1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 12

sp. nov., isolated from a culture sample No Access

Abstract

Strain NIBR12 (=KACC 22094=HAMBI 3739), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture ( NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12 belongs to the genus , with its closest neighbours being SHET (98.8%), RB-3 (97.7%), “ R-30 (95.7 %) and H-8 (95.0 %). Genomic comparison of strain NIBR12 with type species in the genus was conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12 was 70.9 mol%. The major fatty acids of strain NIBR12 were summed feature 8 (C  7 and/or C 6) and summed feature 3 (C 6/C 7). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12 were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12 is identified as represeting a novel species of the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acetobacteraceae , Alphaproteobacteria , coenzyme Q9 , pink pigments , Roseococcus and taxonomy
Funding
This study was supported by the:
  • national institute of biological resources (Award NIBR202002108)
    • Principle Award Recipient: WoojunPark
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005185
2021-12-16
2024-05-13
Loading full text...

Full text loading...

References

  1. Boldareva EN, Tourova TP, Kolganova TV, Moskalenko AA, Makhneva ZK et al. Roseococcus suduntuyensis sp. nov., a new aerobic bacteriochlorophyll a-containing bacterium isolated from a low-mineralized soda lake of Eastern Siberia. Microbiology 2009; 78:92–101 [View Article]
     [Google Scholar]
  2. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 1994; 44:427–434 [View Article]
     [Google Scholar]
  3. Kim M, Shin B, Lee J, Park HY, Park W. Culture-independent and culture-dependent analyses of the bacterial community in the phycosphere of cyanobloom-forming Microcystis aeruginosa. Sci Rep 2019; 9:20416 [View Article] [PubMed]
     [Google Scholar]
  4. Musto H, Naya H, Zavala A, Romero H, Alvarez-Valín F et al. Genomic GC level, optimal growth temperature, and genome size in prokaryotes. Biochem Biophys Res Commun 2006; 347:1–3 [View Article] [PubMed]
     [Google Scholar]
  5. Kim M, Lee J, Yang D, Park HY, Park W. Seasonal dynamics of the bacterial communities associated with cyanobacterial blooms in the Han River. Environ Pollut 2020; 266:115198 [View Article] [PubMed]
     [Google Scholar]
  6. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–6 [View Article] [PubMed]
     [Google Scholar]
  9. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  10. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article] [PubMed]
     [Google Scholar]
  13. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  16. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article] [PubMed]
     [Google Scholar]
  17. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
     [Google Scholar]
  18. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
     [Google Scholar]
  19. Park C, Lee YS, Park SY, Park W. Methylobacterium currus sp. nov., isolated from a car air conditioning system. Int J Syst Evol Microbiol 2018; 68:3621–3626 [View Article] [PubMed]
     [Google Scholar]
  20. Smibert RM, Krieg NR, Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  21. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  22. Saitoh S, Suzuki T, Nishimura Y. Proposal of craurococcus roseus gen. nov., sp. nov. and paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil. Int J Syst Bacteriol 1998; 48:1043–1047 [View Article]
     [Google Scholar]
  23. Margesin R, Zhang D-C. Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil. Int J Syst Evol Microbiol 2013; 63:1411–1416 [View Article] [PubMed]
     [Google Scholar]
  24. Habib N, Khan IU, Hussain F, Zhou E-M, Xiao M et al. Caldovatus sediminis gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:4716–4721 [View Article]
     [Google Scholar]
  25. Alarico S, Rainey FA, Empadinhas N, Schumann P, Nobre MF et al. Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the alpha-1 subclass of the Proteobacteria. Syst Appl Microbiol 2002; 25:198–206 [View Article]
     [Google Scholar]
  26. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI technical note 101. Newark, DE: MIDI Inc; 1990
  27. 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]
  28. Qu J-H, Qu J-Y, He X-B, Li H-F, Luo Y et al. Sediminicoccus rosea gen. nov. sp. nov., isolated from the sediment of a eutrophic lake. J Gen Appl Microbiol 2013; 59:463–468 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005185
Loading
Roseococcus microcysteis sp. nov., isolated from a Microcystis aeruginosa culture sample
Int J Syst Evol Microbiol 71, 005185 (2021); https://doi.org/10.1099/ijsem.0.005185
/content/journal/ijsem/10.1099/ijsem.0.005185
/content/journal/ijsem/10.1099/ijsem.0.005185
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