1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 1

sp. nov., sp. nov., sp. nov. and sp. nov., isolated from diverse environmental sources, and emended description of the genus No Access

Abstract

Bacteria isolated from onion bulbs suffering from bacterial decay in the United States and Norway were previously shown to belong to the genus based on partial housekeeping gene sequences and/or fatty acid analysis. However, many strains could not be assigned to any existing species. Additionally, strains isolated from creek water and oak as well as a strain with bioremediation properties were assigned to based on partial housekeeping gene sequences. The taxonomic status of these 21 strains was investigated using multilocus sequence analysis, whole genome analyses, phenotypic assays and fatty acid analysis. Phylogenetic and phylogenomic analyses separated the strains into five clusters, one of which corresponded to . The remaining four clusters could be differentiated both genotypically and phenotypically from each other and existing species. Based on these results, we propose the description of four novel species: sp. nov. (type strain SL6=LMG 32257=DSM 112609), sp. nov. (H11b=LMG 32256=DSM 112610), sp. nov. (FC061912-K=LMG 32259=DSM 112611) and sp. nov. (FRB 231=LMG 32255=DSM 112612).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): acute oak decline , bacterial decay , onion , Rahnella and Yersiniaceae
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005190
2022-01-20
2024-04-24
Loading full text...

Full text loading...

References

  1. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciacceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article]
     [Google Scholar]
  2. Izard D, Gavini F, Trinel PA, Leclerc H. Rahnella aquatilis, nouveau membre de la famille des Enterobacteriaceae. Ann Microbiol 1979; 130:163–177
     [Google Scholar]
  3. Brenner DJ, Müller HE, Steigerwalt AG, Whitney AM, O’Hara CM et al. Two new Rahnella genomo species that cannot be phenotypically differentiated from Rahnella aquatilis. Int J Syst Bacteriol 1998; 48:141–149 [View Article] [PubMed]
     [Google Scholar]
  4. Kämpfer P. Rahnella. In Bergey’s Manual of Systematics of Archaea and Bacteria Hoboken, New Jersey: John Wiley & Sons; 2015 [View Article]
     [Google Scholar]
  5. Brady C, Hunter G, Kirk S, Arnold D, Denman S. Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella. Syst Appl Microbiol 2014; 37:545–552 [View Article]
     [Google Scholar]
  6. Lee SD, Jeon D, Kim IS, Choe H, Kim JS. Rahnella aceris sp. nov., isolated from sap drawn from Acer pictum. Arch Microbiol 2020; 202:2411–2417 [View Article]
     [Google Scholar]
  7. Jeon D, Kim IS, Lee SD. Rahnella laticis sp. nov. and Rahnella contaminans sp. nov., and emended description of the genus Rahnella. Int J Syst Evol Microbiol 2021; 71:004893 [View Article]
     [Google Scholar]
  8. Berge O, Heulin T, Achouak W, Richard C, Bally R et al. Rahnella aquatilis, a nitrogen-fixing enteric bacterium associated with the rhizosphere of wheat and maize. Can J Microbiol 1991; 37:195–203 [View Article]
     [Google Scholar]
  9. Martinez RJ, Bruce D, Detter C, Goodwin LA, Han J et al. Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil. J Bacteriol 2012; 194:2113–2114 [View Article] [PubMed]
     [Google Scholar]
  10. Chen F, Li J-Y, Guo Y-B, Wang J-H, Wang H-M. Biological control of grapevine crown gall: purification and partial characterisation of an antibacterial substance produced by Rahnella aquatilis strain HX2. Eur J Plant Pathol 2009; 124:427–437 [View Article]
     [Google Scholar]
  11. Doonan J, Denman S, Pachebat JA, McDonald JE. Genomic analysis of bacteria in the Acute Oak Decline pathobiome. Microb Genom 2019; 5:0–15 [View Article] [PubMed]
     [Google Scholar]
  12. Moradi‐Amirabad Y, Khodakaramian G. First report of bleeding canker caused by Rahnella sp. on Populus nigra in Iran. New Disease Rep 2020; 41: [View Article]
     [Google Scholar]
  13. Asselin JE, Eikemo H, Perminow J, Nordskog B, Brurberg MB et al. Rahnella spp. are commonly isolated from onion (Allium cepa) bulbs and are weakly pathogenic. J Appl Microbiol 2019; 127:812–824 [View Article] [PubMed]
     [Google Scholar]
  14. Martinez RJ, Wang Y, Raimondo MA, Coombs JM, Barkay T et al. Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Appl Environ Microbiol 2006; 72:3111–3118 [View Article] [PubMed]
     [Google Scholar]
  15. Niemann S, Pühler A, Tichy HV, Simon R, Selbitschka W. Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 1997; 82:477–484 [View Article] [PubMed]
     [Google Scholar]
  16. Brady C, Cleenwerck I, Venter S, Vancanneyt M, Swings J et al. Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA). Syst Appl Microbiol 2008; 31:447–460 [View Article] [PubMed]
     [Google Scholar]
  17. Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JR et al. Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 1999; 49 Pt 2:405–413 [View Article] [PubMed]
     [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic Acids Symposium Series 1999 pp 95–98
     [Google Scholar]
  19. Lefort V, Longueville J-. E, Gascuel O. SMS: Smart Model Selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [View Article] [PubMed]
     [Google Scholar]
  20. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [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. Versalovic J, Schneider M, de Bruijn F, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 1994; 5:25–40
     [Google Scholar]
  23. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  24. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A et al. Assembling genomes and mini-metagenomes from highly chimeric reads. In Lecture Notes in Computer Science 2013 pp 158–170 [View Article]
     [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. 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]
  28. Farris JS. Estimating phylogenetic trees from distance matrices. The American Naturalist 1972; 106:645–668 [View Article]
     [Google Scholar]
  29. 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]
  30. 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] [PubMed]
     [Google Scholar]
  31. De Maayer P, Pillay T, Coutinho TA. Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales. BMC Genomics 2020; 21:1–16 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005190
Loading
Rahnella perminowiae sp. nov., Rahnella bonaserana sp. nov., Rahnella rivi sp. nov. and Rahnella ecdela sp. nov., isolated from diverse environmental sources, and emended description of the genus Rahnella
Int J Syst Evol Microbiol 72, 005190 (2022); https://doi.org/10.1099/ijsem.0.005190
/content/journal/ijsem/10.1099/ijsem.0.005190
/content/journal/ijsem/10.1099/ijsem.0.005190
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