1887

Abstract

A novel phosphate-solubilizing and 3-indoleacetic acid producing bacterium, designated strain CMYE1, was isolated from the phyllosphere of pomelo () in Meizhou, Guangdong Province, PR China. Cells were Gram-stain-negative, facultative aerobic, non-spore-forming, rod-shaped and motile with peritrichous flagella. It had the highest 16S rRNA gene sequence similarity to NRRL B-65522 (99.0 %), followed by LMG 2657 (98.1 %), B120 (97.7 %), 29Y89B (97.6 %) and other species (<97.6 %). However, phylogenomic analyses clearly showed that strain CMYE1 should be assigned into the genus , and was most closely related to LMG 25322 (96.7 %). Genome comparisons showed that the novel strain shared ≤83.2 % average nucleotide identity and ≤26.5 % digital DNA–DNA hybridization values with closely related strains, respectively. It contained C, C cyclo, summed feature 3 (C 7 and/or C 6) and summed feature 8 (C 7 and/or C 6) as the major fatty acids. Based on the results of phylogenetic, phenotypic and chemotaxonomic analyses, as well as genome comparisons, strain CMYE1 belongs to a novel species of the genus , for which the name sp. nov. is proposed with the type strain CMYE1 (=GDMCC 1.2674=JCM 34792).

Funding
This study was supported by the:
  • the GDAS’ Project of Science and Technology Development (Award 2021GDASYL-20210103020)
    • Principle Award Recipient: Guang-DaFeng
  • Water Resources Department of Guangdong Province (Award 2018B030324001)
    • Principle Award Recipient: HonghuiZhu
  • the National Natural Science Foundation of China (Award 32000007)
    • Principle Award Recipient: Guang-DaFeng
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005316
2022-04-13
2022-05-18
Loading full text...

Full text loading...

References

  1. Pan M-K, Feng G-D, Yao Q, Li J, Liu C. Erwinia phyllosphaerae sp. nov., a novel bacterium isolated from phyllosphere of pomelo (Citrus maxima). Figshare 2022. 10.6084/m9.figshare.19127516.v1
    [Google Scholar]
  2. Winslow CE, Broadhurst J, Buchanan RE, Krumwiede C, Rogers LA et al. The families and genera of the bacteria: final report of the Committee of the Society of American Bacteriologists on characterization and classification of bacterial types. J Bacteriol 1920; 5:191–229 [View Article] [PubMed]
    [Google Scholar]
  3. Adeolu M, Alnajar S, Naushad S, S Gupta R. Genome-based phylogeny and taxonomy of the “Enterobacteriales”: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article]
    [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  5. Gardan L, Christen R, Achouak W, Prior P. Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya). Int J Syst Evol Microbiol 2004; 54:107–113 [View Article] [PubMed]
    [Google Scholar]
  6. López MM, Roselló M, Llop P, Ferrer S, Christen R et al. Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms. Int J Syst Evol Microbiol 2011; 61:561–567 [View Article] [PubMed]
    [Google Scholar]
  7. Matsuura T, Mizuno A, Tsukamoto T, Shimizu Y, Saito N et al. Erwinia uzenensis sp. nov., a novel pathogen that affects European pear trees (Pyrus communis L.). Int J Syst Evol Microbiol 2012; 62:1799–1803 [View Article] [PubMed]
    [Google Scholar]
  8. Mergaert J, Hauben L, Cnockaert MC, Swings J. Reclassification of non-pigmented Erwinia herbicola strains from trees as Erwinia billingiae sp. nov. Int J Syst Bacteriol 1999; 49:377–383 [View Article] [PubMed]
    [Google Scholar]
  9. Geider K, Auling G, Du Z, Jakovljevic V, Jock S et al. Erwinia tasmaniensis sp. nov., a non-phytopathogenic bacterium from apple and pear trees. Int J Syst Evol Microbiol 2006; 56:2937–2943 [View Article] [PubMed]
    [Google Scholar]
  10. Rojas AM, Rios JEG de L, Saux MF-L, Jimenez P, Reche P et al. Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots. Int J Syst Evol Microbiol 2004; 54:2217–2222 [View Article] [PubMed]
    [Google Scholar]
  11. Moretti C, Hosni T, Vandemeulebroecke K, Brady C, De Vos P et al. Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Int J Syst Evol Microbiol 2011; 61:2745–2752 [View Article] [PubMed]
    [Google Scholar]
  12. Rezzonico F, Smits THM, Born Y, Blom J, Frey JE et al. Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. Int J Syst Evol Microbiol 2016; 66:1583–1592 [View Article] [PubMed]
    [Google Scholar]
  13. Liu B, Luo J, Li W, Long X-F, Zhang Y-Q et al. Erwinia teleogrylli sp. nov., a bacterial isolate associated with a Chinese cricket. PLoS One 2016; 11:e0146596 [View Article] [PubMed]
    [Google Scholar]
  14. Campillo T, Luna E, Portier P, Fischer-Le Saux M, Lapitan N et al. Erwinia iniecta sp. nov., isolated from Russian wheat aphid (Diuraphis noxia). Int J Syst Evol Microbiol 2015; 65:3625–3633 [View Article]
    [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 U S A 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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  23. 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]
  24. Singh NK, Wood JM, Mhatre SS, Venkateswaran K. Correction to: Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station. Appl Microbiol Biotechnol 2019; 103:6851–6852 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Lee I, Chalita M, Ha SM, Na SI, Yoon SH 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]
  27. Na SI, Kim YO, Yoon SH, Ha SM, 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]
  28. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. 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]
  37. 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 Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  38. Pikovskaya RI. Mobilization of phosphorus in soil in connection with the vital activity of some microbial species. Mikrobiologiya 1948; 17:362–370
    [Google Scholar]
  39. Pérez-Miranda S, Cabirol N, George-Téllez R, Zamudio-Rivera LS, Fernández FJ. O-CAS, a fast and universal method for siderophore detection. J Microbiol Methods 2007; 70:127–131 [View Article]
    [Google Scholar]
  40. Bric JM, Bostock RM, Silverstone SE. Rapid in situ assay for indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane. Appl Environ Microbiol 1991; 57:535–538 [View Article]
    [Google Scholar]
  41. Poly F, Monrozier LJ, Bally R. Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 2001; 152:95–103 [View Article]
    [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005316
Loading
/content/journal/ijsem/10.1099/ijsem.0.005316
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare

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