sp. nov., isolated from charcoal No Access

Abstract

A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of and (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci , and and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4 and the type strains of and yielded average nucleotide identity values <95 % and DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C, summed feature 3 (Cω7 and/or Cω6) and summed feature 8 (Cω7 and/or C ω6). In addition, physiological and biochemical tests revealed a clear phenotypic difference from . These cumulative data indicate that the isolate represents a novel species of the genus for which the name sp. nov. is proposed with Wesi-4 (=DSM 110367=CIP 111764=CCM 9017) as the type strain.

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2021-04-09
2024-03-28
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References

  1. Migula W. Über ein neues System der Bakterien. Arbeiten aus dem Bakteriologischen Institut der Technischen Hochschule zu Karlsruhe 1894; 1:235–238
    [Google Scholar]
  2. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
    [Google Scholar]
  3. DeVos P, DeLey J. Intra- and intergeneric similarities of Pseudomonas and Xanthomonas ribosomal ribonucleic acid cistrons. Int J Syst Bacteriol 1983; 33:487–509 [View Article]
    [Google Scholar]
  4. Palleroni NJ. Genus I. Pseudomonas Migula 1984, 237AL. In Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology 1 Baltimore: Williams & Wilkins; pp 141–199
    [Google Scholar]
  5. Woese CR, Blanz P, Hahn CM. What isn't a pseudomonad: the importance of nomenclature in bacterial classification. Syst Appl Microbiol 1984; 5:179–195 [View Article]
    [Google Scholar]
  6. Oyaizu H, Komagata K. Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J Gen Appl Microbiol 1983; 29:17–40 [View Article]
    [Google Scholar]
  7. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  8. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  9. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  10. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
    [Google Scholar]
  11. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  12. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  13. Jukes TH, Cantor CR. Evolution of the protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  14. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author Seattle: Department of Genome Sciences, University of Washington; 2005
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  16. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 1978; 75:4801–4805 [View Article][PubMed]
    [Google Scholar]
  17. Criscuolo A, Brisse S. AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics 2013; 102:500–506 [View Article][PubMed]
    [Google Scholar]
  18. Liu Y, Schröder J, Schmidt B. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 2013; 29:308–315 [View Article][PubMed]
    [Google Scholar]
  19. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  20. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018; 34:3094–3100 [View Article][PubMed]
    [Google Scholar]
  21. Lindner MS, Kollock M, Zickmann F, Renard BY. Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinformatics 2013; 29:1260–1267 [View Article][PubMed]
    [Google Scholar]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  23. Anurat P, Duangmal K, Srisuk N. Pseudomonas mangiferae sp. nov., isolated from bark of mango tree in Thailand. Int J Syst Evol Microbiol 2019; 69:3537–3543 [View Article][PubMed]
    [Google Scholar]
  24. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
    [Google Scholar]
  25. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article][PubMed]
    [Google Scholar]
  26. Criscuolo A. A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. Research Ideas and Outcomes 2019; 5:e36178 [View Article]
    [Google Scholar]
  27. Criscuolo A. On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Res 2020; 9:1309 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. 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]
  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. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  32. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21:227–251 [View Article][PubMed]
    [Google Scholar]
  33. Kämpfer P. Evaluation of the Titertek-Enterobac-Automated system (TTE-AS) for identification of members of the family Enterobacteriaceae . Zentralbl Bakteriol 1990; 273:164–172 [View Article][PubMed]
    [Google Scholar]
  34. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  35. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  36. 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]
  37. Altenburgera P, Kämpferb P, Makristathisc A, Lubitza W, Bussea H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
    [Google Scholar]
  38. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
    [Google Scholar]
  39. Ikemoto S, Kuraishi H, Komagata K, Azuma R, Suto T et al. Cellular fatty acid composition in Pseudomonas species. J Gen Appl Microbiol 1978; 24:199–213 [View Article]
    [Google Scholar]
  40. Mulet M, Gomila M, Ramírez A, Lalucat J, Garcia-Valdes E. Pseudomonas nosocomialis sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 2019; 69:3392–3398 [View Article][PubMed]
    [Google Scholar]
  41. Behera P, Mahapatra M, Seuylemezian A, Vaishampayan P, Ramana VV et al. Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka . J Microbiol 2018; 56:458–466 [View Article][PubMed]
    [Google Scholar]
  42. Lin S-Y, Hameed A, Hung M-H, Liu Y-C, Hsu Y-H et al. Pseudomonas matsuisoli sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2015; 65:902–909 [View Article][PubMed]
    [Google Scholar]
  43. Zou Y, He S, Sun Y, Zhang X, Liu Y et al. Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia . Int J Syst Evol Microbiol 2019; 69:1760–1766 [View Article][PubMed]
    [Google Scholar]
  44. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [View Article]
    [Google Scholar]
  45. Auling G, Busse H-J, Pilz F, Webb L, Kneifel H et al. Rapid differentiation, by polyamine analysis, of Xanthomonas strains from phytopathogenic pseudomonads and other members of the class Proteobacteria interacting with plants. Int J Syst Bacteriol 1991; 41:223–228 [View Article]
    [Google Scholar]
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