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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

gen. nov., sp. nov., isolated from forest soil, and reclassification of as gen. nov., comb. nov. No Access

Abstract

A lemon-chiffon strain, designated QH1ED-6-2, was isolated from a soil sample collected from Qinghai Virgin Forests, Qinghai Province, PR China. The strain was Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain QH1ED-6-2 belongs to the family , and has the highest similarity values of 93.6–92.0 % to CCUG 58939, CCUG 58938, SDU1-6 and DSM 24574, respectively. The major cellular fatty acids included iso-C, C 5, iso-C 3-OH and summed feature 3. The major polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone-7. The average amino acid identity values and percentages of conserved proteins between QH1ED-6-2 and its closely related genera were 66.4–69.6 % and 58.9–64.9 %, respectively, which are interspersed in the intra-genera cutoff values. The digital DNA–DNA hybridization values were 17.6–19.2 %. The draft genome size of strain QH1ED-6-2 was 7.98 Mbp with a DNA G+C content of 51.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic data, genomic DNA G+C content, as well as AAI, POCP and dDDH results, strain QH1ED-6-2 represents a novel species of a new genus in the family , for which the name sp. nov. is proposed. The type strain is QH1ED-6-2 (=GDMCC 1.2318=JCM 35041). We also propose the reclassification of as gen. nov., comb. nov. (type strain SDU1-6=CGMCC 1.13492=JCM 32520).

  • Received:
  • Accepted:
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Keyword(s): Fulvivirgaceae , genomic analyses , Parachryseolinea silvisoli , polyphasic identification and Pseudochryseolinea flava
© 2022 The Authors
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2022-10-07
2024-05-18
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References

  1. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:1–74 [View Article]
     [Google Scholar]
  2. Nedashkovskaya OI, Kim SB, Shin DS, Beleneva IA, Mikhailov VV. Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm. Int J Syst Evol Microbiol 2007; 57:1046–1049 [View Article]
     [Google Scholar]
  3. Kim JJ, Alkawally M, Brady AL, Rijpstra WIC, Sinninghe Damsté JS et al. Chryseolinea serpens gen. nov., sp. nov., a member of the phylum bacteroidetes isolated from soil. Int J Syst Evol Microbiol 2013; 63:654–660 [View Article]
     [Google Scholar]
  4. Lee SA, Kim Y, Sang M-K, Song J, Kwon S-W et al. Chryseolinea soli sp. nov., isolated from soil. J Microbiol 2019; 57:122–126 [View Article]
     [Google Scholar]
  5. Maejima Y, Iino T, Muraguchi Y, Fukuda K, Ohkuma M et al. Chryseotalea sanaruensis gen. nov., sp., nov., a member of the family Cytophagaceae, isolated from a brackish lake in Hamamatsu, Japan. Curr Microbiol 2020; 77:306–312 [View Article]
     [Google Scholar]
  6. Yoon JH, Kang SJ, Lee SY, Lee JS, Park S. Ohtaekwangia koreensis gen. nov., sp. nov. and Ohtaekwangia kribbensis sp. nov., isolated from marine sand, deep-branching members of the phylum Bacteroidetes. Int J Syst Evol Microbiol 2011; 61:1066–1072 [View Article]
     [Google Scholar]
  7. Nupur SS, Sharma S, Kumar Singh P, Suresh K, Anil Kumar P. Fulvivirga imtechensis sp. nov., a member of the phylum Bacteroidetes. Int J Syst Evol Microbiol 2012; 62:2213–2217 [View Article]
     [Google Scholar]
  8. Livingstone PG, Morphew RM, Cookson AR, Whitworth DE. Genome analysis, metabolic potential, and predatory capabilities of Herpetosiphon llansteffanense sp. nov. Appl Environ Microbiol 2018; 84:1–14 [View Article]
     [Google Scholar]
  9. Chen DH, Ronald PC. A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep 1999; 17:53–57 [View Article]
     [Google Scholar]
  10. 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]
     [Google Scholar]
  11. Kai AKL, Cheung YK, Yeung PKK, Wong JTY. Development of single-cell PCR methods for the Raphidophyceae. Harmful Algae 2006; 5:649–657 [View Article]
     [Google Scholar]
  12. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article]
     [Google Scholar]
  13. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  16. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger atasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  17. 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]
  18. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  19. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
     [Google Scholar]
  22. Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P. Phylogenomic re-assessment of the thermophilic genus Geobacillus. Syst Appl Microbiol 2016; 39:527–533 [View Article] [PubMed]
     [Google Scholar]
  23. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article]
     [Google Scholar]
  24. Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Alkalihalobacterium elongatum gen. nov. sp. nov.: an antibiotic-producing bacterium isolated from Lonar Lake and reclassification of the genus Alkalihalobacillus into seven novel genera. Front Microbiol 2021; 12:722369 [View Article]
     [Google Scholar]
  25. Lv YY, Wang J, You J, Qiu LH. Chitinophaga dinghuensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4816–4822 [View Article]
     [Google Scholar]
  26. Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA et al. Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 2014; 64:594–598 [View Article]
     [Google Scholar]
  27. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
     [Google Scholar]
  28. Son HM, Kook M, Kim JH, Yi TH. Taibaiella koreensis sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2014; 64:1018–1023 [View Article]
     [Google Scholar]
  29. Wang CL, Lv YY, Li AZ, Bao GG, Feng GD et al. Deminuibacter soli gen. nov., sp. nov., isolated from forest soil, and reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov. Int J Syst Evol Microbiol 2019; 69:1650–1655 [View Article]
     [Google Scholar]
  30. Bode HB, Ring MW, Schwär G, Kroppenstedt RM, Kaiser D et al. 3-Hydroxy-3-methylglutaryl-coenzyme A (CoA) synthase is involved in biosynthesis of isovaleryl-CoA in the myxobacterium Myxococcus xanthus during fruiting body formation. J Bacteriol 2006; 188:6524–6528 [View Article]
     [Google Scholar]
  31. Tindall B, Sikorski J, Smibert R, Krieg N. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Breznak JA, Marzluf G, Schmidt TM. eds Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 384–385
     [Google Scholar]
  32. 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]
  33. Wang JJ, Chen Q, Li YZ. Chryseolinea flava sp. nov., a new species of Chryseolinea isolated from soil. Int J Syst Evol Microbiol 2018; 68:3518–3522 [View Article]
     [Google Scholar]
  34. Goldberg SR, Correa H, Haltli BA, Kerr RG. Fulvivirga aurantia sp. nov. and Xanthovirga aplysinae gen. nov., sp. nov., marine bacteria isolated from the sponge Aplysina fistularis, and emended description of the genus Fulvivirga. Int J Syst Evol Microbiol 2020; 70:2766–2781 [View Article]
     [Google Scholar]
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Parachryseolinea silvisoli gen. nov., sp. nov., isolated from forest soil, and reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov.
Int J Syst Evol Microbiol 72, 005523 (2022); https://doi.org/10.1099/ijsem.0.005523
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