1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 4

sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest No Access

Abstract

A bacterial strain, designated S9-5, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus . Strain S9-5 was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5. Its major fatty acids were summed feature 8 (C 7 and/or C 6) and C. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5 was phylogenetically closely related to DCY91 (98.17 %), K-1-16 (98.11 %) and DSM 17494 (97.39 %). The average nucleotide identity values among strain S9-5 and DCY91, K-1-16 and DSM 17494 were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5 (=JCM 34750=GDMCC 1.2714) should represent a novel species of the genus , for which we propose the name sp. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): moraine , Mount Everest , phylogenetic analysis and Sphingomonas radiodurans
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005312
2022-04-12
2024-05-12
Loading full text...

Full text loading...

References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 1990; 34:99–119 [View Article]
     [Google Scholar]
  2. Akter S, Lee S-Y, Moon S-K, Choi C, Balusamy SR et al. Sphingomonas horti sp. nov., a novel bacterial species isolated from soil of a tomato garden. Arch Microbiol 2021; 203:543–548 [View Article] [PubMed]
     [Google Scholar]
  3. Akter S, Huq MA. Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample. Int J Syst Evol Microbiol 2020; 70:4151–4157 [View Article] [PubMed]
     [Google Scholar]
  4. Wübbeler JH, Oppermann-Sanio FB, Ockenfels A, Röttig A, Osthaar-Ebker A et al. Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil. Int J Syst Evol Microbiol 2017; 67:4057–4063 [View Article]
     [Google Scholar]
  5. Sukweenadhi J, Kim Y-J, Kang CH, Farh ME-A, Nguyen N-L et al. Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field. Arch Microbiol 2015; 197:973–981 [View Article]
     [Google Scholar]
  6. Chaudhary DK, Kim J. Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:2731–2738 [View Article] [PubMed]
     [Google Scholar]
  7. Fan QM, Zhang RG, Chen HY, Feng QQ, Lv J. Sphingomonas floccifaciens sp. nov., isolated from subterranean sediment. Int J Syst Evol Microbiol 2019; 69:1531–1536 [View Article] [PubMed]
     [Google Scholar]
  8. Busse H-J, Denner EBM, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . Int J Syst Evol Microbiol 2003; 53:1253–1260 [View Article] [PubMed]
     [Google Scholar]
  9. Xue H, Piao CG, Wang XZ, Lin CL, Guo MW et al. Sphingomonas aeria sp. nov., isolated from air. Int J Syst Evol Microbiol 2018; 68:2866–2871 [View Article] [PubMed]
     [Google Scholar]
  10. Kämpfer P, Meurer U, Esser M, Hirsch T, Busse HJ. Sphingomonas pseudosanguinis sp. nov., isolated from the water reservoir of an air humidifier. Int J Syst Evol Microbiol 2007; 57:1342–1345 [View Article] [PubMed]
     [Google Scholar]
  11. Cha I, Kang H, Kim H, Joh K. Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba . Int J Syst Evol Microbiol 2019; 69:3224–3229 [View Article]
     [Google Scholar]
  12. Gao J-L, Sun P, Wang X-M, Cheng S, Lv F et al. Sphingomonas zeicaulis sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:3755–3760 [View Article] [PubMed]
     [Google Scholar]
  13. Tanner K, Mancuso CP, Peretó J, Khalil AS, Vilanova C et al. Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts. Int J Syst Evol Microbiol 2020; 70:1814–1821 [View Article] [PubMed]
     [Google Scholar]
  14. Lieberman P, Morey A, Hochstadt J, Larson M, Mather S. Mount Everest: a space analogue for speech monitoring of cognitive deficits and stress. Aviat Space Environ Med 2005; 76:B198–207 [PubMed]
     [Google Scholar]
  15. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
     [Google Scholar]
  16. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  17. Zhou L, Yu H, Wang K, Chen T, Ma Y et al. Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions. BMC Genomics 2020; 21:407 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. 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 [View Article] [PubMed]
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Nishimaki T, Sato K. An extension of the Kimura two-parameter model to the natural evolutionary process. J Mol Evol 2019; 87:60–67 [View Article] [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; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. 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 [View Article] [PubMed]
     [Google Scholar]
  27. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  28. 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 [View Article] [PubMed]
     [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  30. 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:D206–14 [View Article] [PubMed]
     [Google Scholar]
  31. Molina-Menor E, Gimeno-Valero H, Pascual J, Peretó J, Porcar M. High culturable bacterial diversity from a European desert: the Tabernas Desert. Front Microbiol 2020; 11:583120 [View Article] [PubMed]
     [Google Scholar]
  32. Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralbl Bakteriol Mikrobiol Hyg A Med Microbiol Infect Dis Virol Parasitol 1988; 268:433–434 [View Article] [PubMed]
     [Google Scholar]
  33. Kim M, Oh HS, Park SC, Chun J. 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 [View Article] [PubMed]
     [Google Scholar]
  34. Reddy GSN, Garcia-Pichel F. Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA. Int J Syst Evol Microbiol 2007; 57:1028–1034 [View Article] [PubMed]
     [Google Scholar]
  35. Feng GD, Xiong X, Zhu HH, Li HP. Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine. Int J Syst Evol Microbiol 2017; 67:5273–5278 [View Article] [PubMed]
     [Google Scholar]
  36. Jung KW, Lim S, Bahn YS. Microbial radiation-resistance mechanisms. J Microbiol 2017; 55:499–507 [View Article] [PubMed]
     [Google Scholar]
  37. Zhang L, Yang Q, Luo X, Fang C, Zhang Q et al. Knockout of crtB or crtI gene blocks the carotenoid biosynthetic pathway in Deinococcus radiodurans R1 and influences its resistance to oxidative DNA-damaging agents due to change of free radicals scavenging ability. Arch Microbiol 2007; 188:411–419 [View Article] [PubMed]
     [Google Scholar]
  38. Daly MJ. A new perspective on radiation resistance based on Deinococcus radiodurans . Nat Rev Microbiol 2009; 7:237–245 [View Article] [PubMed]
     [Google Scholar]
  39. Tian B, Xu Z, Sun Z, Lin J, Hua Y. Evaluation of the antioxidant effects of carotenoids from Deinococcus radiodurans through targeted mutagenesis, chemiluminescence, and DNA damage analyses. Biochim Biophys Acta 2007; 1770:902–911 [View Article] [PubMed]
     [Google Scholar]
  40. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia . Can J Microbiol 1973; 19:1035–1048 [View Article] [PubMed]
     [Google Scholar]
  41. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  42. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article] [PubMed]
     [Google Scholar]
  43. Logan NA, Berge O, Bishop AH, Busse H-J, De Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article] [PubMed]
     [Google Scholar]
  44. Yang L, Xinyue W, Tuo C, Gaosen Z, Fasi W et al. The diversity of culturable bacteria in the eastern edge of kumtag desertkumtag desert, and the charateristic of their radiation-resistance and anti-oxidation, including the correlation and coupling of these capacities. China Environ Sci 2021; 41 (12):5921–5932 [View Article]
     [Google Scholar]
  45. Li J, Zhang B, Liu G, Liu Y, Yang H et al. Radiobacillus deserti gen. nov., sp. nov., a UV-resistant bacterium isolated from desert soil. Int J Syst Evol Microbiol 2020; 70:6338–6347 [View Article]
     [Google Scholar]
  46. Kang CK, Yang JE, Park HW, Choi YJ. Enhanced lycopene production by UV-C irradiation in radiation-resistant Deinococcus radiodurans R1. J Microbiol Biotechnol 2020; 30:1937–1943 [View Article] [PubMed]
     [Google Scholar]
  47. Nishimura Y, Ino T, Iizuka H. Acinetobacter radioresistens sp. nov. isolated from cotton and soil. Int J Syst Bacteriol 1988; 38:209–211 [View Article]
     [Google Scholar]
  48. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  49. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes . Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  50. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
     [Google Scholar]
  51. 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]
  52. Sasser M. MIDI technical note 101. identification of bacteria by gas chromatography of cellular fatty acids. MIDI, Newark DE 19901–7
     [Google Scholar]
  53. Asaf S, Numan M, Khan AL, Al-Harrasi A. Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth. Crit Rev Biotechnol 2020; 40:138–152 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005312
Loading
Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest
Int J Syst Evol Microbiol 72, 005312 (2022); https://doi.org/10.1099/ijsem.0.005312
/content/journal/ijsem/10.1099/ijsem.0.005312
/content/journal/ijsem/10.1099/ijsem.0.005312
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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