1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 9

sp. nov., isolated from soils in Antarctica Free

Abstract

A set of three psychrotrophic bacterial strains was isolated from different soil samples collected at the deglaciated northern part of James Ross Island (Antarctica) in 2014. All isolates were rod-shaped, Gram-stain-negative, non-motile, catalase-positive and oxidase-negative, and produced moderately slimy red-pink pigmented colonies on Reasoner's 2A (R2A) agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, automated ribotyping, MALDI-TOF MS, chemotaxonomy methods and extensive biotyping using conventional tests and commercial identification kits was applied to the isolates in order to clarify their taxonomic position. Phylogenetic analysis based on the 16S rRNA gene showed that all isolates belonged to the genus with the closest relative being DSM 13606, exhibiting 98.5 % 16S rRNA gene pairwise similarity to the reference isolate P6312. Average nucleotide identity values calculated from the whole-genome sequencing data proved that P6312 represents a distinct species. The major components of the cellular fatty acid composition were summed feature 3 (C 7/C 6), C 5, summed feature 4 (C anteiso B/iso I), C anteiso and C iso. The menaquinone system of strain P6312 contained MK-7 as the major respiratory quinone. The predominant polar lipids were phosphatidylethanolamine and an unidentified phospholipid. Moderate to minor amounts of three unidentified polar lipids, four unidentified aminophospholipids, one unidentified glycolipid and one unidentified phospholipid were also present. Based on the obtained results, we propose a novel species for which the name sp. nov. is suggested, with the type strain P6312 (=CCM 8763=LMG 30612).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Antarctica , Hymenobacter humicola , identification , soil and taxonomy
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003555
2019-09-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/9/2755.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003555&mimeType=html&fmt=ahah

References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article][PubMed]
     [Google Scholar]
  2. Buczolits S, Denner EB, Kämpfer P, Busse HJ. Proposal of Hymenobacter norwichensis sp. nov., classification of 'Taxeobacter ocellatus', 'Taxeobacter gelupurpurascens' and 'Taxeobacter chitinovorans' as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 2006; 56:2071–2078 [View Article][PubMed]
     [Google Scholar]
  3. Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter . Antonie van Leeuwenhoek 2014; 105:971–978 [View Article][PubMed]
     [Google Scholar]
  4. Klassen JL, Foght JM. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 2011; 15:45–57 [View Article][PubMed]
     [Google Scholar]
  5. Kojima H, Watanabe M, Tokizawa R, Shinohara A, Fukui M. Hymenobacter nivis sp. nov., isolated from red snow in Antarctica. Int J Syst Evol Microbiol 2016; 66:4821–4825 [View Article][PubMed]
     [Google Scholar]
  6. Sedláček I, Králová S, Kýrová K, Mašlaňová I, Busse HJ et al. Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. Int J Syst Evol Microbiol 2017; 67:1975–1983 [View Article][PubMed]
     [Google Scholar]
  7. Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L et al. Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2018; 68:663–668 [View Article][PubMed]
     [Google Scholar]
  8. Sedláček I, Pantůček R, Králová S, Mašlaňová I, Holochová P et al. Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica. Syst Appl Microbiol 2019; 42:284–290 [View Article][PubMed]
     [Google Scholar]
  9. Chang X, Zheng J, Jiang F, Liu P, Kan W et al. Hymenobacter arcticus sp. nov., isolated from glacial till. Int J Syst Evol Microbiol 2014; 64:2113–2118 [View Article][PubMed]
     [Google Scholar]
  10. Gu Z, Liu Y, Xu B, Wang N, Jiao N et al. Hymenobacter frigidus sp. nov., isolated from a glacier ice core. Int J Syst Evol Microbiol 2017; 67:4121–4125 [View Article][PubMed]
     [Google Scholar]
  11. Liu K, Liu Y, Wang N, Gu Z, Shen L et al. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793–3798 [View Article][PubMed]
     [Google Scholar]
  12. Liu L, Zhou EM, Jiao JY, Manikprabhu D, Ming H et al. Hymenobacter mucosus sp. nov., isolated from a karst cave soil sample. Int J Syst Evol Microbiol 2015; 65:4121–4127 [View Article][PubMed]
     [Google Scholar]
  13. Zhu HZ, Yang L, Muhadesi JB, Wang BJ, Liu SJ. Hymenobacter cavernae sp. nov., isolated from a karst cave. Int J Syst Evol Microbiol 2017; 67:4825–4829 [View Article][PubMed]
     [Google Scholar]
  14. Zhang G, Niu F, Busse HJ, Ma X, Liu W et al. Hymenobacter psychrotolerans sp. nov., isolated from the Qinghai-Tibet Plateau permafrost region. Int J Syst Evol Microbiol 2008; 58:1215–1220 [View Article][PubMed]
     [Google Scholar]
  15. Kim MC, Kim CM, Kang OC, Zhang Y, Liu Z et al. Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic. Int J Syst Evol Microbiol 2017; 67:856–861 [View Article][PubMed]
     [Google Scholar]
  16. Sun J, Xing M, Wang W, Dai F, Liu J et al. Hymenobacter profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:947–950 [View Article][PubMed]
     [Google Scholar]
  17. 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]
  18. Hrbáček F, Kňažková M, Nývlt D, Láska K, Mueller CW et al. Active layer monitoring at CALM-S site near J.G.Mendel Station, James Ross Island, eastern Antarctic Peninsula. Sci Total Environ 2017; 601-602:987–997 [View Article][PubMed]
     [Google Scholar]
  19. Kýrová K, Sedláček I, Pantůček R, Králová S, Holochová P et al. Rufibacter ruber sp. nov., isolated from fragmentary rock. Int J Syst Evol Microbiol 2016; 66:4401–4405 [View Article][PubMed]
     [Google Scholar]
  20. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
     [Google Scholar]
  21. Buczolits S, Denner EB, Vybiral D, Wieser M, Kämpfer P et al. Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int J Syst Evol Microbiol 2002; 52:445–456 [View Article][PubMed]
     [Google Scholar]
  22. Collins MD, Hutson RA, Grant IR, Patterson MF. Phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of Hymenobacter actinosclerus sp. nov. Int J Syst Evol Microbiol 2000; 50:731–734 [View Article][PubMed]
     [Google Scholar]
  23. Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F et al. Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2011; 61:859–863 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. 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]
  26. 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]
  27. Sedláček I, Kwon SW, Švec P, Mašlaňová I, Kýrová K et al. Aquitalea pelogenes sp. nov., isolated from mineral peloid. Int J Syst Evol Microbiol 2016; 66:962–967 [View Article][PubMed]
     [Google Scholar]
  28. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article][PubMed]
     [Google Scholar]
  29. 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]
  30. 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]
  31. Buczolits S, Busse H-J. Hymenobacter. In: Whitman WB (editor). Bergey's Manual of Systematics of Archaea and Bacteria Indianapolis, IN: John Wiley & Sons; 2015 pp. 1–11
     [Google Scholar]
  32. Freiwald A, Sauer S. Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 2009; 4:732–742 [View Article][PubMed]
     [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE, USA: Microbial ID, Inc; 1990
     [Google Scholar]
  34. Švec P, Králová S, Busse HJ, Kleinhagauer T, Kýrová K et al. Pedobacter psychrophilus sp. nov., isolated from fragmentary rock. Int J Syst Evol Microbiol 2017; 67:2538–2543
     [Google Scholar]
  35. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
     [Google Scholar]
  36. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
     [Google Scholar]
  37. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  38. Carlone GM, Valadez MJ, Pickett MJ. Methods for distinguishing gram-positive from gram-negative bacteria. J Clin Microbiol 1982; 16:1157–1159[PubMed]
     [Google Scholar]
  39. Bernardet JF, 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 [View Article][PubMed]
     [Google Scholar]
  40. 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][PubMed]
     [Google Scholar]
  41. Margesin R, Gander S, Zacke G, Gounot AM, Schinner F. Hydrocarbon degradation and enzyme activities of cold-adapted bacteria and yeasts. Extremophiles 2003; 7:451–458 [View Article][PubMed]
     [Google Scholar]
  42. Patel JB, Cockerill FR, Bradford PA, Eliopoulos GM, Hindler JA et al. Performance Standards for Antimicrobial Susceptibility Testing, Twenty-Fifth Informational Supplement (M100-S25). Wayne, PA: Clinical and Laboratory Standards Institute (CLSI); 2015
     [Google Scholar]
  43. EUCAST Breakpoint tables for interpretation of MICs and zone diameters. The European Committee on Antimicrobial Susceptibility Testing, version 7.1. 2017 www.eucast.org
     [Google Scholar]
  44. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003555
Loading
Hymenobacter humicola sp. nov., isolated from soils in Antarctica
Int J Syst Evol Microbiol 69, 2755 (2019); https://doi.org/10.1099/ijsem.0.003555
/content/journal/ijsem/10.1099/ijsem.0.003555
/content/journal/ijsem/10.1099/ijsem.0.003555
Loading

Data & Media loading...

Supplements

Supplementary File 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