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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 9

sp. nov., a new member of isolated from soil in Norrbyskär island, Sweden No Access

Abstract

A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6, was classified in the family , class , and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with (98.20 % similarity) and (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69–81 % with the members of genera and . On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus with the designation 17-6 (=DSM 115342=CCM 9308).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene analysis , Chromobacteriaceae , Norrbyskär , novel species , Silvimonas , soil bacteria and whole genome sequencing
Funding
This study was supported by the:
  • Ministerstvo Školství, Mládeže a Tělovýchovy (Award LM2023055)
    • Principal Award Recipient: NotApplicable
  • Ministerstvo Obrany České Republiky (Award 907930101413)
    • Principal Award Recipient: NotApplicable
  • Grantová Agentura České Republiky (Award 20-00291S)
    • Principal Award Recipient: MichalStrejcek
© 2023 The Authors
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2023-09-28
2026-01-24

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References

  1. Adeolu M, Gupta RS. Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov. Antonie van Leeuwenhoek 2013; 104:1–24 [View Article] [PubMed]
     [Google Scholar]
  2. Bromberg N, Durán N. Violacein transformation by peroxidases and oxidases: implications on its biological properties. J Mol Catal B Enzym 2001; 11:463–467 [View Article]
     [Google Scholar]
  3. Yang H-C, Im W-T, An D-S, Park W-S, Kim IS et al. Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the “Betaproteobacteria.”. Int J Syst Evol Microbiol 2005; 55:2329–2332 [View Article] [PubMed]
     [Google Scholar]
  4. Muramatsu Y, Suzuki K-I, Nakagawa Y. Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan. Int J Syst Evol Microbiol 2010; 60:174–178 [View Article] [PubMed]
     [Google Scholar]
  5. 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]
  6. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
     [Google Scholar]
  7. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
     [Google Scholar]
  8. Uhlik O, Strejcek M, Junkova P, Sanda M, Hroudova M et al. Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil. Appl Environ Microbiol 2011; 77:6858–6866 [View Article] [PubMed]
     [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics Wiley; 1991 pp 115–175
     [Google Scholar]
  10. 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]
  11. Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics 2015; 16:322 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  14. Li H. Aligning sequence reads, clone sequences and assembly Contigs with BWA-MEM. arXiv preprint arXiv 201313033997
     [Google Scholar]
  15. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ et al. GenBank. Nucleic Acids Res 2013; 41:D36–D42 [View Article] [PubMed]
     [Google Scholar]
  18. Kim J, Na S-I, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
     [Google Scholar]
  19. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–W235 [View Article] [PubMed]
     [Google Scholar]
  20. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
     [Google Scholar]
  21. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  24. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
     [Google Scholar]
  26. Rezanka T, Petránková M, Cepák V, Pribyl P, Sigler K et al. Trachydiscus minutus, a new biotechnological source of eicosapentaenoic acid. Folia Microbiol 2010; 55:265–269 [View Article] [PubMed]
     [Google Scholar]
  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 Met 1984; 2:233–241 [View Article]
     [Google Scholar]
  28. Dyńska-Kukulska K, Ciesielski W, Zakrzewski R. The use of a new, modified Dittmer-Lester spray reagent for phospholipid determination by the TLC image analysis technique. Biomed Chromatogr 2013; 27:458–465 [View Article] [PubMed]
     [Google Scholar]
  29. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  30. Moß KS, Hartmann SC, Müller I, Fritz C, Krügener S et al. Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil. Int J Syst Evol Microbiol 2013; 63:98–103 [View Article] [PubMed]
     [Google Scholar]
  31. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  32. Bruce T, Martinez IB, Maia Neto O, Vicente ACP, Kruger RH et al. Bacterial community diversity in the Brazilian Atlantic forest soils. Microb Ecol 2010; 60:840–849 [View Article] [PubMed]
     [Google Scholar]
  33. Twizeyimana M, Hammer PE, Gachango E, Craig K, Espejo B et al. Diverse environmental bacteria displaying activity against Phakopsora pachyrhizi, the cause of soybean rust. Front Plant Sci 2023; 14:42 [View Article] [PubMed]
     [Google Scholar]
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Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden
Int J Syst Evol Microbiol 73, 006048 (2023); https://doi.org/10.1099/ijsem.0.006048
/content/journal/ijsem/10.1099/ijsem.0.006048
/content/journal/ijsem/10.1099/ijsem.0.006048
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