1887

Abstract

A novel bioplastic-degrading actinomycete, strain SCM_MK2-4, was isolated from paddy soil in Thailand. The 16S rRNA gene sequence showed that strain SCM_MK2-4 belonged to the genus Amycolatopsis , with the highest sequence similarity to Amycolatopsis azurea JCM 3275 (99.4 %), and was phylogenetically clustered with this strain along with Amycolatopsis lurida JCM 3141 (99.3 %), A. japonica DSM 44213 (99.2 %), A. decaplanina DSM 44594 (99.0 %), A. roodepoortensis M29 (98.9 %), A. keratiniphila subsp. nogabecina DSM 44586 (98.8 %), A. keratiniphila subsp. keratiniphila DSM 44409 (98.5 %), A. orientalis DSM 40040 (98.4 %) and A. regifaucium GY080 (98.3 %). A combination of DNA–DNA hybridization results ranging from 42.8±3.2 to 66.2±1.4 % with the type strains of A. azurea and A. lurida and some different phenotypic characteristics indicated that the strain could be distinguished from its closest phylogenetic neighbours. Whole-cell hydrolysates of the strain were shown to contain meso-diaminopimelic acid, arabinose, galactose, glucose, ribose, mannose, rhamnose and xylose. The predominant menaquinone was MK-9(H4). The major cellular fatty acid profile consisted of iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2OH) and C16 : 0. The polar lipid composition of the strain consisted of phosphatidyl-N-methylethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylglycerol, aminophospholipids, an unidentified phospholipid and two unidentified glycolipids. The G+C content of the genomic DNA was 68.2 mol%. On the basis of phylogenetic analyses, DNA–DNA hybridization experimentation and the phenotypic characteristics, it was concluded that strain SCM_MK2-4 represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis oliviviridis sp. nov. is proposed. The type strain is SCM_MK2-4 (=TBRC 7186=JCM 32134).

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2018-03-08
2019-10-17
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References

  1. Lechevalier MP, Prauser H, Labeda DP, Ruan JS. Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 1986; 36: 29– 37 [CrossRef]
    [Google Scholar]
  2. Embley MT, Smida J, Stackebrandt E. The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 1988; 11: 44– 52 [CrossRef]
    [Google Scholar]
  3. Sensi P, Greco AM, Ballotta R. Rifomycin. I. Isolation and properties of rifomycin B and rifomycin complex. Antibiot Annu 1959; 7: 262– 270 [PubMed]
    [Google Scholar]
  4. Wink JM, Kroppenstedt RM, Ganguli BN, Nadkarni SR, Schumann P et al. Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov. Syst Appl Microbiol 2003; 26: 38– 46 [CrossRef] [PubMed]
    [Google Scholar]
  5. Bala S, Khanna R, Dadhwal M, Prabagaran SR, Shivaji S et al. Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov. Int J Syst Evol Microbiol 2004; 54: 1145– 1149 [CrossRef] [PubMed]
    [Google Scholar]
  6. Pranamuda H, Tokiwa Y. Degradation of poly(l-lactide) by strains belonging to genus Amycolatopsis. Biotechnol Lett 1999; 21: 901– 905 [CrossRef]
    [Google Scholar]
  7. Jarerat A, Pranamuda H, Tokiwa Y. Poly(l-lactide)-degrading activity in various actinomycetes. Macromol Biosci 2002; 2: 420– 428 [CrossRef]
    [Google Scholar]
  8. Li F, Wang S, Liu W, Chen G. Purification and characterization of poly(l-lactic acid)-degrading enzymes from Amycolatopsis orientalis ssp. orientalis. FEMS Microbiol Lett 2008; 282: 52– 58 [CrossRef] [PubMed]
    [Google Scholar]
  9. Chomchoei A, Pathom-Aree W, Yokota A, Kanongnuch C, Lumyong S. Amycolatopsis thailandensis sp. nov., a poly(l-lactic acid)-degrading actinomycete, isolated from soil. Int J Syst Evol Microbiol 2011; 61: 839– 843 [CrossRef] [PubMed]
    [Google Scholar]
  10. Penkhrue W, Khanongnuch C, Masaki K, Pathom-Aree W, Punyodom W et al. Isolation and screening of biopolymer-degrading microorganisms from northern Thailand. World J Microbiol Biotechnol 2015; 31: 1431– 1442 [CrossRef] [PubMed]
    [Google Scholar]
  11. Penkhrue W, Kanpiengjai A, Khanongnuch C, Masaki K, Pathom-Aree W et al. Effective enhancement of polylactic acid-degrading enzyme production by Amycolatopsis sp. strain SCM_MK2-4 using statistical and one-factor-at-a-time approaches. Prep Biochem Biotechnol 2017; 47: 730– 738 [CrossRef] [PubMed]
    [Google Scholar]
  12. Tomita K, Tsuji H, Nakajima T, Kikuchi Y, Ikarashi K et al. Degradation of poly(d-lactic acid) by a thermophile. Polym Degrad Stab 2003; 81: 167– 171 [CrossRef]
    [Google Scholar]
  13. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16: 313– 340 [CrossRef]
    [Google Scholar]
  14. Jacobson E, Grauville W, Fogs CE. Color Harmony Manual, 4th ed. Chicago: Container Corporation of America; 1958
    [Google Scholar]
  15. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55: 1149– 1153 [CrossRef] [PubMed]
    [Google Scholar]
  16. Kilian M. Rapid identification of Actinomycetaceae and related bacteria. J Clin Microbiol 1978; 8: 127– 133 [PubMed]
    [Google Scholar]
  17. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28: 226– 231 [PubMed]
    [Google Scholar]
  18. Mikami H, Ishida Y. Post-column fluorometric detection of reducing sugars in high performance liquid chromatography using arginine. Bunseki kagaku 1983; 32: E207 E210 [CrossRef]
    [Google Scholar]
  19. 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]
  20. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54: 31– 36 [PubMed] [Crossref]
    [Google Scholar]
  21. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188: 221– 233 [CrossRef]
    [Google Scholar]
  22. Yano I, Saito K, Furukawa Y, Kusunose M. Structural analysis of molecular species of nocardomycolic acids from Nocardia erythropolis by the combined system of gas chromatography and mass spectrometry. FEBS Lett 1972; 21: 215– 219 [CrossRef] [PubMed]
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  24. 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]
  25. Nakajima Y, Kitpreechavanich V, Suzuki K, Kudo T. Microbispora corallina sp. nov., a new species of the genus Microbispora isolated from Thai soil. Int J Syst Bacteriol 1999; 49: 1761– 1767 [CrossRef] [PubMed]
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  27. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18: 1– 32 [CrossRef]
    [Google Scholar]
  28. 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]
  29. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870– 1874 [CrossRef] [PubMed]
    [Google Scholar]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  31. 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 [CrossRef] [PubMed]
    [Google Scholar]
  32. 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]
  33. Everest GJ, Meyers PR. The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis. Antonie van Leeuwenhoek 2009; 95: 1– 11 [CrossRef] [PubMed]
    [Google Scholar]
  34. Everest GJ, Cook AE, Kirby BM, Meyers PR. Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis. Antonie van Leeuwenhoek 2011; 100: 483– 496 [CrossRef] [PubMed]
    [Google Scholar]
  35. Raeder U, Broda P. Rapid preparation of DNA from filamentous fungi. Lett Appl Microbiol 1985; 1: 17– 20 [CrossRef]
    [Google Scholar]
  36. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25: 125– 128 [CrossRef]
    [Google Scholar]
  37. 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]
  38. Yassin AF, Haggenel B, Budzikiewicz H, Schaal KP. Fatty acid and polar lipid composition of the genus Amycolatopsis: application of fast atom bombardment-mass spectrometry to structure analysis of underivatized phospholipids. Int J Syst Bacteriol 1993; 43: 414– 420 [CrossRef]
    [Google Scholar]
  39. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37: 463– 464 [CrossRef]
    [Google Scholar]
  40. Everest GJ, Le Roes-Hill M, Rohland J, Enslin S, Meyers PR. Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils. J Antibiot 2014; 67: 813– 818 [CrossRef] [PubMed]
    [Google Scholar]
  41. Wink J, Gandhi J, Kroppenstedt RM, Seibert G, Sträubler B et al. Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology. Int J Syst Evol Microbiol 2004; 54: 235– 239 [CrossRef] [PubMed]
    [Google Scholar]
  42. Henssen A, Kothe HW, Kroppenstedt RM. Transfer of Pseudonocardia azurea and "Pseudonocardia fastidiosa" to the genus Amycolatopsis, with emended species description. Int J Syst Bacteriol 1987; 37: 292– 295 [CrossRef]
    [Google Scholar]
  43. Tan GY, Robinson S, Lacey E, Brown R, Kim W et al. Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins. Int J Syst Evol Microbiol 2007; 57: 2562– 2567 [CrossRef] [PubMed]
    [Google Scholar]
  44. Stackebrandt E, Kroppenstedt RM, Wink J, Schumann P. Reclassification of Amycolatopsis orientalis subsp. lurida Lechevalier et al. 1986 as Amycolatopsis lurida sp. nov., comb. nov. Int J Syst Evol Microbiol 2004; 54: 267– 268 [CrossRef] [PubMed]
    [Google Scholar]
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