1887

Abstract

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144 and 4053, were isolated from leaves of on the Qinghai–Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner’s 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144 belonged to the genus and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were DSM 103718 (98.4 %), DSM 23986 (98.2%) and DSM 11054 (97.8 %). The genome of strain S-1144 showed less than 70 % digital DNA–DNA hybridization and < 95–96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144 was 73.5 mol%. MK-8(H) was the predominant respiratory quinone (96.0 %) and -2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144 consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C, C 8, C and C 9. On the basis of obtained data, strain S-1144 represented a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S-1144 (=CGMCC 4.7568=JCM 33469).

Funding
This study was supported by the:
  • Jianguo Xu , Research Units of Discovery of Unknown Bacteria and Function , (Award 2018RU010)
  • Jianguo Xu , Sanming Project of Medicine in Shenzhen , (Award SZSM201811071)
  • Dong Jin , National Key R&D Program of China , (Award 2018YFC1200102)
  • Shan Lu , National Science and Technology Major Project of China , (Award 2018ZX10712001-018)
  • Jing Yang , National Science and Technology Major Project of China , (Award 2018ZX10712001-007)
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2020-04-28
2020-06-02
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References

  1. Nocardioides PH. a new genus of the order Actinomycetales . Int J Syst Evol Microbiol 1976; 26:58–65
    [Google Scholar]
  2. Wang X, Yang J, Lu S, Lai X-H, Jin D et al. Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2018; 68:3874–3880 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Li F, Tuo L, Su Z-W, Wei X-Q, Zhang X-Y et al. Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala . Int J Syst Evol Microbiol 2017; 67:2592–2597 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Liu J, Li F, Gao C-H, Han Y, Hao H et al. Nocardioides kandeliae sp. nov., an endophytic actinomycete isolated from leaves of Kandelia candel . Int J Syst Evol Microbiol 2017; 67:3888–3893 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Song GC, Yasir M, Bibi F, Chung EJ, Jeon CO et al. Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud . Int J Syst Evol Microbiol 2011; 61:105–109 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Han J-H, Kim T-S, Joung Y, Kim MN, Shin K-S et al. Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots. Int J Syst Evol Microbiol 2013; 63:4730–4734 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Du H-J, Wei Y-Z, Su J, Liu H-Y, Ma B-P et al. Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens . Int J Syst Evol Microbiol 2013; 63:1068–1072 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Xu H, Zhang S, Cheng J, Asem MD, Zhang M-Y et al. Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L. Int J Syst Evol Microbiol 2016; 66:2013–2018 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Huang M-J, Huang H-Q, Salam N, Xiao M, Duan Y-Q et al. Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu. Int J Syst Evol Microbiol 2016; 66:3841–3847 [CrossRef]
    [Google Scholar]
  10. Qin S, Yuan B, Zhang Y-J, Bian G-K, Tamura T et al. Nocardioides panzhihuaensis sp. nov., a novel endophytic actinomycete isolated from medicinal plant Jatropha curcas L. Antonie Van Leeuwenhoek 2012; 102:353–360 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Glaeser SP, McInroy JA, Busse H-J, Kämpfer P. Nocardioides zeae sp. nov., isolated from the stem of Zea mays . Int J Syst Evol Microbiol 2014; 64:2491–2496 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Kämpfer P, Glaeser SP, McInroy JA, Busse H-J. Nocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize. Int J Syst Evol Microbiol 2016; 66:1869–1874 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Liu J, Wang L, Geng Y, Wang Q, Luo L et al. Genetic diversity and population structure of Lamiophlomis rotata (Lamiaceae), an endemic species of Qinghai–Tibet plateau. Genetica 2006; 128:385–394 [CrossRef]
    [Google Scholar]
  14. Pan Z, Fan G, Yang R-ping, Luo W-zao, Zhou X-dong et al. Discriminating Lamiophlomis rotata according to geographical origin by (1)H-NMR spectroscopy and multivariate analysis. Phytochem Anal 2015; 26:247–252 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Zhu B, Gong N, Fan H, Peng C-S, Ding X-J et al. Lamiophlomis rotata, an orally available Tibetan herbal painkiller, specifically reduces pain hypersensitivity states through the activation of spinal glucagon-like peptide-1 receptors. Anesthesiology 2014; 121:835–851 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Zhang W, Bai Y, Qiao Y, Wang J, Li M-Y et al. 8-O-Acetyl shanzhiside methylester from Lamiophlomis Rotata reduces neuropathic pain by inhibiting the ERK/TNF-α pathway in spinal astrocytes. Front Cell Neurosci 2018; 12:54 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Li J, Yang J, Lu S, Jin D, Lai X-H et al. Mycetocola zhujimingii sp. nov., isolated from faeces of Tibetan antelopes (Pantholops hodgsonii). Int J Syst Evol Microbiol 2019; 69:1117–1122 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  22. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. 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][PubMed]
    [Google Scholar]
  26. 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]
  27. Huang Y, Wang X, Yang J, Lu S, Lai XH et al. Nocardioides yefusunii sp. nov. isolated from Equus kiang (Tibetan wild ass) faeces. J Mol Evol 2019
    [Google Scholar]
  28. Chen C, Zhang W, Zheng H, Lan R, Wang H et al. Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol 2013; 51:2582–2591 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  29. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  30. 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]
  31. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
    [Google Scholar]
  35. 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]
  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][PubMed]
    [Google Scholar]
  37. 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]
  38. Cho Y, Jang GI, Cho BC. Nocardioides marinquilinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2594–2599 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  39. Lee DW, Lee AH, Lee H, Kim J-J, Khim JS et al. Nocardioides litoris sp. nov., isolated from the Taean seashore. Int J Syst Evol Microbiol 2017; 67:2332–2336 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  40. Lee SD, Lee DW. Nocardioides rubroscoriae sp. nov., isolated from volcanic ash. Antonie van Leeuwenhoek 2014; 105:1017–1023 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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