1887

Abstract

Strains P8930 and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus and showed and to be their closest phylogenetic neighbours, with 97.4 and 97.2 % 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA–DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930 and RP-3-11 and DSM 17933 were 79.7 and 77.6 %, respectively, and the value between RP-3-11 and DSM 17933 was 77.7 %, clearly demonstrating the phylogenetic distance and the novelty of strain P8930. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930 and 478 from the other validly named species, and confirmed that they represent a new species for which the name sp. nov. is proposed. The type strain is P8930 (=CCM 8938=LMG 32098).

Funding
This study was supported by the:
  • ministerstvo školství, mládeže a tělovýchovy (Award CZ.02.1.01/0.0/0.0/16_013/0001708)
    • Principle Award Recipient: PavelŠvec
  • ministerstvo školství, mládeže a tělovýchovy (Award LM2015078)
    • Principle Award Recipient: NotApplicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005309
2022-04-20
2024-03-28
Loading full text...

Full text loading...

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; 48:165–177 [View Article]
    [Google Scholar]
  2. Margesin R, Shivaji S. Pedobacter. In Whitman WB, Rainey F, Kämpfer P, Trujillo J, Chun P. eds Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc; 2015 pp 1–17
    [Google Scholar]
  3. 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]
  4. Dahal RH, Chaudhary DK, Kim D-U, Kim J. Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities. Int J Syst Evol Microbiol 2020; 70:2537–2553 [View Article] [PubMed]
    [Google Scholar]
  5. He R-H, Liu Z-W, Yu Y, Li H-R, Du Z-J. Pedobacter changchengzhani sp. nov., isolated from soil of Antarctica. Antonie van Leeuwenhoek 2019; 112:1747–1754 [View Article] [PubMed]
    [Google Scholar]
  6. Kämpfer P, Irgang R, Fernández-Negrete G, Busse H-J, Poblete-Morales M et al. Proposal of Pedobacter nototheniae sp. nov., isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) from the Chilean Antarctica. Antonie van Leeuwenhoek 2019; 112:1465–1475 [View Article] [PubMed]
    [Google Scholar]
  7. Jones D, Pell PA, Sneath PHA. Maintenance of bacteria on glass beads at -60 °C to -76°C. In Maintenance of Microorganism and Cultured Cells A Manual of Laboratory Methods London: Academic Press; 1991 pp 45–50
    [Google Scholar]
  8. Ciok A, Budzik K, Zdanowski MK, Gawor J, Grzesiak J et al. Plasmids of psychrotolerant Polaromonas spp. isolated from arctic and antarctic glaciers - diversity and role in adaptation to polar environments. Front Microbiol 2018; 9:1285 [View Article] [PubMed]
    [Google Scholar]
  9. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article] [PubMed]
    [Google Scholar]
  10. Švec P, 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. Rogala MM, Gawor J, Gromadka R, Kowalczyk M, Grzesiak J. Biodiversity and habitats of polar region polyhydroxyalkanoic acid-producing bacteria: bioprospection by popular screening methods. Genes (Basel) 2020; 11:E873 [View Article] [PubMed]
    [Google Scholar]
  12. 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]
  13. 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]
  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] [PubMed]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. Jukes T, Cantor C. Evolution of protein molecules. In Munro H. eds Mammalian Protein Metabolism Academic Press; 1969 pp 21–132
    [Google Scholar]
  17. Freiwald A, Sauer S. Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 2009; 4:732–742 [View Article] [PubMed]
    [Google Scholar]
  18. Wu L, McCluskey K, Desmeth P, Liu S, Hideaki S et al. The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species. Gigascience 2018; 7:giy026 [View Article] [PubMed]
    [Google Scholar]
  19. Wu L, Ma J. The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation. Int J Syst Evol Microbiol 2019; 69:895–898 [View Article] [PubMed]
    [Google Scholar]
  20. Lee I, Ouk Kim Y, Park S-C, 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]
  21. 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] [PubMed]
    [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. PNAS 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Klenk H-P, 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]
  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] [PubMed]
    [Google Scholar]
  25. Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 2018; 46:W282–W288 [View Article] [PubMed]
    [Google Scholar]
  26. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article] [PubMed]
    [Google Scholar]
  27. Taboada B, Estrada K, Ciria R, Merino E. Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics 2018; 34:4118–4120 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Song W, Sun H-X, Zhang C, Cheng L, Peng Y et al. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic Acids Res 2019; 47:W74–W80 [View Article] [PubMed]
    [Google Scholar]
  30. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
    [Google Scholar]
  31. Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM. CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics 2016; 17:356 [View Article] [PubMed]
    [Google Scholar]
  32. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
    [Google Scholar]
  33. Gudeta DD, Bortolaia V, Amos G, Wellington EMH, Brandt KK et al. The soil microbiota harbors a diversity of carbapenem-hydrolyzing β-lactamases of potential clinical relevance. Antimicrob Agents Chemother 2016; 60:151–160 [View Article] [PubMed]
    [Google Scholar]
  34. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008; 36:D480–4 [View Article] [PubMed]
    [Google Scholar]
  35. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  36. Moyer CL, Morita RY. Psychrophiles and psychrotrophs. In ELS John Wiley & Sons, Ltd; 2001
    [Google Scholar]
  37. Jung YH, Yi J-Y, Jung HJ, Lee YK, Lee HK et al. Overexpression of cold shock protein A of Psychromonas arctica KOPRI 22215 confers cold-resistance. Protein J 2010; 29:136–142 [View Article] [PubMed]
    [Google Scholar]
  38. Jung YH, Lee YK, Lee HK, Lee K, Im H. CspB of an arctic bacterium, Polaribacter irgensii KOPRI 22228, confers extraordinary freeze-tolerance. Braz J Microbiol 2018; 49:97–103 [View Article] [PubMed]
    [Google Scholar]
  39. Mojib N, Andersen DT, Bej AK. Structure and function of a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East Antarctica. FEMS Microbiol Lett 2011; 319:106–114 [View Article]
    [Google Scholar]
  40. Sajjad W, Din G, Rafiq M, Iqbal A, Khan S et al. Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications. Extremophiles 2020; 24:447–473 [View Article] [PubMed]
    [Google Scholar]
  41. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953; 66:24–26 [View Article] [PubMed]
    [Google Scholar]
  42. Baron EJ, Antonson S. Identification of unusual pathogenic gram-negative aerobic and facultatively anaerobic bacteria. Clin Infect Dis 1997; 24:537 [View Article]
    [Google Scholar]
  43. Brooks K, Sodeman T. A rapid method for determining decarboxylase and dihydrolase activity. J Clin Pathol 1974; 27:148–152 [View Article] [PubMed]
    [Google Scholar]
  44. Oberhofer TR, Rowen JW. Acetamide agar for differentiation of nonfermentative bacteria. Appl Microbiol 1974; 28:720–721 [View Article] [PubMed]
    [Google Scholar]
  45. Ewing WH. Enterobacteriaceae. Biochemical methods for group differentiation. Atlanta: Public Health Service Publication No 734, CDC; 1960 https://www.cabdirect.org/cabdirect/abstract/19612200045 accessed 27 February 2018
  46. Christensen WB. Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 1946; 52:461–466 [View Article] [PubMed]
    [Google Scholar]
  47. Kurup VP, Babcock JB. Use of casein, tyrosine, and hypoxanthine in the identification of nonfermentative gram-negative bacilli. Med Microbiol Immunol 1979; 167:71–75 [View Article] [PubMed]
    [Google Scholar]
  48. Páčová Z, Kocur M. New medium for detection of esterase and gelatinase activity. Zentralbl Bakteriol Mikrobiol Hyg A 1984; 258:69–73 [View Article] [PubMed]
    [Google Scholar]
  49. Owens JJ. The egg yolk reaction produced by several species of bacteria. J Appl Bacteriol 1974; 37:137–148 [View Article] [PubMed]
    [Google Scholar]
  50. Lowe GH. The rapid detection of lactose fermentation in paracolon organisms by the demonstration of beta-d-galactosidase. J Med Lab Technol 1962; 19:21–25 [PubMed]
    [Google Scholar]
  51. Barrow GI, Feltham RKA. eds Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  52. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
    [Google Scholar]
  53. CLSI Performance standards for antimicrobial susceptibility testing; Twenty-Fifth Informational Supplement (M100-S25) Wayne, PA: Clinical and Laboratory Standards Institute; 2015
    [Google Scholar]
  54. EUCAST Breakpoint Tables for Interpretation of MICs and Zone Diameters, Version 7.1 The European Committee on Antimicrobial Susceptibility Testing; 2017
    [Google Scholar]
  55. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101 Newark, Del: MIDI, Inc; 1990 pp 1–7
    [Google Scholar]
  56. Bajerski F, Wagner D, Mangelsdorf K. Cell membrane fatty acid composition of Chryseobacterium frigidisoli PB4T, isolated from antarctic glacier forefield soils, in response to changing temperature and pH conditions. Front Microbiol 2017; 8:6778 [View Article] [PubMed]
    [Google Scholar]
  57. Králová S. Role of fatty acids in cold adaptation of Antarctic psychrophilic Flavobacterium spp. Syst Appl Microbiol 2017; 40:329–333 [View Article] [PubMed]
    [Google Scholar]
  58. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
    [Google Scholar]
  59. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  60. 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] [PubMed]
    [Google Scholar]
  61. 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] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005309
Loading
/content/journal/ijsem/10.1099/ijsem.0.005309
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