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Abstract

A Gram-stain-positive, rod-shaped, aerobic, non-motile, non-sporulating bacterial strain, designated CSA1, was isolated from chromium-containing soil sampled at a chemical plant. Growth of strain CSA1 occurred at pH 6–10 (optimum, pH 7), 15–45 °C (optimum, 30 °C) and in the presence of 0.5–6.5 % (w/v) NaCl (optimum, 2 %). The 16S rRNA gene sequence of strain CSA1 revealed the highest similarity to A2 (97.5 %), K 70/01 (97.3 %), Re6 (96.6 %), F3-P9 (96.2 %), CC-MF41 (96.1 %) and S27 (96.0 %). The draft genome of CSA1 was approximately 3 350 931 bp in size with a G+C content of 70.6 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values among strain CSA1 and the selected species were 74.0–79.2 % (ANIb), 84.3–87.1 % (ANIm) and 21.5–25.4 % (dDDH), which are below the recommended cutoff values for species delineation. The major fatty acids were anteiso-C, iso-C and anteiso-C. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The predominant menaquinones were MK-11, MK-8 and MK-6. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. From the phenotypic, chemotaxonomic and molecular features, strain CSA1 was considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CSA1 (=JCM 34359=CGMCC 1.18746).

Funding
This study was supported by the:
  • Key Research and Development Program of Jiangxi Province (Award 2020YFS0287)
    • Principle Award Recipient: YongqiangTian
  • National Key Research and Development Program of China (Award 2018YFC1802201)
    • Principle Award Recipient: YongqiangTian
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2021-07-28
2022-01-21
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References

  1. Takeuchi M, Weiss N, Schumann P, Yokota A. Leucobacter komagatae gen. nov., sp. nov., a new aerobic Gram-positive, nonsporulating rod with 2,4-diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:967–971 [View Article] [PubMed]
    [Google Scholar]
  2. Parte AC. LPSN-List of Prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  3. Behrendt U, Ulrich A, Schumann P. Leucobacter tardus sp. nov., isolated from the phyllosphere of Solanum tuberosum L. Int J Syst Evol Microbiol 2008; 58:2574–2578 [View Article] [PubMed]
    [Google Scholar]
  4. Schumann P, Pukall R. Leucobacter weissii sp. nov., an isolate from activated sludge once described as first representative of the peptidoglycan variation B2delta, and emended description of the genus Leucobacter. Int J Syst Evol Microbiol 2017; 67:5244–5251 [View Article] [PubMed]
    [Google Scholar]
  5. Chun BH, Lee HJ, Jeong SE, Schumann P, Jeon CO. Leucobacter ruminantium sp. nov., isolated from the bovine rumen. Int J Syst Evol Microbiol 2017; 67:2634–2639 [View Article] [PubMed]
    [Google Scholar]
  6. Benga L, Sproer C, Schumann P, Verbarg S, Bunk B. Leucobacter muris sp. nov., isolated from the nose of a laboratory mouse. Int J Syst Evol Microbiol 2019; 69:2095–2100 [View Article] [PubMed]
    [Google Scholar]
  7. Li Y, Fang W, Xie SJ, Yang X, Wang LF. Leucobacter corticis sp. nov., isolated from symptomatic bark of Populus x euramericana canker. Int J Syst Evol Microbiol 2017; 67:2248–2252 [View Article] [PubMed]
    [Google Scholar]
  8. Sun L-N, Pan D-D, Wu X-W, Yang E-D, Hua R-M et al. Leucobacter triazinivorans sp. nov., a s-triazine herbicide prometryn-degrading bacterium isolated from sludge. Int J Syst Evol Microbiol 2018; 68:204–210 [View Article] [PubMed]
    [Google Scholar]
  9. Martin E, Lodders N, Jackel U, Schumann P, Kampfer P. Leucobacter aerolatus sp. nov., from the air of a duck barn. Int J Syst Evol Microbiol 2010; 60:2838–2842 [View Article] [PubMed]
    [Google Scholar]
  10. Yun JH, Roh SW, Kim MS, Jung MJ, Park EJ et al. Leucobacter salsicius sp. nov., from a salt-fermented food. Int J Syst Evol Microbiol 2011; 61:502–506 [View Article] [PubMed]
    [Google Scholar]
  11. Kim HJ, Lee SS. Leucobacter kyeonggiensis sp. nov., a new species isolated from dye waste water. J Microbiol 2011; 49:1044–1049 [View Article]
    [Google Scholar]
  12. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article] [PubMed]
    [Google Scholar]
  13. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. 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]
  16. Sudhir K, Glen S, Michael L, Christina K, Koichiro T et al. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 6:
    [Google Scholar]
  17. Saitou NNM, Nei MC. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: Minimum change for a specific tree topology. Systematic Biology 1971; 20:406–416 [View Article]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  20. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  21. Li R, Zhu HM, Ruan J, Qian WB, Fang XD et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2009; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  22. Lin SH, Liao YC. CISA: Contig integrator for sequence assembly of bacterial genomes. PLoS One 2013; 8:e60843 [View Article]
    [Google Scholar]
  23. Meier-Kolthoff JP, Gker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  24. Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  27. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  28. Overbeek R, Olson R, Pusch GD, Olsen GJ, Stevens R et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST. Nucleic Acids Res 2013; 42:
    [Google Scholar]
  29. Muir RE, Tan MW. Leucobacter chromiireducens subsp. solipictus subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis elegans, and emended description of L. chromiireducens. Int J Syst Evol Microbiol 2007; 57:2770–2776 [View Article] [PubMed]
    [Google Scholar]
  30. Morais PV, Francisco R, Branco R, Chung AP, da Costa MS. Leucobacter chromiireducens sp. nov, and Leucobacter aridicollis sp. nov., two new species isolated from a chromium contaminated environment. Syst Appl Microbiol 2004; 27:646–652 [View Article] [PubMed]
    [Google Scholar]
  31. Joutey NT, Bahafid W, Sayel H, Nassef S, Ghachtouli NE. Leucobacter chromiireducens CRB2, a new strain with high Cr(VI) reduction potential isolated from tannery-contaminated soil (Fez, Morocco. Ann Microbiol 2016; 66:425–436 [View Article]
    [Google Scholar]
  32. Sturm G, Jacobs J, Spröer C, Schumann P, Gescher J. Leucobacter chromiiresistens sp. nov., a chromate-resistant strain. Int J Syst Evol Microbiol 2011; 61:956–960 [View Article] [PubMed]
    [Google Scholar]
  33. Philipp G, Murray RGE, Wood W, Krieg N. Methods for General and Molecular Bacteriology American Society for Microbiology; 1994
    [Google Scholar]
  34. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article] [PubMed]
    [Google Scholar]
  35. Li X, Gan L, Hu M, Wang S, Tian Y et al. Halomonas pellis sp. nov., a moderately halophilic bacterium isolated from wetsalted hides. Int J Syst Evol Microbiol 2020; 70:5417–5424 [View Article] [PubMed]
    [Google Scholar]
  36. Mata JA, Martinez-Canovas J, Quesada E, Bejar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 2002; 25:360–375 [View Article] [PubMed]
    [Google Scholar]
  37. Somvanshi VS, Lang E, Schumann P, Pukall R, Kroppenstedt RM et al. Leucobacter iarius sp. nov., in the family Microbacteriaceae. Int J Syst Evol Microbiol 2007; 57:682–686 [View Article] [PubMed]
    [Google Scholar]
  38. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 2011; 42:989–1005
    [Google Scholar]
  39. Xiang W, Liu C, Wang X, Du J, Xi L et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa. Int J Syst Evol Microbiol 2011; 61:1165–1169 [View Article] [PubMed]
    [Google Scholar]
  40. 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
    [Google Scholar]
  41. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  42. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  43. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
    [Google Scholar]
  44. Muir RE, Tan MW. Leucobacter chromiireducens subsp. solipictus subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis elegans, and emended description of L. chromiireducens. Int J Syst Evol Microbiol 2007; 57:2770–2776 [View Article] [PubMed]
    [Google Scholar]
  45. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
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