Skip to content
1887

Abstract

Four actinobacterial strains, designated NEAU-PBA1, NEAU-PB14, NEAU-PB65 and NEAU-PB77, were isolated from the frass of collected from Harbin, Heilongjiang Province, China. These strains were Gram-stain positive, aerobic and produced branched substrate mycelium and aerial hyphae, without producing diffusible pigments in the tested media. Upon maturity, spore chains formed on the aerial hyphae, while the mycelium fragmented with age. The genome sizes of these four strains ranged from 7.41 to 7.49 Mbp, with the genomic DNA G+C content varying from 71.8% to 72.9%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these four strains belonged to the genus and exhibited high sequence similarity with Mg02. The average nucleotide identity and digital DNA–DNA hybridization values between these four isolates exceeded the threshold for species delineation, while the values between the four isolates and their close relatives were below the threshold. The predominant menaquinones in strain NEAU-PBA1 are MK-10 (H, H, H) and MK-10, while the phospholipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphoglycolipid, phosphatidylcholine, one phospholipid and one lipid. The major cellular fatty acids comprised -C, -C, -C and C 9. Based on polyphasic taxonomic analysis, strains NEAU-PBA1, NEAU-PB14, NEAU-PB65 and NEAU-PB77 were identified as a novel species within the genus , and the name sp. nov. was proposed. The type strain is NEAU-PBA1 (=MCCC 1K08877=JCM 37021).

Funding
This study was supported by the:
  • Research Team Project of Natural Science Foundation of Heilongjiang Province (Award TD2022C002)
    • Principle Award Recipient: YongqiangLiu
  • National Key Research and Development Program of China (Award 2022YFD1700205)
    • Principle Award Recipient: XiangjingWang
  • Key Programme (Award U22A20483)
    • Principle Award Recipient: XiangjingWang
  • Key Programme (Award 32030090)
    • Principle Award Recipient: WenshengXiang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006832
2025-07-02
2025-07-10
Loading full text...

Full text loading...

References

  1. Meyer J. Nocardiopsis, a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 1976; 26:487–493 [View Article]
    [Google Scholar]
  2. Rainey FA, Ward-rainey N, Kroppenstedt RM, Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 1996; 46:1088–1092 [View Article]
    [Google Scholar]
  3. Salam N, Jiao JY, Zhang XT, Li WJ. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
    [Google Scholar]
  4. Hozzein WN, Trujillo ME. Nocardiopsis. In Bergey’s Manual of Systematics of Archaea and Bacteria 2015
    [Google Scholar]
  5. Kumar S, Solanki DS, Parihar K, Tak A, Gehlot P et al. Actinomycetes isolates of arid zone of Indian Thar Desert and efficacy of their bioactive compounds against human pathogenic bacteria. Biol Futur 2021; 72:431–440 [View Article] [PubMed]
    [Google Scholar]
  6. Xu S, Yan L, Zhang X, Wang C, Feng G et al. Nocardiopsis fildesensis sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2014; 64:174–179 [View Article] [PubMed]
    [Google Scholar]
  7. Pinto-Almeida A, Bauermeister A, Luppino L, Grilo IR, Oliveira J et al. The diversity, metabolomics profiling, and the pharmacological potential of actinomycetes isolated from the Estremadura Spur pockmarks (Portugal). Mar Drugs 2021; 20:21 [View Article] [PubMed]
    [Google Scholar]
  8. Chen L, Wang Z, Du S, Wang G. Antimicrobial activity and functional genes of actinobacteria from coastal wetland. Curr Microbiol 2021; 78:3058–3067 [View Article] [PubMed]
    [Google Scholar]
  9. Tatar D. Isolation, phylogenetic analysis and antimicrobial activity of halophilic actinomycetes from different saline environments located near Çorum province. Biologia 2021; 76:773–780
    [Google Scholar]
  10. Shi T, Wang Y-F, Wang H, Wang B. Genus Nocardiopsis: a prolific producer of natural products. Mar Drugs 2022; 20:374 [View Article] [PubMed]
    [Google Scholar]
  11. Hozzein WN, Li W-J, Ali MIA, Hammouda O, Mousa AS et al. Nocardiopsis alkaliphila sp. nov., a novel alkaliphilic actinomycete isolated from desert soil in Egypt. Int J Syst Evol Microbiol 2004; 54:247–252 [View Article] [PubMed]
    [Google Scholar]
  12. Peltola JS, Andersson MA, Kämpfer P, Auling G, Kroppenstedt RM et al. Isolation of toxigenic Nocardiopsis strains from indoor environments and description of two new Nocardiopsis species, N. exhalans sp. nov. and N. umidischolae sp. nov. Appl Environ Microbiol 2001; 67:4293–4304 [View Article] [PubMed]
    [Google Scholar]
  13. Evtushenko LI, Taran VV, Akimov VN, Kroppenstedt RM, Tiedje JM et al. Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 1:73–81 [View Article] [PubMed]
    [Google Scholar]
  14. Muangham S, Suksaard P, Mingma R, Matsumoto A, Takahashi Y et al. Nocardiopsis sediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2016; 66:3835–3840 [View Article] [PubMed]
    [Google Scholar]
  15. Asem MD, Salam N, Idris H, Zhang X-T, Bull AT et al. Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil. Int J Syst Evol Microbiol 2020; 70:3210–3218 [View Article] [PubMed]
    [Google Scholar]
  16. Zhang Y-G, Lu X-H, Ding Y-B, Zhou X-K, Wang H-F et al. Nocardiopsis rhizosphaerae sp. nov., isolated from rhizosphere soil of Halocnermum strobilaceum (Pall.) Bieb. Int J Syst Evol Microbiol 2016; 66:5129–5133 [View Article] [PubMed]
    [Google Scholar]
  17. Li W-J, Park D-J, Tang S-K, Wang D, Lee J-C et al. Nocardiopsis salina sp. nov., a novel halophilic actinomycete isolated from saline soil in China. Int J Syst Evol Microbiol 2004; 54:1805–1809 [View Article] [PubMed]
    [Google Scholar]
  18. Grund E, Kroppenstedt R. Chemotaxonomy and numerical taxonomy of the genus Nocardiopsis Meyer 1976. Int J Syst Evol Microbiol 1990; 40:5–11
    [Google Scholar]
  19. 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]
  20. Shirling ET, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Evol Microbiol 1966; 16:313–340
    [Google Scholar]
  21. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50 Pt 6:2031–2036 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Nikodinovic J, Barrow KD, Chuck J-A. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003; 35:932–934 [View Article] [PubMed]
    [Google Scholar]
  27. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  28. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  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; 14:1–14 [View Article] [PubMed]
    [Google Scholar]
  31. 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 [View Article] [PubMed]
    [Google Scholar]
  32. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article]
    [Google Scholar]
  33. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Research 2004; 32:277D–280 [View Article]
    [Google Scholar]
  34. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 2009; 37:D233–8 [View Article] [PubMed]
    [Google Scholar]
  35. Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A et al. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nat Biotechnol 2022; 40:711–719 [View Article] [PubMed]
    [Google Scholar]
  36. Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG et al. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e0269623 [View Article] [PubMed]
    [Google Scholar]
  37. 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]
  38. 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]
  39. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  40. Kelly K. Inter-Society Color Council–National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  41. Hozzein WN, Goodfellow M. Nocardiopsis arabia sp. nov., a halotolerant actinomycete isolated from a sand-dune soil. Int J Syst Evol Microbiol 2008; 58:2520–2524 [View Article] [PubMed]
    [Google Scholar]
  42. Han L, Yu M, Zhao J, Jiang H, Guo X et al. Herbidospora galbida sp. nov., a novel actinobacterium isolated from soil. Int J Syst Evol Microbiol 2020; 70:1364–1371 [View Article]
    [Google Scholar]
  43. Ruan Z, Wang Y, Song J, Jiang S, Wang H et al. Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia. Int J Syst Evol Microbiol 2014; 64:518–521 [View Article]
    [Google Scholar]
  44. Gerhardt P. Methods for general and molecular bacteriology. In Methods for General & Molecular Microbiology 1994
    [Google Scholar]
  45. Xu L, Li W, Liu Z, Jiang C. Actinomycete Systematic—Principle, Methods and Practice Science press Beijing; 2007
    [Google Scholar]
  46. Ruan J, Huang Y. Rapid Identification and Systematics of Actinobacteria Beijing: Science Press; 2011
    [Google Scholar]
  47. 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 [View Article]
    [Google Scholar]
  48. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  49. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  50. Kroppenstedt R. Fatty acid and menaquinone analysis of actinomycetes and related organisms. Chem Methods Bacter Syst 1985173–199
    [Google Scholar]
  51. Collins M, Pirouz T, Goodfellow M, Minnikin D. Distribution of menaquinones in actinomycetes and corynebacteria. Microbiology 1977; 100:221–230
    [Google Scholar]
  52. Ariffin H, Abdullah N, Umi Kalsom M, Shirai Y, Hassan M. Production and characterization of cellulase by Bacillus pumilus EB3. Int J Eng Technol 2006; 3:47–53
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006832
Loading
/content/journal/ijsem/10.1099/ijsem.0.006832
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error