1887

Abstract

A novel species of endophytic actinobacterium, designated strain GBK3QG-3, was isolated from surface-sterilized root of collected from Beilun Estuary, Guangxi Zhuang Autonomous Region, PR China. Cells of strain GBK3QG-3 were Gram-stain-positive, aerobic, non-spore-forming and rod-shaped. Growth of GBK3QG-3 was observed at 10–40 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–3 % (w/v) NaCl (optimum, 0 %). The G+C content of genomic DNA was determined to be 72.2 mol%. On the basis of 16S rRNA gene sequence analysis, strain GBK3QG-3 was most related to the type strain of CCTCC AB 2017058 (97.7 % 16S rRNA gene sequence similarity), followed by SYP-A7303 (97.0 %) and GW-9 (96.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain GBK3QG-3 and some strains of the genus with publicly available genomes were below 84.3 and 30.0 %, respectively. The cell-wall peptidoglycan contained -diaminopimelic acid. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown lipid. The major menaquinone was identified as MK-8(H), and the major fatty acids were identified as iso-C, iso-C and anteiso-C. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, we propose a novel species named sp. nov. The type strain is GBK3QG-3 (=CGMCC 4.7708=JCM 34553).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 81960642)
    • Principle Award Recipient: LiTuo
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005295
2022-03-25
2022-07-06
Loading full text...

Full text loading...

References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 1976; 26:58–65 [View Article]
    [Google Scholar]
  2. Chen X-H, Li F, Li F-N, Chen M-S, Yan X-R et al. Nocardioides acrostichi sp. nov., a novel endophytic actinobacterium isolated from leaf of Acrostichum aureum. Antonie van Leeuwenhoek 2021; 114:479–486 [View Article] [PubMed]
    [Google Scholar]
  3. Chhetri G, Kim I, Kang M, Kim J, So Y et al. Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  4. Suh MK, Lee KC, Kim J-S, Han K-I, Kim HS et al. Nocardioides cynanchi sp. nov., isolated from soil of rhizosphere of Cynanchum wilfordii. Int J Syst Evol Microbiol 2021; 71:4640 [View Article] [PubMed]
    [Google Scholar]
  5. Cheng Y, Jiao Y, Zhang S, Yang J, Lu S et al. Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) and leaves of dandelion (Taraxacum officinale), respectively, on the Qinghai–Tibet Plateau. Int J Syst Evol Microbiol 2021; 71:4920 [View Article]
    [Google Scholar]
  6. Zhang X, Wu Z, Yan C, Chen C, Zheng G et al. Nocardioides malaquae sp. nov., a novel actinobacterium isolated from sewage sludge of a fisheries processing factory. Int J Syst Evol Microbiol 2021; 71:4852 [View Article] [PubMed]
    [Google Scholar]
  7. Zhou X-K, Huang Y, Zhang T-K, Liu J-J, Liu Z-Y et al. Nocardioides stalactiti sp. nov., isolated from a cave stalactite surface. Int J Syst Evol Microbiol 2021; 71:4636 [View Article] [PubMed]
    [Google Scholar]
  8. Singh H, Du J, Trinh H, Won K, Yang J-E et al. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:371–378 [View Article] [PubMed]
    [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley Sons; 1991 pp 115–147
    [Google Scholar]
  10. 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]
  11. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  16. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  17. 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 [View Article] [PubMed]
    [Google Scholar]
  18. Lim HJ, Lee EH, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
    [Google Scholar]
  19. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  20. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  23. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
    [Google Scholar]
  24. 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]
  25. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–9 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  28. 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 [View Article] [PubMed]
    [Google Scholar]
  29. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  30. 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]
  31. 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 [View Article]
    [Google Scholar]
  32. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
    [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI inc; 1990
    [Google Scholar]
  34. Tuo L, Yan X-R, Li F-N, Bao Y-X, Shi H-C et al. Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi. Int J Syst Evol Microbiol 2018; 68:3563–3568 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. Guo L, Tuo L, Habden X, Zhang Y, Liu J et al. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015; 65:206–213 [View Article]
    [Google Scholar]
  37. 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]
  38. Wang X, Jiang W-K, Cui M-D, Yang Z-G, Yu X et al. Nocardioides agrisoli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2017; 67:3722–3727 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005295
Loading
/content/journal/ijsem/10.1099/ijsem.0.005295
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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