1887

Abstract

In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to KCTC 42859 (98.2%) followed by KCTC 42562 (98%), II-D5 (97.9%) and MWH-BRAZ-DAM2D (97.4%). Growth of strain JUR4 occurred at 10–37 °C (optimum, 30 °C), at pH 5.5–8.0 (optimum, 6.5–7) and in the presence of 0–0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4 was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4 and closely related reference strains were 21.0–24.8% and 74.7–81.4%, respectively. Strain JUR4 contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C and summed feature 3 (comprising C 7 and/or C 6), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is JUR4 (=KACC 21745=NBRC 114484).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004957
2021-08-17
2024-06-14
Loading full text...

Full text loading...

References

  1. Hahn MW, Kasalický V, Jezbera J, Brandt U, Jezberová J et al. Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2010; 60:1358–1365 [View Article] [PubMed]
    [Google Scholar]
  2. Kasalický V, Jezbera J, Šimek K, Hahn MW. Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2710–2714 [View Article] [PubMed]
    [Google Scholar]
  3. Hahn MW, Kasalický V, Jezbera J, Brandt U, Šimek K. Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2946–2950 [View Article] [PubMed]
    [Google Scholar]
  4. Gich F, Schubert K, Bruns A, Hoffelner H, Overmann J. Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. Appl Environ Microbiol 2005; 7:5908–5919 [View Article]
    [Google Scholar]
  5. Kasalický V, Jezbera J, Hahn MW, Šimek K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One 2013; 8:e58209 [View Article] [PubMed]
    [Google Scholar]
  6. Salcher MM, Šimek K. Isolation and cultivation of planktonic freshwater microbes is essential for a comprehensive understanding of their ecology. Aquat Microb Ecol 2016; 77:183–196 [View Article]
    [Google Scholar]
  7. Kasalický V, Zeng Y, Piwosz K, Šimek K, Kratochvilová H et al. Aerobic anoxygenic photosynthesis is commonly present within the genus Limnohabitans. Appl Environ Microbiol 2018; 84:e02116 [View Article]
    [Google Scholar]
  8. Zeng Y, Kasalický V, Šimek K, Koblížeka M. Genome sequences of two freshwater betaproteobacterial isolates, Limnohabitans species strains Rim28 and Rim47, indicate their capabilities as both photoautotrophs and ammonia oxidizers. J Bacteriol 2012; 194:6302–6303 [View Article] [PubMed]
    [Google Scholar]
  9. Salah Ud-Din AIM, Roujeinikova A. Methyl-accepting chemotaxis proteins: a core sensing element in prokaryotes and archaea. Cell Mol Life Sci 2017; 74:3293–3303 [View Article] [PubMed]
    [Google Scholar]
  10. Clausznitzer D, Micali G, Neumann S, Sourjik V, Endres RG. Predicting chemical environments of bacteria from receptor signaling. PLoS Comput Biol 2014; 10:e1003870 [View Article] [PubMed]
    [Google Scholar]
  11. Bandumula N. Rice production in Asia: Key to global food security. Proc Natl Acad Sci, India, Sect B Biol Sci 2017; 88:1323–1328 [View Article]
    [Google Scholar]
  12. Edwards J, Johnson C, Santos-Medellin C. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A 2015; 112:E911–20 [View Article] [PubMed]
    [Google Scholar]
  13. Chhetri G, Kim J, Kim I, Lee B, Jang W et al. Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant. Int J Syst Evol Microbiol 2020; 70:5382–5388 [View Article] [PubMed]
    [Google Scholar]
  14. Kim J, Chhetri G, Kim I. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol 2020; 959–966:
    [Google Scholar]
  15. Choi J, Lee D, Jang JH. Aestuariibaculum marinum sp. nov., a marine bacterium isolated from seawater in. South Korea J Microbiol 2018; 56:614
    [Google Scholar]
  16. 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 Microbial 2012; 62:716–721 [View Article]
    [Google Scholar]
  17. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  20. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [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 [View Article] [PubMed]
    [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. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293
    [Google Scholar]
  24. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. 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 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA. Blast Ring image generator (BRIG): Simple prokaryote genome comparisons. BMC Genomics 2011; 12:402 [View Article] [PubMed]
    [Google Scholar]
  29. 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 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Chhetri G, Kim J, Kim I, Kim H, Seo T. Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis. Int J Syst Evol Microbiol 2020; 70:3724–3730 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Gerhardt P, Murray R, Wood W, Krieg N. Phenotypic characterization. In Methods for General and Molecular Bacteriology 1994 pp 607–654
    [Google Scholar]
  34. Kim H, Chhetri G, Kim J, Kang M, Seo T. Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6180–6187 [View Article] [PubMed]
    [Google Scholar]
  35. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
    [Google Scholar]
  36. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988; 38:358–361
    [Google Scholar]
  37. 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 Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  38. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Meth Microbiol 1987; 19:205
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004957
Loading
/content/journal/ijsem/10.1099/ijsem.0.004957
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