1887

Abstract

A yellow-coloured, Gram-stain-negative, non-sporulating, psychrotolerant and motile bacterium, designated AR-3-1, was isolated from the Arctic soil of Cambridge Bay, Nunavut, Canada. Strain AR-3-1 could grow at 4–32 °C and pH 5.0– 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain AR-3-1 formed a lineage within the family and clustered as a member of the genus . The closest members within this genus were CU4 (98.1 % sequence similarity), VC-230 (97.6 %) and DS20 (97.5 %). The only respiratory quinone was the ubiquinone Q-10. Spermidine was the predominant polyamine. The principal cellular fatty acids were summed feature 8 (C 7 and/or C 6), summed feature 3 (iso-C 2-OH and/or C 7), C and C 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid and phosphoglycolipid. The DNA G+C content was 63.1 %. The average nucleotide identity and DNA–DNA hybridization relatedness values between strain AR-3-1 and its most closely related genus members were ≤89.6 and 39.6 %, respectively. The genome was 5 162 327 bp long, with 83 scaffolds and 4824 protein-coding genes. The genome showed six putative biosynthetic gene clusters responsible for various secondary metabolites. Based on this polyphasic study, strain AR-3-1 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is AR-3-1 (=KACC 21613=NBRC 114604).

Funding
This study was supported by the:
  • JaisooKim , National Research Foundation (KR) , (Award 2019R1F1A1058501)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004705
2021-02-17
2021-03-02
Loading full text...

Full text loading...

References

  1. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51: 1405 1417 [CrossRef] [PubMed]
    [Google Scholar]
  2. Li L, Liu H, Shi Z, Wang G. Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus Sphingobium . Int J Syst Evol Microbiol 2013; 63: 604 609 [CrossRef] [PubMed]
    [Google Scholar]
  3. Chaudhary DK, Jeong SW, Kim J. Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67: 2986 2993 [CrossRef] [PubMed]
    [Google Scholar]
  4. Park YJ, Kim KH, Han DM, Lee DH, Jeon CO. Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil. Int J Syst Evol Microbiol 2019; 69: 2459 2464 [CrossRef] [PubMed]
    [Google Scholar]
  5. Kumari H, Gupta SK, Jindal S, Katoch P, Lal R. Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59: 2291 2296 [CrossRef] [PubMed]
    [Google Scholar]
  6. Révész F, Tóth EM, Kriszt B, Bóka K, Benedek T et al. Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater. Int J Syst Evol Microbiol 2018; 68: 2807 2812 [CrossRef] [PubMed]
    [Google Scholar]
  7. Vaz-Moreira I, Faria C, Lopes AR, Svensson L, Falsen E et al. Sphingobium vermicomposti sp. nov., isolated from vermicompost. Int J Syst Evol Microbiol 2009; 59: 3145 3149 [CrossRef] [PubMed]
    [Google Scholar]
  8. Young CC, Arun AB, Kämpfer P, Busse HJ, Lai WA et al. Sphingobium rhizovicinum sp. nov., isolated from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle. Int J Syst Evol Microbiol 2008; 58: 1801 1806 [CrossRef] [PubMed]
    [Google Scholar]
  9. Sheu SY, Shiau YW, Chen WM. Sphingobium sufflavum sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2013; 63: 3444 3450 [CrossRef] [PubMed]
    [Google Scholar]
  10. Lee JC, Kim SG, Whang KS. Sphingobium subterraneum sp. nov., isolated from ground water. Int J Syst Evol Microbiol 2015; 65: 393 398 [CrossRef] [PubMed]
    [Google Scholar]
  11. Chen WM, Guo YP, Sheu C, Sheu SY. Sphingobium algorifonticola sp. nov., isolated from a cold spring. Int J Syst Evol Microbiol 2020; 70: 309 316 [CrossRef] [PubMed]
    [Google Scholar]
  12. Dahal RH, Kim J. Glaciihabitans arcticus sp. nov., a psychrotolerant bacterium isolated from Arctic soil. Int J Syst Evol Microbiol 2019; 69: 2492 2497 [CrossRef] [PubMed]
    [Google Scholar]
  13. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74: 2461 2470 [CrossRef] [PubMed]
    [Google Scholar]
  14. Yoon SH, 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 [CrossRef] [PubMed]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870 1874 [CrossRef] [PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783 791 [CrossRef] [PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7: 203 214 [CrossRef] [PubMed]
    [Google Scholar]
  20. 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 [CrossRef] [PubMed]
    [Google Scholar]
  21. 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]
  22. 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 [CrossRef] [PubMed]
    [Google Scholar]
  23. 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 [CrossRef] [PubMed]
    [Google Scholar]
  24. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56: 281 285 [CrossRef] [PubMed]
    [Google Scholar]
  25. 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 [CrossRef] [PubMed]
    [Google Scholar]
  26. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005; 33: W686 W689 [CrossRef] [PubMed]
    [Google Scholar]
  27. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35: 3100 3108 [CrossRef] [PubMed]
    [Google Scholar]
  28. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47: W81 W87 [CrossRef] [PubMed]
    [Google Scholar]
  29. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106: 19126 19131 [CrossRef] [PubMed]
    [Google Scholar]
  30. Goordial J, Raymond-Bouchard I, Zolotarov Y, de Bethencourt L, Ronholm J et al. Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiol Ecol 2016; 92: fiv154 [CrossRef] [PubMed]
    [Google Scholar]
  31. Raymond-Bouchard I, Goordial J, Zolotarov Y, Ronholm J, Stromvik M et al. Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria. FEMS Microbiol Ecol 2018; 94: 23 [CrossRef] [PubMed]
    [Google Scholar]
  32. Doetsch RN. Determinative methods of light microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. (editors) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp 21 33
    [Google Scholar]
  33. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC. USA: American Society for Microbiology; 1994 pp 607 654
    [Google Scholar]
  34. Dahal RH, Kim J. Fluviicola kyonggii sp. nov., a bacterium isolated from forest soil and emended description of the genus Fluviicola. Int J Syst Evol Microbiol 2018; 68: 1885 1889 [CrossRef] [PubMed]
    [Google Scholar]
  35. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acid Methyl Esters (Gc-Fame) , MIDI Tech Note 101. Newark: MIDI Inc; 1990
    [Google Scholar]
  36. 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 [CrossRef]
    [Google Scholar]
  37. Komagata K, Suzuki K. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19: 161 207
    [Google Scholar]
  38. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57: 572 576 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004705
Loading
/content/journal/ijsem/10.1099/ijsem.0.004705
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error