Skip to content
1887

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

Volume 74, Issue 11

sp. nov. and sp. nov., isolated from wilted pepper plants No Access

Abstract

Two Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming bacteria, designated as strain MH1 and MH2, were isolated from branches of wilted pepper plants () collected from a farmland in Machong town, Guangdong, China, and investigated using a polyphasic approach. MH1 grew at temperatures of 4–42 °C (optimum 28 °C), with 0–6.0 % (w/v) NaCl and at pH 4.0–10.0 (optimum pH 4.0). MH2 grew at temperatures of 4–42 °C (optimum 28 °C), with 0–6.0% (w/v) NaCl and at pH 4.0–10.0 (optimum pH 5.0). Analysis of the 16S rRNA gene sequence indicated that MH1 belongs to and MH2 belongs to . Genome-based phylogenetic analysis further established that MH1 shares the closest evolutionary relationships with DSM 18929 and DSM 18941, and MH2 is sister to RW3S1. Whole-genome comparisons between MH1 and known species revealed average nucleotide identity (ANI) values up to 84.5%, as well as digital DNA–DNA hybridization (dDDH) values up to 28.3%, both substantially lower than the accepted thresholds for species delineation (ANI: 95%; dDDH: 70%). The ANI and dDDH values between MH2 and known species were at most 94.6 and 59.2 %, respectively. Additional biochemical and physiological analyses further support that MH1 and MH2 represent a novel species in and , respectively. Notably, the differences in carbon source utilization could differentiate MH1 and its close relatives in . The major fatty acids were iso-C, iso-C and iso-C for MH1 and were C, C ω7c/C ω6c (summed feature 8), C ω7c/C ω6c (summed feature 3) and C cyclo for MH2. Therefore, we propose a new species sp. nov., with MH1 (=GDMCC 1.3749=JCM 36317) as the type strain, and a new species sp. nov., with MH2 (=GDMCC 1.3750=JCM 36318) as the type strain. The MH1 genome has a size of 4.18 Mb and a GC-content of 67.19 mol%, while the MH2 genome has a size of 5.71 Mb and a GC-content of 63.12 mol%.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): novel species , pepper , Pseudomonas machongensis and Stenotrophomonas capsici
Funding
This study was supported by the:
  • National Key Area Research and Development Program of China (Award 2022YFA1304401)
    • Principle Award Recipient: XiaofanZhou
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006550
2024-11-26
2025-07-12
Loading full text...

Full text loading...

References

  1. 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]
  2. Peix A, Ramírez-Bahena M-H, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: an update. Infect Genet Evol 2018; 57:106–116 [View Article] [PubMed]
     [Google Scholar]
  3. 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]
  4. Migula W. System der bakterien: Handbuch der morphologie, entwicklungsgeschichte und systematik der bakterien. In vol 2 1900: Fischer;
  5. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Mehmood N, Saeed M, Zafarullah S, Hyder S, Rizvi ZF et al. Multifaceted impacts of plant-beneficial Pseudomonas spp. in managing various plant diseases and crop yield improvement. ACS Omega 2023; 8:22296–22315 [View Article] [PubMed]
     [Google Scholar]
  8. Barreteau H, Bouhss A, Fourgeaud M, Mainardi J-L, Touzé T et al. Human- and plant-pathogenic Pseudomonas species produce bacteriocins exhibiting colicin M-like hydrolase activity towards peptidoglycan precursors. J Bacteriol 2009; 191:3657–3664 [View Article] [PubMed]
     [Google Scholar]
  9. Ikemoto S, Suzuki K, Kaneko T, Komagata K. Characterization of strains of Pseudomonas maltophilia which do not require methionine. Int J Syst Evol Microbiol 1980; 30:437–447 [View Article]
     [Google Scholar]
  10. Palleroni NJ, Bradbury JF. Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia. Int J Syst Bacteriol 1993; 43:606–609 [View Article] [PubMed]
     [Google Scholar]
  11. Kaiser S, Biehler K, Jonas D. A Stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure. J Bacteriol 2009; 191:2934–2943 [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. Wolf A, Fritze A, Hagemann M, Berg G. Stenotrophomonas rhizophila sp. nov., a novel plant-associated bacterium with antifungal properties. Int J Syst Evol Microbiol 2002; 52:1937–1944 [View Article] [PubMed]
     [Google Scholar]
  14. Juhnke ME, des Jardin E. Selective medium for isolation of Xanthomonas maltophilia from soil and rhizosphere environments. Appl Environ Microbiol 1989; 55:747–750 [View Article] [PubMed]
     [Google Scholar]
  15. Berg G, Marten P, Ballin G. Stenotrophomonas maltophilia in the rhizosphere of oilseed rape — occurrence, characterization and interaction with phytopathogenic fungi. Microbiol Res 1996; 151:19–27 [View Article]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL et al. The MaSuRCA genome assembler. Bioinformatics 2013; 29:2669–2677 [View Article] [PubMed]
     [Google Scholar]
  19. Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol 2021; 38:4647–4654 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  22. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 2022; 38:5315–5316 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Gosselin S, Fullmer MS, Feng Y, Gogarten JP. Improving phylogenies based on average nucleotide identity, incorporating saturation correction and nonparametric bootstrap support. Syst Biol 2022; 71:396–409 [View Article]
     [Google Scholar]
  28. Heylen K, Vanparys B, Peirsegaele F, Lebbe L, De Vos P. Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil. Int J Syst Evol Microbiol 2007; 57:2056–2061 [View Article] [PubMed]
     [Google Scholar]
  29. Pellegrinetti TA, Monteiro GGTN, Lemos LN, Santos RAC dos, Barros AG et al. PGPg_finder: a comprehensive and user-friendly pipeline for identifying plant growth-promoting genes in genomic and metagenomic data. Rhizosphere 2024; 30:100905 [View Article]
     [Google Scholar]
  30. 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]
/content/journal/ijsem/10.1099/ijsem.0.006550
Loading
Pseudomonas machongensis sp. nov. and Stenotrophomonas capsici sp. nov., isolated from wilted pepper plants
Int J Syst Evol Microbiol 74, 006550 (2024); https://doi.org/10.1099/ijsem.0.006550
/content/journal/ijsem/10.1099/ijsem.0.006550
/content/journal/ijsem/10.1099/ijsem.0.006550
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