1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 5

sp. nov. sp. nov. sp. nov. and sp. nov., isolated from subtropical forest soil No Access

Abstract

Four novel bacterial strains, designated RBB1W86, RXD159, RBB189 and RLT163, were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus , among which strains RBB1W86 and RXD159 were closely related to CGMCC 1.15435 with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189 and RLT163 were closely related to CGMCC 1.16273 (98.8 %) and JCM 21530 (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86, RBB189 and RLT163, while strain RXD159 showed a closer relationship with CGMCC 1.16273 and strain RBB189. The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA–DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C and summed feature 9 (10-methyl C and/or iso-C 9) as the major fatty acids. Moreover, C, iso-C, iso-C and summed feature 3 (C 7 and/or C 6) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189 as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus , for which the names sp. nov. (type strain RBB1W86=GDMCC 1.1901=KACC 21988), sp. nov. (type strain RXD159=GDMCC 1.1902=KACC 21989), sp. nov. (type strain RBB189=GDMCC 1.1900=KACC 21990 ) and sp. nov. (type strain RLT163=GDMCC 1.1916=KACC 21991) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Dyella , forest soil , genome comparison and Nanling National Nature Reserve
Funding
This study was supported by the:
  • Guangdong Special Support Plan (Award 2021JC06N628)
    • Principle Award Recipient: HonghuiZhu
  • the GDAS’ Project of Science and Technology Development (Award 2021GDASYL-20210103020)
    • Principle Award Recipient: HonghuiZhu
  • the Science and Technology Program of Guangdong Province (Award 2021B1212050022; 2018B030324001)
    • Principle Award Recipient: HonghuiZhu
  • the Natural Science Foundation of China (Award 32170118)
    • Principle Award Recipient: HonghuiZhu
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005878
2023-05-15
2024-12-05
Loading full text...

Full text loading...

References

  1. Xie CH, Yokota A. Dyella japonica gen. nov., sp. nov., a gamma-proteobacterium isolated from soil. Int J Syst Evol Microbiol 2005; 55:753–756 [View Article] [PubMed]
     [Google Scholar]
  2. 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]
  3. Huang T, Fu J-C, Dong S-H, Zhang Q-M, Wu T-T et al. Dyella telluris sp. nov. and Dyella acidiphila sp. nov., isolated from forest soil of Dinghushan Biosphere Reserve, China. Int J Syst Evol Microbiol 2021; 71:4985 [View Article] [PubMed]
     [Google Scholar]
  4. Chen M-H, Xia F, Lv Y-Y, Zhou X-Y, Qiu L-H. Dyella acidisoli sp. nov., D. flagellata sp. nov. and D. nitratireducens sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:736–743 [View Article] [PubMed]
     [Google Scholar]
  5. Fu JC, Gao ZH, Wu TT, Chen MH, Qiu LH. Dyella amyloliquefaciens sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:3560–3566 [View Article] [PubMed]
     [Google Scholar]
  6. Xia F, Chen MH, Lv YY, Zhang HY, Qiu LH. Dyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:3237–3245 [View Article] [PubMed]
     [Google Scholar]
  7. Zhao F, Guo X-Q, Wang P, He L-Y, Huang Z et al. Dyella jiangningensis sp. nov., a γ-proteobacterium isolated from the surface of potassium-bearing rock. Int J Syst Evol Microbiol 2013; 63:3154–3157 [View Article] [PubMed]
     [Google Scholar]
  8. Anandham R, Kwon S-W, Indira Gandhi P, Kim S-J, Weon H-Y et al. Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L.). Int J Syst Evol Microbiol 2011; 61:392–398 [View Article] [PubMed]
     [Google Scholar]
  9. An DS, Im WT, Yang HC, Yang DC, Lee ST. Dyella koreensis sp. nov., a beta-glucosidase-producing bacterium. Int J Syst Evol Microbiol 2005; 55:1625–1628 [View Article] [PubMed]
     [Google Scholar]
  10. Chaudhary DK, Kim J. Dyella agri sp. nov., isolated from reclaimed grassland soil. Int J Syst Evol Microbiol 2017; 67:4246–4252 [View Article] [PubMed]
     [Google Scholar]
  11. Wang S, Yin Y, Wang J. Microbial degradation of triclosan by a novel strain of Dyella sp. Appl Microbiol Biotechnol 2018; 102:1997–2006 [View Article] [PubMed]
     [Google Scholar]
  12. Li A, Qu Y, Zhou J, Ma F. Characterization of a newly isolated biphenyl-degrading bacterium, Dyella ginsengisoli LA-4. Appl Biochem Biotechnol 2009; 159:687–695 [View Article] [PubMed]
     [Google Scholar]
  13. Silano V, Barat Baviera JM, Bolognesi C, Cocconcelli PS, Crebelli R et al. Safety evaluation of the food enzyme isoamylase from a Dyella sp. strain. EFSA J 2020; 18:e06250 [View Article] [PubMed]
     [Google Scholar]
  14. Desiderato JG, Alvarenga DO, Constancio MTL, Alves LMC, Varani AM. The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications. Genet Mol Biol 2018; 41:507–513 [View Article] [PubMed]
     [Google Scholar]
  15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  16. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci 2008; 105:17994–17999 [View Article] [PubMed]
     [Google Scholar]
  17. Nübel U, Garcia-Pichel F, Muyzer G. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 1997; 63:3327–3332 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
     [Google Scholar]
  26. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  27. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. 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]
  31. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  34. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  35. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds Methods for General and Molecular Microbiology, 3rd edn. Washington, DC: ASM Press; 2007 pp 330–393 [View Article]
     [Google Scholar]
  36. 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]
  37. Collins MD. Isoprenoidquinones. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons Ltd; 1994 pp 265–309
     [Google Scholar]
  38. Sasser M. Technical note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Inc; 1990
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005878
Loading
Dyella humicola sp. nov., Dyella subtropica sp. nov., Dyella silvatica sp. nov. and Dyella silvae sp. nov., isolated from subtropical forest soil
Int J Syst Evol Microbiol 73, 005878 (2023); https://doi.org/10.1099/ijsem.0.005878
/content/journal/ijsem/10.1099/ijsem.0.005878
/content/journal/ijsem/10.1099/ijsem.0.005878
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