1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 5

sp. nov., a novel representative of the order isolated from temperate grassland soil Open Access

Abstract

Strain 0141_2 was isolated from a temperate grassland soil in Germany and was found to be affiliated with the order . It is most closely related to BR7-21, with 98.1 % 16S rRNA gene sequence similarity. Cells are rod-shaped, non-motile, stain Gram-positive and can have multiple vesicles in the cell surface. Polyhydroxybutyrate is accumulated within the cells. Catalase- and oxidase-positive. It is a mesophilic aerobe and grows best around neutral to slightly acidic pH in R2A medium. The major fatty acids are C 9, iso-C, C, C, C 7 and C 8. Diphosphatidylglycerol is present. The predominant respiratory quinone is MK-7(H). Meso-diaminopimelic acid is the diagnostic diamino acid in the cell-wall peptidoglycan. The G+C content of genomic DNA is 72.9 mol%. Based on the results of phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the novel species sp. nov. with the type strain 0141_2 (=DSM 104299=LMG 30000=CECT 9239).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Baekduia , high G+C content , polyhydroxybutyrate and soil bacterium
Funding
This study was supported by the:
  • Deutsche Forschungsgemeinschaft (Award OV 20/27)
    • Principle Award Recipient: JörgOvermann
  • Deutsche Forschungsgemeinschaft (Award OV 20/21-1)
    • Principle Award Recipient: JörgOvermann
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005918
2023-05-30
2024-05-01
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/73/5/ijsem005918.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005918&mimeType=html&fmt=ahah

References

  1. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608 [View Article] [PubMed]
     [Google Scholar]
  2. Reddy GSN, Garcia-Pichel F. Description of Patulibacter americanus sp. nov., isolated from biological soil crusts, emended description of the genus Patulibacter Takahashi et al. 2006 and proposal of Solirubrobacterales ord. nov. and Thermoleophilales ord. nov. Int J Syst Evol Microbiol 2009; 59:87–94 [View Article] [PubMed]
     [Google Scholar]
  3. Fischer M, Bossdorf O, Gockel S, Hänsel F, Hemp A et al. Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic Appl Ecol 2010; 11:473–485 [View Article]
     [Google Scholar]
  4. Solly EF, Schöning I, Boch S, Kandeler E, Marhan S et al. Factors controlling decomposition rates of fine root litter in temperate forests and grasslands. Plant Soil 2014; 382:203–218 [View Article]
     [Google Scholar]
  5. Vieira S, Pascual J, Boedeker C, Geppert A, Riedel T et al. Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil. Int J Syst Evol Microbiol 2020; 70:4966–4977 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. An D-S, Siddiqi MZ, Kim K-H, Yu H-S, Im W-T. Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu mountain and proposal of a novel family name, Baekduiaceae fam. nov. J Microbiol 2018; 56:24–29 [View Article] [PubMed]
     [Google Scholar]
  8. Vieira S, Huber KJ, Geppert A, Wolf J, Neumann-Schaal M et al. Capillimicrobium parvum gen. nov., sp. nov., a novel representative of Capillimicrobiaceae fam. nov. within the order Solirubrobacterales, isolated from a grassland soil. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  9. Gerhardt P. Methods for General and Molecular Bacteriology Washington, D.C: American Society for Microbiology; 1994
     [Google Scholar]
  10. Bast E. Mikrobiologische Methoden. 3rd edn Springer Spektrum; 2014
     [Google Scholar]
  11. Ostle AG, Holt JG. Nile blue A as a fluorescent stain for poly-beta-hydroxybutyrate. Appl Environ Microbiol 1982; 44:238–241 [View Article] [PubMed]
     [Google Scholar]
  12. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria. 3rd Edition Cambridge University Press; 1993 [View Article]
     [Google Scholar]
  13. Huber KJ, Wüst PK, Rohde M, Overmann J, Foesel BU. Aridibacter famidurans gen nov. sp. nov and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil. Int J Syst Evol Microbiol 2014; 64:1866–1875 [View Article]
     [Google Scholar]
  14. Pascual J, Wüst PK, Geppert A, Foesel BU, Huber KJ et al. Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 2015; 38:534–544 [View Article] [PubMed]
     [Google Scholar]
  15. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 2001
     [Google Scholar]
  16. Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M et al. Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  17. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 330–393 [View Article]
     [Google Scholar]
  18. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  19. Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D et al. Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., nov, with an emended description of the genus Ruania, recognition tha. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  20. Schumann P. Peptidoglycan structure. In Methods in Microbiology 2011 pp 101–129 [PubMed]
     [Google Scholar]
  21. Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 1999; 46:327–338 [View Article] [PubMed]
     [Google Scholar]
  22. Lane D. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Wiley; 1991 pp 115–175
     [Google Scholar]
  23. Chun S-J, Cui Y, Jin C, Cho AR, Wong S-K et al. Paraconexibacter algicola gen. nov., sp. nov., a novel actinobacterium isolated from a eutrophic lake during the end of cyanobacterial harmful algal blooms, and proposal of Paraconexibacteraceae fam. nov. in the order Solirubrobacterales. Int J Syst Evol Microbiol 2020; 70:915–922 [View Article]
     [Google Scholar]
  24. Davis KER, Joseph SJ, Janssen PH. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 2005; 71:826–834 [View Article]
     [Google Scholar]
  25. 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]
     [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  27. Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 2010; 26:589–595 [View Article] [PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [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. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  31. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  33. 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]
  34. 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]
  35. 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]
  36. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article] [PubMed]
     [Google Scholar]
  37. Watzer B, Forchhammer K. Cyanophycin: s nitrogen-rich reserve polymer. In Tiwari A. eds Cyanobacteria. IntechOpen pp 85–107 [View Article]
     [Google Scholar]
  38. Kim CS, Liu Z, Peng X, Qin K, Huang J et al. Paraconexibacter antarcticus sp. nov., a novel actinobacterium isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  39. Monciardini P, Cavaletti L, Schumann P, Rohde M, Donadio S. Conexibacter woesei gen nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria. Int J Syst Evol Microbiol 2003; 53:569–576 [View Article]
     [Google Scholar]
  40. Seki T, Matsumoto A, Shimada R, Inahashi Y, Ōmura S et al. Conexibacter arvalis sp. nov., isolated from a cultivated field soil sample. Int J Syst Evol Microbiol 2012; 62:2400–2404 [View Article] [PubMed]
     [Google Scholar]
  41. Lee SD. Conexibacter stalactiti sp. nov., isolated from stalactites in a lava cave and emended description of the genus Conexibacter. Int J Syst Evol Microbiol 2017; 67:3214–3218 [View Article] [PubMed]
     [Google Scholar]
  42. Foesel BU, Geppert A, Rohde M, Overmann J. Parviterribacter kavangonensis gen nov. sp. nov and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families. Int J Syst Evol Microbiol 2016; 66:652–665 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005918
Loading
Baekduia alba sp. nov., a novel representative of the order Solirubrobacterales isolated from temperate grassland soil
Int J Syst Evol Microbiol 73, 005918 (2023); https://doi.org/10.1099/ijsem.0.005918
/content/journal/ijsem/10.1099/ijsem.0.005918
/content/journal/ijsem/10.1099/ijsem.0.005918
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