1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 6

sp. nov., a bacterium isolated from root-zone soil of a native legume, (L.) Fernald, in Quebec, Canada Open Access

Abstract

Four bacterial strains (S1Bt3, S1Bt7, S1Bt30 and S1Bt42) isolated from soil collected from the rhizosphere of a native legume, , were investigated using a polyphasic approach. Colonies were fluorescent, white-yellowish, circular and convex with regular margins on King’s B medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming rods. Oxidase- and catalase-positive. The optimal growth temperature of the strains was 37 °C. Phylogenetic analysis of the 16S rRNA gene sequences placed the strains within the genus . Analysis of the 16S rRNA- concatenated sequences clustered the strains and well separated from CIP 104664 and CFM 97-514 with the type strains of the closest species. Phylogenomic analysis of 92 up-to-date bacterial core gene and matrix-assisted laser desorption/ionization-time-of-flight MS biotyper data confirmed the distinct clustering pattern of these four strains. Digital DNA–DNA hybridization (41.7 %–31.2 %) and average nucleotide identity (91.1 %–87.0 %) values relative to closest validly published species were below the species delineation thresholds of 70 and 96 %, respectively. Fatty acid composition results validated the taxonomic position of the novel strains in the genus . Phenotypic characteristics from carbon utilization tests differentiated the novel strains from closely related species. prediction of secondary metabolite biosynthesis gene clusters in the whole-genome sequences of the four strains revealed the presence of 11 clusters involved in the production of siderophore, redox-cofactor, betalactone, terpene, arylpolyene and nonribosomal peptides. Based on phenotypic and genotypic data, strains S1Bt3, S1Bt7, S1Bt30 and S1Bt42 represent a novel species for which the name sp. nov. is proposed. The type strain is S1Bt42 (=DOAB 746=LMG 32141=CECT 30251). The genomic DNA G+C content is 60.95 mol%.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Amphicarpaea bracteata , Canadian woodland soils , genome-based DNA–DNA hybridization , Pseudomonas , Pseudomonas quebecensis , whole genome and whole-genome average nucleotide identity
Funding
This study was supported by the:
  • Agriculture and Agri-Food Canada (Award J-002272, J-002295 and J-000409)
    • Principle Award Recipient: JamesT. Tambong
© 2023 Crown Copyright
  • 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.0.005890
2023-06-16
2024-05-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/73/6/ijsem005890.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005890&mimeType=html&fmt=ahah

References

  1. 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]
  2. 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]
  3. Palleroni NJ. Introduction to the Family Pseudomonadaceae New York: Springer; 1992
     [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. Diallo S, Crépin A, Barbey C, Orange N, Burini J-F et al. Mechanisms and recent advances in biological control mediated through the potato rhizosphere. FEMS Microbiol Ecol 2011; 75:351–364 [View Article] [PubMed]
     [Google Scholar]
  6. Furmanczyk EM, Kaminski MA, Spolnik G, Sojka M, Danikiewicz W et al. Isolation and characterization of Pseudomonas spp. strains that efficiently decompose sodium dodecyl sulfate. Front Microbiol 2017; 8:1872 [View Article] [PubMed]
     [Google Scholar]
  7. Mannaa M, Oh JY, Kim KD. Biocontrol activity of volatile-producing Bacillus megaterium and pseudomonas protegens against Aspergillus flavus and aflatoxin production on stored rice grains. Mycobiology 2017; 45:213–219
     [Google Scholar]
  8. Sah S, Singh N, Singh R. Iron acquisition in maize (Zea mays L.) using Pseudomonas siderophore. 3 Biotech 2017; 7:121 [View Article] [PubMed]
     [Google Scholar]
  9. Zamioudis C, Mastranesti P, Dhonukshe P, Blilou I, Pieterse CMJ. Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria. Plant Physiol 2013; 162:304–318 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. Hoagland DR, Arnon DI. The Water-Culture Method for Growing Plants without Soil Berkeley, California: University of California CoA, Agricultural Experiment; 1950
     [Google Scholar]
  12. Tambong JT, Xu R, Bromfield ESP. Intercistronic heterogeneity of the 16S-23S rRNA spacer region among Pseudomonas strains isolated from subterranean seeds of hog peanut (Amphicarpa bracteata). Microbiology 2009; 155:2630–2640 [View Article] [PubMed]
     [Google Scholar]
  13. 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]
  14. Mise K, Iwasaki W. Environmental atlas of prokaryotes enables powerful and intuitive habitat-based analysis of community structures. iScience 2020; 23:101624 [View Article] [PubMed]
     [Google Scholar]
  15. Lane D. 16S/23S rRNA Sequencing In. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematic New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  16. 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]
  17. Tambong JT, Xu R, Gerdis S, Daniels GC, Chabot D et al. Molecular analysis of bacterial isolates from necrotic wheat leaf lesions caused by Xanthomonas translucens, and description of three putative novel species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov. Front Microbiol 2021; 12:666689 [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. Lalucat J, Mulet M, Gomila M, García-Valdés E. Genomics in bacterial taxonomy: impact on the genus Pseudomonas. Genes 2020; 11:139 [View Article] [PubMed]
     [Google Scholar]
  20. González AJ, Cleenwerck I, De Vos P, Fernández-Sanz AM. Pseudomonas asturiensis sp. nov., isolated from soybean and weeds. Syst Appl Microbiol 2013; 36:320–324 [View Article] [PubMed]
     [Google Scholar]
  21. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Andrews S. FastQC: A quality control tool for high throughput sequence data; 2010 https://www.bioinformatics.babraham.ac.uk/projects/fastqc
  26. 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] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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]
  29. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
     [Google Scholar]
  30. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 2014; 42:D581–91 [View Article] [PubMed]
     [Google Scholar]
  31. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  32. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. 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]
  35. 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]
  36. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  37. 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]
  38. Meier-Kolthoff JP, 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]
  39. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  40. Na S-I, Kim YO, Yoon S-H, Ha S-M, 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] [PubMed]
     [Google Scholar]
  41. 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]
  42. Zeng Q, Xie J, Li Y, Chen X, Gu X et al. Organization, evolution and function of fengycin biosynthesis gene clusters in the Bacillus amyloliquefaciens group. Phytopathol Res 2021; 3: [View Article]
     [Google Scholar]
  43. Lee X, Azevedo MD, Armstrong DJ, Banowetz GM, Reimmann C. The Pseudomonas aeruginosa antimetabolite L-2-amino-4-methoxy-trans-3-butenoic acid inhibits growth of Erwinia amylovora and acts as a seed germination-arrest factor. Environ Microbiol Rep 2013; 5:83–89 [View Article] [PubMed]
     [Google Scholar]
  44. Maier T, Klepel S, Renner U, Kostrzewa M. Fast and reliable MALDI-TOF MS–based microorganism identification. Nat Methods 2006; 3:i–ii [View Article]
     [Google Scholar]
  45. Sasser M. Techinical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI; 1990
     [Google Scholar]
  46. Oyaizu H, Komagata K. Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J Gen Appl Microbiol 1983; 29:17–40 [View Article]
     [Google Scholar]
  47. Tambong JT, Xu R, Bromfield ESP. Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization. Int J Syst Evol Microbiol 2017; 67:889–895 [View Article] [PubMed]
     [Google Scholar]
  48. Ryu E. A simple method of differentiation between Gram-positive and Gram-negative organisms without staining. Kitasato Archives Exp Med J 1940; 58:
     [Google Scholar]
  49. Rademaker JL, De Bruijn FJ. Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer-assisted pattern analysis. In Caetano-Anolles G, Gresshoff PM. eds DNA Markers: Protocols, Applications and Overviews New York: John Wiley & Sons; 1997 pp 151–171
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005890
Loading
Pseudomonas quebecensis sp. nov., a bacterium isolated from root-zone soil of a native legume, Amphicarpaea bracteata (L.) Fernald, in Quebec, Canada
Int J Syst Evol Microbiol 73, 005890 (2023); https://doi.org/10.1099/ijsem.0.005890
/content/journal/ijsem/10.1099/ijsem.0.005890
/content/journal/ijsem/10.1099/ijsem.0.005890
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