1887

Abstract

A novel protease-producing actinomycete, designated strain NEAU-ZS1, was isolated from the root of (Linn.) Britt collected from Jiamusi, Heilongjiang, PR China. Comparative 16S rRNA gene sequencing showed that strain NEAU-ZS1 belonged to the genus and was most closely related to ‘’ NEAU-YHS15 (99.2%) and JCM 3291 (99.0%). Phylogenetic tree analysis revealed that strain NEAU-ZS1 formed a monophyletic clade with ‘’ NEAU-YHS15. The genome size was 9.3 Mbp with a DNA G+C content of 70.3 mol%. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between the genome sequence of strain NEAU-ZS1 and those of ‘’ NEAU-YHS15 (28.6, 83.9 and 79.1 %) and JCM 3291 (18.5, 70.6 and 50.2 %) were below the recommended thresholds for species delineation. The strain formed spherical spore vesicles produced on the aerial hyphae. The cell wall contained -diaminopimelic acid and the whole-cell sugars were glucose and madurose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid and an unidentified glycolipid. The menaquinones were MK-9(H), MK-9(H) and MK-9(H). The major fatty acids were iso-C, C ω5, 10-methy C and C ω7. On the basis of the results of a polyphasic taxonomic study, it is concluded that strain NEAU-ZS1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-ZS1 (=CCTCC AA 2021019= JCM 35655).

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2023-04-12
2024-05-14
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References

  1. Ara I, Kudo T. Sphaerosporangium gen. nov., a new member of the family Streptosporangiaceae, with descriptions of three new species as Sphaerosporangium melleum sp. nov., Sphaerosporangium rubeum sp. nov. and Sphaerosporangium cinnabarinum sp. nov., and transfer of Streptosporangium viridialbum Nonomura and Ohara 1960 to Sphaerosporangium viridialbum comb. nov. Actinomycetologica 2007; 21:11–21 [View Article]
    [Google Scholar]
  2. Wang X, Liu CX, Cheng JX, Zhang YJ, Ma ZX et al. Sphaerisporangium corydalis sp. nov., isolated from the root of Corydalis yanhusuo L. Antonie van Leeuwenhoek 2015; 108:133–139
    [Google Scholar]
  3. Cao YR, Jiang Y, Xu LH, Jiang CL. Sphaerisporangium flaviroseum sp. nov. and Sphaerisporangium album sp. nov., isolated from forest soil in China. Int J Syst Evol Microbiol 2009; 59:1679–1684
    [Google Scholar]
  4. Duangmal K, Mingma R, Pathom-Aree W, Inahashi Y, Matsumoto A et al. Sphaerisporangium siamense sp. nov., an actinomycete isolated from rubber-tree rhizospheric soil. J Antibiot (Tokyo) 2011; 64:293–296 [View Article] [PubMed]
    [Google Scholar]
  5. Suriyachadkun C, Chunhametha S, Ngaemthao W, Tamura T, Kirtikara K et al. Sphaerisporangium krabiense sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:2890–2894 [View Article] [PubMed]
    [Google Scholar]
  6. Guo LF, Zhao JW, Liu CX, Bai L, Sun PY et al. Sphaerisporangium aureirubrum sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2015; 65:4157–4162 [View Article]
    [Google Scholar]
  7. Mu S, Zhao QN, Zhao JW, Cao TT, Zhao XL et al. Sphaerisporangium rhizosphaerae sp. nov., an actinomycete isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg). Int J Syst Evol Microbiol 2018; 68:2860–2865 [View Article]
    [Google Scholar]
  8. Mingma R, Duangmal K, Trakulnaleamsai S, Thamchaipenet A, Matsumoto A et al. Sphaerisporangium rufum sp. nov., an endophytic actinomycete from roots of Oryza sativa L. Int J Syst Evol Microbiol 2014; 64:1077–1082 [View Article] [PubMed]
    [Google Scholar]
  9. Xing J, Liu CX, Zhang YJ, He HR, Zhou Y et al. Sphaerisporangium dianthi sp. nov., an endophytic actinomycete isolated from a root of Dianthus chinensis L. Antonie van Leeuwenhoek 2015; 107:9–14 [View Article]
    [Google Scholar]
  10. Bond JS. Proteases: history, discovery, and roles in health and disease. J Biol Chem 2019; 294:1643–1651 [View Article] [PubMed]
    [Google Scholar]
  11. Jessika GDSA, Helia HS. Microbial proteases: production and application in obtaining protein hydrolysates. Food Res Int 2018; 103:253–262 [View Article]
    [Google Scholar]
  12. Liu CX, Wang XJ, Zhao JW, Liu QF, Wang L et al. Streptomyces harbinensis sp. nov., an endophytic, ikarugamycin-producing actinomycete isolated from soybean root [Glycine max (L.) Merr]. Int J Syst Evol Microbiol 2013; 63:3579–3584
    [Google Scholar]
  13. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987; 65:501–509 [View Article]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  15. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003; 35:932–934 [View Article] [PubMed]
    [Google Scholar]
  16. 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 [View Article]
    [Google Scholar]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  19. Tamura K, Stecher G, Kumar S. MEGA 11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  21. 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 [View Article] [PubMed]
    [Google Scholar]
  22. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  23. Li RQ, Zhu HM, Ruan J, Qian WB, Fang XD et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 2010; 20:265–272 [View Article]
    [Google Scholar]
  24. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  26. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  27. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
    [Google Scholar]
  28. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. AntiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  29. Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA et al. Pfam: the protein families database in 2021. Nucleic Acids Res 2021; 49:D412–D419 [View Article] [PubMed]
    [Google Scholar]
  30. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O 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]
  31. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
    [Google Scholar]
  32. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
    [Google Scholar]
  33. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  34. Conway V, Gauthier SF, Pouliot Y. Antioxidant activities of buttermilk proteins, whey proteins, and their enzymatic hydrolysates. J Agric Food Chem 2013; 61:364–372 [View Article] [PubMed]
    [Google Scholar]
  35. Jin L, Zhao Y, Song W, Duan L, Jiang S et al. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:688–695 [View Article] [PubMed]
    [Google Scholar]
  36. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  37. Waksman SA. The Actinomycetes. In Classification, Identification and Descriptions of Genera and Species vol 2 Baltimore: Williams & Wilkins; 1961
    [Google Scholar]
  38. 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]
  39. Kelly KL. Inter-Society Color Council–National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington: US Government Printing Office; 1964
    [Google Scholar]
  40. Zhao JW, Han LY, Yu MY, Cao P, Li DM et al. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum. Microorganisms 2019; 7:360 [View Article]
    [Google Scholar]
  41. Zhang CH, Cao K, Zhang JS, Wu C. Screening of a strain of Bacillus salicus and study on its enzymatic properties. J Anhui Agri Uni 2020; 47:122–128
    [Google Scholar]
  42. Smibert RM, Krieg NR. Phenotypic characterisation. In Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  43. Gordon RE, Barnett DA, Handerhan JE, Pang C. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  44. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812
    [Google Scholar]
  45. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM et al. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000; 30:178–182 [View Article] [PubMed]
    [Google Scholar]
  46. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. eds Actinomycete Taxonomy Arlington: Special Publications Society for Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  47. 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 [View Article]
    [Google Scholar]
  48. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–284
    [Google Scholar]
  49. Yu Z, Han C, Yu B, Zhao J, Yan Y et al. Taxonomic characterization, and secondary metabolite analysis of Streptomyces triticiradicis sp. nov.: a novel actinomycete with antifungal activity. Microorganisms 2020; 8:77 [View Article] [PubMed]
    [Google Scholar]
  50. Zhuang XX, Peng JW, Wang CH, Zhao ZY, Shen Y et al. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113:677–685 [View Article]
    [Google Scholar]
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