sp. nov., a novel Actinobacterium with antimicrobial activity isolated from soil of the Qinghai–Tibet Plateau No Access

Abstract

A novel filamentous Actinobacterium, designated strain FXJ1.1311, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and . Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311 belonged to the genus and showed the highest sequence similarity to DHS C013 (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus . The genome-wide average nucleotide identity between strain FXJ1.1311 and DHS C013 as well as other type strains was <82.2 %. Strain FXJ1.1311 also formed a monophyletic line distinct from the known species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from . Based on the evidence presented here, strain FXJ1.1311 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FXJ1.1311 (=CGMCC 4.7383=DSM 104975).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31670502)
    • Principle Award Recipient: HuangYing
  • Science and Technology Infrastructure Work Project of China (Award 2015FY110100)
    • Principle Award Recipient: HuangYing
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2021-08-24
2024-03-28
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References

  1. Yassin AF, Rainey FA, Brzezinka H, Jahnke KD, Weissbrodt H et al. Lentzea gen. nov., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1995; 45:357–363 [View Article] [PubMed]
    [Google Scholar]
  2. Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ et al. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae. Int J Syst Evol Microbiol 2011; 61:1259–1264
    [Google Scholar]
  3. Lee SD, Kim ES, Roe JH, Kim J, Kang SO et al. Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov. Int J Syst Evol Microbiol 2000; 50:1315–1323 [View Article] [PubMed]
    [Google Scholar]
  4. Labeda DP, Hatano K, Kroppenstedt RM, Tamura T. Revival of the genus Lentzea and proposal for Lechevalieria gen. nov. Int J Syst Evol Microbiol 2001; 51:1045–1050 [View Article] [PubMed]
    [Google Scholar]
  5. Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
    [Google Scholar]
  6. Yang LL, Zhi XY. Reclassification of Friedmanniella endophytica, Lysinimicrobium sediminis and Lechevalieria rhizosphaerae as Microlunatus kandeliicorticis nom. nov., Demequina sediminis comb. nov. and Lentzea rhizosphaerae comb. nov., respectively. Int J Syst Evol Microbiol 2020; 70:3930–3931 [View Article] [PubMed]
    [Google Scholar]
  7. Labeda DP. Genus XI. Lentzea Yassin, Rainey, Brzezinka, Jahnke, Weissbrodt, Budzikiewicz, Stackebrandt and Schaal 1995, 1125VP emend. Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049. Goodfellow M, Kampfer P, Busse H-J, Trujillo M, Suzuki K-I. eds In Bergey’s Manual of Systematic Bacteriology, Part A, 2nd. edn New York: Springer; 2012 pp 1379–1383
    [Google Scholar]
  8. Zhang YQ, Liu HY, Chen J, Yuan LJ, Sun W et al. Diversity of culturable actinobacteria from Qinghai–Tibet plateau, China. Antonie van Leeuwenhoek 2010; 98:213–223 [View Article] [PubMed]
    [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  10. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article] [PubMed]
    [Google Scholar]
  11. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  12. Kelly KL. Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  13. Kampfer P, Kroppenstedt RM, Dott W. A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J Gen Microbiol 1991; 137:1831–1891 [View Article]
    [Google Scholar]
  14. Gottlieb D. An evaluation of criteria and procedures used in the description and characterization of the Streptomycetes. Appl Microbiol 1961; 9:55–65 [View Article] [PubMed]
    [Google Scholar]
  15. Frazier NC. A method for the detection of changes in gelatin due to bacteria. J Infect Dis 1926; 39:302–309 [View Article]
    [Google Scholar]
  16. Hendricks CW, Doyle JD, Hugley B. A new solid medium for enumerating cellulose-utilizing bacteria in soil. Appl Environ Microbiol 1995; 61:2016–2019 [View Article] [PubMed]
    [Google Scholar]
  17. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  18. Kuester E, Williams ST. Production of hydrogen sulfide by streptomycetes and methods for its detection. Appl Microbiol 1964; 12:46–52 [PubMed]
    [Google Scholar]
  19. Pridham TG, Gottlieb D. The utilization of carbon compounds by some Actinomycetales as an aid for species determination. J Bacteriol 1948; 56:107–114 [View Article] [PubMed]
    [Google Scholar]
  20. Nie GX, Ming H, Li S, Zhou EM, Cheng J 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; 62:2650–2656
    [Google Scholar]
  21. de Louvois J. Factors influencing the assay of antimicrobial drugs in clinical samples by the agar plate diffusion method. J Antimicrob Chemother 1982; 9:253–265 [View Article] [PubMed]
    [Google Scholar]
  22. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  23. Tamaoka J, Katayamafujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high-performance liquid-chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [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
    [Google Scholar]
  25. 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; 48:459–470 [View Article]
    [Google Scholar]
  26. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
    [Google Scholar]
  27. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  28. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article] [PubMed]
    [Google Scholar]
  29. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  31. 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 [View Article] [PubMed]
    [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  33. 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 [View Article] [PubMed]
    [Google Scholar]
  34. Bankevich A, Nurk S, Antipov D. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  35. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  36. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  37. Chaudhari NM, Gupta VK, Dutta C. BPGA–an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
    [Google Scholar]
  38. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90k prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  39. Yabutani T, Tsujimoto M, Ohira S, Shimizu S, Nakano H. Strain improvement of Lentzea sp. 7887 for higher yield per unit volume on hydroxylation of cyclosporine derivative FR901459. Biosci Biotechnol Biochem 2017; 81:1456–1459 [View Article] [PubMed]
    [Google Scholar]
  40. Nakano H, Omura S. Chemical biology of natural indolocarbazole products: 30 years since the discovery of staurosporine. J Antibiot 2009; 62:17–26 [View Article]
    [Google Scholar]
  41. Tamaoki T, Nomoto H, Takahashi I, Kato Y, Morimoto M et al. Staurosporine, a potent inhibitor of phospholipid/Ca++dependent protein kinase. Biochem Biophys Res Commun 1986; 135:397–402 [View Article] [PubMed]
    [Google Scholar]
  42. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2015; 43:W237–243
    [Google Scholar]
  43. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  44. Atkinson DJ, Brimble MA. Isolation, biological activity, biosynthesis and synthetic studies towards the rubromycin family of natural products. Nat Prod Rep 2015; 32:811–840 [View Article] [PubMed]
    [Google Scholar]
  45. Karwowski JP, Jackson M, Sunga G, Sheldon P, Poddig JB et al. Dorrigocins: Novel antifungal antibiotics that change the morphology of ras-transformed NIH/3T3 cells to that of normal cells. I. Taxonomy of the producing organism, fermentation and biological activity. J Antibiot 1994; 47:862–869 [View Article]
    [Google Scholar]
  46. Kluepfel D, Baker HA, Piattoni G, Sehgal SN, Sidorowicz A et al. Naphthyridinomycin, a new broad-spectrum antibiotic. J Antibiot 1975; 28:497–502 [View Article]
    [Google Scholar]
  47. Izaguirre G, Hwang CJ, Krasner SW, McGuire MJ. Geosmin and 2-methylisoborneol from cyanobacteria in three water supply systems. Appl Environ Microbiol 1982; 43:708–714 [View Article] [PubMed]
    [Google Scholar]
  48. Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO et al. Function-related replacement of bacterial siderophore pathways. ISME J 2018; 12:320–329 [View Article] [PubMed]
    [Google Scholar]
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