1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 4

sp. nov. isolated from var. Rijnsburger, an onion landrace Open Access

Abstract

The novel, aerobic, Gram-stain-positive, rod-shaped bacterial strain, ZW T2_19, was isolated from an onion sample ( var. Rijnsburger). Analyses of the 16S rRNA gene sequence revealed that ZW T2_19 represented a member of the genus but may represent a novel species of this genus. Analyses of the whole draft genome sequences, i.e. digital DNA–DNA hybridisation (dDDH) and average nucleotide identity (ANI) of ZW T2_19 and all type strains of species of the genus confirmed that ZW T2_19 represents a novel species of the genus . The genome size of ZW T2_19 is 4.01 Mbp and the DNA G+C content is 71.8 mol%. Glucose, mannose, rhamnose and ribose were detected as whole-cell sugars of ZW T2_19. The major respiratory quinone of ZW T2_19 is menaquinone MK-10, at 78.9 %. The detected peptidoglycan type in ZW T2_19 is a variant of type B2γ with {Gly} [-diaminobutyric acid (-DAB)/-homoserine (-Hse)] -Glu--DAB. Polar lipids in ZW T2_19 consisted of one diphosphatidylglycerol, one phosphatidylglycerol, seven glycolipids, one phospholipid and one lipid. The fatty acid profile of ZW T2_19 predominantly consisted of anteiso-C (53 %), iso-C (21 %) and anteiso-C (18 %). In addition, API 20NE, API 50CH, API Coryne, API ZYM, antibiotic susceptibility, haemolysis and growth at different temperatures and with different supplements was investigated. On the basis of the results obtained using this polyphasic approach, including molecular, phenotypic and biochemical analyses, we propose the novel species with the type and only strain ZW T2_19 (= DSM 114294 = LMG 32700).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Microbacteriaceae , onion landrace and Rathayibacter
Funding
This study was supported by the:
  • Bundesanstalt für Landwirtschaft und Ernährung (Award 2819OE019)
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005811
2023-04-11
2024-05-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/73/4/ijsem005811.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005811&mimeType=html&fmt=ahah

References

  1. Ráthay E. Über eine Bakteriose von Dactylis glomerata L. In Aus Der KK Hof-Und Staatsdruckerei, in Commission Bei Carl Gerold’s Sohn (Wien) 1899
     [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Kalakoutskii LV. Rathayibacter gen. nov., including the species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses. Int J Syst Bacteriol 1993; 43:143–149 [View Article]
     [Google Scholar]
  3. Schroeder BK, Schneider WL, Luster DG, Sechler A, Murray TD. Rathayibacter agropyri (non O’Gara 1916) comb. nov., nom. rev., isolated from western wheatgrass (Pascopyrum smithii). Int J Syst Evol Microbiol 2018; 68:1519–1525 [View Article]
     [Google Scholar]
  4. Dorofeeva LV, Evtushenko LI, Krausova VI, Karpov AV, Subbotin SA et al. Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively. Int J Syst Evol Microbiol 2002; 52:1917–1923 [View Article]
     [Google Scholar]
  5. Dorofeeva LV, Starodumova IP, Krauzova VI, Prisyazhnaya NV, Vinokurova NG et al. Rathayibacter oskolensis sp. nov., a novel actinobacterium from Androsace koso-poljanskii Ovcz. (Primulaceae) endemic to the Central Russian Upland. Int J Syst Evol Microbiol 2018; 68:1442–1447 [View Article]
     [Google Scholar]
  6. Vasilenko OV, Starodumova IP, Tarlachkov SV, Dorofeeva LV, Avtukh AN et al. Draft genome sequence of "Rathayibacter tanaceti" strain VKM Ac-2596 isolated from Tanacetum vulgare infested by a foliar nematode. Genome Announc 2016; 4:e00512-16 [View Article]
     [Google Scholar]
  7. Sasaki J, Chijimatsu M, Suzuki K. Taxonomic significance of 2,4-diaminobutyric acid isomers in the cell wall peptidoglycan of actinomycetes and reclassification of Clavibacter toxicus as Rathayibacter toxicus comb. nov. Int J Syst Bacteriol 1998; 48 Pt 2:403–410 [View Article]
     [Google Scholar]
  8. Riley IT, Ophel KM. Clavibacter toxicus sp. nov., the bacterium responsible for annual ryegrass toxicity in Australia. Int J Syst Bacteriol 1992; 42:64–68 [View Article]
     [Google Scholar]
  9. Davis MJ, Gillaspie AG, Vidaver AK, Harris RW. Clavibacter: a new genus containing some phytopathogenic coryneform bacteria, including Clavibacter xyli subsp. xyli sp. nov., subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease. Int J Syst Bacteriol 1984; 34:107–117 [View Article]
     [Google Scholar]
  10. Sabet KA. On the host range and systematic position of the bacteria responsible for the yellow slime diseases of wheat (Triticum vulgare Vill.) and cocksfoot grass (Dactylis glomerata L). Ann Appl Biol 1954; 41:606–611 [View Article]
     [Google Scholar]
  11. Gupta P, Swarup G. Ear-cockle and yellow ear-rot disease of wheat. II. Nematode bacterial association. Nematol 1972; 18:320–324 [View Article]
     [Google Scholar]
  12. Kerr A, Price PC, Fisher JM. On Anguina funesta n. sp. and its association with Corynebacterium sp., in infecting Lolium rigidum. Nematol 1979; 25:76–85 [View Article]
     [Google Scholar]
  13. Riley IT. Serological relationships between strains of Coryneform bacteria responsible for annual ryegrass toxicity and other plant-pathogenic Corynebacteria. Int J Syst Bacteriol 1987; 37:153–159 [View Article]
     [Google Scholar]
  14. Riley ITM AC. Specificity of the adhesion of some plant pathogenic micro-organisms to the cuticle of nematodes in the genus Anguina (Nematoda: Anguinidae). Nematol 1990; 36:90–103 [View Article]
     [Google Scholar]
  15. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
     [Google Scholar]
  16. Stoll DA, Danylec N, Soukup ST, Hetzer B, Kulling SE et al. Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia. Int J Syst Evol Microbiol 2021; 71:004987 [View Article]
     [Google Scholar]
  17. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9:671–675 [View Article] [PubMed]
     [Google Scholar]
  18. Danylec N, Göbl A, Stoll DA, Hetzer B, Kulling SE et al. Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1533–1540 [View Article]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. 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]
  21. 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]
  22. 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]
     [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  24. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  25. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  26. Weimann A, Mooren K, Frank J, Pope PB, Bremges A et al. From genomes to phenotypes: traitar, the microbial trait analyzer. mSystems 2016; 1:e00101–00116 [View Article]
     [Google Scholar]
  27. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020; 75:3491–3500 [View Article] [PubMed]
     [Google Scholar]
  28. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinform 2009; 10:421 [View Article]
     [Google Scholar]
  29. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  30. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202
     [Google Scholar]
  31. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  32. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
     [Google Scholar]
  33. Schumann P. 5 - Peptidoglycan structure. In Rainey F, Oren A. eds Methods Microbiol 2011 pp 101–129
     [Google Scholar]
  34. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
     [Google Scholar]
  35. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  36. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985123–156
     [Google Scholar]
  37. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
  38. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article]
     [Google Scholar]
  39. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. Method Gen Mol Microbiol 2007330–393
     [Google Scholar]
  40. 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]
     [Google Scholar]
  41. Farris JS. Estimating phylogenetic trees from distance matrices. Am Natural 1972; 106:645–668 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005811
Loading
Rathayibacter rubneri sp. nov. isolated from Allium cepa var. Rijnsburger, an onion landrace
Int J Syst Evol Microbiol 73, 005811 (2023); https://doi.org/10.1099/ijsem.0.005811
/content/journal/ijsem/10.1099/ijsem.0.005811
/content/journal/ijsem/10.1099/ijsem.0.005811
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