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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 11

gen. nov., sp. nov., a novel member of the family isolated from toxin-producing dinoflagellate No Access

Abstract

A Gram-stain-negative, aerobic, rod-shaped strain (R2A-3) was isolated from the toxin-producing dinoflagellate and identified as a novel genus and new species based on a polyphasic taxonomic approach. The optimum conditions for growth of the strain were at 25 °C, pH 8.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA genes and 92 core genes sets revealed that strain R2A-3 belongs to the family in the class and represented an independent taxon separated from other genera. The 16S rRNA gene of strain R2A-3 showed the highest sequence similarity to TG408 (95.2%), HA-01 (94.1%) and NH6-24 (93.2%), and less than 92.8 % similarity to other genera in the family . The genome length of strain R2A-3 was 3608892 bp with 65.2 mol% G+C content. Summed feature 8 (comprising C 7 and/or C 6) was the major fatty acid (>10 %). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected as the major polar lipids. The major respiratory quinone was ubiquinone-8. According to its phylogenetic, phenotypic, chemotaxonomic and genomic features, strain R2A-3 represents a new species in the new genus of the family . It is recommended to name it gen. nov., sp. nov. The type strain is R2A-3 (=KCTC 82469=GDMCC 1.2523).

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Keyword(s): dinoflagellate , novel genus , novel species , phylogeny and polyphasic taxonomy
© 2021 The Authors
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2021-11-05
2024-05-02
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References

  1. Henrici AT, Johnson DE. Studies of freshwater bacteria: Ii. Stalked bacteria, a new order of schizomycetes 1. J Bacteriol Res 1935; 30:61
     [Google Scholar]
  2. 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]
  3. Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2015; 107:467–485 [View Article] [PubMed]
     [Google Scholar]
  4. Liu Q, Liu HC, Zhou YG, Xin YH. Stenotrophobium rhamnosiphilum gen. nov., sp. nov., isolated from a glacier, proposal of Steroidobacteraceae fam. nov. in Nevskiales and emended description of the family Nevskiaceae. Int J Syst Evol Microbiol 2019; 69:1404–1410 [View Article] [PubMed]
     [Google Scholar]
  5. Zhang XQ, Sun C, Wang CS, Zhang X, Zhou X. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:3541–3546 [View Article] [PubMed]
     [Google Scholar]
  6. Weon HY, Kim BY, Son JA, Song MH, Kwon SW. Nevskia soli sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2008; 58:578–580 [View Article] [PubMed]
     [Google Scholar]
  7. Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ERB. Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008. Int J Syst Evol Microbiol 2013; 63:254–259 [View Article] [PubMed]
     [Google Scholar]
  8. Liu Y, Song XF, Jiang JT, Liu YH, Xu CJ. Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2011; 61:408–411 [View Article] [PubMed]
     [Google Scholar]
  9. Kim JH, Baek J, Yoon JH, Sukhoom A, Kim W. Polyphasic taxonomic analysis of Sinimarinibacterium arenosum sp. nov., a halophilic bacterium isolated from marine sediment. FEMS Microbiol Lett 2020367 [View Article]
     [Google Scholar]
  10. Friedrich MM, Lipski A. Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter. Int J Syst Evol Microbiol 2008; 58:2324–2329 [View Article] [PubMed]
     [Google Scholar]
  11. Sheu S-Y, Chen T-Y, Young C-C, Chen W-M. Stagnimonas aquatica gen. nov., sp. nov., a new member of the family Nevskiaceae isolated from a freshwater mesocosm. Int J Syst Evol Microbiol 2019; 69:1606–1612 [View Article] [PubMed]
     [Google Scholar]
  12. Liu Q, Liu H-C, Zhou Y-G, Xin Y-H. Stenotrophobium rhamnosiphilum gen. nov., sp. nov., isolated from a glacier, proposal of Steroidobacteraceae fam. nov. in Nevskiales and emended description of the family Nevskiaceae. Int J Syst Evol Microbiol 2019; 69:1404–1410 [View Article] [PubMed]
     [Google Scholar]
  13. Kim MK, Kim Y-J, Cho D-H, Yi T-H, Soung N-K et al. Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2007; 57:2591–2594 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. 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]
  16. Hall TA. Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic Acids Symposium Series London: Oxford University Press; pp c1979–c2000
     [Google Scholar]
  17. 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]
  18. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945 [View Article]
     [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. 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]
  23. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  24. M-K JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 186:1471–2105
     [Google Scholar]
  25. 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]
  26. Luo C, Rodriguez-R LM, Konstantinidis KT. Mytaxa: An advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
  27. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  30. Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol 2020; 70:2937–2948 [View Article] [PubMed]
     [Google Scholar]
  31. Li Z, Mertens KN, Nézan E, Chomérat N, Bilien G et al. Discovery of a new clade nested within the genus Alexandrium (Dinophyceae): Morpho-molecular characterization of Centrodinium punctatum (Cleve) F.J.R. Taylor. Protist 2019; 170:168–186 [View Article]
     [Google Scholar]
  32. Jiang L, Lim CJ, Kim S-G, Jeong JC, Kim CY et al. Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds. J Microbiol 2020; 58:24–29 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 1980; 48:277–282 [View Article] [PubMed]
     [Google Scholar]
  35. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). In MIDI Technical MIDI Technical Note #101, 2006 Newark, DE, USA: MIDI Inc;
     [Google Scholar]
  36. Gutierrez T, Green DH, Nichols PD, Whitman WB, Semple KT et al. Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton. Appl Environ Microbiol 2013; 79:205–214 [View Article] [PubMed]
     [Google Scholar]
  37. Kim MK, Kim Y-J, Cho D-H, Yi T-H, Soung N-K et al. Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2007; 57:2591–2594 [View Article] [PubMed]
     [Google Scholar]
  38. Zhou Y, Zhang Y-Q, Zhi X-Y, Wang X, Dong J et al. Description of Sinobacter flavus gen. nov., sp. nov., and proposal of Sinobacteraceae fam. nov. Int J Syst Evol Microbiol 2008; 58:184–189 [View Article] [PubMed]
     [Google Scholar]
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Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum
Int J Syst Evol Microbiol 71, 005084 (2021); https://doi.org/10.1099/ijsem.0.005084
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