1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 4

sp. nov., from the acidic soil of a deciduous forest Free

Abstract

A bacterial strain designated strain SK-11 was isolated from the acidic soil of a deciduous forest in the Shirakami Mountains in Japan. Cells of strain SK-11 were aerobic, non-motile, Gram-stain-negative rods, 0.7–1.0 µm in width and 1.0–1.4 µm in length. The pH range for growth was between pH 4.0 and 5.5, with an optimum at pH 5.0. The temperature range for growth was between 10 and 35 °C, with an optimum at around 25–30 °C. Strain SK-11 utilized various carbohydrates as growth substrates as well as yeast extract and protein hydrolysates. The major cellular fatty acids (>10 % of total fatty acid contents) were iso-C (55.4 %), iso-C (16.7 %) and iso-Cω9c/10 methyl-hexadecanoic acid (17.7 %). The major respiratory quinone was MK-8. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and an unidentified polar lipid. The DNA G+C content of strain SK-11 was 56.9 %. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SK-11 belonged to the family within subdivision 1 of the phylum and the closest relatives of strain SK-11 were WH120 and KA1, with 16S rRNA gene sequence similarities of 96.6 and 96.5 %, respectively. On the basis of the evidence from our polyphasic study, we concluded that strain SK-11 represents a novel species of the genus , and propose the name sp. nov. The type strain of sp nov. is SK-11 (=DSM 100508=NBRC 111227).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acidobacteria and subdivision I
© 2017 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001688
2017-04-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/4/862.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001688&mimeType=html&fmt=ahah

References

  1. Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998; 180:4765–4774[PubMed]
     [Google Scholar]
  2. Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006; 72:1719–1728 [View Article][PubMed]
     [Google Scholar]
  3. Barns SM, Cain EC, Sommerville L, Kuske CR. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 2007; 73:3113–3116 [View Article][PubMed]
     [Google Scholar]
  4. George IF, Hartmann M, Liles MR, Agathos SN. Recovery of as-yet-uncultured soil Acidobacteria on dilute solid media. Appl Environ Microbiol 2011; 77:8184–8188 [View Article][PubMed]
     [Google Scholar]
  5. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 1989; 39:224–229 [View Article]
     [Google Scholar]
  6. Dianou D, Miyaki T, Asakawa S, Morii H, Nagaoka K et al. Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA–DNA hybridization among Methanoculleus species. Int J Syst Evol Microbiol 2001; 51:1663–1669 [View Article][PubMed]
     [Google Scholar]
  7. 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 [View Article]
     [Google Scholar]
  8. 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]
  9. Horino H, Ito M, Tonouchi A. Clostridium oryzae sp. nov., from soil of a Japanese rice field. Int J Syst Evol Microbiol 2015; 65:943–951 [View Article][PubMed]
     [Google Scholar]
  10. 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]
  11. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  13. 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[PubMed]
     [Google Scholar]
  14. 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]
  15. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  16. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  17. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article][PubMed]
     [Google Scholar]
  18. Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol 2016; 7:744 [View Article][PubMed]
     [Google Scholar]
  19. Kulichevskaya IS, Kostina LA, Valásková V, Rijpstra WI, Damsté JS et al. Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood. Int J Syst Evol Microbiol 2012; 62:1512–1520 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001688
Loading
Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest
Int J Syst Evol Microbiol 67, 862 (2017); https://doi.org/10.1099/ijsem.0.001688
/content/journal/ijsem/10.1099/ijsem.0.001688
/content/journal/ijsem/10.1099/ijsem.0.001688
Loading

Data & Media loading...

Supplements

Supplementary File 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