Pseudomonas rhizozeae sp. nov., originated from rhizosphere soil of corn field

pseudomonas-rhizozeae-sp-nov.,-originated-from-rhizosphere-soil-of-corn-field
Pseudomonas rhizozeae sp. nov., originated from rhizosphere soil of corn field

References

  1. Migula, W. Über Ein neues system der Bakterien. Arbeiten Aus Dem Bakteriologischen Inst. Der Technischen Hochschule Zu Karlsruhe. 1, 235–238 (1894).

    Google Scholar 

  2. Parte, A. C., Carbasse, J. S., Meier-Kolthoff, J. P., Reimer, L. C. & Göker, M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int. J. Syst. Evol. Microbiol. 70, 5607 (2020).

    Google Scholar 

  3. Palleroni, J. N. Pseudomonas classification. A new case history in the taxonomy of gram-negative bacteria. Antonie Van Leeuwenhoek. 64, 231–251 (1993).

    Google Scholar 

  4. Girard, L. et al. The ever-expanding Pseudomonas genus: description of 43 new species and partition of the Pseudomonas Putida group. Microorganisms 9, 1766 (2021).

    Google Scholar 

  5. Höfte, M. & De Vos, P. Plant pathogenic Pseudomonas species. Plant-Associated Bacteria. 507, 533 (2007).

    Google Scholar 

  6. Wiklund Tom. Pseudomonas anguilliseptica infection as a threat to wild and farmed fish in the Baltic sea. Microbiol. Australia. 37, 135–136 (2016).

    Google Scholar 

  7. Gross, H. & Loper, J. E. Genomics of secondary metabolite production by Pseudomonas spp. Nat. Prod. Rep. 26, 1408–1446 (2009).

    Google Scholar 

  8. Sah, S., Singh, N. & Singh, R. Iron acquisition in maize (Zea mays) using Pseudomonas siderophore. 3 Biotech. 7, 121 (2017).

    Google Scholar 

  9. Raaijmakers, J. M. & Mazzola, M. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu. Rev. Phytopathol. 50, 403–424 (2012).

    Google Scholar 

  10. Haas, D. & Défago, G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat. Reviews Microbiol.. 3:4 (3), 307–319 (2005).

    Google Scholar 

  11. Papp, D. A. et al. Aflatoxin B1 control by various Pseudomonas isolates. Toxins (Basel). 16, 367 (2024).

    Google Scholar 

  12. Rudra, B. & Gupta, R. S. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front. Microbiol. 14, 1273665 (2023).

    Google Scholar 

  13. Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

    Google Scholar 

  14. Travin, D. Y. et al. Structure of ribosome-bound azole-modified peptide Phazolicin rationalizes its species-specific mode of bacterial translation Inhibition. Nat. Commun. 10, 4563 (2019).

    Google Scholar 

  15. Schöner, T. A. et al. Aryl polyenes, a highly abundant class of bacterial natural products, are functionally related to antioxidative carotenoids. ChemBioChem 17, 247–253 (2016).

    Google Scholar 

  16. Kang, B. R., Anderson, A. J. & Kim, Y. C. Hydrogen cyanide produced by Pseudomonas chlororaphis O6 is a key aphicidal metabolite. Can. J. Microbiol. 65, 185–190 (2019).

    Google Scholar 

  17. Kang, B. R., Anderson, A. J. & Kim, Y. C. Hydrogen cyanide produced by Pseudomonas chlororaphis O6 exhibits nematicidal activity against Meloidogyne hapla. Plant. Pathol. J. 34, 35 (2018).

    Google Scholar 

  18. Czech, L. et al. Role of the extremolytes Ectoine and hydroxyectoine as stress protectants and nutrients: genetics, phylogenomics, biochemistry, and structural analysis. Genes (Basel). 9, 177 (2018).

    Google Scholar 

  19. Díaz, M. et al. Agronomic efficiency and genome mining analysis of the wheat-biostimulant rhizospheric bacterium Pseudomonas pergaminensis sp. nov. Strain 1008T. Front. Plant. Sci. 13, 894985 (2022).

    Google Scholar 

  20. Verhille, S., Baida, N., Dabboussi, F., Izard, D. & Leclerc, H. Taxonomic study of bacteria isolated from natural mineral waters: proposal of Pseudomonas jessenii sp. nov. And Pseudomonas mandelii sp. nov. Syst. Appl. Microbiol. 22, 45–58 (1999).

    Google Scholar 

  21. Duman, M. et al. Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout. Int J Syst Evol Microbiol 71, (2021).

  22. Kaminski, M. A., Furmanczyk, E. M., 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. 41, 13–22 (2018).

    Google Scholar 

  23. Ntana, F., Hennessy, R. C., Zervas, A. & Stougaard, P. Pseudomonas Nunensis sp. nov. Isolated from a suppressive potato field in Greenland. Int J. Syst. Evol. Microbiol. 73, (2023).

  24. Verhille, S. et al. Pseudomonas gessardii sp. nov. And Pseudomonas migulae sp. nov., two new species isolated from natural mineral waters. Int. J. Syst. Bacteriol. 49, 1559–1572 (1999).

    Google Scholar 

  25. Campos, V. L. et al. Pseudomonas arsenicoxydans Sp nov., an arsenite-oxidizing strain isolated from the Atacama desert. Syst. Appl. Microbiol. 33, 193–197 (2010).

    Google Scholar 

  26. Kosina, M. et al. Pseudomonas prosekii sp. nov., a novel psychrotrophic bacterium from Antarctica. Curr. Microbiol. 67, 637–646 (2013).

    Google Scholar 

  27. Delorme, S. et al. Pseudomonas Lini sp. nov., a novel species from bulk and rhizospheric soils. Int. J. Syst. Evol. Microbiol. 52, 513–523 (2002).

    Google Scholar 

  28. Liao, K., Liu, J., Gu, Y. L., Wang, C. & Wei, H. L. Pseudomonas cucumis sp. nov., isolated from the rhizosphere of crop plants. Int J. Syst. Evol. Microbiol 73, (2023).

  29. Kwon, S. W. et al. Pseudomonas Koreensis sp. nov., Pseudomonas umsongensis sp. nov. And Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. Int. J. Syst. Evol. Microbiol. 53, 21–27 (2003).

    Google Scholar 

  30. Jia, J. et al. Pseudomonas glycinae sp. nov. isolated from the soybean rhizosphere. MicrobiologyOpen 9, (2020).

  31. Chang, D. H. et al. Pseudomonas kribbensis sp. nov., isolated from garden soils in Daejeon, Korea. Antonie Van Leeuwenhoek. Int. J. Gen. Mol. Microbiol. 109, 1433–1446 (2016).

    Google Scholar 

  32. Cámara, B. et al. Pseudomonas Reinekei sp. nov., Pseudomonas moorei sp. nov. And Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid. Int. J. Syst. Evol. Microbiol. 57, 923–931 (2007).

    Google Scholar 

  33. Poblete-Morales, M. et al. Pseudomonas atacamensis sp. nov., isolated from the rhizosphere of desert bloom plant in the region of Atacama, Chile. Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 113, 1201–1211 (2020).

    Google Scholar 

  34. Furmanczyk, E. M., Kaminski, M. A., Lipinski, L., Dziembowski, A. & Sobczak, A. Pseudomonas laurylsulfatovorans sp. nov., sodium Dodecyl sulfate degrading bacteria, isolated from the peaty soil of a wastewater treatment plant. Syst. Appl. Microbiol. 41, 348–354 (2018).

    Google Scholar 

  35. Andersen, S. M., Johnsen, K., Sørensen, J., Nielsen, P. & Jacobsen, C. S. Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site. International J. Syst. Evolutionary Microbiology 50 (2000).

  36. Rühl, J., Hein, E. M., Hayen, H., Schmid, A. & Blank, L. M. The glycerophospholipid inventory of Pseudomonas Putida is conserved between strains and enables growth condition-related alterations. Microb. Biotechnol. 5, 45 (2011).

    Google Scholar 

  37. Lu, C. H. et al. Pseudomonas lijiangensis sp. nov., a novel phytopathogenic bacterium isolated from black spots of tobacco. Int. J. Syst. Evol. Microbiol. 72, 005591 (2022).

    Google Scholar 

  38. Vo, C. D. T. et al. The O2-independent pathway of ubiquinone biosynthesis is essential for denitrification in Pseudomonas aeruginosa. J. Biol. Chem. 295, 9021 (2020).

    Google Scholar 

  39. Liao, K., Li, Q., Li, J. Z. & Wei, H. L. Pseudomonas hefeiensis sp. nov., isolated from the rhizosphere of multiple cash crops in China. Int. J. Syst. Evol. Microbiol. 74, 006303 (2024).

    Google Scholar 

  40. Ait Tayeb, L., Ageron, E., Grimont, F. & Grimont, P. A. D. Molecular phylogeny of the genus Pseudomonas based on RpoB sequences and application for the identification of isolates. Res. Microbiol. 156, 763–773 (2005).

    Google Scholar 

  41. 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. 23, 140–147 (2009).

    Google Scholar 

  42. Pei, A. Y. et al. Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl. Environ. Microbiol. 76, 3886 (2010).

    Google Scholar 

  43. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30, 2114 (2014).

    Google Scholar 

  44. Souvorov, A., Agarwala, R. & Lipman, D. J. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology 2018 19:1 19, 1–13 (2018).

  45. Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications 2018 9:1 9, 1–8 (2018).

  46. Pritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G. & Toth, I. K. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal. Methods. 8, 12–24 (2015).

    Google Scholar 

  47. Meier-Kolthoff, J. P., Carbasse, J. S., Peinado-Olarte, R. L. & Göker, M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 50, D801 (2021).

    Google Scholar 

  48. Blin, K. et al. AntiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51, W46–W50 (2023).

    Google Scholar 

  49. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772 (2013).

    Google Scholar 

  50. Kück, P. & Longo, G. C. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front. Zool. 11, 81 (2014).

    Google Scholar 

  51. Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. 14, 587 (2017).

    Google Scholar 

  52. Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).

    Google Scholar 

  53. Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).

    Google Scholar 

  54. Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).

    Google Scholar 

  55. Wang, X. et al. Pseudomonas rhizoryzae sp. nov., isolated from rice. Int. J. Syst. Evol. Microbiol. 70, 944–950 (2020).

    Google Scholar 

  56. Bartholomew, J. W. & Mittwer, T. The gram stain. Bacteriol. Rev. 16, 1 (1952).

    Google Scholar 

  57. de Sousa, T. et al. Study of antimicrobial resistance, biofilm formation, and motility of Pseudomonas aeruginosa derived from urine samples. Microorganisms 11, (2023).

  58. King, E. O., Ward, M. K. & Raney, D. E. Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med. 44, 301–307 (1954).

    Google Scholar 

  59. Kovacs, N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956 178:4535 178, 703–703 (1956).

  60. Lelliott, R. A., Billing, E. & Hayward, A. C. A determinative scheme for the fluorescent plant pathogenic pseudomonads. J. Appl. Bacteriol. 29, 470–489 (1966).

    Google Scholar 

  61. Castric, K. F. & Castric, P. A. Method for rapid detection of cyanogenic bacteria. Appl. Environ. Microbiol. 45, 701–702 (1983).

    Google Scholar 

  62. Feigl, F. & Anger, V. Replacement of benzidine by copper ethylacetoacetate and tetra base as spot-test reagent for hydrogen cyanide and cyanogen. Analyst 91, 282–284 (1966).

    Google Scholar 

  63. Sasser, M. Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101. MIDI (1990).

  64. Minnikin, D. E. et al. An integrated procedure for the extraction of bacterial isoprenoid Quinones and Polar lipids. J. Microbiol. Methods. 2, 233–241 (1984).

    Google Scholar 

Download references