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Hyphomicrobium album sp. nov., isolated from mountain soil and emended description of genus Hyphomicrobium


A soil bacterium, designated XQ2T, was isolated from Lang Mountain in Hunan province, P. R. China. The strain is Gram stain negative, facultative anaerobic, and the cells are motile and rod-shaped. The 16S rRNA gene sequence of strain XQ2T shared the highest similarities with Hyphomicrobium sulfonivorans S1T (97.1%), Pedomicrobium manganicum ACM 3038T (95.9%) and Hyphomicrobium aestuarii DSM 1564T (95.4%) and grouped with H. sulfonivorans S1T. The average nucleotide identity (ANI) values and the DNA–DNA hybridization (dDDH) values between strain XQ2T and H. sulfonivorans S1T were 86.6% and 55.4% respectively. Strain XQ2T had a genome size of 3.91 Mb and the average G+C content was 65.1%. The major fatty acids (> 5%) were C18:1ω6c, C18:1ω7c, C19:0 cyclo ω8c, C16:0 and C18:0. The major respiratory quinone was Q-9 (82.8%) and the minor one was Q-8 (17.2%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and two unidentified lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain XQ2T represents a novel species of the genus Hyphomicrobium, for which the name Hyphomicrobium album sp. nov. is proposed. The type strain is XQ2T (= KCTC 82378T = CCTCC AB 2020178T). The genus description is also emended.

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  1. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  Google Scholar 

  2. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in Actinomycetes and Corynebacteria. J Gen Microbiol 100:22–230

    Article  Google Scholar 

  3. Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. Cambridge University Press, London

    Google Scholar 

  4. Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Scientific Press, Beijing

    Google Scholar 

  5. Fan H, Su C, Wang Y, Yao J, Zhao K et al (2008) Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 105:529–539

    Article  CAS  Google Scholar 

  6. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  7. Gebers R (1981) Enrichment, isolation, and emended description of Pedomicrobium ferrugineum Aristovskaya and Pedomicrobium manganicum Aristovskaya. Int J Syst Evol Microbiol 31:302–316

    Google Scholar 

  8. Gliesche CG, Fesefeldt A, Hirsch P (2005) Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey’s manual of systematic bacteriology. Williams and Wilkins, Baltimore, pp 476–494

    Chapter  Google Scholar 

  9. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  Google Scholar 

  10. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  Google Scholar 

  11. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  Google Scholar 

  12. Leifson E (1963) Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85:1183–1184

    Article  CAS  Google Scholar 

  13. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60

    Article  Google Scholar 

  14. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  15. Moore RL, Weiner RM, Gebers R (1984) Genus Hyphomonas Pongratz 1957 nom. rev. emend. Hyphomonas polymorpha Pongratz 1957 nom. rev. emend. and Hyphomonas neptunium (Leifson 1964) comb. nov. emend. (Hyphomicrobium neptunium). Int J Syst Evol Microbiol 34:71–73

    Google Scholar 

  16. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285

    Article  CAS  Google Scholar 

  17. Nei M, Kumar S (2013) Molecular evolution and phylogenetics. Heredity 86:385

    Google Scholar 

  18. Saitou NNM, Nei MC (1987) The neighbor-joining method-a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  19. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note, vol 101. MIDI Inc, Newark

    Google Scholar 

  20. Skerman VBD, McGowan V, Sneath PHA (1980) Approved list of bacterial names. Int J Syst Bacteriol 30:225–420

    Article  Google Scholar 

  21. Stutzer A, Hartleb R (1899) Untersuchungen über die bei der Bildung von Salpeter beobachteten Mikroorganismen. Mitteilungen Des Landwirtschaftlichen Institutes Der Kaiserlichen Universität Breslau 1:75–100

    Google Scholar 

  22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  Google Scholar 

  23. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    Article  CAS  Google Scholar 

  24. Urakami T, Komagata K (1987) Characterization and identification of methanol-utilizing Hyphomicrobium strains and a comparison with species of Hyphomonas and Rhodomicrobium. J Gen Appl Microbiol 33:521–542

    Article  CAS  Google Scholar 

  25. Vila J, Gene A, García C, Vidal C, Barranco M et al (1992) Rapid method for identifying Escherichia coli and species of the Proteeae tribe in urine. Med Clin 99:601–604

    CAS  Google Scholar 

  26. Wayne LG, Brenner DJ, Colwell RR et al (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  27. Xie CH, Yokota A (2003) Phylogenetic analyses of Lampropedia hyaline based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49:345–349

    Article  CAS  Google Scholar 

  28. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 110:1281–1286

    Article  CAS  Google Scholar 

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We are grateful to Professor Bernhard Schink for the Latin construction of the species name. Fatty acid and polar lipid analyses were performed by Guangdong Detection Centre of Microbiology, P. R. China.


The present study was supported National Natural Science Foundation of China (31670108).

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Correspondence to Gejiao Wang.

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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain XQ2T is MN647626. The genome number of strain XQ2T is NZ_WMBQ01000000, and the genome number of Hyphomicrobium sulfonivorans S1T is NZ_PZPO01000000.

Communicated by Erko Stackebrandt.

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Xu, Q., Zhang, Y., Wang, X. et al. Hyphomicrobium album sp. nov., isolated from mountain soil and emended description of genus Hyphomicrobium. Arch Microbiol 203, 5931–5936 (2021).

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  • Hyphomicrobium
  • Hyphomicrobium album
  • Phylogenetic analysis
  • Polyphasic analysis