van Leeuwenhoek 104:315–320

    CAS  Article  PubMed  Google Scholar 

  46. Ying JY, Liu ZP, Wang BJ, Dai X, Yang SS, Liu SJ (2007) Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter. Int J Syst Evol Microbiol 57:219–222

    CAS  Article  PubMed  Google Scholar 

  47. Yoon J, Lee KC, Lee JS (2016) Cribrihabitans pelagius sp. nov., a marine alphaproteobacterium isolated from seawater. Int J Syst Evol Microbiol 66:3195–3200

    CAS  Article  PubMed  Google Scholar 

  48. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  PubMed  PubMed Central  Google Scholar 

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Correspondence to Sang-Jip Nam.

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Additional information

The digital protologue database (DPD) number for the strain SNA426T is TA00277. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SNA426T is LC212983.

Communicated by Erko Stackebrandt.

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Yoon, J., Choi, M.K. & Nam, SJ. Citreibacter salsisoli gen. nov., sp. nov., a bacterium isolated from marine soil. Arch Microbiol 200, 445–451 (2018). https://doi.org/10.1007/s00203-017-1451-5

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Keywords

  • Flavobacteriaceae
  • Citreibacter salsisoli gen. nov., sp. nov.
  • Marine soil
  • 16S rRNA gene
  • Polyphasic taxonomy