1887

Abstract

Phylogenetic and taxonomic characterization was performed for bacterium RB-25, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20–37 °C at pH 5–8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C, Cω7 and summed feature 3 (Cω7 and/or iso-C 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25 formed a distinct lineage within the family of the class . It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours LMG 26275(96.6 %), CIP 78.65 (96.5 %), ATCC 43762(96.4 %), LMG 26273 (96.3 %), NUM 1720(96.3 %) and C1 (96.2 %). Multilocus sequence analyses based on and sequences showed a clear distinction of strain RB-25 from the most closely related genera. Isolate RB-25 could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25 represents a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain is RB-25 (=DSM 28811=LMG 28304).

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2016-06-10
2020-01-28
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J.. 1997; Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res25:3389–3402 [CrossRef][PubMed]
    [Google Scholar]
  2. Bligh E. G., Dyer W. J.. 1959; A rapid method of total lipid extraction and purification. Can J Biochem Physiol37:911–917[CrossRef]
    [Google Scholar]
  3. Brady C. L., Cleenwerck I., van der Westhuizen L., Venter S. N., Coutinho T. A., De Vos P.. 2012; Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus . Int J Syst Evol Microbiol62:1457–1464 [CrossRef][PubMed]
    [Google Scholar]
  4. Brady C., Hunter G., Kirk S., Arnold D., Denman S.. 2014; Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella . Syst Appl Microbiol37:545–552 [CrossRef][PubMed]
    [Google Scholar]
  5. Brenner D. J., Farmer J. J.. 2015; Enterobacteriaceae. In Bergey's Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd;
    [Google Scholar]
  6. Brenner D. J., Müller H. E., Steigerwalt A. G., Whitney A. M., O'Hara C. M., Kämpfer P.. 1998; Two new Rahnella genomospecies that cannot be phenotypically differentiated from Rahnella aquatilis . Int J Syst Bacteriol48:141–149 [CrossRef][PubMed]
    [Google Scholar]
  7. Ee R., Lim Y. L., Tee K. K., Yin W. F., Chan K. G.. 2014a; Quorum sensing activity of Serratia fonticola strain RB-25 isolated from an ex-landfill site. Sensors14:5136–5146 [CrossRef]
    [Google Scholar]
  8. Ee R., Lim Y. L., Kin L. X., Yin W. F., Chan K. G.. 2014b; Quorum sensing activity in Pandoraea pnomenusa RB38. Sensors14:10177–10186 [CrossRef]
    [Google Scholar]
  9. Ewing W. H., Farmer J. J., Brenner D. J.. 1980; Proposal of Enterobacteriaceae fam. nov., nom. rev. to replace Enterobacteriaceae Rahn 1937, nom. fam. cons. (Opin. 15, Jud. Comm. 1958), which lost standing in nomenclature on 1 January 1980. Int J Syst Bacteriol30:674–675[CrossRef]
    [Google Scholar]
  10. Geiger A., Fardeau M. L., Falsen E., Ollivier B., Cuny G.. 2010; Serratia glossinae sp. nov., isolated from the midgut of the tsetse fly Glossina palpalis gambiensis . Int J Syst Evol Microbiol60:1261–1265 [CrossRef][PubMed]
    [Google Scholar]
  11. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M.. 2007; DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  12. Grimont F., Grimont P. D.. 2006; The Genus Serratia . In The Prokaryotes, pp.219–244 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E.. New York: Springer;[CrossRef]
    [Google Scholar]
  13. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  14. Lau Y., Yin W.-F., Chan K.-G.. 2014; Enterobacter asburiae strain L1: complete genome and whole genome optical mapping analysis of a quorum sensing bacterium. Sensors14:13913–13924 [CrossRef][PubMed]
    [Google Scholar]
  15. Le Flèche-Matéos A., Levast M., Lomprez F., Arnoux Y., Andonian C., Perraud M., Vincent V., Ar Gouilh M., Thiberge J. M. et al. 2015; Rouxiella chamberiensis gen. nov., sp. nov., a member of the family Enterobacteriaceae isolated from parenteral nutrition bags. Int J Syst Evol Microbiol65:1812–1818 [CrossRef][PubMed]
    [Google Scholar]
  16. Lee I., Kim Y. O., Park S. C., Chun J.. 2016; OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol66:1100–1103[CrossRef]
    [Google Scholar]
  17. Lim Y. L., Ee R., Yin W. F., Chan K. G.. 2014; Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost. Sensors14:7026–7040 [CrossRef][PubMed]
    [Google Scholar]
  18. Lim Y. L., Yong D., Ee R., Tee K. K., Yin W. F., Chan K. G.. 2015a; Complete genome sequence of Serratia multitudinisentens RB-25(T), a novel chitinolytic bacterium. J Biotechnol207:32–33[CrossRef]
    [Google Scholar]
  19. Lim Y. L., Ee R., How K. Y., Lee S. K., Yong D., Tee K. K., Yin W. F., Chan K. G.. 2015b; Complete genome sequencing of Pandoraea pnomenusa RB38 and molecular characterization of its N-acyl homoserine lactone synthase gene ppnI . PeerJ3:e1225
    [Google Scholar]
  20. McClean K. H., Winson M. K., Fish L., Taylor A., Chhabra S. R., Camara M., Daykin M., Lamb J. H., Swift S., other authors. 1997; Quorum sensing and Chromobacterium violaceum: exploitation of violacein production and inhibition for the detection of N-acylhomoserine lactones. Microbiology143:3703–3711 [CrossRef][PubMed]
    [Google Scholar]
  21. Miller L. T.. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. Clin Microbiol16:584–586
    [Google Scholar]
  22. Munoz R., Yarza P., Ludwig W., Euzéby J., Amann R., Schleifer K. H., Glöckner F. O., Rosselló-Móra R.. 2011; Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol34:169–170 [CrossRef][PubMed]
    [Google Scholar]
  23. Nabhan S., De Boer S. H., Maiss E., Wydra K.. 2013; Pectobacterium aroidearum sp. nov., a soft rot pathogen with preference for monocotyledonous plants. Int J Syst Evol Microbiol63:2520–2525 [CrossRef][PubMed]
    [Google Scholar]
  24. Octavia S., Lan R.. 2014; The Family Enterobacteriaceae . In The Prokaryotes, pp.225–286 Edited by Rosenberg E., DeLong E., Lory S., Stackebrandt E., Thompson F.. Berlin Heidelberg: Springer;
    [Google Scholar]
  25. Richter M., Rosselló-Móra R.. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  26. Saito M., Shinozaki-Kuwahara N., Takada K.. 2012; Gibbsiella dentisursi sp. nov., isolated from the bear oral cavity. Microbiol Immunol56:506–512 [CrossRef][PubMed]
    [Google Scholar]
  27. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  28. Thompson J. D., Higgins D. G., Gibson T. J.. 1994; CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res22:4673–4680[PubMed][CrossRef]
    [Google Scholar]
  29. Thomson S. V., Hildebrand D. C., Schroth M. N.. 1981; Identification and nutritional differentiation of the Erwinia sugar beet pathogen from members of Erwinia carotovora and Erwinia chrysanthemi . Phytopathology71:1037–1042 [CrossRef]
    [Google Scholar]
  30. Tindall B. J.. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol13:128–130[CrossRef]
    [Google Scholar]
  31. Tindall B. J.. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett66:199–202[CrossRef]
    [Google Scholar]
  32. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R.. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. Washington: American Society of Microbiology;
    [Google Scholar]
  33. Wattam A. R., Abraham D., Dalay O., Disz T. L., Driscoll T., Gabbard J. L., Gillespie J. J., Gough R., Hix D. et al. 2014; PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res42:D581–591 [CrossRef][PubMed]
    [Google Scholar]
  34. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R.. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol31:241–250 [CrossRef][PubMed]
    [Google Scholar]
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