1887

Abstract

A novel endophytic actinobacterium, designated strain EGI 650086, was isolated from the roots of (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15–40 °C, pH 6.0–8.0 and in the presence of 0–6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086 formed a monophyletic clade within the genus and shared the highest sequence similarities with JCM 14717 (97.1 %) and DSM 44468 (97.0 %). Sequence similarities with type strains of other species of the genus were less than 97.0 %. The average nucleotide identity and DNA–DNA hybridization values between strain EGI 650086 and the reference strains were 78.1–79.8 % and 22.1–23.0 %, respectively. The genome of strain EGI 650086 was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was -diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H) and MK-9 (H). Major fatty acids were -C and summed feature 4 (-C I and/or -C B). The polar lipid profile of strain EGI 650086 included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is EGI 650086 (=KCTC 49044=CGMCC 4.7188).

Funding
This study was supported by the:
  • Hong-Fei Wang , Department of Education of Liaoning Province , (Award L201683673)
  • Hong-Fei Wang , Natural Science Foundation of Liaoning Province , (Award 2019-ZD-0466)
  • Wen-Jun Li , Key-Area Research and Development Program of Guangdong Province , (Award 2018B020206001)
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2020-05-04
2020-06-02
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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. Lee SD. Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis . Int J Syst Evol Microbiol 2009; 59:1401–1404 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Tang S-K, Wang Y, Guan T-W, Lee J-C, Kim C-J et al. Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 2010; 60:1073–1078 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2018; 9:9 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Peng G, Xiong D-S, Li L-C, Hu J-Y, Bao S et al. Amycolatopsis panacis sp. nov., isolated from Panax notoginseng rhizospheric soil. Int J Syst Evol Microbiol 2019; 69:567–571 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Tatar D, Sazak A, Guven K, Cetin D, Sahin N. Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:3739–3743 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Lee SD. Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave. Int J Syst Evol Microbiol 2006; 56:549–553 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Bian J, Li Y, Wang J, Song F-H, Liu M et al. Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol 2009; 59:477–481 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Groth I, Tan GYA, González JM, Laiz L, Carlsohn MR et al. Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb. Int J Syst Evol Microbiol 2007; 57:513–519 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Huang Y, Paściak 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; 54:359–363 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Chantavorakit T, Suksaard P, Matsumoto A, Duangmal K. Amycolatopsis suaedae sp. nov., an endophytic actinomycete isolated from Suaeda maritima roots. Int J Syst Evol Microbiol 2019; 69:2591–2596 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Duangmal K, Mingma R, Pathom-Aree W, Thamchaipenet A, Inahashi Y et al. Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr. Int J Syst Evol Microbiol 2011; 61:951–955 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Klykleung N, Tanasupawat S, Pittayakhajonwut P, Ohkuma M, Kudo T. Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant. Int J Syst Evol Microbiol 2015; 65:3894–3899 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Xing K, Liu W, Zhang Y-J, Bian G-K, Zhang W-D et al. Amycolatopsis jiangsuensis sp. nov., a novel endophytic actinomycete isolated from a coastal plant in Jiangsu, China. Antonie van Leeuwenhoek 2013; 103:433–439 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Miao Q, Qin S, Bian G-K, Yuan B, Xing K et al. Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. Antonie van Leeuwenhoek 2011; 100:333–339 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Qin S, Wang H-B, Chen H-H, Zhang Y-Q, Jiang C-L et al. Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees. Int J Syst Evol Microbiol 2008; 58:2525–2528 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [CrossRef]
    [Google Scholar]
  18. 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]
  19. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z 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][PubMed]
    [Google Scholar]
  20. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [CrossRef]
    [Google Scholar]
  21. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL . In Williams ST. editor Bergey’s Manual of Systematic Bacteriology 4 Baltimore: Williams & Wilkins; 1989 pp 2463–2468
    [Google Scholar]
  22. Tseng M, Yang S-F, Li W-J, Jiang C-L. Amycolatopsis taiwanensis sp. nov., from soil. Int J Syst Evol Microbiol 2006; 56:1811–1815 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  23. Tamura T, Ishida Y, Otoguro M, Suzuki K-ichiro, Suzuki K. Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2629–2633 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  24. Goodfellow M, Kim SB, Minnikin DE, Whitehead D, Zhou ZH et al. Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter. Int J Syst Evol Microbiol 2001; 51:187–193 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  26. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  27. 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; 5:2359–2367 [CrossRef]
    [Google Scholar]
  28. 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]
  29. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. In Colwell PR. editor Methods in Microbiology Orlando: Academic Press; 1987
    [Google Scholar]
  30. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides . J Bacteriol 1982; 151:828–837 [CrossRef][PubMed][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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. 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]
  33. Thawai C. Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil. Int J Syst Evol Microbiol 2018; 68:1546–1551 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  34. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [CrossRef]
    [Google Scholar]
  35. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E. editor Nucleic Acid Techniques in Bacterial Systematic Wiley: Chichester; 1991 pp 115–175
    [Google Scholar]
  36. Yoon S-H, Ha S-M, 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][PubMed]
    [Google Scholar]
  37. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  38. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  39. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  40. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  41. 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][PubMed]
    [Google Scholar]
  42. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  43. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  44. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  45. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  46. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  47. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  48. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  49. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  50. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  51. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  52. Zucchi TD, Bonda ANV, Frank S, Kim B-Y, Kshetrimayum JD et al. Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils. Antonie van Leeuwenhoek 2012; 102:91–98 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  53. Zhang G, Wang L, Li J, Zhou Y. Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:3860–3864 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  54. Camas M, Sahin N, Sazak A, Spröer C, Klenk H-P. Amycolatopsis magusensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:1254–1260 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  55. Jamjan W, Suriyachadkun C, Tanasupawat S, Sakai K, Tashiro Y et al. Amycolatopsis silviterrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2018; 68:1455–1460 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  56. Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T et al. Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 2006; 24:1384–1390 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  57. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler OK 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]
  58. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  59. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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