1887

Abstract

Three rod-shaped, non-spore-forming, yellow or pale-yellow pigmented bacteria with distinct MALDI-TOF mass spectra were isolated from the phyllosphere of seedlings. Their 16S rRNA gene sequences demonstrated that these isolates belong to the genus . The nearest phylogenetic neighbours of strain LMG 31462 were DSM 19110 (98.3 % 16S rRNA sequence similarity) and LMG 22862 (98.3 %); the nearest phylogenetic neighbours of strain LMG 31463 were Gsoil 042 (98.3 %) and DSM 27372 (98.1 %); and the nearest phylogenetic neighbours of strain LMG 31464 were BR-9 (99.0 %) and THG-DN3.18 (98.7 %). Average nucleotide identity analyses between the whole genome sequences of the three strains and of the type strains of their respective nearest-neighbour taxa yielded values well below the species delineation threshold and thus confirmed that the three strains represented a novel species each. An extensive phenotypic comparison and an analysis of whole-cell fatty acid components yielded distinctive phenotypic characteristics for each of these strains. We therefore propose to classify these isolates as three novel species, for which we propose the names with LMG 31462 (=R-74704=CECT 30149) as the type strain, with LMG 31463 (=R-74623=CECT 30150) as the type strain and with LMG 31464 (=R-74626=CECT 30151) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004667
2021-01-27
2021-03-02
Loading full text...

Full text loading...

References

  1. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48: 165 177 [CrossRef] [PubMed]
    [Google Scholar]
  2. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66: 2205 2211 [CrossRef] [PubMed]
    [Google Scholar]
  3. Singh H, Du J, Ngo HTT, Won KH, Kim K-Y et al. Pedobacter edaphicus sp. nov. isolated from forest soil in South Korea. Arch Microbiol 2015; 197: 781 787 [CrossRef] [PubMed]
    [Google Scholar]
  4. Gao J-L, Sun P, Mao X-J, Du Y-L, Liu B-Y et al. Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2017; 67: 231 236 [CrossRef] [PubMed]
    [Google Scholar]
  5. Crawford DL, Lynch JM, Whipps JM, Ousley MA. Isolation and characterization of actinomycete antagonists of a fungal root pathogen. Appl Environ Microbiol 1993; 59: 3899 3905 [CrossRef] [PubMed]
    [Google Scholar]
  6. Murashige T, Skoog F. A revised medium for rapid growth and BIO assays with tobacco tissue cultures. Physiol Plant 1962; 15: 473 497 [CrossRef]
    [Google Scholar]
  7. Dumolin C, Aerts M, Verheyde B, Schellaert S, Vandamme T et al. Introducing SPeDE: high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data. mSystems 2019; 4: e00437-19 10 09 2019 [CrossRef] [PubMed]
    [Google Scholar]
  8. Niemann S, Pu A, 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. 1997 477 484
  9. 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 [CrossRef] [PubMed]
    [Google Scholar]
  10. Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2018; 34: 2490 2492 [CrossRef] [PubMed]
    [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870 1874 [CrossRef] [PubMed]
    [Google Scholar]
  12. Guindon S, Delsuc F, Dufayard J-F, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 2009; 537: 113 137 [CrossRef] [PubMed]
    [Google Scholar]
  13. Lefort V, Longueville J-E, Gascuel O. Sms: smart model selection in PhyML. Mol Biol Evol 2017; 34: 2422 2424 [CrossRef] [PubMed]
    [Google Scholar]
  14. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30: 2114 2120 [CrossRef] [PubMed]
    [Google Scholar]
  15. Souvorov A, Agarwala R, Lipman DJ. Software open access SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 2018; 19: 153
    [Google Scholar]
  16. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29: 1072 1075 [CrossRef] [PubMed]
    [Google Scholar]
  17. Dumolin C, Peeters C, Ehsani E, Tahon G, De Canck E et al. Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production. Int J Syst Evol Microbiol 2019
    [Google Scholar]
  18. Vandamme P, Vancanneyt M, Pot B, Mels L, Hoste B et al. Polyphasic taxonomic study of the emended genus Arcobacter with Arcobacter butzleri comb. nov. and Arcobacter skirrowii sp. nov., an aerotolerant bacterium isolated from veterinary specimens. Int J Syst Bacteriol 1992; 42: 344 356 [CrossRef] [PubMed]
    [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111 120 [CrossRef] [PubMed]
    [Google Scholar]
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35: 1547 1549 [CrossRef] [PubMed]
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783 791 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004667
Loading
/content/journal/ijsem/10.1099/ijsem.0.004667
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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