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Volume 68, Issue 4

sp. nov., an atypical, non-infective (Nod–) and non-nitrogen fixing (Fix–) actinobacterium isolated from root nodules Free

Abstract

Strain CN3, a isolate, appears to form hyphae and sporangia typical of members fo the genus . However, it failed to form vesicles, to reduce acetylene and to induce nodules on its original host plant. A polyphasic approach was used here to determine the taxonomic status of strain CN3. The 16S rRNA gene sequence of strain CN3 showed the highest sequence identity with type strain M16386 (99.4 %). Digital DNA–DNA hybridization between strains CN3 and M16386 was 25.7 %, which is clearly below the accepted cut-off point of 70 %. The G+C content of DNA was 71.8 mol%. Whole-cell hydrolysates of strain CN3 were rich in -diaminopimelic acid. Cell-wall sugars were composed of galactose, glucose, mannose, rhamnose and traces of ribose. The polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipids, phospholipid, six uncharacterized glycolipids and two uncharacterized lipids. The predominant menaquinone (>25 %) was MK-9(H). Major fatty acids (>15 %) of strain CN3 consisted of iso-C, Cω8 and C. Based on 16S rRNA gene phylogeny, genome sequence analysis and phenotypic results, strain CN3 (=DSM 105290=CECT 9314) is proposed to represent the type strain of a novel species, sp. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): actinobacteria , actinorhizas , polyphasic taxonomy and symbiosis
© 2018 IUMS
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2018-04-01
2024-04-24
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References

  1. Lechevalier MP. Taxonomy of the genus Frankia (Actinomycetales) . Int J Syst Bacteriol 1994; 44:1–8 [View Article]
     [Google Scholar]
  2. Gtari M, Tisa LS, Normand P. Diversity of Frankia strains, actinobacterial symbionts of actinorhizal plants. In Aroca R. (editor) Symbiotic Endophytes Berlin, Heidelberg: Springer-Verlag; 2013 pp. 123–148 [Crossref]
     [Google Scholar]
  3. Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz MD, Göker M, Meier-Kolthoff JP et al. Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Int J Syst Evol Microbiol 2016; 66:5201–5210 [View Article][PubMed]
     [Google Scholar]
  4. Nouioui I, Ghodhbane-Gtari F, Rohde M, Klenk HP, Gtari M. Frankia coriariae sp. nov., an infective and effective microsymbiont isolated from Coriaria japonica . Int J Syst Evol Microbiol 2017; 67:1266–1270 [View Article][PubMed]
     [Google Scholar]
  5. Nouioui I, del Carmen Montero-Calasanz M, Ghodhbane-Gtari F, Rohde M, Tisa LS et al. Frankia discariae sp. nov.: an infective and effective microsymbiont isolated from the root nodule of Discaria trinervis . Arch Microbiol 2017; 199:641–647 [View Article][PubMed]
     [Google Scholar]
  6. Baker D, Newcomb W, Torrey JG. Characterization of an ineffective actinorhizal microsymbiont, Frankia sp. EuI1 (Actinomycetales). Can J Microbiol 1980; 26:1072–1089 [View Article][PubMed]
     [Google Scholar]
  7. Hahn D, Starrenburg MJC, Akkermans ADL. Variable compatibility of cloned Alnus glutinosa ecotypes against ineffective Frankia strains. Plant Soil 1988; 107:233–243 [View Article]
     [Google Scholar]
  8. Ramírez-Saad H, Janse JD, Akkermans ADL. Root nodules of Ceanothus caeruleus contain both the N2-fixing Frankia endophyte and a phylogetically related Nod-/Fix- actinomycete. Can J Microbiol 1998; 44:140–148 [Crossref]
     [Google Scholar]
  9. Mirza MS, Hahn D, Akkermans ADL. Isolation and characterization of Frankia strains from Coriaria nepaknsis. Syst Appl Microbiol 1992; 15:289–295 [View Article]
     [Google Scholar]
  10. Mirza MS, Janse JD, Hahn D, Akkermans ADL. Identification of atypical Frankia strains by fatty acid analysis. FEMS Microbiol Lett 1991; 83:91–98 [View Article]
     [Google Scholar]
  11. Nouioui I, Ghodhbane-Gtari F, del Carmen Montero-Calasanz M, Rohde M, Tisa LS et al. Frankia inefficax sp. nov., an actinobacterial endophyte inducing ineffective, non nitrogen-fixing, root nodules on its actinorhizal host plants. Antonie van Leeuwenhoek 2017; 110:313–320 [View Article][PubMed]
     [Google Scholar]
  12. Nouioui I, Gueddou A, Ghodhbane-Gtari F, Rhode M, Gtari M et al. Frankia asymbiotica sp. nov., a non-infective actinobacterium isolated from Morella californica root nodule. Int J Syst Evol Microbiol 2017; 67:4897–4901 [View Article][PubMed]
     [Google Scholar]
  13. Mirza MS, Hameed S, Akkermans AD. Genetic diversity of Datisca cannabina-compatible Frankia strains as determined by sequence analysis of the PCR-amplified 16S rRNA gene. Appl Environ Microbiol 1994; 60:2371–2376[PubMed]
     [Google Scholar]
  14. Murry MA, Fontaine MS, Torrey JG. Growth kinetics and nitrogenase induction in Frankia sp. HFPArI 3 grown in batch culture. Plant Soil 1984; 78:61–78 [View Article]
     [Google Scholar]
  15. Vaas LA, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012; 7:e34846 [View Article][PubMed]
     [Google Scholar]
  16. Broughton WJ, Dilworth MJ. Control of leghaemoglobin synthesis in snake beans. Biochem J 1971; 125:1075–1080 [View Article][PubMed]
     [Google Scholar]
  17. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  18. Lechavalier MP A, Lechevalier H. Composition of whole-cell hydrolysates as a criterion in the classification of aerobic actinomycetes. In Prauser H. (editor) The Actinomycetales Jena: Gustav Fischer Verlag; 1970 pp. 311–316
     [Google Scholar]
  19. Collins MD. Analysis of isoprenoid quinones. Meth Microbiol 1985; 18:329–366 [Crossref]
     [Google Scholar]
  20. 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]
  21. 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[PubMed]
     [Google Scholar]
  22. 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]
  23. Sasser MJ. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101, Microbial ID. Newark, DE: MIDI, Inc.; 1990
     [Google Scholar]
  24. Nouioui I, Ghodhbane-Gtari F, Beauchemin NJ, Tisa LS, Gtari M. Phylogeny of members of the Frankia genus based on gyrB, nifH and glnII sequences. Antonie van Leeuwenhoek 2011; 100:579–587 [View Article][PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
     [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, 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. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article][PubMed]
     [Google Scholar]
  28. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  29. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
     [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  31. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 Sunderland: Sinauer Associates; 2002
     [Google Scholar]
  32. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
     [Google Scholar]
  33. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
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Frankia saprophytica sp. nov., an atypical, non-infective (Nod–) and non-nitrogen fixing (Fix–) actinobacterium isolated from Coriaria nepalensis root nodules
Int J Syst Evol Microbiol 68, 1090 (2018); https://doi.org/10.1099/ijsem.0.002633
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