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Amycolatopsis alkalitolerans sp. nov., isolated from Gastrodia elata Blume

The Journal of Antibiotics volume 73, pages 35–39 (2020)Cite this article

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Abstract

A Gram-staining positive and nonmotile strain designated SYSUP0005T was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result showed that strain SYSUP0005T shared highest sequence similarity with the type strain of Amycolatopsis cappadoca (95.7%), Amycolatopsis taiwanensis (95.4%), Amycolatopsis pigmentata (95.4%), Amycolatopsis ruanii (95.1%), and Amycolatopsis helveola (94.8%). Growth occurs at 14–37 °C (optimum temperature, 28 °C), at pH 6–9 (optimum, pH 8) and in the presence of up to 6% (w/v) NaCl. Strain SYSUP0005T had meso-diaminopimelic acid in its peptidoglycan. The whole cell sugars were galactose, ribose, and xylose. The predominant menaquinone was MK-9(H4) and minor menaquinones were MK-9(H2) and MK-9(H8). The polar lipids were diphosphatidylglycerol (DPG); phosphatidylmonomethylethanolamine (PME), phosphatidylethanolamine (PE), phosphatidylinositol (PI), unidentified glycolipid (GL), and unidentified phospholipid (PL). The genomic DNA G + C content was 69.6 mol%. The major fatty acids were iso-C16:0, anteiso-C17:0, C16:0, iso-C14:0, C17:1 ω6c, C17:0, and Summed Feature 3 (C16:1 ω7c/C16:1 ω6c). On the basis of the phenotypic, phylogenetic, chemotaxonomic characters, and genomic comparison, SYSUP0005T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis alkalitolerans sp. nov. is proposed. The type strain is SYSUP0005T (=KCTC 49024T = CGMCC4.7463T).

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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.

    Article  Google Scholar 

  2. Thawai C. Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil. Int J Syst Evol Microbiol. 2018;68:1546–51.

    Article  CAS  PubMed  Google Scholar 

  3. Bian J, et al. Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol. 2009;59:477–81.

    Article  CAS  PubMed  Google Scholar 

  4. Işık K, et al. Amycolatopsis cappadoca sp. nov., isolated from soil. Antonie van Leeuwenhoek. 2018;111:1175–82.

    Article  PubMed  Google Scholar 

  5. Miao Q, et al. Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. Antonie van Leeuwenhoek. 2011;100:333–9.

    Article  PubMed  Google Scholar 

  6. Huang Y, Pas´ciak M, Liu Z, Xie Q, Gamian A. Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source. Int J Syst Evol Microbiol. 2004;54:359–63.

    Article  CAS  PubMed  Google Scholar 

  7. Wang J, Leiva S, Huang J, Huang Y. Amycolatopsis antarctica sp. nov., isolated from the surface of an Antarctic brown macroalga. Int J Syst Evol Microbiol. 2018;68:2348–56.

    Article  CAS  PubMed  Google Scholar 

  8. Murakami R, et al. A-102395, a new inhibitor of bacterial Translocase I, produced by Amycolatopsis sp. SANK 60206. J Antibiot. 2007;60:690–5.

    Article  CAS  Google Scholar 

  9. Dasari VR, Muthyala MK, Nikku MY, Donthireddy SR. Novel Pyridinium compound from marine actinomycete, Amycolatopsis alba var. nov. DVR D4 showing antimicrobial and cytotoxic activities in vitro. Microbiol Res. 2012;167:346–51.

    Article  CAS  PubMed  Google Scholar 

  10. Zhang H, et al. Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol. 2019;69:261–5.

    Article  CAS  PubMed  Google Scholar 

  11. Li YQ, et al. Description of Sphingomonas mesophila sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol. 2019. https://doi.org/10.1099/ijsem.0.003263.

    Article  CAS  PubMed  Google Scholar 

  12. Prabhu DM, et al. Sinomonas mesophila sp. nov., isolated from ancient fort soil. J Antibiot. 2015;68:318–21.

    Article  CAS  Google Scholar 

  13. Xu P, et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol. 2005;55:1149–53.

    Article  CAS  PubMed  Google Scholar 

  14. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature. 1956;178:703–4.

    Article  CAS  PubMed  Google Scholar 

  15. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov.: an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol. 1978;24:710–5.

    Article  CAS  PubMed  Google Scholar 

  16. Pridham TG, Gottlieb D. The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol. 1948;56:107–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Nie GX, et al. Amycolatopsis dongchuanensis sp. nov., a novel actinobacterium isolated from dry-hot valley in Yunnan, south-west China. Int J Syst Evol Microbiol. 2012;62:2650–6.

    Article  CAS  PubMed  Google Scholar 

  18. Li WJ, et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol. 2007;57:1424–8.

    Article  PubMed  Google Scholar 

  19. Yoon SH, et al. Introducing EzBio-Cloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.

    CAS  PubMed  Google Scholar 

  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–76.

    Article  CAS  PubMed  Google Scholar 

  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool. 1971;20:406–16.

    Article  Google Scholar 

  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111–20.

    CAS  PubMed  Google Scholar 

  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.

    Article  PubMed  Google Scholar 

  27. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol. 1983;29:319–22.

    Article  CAS  Google Scholar 

  28. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol. 1977;100:221–30.

    Article  CAS  PubMed  Google Scholar 

  29. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr. 1982;5:2359–67.

    Article  CAS  Google Scholar 

  30. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101.Newark: Microbial ID, Inc; 1990. .

  31. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol. 1979;47:87–95.

    Article  CAS  Google Scholar 

  32. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4- diaminobutyric acid. J Appl Bacteriol. 1980;48:459–70.

    Article  CAS  Google Scholar 

  33. Bankevich A, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57:81–91.

    Article  CAS  PubMed  Google Scholar 

  37. Kurtz S, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.

    Article  PubMed  PubMed Central  Google Scholar 

  38. 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;32:929–31.

    Article  CAS  PubMed  Google Scholar 

  39. Blin K, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;W1:W81–W87.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Tamura T, Ishida Y, Otoguro M, Suzuki K. Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil. Int J Syst Evol Microbiol. 2010;60:2629–33.

    Article  CAS  PubMed  Google Scholar 

  41. Tseng M, Yang SF, Li WJ, Jiang CL. Amycolatopsis taiwanensis sp. nov., from soil. Int J Syst Evol Microbiol. 2006;56:1811–5.

    Article  CAS  PubMed  Google Scholar 

  42. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009;106:19126–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are grateful to Professor Jung-Sook Lee (KCTC, Korea) for kindly providing the reference type strain. This research was supported by Natural Science Foundation of Guangdong Province, PR China (number 2016A030312003).

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  1. These authors contributed equally: Manik Prabhu Narsing Rao, Yan-Qiong Li, Hui Zhang

Authors and Affiliations

  1. State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, 510275, PR China

    Manik Prabhu Narsing Rao, Zhou-Yan Dong, Min Xiao & Wen-Jun Li

  2. Kunming Medical University Haiyuan College, Kunming, 650106, PR China

    Yan-Qiong Li & Hui Zhang

  3. Department of Microbiology, Maharani’s Science College for Women, Bangalore, 560001, India

    Awalagaway Dhulappa

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Narsing Rao, M.P., Li, YQ., Zhang, H. et al. Amycolatopsis alkalitolerans sp. nov., isolated from Gastrodia elata Blume. J Antibiot 73, 35–39 (2020). https://doi.org/10.1038/s41429-019-0222-8

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