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

Volume 75, Issue 3

Description of sp. nov., a plant growth-promoting bacterium that modulates stomatal aperture No Access

Abstract

A polyphasic taxonomic approach was used to characterize a previously isolated plant growth-promoting strain designated as NT2 and a strain designated as TKP (JCM 19688), both of which were found to manipulate plant stomatal immunity. Both strains shared 100% 16S rRNA gene sequence identity. Phylogenetic trees based on single and concatenated sequences of the housekeeping genes , , and 16S rRNA, as well as whole-genome sequences, clustered NT2 and TKP together, clearly separated from the closest spp., which belonged to the complex. NT2 showed average nucleotide identities (ANIs) of 87.8% (ANIb) and 89.9% (ANIm) and a 37.4% digital DNA–DNA hybridization score with DSM 17515, the species with the highest genome sequence similarity. On the contrary, the comparison between NT2 and TKP showed very high ANI (ANIb=99.67, ANIm=99.93) and digital DNA–DNA hybridization scores (98.90%). NT2 and TKP differed from closely related species in relation to arginine dihydrolase activity, aesculin and gelatin hydrolysis, -acetyl--glucosamine, maltose, adipate, phenylacetate, p-hydroxy-phenylacetic acid, Tween 40, glycyl--proline, -maltose, -galactonic acid lactone, -hydroxy butyric acid, myo-inositol, sucrose, -histidine, -malic acid, -rhamnose and acetic acid assimilation, NaCl-tolerance range and pyocyanin production (fluorescence on King A medium). The major fatty acids in NT2 and TKP were C16 : 0, C16 : 1 and C18 : 1. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of NT2 and TKP from the closest and confirmed that these strains represent a novel species, for which the name sp. nov. is proposed with NT2 (DSM 114757=LMG 32751) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): endophytic bacteria , plant growth-promoting bacteria and stomatal immunity
Funding
This study was supported by the:
  • Consejo Nacional de Investigaciones Científicas y Técnicas (Award PIP 11220200102958CO)
    • Principal Award Recipient: GustavoEduardo Gudesblat
  • Consejo Nacional de Investigaciones Científicas y Técnicas (Award PIP 11220200103017CO)
    • Principal Award Recipient: FernandoLuis Pieckenstain
  • Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Award PICT 2017-02075)
    • Principal Award Recipient: GustavoEduardo Gudesblat
  • Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Award PICT 2019-03857)
    • Principal Award Recipient: FernandoLuis Pieckenstain
  • Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Award PICT Aplicado 2021-92)
    • Principal Award Recipient: FernandoLuis Pieckenstain
© 2025 The Authors
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2025-03-31
2026-01-18

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References

  1. Lindow SE, Leveau JH. Phyllosphere microbiology. Curr Opin Biotechnol 2002; 13:238–243 [View Article] [PubMed]
     [Google Scholar]
  2. Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE et al. Shaping the leaf microbiota: plant-microbe-microbe interactions. J Exp Bot 2021; 72:36–56 [View Article] [PubMed]
     [Google Scholar]
  3. Gudesblat GF, Torres PS, Vojnov AA. Xanthomonas campestris overcomes arabidopsis stomatal innate immunity through a DSF cell-to-cell signal-regulated virulence factor. Plant Physiol 2009; 149:1017–1027 [View Article] [PubMed]
     [Google Scholar]
  4. Melotto M, Fochs B, Jaramillo Z, Rodrigues O. Fighting for survival at the stomatal gate. Annu Rev Plant Biol 2024; 75:551–577 [View Article] [PubMed]
     [Google Scholar]
  5. Frank AC, Saldierna Guzmán JP, Shay JE. Transmission of bacterial endophytes. Microorganisms 2017; 5:70 [View Article] [PubMed]
     [Google Scholar]
  6. Romero FM, Marina M, Pieckenstain FL. Novel components of leaf bacterial communities of field-grown tomato plants and their potential for plant growth promotion and biocontrol of tomato diseases. Res Microbiol 2016; 167:222–233 [View Article] [PubMed]
     [Google Scholar]
  7. Ohtsubo Y, Kishida K, Sato T, Tabata M, Kawasumi T et al. Complete genome sequence of Pseudomonas sp. strain TKP, isolated from a γ-hexachlorocyclohexane-degrading mixed culture. Genome Announc 2014; 2:e01241–13 [View Article] [PubMed]
     [Google Scholar]
  8. Vincent JM. A Manual for Practical Study of Root Nodule Bacteria Oxford. Blackwell Scientific Publishers; 1970
     [Google Scholar]
  9. Sambrook J, Russell DW. Molecular Cloning, a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001
     [Google Scholar]
  10. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012; 9:676–682 [View Article] [PubMed]
     [Google Scholar]
  11. Brooks ME, Kristensen K, Van Benthem KJ, Magnusson A, Berg CW et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J 2017; 9:378–400 [View Article]
     [Google Scholar]
  12. Dauga C. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int J Syst Evol Microbiol 2002; 52:531–547 [View Article] [PubMed]
     [Google Scholar]
  13. Giammanco G, Pignato S, Grimont PAD, Grimont F, Giammanco GM. Genotyping of the genus Proteus by rpoB sequence analysis. Ital J Publ Health 2005; 2:19–22 [View Article]
     [Google Scholar]
  14. Mulet M, Bennasar A, Lalucat J, García-Valdés E. An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 2009; 23:140–147 [View Article] [PubMed]
     [Google Scholar]
  15. Rahman MT, Crombie A, Chen Y, Stralis-Pavese N, Bodrossy L et al. Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J 2011; 5:1061–1066 [View Article] [PubMed]
     [Google Scholar]
  16. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
     [Google Scholar]
  17. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  18. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article]
     [Google Scholar]
  19. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:206–214 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [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 Bioinform 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Sardà Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–667 [View Article]
     [Google Scholar]
  26. 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]
  27. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  28. Altabe SG, Aguilar P, Caballero GM, de Mendoza D. The Bacillus subtilis acyl lipid desaturase is a delta5 desaturase. J Bacteriol 2003; 185:3228–3231 [View Article] [PubMed]
     [Google Scholar]
  29. Christie WW. Gas Chromatography and Lipids: A Practical Guide, 1st edn Ayr, Scotland: The Oily Press; 1990 [View Article]
     [Google Scholar]
  30. Versalovic J, Schneider M, Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Meth Mol Cell Biol 1994; 5:25–40
     [Google Scholar]
  31. Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991; 19:6823–6831 [View Article] [PubMed]
     [Google Scholar]
  32. Hematzadeh A, Haghkhah M. Biotyping of isolates of Pseudomonas aeruginosa isolated from human infections by RAPD and ERIC-PCR. Heliyon 2021; 7:e07967 [View Article] [PubMed]
     [Google Scholar]
  33. Mahenthiralingam E, Campbell ME, Foster J, Lam JS, Speert DP. Random amplified polymorphic DNA typing of Pseudomonas aeruginosa isolates recovered from patients with cystic fibrosis. J Clin Microbiol 1996; 34:1129–1135 [View Article] [PubMed]
     [Google Scholar]
  34. Hafiane A, Ravaoarinoro M. Characterization of Pseudomonas aeruginosa strains isolated from cystic fibrosis patients by different typing methods. Pathol Biol 2011; 59:109–144 [View Article] [PubMed]
     [Google Scholar]
  35. Wu J, Liu Y. Stomata-pathogen interactions: over a century of research. Trends Plant Sci 2022; 27:964–967 [View Article] [PubMed]
     [Google Scholar]
  36. Melotto M, Underwood W, Koczan J, Nomura K, He SY. Plant stomata function in innate immunity against bacterial invasion. Cell 2006; 126:969–980 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. 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]
  39. Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985; 22:160–174 [View Article] [PubMed]
     [Google Scholar]
  40. Stecher G, Tamura K, Kumar S. Molecular evolutionary genetics analysis (MEGA) for macOS. Mol Biol Evol 2020; 37:1237–1239 [View Article] [PubMed]
     [Google Scholar]
  41. López NI, Pettinari MJ, Stackebrandt E, Tribelli PM, Põtter M et al. Pseudomonas extremaustralis sp. nov., a poly(3-hydroxybutyrate) producer isolated from an antarctic environment. Curr Microbiol 2009; 59:514–519 [View Article] [PubMed]
     [Google Scholar]
  42. Pavlov MS, Lira F, Martinez JL, Olivares-Pacheco J, Marshall SH. Pseudomonas fildesensis sp. nov., a psychrotolerant bacterium isolated from antarctic soil of king george island, South Shetland Islands. Int J Syst Evol Microbiol 2020; 70:3255–3263 [View Article] [PubMed]
     [Google Scholar]
  43. 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]
     [Google Scholar]
  44. Lick S, Wibberg D, Busche T, Blom J, Grimmler C et al. Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast. Int J Syst Evol Microbiol 2024; 74: [View Article] [PubMed]
     [Google Scholar]
  45. Sawada H, Fujikawa T, Osada S, Satou M. Pseudomonas petroselini sp. nov., a pathogen causing bacterial rot of parsley in Japan. Int J Syst Evol Microbiol 2022; 72:10 [View Article] [PubMed]
     [Google Scholar]
  46. Duman M, Mulet M, Saticioglu IB, Altun S, Gomila M et al. Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey. Syst Appl Microbiol 2020; 43:126103 [View Article] [PubMed]
     [Google Scholar]
  47. Elomari M, Coroler L, Hoste B, Gillis M, Izard D et al. DNA relatedness among Pseudomonas strains isolated from natural mineral waters and proposal of Pseudomonas veronii sp. nov. Int J Syst Bacteriol 1996; 46:1138–1144 [View Article] [PubMed]
     [Google Scholar]
  48. Kosina M, Barták M, Mašlaňová I, Pascutti AV, Sedo O et al. Pseudomonas prosekii sp. nov., a novel psychrotrophic bacterium from antarctica. Curr Microbiol 2013; 67:637–646 [View Article] [PubMed]
     [Google Scholar]
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Description of Pseudomonas gorinensis sp. nov., a plant growth-promoting bacterium that modulates stomatal aperture
Int J Syst Evol Microbiol 75, 006739 (2025); https://doi.org/10.1099/ijsem.0.006739
/content/journal/ijsem/10.1099/ijsem.0.006739
/content/journal/ijsem/10.1099/ijsem.0.006739
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