1887

Abstract

A Gram-stain-negative bacterium, designated as R-40, was isolated from sediment of the Mulong river in Mianyang city, Sichuan province, PR China. The cells of strain R-40 were aerobic non-motile and formed translucent white colonies on R2A agar. Growth occurred at 15–37 °C (optimum 30 °C), pH 5.0–9.0 (optimum 7.0) and salinities of 0–3.0 % (w/v, optimum 0 %). R-40 showed 95.2–96.6 % 16S rRNA gene sequence similarities with the type strains of species of the genera , , , and in the family . The results of phylogenetic analysis based on genome sequences indicated that the strain was clustered with type strains of species of the genera and in the family but formed a distinct lineage. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH) and average amino acid identity (AAI) values between R-40 and type strains of species of the genera , , , and ranged from 69.3 to 74.1 %, from 18.2 to 21.4 % and from 60.1 to 67.4 %, respectively. The major cellular fatty acids were C, C cyclo and summed feature 3 (Cω7 and/or Cω6). The major quinone was ubiquinone-8 (Q-8). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and small amounts of glycophospholipids. The genome size of R-40 was 5.1 Mbp with 54.0 % DNA G+C content. On the basis of the evidence presented in this study, strain R-40 represents a novel species of a novel genus in the family , for which the name gen. nov., sp. nov. (type strain R-40=MCCC 1K08818=KCTC 8137) is proposed.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award No. 32170128)
    • Principle Award Recipient: ShiyuZhao
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006289
2024-03-28
2024-04-13
Loading full text...

Full text loading...

References

  1. 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]
  2. Felföldi T, Szabó A, Tóth E, Schumann P, Kéki Z et al. Sapientia aquatica gen. nov., sp. nov., isolated from a crater lake. Int J Syst Evol Microbiol 2020; 70:346–351 [View Article] [PubMed]
    [Google Scholar]
  3. Yoon JH, Lee ST, Park YH. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48 Pt 1:187–194 [View Article] [PubMed]
    [Google Scholar]
  4. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
    [Google Scholar]
  5. Zhang W, Sun Z. Random local neighbor joining: a new method for reconstructing phylogenetic trees. Mol Phylogenet Evol 2008; 47:117–128 [View Article] [PubMed]
    [Google Scholar]
  6. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  7. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  8. 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]
  9. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  10. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  11. Sambrook J, Fritsch FE, Maniatis T. Molecular cloning: a laboratory manual. CSH 1982
    [Google Scholar]
  12. Luo R, Liu B, Xie Y, Li Z, Huang W et al. Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2015; 4:30 [View Article] [PubMed]
    [Google Scholar]
  13. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  14. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
    [Google Scholar]
  15. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
    [Google Scholar]
  16. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
    [Google Scholar]
  17. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Hua Z-S, Qu Y-N, Zhu Q, Zhou E-M, Qi Y-L et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832 [View Article] [PubMed]
    [Google Scholar]
  20. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak TA, Marzluf G. eds Methods for General and Molecular Microbiology 2007 pp 19–33 [View Article]
    [Google Scholar]
  21. Joseph NM, Sistla S, Dutta TK, Badhe AS, Rasitha D et al. Reliability of Kirby-Bauer disk diffusion method for detecting meropenem resistance among non-fermenting gram-negative bacilli. Indian J Pathol Microbiol 2011; 54:556–560 [View Article] [PubMed]
    [Google Scholar]
  22. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Usfcc Newsl 1990
    [Google Scholar]
  23. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
    [Google Scholar]
  24. 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 Met 1984; 2:233–241 [View Article]
    [Google Scholar]
  25. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. J Microbiol Methods 1988; 19:161–207
    [Google Scholar]
  26. Sagot B, Gaysinski M, Mehiri M, Guigonis J-M, Le Rudulier D et al. Osmotically induced synthesis of the dipeptide N-acetylglutaminylglutamine amide is mediated by a new pathway conserved among bacteria. Proc Natl Acad Sci U S A 2010; 107:12652–12657 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Jin C-Z, Jin L, Liu M-J, Lee J-M, Park D-J et al. Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  29. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
  30. Zhang J, Kim Y-J, Hoang V-A, Lan Nguyen N, Wang C et al. Duganella ginsengisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2016; 66:56–61 [View Article] [PubMed]
    [Google Scholar]
  31. Sahin N, Gonzalez JM, Iizuka T, Hill JE. Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov. FEMS Microbiol Lett 2010; 307:25–29 [View Article] [PubMed]
    [Google Scholar]
  32. Fernandes C, Rainey FA, Nobre MF, Pinhal I, Folhas F et al. Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water. Syst Appl Microbiol 2005; 28:596–603 [View Article] [PubMed]
    [Google Scholar]
  33. Kämpfer P, P. Glaeser S, Lodders N, Busse H-J, Falsen E. Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals. Int J Syst Evol Microbiol 2013; 63:412–417 [View Article]
    [Google Scholar]
  34. Wu X, Jin C-Z, Jin F-J, Li T, Sung YJ et al. Lacisediminimonas profundi gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from freshwater sediment. Antonie van Leeuwenhoek 2020; 113:253–264 [View Article] [PubMed]
    [Google Scholar]
  35. Ishii S, Ashida N, Ohno H, Segawa T, Yabe S et al. Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. Int J Syst Evol Microbiol 2017; 67:1841–1848 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006289
Loading
/content/journal/ijsem/10.1099/ijsem.0.006289
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