1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 9

sp. nov. and sp. nov., isolated from abandoned lead–zinc mine Free

Abstract

Two novel strains, designated 92R-1 and 9PBR-1, were isolated from abandoned lead–zinc ore collected in Meizhou, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that they fell into the genus of r and formed two distinct lineages. Strain 92R-1 was most closely related to JCM 19491 (98.7 %) and LMG 21873 (98.5 %), while strain 9PBR-1 was most closely related to LMG 21951 (99.0 %), JCM 17223 (98.7 %) and JCM 31653 (98.1 %). Strain 92R-1shared average nucleotide identity values of 80.0–83.7 % and digital DNA–DNA hybridization values of 23.1–27.1 % with its closely related type strains, respectively, while strain 9PBR-1 shared corresponding values of 80.3–83.2 % and 23.6–26.7 % with its closely related type strains, respectively. The two novel strains could be clearly distinguished from their closely related type strains by enzyme activities and substrates assimilation, respectively. Both of them took iso-C summed feature 3 (C 7 and/or C 6), summed feature 4 (iso-C I and/or anteiso-C B) and C 5 as major fatty acids, and showed clear differences from their closely relatives in the contents of several components. They contained menaquinone 7 as the major respiratory quinone and phosphatidylethanolamine as the dominant polar lipid. The G+C contents of strains 92R-1 and 9PBR-1 were 56.7 and 59.5 mol%, respectively. The results clearly supported that strains 92R-1 and 9PBR-1 represent two distinct novel species within the genus , for which the names sp. nov. (type strain 92R-1=GDMCC 1.1493=JCM 32697) and sp. nov. (type strain 9PBR-1=GDMCC 1.1491=JCM 32698) are proposed.

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Keyword(s): abandoned lead–zinc ore , Hymenobacter fodinae , Hymenobacter metallicola and whole genome sequence
© 2020 The Authors
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2020-08-04
2024-04-18
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References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article][PubMed]
     [Google Scholar]
  2. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296 [View Article][PubMed]
     [Google Scholar]
  3. Klassen JL, Foght JM. Differences in carotenoid composition among Hymenobacter and related strains support a tree-like model of carotenoid evolution. Appl Environ Microbiol 2008; 74:2016–2022 [View Article][PubMed]
     [Google Scholar]
  4. Kang H, Kim H, Joung Y, Kim K-J, Joh K. Hymenobacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2016; 66:2212–2217 [View Article][PubMed]
     [Google Scholar]
  5. Liang Y, Tang K, Wang Y, Yuan B, Tan F et al. Hymenobacter crusticola sp. nov., isolated from biological soil crust. Int J Syst Evol Microbiol 2019; 69:547–551 [View Article][PubMed]
     [Google Scholar]
  6. Chen H, Han L, Feng Q, Fan Q, Lv J. Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment. Int J Syst Evol Microbiol 2018; 68:2749–2754 [View Article][PubMed]
     [Google Scholar]
  7. Zhang Q, Liu C, Tang Y, Zhou G, Shen P et al. Hymenobacter xinjiangensis sp. nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2007; 57:1752–1756 [View Article][PubMed]
     [Google Scholar]
  8. Liu K, Liu Y, Wang N, Gu Z, Shen L et al. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793–3798 [View Article][PubMed]
     [Google Scholar]
  9. Chen W-M, Chen W-T, Young C-C, Sheu S-Y. Hymenobacter gummosus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2017; 67:4728–4735 [View Article][PubMed]
     [Google Scholar]
  10. Hoang V-A, Kim Y-J, Nguyen NL, Yang D-C. Hymenobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2013; 63:661–666 [View Article][PubMed]
     [Google Scholar]
  11. Zou WL, Feng GD, HP L, Zhu HH. Diversity analyses of culturable bacteria in abandoned lead-zinc ore and tungsten sands. Current Biotechnology 2018; 8:450–458
     [Google Scholar]
  12. Feng G-D, Wang Y-H, Zhang X-J, Chen W-D, Zhang J et al. Sphingomonas lenta sp. nov., a slowly growing bacterium isolated from an abandoned lead-zinc mine. Int J Syst Evol Microbiol 2019; 69:2214–2219 [View Article][PubMed]
     [Google Scholar]
  13. Feng G-D, Zhang J, Zhang X-J, Wang S-N, Xiong X et al. Hymenobacter metallilatus sp. nov., isolated from abandoned lead-zinc ore. Int J Syst Evol Microbiol 2019; 69:2142–2146 [View Article][PubMed]
     [Google Scholar]
  14. Feng GD, Yang SZ, Wang YH, Zhao GZ, Deng MR et al. Sphingomonas gimensis sp. nov., a novel Gram-negative bacterium isolated from abandoned lead-zinc ore mine. Antonie van Leeuwenhoek 2014; 105:1091–1097 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. 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]
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  21. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687 [View Article][PubMed]
     [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Göker 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]
  26. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  29. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
     [Google Scholar]
  30. Richter M, Rosselló-Móra 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]
  31. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article][PubMed]
     [Google Scholar]
  32. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1861–1868 [View Article][PubMed]
     [Google Scholar]
  33. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp 330–393
     [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  35. 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]
  36. Collins MD. Isoprenoidquinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Johb Wiley & Sons Ltd; 1994 pp 265–309
     [Google Scholar]
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Hymenobacter fodinae sp. nov. and Hymenobacter metallicola sp. nov., isolated from abandoned lead–zinc mine
Int J Syst Evol Microbiol 70, 4867 (2020); https://doi.org/10.1099/ijsem.0.004313
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