1887

Abstract

A Gram-stain-negative strain, designated GT1R17, was isolated from an ervoconite sample collected from Gawalong glacier in the Tibet Autonomous Region, PR China. Strain GT1R17 was catalase- and oxidase-positive, and grew optimally at 20–25°C and pH 7.0. The highest level of 16S rRNA gene sequence similarities were found to members of the genera Nevskia (92.27–93.15 %) and Hydrocarboniphaga (91.92–92.96 %). Phylogenetic analyses based on 16S rRNA gene sequences and genomic data revealed that the strain GT1R17 belonged to the family Nevskiaceae , but could not be assigned to any known genera. The genomic DNA G+C content was 54.4 mol%. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1  ω7c and/or C18 : 1ω6c), C16 : 0, iso-C16 : 0 and summed feature 2 (C14 : 0 3OH and/or iso-C16 : 1 I). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified lipid. The ubiquinone was Q-8. On the basis of the phenotypic, chemotaxonomic, genotypic and phylogenetic data, a novel species of a new genus,Stenotrophobiumrhamnosiphilum gen. nov., sp. nov. within the family Nevskiaceae , is proposed, with GT1R17 (=CGMCC 1.16137=NBRC 113346) as the type strain. In addition, phylogenetic analyses revealed that Steroidobacter and Povalibacter formed an independent clade in the order Nevskiales and were away from the families Nevskiaceae , Algiphilaceae and Salinisphaeraceae . Therefore, we propose to remove Steroidobacter and Povalibacter from the family Nevskiaceae and propose a new family Steroidobacteraceae in the order Nevskiales .

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2019-03-01
2019-09-22
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References

  1. Henrici AT, Johnson DE. Studies of freshwater bacteria: II. stalked bacteria, a new order of schizomycetes. J Bacteriol 1935;30:61–93[PubMed]
    [Google Scholar]
  2. Skerman VBD, Sneath PHA, Mcgowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980;30:225–420 [CrossRef]
    [Google Scholar]
  3. Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE et al. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2015;107:467–485 [CrossRef][PubMed]
    [Google Scholar]
  4. Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ER et al. Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008. Int J Syst Evol Microbiol 2013;63:254–259 [CrossRef][PubMed]
    [Google Scholar]
  5. Tindall BJ. The family name Solimonadaceae Losey et al. 2013 is illegitimate, proposals to create the names 'Sinobacter soli' comb. nov. and 'Sinobacter variicoloris' contravene the Code, the family name Xanthomonadaceae Saddler and Bradbury 2005 and the order name Xanthomonadales Saddler and Bradbury 2005 are illegitimate and notes on the application of the family names Solibacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and order name Lysobacteriales Christensen and Cook 1978 (Approved Lists 1980) with respect to the classification of the corresponding type genera Solibacter Zhou et al. 2008, Nevskia Famintzin 1892 (Approved Lists 1980) and Lysobacter Christensen and Cook 1978 (Approved Lists 1980) and importance of accurately expressing the link between a taxonomic name, its authors and the corresponding description/circumscription/emendation. Int J Syst Evol Microbiol 2014;64:293–297 [CrossRef][PubMed]
    [Google Scholar]
  6. Whitman WB, Lawson PA, Losey NA. Response to tindall (2014) on the legitimacy of the names Solimonadaceae Losey et al. 2013, xanthomonadaceae saddler and bradbury 2005 and xanthomonadales saddler and bradbury 2005. Int J Syst Evol Microbiol 2015;65:1086–1087 [CrossRef][PubMed]
    [Google Scholar]
  7. Parker CT, Tindall BJ, Garrity GM. International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 2019;69:S1–S111 [CrossRef][PubMed]
    [Google Scholar]
  8. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991
    [Google Scholar]
  10. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  11. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  12. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  13. Yoon SH, Ha SM, 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 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:280–285
    [Google Scholar]
  16. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30:772–780 [CrossRef][PubMed]
    [Google Scholar]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25:1043–1055 [CrossRef][PubMed]
    [Google Scholar]
  19. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614–6624 [CrossRef][PubMed]
    [Google Scholar]
  20. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice. Int J Syst Evol Microbiol 2015;65:2955–2959 [CrossRef][PubMed]
    [Google Scholar]
  21. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  22. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977;27:104–117 [CrossRef]
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  24. Li G, Lai Q, Liu X, Sun F, Du Y et al. Maricoccus atlantica gen. nov. sp. nov., isolated from deep sea sediment of the Atlantic Ocean. Antonie van Leeuwenhoek 2013;104:1073–1081 [CrossRef][PubMed]
    [Google Scholar]
  25. Zhou S, Ren Q, Li Y, Liu J, Wang X et al. Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. Int J Syst Evol Microbiol 2018;68:3424–3429 [CrossRef][PubMed]
    [Google Scholar]
  26. Nogi Y, Yoshizumi M, Hamana K, Miyazaki M, Horikoshi K. Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes. Int J Syst Evol Microbiol 2014;64:2712–2717 [CrossRef][PubMed]
    [Google Scholar]
  27. Zhang XQ, Sun C, Wang CS, Zhang X, Zhou X et al. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015;65:3541–3546 [CrossRef][PubMed]
    [Google Scholar]
  28. Fahrbach M, Kuever J, Remesch M, Huber BE, Kämpfer P et al. Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. Int J Syst Evol Microbiol 2008;58:2215–2223 [CrossRef][PubMed]
    [Google Scholar]
  29. Kim MK, Kim YJ, Cho DH, Yi TH, Soung NK et al. Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2007;57:2591–2594 [CrossRef][PubMed]
    [Google Scholar]
  30. Sheu SY, Cho NT, Arun AB, Chen WM. Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli. Int J Syst Evol Microbiol 2011;61:2284–2291 [CrossRef][PubMed]
    [Google Scholar]
  31. Palleroni NJ, Port AM, Chang HK, Zylstra GJ. Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the gamma-Proteobacteria active in alkane and aromatic hydrocarbon degradation. Int J Syst Evol Microbiol 2004;54:1203–1207 [CrossRef][PubMed]
    [Google Scholar]
  32. Leandro T, França L, Nobre MF, Schumann P, Rosselló-Móra R et al. Nevskia aquatilis sp. nov. and Nevskia persephonica sp. nov., isolated from a mineral water aquifer and the emended description of the genus Nevskia. Syst Appl Microbiol 2012;35:297–301 [CrossRef][PubMed]
    [Google Scholar]
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