1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 5

sp. nov., isolated from high Arctic glacial till, and emended description of the genus Open Access

Abstract

A yellow pigmented, Gram-stain-positive, motile, facultatively anaerobic and irregular rod-shaped bacteria (strain M0-14) was isolated from a till sample collected from the foreland of a high Arctic glacier near the settlement of Ny-Ålesund in the Svalbard Archipelago, Norway. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that M0-14 formed a lineage within the family , suborder . M0-14 represented a novel member of the genus and had highest 16S rRNA gene sequence similarity to LRZ-2 (97.3 %). Growth occurred at 4–25 °C (optimum 4–18 °C), at pH 6.0–9.0 (optimum pH 7.0), and in the presence of 0–5 % (w/v) NaCl. The predominant menaquinone was MK-9(H) and the major fatty acids were anteiso-C, C and summed feature 3 (comprising Cω7 and/or Cω6). The major polar lipids were phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylinositol, one undefined phospholipid and five undefined phosphoglycolipids. The cell-wall diamino acid was -ornithine whereas rhamnose and mannose were the cell-wall sugars. Polyphosphate particles were found inside the cells of M0-14. Polyphosphate kinase and polyphosphate-dependent glucokinase genes were detected during genomic sequencing of M0-14. In addition, the complete gene cluster and synthesis genes, which are important for the uptake and transport of phosphorus in cells, were annotated in the genomic data. According to the genomic data, M0-14 has a metabolic pathway related to phosphorus accumulation. The DNA G+C content of the genomic DNA was 70.8 %. On the basis of its phylogenetic relationship, phenotypic properties and chemotaxonomic distinctiveness, strain M0-14 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is M0-14 (= CCTCC AB 2012967 = NRRL B-59105).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): high-Arctic glacial till , Pengzhenrongella phosphoraccumulans and Svalbard Archipelago
Funding
This study was supported by the:
  • Chinese Polar Scientific Strategy Research Fund (Award IC201706)
    • Principle Award Recipient: FangPeng
  • the R and D Infrastructure and Facility Development Programme of the Ministry of Science and Technology of the People’s Republic of China (Award NIMR-2023-8)
    • Principle Award Recipient: FangPeng
  • National Key R&D Program of China (Award 2022YFC2807501)
    • Principle Award Recipient: FangPeng
  • National Natural Science Foundation of China (Award 42076230)
    • Principle Award Recipient: FangPeng
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006368
2024-05-09
2024-05-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/74/5/ijsem006368.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006368&mimeType=html&fmt=ahah

References

  1. Stackebrandt E, Rainey FA, Ward-rainey NL. Proposal for a new hierarchic classification system, actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  2. Kim MC, Ju YH, Hwang UA, Liu P, Pak SH et al. Pengzhenrongella sicca gen. nov., sp. nov., a new member of suborder Micrococcineae isolated from high Arctic tundra soil. Int J Syst Evol Microbiol 2021; 71:004988 [View Article] [PubMed]
     [Google Scholar]
  3. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley Press; 1991 pp 115–147
     [Google Scholar]
  4. 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]
  5. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  8. Mount DW. Maximum parsimony method for phylogenetic prediction. Cold Spring Harb Protoc 2008; 2008:db [View Article]
     [Google Scholar]
  9. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  10. Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing. Genome Biol 2013; 14:405 [View Article] [PubMed]
     [Google Scholar]
  11. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  15. 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] [PubMed]
     [Google Scholar]
  16. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  17. Zuo G-H. CVTree: a parallel alignment-free phylogeny and taxonomy tool based on composition vectors of genomes. Genom Proteom Bioinform 2021; 19:662–667 [View Article] [PubMed]
     [Google Scholar]
  18. Doetsch RN. Determinative methods of light microscopy. In Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 21–33
     [Google Scholar]
  19. Duckworth AW, Grant WD, Jones BE, Steenbergen R. Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 1996; 19:181–191 [View Article]
     [Google Scholar]
  20. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article] [PubMed]
     [Google Scholar]
  21. Rodriguez-Kabana R, Godoy G, Morgan-Jones G, Shelby RA. The determination of soil chitinase activity: conditions for assay and ecological studies. Plant Soil 1983; 75:95–106 [View Article]
     [Google Scholar]
  22. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings; 2002
     [Google Scholar]
  23. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
  24. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  25. Xie C-H, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article] [PubMed]
     [Google Scholar]
  26. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  27. 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]
  28. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  29. Stackebrandt E, Kandler O. Taxonomy of the Genus Cellulomonas, Based on Phenotypic Characters and Deoxyribonucleic Acid-Deoxyribonucleic Acid Homology, and Proposal of Seven Neotype Strains. International Journal of Systematic Bacteriology 1979; 29:273–282 [View Article]
     [Google Scholar]
  30. Yi H, Schumann P, Chun J. Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov. International Journal of Systematic and Evolutionary Microbiology 2007; 57:151–156 [View Article]
     [Google Scholar]
  31. Yoon M-H, Ten LN, Im W-T, Lee S-T. Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 2008; 58:1878–1884 [View Article]
     [Google Scholar]
  32. Jones BE, Grant WD, Duckworth AW, Schumann P, Weiss N et al. Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad. International Journal of Systematic and Evolutionary Microbiology 2005; 55:1711–1714 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006368
Loading
Pengzhenrongella phosphoraccumulans sp. nov., isolated from high Arctic glacial till, and emended description of the genus Pengzhenrongella
Int J Syst Evol Microbiol 74, 006368 (2024); https://doi.org/10.1099/ijsem.0.006368
/content/journal/ijsem/10.1099/ijsem.0.006368
/content/journal/ijsem/10.1099/ijsem.0.006368
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