Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 7

sp. nov., an oligotrophic, slightly acidophilic mesophile isolated from sandy soil No Access

Abstract

A bacterial strain, designated S6, was isolated from the sandy soil on a rocky mountain in South China. Cells of S6 were Gram-stain-negative, aerobic, non-spore-forming, non-motile and non-prosthecae-producing. 16S rRNA gene sequence analysis revealed the highest similarities to 12 uncultured bacteria, followed by sp. B6.10-61 (97.14 %). The closest related validly published strains are ATCC 15253 (96.15 %), FWC 21 (96.08 %) and FWC 38 (96.08 %). Phylogenetic analysis based on 16S rRNA gene, genome and proteome sequences demonstrated that S6 formed a separated lineage in the genus . Strain S6 contained Q-10 (97.5 %) as the major ubiquinone and C ω7 and C as the major fatty acids. The polar lipid profile consisted of phosphatidylglycerol, an unknown phosphoglycolipid and three unknown glycolipids. The assembled genome comprises a chromosome with a length of 5.5 Mb and a plasmid of 96 014 bp. The G+C content was 67.6 mol%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus it is proposed that strain S6 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is S6 (=NBRC 115419=GCMCC 1.18594).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Caulobacter , genome , Phenylobacterium , polyphasic taxonomy and uncultured bacteria
Funding
This study was supported by the:
  • Science and Technology Bureau, Changsha (Award kq2208130)
    • Principle Award Recipient: QingshuLiu
  • Science and Technology Bureau, Changsha (Award kq2014171)
    • Principle Award Recipient: QingshanLong
  • Natural Science Foundation of Hunan Province (Award 2023JJ30354)
    • Principle Award Recipient: QingshanLong
  • Department of Science and Technology of Hunan Province (Award 2021NK1040)
    • Principle Award Recipient: QingshuLiu
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006463
2024-07-17
2025-07-20
Loading full text...

Full text loading...

References

  1. Lingens F, Blecher R, Blecher H, Blobel F, Eberspacher J et al. Phenylobacterium immobile gen. nov., sp. nov., a Gram-negative bacterium that degrades the herbicide chloridazon. Int J Syst Bacteriol 1985; 35:26–39 [View Article]
     [Google Scholar]
  2. Kanso S, Patel BKC. Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2004; 54:2141–2146 [View Article] [PubMed]
     [Google Scholar]
  3. Tiago I, Mendes V, Pires C, Morais PV, Verśsimo A. Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium. Syst Appl Microbiol 2005; 28:295–302 [View Article] [PubMed]
     [Google Scholar]
  4. Abraham WR, Macedo AJ, Lünsdorf H, Fischer R, Pawelczyk S et al. Phylogeny by a polyphasic approach of the order Caulobacterales, proposal of Caulobacter mirabilis sp. nov., Phenylobacterium haematophilum sp. nov. and Phenylobacterium conjunctum sp. nov., and emendation of the genus Phenylobacterium. Int J Syst Evol Microbiol 2008; 58:1939–1949 [View Article]
     [Google Scholar]
  5. Oh YS, Roh DH. Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2012; 62:977–983 [View Article] [PubMed]
     [Google Scholar]
  6. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  7. Pascual J, Wüst PK, Geppert A, Foesel BU, Huber KJ et al. Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 2015; 38:534–544 [View Article] [PubMed]
     [Google Scholar]
  8. Payne A, Holmes N, Rakyan V, Loose M. BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics 2019; 35:2193–2198 [View Article]
     [Google Scholar]
  9. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  10. Tatiana T, Michael DC, Azat B, Vyacheslav C, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  11. 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] [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. 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]
  14. 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]
  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. 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]
  17. 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]
  18. Kimura MJ. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1979; 16:111–120 [View Article]
     [Google Scholar]
  19. Felsenstein J. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  20. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
     [Google Scholar]
  21. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  22. Rodriguez-R LM, Konstantinidis KTJM. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  23. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
     [Google Scholar]
  24. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  25. Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88–W92 [View Article] [PubMed]
     [Google Scholar]
  26. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Tang J, Li Y, Zhang L, Mu J, Jiang Y et al. Biosynthetic pathways and functions of indole-3-acetic acid in microorganisms. Microorganisms 2023; 11:2077 [View Article] [PubMed]
     [Google Scholar]
  29. Siles JA, Starke R, Martinovic T, Parente Fernandes ML, Orgiazzi A et al. Distribution of phosphorus cycling genes across land uses and microbial taxonomic groups based on metagenome and genome mining. Soil Biol Biochem 2022; 174:108826 [View Article]
     [Google Scholar]
  30. Vazquez P, Holguin G, Puente ME, Lopez-Cortes A, Bashan YJB. Phosphate-solubilizing microorganisms associated with the rhizosphere of mangroves in a semiarid coastal lagoon. Biol Fertil Soils 2000; 30:460–468 [View Article]
     [Google Scholar]
  31. 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]
  32. Shin YK, Lee JS, Chun CO, Kim HJ, Park YH. Isoprenoid quinone profiles of the Leclercia Adecarboxylata KCTC 1036T. J Microbiol Biotechnol 1996; 6:68–69
     [Google Scholar]
  33. Baek C, Shin SK, Yi H. Phenylobacterium parvum sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2019; 69:1169–1172 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006463
Loading
Phenylobacterium montanum sp. nov., an oligotrophic, slightly acidophilic mesophile isolated from sandy soil
Int J Syst Evol Microbiol 74, 006463 (2024); https://doi.org/10.1099/ijsem.0.006463
/content/journal/ijsem/10.1099/ijsem.0.006463
/content/journal/ijsem/10.1099/ijsem.0.006463
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