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Volume 70, Issue 4

Nine novel psychrotolerant species of the genus isolated from Arctic soil with potential antioxidant activities Free

Abstract

Fifteen isolates of the genus were obtained from Arctic soil samples. All isolates were Gram-stain-negative and rod-shaped. Cells were strictly aerobic, psychrotolerant and grew optimally at 15–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all the isolated strains formed a lineage within the family and clustered as members of the genus . The sole respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (iso-C2-OH/Cω7ω6), iso-C and iso-C 3-OH. The DNA G+C content of the novel strains was 33.9–41.8 mol%. In addition, the average nucleotide identity and DNA–DNA hybridization relatedness values between the novel type strains and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, phylogenetic and phylogenomic analyses, the isolated strains represent novel species in the genus , for which the names sp. nov. (type strain AR-2-6=KEMB 9005-717=KACC 19998=NBRC 113826), sp. nov. (type strain AR-3-17=KEMB 9005-718=KACC 19999=NBRC 113827), sp. nov. (type strain RP-1-13=KEMB 9005-720=KACC 21147=NBRC 113829), sp. nov. (type strain RP-1-14=KEMB 9005-721=KACC 21148=NBRC 113830), sp. nov. (type strain RP-3-8=KEMB 9005-724=KACC 21152=NBRC 113833), sp. nov. (type strain RP-3-11=KEMB 9005-725=KACC 21153=NBRC 113927), sp. nov. (type strain RP-3-15=KEMB 9005-726=KACC 21154=NBRC 113834), sp. nov. (type strain RP-3-21=KEMB 9005-728=KACC 21156=NBRC 113835) and sp. nov. (type strain RP-3-22=KEMB 9005-729=KACC 21157=NBRC 113836) are proposed.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): antioxidant , Arctic soil , Bacteroidetes , Pedobacter , psychrotolerant and Sphingobacteriaceae
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2019R1F1A1058501)
    • Principle Award Recipient: Jaisoo Kim
© 2020 The Authors
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2020-03-11
2024-04-26
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References

  1. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48 Pt 1:165–177 [View Article]
     [Google Scholar]
  2. Du J, Singh H, Ngo HTT, Won K-H, Kim K-Y et al. Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 2015; 65:1241–1246 [View Article]
     [Google Scholar]
  3. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article]
     [Google Scholar]
  4. Chaudhary DK, Lee SD, Kim J. Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:5120–5127 [View Article]
     [Google Scholar]
  5. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus . Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article]
     [Google Scholar]
  6. Shivaji S, Chaturvedi P, Reddy GSN, Suresh K. Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India. Int J Syst Evol Microbiol 2005; 55:1083–1088 [View Article]
     [Google Scholar]
  7. Da X, Jiang F, Chang X, Ren L, Qiu X et al. Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica. Int J Syst Evol Microbiol 2015; 65:3841–3846 [View Article]
     [Google Scholar]
  8. Margesin R, Spröer C, Schumann P, Schinner F. Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 2003; 53:1291–1296 [View Article]
     [Google Scholar]
  9. Manandhar P, Zhang G, Lama A, Hu Y, Gao F. Pedobacter psychrotolerans sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:4560–4566 [View Article]
     [Google Scholar]
  10. Králová S, Busse H-J, Kleinhagauer T, Pantůček R et al. Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment. Int J Syst Evol Microbiol 2017; 67:1499–1507 [View Article]
     [Google Scholar]
  11. Dahal RH, Chaudhary DK, Kim J. Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968. Int J Syst Evol Microbiol 2018; 68:1955–1962 [View Article]
     [Google Scholar]
  12. 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 [View Article]
     [Google Scholar]
  13. 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]
     [Google Scholar]
  14. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  18. 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 [View Article]
     [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  20. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article]
     [Google Scholar]
  21. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article]
     [Google Scholar]
  22. 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]
     [Google Scholar]
  23. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
     [Google Scholar]
  24. 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 [View Article]
     [Google Scholar]
  25. 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]
     [Google Scholar]
  26. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4:770–773 [View Article]
     [Google Scholar]
  27. 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 [View Article]
     [Google Scholar]
  28. 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 [View Article]
     [Google Scholar]
  29. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  30. Kim I, Kim D-U, Kim N-H, Ka J-O. Isolation and characterization of fenobucarb-degrading bacteria from rice paddy soils. Biodegradation 2014; 25:383–394 [View Article]
     [Google Scholar]
  31. Pavel AB, Vasile CI. PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinformatics 2012; 13:9 [View Article]
     [Google Scholar]
  32. Kook M, Park Y, Yi T-H. Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 2014; 64:1789–1794 [View Article]
     [Google Scholar]
  33. 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 [View Article]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  36. Doetsch RN et al. Determinative Methods of Light Microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. (editors) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp 21–33
     [Google Scholar]
  37. Breznak JA, Costilow RN et al. Physicochemical factors in growth. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Bacteriology Washinton, DC, USA: American Society of Microbiology; 2007 pp 309–329
     [Google Scholar]
  38. 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]
  39. 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]
  40. 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]
  41. Komagata K, Suzuki K. 4 lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  42. Zeng Y, Feng H, Huang Y. Pedobacter xixiisoli sp. nov., isolated from bank soil. Int J Syst Evol Microbiol 2014; 64:3683–3689 [View Article]
     [Google Scholar]
  43. Dahal RH, Shim DS, Kim J. Development of actinobacterial resources for functional cosmetics. J Cosmet Dermatol 2017; 16:243–252 [View Article]
     [Google Scholar]
  44. 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 [View Article]
     [Google Scholar]
  45. González-Burgos E, Gómez-Serranillos MP. Terpene compounds in nature: a review of their potential antioxidant activity. Curr Med Chem 2012; 19:5319–5341 [View Article]
     [Google Scholar]
  46. Bendary E, Francis RR, Ali HMG, Sarwat MI, El Hady S. Antioxidant and structure–activity relationships (SARS) of some phenolic and anilines compounds. Annals of Agricultural Sciences 2013; 58:173–181 [View Article]
     [Google Scholar]
  47. Özyürek M, Bekdeşer B, Güçlü K, Apak R. Resorcinol as a spectrofluorometric probe for the hypochlorous acid scavenging activity assay of biological samples. Anal Chem 2012; 84:9529–9536 [View Article]
     [Google Scholar]
  48. An D-S, Kim S-G, Ten LN, Cho C-H. Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea. Int J Syst Evol Microbiol 2009; 59:69–72 [View Article]
     [Google Scholar]
  49. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014; 64:2431–2436 [View Article]
     [Google Scholar]
  50. Baik KS, Park Y-D, Kim MS, Park SC, Moon EY et al. Pedobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007; 57:2079–2083 [View Article]
     [Google Scholar]
  51. Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL et al. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 2009; 59:1720–1726 [View Article]
     [Google Scholar]
  52. Yoon M-H, Ten LN, Im W-T, Lee S-T. Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. Int J Syst Evol Microbiol 2007; 57:381–386 [View Article]
     [Google Scholar]
  53. Ngo HTT, Son H-M, Park S-Y, Kim K-Y, Yi T-H. Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field. Antonie Van Leeuwenhoek 2014; 105:961–970 [View Article]
     [Google Scholar]
  54. Yoon J-H, Kang S-J, Oh T-K. Pedobacter terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:2462–2466 [View Article]
     [Google Scholar]
  55. Joung Y, Kim H, Joh K. Pedobacter yonginense sp. nov., isolated from a mesotrophic artificial lake in Korea. J Microbiol 2010; 48:536–540 [View Article]
     [Google Scholar]
  56. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 2014; 37:342–350 [View Article]
     [Google Scholar]
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Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities
Int J Syst Evol Microbiol 70, 2537 (2020); https://doi.org/10.1099/ijsem.0.004071
/content/journal/ijsem/10.1099/ijsem.0.004071
/content/journal/ijsem/10.1099/ijsem.0.004071
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