1887

Abstract

A novel Gram-stain-positive, yellow, short-rod-shaped or coccoid bacterial strain, W204, was isolated from a soil sample collected from Jiadengyu national forest park in China and characterized using a polyphasic approach. The cell-wall peptidoglycan contained ornithine as the diagnostic diamino acid. 16S rRNA gene sequence analysis indicated that strain W204 was closely related to CPCC 203535 (97.4 %, similarity), CGMCC 4.5582 (96.9 %), GP-T3-3 (96.8 %), JLT9 (96.7 %), CPCC 203383 (96.6 %) and K22-20 (96.6 %). However, the digital DNA–DNA genome hybridization value between strain W204 and the closest related strain CPCC 203535 was 21.90 %. Complete genome analyses revealed that the size of the genome was 3.54 Mb and the genomic DNA G+C content was 70.79 mol%. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The major menaquinone was MK-8(H). The predominant cellular fatty acids were iso-C, anteiso-C and C. The phenotypic, chemotaxonomic and phylogenetic data suggested that strain W204 should be classified as representative of a novel species of the genus , for which the name sp. nov. is proposed. The type strain is W204 (=GDMCC 1.1391=KCTC 49237).

Funding
This study was supported by the:
  • Xiubin Ke , Fundamental Research Fund for Central Non-Profit Scientific Institution , (Award 1610392019006)
  • , National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809, (Award 31560023)
  • , National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809, (Award 31930004)
  • , Ministry of Agriculture of China , (Award 2019ZX08010-004)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004557
2020-11-11
2021-01-15
Loading full text...

Full text loading...

References

  1. Groth I, Schumann P, Weiss N, Schuetze B, Augsten K et al. Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with L-ornithine in the peptidoglycan. Int J Syst Evol Microbiol 2001; 51:81–87 [CrossRef][PubMed]
    [Google Scholar]
  2. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2018; 9:2007 [CrossRef][PubMed]
    [Google Scholar]
  3. Parte AC, Aidan C. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [CrossRef][PubMed]
    [Google Scholar]
  4. Mayilraj S, Saha P, Suresh K, Saini HS. Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 2006; 56:1657–1661 [CrossRef][PubMed]
    [Google Scholar]
  5. Liu XY, Wang BJ, Jiang CY, Liu SJ. Ornithinimicrobium pekingense sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2008; 58:116–119 [CrossRef][PubMed]
    [Google Scholar]
  6. Kämpfer P, Glaeser SP, Schäfer J, Lodders N, Martin K et al. Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds. Int J Syst Evol Microbiol 2013; 63:119–123 [CrossRef][PubMed]
    [Google Scholar]
  7. Liu LZ, Liu Y, Chen Z, Liu HC, Zhou YG et al. Ornithinimicrobium tianjinense sp. nov., isolated from a recirculating aquaculture system. Int J Syst Evol Microbiol 2013; 63:4489–4494 [CrossRef][PubMed]
    [Google Scholar]
  8. Ramaprasad EVV, Sasikala C, Ramana CV, Ch R. Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva . Int J Syst Evol Microbiol 2015; 65:4627–4631 [CrossRef][PubMed]
    [Google Scholar]
  9. Fang XM, Yan D, Bai JL, Su J, Liu HY et al. Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla. Int J Syst Evol Microbiol 2017; 67:4541–4545 [CrossRef][PubMed]
    [Google Scholar]
  10. Huo Y, Kang JP, Ahn JC, Yang DU, Yang DC. Ornithinimicrobium panacihumi sp. nov., antagonistic bacteria against root rot fungal pathogens, isolated from cultivated ginseng soil. Curr Microbiol 2019; 76:22–28 [CrossRef][PubMed]
    [Google Scholar]
  11. Zhang LY, Ming H, Meng XL, Fang BZ, Jiao JY et al. Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave. Antonie van Leeuwenhoek 2019; 112:179–186 [CrossRef][PubMed]
    [Google Scholar]
  12. Fang X-M, Du H-J, Bai J-L, He W-N, Li J et al. Ornithinimicrobium cerasi sp. nov., isolated from the fruit of Cerasus pseudocerasus and emended description of the genus Ornithinimicrobium . Int J Syst Evol Microbiol 2020; 70:1691–1697 [CrossRef][PubMed]
    [Google Scholar]
  13. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [CrossRef][PubMed]
    [Google Scholar]
  14. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991125–175
    [Google Scholar]
  15. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [CrossRef][PubMed]
    [Google Scholar]
  16. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [CrossRef][PubMed]
    [Google Scholar]
  17. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–W57 [CrossRef][PubMed]
    [Google Scholar]
  18. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  20. Yoon SH, Ha SM, 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  24. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  26. 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 [CrossRef][PubMed]
    [Google Scholar]
  27. Wayne LG. International committee on systematic bacteriology: announcement of the report of the AD hoc committee on reconciliation of approaches to bacterial systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433–434 [CrossRef][PubMed]
    [Google Scholar]
  28. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  29. Park M, Ryu SH, Vu T-HT, Ro H-S, Yun P-Y et al. Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2007; 57:233–237 [CrossRef][PubMed]
    [Google Scholar]
  30. Yoon M-H, Ten LN, Im W-T, Lee S-T. Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost. Int J Syst Evol Microbiol 2008; 58:1878–1884 [CrossRef][PubMed]
    [Google Scholar]
  31. Schumann P. Peptidoglycan structure. Method Microbiol 2011; 38:101–129
    [Google Scholar]
  32. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
    [Google Scholar]
  33. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial Systematics. Method Microbiol 1987; 19:161–207
    [Google Scholar]
  34. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [CrossRef]
    [Google Scholar]
  35. 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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004557
Loading
/content/journal/ijsem/10.1099/ijsem.0.004557
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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