1887

Abstract

A novel bacterium, designated strain ANT13_2, was isolated from a phenanthrene-degrading consortium enriched from a soil sample collected near the Great Wall Station located in the southwestern area of King George Island, Antarctica. Following a polyphasic taxonomic study, a novel species belonging to the genus was described. The strain was a Gram-stain-positive bacterium that exhibited a rod–coccus growth cycle. Strain ANT13_2 grew aerobically at an optimum temperature of 20–25 °C and at pH 7.0–8.0. Ribose, arabinose and glucose were detected as whole-cell sugars. The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C (67.7 %) and anteiso-C (11.2 %). The DNA G+C content of the genomic DNA was 60.6 mol%. Based on 16S rRNA gene sequence analysis, strain ANT13_2 showed the highest similarities to SPC26 (98.9 %) followed by Lz1y (98.4 %), DSM 20167 (98.3%) and KGN15 (97.9 %). The average nucleotide identity values between strain ANT13_2 and the type strains of SPC26 and Lz1y were 73.8 and 77.5 %, respectively, which are well below the 95–96 % species circumscription threshold. On the basis of this polyphasic taxonomic study, strain ANT13_2 is proposed to represent a novel species to be named sp. nov. The type strain is ANT13_2 (=TBRC 11756=NBRC 114615).

Funding
This study was supported by the:
  • ChatsudaSakdapetsiri , Ratchadapisek Somphot Fund for Postdoctoral Fellowship, Chulalongkorn University.
  • OnruthaiPinyakong , Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Thailand
  • ChenBo , Technology Development Agency, Chinese Arctic and Antarctic Administration
  • OnruthaiPinyakong , the Information Technology Foundation under the Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn, Polar Research Project under the Initiatives of Her Royal Highness Princess Maha Chakri Sirindhorn, National Science
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2021-02-08
2021-02-26
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References

  1. Conn H, Dimmick I. Soil bacteria similar in morphology to Mycobacterium and Corynebacterium . J Bacteriol 1947; 54: 291 303 [CrossRef] [PubMed]
    [Google Scholar]
  2. Busse HJ. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus . Int J Syst Evol Microbiol 2016; 66: 9 37 [CrossRef] [PubMed]
    [Google Scholar]
  3. Hughes KA, Cowan DA, Wilmotte A. Protection of Antarctic microbial communities - 'out of sight, out of mind'. Front Microbiol 2015; 6: 151 [CrossRef] [PubMed]
    [Google Scholar]
  4. Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV et al. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol Rev 2013; 37: 303 335 [CrossRef] [PubMed]
    [Google Scholar]
  5. Pongpiachan S, Hattayanone M, Pinyakong O, Viyakarn V, Chavanich SA et al. Quantitative ecological risk assessment of inhabitants exposed to polycyclic aromatic hydrocarbons in terrestrial soils of King George Island, Antarctica. Polar Sci 2017; 11: 19 29 [CrossRef]
    [Google Scholar]
  6. Gran-Scheuch A, Fuentes E, Bravo DM, Jiménez JC, Pérez-Donoso JM. Isolation and characterization of phenanthrene degrading bacteria from diesel fuel-contaminated Antarctic soils. Front Microbiol 2017; 8: 1634 [CrossRef] [PubMed]
    [Google Scholar]
  7. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual , 10th ed. USA: Benjamin-Cummings Publishing company; 2014
    [Google Scholar]
  8. Ganzert L, Bajerski F, Mangelsdorf K, Lipski A, Wagner D. Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil. Int J Syst Evol Microbiol 2011; 61: 979 984 [CrossRef] [PubMed]
    [Google Scholar]
  9. Lányi B. 1 Classical and rapid identification methods for medically important bacteria. In Colwell RR, Grigorova R. (editors) Methods in Microbiology New York: Academic Press; 1988 pp 1 67
    [Google Scholar]
  10. Lisowska K, Długoński J. Concurrent corticosteroid and phenanthrene transformation by filamentous fungus Cunninghamella elegans . J Steroid Biochem Mol Biol 2003; 85: 63 69 [CrossRef] [PubMed]
    [Google Scholar]
  11. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids , Technical note 101. Newark, DE: MIDI inc; 1990
    [Google Scholar]
  12. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42: 989 1005 [CrossRef]
    [Google Scholar]
  13. Komagata K, Suzuki KI. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19: 161 207
    [Google Scholar]
  14. 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]
  15. 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]
  16. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16: 176 178
    [Google Scholar]
  17. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72: 619 629 [CrossRef] [PubMed]
    [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41: 95 98
    [Google Scholar]
  19. 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]
  20. 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]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406 425 [CrossRef] [PubMed]
    [Google Scholar]
  22. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 1983; 14: 313 333 [CrossRef]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368 376 [CrossRef] [PubMed]
    [Google Scholar]
  24. 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 [CrossRef] [PubMed]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783 791 [CrossRef] [PubMed]
    [Google Scholar]
  26. Brown J, Pirrung M, McCue LA. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics 2017; 33: 3137 3139 [CrossRef] [PubMed]
    [Google Scholar]
  27. Krueger F. Trim Galore! Babraham bioinformatics. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ . 2014
  28. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20: 714 737 [CrossRef] [PubMed]
    [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30: 2068 2069 [CrossRef] [PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32: 929 931 [CrossRef] [PubMed]
    [Google Scholar]
  31. 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 [CrossRef] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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 [CrossRef] [PubMed]
    [Google Scholar]
  34. Kim M, Oh H-S, Park S-C, Chun J, HS O. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64: 346 351 [CrossRef] [PubMed]
    [Google Scholar]
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