1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 1

sp. nov., an oligotrophic bacterium isolated from a tomato plant in China No Access

Abstract

A Gram-positive, rod-shaped, motile, endospore-forming strain, DXFW5, was isolated from the rhizosphere soil of tomato. Strain DXFW5 grew at 20–50 °C (optimum, 25–37 °C), pH 5–8 (optimum, pH 7) and in the presence of 3 % NaCl. It was positive for catalase and oxidase. Phylogenetic analysis using 16S rRNA gene sequences showed this strain was most closely related to DSM 16943 (98.0 %) and DSM 22255 (97.4 %). The DNA G+C content was 52.9 mol%. The digital DNA–DNA hybridization values between strain DXFW5 and DSM 16943, DSM 22255 and DSM 24 were 33.1, 24.9 and 21.2 %, respectively. The average nucleotide identity values between strain DXFW5 and DSM 16943 DSM 22255 and DSM 24 were 86.93, 81.77 and 75.98 %, respectively. The major fatty acids were anteiso-C (55.1 %), iso-C (13.2 %) and C (10 %). The polar lipids of strain DXFW5 consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine two unidentified phospholipids and three unidentified lipids. MK-7 was the major isoprenoid quinone. Based on these results, it was concluded that the isolate represents a novel species of the genus for which the name sp. nov. is proposed, with DXFW5 (=ACCC 61751=JCM 34488) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Paenibacillus rhizolycopersici sp. nov. , polyphasic , rhizobacteria , rhizospheric soil and tomato plants
Funding
This study was supported by the:
  • the Beijing Innovation Consortium of Agriculture Research System (Award BAIC04-2022)
    • Principle Award Recipient: Xiao-XiaZhang
  • the Fundamental Research Funds for Central Public-interest Scientific Institutions (Award Y2022PT12)
    • Principle Award Recipient: Xiao-XiaZhang
  • Agricultural Science and Technology Innovation Program (Award CAAS-ZDRW202201)
    • Principle Award Recipient: Xiao-XiaZhang
  • Key Technologies Research and Development Program of China (CN) (Award 2019YFD1002001)
    • Principle Award Recipient: Xiao-XiaZhang
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005698
2023-01-27
2024-04-26
Loading full text...

Full text loading...

References

  1. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 1994; 64:253–260 [View Article] [PubMed]
     [Google Scholar]
  2. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 1997; 47:289–298 [View Article] [PubMed]
     [Google Scholar]
  3. Huang Z, Zhao F, Li YH. Isolation of Paenibacillus tumbae sp. nov., from the tomb of the emperor Yang of the Sui dynasty, and emended description of the genus Paenibacillus. Antonie Van Leeuwenhoek 2017; 110:357–364 [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. Qi SS, Cnockaert M, Carlier A, Vandamme PA. Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov. and Paenibacillus germinis sp. nov., isolated from the Arabidopsis thaliana phyllosphere. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  6. Yang R-J, Zhou D, Wang Q-M, Wang X-H, Zhang W-J et al. Paenibacillus puerhi sp. nov., isolated from the rhizosphere soil of Pu-erh tea plants (Camellia sinensis var. assamica). Arch Microbiol 2021; 203:1375–1382 [View Article] [PubMed]
     [Google Scholar]
  7. Narsing Rao MP, Dong Z-Y, Kan Y, Zhang K, Fang B-Z et al. Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2020; 70:1048–1054 [View Article] [PubMed]
     [Google Scholar]
  8. Kim J, Jung HS, Baek JH, Chun BH, Khan SA et al. Paenibacillus silvestris sp. nov., isolated from forest soil. Curr Microbiol 2021; 78:822–829 [View Article]
     [Google Scholar]
  9. Kiran S, Swarnkar MK, Mayilraj S, Tewari R, Gulati A. Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal lake in the Indian trans-Himalayas. Syst Appl Microbiol 2017; 40:430–439 [View Article]
     [Google Scholar]
  10. Chen Y, Ye L, Huang H, Jiang M, Hu Y et al. Paenibacillus oceani sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  11. Yun JH, Lee JY, Kim PS, Jung MJ, Bae JW. Paenibacillus apis sp. nov. and Paenibacillus intestini sp. nov., isolated from the intestine of the honey bee Apis mellifera. Int J Syst Evol Microbiol 2017; 67:1918–1924 [View Article] [PubMed]
     [Google Scholar]
  12. Heo J, Kim SJ, Kim JS, Hong SB, Kwon SW. Paenibacillus protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int J Syst Evol Microbiol 2020; 70:989–994 [View Article] [PubMed]
     [Google Scholar]
  13. Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203 [View Article] [PubMed]
     [Google Scholar]
  14. Dai X, Shi K, Wang X, Fan J, Wang R et al. Paenibacillus flagellatus sp. nov., isolated from selenium mineral soil. Int J Syst Evol Microbiol 2019; 69:183–188 [View Article] [PubMed]
     [Google Scholar]
  15. Logan NA, Berge O, Bishop AH, Busse H-J, De Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article] [PubMed]
     [Google Scholar]
  16. Zhang L, Wang Y, Dai J, Tang Y, Yang Q et al. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China. Int J Syst Evol Microbiol 2009; 59:1787–1792 [View Article]
     [Google Scholar]
  17. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article]
     [Google Scholar]
  18. Tanasupawat S, Thawai C, Yukphan P, Moonmangmee D, Itoh T et al. Gluconobacter thailandicus sp. nov., an acetic acid bacterium in the alpha-Proteobacteria. J Gen Appl Microbiol 2004; 50:159–167 [View Article]
     [Google Scholar]
  19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  20. Saitou N. The neighbor-joining methods: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
     [Google Scholar]
  21. Sourdis J, Nei M. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 1988; 5:298–311 [View Article] [PubMed]
     [Google Scholar]
  22. Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 1997; 28:437–466 [View Article]
     [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. 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]
  25. 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]
  26. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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]
  29. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. 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:D206–14 [View Article] [PubMed]
     [Google Scholar]
  32. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article] [PubMed]
     [Google Scholar]
  33. Sasser M. Technical note 101: Identification of bacteria by gas chromatography of cellular fatty acids Newark, DE: MIDI; 1990
     [Google Scholar]
  34. 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]
  35. Collins MD, Jones D. Lipids in the classification and identification of Coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  36. Collins MD. 11 analysis of isoprenoid quinones. Method Microbiol 1985; 18:329–366 [View Article]
     [Google Scholar]
  37. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article]
     [Google Scholar]
  38. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  39. 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]
  40. Shao J, Li S, Zhang N, Cui X, Zhou X et al. Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9. Microb Cell Fact 2015; 14:130 [View Article] [PubMed]
     [Google Scholar]
  41. Trinh NH, Kim J. Paenibacillus piri sp. nov., isolated from urban soil. Int J Syst Evol Microbiol 2020; 70:656–661 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005698
Loading
Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China
Int J Syst Evol Microbiol 73, 005698 (2023); https://doi.org/10.1099/ijsem.0.005698
/content/journal/ijsem/10.1099/ijsem.0.005698
/content/journal/ijsem/10.1099/ijsem.0.005698
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