Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 4

sp. nov., a novel endophytic actinobacterium isolated from bark of and emended description of the genus No Access

Abstract

A novel strain, KQZ13P-5, was isolated from the bark of collected from Maowei Sea Mangrove Nature Reserve of Guangxi Zhuang Autonomous Region, China. Cells of strain KQZ13P-5 were Gram-stain-positive, aerobic and non-spore producing. A polyphasic taxonomic approach was investigated to resolve its taxonomic position. The conditions for the growth of strain KQZ13P-5 were at 20–37 °C (optimum 30–37 °C), pH 5.0–8.5 (optimum pH 6.5–7.5) and with 0–4% (w/v) NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequence and genome sequence showed that strain KQZ13P-5 formed a stable and coherent branch with Lg2 and shared the highest 16S rRNA gene sequence similarity of 98.2% with Lg2. The average nucleotide identity and estimated digital DNA–DNA hybridization values between strain KQZ13P-5 and Lg2 were 80.2% and 24.0%, respectively, far below the interspecies threshold. The G+C content of DNA of strain KQZ13P-5 was 70.5%. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, two unidentified lipids and one unidentified glycolipid. It contained anteiso-C, iso-C and C as the major fatty acids and MK-9(H) as the predominant menaquinone. The cell wall diagnostic diamino acid was -diaminopimelic acid (DAP). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, strain KQZ13P-5 represents a novel species of genus for which the name sp. nov. is proposed. The type strain is KQZ13P-5 (=JCM 34552= CGMCC 1.18968). The description of the genus has also been emended.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Endophytic actinobacterium , KQZ13P-5T , Micropruina and novel species
Funding
This study was supported by the:
  • Guizhou Provincial Science and Technology Foundation (Award Qian Ke He Jichu-ZK [2024] Yiban 270)
    • Principal Award Recipient: LiTuo
  • Construction Project of the Educational Department of Guizhou (Award [2022]027)
    • Principal Award Recipient: Hai-BoYi
  • Guizhou Science and Technology Plan Project (Award Qian Kehe Platform Talent [2018] No. 5772-037)
    • Principal Award Recipient: Hai-BoYi
  • Natural Science Foundation of Guizhou Provincial Education Department for Young Talents (Award Qian Education Contract KY [2022]279)
    • Principal Award Recipient: Hai-BoYi
  • National Natural Science Foundation of China (Award 32360004)
    • Principal Award Recipient: LiTuo
© 2025 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006759
2025-04-23
2026-01-21

Metrics

Loading full text...

Full text loading...

References

  1. Shintani T, Liu WT, Hanada S, Kamagata Y, Miyaoka S et al. Micropruina glycogenica gen. nov., sp. nov., a new Gram-positive glycogen-accumulating bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2000; 50 Pt 1:201–207 [View Article] [PubMed]
     [Google Scholar]
  2. Chen MS, Pu XL, Weng MD, Chen L, Zhu LY et al. Description and genomic characterization of Jiella flava sp. nov., isolated from Acrostichum aureum. Int J Syst Evol Microbiol 2022; 72:005514
     [Google Scholar]
  3. Bai X, Xiong Y, Lu S, Jin D, Lai X et al. Streptococcus pantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2016; 66:3281–3286 [View Article] [PubMed]
     [Google Scholar]
  4. 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]
  5. 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]
  6. 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]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  8. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology, systematic. Zoology 1971; 20:406–416 [View Article]
     [Google Scholar]
  9. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. 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]
  12. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  13. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The rast server: rapid annotations using subsystems technology. BMC Genom 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Taghavi S, van der Lelie D, Hoffman A, Zhang Y-B, Walla MD et al. Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. PLoS Genet 2010; 6:e1000943 [View Article] [PubMed]
     [Google Scholar]
  16. Bremer E, Krämer R. Responses of microorganisms to osmotic stress. Annu Rev Microbiol 2019; 73:313–334 [View Article] [PubMed]
     [Google Scholar]
  17. Csonka LN. Physiological and genetic responses of bacteria to osmotic stress. Microbiol Rev 1989; 53:121–147 [View Article] [PubMed]
     [Google Scholar]
  18. Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front Plant Sci 2018; 9:1473 [View Article] [PubMed]
     [Google Scholar]
  19. 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] [PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. 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 [View Article] [PubMed]
     [Google Scholar]
  23. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  24. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  27. Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C. MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics 2017; 33:3808–3810 [View Article] [PubMed]
     [Google Scholar]
  28. Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol 2021; 39:499–509 [View Article] [PubMed]
     [Google Scholar]
  29. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI inc; 1990
     [Google Scholar]
  34. Tuo L, Yan X-R, Li F-N, Yang C, An M-B et al. Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill. Int J Syst Evol Microbiol 2019; 69:285–290 [View Article] [PubMed]
     [Google Scholar]
  35. Lechevalier HA, Lechevalier MP. The chemotaxonomy of actinomycetes. In Dietz A, Thayer J. eds Actinomycete Taxonomy (Special Publication No. 6) Arlington, VA: Society for Industrial Microbiology; 1980 pp 227–291
     [Google Scholar]
  36. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  37. 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]
  38. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. is an anamylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  39. Lee Y, Jeon CO. Sphingomonas frigidaeris sp. nov., isolated from an air conditioning system. Int J Syst Evol Microbiol 2017; 67:3907–3912 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006759
Loading
Micropruina sonneratiae sp. nov., a novel endophytic actinobacterium isolated from bark of Sonneratia apetala and emended description of the genus Micropruina
Int J Syst Evol Microbiol 75, 006759 (2025); https://doi.org/10.1099/ijsem.0.006759
/content/journal/ijsem/10.1099/ijsem.0.006759
/content/journal/ijsem/10.1099/ijsem.0.006759
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited 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