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).

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2014-03-01
2019-10-20
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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:, 540–552. [CrossRef][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:, 3807–3818. [CrossRef]
    [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:, 717–727. [CrossRef][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:, 149–158. [CrossRef]
    [Google Scholar]
  5. Edgar R. C.. ( 2004;). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32:, 1792–1797. [CrossRef][PubMed]
    [Google Scholar]
  6. Ehrenberg C. G.. ( 1836;). Vorläufige Mittheilungen über das wirkliche Vorkommen fossiler Infusorien und ihre grosse Verbreitung. . Ann Phys 114:, 213–227 (in German). [CrossRef]
    [Google Scholar]
  7. Emerson D., Merrill Floyd M.. ( 2005;). Enrichment and isolation of iron-oxidizing bacteria at neutral pH. . Methods Enzymol 397:, 112–123. [CrossRef][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:, 4784–4792.[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:, 3085–3093. [CrossRef][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:, 4022–4031.[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. [CrossRef][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:, 561–583. [CrossRef][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. [CrossRef][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:, 307–321. [CrossRef][PubMed]
    [Google Scholar]
  15. Hallbeck L., Pedersen K.. ( 1990;). Culture parameters regulating stalk formation and growth rate of Gallionella ferruginea. . J Gen Microbiol 136:, 1675–1680. [CrossRef]
    [Google Scholar]
  16. Hallbeck L., Pedersen K.. ( 1991;). Autotrophic and mixotrophic growth of Gallionella ferruginea. . J Gen Microbiol 137:, 2657–2661. [CrossRef]
    [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:, 1531–1535. [CrossRef][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:, 2094–2111. [CrossRef][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:, 5283–5290. [CrossRef][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:, 1701–1710. [CrossRef]
    [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:, 1671–1680. [CrossRef][PubMed]
    [Google Scholar]
  22. Kucera S., Wolfe R. S.. ( 1957;). A selective enrichment method for Gallionella ferruginea. . J Bacteriol 74:, 344–349.[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:, 2814–2825.[PubMed]
    [Google Scholar]
  24. Tamaoka J.. ( 1994;). Determination of DNA base composition. . In Chemical Methods in Prokaryotic Systematics, pp. 463–470. 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:, 248–252.[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:, 559–570. [CrossRef]
    [Google Scholar]
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