1887

Abstract

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29k, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5–0.7×1.7–3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C ω7, C cyclo and C. The genomic DNA G+C content was 67.95 mol%. Strain 29k was able to grow at 4–37 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 6.5–7.0) and at salinities of 0–0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29k could grow chemolithoautotrophically in mineral media under an atmosphere of H, O and CO as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus with 7c (99.9% similarity) and 7d (99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA–DNA hybridization values of 92.7 and 44.9%, respectively, of the 29k to the genome of the most closely related species, 7c, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, sp. nov. The type strain is 29k (=KCTC 72777=VKM B-3453).

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2021-08-19
2024-02-28
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References

  1. Baumgarten J, Reh M, Schlegel HG. Taxonomic studies on some Gram-positive coryneform hydrogen bacteria. Arch Microbiol 1974; 100:207–217 [View Article]
    [Google Scholar]
  2. Wiegel J, Wilke D, Baumgarten J, Opitz R, Schlegel HG. Transfer of the nitrogen-fixing hydrogen bacterium Corynebacterium autotrophicum Baumgarten et al. to Xanthobacter gen. nov. Int J Syst Bacteriol 1978; 28:573–581 [View Article]
    [Google Scholar]
  3. Malik KA, Claus D. Xanthobacter flavus, a new species of nitrogen-fixing hydrogen bacteria. Int J Syst Bacteriol 1979; 29:283–287 [View Article]
    [Google Scholar]
  4. Jenni B, Aragno M. Xanthobacter agilis sp. nov., a motile, dinitrogen-fixing, hydrogen-oxidizing bacterium. Syst Appl Microbiol 1987; 9:254–257
    [Google Scholar]
  5. Padden AN, Rainey FA, Kelly DP, Wood AP. Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. Int J Syst Bacteriol 1997; 47:394–401 [View Article] [PubMed]
    [Google Scholar]
  6. Doronina NV, Trotsenko YA. Reclassification of “Blastobacter viscosus” 7d and “Blastobacter aminooxidans” 14a as Xanthobacter viscosus sp. Int J Syst Evol Microbiol 2003; 53:179–182 [View Article] [PubMed]
    [Google Scholar]
  7. Doronina NV, Braus-Strohmeyer SA, Leisinger T, Trotsenko YA. Isolation and characterization of a new facultatively methylotrophic bacterium: description of Methylorhabdus multivorans gen. nov., sp. nov. Syst Appl Microbiol 1995; 18:92–98
    [Google Scholar]
  8. Hirano S, Kitauchi F, Haruki M, Imanaka T, Morikawa M et al. Isolation and characterization of Xanthobacter polyaromaticivorans sp. nov. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions. Biosci Biotechnol Biochem 2004; 68:557–564 [View Article] [PubMed]
    [Google Scholar]
  9. Spiess E, Sommer C, Görisch H. Degradation of 1,4-dichlorobenzene by Xanthobacter flavus 14p1. Appl Environ Microbiol 1995; 61:3884–3888 [View Article] [PubMed]
    [Google Scholar]
  10. Meijer WG, Croes LM, Jenni B, Lehmicke LG, Lidstrom ME et al. Characterization of Xanthobacter strains H4-14 and 25a and enzyme profiles after growth under autotrophic and heterotrophic conditions. Arch Microbiol 1990; 153:360–367 [View Article] [PubMed]
    [Google Scholar]
  11. Reding KH, Hartel PG, Wiegel J. Effect of Xanthobacter isolated and characterized from rice roots, on growth on wetland rice. Plant and Soil 1991; 138:221–229
    [Google Scholar]
  12. Wilson K. Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology John Wiley & Sons; 2001
    [Google Scholar]
  13. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, M Goodfellow. eds In Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley& Sons; 1991 pp 115–175
    [Google Scholar]
  14. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  15. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
    [Google Scholar]
  16. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  17. Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2017; 35:518–522
    [Google Scholar]
  18. Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A et al. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC EvolBiol 2018; 18:11 [View Article]
    [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2016; 33:1870–1874
    [Google Scholar]
  20. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y. 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]
  21. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  22. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M. 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]
  24. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S et al. Prokaryotic Genome Annotation Pipeline. The NCBI handbook, 2nd ed. Bethesda, MD: National Center for Biotechnology Information; 2013
    [Google Scholar]
  25. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  27. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020; 36:1925–1927
    [Google Scholar]
  28. Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol Biol 2018; 18:11 [View Article] [PubMed]
    [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. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  31. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J. blast+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Whittenbury R, Phillips KC, Wilkinson JF. Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 1970; 61:205–218 [View Article] [PubMed]
    [Google Scholar]
  34. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296 [View Article] [PubMed]
    [Google Scholar]
  35. Slobodkina GB, Panteleeva AN, Kostrikina NA, Kopitsyn DS, Bonch-Osmolovskaya EA. Tepidibacillus fermentans gen. nov., sp. nov.: a moderately thermophilic anaerobic and microaerophilic bacterium from an underground gas storage. Extremophiles 2013; 17:833–839 [View Article] [PubMed]
    [Google Scholar]
  36. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
    [Google Scholar]
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