1887

Abstract

A Gram-stain-positive, aerobic, non-mobile and spherical strain, designated ZS9-10, belonging to the genus was isolated from soil sampled at the Chinese Zhong Shan Station, Antarctica. Growth was observed in the presence of 0–4 % (w/v) NaCl, at pH 7.0–8.0 and at 4–25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZS9-10 formed a lineage in the genus . It exhibited highest sequence similarity (97.4 %) to DSM 12784. The major phospholipids of ZS9-10 were unidentified phosphoglycolipid, unidentified glycolipids and unidentified lipids. The major fatty acids were summed feature 3 (C 7 and/or C 6), C and C 7. MK-8 was the predominant respiratory quinone. The digital DNA–DNA hybridization and average nucleotide identity values between strain ZS9-10 and its close relative DSM 12784 were 27.4 and 83.9 %, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, named sp. nov., is proposed. The type strain iis ZS9-10 (=CCTCC AB 2019392=KCTC43192).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006397
2024-05-24
2024-06-19
Loading full text...

Full text loading...

References

  1. Brooks BW, Murray RGE. Nomenclature for “Micrococcus radiodurans” and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Bacteriol 1981; 31:353–360 [View Article]
    [Google Scholar]
  2. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  3. Hussain F, Khan IU, Habib N, Xian W-D, Hozzein WN et al. Deinococcus saudiensis sp. nov., isolated from desert. Int J Syst Evol Microbiol 2016; 66:5106–5111 [View Article] [PubMed]
    [Google Scholar]
  4. Asker D, Awad TS, McLandsborough L, Beppu T, Ueda K. Deinococcus depolymerans sp. nov., a gamma- and UV-radiation-resistant bacterium, isolated from a naturally radioactive site. Int J Syst Evol Microbiol 2011; 61:1448–1453 [View Article] [PubMed]
    [Google Scholar]
  5. Chen W, Wang B, Hong H, Yang H, Liu SJ. Deinococcus reticulitermitis sp. nov., isolated from a termite gut. Int J Syst Evol Microbiol 2012; 62:78–83 [View Article]
    [Google Scholar]
  6. Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R et al. Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 1997; 47:939–947 [View Article] [PubMed]
    [Google Scholar]
  7. de Groot A, Chapon V, Servant P, Christen R, Saux MF-L et al. Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 2005; 55:2441–2446 [View Article] [PubMed]
    [Google Scholar]
  8. Hirsch P, Gallikowski CA, Siebert J, Peissl K, Kroppenstedt R et al. Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Syst Appl Microbiol 2004; 27:636–645 [View Article] [PubMed]
    [Google Scholar]
  9. Kim D-U, Lee H, Lee J-H, Ahn J-H, Lim S et al. Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system. Int J Syst Evol Microbiol 2015; 65:3175–3182 [View Article] [PubMed]
    [Google Scholar]
  10. Lai W-A, Kämpfer P, Arun AB, Shen F-T, Huber B et al. Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. Int J Syst Evol Microbiol 2006; 56:787–791 [View Article] [PubMed]
    [Google Scholar]
  11. Shashidhar R, Bandekar JR. Deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish. Int J Syst Evol Microbiol 2009; 59:2714–2717 [View Article] [PubMed]
    [Google Scholar]
  12. Lee J-J, Lee HJ, Jang GS, Yu JM, Cha JY et al. Deinococcus swuensis sp. nov., a gamma-radiation-resistant bacterium isolated from soil. J Microbiol 2013; 51:305–311 [View Article] [PubMed]
    [Google Scholar]
  13. Ahmed I, Abbas S, Kudo T, Iqbal M, Fujiwara T et al. Deinococcus citri sp. nov., isolated from citrus leaf canker lesions. Int J Syst Evol Microbiol 2014; 64:4134–4140 [View Article] [PubMed]
    [Google Scholar]
  14. Wang X-P, Li C-M, Yu Y, Li H-R, Du Z-J et al. Deinococcus arcticus sp. nov., isolated from silene acaulis rhizosphere soil of the Arctic tundra. Int J Syst Evol Microbiol 2019; 69:3437–3442 [View Article] [PubMed]
    [Google Scholar]
  15. Makk J, Tóth EM, Anda D, Pál S, Schumann P et al. Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave. Int J Syst Evol Microbiol 2016; 66:5345–5351 [View Article] [PubMed]
    [Google Scholar]
  16. Rollo F, Martins GD, Gouveia AG, Ithurbide S, Servant P et al. Insights into the role of three Endonuclease III enzymes for oxidative stress resistance in the extremely radiation resistant bacterium Deinococcus radiodurans. Front Microbiol 2023; 14:1266785 [View Article] [PubMed]
    [Google Scholar]
  17. Cai J, Zhang M, Chen Z, Zhao Y, Xu H et al. MoaE is involved in response to oxidative stress in Deinococcus radiodurans. Int J Mol Sci 2023; 24:2441 [View Article] [PubMed]
    [Google Scholar]
  18. Chaudhary R, Mishra S, Maurya GK, Rajpurohit YS, Misra HS. FtsZ phosphorylation brings about growth arrest upon DNA damage in Deinococcus radiodurans. FASEB Bioadv 2023; 5:27–42 [View Article] [PubMed]
    [Google Scholar]
  19. Battista JR. Against all odds: the survival strategies of Deinococcus radiodurans. Annu Rev Microbiol 1997; 51:203–224 [View Article] [PubMed]
    [Google Scholar]
  20. Wang J-J, Wu S-G, Chen Q, Sheng D-H, Du Z-J et al. Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil. Int J Syst Evol Microbiol 2020; 70:4993–5000 [View Article] [PubMed]
    [Google Scholar]
  21. Monciardini P, Sosio M, Cavaletti L, Chiocchini C, Donadio S. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol Ecol 2002; 42:419–429 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 2001; 51:357–363 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  27. Lakra P, Verma H, Talwar C, Singh DN, Singhvi N et al. Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans. Int J Syst Evol Microbiol 2021; 71:71 [View Article] [PubMed]
    [Google Scholar]
  28. Sun W, Dai S, Jiang S, Wang G, Liu G et al. Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek 2010; 98:65–75 [View Article] [PubMed]
    [Google Scholar]
  29. 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 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  33. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
    [Google Scholar]
  34. Meier-Kolthoff JP, Klenk HP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  35. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
  36. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article] [PubMed]
    [Google Scholar]
  37. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–W185 [View Article] [PubMed]
    [Google Scholar]
  38. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
    [Google Scholar]
  39. UniProt Consortium UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515 [View Article] [PubMed]
    [Google Scholar]
  40. Conesa A, Götz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genom 2008; 2008:619832 [View Article] [PubMed]
    [Google Scholar]
  41. 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]
  42. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
    [Google Scholar]
  43. Hoffmann T, Frankenberg N, Marino M, Jahn D. Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J Bacteriol 1998; 180:186–189 [View Article] [PubMed]
    [Google Scholar]
  44. Mccarthy AJ, Cross T. A Taxonomic Study of Thermomonospora and Other Monosporic Actinomycetes. Microbiology 1984; 130:5–25 [View Article]
    [Google Scholar]
  45. Yan L, Wang J, Chen Z, Guan Y, Li J. Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment. Int J Syst Evol Microbiol 2015; 65:3697–3702 [View Article] [PubMed]
    [Google Scholar]
  46. Anand S, Bala K, Saxena A, Schumann P, Lal R. Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site. International Journal of Systematic and Evolutionary Microbiology 2012; 62:2114–2120 [View Article]
    [Google Scholar]
  47. Cowan and Steel’s Manual for the Identification of Medical Bacteria. 28 January 1993; 1993
  48. Minnikin DE, Dobson G, Draper P. Characterization of Mycobacterium leprae by lipid analysis. Acta Leprol 1984; 2:113–120 [PubMed]
    [Google Scholar]
  49. Sabry SA, Ghanem NB, Abu-Ella GA, Schumann P, Stackebrandt E et al. Nocardiopsis aegyptia sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2004; 54:453–456 [View Article] [PubMed]
    [Google Scholar]
  50. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
    [Google Scholar]
  51. Srinivasan S, Lee JJ, Lim S, Joe M, Kim MK. Deinococcus humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 62:2844–2850 [View Article] [PubMed]
    [Google Scholar]
  52. Im W-T, Jung H-M, Ten LN, Kim MK, Bora N et al. Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2008; 58:2348–2353 [View Article] [PubMed]
    [Google Scholar]
  53. Wang W, Mao J, Zhang Z, Tang Q, Xie Y et al. Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol 2010; 60:2006–2010 [View Article] [PubMed]
    [Google Scholar]
  54. Rainey FA, Ray K, Ferreira M, Gatz BZ, Nobre MF et al. Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl Environ Microbiol 2005; 71:5225–5235 [View Article] [PubMed]
    [Google Scholar]
  55. Bentchikou E, Servant P, Coste G, Sommer S. A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans. PLoS Genet 2010; 6:e1000774 [View Article] [PubMed]
    [Google Scholar]
  56. Rocha EPC, Cornet E, Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet 2005; 1:e15 [View Article] [PubMed]
    [Google Scholar]
  57. Lim S, Jung J-H, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19–52 [View Article] [PubMed]
    [Google Scholar]
  58. Liu T, Zhu L, Zhang Z, Huang H, Zhang Z et al. Protective role of trehalose during radiation and heavy metal stress in Aureobasidium subglaciale F134. Sci Rep 2017; 7:17586 [View Article] [PubMed]
    [Google Scholar]
  59. Xu R, Wu K, Han H, Ling Z, Chen Z et al. Co-expression of YieF and PhoN in Deinococcus radiodurans R1 improves uranium bioprecipitation by reducing chromium interference. Chemosphere 2018; 211:1156–1165 [View Article] [PubMed]
    [Google Scholar]
  60. Gogada R, Singh SS, Lunavat SK, Pamarthi MM, Rodrigue A et al. Engineered Deinococcus radiodurans R1 with NiCoT genes for bioremoval of trace cobalt from spent decontamination solutions of nuclear power reactors. Appl Microbiol Biotechnol 2015; 99:9203–9213 [View Article] [PubMed]
    [Google Scholar]
  61. Misra CS, Appukuttan D, Kantamreddi VSS, Rao AS, Apte SK. Recombinant D. radiodurans cells for bioremediation of heavy metals from acidic/neutral aqueous wastes. Bioengineered 2012; 3:44–48 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006397
Loading
/content/journal/ijsem/10.1099/ijsem.0.006397
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