1887

Abstract

The taxonomic position of an actinomycete designated AMA 120, isolated from mangrove sediment, was clarified by phenotypic, chemotaxonomic and phylogenetic studies. The 16S rRNA gene sequence revealed that strain AMA 120 was most closely related to Gordonia rhizosphera NBRC 16068 (98.9 %), Gordonia polyisoprenivorans NBRC 16320 (98.1 %) and Gordonia bronchialis NBRC 16047 (98.1 %). A fragment of the gyrB gene of strain AMA 120 formed a distinct phyletic line with G. rhizosphera NBRC 16068 (95.4 %). Strain AMA 120 contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, and MK-9(H2) was the predominant menaquinone. The polar lipid profile for this strain consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. Mycolic acid was present. The major fatty acids were C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The DNA–DNA relatedness values between AMA 120 and close species were below 70 %. There was an obvious distinction in the average nucleotide identity distribution between strain AMA 120 and its closely related strains at around 75–92%. The DNA G+C content of strain AMA 120 was 66.6 mol%. These results, coupled with the phenotypic and chemotaxonomic data, indicated that strain AMA 120 represents a novel species of the genus Gordonia , for which the name Gordonia sediminis sp. nov. is proposed. The type strain is AMA 120 (=TBRC 7109=NBRC 113236).

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2019-04-17
2019-08-25
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References

  1. Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971;68:15–26 [CrossRef][PubMed]
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997;47:479–491 [CrossRef]
    [Google Scholar]
  3. Kim SB, Brown R, Oldfield C, Gilbert SC, Goodfellow M. sp. nov., a benzothiophene-desulphurizing actinomycete. Int J Syst Bacteriol 1999;49:1845–1851 [CrossRef][PubMed]
    [Google Scholar]
  4. Park S, Kang SJ, Kim W, Yoon JH. Gordonia hankookensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009;59:3172–3175 [CrossRef][PubMed]
    [Google Scholar]
  5. Kämpfer P, Young CC, Chu JN, Frischmann A, Busse HJ et al. Gordonia humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011;61:65–70 [CrossRef][PubMed]
    [Google Scholar]
  6. Drzyzga O, Navarro Llorens JM, Fernández de Las Heras L, García Fernández E, Perera J. Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge. Int J Syst Evol Microbiol 2009;59:1011–1015 [CrossRef][PubMed]
    [Google Scholar]
  7. Srinivasan S, Park G, Yang H, Hwang S, Bae Y et al. Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant. Int J Syst Evol Microbiol 2012;62:2703–2709 [CrossRef][PubMed]
    [Google Scholar]
  8. Linos A, Berekaa MM, Steinbüchel A, Kim KK, Spröer C et al. Gordonia westfalica sp. nov., a novel rubber-degrading actinomycetes. Int J Syst Bacteriol 2002;52:1133–1139
    [Google Scholar]
  9. Kämpfer P, Martin K, Dott W. Gordonia phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal. Int J Syst Evol Microbiol 2013;63:230–235 [CrossRef][PubMed]
    [Google Scholar]
  10. de Menezes CB, Afonso RS, de Souza WR, Parma M, de Melo IS et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp. Antonie van Leeuwenhoek 2016;109:297–303 [CrossRef][PubMed]
    [Google Scholar]
  11. Kummer C, Schumann P, Stackebrandt E. Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int J Syst Bacteriol 1999;49 Pt 4:1513–1522 [CrossRef][PubMed]
    [Google Scholar]
  12. Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2018;44:1–21 [CrossRef][PubMed]
    [Google Scholar]
  13. Hayakawa M, Otoguro M, Takeuchi T, Yamazaki T, Iimura Y. Application of a method incorporating differential centrifugation for selective isolation of motile actinomycetes in soil and plant litter. Antonie van Leeuwenhoek 2000;78:171–185 [CrossRef][PubMed]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  15. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963;72:619–629 [CrossRef][PubMed]
    [Google Scholar]
  16. 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 [CrossRef][PubMed]
    [Google Scholar]
  17. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids SympSer 1999;41:95–98
    [Google Scholar]
  19. Serrano W, Tarazona UI, Olaechea RM, Friedrich MW. Draft genome sequence of a new Vibrio strain with the potential to produce bacteriocin-like inhibitory substances, isolated from the gut microflora of scallop (Argopecten purpuratus). Genome Announc 2018;6:e0041918 [CrossRef][PubMed]
    [Google Scholar]
  20. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 1983;14:313–333 [CrossRef]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  26. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989;39:224–229 [CrossRef]
    [Google Scholar]
  27. Verlander CP. Detection of horseradish peroxidase by colorimetry. In Kricka LJ. (editor) Nonisotopic DNA Probe Techniques New York: Academic Press; 1992; pp.185–201
    [Google Scholar]
  28. Shen FT, Lu HL, Lin JL, Huang WS, Arun AB et al. Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene. Res Microbiol 2006;157:367–375 [CrossRef][PubMed]
    [Google Scholar]
  29. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464
    [Google Scholar]
  30. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102:2567–2572 [CrossRef][PubMed]
    [Google Scholar]
  31. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  32. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207
    [Google Scholar]
  33. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note#101. 2001
    [Google Scholar]
  35. Minnikin DE, Alshamaony L, Goodfellow M. Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 1975;88:200–204 [CrossRef][PubMed]
    [Google Scholar]
  36. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  37. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970;20:435–443 [CrossRef]
    [Google Scholar]
  38. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  39. Kelly KL. Inter-Society Color Council-National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  40. Blackall LL, Parlett JH, Hayward AC, Minnikin DE, Greenfield PF et al. Nocardia pinensis sp. nov., an actinomycete found in activated sludge foams in Australia. Microbiology 1989;135:1547–1558 [CrossRef]
    [Google Scholar]
  41. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
    [Google Scholar]
  42. Greenwood JR, Pickett MJ. Salient features of Haemophilus vaginalis. J Clin Microbiol 1979;9:200–204[PubMed]
    [Google Scholar]
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