1887

Abstract

A neutrophilic, stalk-forming, iron-oxidizing bacterium, strain OYT1, which was isolated from a groundwater seep in Ohyato Park, Tokyo, Japan, was subjected to taxonomic analysis. OYT1 was a motile, bean-shaped, Gram-negative bacterium that was able to grow at 8–30 °C (optimally at 25–30 °C) and at pH 5.6–7.3 (optimally at pH 6.1–6.5). The strain grew microaerobically and autotrophically. Major cellular fatty acids detected were Cω7/Cω6 and C. The total DNA G+C content was 57.6 mol%. 16S rRNA gene sequence analysis revealed that strain OYT1 was affiliated with the class and clustered with iron-oxidizing bacteria isolated from groundwater seeps and wetlands and with uncultured clones detected in freshwater iron-rich environments. Based on the phenotypic and phylogenetic characteristics of strain OYT1, we propose that the strain represents a novel species in a new genus, for which the name gen. nov., sp. nov. is proposed; the type strain of is OYT1 ( = JCM 18545 = DSM 26810).

Funding
This study was supported by the:
  • RIKEN Special Postdoctoral Researchers’ Program
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/content/journal/ijsem/10.1099/ijs.0.058487-0
2014-03-01
2024-03-29
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References

  1. Castresana J. ( 2000 ). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. . Mol Biol Evol 17, 540552. [View Article] [PubMed]
    [Google Scholar]
  2. Chan C. S., Fakra S. C., Edwards D. C., Emerson D., Banfield J. F. ( 2009 ). Iron oxyhydroxide mineralization on microbial extracellular polysaccharides. . Geochim Cosmochim Acta 73, 38073818. [View Article]
    [Google Scholar]
  3. Chan C. S., Fakra S. C., Emerson D., Fleming E. J., Edwards K. J. ( 2011 ). Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation. . ISME J 5, 717727. [View Article] [PubMed]
    [Google Scholar]
  4. Duckworth O. W., Holmström S. J. M., Peña J., Sposito G. ( 2009 ). Biogeochemistry of iron oxidation in a circumneutral freshwater habitat. . Chem Geol 260, 149158. [View Article]
    [Google Scholar]
  5. Edgar R. C. ( 2004 ). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32, 17921797. [View Article] [PubMed]
    [Google Scholar]
  6. Ehrenberg C. G. ( 1836 ). Vorläufige Mittheilungen über das wirkliche Vorkommen fossiler Infusorien und ihre grosse Verbreitung. . Ann Phys 114, 213227 (in German). [View Article]
    [Google Scholar]
  7. Emerson D., Merrill Floyd M. ( 2005 ). Enrichment and isolation of iron-oxidizing bacteria at neutral pH. . Methods Enzymol 397, 112123. [View Article] [PubMed]
    [Google Scholar]
  8. Emerson D., Moyer C. ( 1997 ). Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. . Appl Environ Microbiol 63, 47844792. [PubMed]
    [Google Scholar]
  9. Emerson D., Moyer C. L. ( 2002 ). Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. . Appl Environ Microbiol 68, 30853093. [View Article] [PubMed]
    [Google Scholar]
  10. Emerson D., Revsbech N. P. ( 1994 ). Investigation of an iron-oxidizing microbial mat community located near Aarhus, Denmark: field studies. . Appl Environ Microbiol 60, 40224031. [PubMed]
    [Google Scholar]
  11. Emerson D., Rentz J. A., Lilburn T. G., Davis R. E., Aldrich H., Chan C., Moyer C. L. ( 2007 ). A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. . PLoS ONE 2, e667. [View Article] [PubMed]
    [Google Scholar]
  12. Emerson D., Fleming E. J., McBeth J. M. ( 2010 ). Iron-oxidizing bacteria: an environmental and genomic perspective. . Annu Rev Microbiol 64, 561583. [View Article] [PubMed]
    [Google Scholar]
  13. Emerson D., Field E. K., Chertkov O., Davenport K. W., Goodwin L., Munk C., Nolan M., Woyke T. ( 2013 ). Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics. . Front Microbiol 4, 254. [View Article] [PubMed]
    [Google Scholar]
  14. Guindon S., Dufayard J. F., Lefort V., Anisimova M., Hordijk W., Gascuel O. ( 2010 ). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. . Syst Biol 59, 307321. [View Article] [PubMed]
    [Google Scholar]
  15. Hallbeck L., Pedersen K. ( 1990 ). Culture parameters regulating stalk formation and growth rate of Gallionella ferruginea . . J Gen Microbiol 136, 16751680. [View Article]
    [Google Scholar]
  16. Hallbeck L., Pedersen K. ( 1991 ). Autotrophic and mixotrophic growth of Gallionella ferruginea . . J Gen Microbiol 137, 26572661. [View Article]
    [Google Scholar]
  17. Hallbeck L., Ståhl F., Pedersen K. ( 1993 ). Phylogeny and phenotypic characterization of the stalk-forming and iron-oxidizing bacterium Gallionella ferruginea . . J Gen Microbiol 139, 15311535. [View Article] [PubMed]
    [Google Scholar]
  18. Kato S., Kobayashi C., Kakegawa T., Yamagishi A. ( 2009 ). Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. . Environ Microbiol 11, 20942111. [View Article] [PubMed]
    [Google Scholar]
  19. Kato S., Chan C., Itoh T., Ohkuma M. ( 2013 ). Functional gene analysis of freshwater iron-rich flocs at circumneutral pH and isolation of a stalk-forming microaerophilic iron-oxidizing bacterium. . Appl Environ Microbiol 79, 52835290. [View Article] [PubMed]
    [Google Scholar]
  20. Kostka J. E., Luther G. W. III ( 1994 ). Partitioning and speciation of solid phase iron in saltmarsh sediments. . Geochim Cosmochim Acta 58, 17011710. [View Article]
    [Google Scholar]
  21. Krepski S. T., Hanson T. E., Chan C. S. ( 2012 ). Isolation and characterization of a novel biomineral stalk-forming iron-oxidizing bacterium from a circumneutral groundwater seep. . Environ Microbiol 14, 16711680. [View Article] [PubMed]
    [Google Scholar]
  22. Kucera S., Wolfe R. S. ( 1957 ). A selective enrichment method for Gallionella ferruginea . . J Bacteriol 74, 344349. [PubMed]
    [Google Scholar]
  23. Lüdecke C., Reiche M., Eusterhues K., Nietzsche S., Küsel K. ( 2010 ). Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen. . Environ Microbiol 12, 28142825. [PubMed]
    [Google Scholar]
  24. Tamaoka J. ( 1994 ). Determination of DNA base composition. . In Chemical Methods in Prokaryotic Systematics, pp. 463470. Edited by Goodfellow M., O’Donnell A. G. . Chichester:: Wiley;.
    [Google Scholar]
  25. Vatter A. E., Wolfe R. S. ( 1956 ). Electron microscopy of Gallionella ferruginea . . J Bacteriol 72, 248252. [PubMed]
    [Google Scholar]
  26. Weiss J. V., Rentz J. A., Plaia T., Neubauer S. C., Merrill-Floyd M., Lilburn T., Bradburne C., Megonigal J. P., Emerson D. ( 2007 ). Characterization of neutrophilic Fe(II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov.. Geomicrobiol J 24, 559570. [View Article]
    [Google Scholar]
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