Skip to content
1887

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

Volume 74, Issue 7

sp. nov., a novel species widely colonizing plant rhizosphere Open Access

Abstract

A polyphasic taxonomic approach was used to characterize the three bacterial strains (FP830, FP2034, and FP2262) isolated from the rhizosphere soil of rice, corn, and highland barley in Beijing, Heilongjiang, and Tibet, respectively, in PR China. These strains were Gram-negative, rod-shaped, and have one or two polar flagella. They exhibited optimal growth at 28 °C and pH 7.0 in the presence of 1 % (w/v) NaCl and showed fluorescence under ultraviolet light when cultivated on King’s B plates. The FP830 genome size is 6.4 Mbp with a G+C content of 61.0 mol%. FP830 has the potential to promote plant growth by producing various metabolites such as fengycin, pyoverdin, indole-3-acetic acid, and the volatile substance 2,3-butanediol. Phylogenetic analysis indicated that three isolates formed an independent branch, which most closely related to type strains DSM 13194 and SWRI12. The values of average nucleotide identity and digital DNA–DNA hybridization between three isolates and closest relatives were not higher than 93.7 and 52.3 %, respectively. The dominant cellular fatty acids were C, summed feature 3 (C 7/C ω6), and summed feature 8 (Cω7/Cω6). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and aminophospholipid. The predominant respiratory quinone was ubiquinone (Q-9). Based on polyphasic taxonomic analysis, it was concluded that strains FP830, FP2034, and FP2262 represented a novel species within the genus , and sp. nov. was proposed for the name of novel species. The type strain is FP830 (=ACCC 62448=JCM 35689).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): novel species , plant growth-promoting rhizobacteria , polyphasic taxonomy and Pseudomonas
Funding
This study was supported by the:
  • the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Award CAAS-ZDRW202308, Y2022PT12)
    • Principle Award Recipient: Hai-LeiWei
  • the Beijing Innovation Consortium of Agriculture Research System (Award BAIC04-2023)
    • Principle Award Recipient: Hai-LeiWei
  • the National Key R&D Program of China (Award 2022YFD1901300)
    • Principle Award Recipient: Hai-LeiWei
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006473
2024-07-26
2025-05-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/74/7/ijsem006473.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006473&mimeType=html&fmt=ahah

References

  1. Migula W. Über ein neues system der bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–328
     [Google Scholar]
  2. Holt JG. Genus I Pseudomonas Migula 1894. In Krieg NR, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol 1 Baltimore, MD: Williams & Wilkins; 1984 pp 141–171
     [Google Scholar]
  3. Woese CR, Blanz P, Hahn CM. What isn’t a Pseudomonad: the Importance of nomenclature in bacterial classification. Syst Appl Microbiol 1984; 5:179–195 [View Article]
     [Google Scholar]
  4. Tchagang CF, Xu R, Overy D, Blackwell B, Chabot D et al. Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov. Heliyon 2018; 4:e00761 [View Article] [PubMed]
     [Google Scholar]
  5. Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H et al. The ever-expanding Pseudomonas genus: description of 43 new species and partition of the Pseudomonas putida group. Microorganisms 2021; 9:1766 [View Article] [PubMed]
     [Google Scholar]
  6. Veena VK, Popavath RN, Kennedy K, Sakthivel N. In vitro antiproliferative, pro-apoptotic, antimetastatic and anti-inflammatory potential of 2,4-diacetylphloroglucinol (DAPG) by Pseudomonas aeruginosa strain FP10. Apoptosis 2015; 20:1281–1295 [View Article] [PubMed]
     [Google Scholar]
  7. Biessy A, Novinscak A, Blom J, Léger G, Thomashow LS et al. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environ Microbiol 2019; 21:437–455 [View Article] [PubMed]
     [Google Scholar]
  8. Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M. Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev 2010; 34:1037–1062 [View Article] [PubMed]
     [Google Scholar]
  9. Popržen T, Nikolić I, Krstić-Milošević D, Uzelac B, Trifunović-Momčilov M et al. Characterization of the IAA-producing and -degrading Pseudomonas strains regulating growth of the common duckweed (Lemna minor L.). Int J Mol Sci 2023; 24:17207 [View Article] [PubMed]
     [Google Scholar]
  10. Yang J, Im Y, Kim TH, Lee MJ, Cho S et al. Engineering Pseudomonas putida KT2440 to convert 2,3-butanediol to mevalonate. Enzyme Microb Technol 2020; 132:109437 [View Article] [PubMed]
     [Google Scholar]
  11. Stringlis IA, Zamioudis C, Berendsen RL, Bakker P, Pieterse CMJ. Type III secretion system of beneficial rhizobacteria Pseudomonas simiae WCS417 and Pseudomonas defensor WCS374. Front Microbiol 2019; 10:1631 [View Article] [PubMed]
     [Google Scholar]
  12. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  13. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas. Front Microbiol 2015; 6:214 [View Article] [PubMed]
     [Google Scholar]
  14. Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q et al. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol 2018; 20:2142–2159 [View Article] [PubMed]
     [Google Scholar]
  15. Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 2020; 38:1079–1086 [View Article] [PubMed]
     [Google Scholar]
  16. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K et al. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996; 60:407–438 [View Article] [PubMed]
     [Google Scholar]
  17. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  22. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  25. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  26. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  27. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  28. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  30. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  31. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
     [Google Scholar]
  32. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
     [Google Scholar]
  33. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014; 42:D490–5 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One 2014; 9:e110726 [View Article] [PubMed]
     [Google Scholar]
  36. Jenul C, Sieber S, Daeppen C, Mathew A, Lardi M et al. Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nat Commun 2018; 9:1297 [View Article] [PubMed]
     [Google Scholar]
  37. Gimenez D, Phelan A, Murphy CD, Cobb SL. Fengycin A analogues with enhanced chemical stability and antifungal properties. Org Lett 2021; 23:4672–4676 [View Article] [PubMed]
     [Google Scholar]
  38. Cai L, Yao Y, Yeon SK, Seiple IB. Modular approaches to lankacidin antibiotics. J Am Chem Soc 2020; 142:15116–15126 [View Article] [PubMed]
     [Google Scholar]
  39. Visca P, Imperi F, Lamont IL. Pyoverdine siderophores: from biogenesis to biosignificance. Trends Microbiol 2007; 15:22–30 [View Article] [PubMed]
     [Google Scholar]
  40. Cunnac S, Lindeberg M, Collmer A. Pseudomonas syringae type III secretion system effectors: repertoires in search of functions. Curr Opin Microbiol 2009; 12:53–60 [View Article] [PubMed]
     [Google Scholar]
  41. Viollet A, Pivato B, Mougel C, Cleyet-Marel J-C, Gubry-Rangin C et al. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. Mycorrhiza 2017; 27:23–33 [View Article] [PubMed]
     [Google Scholar]
  42. Rezzonico F, Binder C, Défago G, Moënne-Loccoz Y. The type III secretion system of biocontrol Pseudomonas fluorescens KD targets the phytopathogenic Chromista Pythium ultimum and promotes cucumber protection. Mol Plant Microbe Interact 2005; 18:991–1001 [View Article] [PubMed]
     [Google Scholar]
  43. 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] [PubMed]
     [Google Scholar]
  44. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307 [PubMed]
     [Google Scholar]
  45. Zhao H, Ma Y, Wu X, Zhang L. Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean. Int J Syst Evol Microbiol 2020; 70:5012–5018 [View Article] [PubMed]
     [Google Scholar]
  46. Yu QT, Liu BN, Zhang JY, Huang ZH. Location of methyl branchings in fatty acids: fatty acids in uropygial secretion of Shanghai duck by GC-MS of 4,4-dimethyloxazoline derivatives. Lipids 1988; 23:804–810 [View Article] [PubMed]
     [Google Scholar]
  47. Spitzer V. Structure analysis of fatty acids by gas chromatography–low resolution electron impact mass spectrometry of their 4,4-dimethyloxazoline derivatives–a review. Prog Lipid Res 1996; 35:387–408 [View Article] [PubMed]
     [Google Scholar]
  48. 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]
  49. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006473
Loading
Pseudomonas beijingensis sp. nov., a novel species widely colonizing plant rhizosphere
Int J Syst Evol Microbiol 74, 006473 (2024); https://doi.org/10.1099/ijsem.0.006473
/content/journal/ijsem/10.1099/ijsem.0.006473
/content/journal/ijsem/10.1099/ijsem.0.006473
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

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