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Volume 73, Issue 12

sp. nov., isolated from the rhizosphere of crop plants Open Access

Abstract

Two bacterial strains, FP1935 and FP1962, were isolated from the rhizosphere soil of cucumber and Chieh-qua plants, respectively, in Jilin Province, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and motile with one or two polar flagella. Analysis of the 16S rRNA gene sequences revealed that they represented members of the genus , with the highest similarity to A3 (99.45 %), JAJ28 (99.45 %), NBRC 103147 (99.38 %), P50 (99.27 %) and CFBP 3225 (99.18 %). The DNA G+C contents of FP1935 and FP1962 were 58.99 mol% and 58.98 mol%, respectively. The results of genome-based analyses indicated that these strains were distinct from other species in the genus , as the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values were below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation, with no values exceeding 94.1 and 55.8 %, respectively, compared with any other related species. The results of phenotypic and chemotaxonomic tests confirmed their differentiation from their closest relatives. The fatty acid profiles of both strains mainly consisted of summed feature 3 (Cω6 and/or Cω7), summed feature 8 (Cω7 and/or Cω6), C and C. The predominant respiratory quinone was Q-9. Polar lipids include phosphatidylethanolamine, unidentified aminophospholipids, unidentified lipids and an unidentified phospholipid. On the basis of these phenotypic and genotypic results, we propose the name sp. nov. for these novel strains. The type strain is FP1935 (=ACCC 62445=JCM 35690).

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  • Accepted:
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Keyword(s): cucumber rhizosphere , plant growth-promoting rhizobacteria , polyphasic taxonomy and Pseudomonas
Funding
This study was supported by the:
  • Key Laboratory of Agricultural Information Service Technology (Award CAAS-ZDRW202308, Y2022PT12)
    • Principle Award Recipient: WeiHai-Lei
  • Beijing Innovation Consortium of Agriculture Research System (Award BAIC04-2023)
    • Principle Award Recipient: WeiHai-Lei
  • National Key R&D Program of China (Award 2022YFD1901300)
    • Principle Award Recipient: WeiHai-Lei
© 2023 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.
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References

  1. Migula W. Über ein Neues system der Bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–328
     [Google Scholar]
  2. Madigan M, Martinko J. Procaryotic Diversity: Bacteria. Brock Biology of Microorganisms. Upper Saddle River New Jersey: Prentice Hall International, Inc; 1997
     [Google Scholar]
  3. Spiers AJ, Buckling A, Rainey PB. The causes of Pseudomonas diversity. Microbiology (Reading) 2000; 146 (Pt 10):2345–2350 [View Article] [PubMed]
     [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on.. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  5. 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]
  6. 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]
  7. Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R et al. Correction: genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 2016; 11:e0153733 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. 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]
  10. Gross H, Loper JE. Genomics of secondary metabolite production by Pseudomonas spp. Nat Prod Rep 2009; 26:1408–1446 [View Article] [PubMed]
     [Google Scholar]
  11. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652–680 [View Article] [PubMed]
     [Google Scholar]
  12. Mercado-Blanco J. Pseudomonas strains that exert biocontrol of plant pathogens. In Ramos J-L, Goldberg JB, Filloux A. eds Pseudomonas: Volume 7: New Aspects of Pseudomonas Biology Dordrecht: Springer Netherlands; pp 121–172 [View Article]
     [Google Scholar]
  13. Narendra Babu A, Jogaiah S, Ito S-I, Kestur Nagaraj A, Tran L-SP. Improvement of growth, fruit weight and early blight disease protection of tomato plants by rhizosphere bacteria is correlated with their beneficial traits and induced biosynthesis of antioxidant peroxidase and polyphenol oxidase. Plant Sci 2015; 231:62–73 [View Article] [PubMed]
     [Google Scholar]
  14. Saharan B, Nehra V. Plant growth promoting rhizobacteria: a critical review. Life Sci Med Res 2011; 21:1–30
     [Google Scholar]
  15. 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]
  16. 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]
  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. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A et al. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology (Reading) 2000; 146 (Pt 10):2385–2394 [View Article] [PubMed]
     [Google Scholar]
  19. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [View Article] [PubMed]
     [Google Scholar]
  22. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
     [Google Scholar]
  23. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP et al. A whole-genome assembly of Drosophila. Science 2000; 287:2196–2204 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  33. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997; 278:631–637 [View Article] [PubMed]
     [Google Scholar]
  34. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000; 28:27–30 [View Article] [PubMed]
     [Google Scholar]
  35. 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]
  36. Peypoux F, Besson F, Michel G, Delcambe L. Structure of bacillomycin D, a new antibiotic of the iturin group. Eur J Biochem 1981; 118:323–327 [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. Patz S, Gautam A, Becker M, Ruppel S, Rodríguez-Palenzuela P et al. PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria. Bioinformatics 2021 [View Article]
     [Google Scholar]
  40. 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
     [Google Scholar]
  41. 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]
  42. Campos VL, Valenzuela C, Yarza P, Kämpfer P, Vidal R et al. Pseudomonas arsenicoxydans sp nov., an arsenite-oxidizing strain isolated from the Atacama desert. Syst Appl Microbiol 2010; 33:193–197 [View Article] [PubMed]
     [Google Scholar]
  43. Kaminski MA, Furmanczyk EM, Sobczak A, Dziembowski A, Lipinski L. Pseudomonas silesiensis sp. nov. strain A3T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence. Syst Appl Microbiol 2018; 41:13–22 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. 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]
  46. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  47. Garrity GM, Bell JA, Lilburn T. Genus I. Pseudomonas Orla-Jensen 1921, 270 AL. In Garrity GM, Brenner DJ, Krieg NR, Staley JR. eds Bergey’s Manual of Systematic Bacteriology (The Proteobacteria Part B The Gammaproteobacteria), 2nd ed. vol 2 New York: Springer; 2005 pp 323–379 [View Article]
     [Google Scholar]
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Pseudomonas cucumis sp. nov., isolated from the rhizosphere of crop plants
Int J Syst Evol Microbiol 73, 006208 (2023); https://doi.org/10.1099/ijsem.0.006208
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