1887

Abstract

A novel species of Fe(III)-reducing bacterium, designated strain OSK6, belonging to the genus , was isolated from lotus field mud in Japan. Strain OSK6 was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, Gram-negative, motile, straight rod-shaped bacterium, 0.6–1.9 µm long and 0.2–0.4 µm wide. The growth of the isolate occurred at 20–40 °C with optima of 30–37 °C and pH 6.5–7.5 in the presence of up to 0.5 g NaCl l. The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7 and 16 : 0. Strain OSK6 was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6 is closely related to and with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6 is described as a representative of a novel species, sp. nov.; the type strain is OSK6 ( = DSM 24905 = JCM 17780).

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2013-02-01
2024-03-29
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References

  1. Akob D. M., Mills H. J., Gihring T. M., Kerkhof L., Stucki J. W., Anastácio A. S., Chin K. J., Küsel K., Palumbo A. V. & other authors ( 2008 ). Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide-contaminated subsurface sediments. . Appl Environ Microbiol 74, 31593170. [View Article] [PubMed]
    [Google Scholar]
  2. Anderson R. T., Rooney-Varga J. N., Gaw C. V., Lovley D. R. ( 1998 ). Anaerobic benzene oxidation in the Fe(III) reduction zone of petroleum-contaminated aquifers. . Environ Sci Technol 32, 12221229. [View Article]
    [Google Scholar]
  3. Anderson R. T., Vrionis H. A., Ortiz-Bernad I., Resch C. T., Long P. E., Dayvault R., Karp K., Marutzky S., Metzler D. R. & other authors ( 2003 ). Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. . Appl Environ Microbiol 69, 58845891. [View Article] [PubMed]
    [Google Scholar]
  4. Balderston W. L., Sherr B., Payne W. J. ( 1976 ). Blockage by acetylene of nitrous oxide reduction in Pseudomonas perfectomarinus . . Appl Environ Microbiol 31, 504508.[PubMed]
    [Google Scholar]
  5. Childers S. E., Ciufo S., Lovley D. R. ( 2002 ). Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. . Nature 416, 767769. [View Article] [PubMed]
    [Google Scholar]
  6. Coates J. D., Phillips E. J., Lonergan D. J., Jenter H., Lovley D. R. ( 1996 ). Isolation of Geobacter species from diverse sedimentary environments. . Appl Environ Microbiol 62, 15311536.[PubMed]
    [Google Scholar]
  7. De Wever H., Cole J. R., Fettig M. R., Hogan D. A., Tiedje J. M. ( 2000 ). Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov.. Appl Environ Microbiol 66, 22972301. [View Article] [PubMed]
    [Google Scholar]
  8. Finkmann W., Altendorf K., Stackebrandt E., Lipski A. ( 2000 ). Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov.. Int J Syst Evol Microbiol 50, 273282. [View Article] [PubMed]
    [Google Scholar]
  9. Guindon S., Gascuel O. ( 2003 ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol 52, 696704. [View Article] [PubMed]
    [Google Scholar]
  10. Hall B. G. ( 2008 ). Maximum likelihood. . In Phylogenetic Trees Made Easy: a How-to Manual, , 3rd edn., pp. 125141. Sunderland, MA:: Sinauer Associates;.
    [Google Scholar]
  11. Hedrick D. B., Peacock A. D., Lovley D. R., Woodard T. L., Nevin K. P., Long P. E., White D. C. ( 2009 ). Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor. . J Ind Microbiol Biotechnol 36, 205209. [View Article] [PubMed]
    [Google Scholar]
  12. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21132. Edited by Munro H. N. . NY:: Academic Press;.
    [Google Scholar]
  13. Kunapuli U., Jahn M. K., Lueders T., Geyer R., Heipieper H. J., Meckenstock R. U. ( 2010 ). Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons. . Int J Syst Evol Microbiol 60, 686695. [View Article] [PubMed]
    [Google Scholar]
  14. Lovley D. R. ( 2006 ). Dissimilatory Fe(III)- and Mn(IV)-reducing prokaryotes. . Prokaryotes 2, 635658. [View Article]
    [Google Scholar]
  15. Lovley D. R., Phillips E. J. P. ( 1986 ). Organic matter mineralization with reduction of ferric iron in anaerobic sediments. . Appl Environ Microbiol 51, 683689.[PubMed]
    [Google Scholar]
  16. Lovley D. R., Phillips E. J. P. ( 1988 ). Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. . Appl Environ Microbiol 54, 14721480.[PubMed]
    [Google Scholar]
  17. Lovley D. R., Giovannoni S. J., White D. C., Champine J. E., Phillips E. J. P., Gorby Y. A., Goodwin S. ( 1993 ). Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. . Arch Microbiol 159, 336344. [View Article] [PubMed]
    [Google Scholar]
  18. Lovley D. R., Coates J. D., Saffarini D., Lonergan D. J. ( 1997 ). Dissimilatory iron reduction. . In Transition Metals in Microbial Metabolism, pp. 187215. Edited by Winkelmann G., Carrano C. J. . Lausanne:: Harwood Academic;.
    [Google Scholar]
  19. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar A., Buchner A., Lai T., Steppi S. & other authors ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 13631371. [View Article] [PubMed]
    [Google Scholar]
  20. Luu Y.-S., Ramsay J. A. ( 2003 ). Review: microbial mechanisms of accessing insoluble Fe(III) as an energy source. . World J Microbiol Biotechnol 19, 215225. [View Article]
    [Google Scholar]
  21. Mahadevan R., Palsson B. O., Lovley D. R. ( 2011 ). In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. . Nat Rev Microbiol 9, 3950. [View Article] [PubMed]
    [Google Scholar]
  22. Nakamura K., Tamaki H., Kang M. S., Mochimaru H., Lee S. T., Nakamura K., Kamagata Y. ( 2011 ). A six-well plate method: less laborious and effective method for cultivation of obligate anaerobic microorganisms. . Microbes Environ 26, 301306. [View Article] [PubMed]
    [Google Scholar]
  23. Nevin K. P., Holmes D. E., Woodard T. L., Covalla S. F., Lovley D. R. ( 2007 ). Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.. Int J Syst Evol Microbiol 57, 463466. [View Article] [PubMed]
    [Google Scholar]
  24. Prakash O., Gihring T. M., Dalton D. D., Chin K.-J., Green S. J., Akob D. M., Wanger G., Kostka J. E. ( 2010 ). Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. . Int J Syst Evol Microbiol 60, 546553. [View Article] [PubMed]
    [Google Scholar]
  25. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., Glöckner F. O. ( 2007 ). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. . Nucleic Acids Res 35, 71887196. [View Article] [PubMed]
    [Google Scholar]
  26. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  27. Schwertmann U., Cornell R. M. ( 2000 ). 8.3 2-Line Ferrihydrite. . In Iron Oxides in the Laboratory, p. 105. Weinheim:: Wiley;. [View Article]
    [Google Scholar]
  28. Senko J. M., Stolz J. F. ( 2001 ). Evidence for iron-dependent nitrate respiration in the dissimilatory iron-reducing bacterium Geobacter metallireducens . . Appl Environ Microbiol 67, 37503752. [View Article] [PubMed]
    [Google Scholar]
  29. Shelobolina E. S., Nevin K. P., Blakeney-Hayward J. D., Johnsen C. V., Plaia T. W., Krader P., Woodard T., Holmes D. E., Vanpraagh C. G., Lovley D. R. ( 2007 ). Geobacter pickeringii sp. nov., Geobacter argillaceus sp. nov. and Pelosinus fermentans gen. nov., sp. nov., isolated from subsurface kaolin lenses. . Int J Syst Evol Microbiol 57, 126135. [View Article] [PubMed]
    [Google Scholar]
  30. Shelobolina E. S., Vrionis H. A., Findlay R. H., Lovley D. R. ( 2008 ). Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation. . Int J Syst Evol Microbiol 58, 10751078. [View Article] [PubMed]
    [Google Scholar]
  31. Sung Y., Fletcher K. E., Ritalahti K. M., Apkarian R. P., Ramos-Hernández N., Sanford R. A., Mesbah N. M., Löffler F. E. ( 2006 ). Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium. . Appl Environ Microbiol 72, 27752782. [View Article] [PubMed]
    [Google Scholar]
  32. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [Google Scholar]
  33. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  34. Weber K. A., Achenbach L. A., Coates J. D. ( 2006 ). Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. . Nat Rev Microbiol 4, 752764. [View Article] [PubMed]
    [Google Scholar]
  35. Yun J., Ueki T., Miletto M., Lovley D. R. ( 2011 ). Monitoring the metabolic status of Geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies. . Appl Environ Microbiol 77, 45974602. [View Article] [PubMed]
    [Google Scholar]
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