1887

Abstract

An aerobic bacterial strain designated AX-7 was isolated from the trunk surface of a Japanese beech (Fagus crenata). Cells of strain AX-7 were Gram-stain-negative, non-spore-forming, non-motile rods (1.0–1.2 µm in width and 1.2–3.0 µm in length) with peritrichous fimbriae. Cells were capsulated, and a number of them were surrounded by a thick slime layer. During growth, large aggregates formed, and the culture medium became viscous probably owing to exopolysaccharide release from the slime layer. The temperature range for growth was 10–37 °C, with an optimum at 30 °C. The pH range for growth was 5.0–7.0, with an optimum at pH 6.0. Strain AX-7 used various sugars, including polysaccharides, and yeast extract as growth substrates. Strain AX-7 contained menaquinones MK-9 and MK-10 as the respiratory quinones, and C16 : 1ω5c, C16 : 1ω11c, C16 : 0 and C14 : 0 as the major cellular fatty acids. Four unidentified phospholipids and 11 unidentified polar lipids constituted the polar lipids. The DNA G+C content was 61.0 mol%. The cell-wall peptidoglycan contained ll-diaminopimelic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AX-7 belonged to the class Armatimonadia , its closest relative being Armatimonas rosea YO-36, with sequence similarity of 88.1%. Based on data from this polyphasic study, we propose that strain AX-7 represents a new genus of a novel species within the novel order Capsulimonadales ord. nov. of the class Armatimonadia , for which the name Capsulimonas corticalis gen. nov., sp. nov. is proposed. The type strain of C. corticalis is AX-7 (=DSM 105890=NBRC 113044).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003135
2018-11-26
2020-01-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/1/220.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003135&mimeType=html&fmt=ahah

References

  1. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998;180:366–376[PubMed]
    [Google Scholar]
  2. Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng XY et al. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int J Syst Evol Microbiol 2011;61:1442–1447 [CrossRef][PubMed]
    [Google Scholar]
  3. Parte AC. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42:D613–D616 [CrossRef][PubMed]
    [Google Scholar]
  4. Lee KCY, Dunfield PF, Morgan XC, Crowe MA, Houghton KM et al. Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int J Syst Evol Microbiol 2011;61:2482–2490 [CrossRef][PubMed]
    [Google Scholar]
  5. Im WT, Hu ZY, Kim KH, Rhee SK, Meng H et al. Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes. Antonie van Leeuwenhoek 2012;102:307–317 [CrossRef][PubMed]
    [Google Scholar]
  6. Dunfield PF, Tamas I, Lee KC, Morgan XC, Mcdonald IR et al. Electing a candidate: a speculative history of the bacterial phylum OP10. Environ Microbiol 2012;14:3069–3080 [CrossRef][PubMed]
    [Google Scholar]
  7. Lee KCY, Herbold CW, Dunfield PF, Morgan XC, Mcdonald IR et al. Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions. Appl Environ Microbiol 2013;79:2484–2487 [CrossRef][PubMed]
    [Google Scholar]
  8. Wilhelm RC, Cardenas E, Leung H, Szeitz A, Jensen LD et al. Long-term enrichment of stress-tolerant cellulolytic soil populations following timber harvesting evidenced by multi-omic stable Isotope Probing. Front Microbiol 2017;8:537 [CrossRef][PubMed]
    [Google Scholar]
  9. Lee KCY, Dunfield PF, Stott MB. The Phylum Armatimonadetes. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes: Other major lineages of bacteria and the Archaea Berlin, Heidelberg: Springer Berlin Heidelberg; 2014; pp.447–458
    [Google Scholar]
  10. Li J, Kudo C, Tonouchi A. Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree. Arch Microbiol 2018;200:291–297 [CrossRef][PubMed]
    [Google Scholar]
  11. Matsuo H, Kudo C, Li J, Tonouchi A. Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest. Int J Syst Evol Microbiol 2017;67:862–867 [CrossRef][PubMed]
    [Google Scholar]
  12. Tonouchi A, Tazawa D, Fujita T. Paenibacillus shirakamiensis sp. nov., isolated from the trunk surface of a Japanese oak (Quercus crispula). Int J Syst Evol Microbiol 2014;64:1763–1769 [CrossRef][PubMed]
    [Google Scholar]
  13. Eichorst SA, Kuske CR, Schmidt TM. Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. Appl Environ Microbiol 2011;77:586–596 [CrossRef][PubMed]
    [Google Scholar]
  14. Yamaguchi M, Okada H, Namiki Y. Smart specimen preparation for freeze substitution and serial ultrathin sectioning of yeast cells. J Electron Microsc 2009;58:261–266 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef]
    [Google Scholar]
  16. da Costa MS, Albuquerque L, Nobre MF, Wait R. The Identification of Polar Lipids in Prokaryotes. In Rainey F, Oren A. (editors) Methods in Microbiology London U. K.: Academic Press; 2011; pp.165–181
    [Google Scholar]
  17. Nishijima M, Araki-Sakai M, Sano H. Identification of isoprenoid quinones by frit-FAB liquid chromatography–mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 1997;28:113–122 [CrossRef]
    [Google Scholar]
  18. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988;19:161–207
    [Google Scholar]
  19. Wilson K. Preparation of genomic DNA from bacteria. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG. et al. (editors) Current Protocols in Molecular Biology Hoboken, NJ: John Wiley & Sons, Inc; 1997; pp.2.4.1–2.4.2
    [Google Scholar]
  20. Lane DJ. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, NY: John Wiley & Sons, Inc; 1991; pp.115–175
    [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 [CrossRef][PubMed]
    [Google Scholar]
  22. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009;75:7537–7541 [CrossRef][PubMed]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis Version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  24. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 [CrossRef][PubMed]
    [Google Scholar]
  28. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512–526 [CrossRef][PubMed]
    [Google Scholar]
  29. Gu X, Fu YX, Li WH. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 1995;12:546–557 [CrossRef][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  31. Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R et al. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 2001;67:1874–1884 [CrossRef][PubMed]
    [Google Scholar]
  32. Yoon SH, Ha SM, 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 [CrossRef][PubMed]
    [Google Scholar]
  33. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000;28:33–36 [CrossRef][PubMed]
    [Google Scholar]
  34. 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 [CrossRef][PubMed]
    [Google Scholar]
  35. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene ontology: tool for the unification of biology. Nat Genet 2000;25:25–29 [CrossRef][PubMed]
    [Google Scholar]
  36. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002;18:77–82 [CrossRef][PubMed]
    [Google Scholar]
  37. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003135
Loading
/content/journal/ijsem/10.1099/ijsem.0.003135
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

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