1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

gen. nov., sp. nov., a novel member of the family isolated from a glacier No Access

Abstract

A novel Gram-stain-negative, rod-shaped, yellow bacterium, designated as LB1R16, was isolated from the Laigu glacier on the Tibetan Plateau, PR China. Strain LB1R16 was catalase-positive, oxidase-negative and grew at 0–28 °C, pH 6.0–8.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB1R16 belongs to the family but formed an independent lineage. The highest level of 16S rRNA gene sequence similarities were found to DJ1R-1 (95.24 %), YLT33 (94.78 %) and DSM 17366 (94.67 %). The genomic DNA G+C content was 68.8 mol%. The main cellular fatty acids were summed feature 8 (C 7/C 6), summed feature 3 (C 7/C 6), C and C-OH. The respiratory quinone was ubiquinone-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid, one unidentified phospholipid and two unidentified polar lipids, which were different from the type strains of , and . Based on a polyphasic approach, a novel species of a new genus, gen. nov., sp. nov., within the family is proposed. The type strain is LB1R16 (=CGMCC 1.11941=NBRC 113873).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cold-adapted , Glacieibacterium , glacier and Tibetan Plateau
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31670003)
    • Principle Award Recipient: Yu-HuaXin
© 2021 Institute of Microbiology, Chinese Academy of Sciences
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004886
2021-07-15
2024-04-20
Loading full text...

Full text loading...

References

  1. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM et al. Analysis of 1000+ type-strain genomes substantially improves taxonomic classification of Aalphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
     [Google Scholar]
  2. Liu K, Li S, Jiao N, Tang K. Pacificamonas flava gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Southeastern Pacific. Curr Microbiol 2014; 9:96–101
     [Google Scholar]
  3. Fukuda W, Chino Y, Araki S, Kondo Y, Imanaka H et al. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock. Int J Syst Evol Microbiol 2014; 64:2034–2040 [View Article] [PubMed]
     [Google Scholar]
  4. Yurkov V, Stackebrandt E, Buss O, Vermeglio A, Gorlenko V et al. Reorganization of the genus Erythromicrobium: description of “Erythromicrobium sibiricum” as Sandaracinobacter sibiricus gen. nov., sp. nov., and of “Erythromicrobium ursincola” as Erythromonas ursincola gen. nov., sp. nov. Int J Syst Bacteriol 1997; 47:1172–1178 [View Article] [PubMed]
     [Google Scholar]
  5. Gich F, Overmann J. Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes. Int J Syst Evol Microbiol 2006; 56:847–854 [View Article] [PubMed]
     [Google Scholar]
  6. Kim M, Kang O, Zhang Y, Ren L, Chang X et al. Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii. Int J Syst Evol Microbiol 2016; 66:91–100 [View Article] [PubMed]
     [Google Scholar]
  7. Geueke B, Busse HJ, Fleischmann T, Kämpfer P, Kohler HE. Description of Sphingosinicella xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans. Int J Syst Evol Microbiol 2007; 57:107–113 [View Article] [PubMed]
     [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 p 115
     [Google Scholar]
  9. 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
     [Google Scholar]
  10. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  14. 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]
  15. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  16. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  17. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
     [Google Scholar]
  18. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  19. Zhang GQ, Yang LL, Liu Q, Liu HC, Zhou YG et al. Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers. Int J Syst Evol Microbiol 2020; 70:4583–4590 [View Article] [PubMed]
     [Google Scholar]
  20. Smibert RM, Krieg NR. Phenotypic characterization. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark: DE: MIDI; 1990
     [Google Scholar]
  22. Collins MD. Isoprenoid quinone analysis in classification and identification. Goodfellow M, Minnikin D. eds In Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
  23. Komagata K, Suzuki K. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988161–207
     [Google Scholar]
  24. Phurbu D, Liu ZX, Liu HC, Lhamo Y, Yangzom P et al. Polymorphobacter arshaanensis sp. nov., containing the photosynthetic gene pufML, isolated from a volcanic lake. Int J Syst Evol Microbiol 2020; 70:1093–1098 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004886
Loading
Glacieibacterium frigidum gen. nov., sp. nov., a novel member of the family Sphingosinicellaceae isolated from a glacier
Int J Syst Evol Microbiol 71, 004886 (2021); https://doi.org/10.1099/ijsem.0.004886
/content/journal/ijsem/10.1099/ijsem.0.004886
/content/journal/ijsem/10.1099/ijsem.0.004886
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