1887

Abstract

A moderately thermophilic, aerobic, stalked bacterium (strain MA2) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MA2 was most closely related to the genera , and (92–93 % similarity) within the class . Strain MA2 was a Gram-stain-negative and stalked dimorphic bacteria. The temperature range for growth was 16–48 °C (optimum growth at 42 °C). This strain required yeast extract and NaCl (>1 %, w/v) for growth, tolerated up to 11 % (w/v) NaCl, and was capable of utilizing various carbon sources. The major cellular fatty acid and major respiratory quinone were Cω7 and ubiquinone-10, respectively. The DNA G+C content was 60.7 mol%. Strain MA2 performed denitrification and produced NO from nitrate under strictly microaerobic conditions. Strain MA2 possessed periplasmic nitrate reductase (Nap) genes but not membrane-bound nitrate reductase (Nar) genes. On the basis of this morphological, physiological, biochemical and genetic information a novel genus and species, gen. nov., sp. nov., are proposed, with MA2 ( = NBRC 109643 = DSM 27167) as the type strain of the species.

Funding
This study was supported by the:
  • Ministry of Education, Culture, Sports, Science and Technology of Japan (Award 221S0002 and 225450265)
  • The University of Tokyo (Award 005, 2013)
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2015-06-01
2024-04-19
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References

  1. Albuquerque L., Rainey F. A., Pena A., Tiago I., Veríssimo A., Nobre M. F., da Costa M. S. ( 2010 ). Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria . . Syst Appl Microbiol 33, 6066. [View Article] [PubMed]
    [Google Scholar]
  2. Bazylinski D. A., Blakemore R. P. ( 1983 ). Denitrification and assimilatory nitrate reduction in Aquaspirillum magnetotacticum . . Appl Environ Microbiol 46, 11181124.[PubMed]
    [Google Scholar]
  3. Bell L. C., Richardson D. J., Ferguson S. J. ( 1990 ). Periplasmic and membrane-bound respiratory nitrate reductases in Thiosphaera pantotropha: the periplasmic enzyme catalyzes the first step in aerobic denitrification. . FEBS Lett 265, 8587. [View Article] [PubMed]
    [Google Scholar]
  4. Blakemore R. P., Maratea D., Wolfe R. S. ( 1979 ). Isolation and pure culture of a freshwater magnetic spirillum in chemically defined medium. . J Bacteriol 140, 720729.[PubMed]
    [Google Scholar]
  5. Bowman J. P. ( 2006 ). The methanotrophs—the families Methylococcaceae and Methylocystaceae . . In The Prokaryotes, vol. 5, pp. 266289. Edited by Dworkin M., Falkow S., Rosenberg E. . New York:: Springer;. [View Article]
    [Google Scholar]
  6. Brettar I., Christen R., Bötel J., Lünsdorf H., Höfle M. G. ( 2007 ). Anderseniella baltica gen. nov., sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea. . Int J Syst Evol Microbiol 57, 23992405. [View Article] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  8. Frette L., Gejlsbjerg B., Westermann P. ( 1997 ). Aerobic denitrifiers isolated from an alternating activated sludge system. . FEMS Microbiol Ecol 24, 363370. [View Article]
    [Google Scholar]
  9. Fukuda W., Yamada K., Miyoshi Y., Okuno H., Atomi H., Imanaka T. ( 2012 ). Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake. . Int J Syst Evol Microbiol 62, 19451950. [View Article] [PubMed]
    [Google Scholar]
  10. Hanada S., Takaichi S., Matsuura K., Nakamura K. ( 2002 ). Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. . Int J Syst Evol Microbiol 52, 187193.[PubMed] [CrossRef]
    [Google Scholar]
  11. Hiraishi A., Urata K., Satoh T. ( 1995 ). A new genus of marine budding phototrophic bacteria, Rhodobium gen. nov., which includes Rhodobium orientis sp. nov. and Rhodobium marinum comb. nov.. Int J Syst Bacteriol 45, 226234. [View Article] [PubMed]
    [Google Scholar]
  12. Ishibashi J.-I., Nakaseama M., Seguchi M., Yamashita T., Doi S., Sakamoto T., Shimada K., Shimada N., Noguchi T. et al. ( 2008 ). Marine shallow-water hydrothermal activity and mineralization at the Wakamiko Crater in Kagoshima Bay, South Kyushu, Japan. . J Volcanol Geotherm Res 173, 8498. [View Article]
    [Google Scholar]
  13. Kamagata Y., Mikami E. ( 1991 ). Isolation and characterization of a novel thermophilic Methanosaeta strain. . Int J Syst Evol Microbiol 41, 191196.
    [Google Scholar]
  14. Katsuyama C., Kondo N., Suwa Y., Yamagishi T., Itoh M., Ohte N., Kimura H., Nagaosa K., Kato K. ( 2008 ). Denitrification activity and relevant bacteria revealed by nitrite reductase gene fragments in soil of temperate mixed forest. . Microbes Environ 23, 337345. [View Article] [PubMed]
    [Google Scholar]
  15. Lai Q., Wang L., Liu Y., Yuan J., Sun F., Shao Z. ( 2011 ). Parvibaculum indicum sp. nov., isolated from deep-sea water. . Int J Syst Evol Microbiol 61, 271274. [View Article] [PubMed]
    [Google Scholar]
  16. Nevison C., Butler J. H., Elkins J. W. ( 2003 ). Global distribution of N2O and the AN2O-AOU yield in the subsurface ocean. . Global Biogeochem Cycles 17, 1119, 30-130-18. [View Article]
    [Google Scholar]
  17. Okada N., Nomura N., Nakajima-Kambe T., Uchiyama H. ( 2005 ). Characterization of the aerobic denitrification in Mesorhizobium sp. strain NH-14 in comparison with that in related rhizobia. . Microbes Environ 20, 208215. [View Article]
    [Google Scholar]
  18. Osborn A. M., Moore E. R., Timmis K. N. ( 2000 ). An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. . Environ Microbiol 2, 3950. [View Article] [PubMed]
    [Google Scholar]
  19. Patureau D., Godon J. J., Dabert P., Bouchez T., Bernet N., Delgenes J. P., Moletta R. ( 1998 ). Microvirgula aerodenitrificans gen. nov., sp. nov., a new gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions. . Int J Syst Bacteriol 48, 775782. [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Ravishankara A. R., Daniel J. S., Portmann R. W. ( 2009 ). Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. . Science 326, 123125. [View Article] [PubMed]
    [Google Scholar]
  22. Robertson L. A., Kuenen J. G. ( 1983 ). Thiosphaera pantotropha gen. nov., sp. nov., a facultatively anaerobic, facultatively autotrophic sulphur bacterium. . J Gen Microbiol 129, 28472855.
    [Google Scholar]
  23. Robertson L. A., Dalsgaard T., Revsbech N.-P., Kuenen J. G. ( 1995 ). Confirmation of ‘aerobic denitrification’ in batch cultures, using gas chromatography and 15N mass spectrometry. . FEMS Microbiol Ecol 18, 113120. [View Article]
    [Google Scholar]
  24. Rönner U., Sörensson F. ( 1985 ). Denitrification rates in the low-oxygen waters of the stratified baltic proper. . Appl Environ Microbiol 50, 801806.[PubMed]
    [Google Scholar]
  25. Rosario-Passapera R., Keddis R., Wong R., Lutz R. A., Starovoytov V., Vetriani C. ( 2012 ). Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise. . Int J Syst Evol Microbiol 62, 29212926. [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. Schleheck D., Tindall B. J., Rosselló-Mora R., Cook A. M. ( 2004 ). Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. . Int J Syst Evol Microbiol 54, 14891497. [View Article] [PubMed]
    [Google Scholar]
  28. Schloss P. D., Westcott S. L., Ryabin T., Hall J. R., Hartmann M., Hollister E. B., Lesniewski R. A., Oakley B. B., Parks D. H. et al. ( 2009 ). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. . Appl Environ Microbiol 75, 75377541. [View Article] [PubMed]
    [Google Scholar]
  29. Scholten E., Lukow T., Auling G., Kroppenstedt R. M., Rainey F. A., Diekmann H. ( 1999 ). Thauera mechernichensis sp. nov., an aerobic denitrifier from a leachate treatment plant. . Int J Syst Bacteriol 49, 10451051. [View Article] [PubMed]
    [Google Scholar]
  30. Sears H. J., Spiro S., Richardson D. J. ( 1997 ). Effect of carbon substrate and aeration on nitrate reduction and expression of the periplasmic and membrane-bound nitrate reductases in carbon-limited continuous cultures of Paracoccus denitrificans Pd1222. . Microbiology 143, 37673774. [View Article]
    [Google Scholar]
  31. Smith C. J., Nedwell D. B., Dong L. F., Osborn A. M. ( 2007 ). Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. . Appl Environ Microbiol 73, 36123622. [View Article] [PubMed]
    [Google Scholar]
  32. Srinivas T. N., Kumar P. A., Sasikala Ch., Ramana ChV., Imhoff J. F. ( 2007 ). Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern. . Int J Syst Evol Microbiol 57, 932935. [View Article] [PubMed]
    [Google Scholar]
  33. Stewart V., Lu Y., Darwin A. J. ( 2002 ). Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. . J Bacteriol 184, 13141323. [View Article] [PubMed]
    [Google Scholar]
  34. Takaya N., Catalan-Sakairi M. A. B., Sakaguchi Y., Kato I., Zhou Z., Shoun H. ( 2003 ). Aerobic denitrifying bacteria that produce low levels of nitrous oxide. . Appl Environ Microbiol 69, 31523157. [View Article] [PubMed]
    [Google Scholar]
  35. Takeuchi M., Yoshioka H., Seo Y., Tanabe S., Tamaki H., Kamagata Y., Takahashi H. A., Igari S., Mayumi D., Sakata S. ( 2011 ). A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan. . Environ Microbiol 13, 32063218. [View Article] [PubMed]
    [Google Scholar]
  36. Takeuchi M., Katayama T., Yamagishi T., Hanada S., Tamaki H., Kamagata Y., Oshima K., Hattori M., Marumo K. et al. ( 2014 a). Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent. . Int J Syst Evol Microbiol 64, 462468. [View Article] [PubMed]
    [Google Scholar]
  37. Takeuchi M., Kamagata Y., Oshima K., Hanada S., Tamaki H., Marumo K., Maeda H., Nedachi M., Hattori M. et al. ( 2014 b). Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum. . Int J Syst Evol Microbiol 64, 32403246. [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. Taoka A., Yoshimatsu K., Kanemori M., Fukumori Y. ( 2003 ). Nitrate reductase from the magnetotactic bacterium Magnetospirillum magnetotacticum MS-1: purification and sequence analyses. . Can J Microbiol 49, 197206. [View Article] [PubMed]
    [Google Scholar]
  40. Torres M. J., Rubia M. I., Bedmar E. J., Delgado M. J. ( 2011 ). Denitrification in Sinorhizobium meliloti . . Biochem Soc Trans 39, 18861889. [View Article] [PubMed]
    [Google Scholar]
  41. US EPA (2010). Methane and Nitrous Oxide Emissions from Natural Sources, US Environmental Protection Agency, Washington, DC, USA, available at: http://www.epa.gov/outreach/pdfs/Methane-and-Nitrous-Oxide-Emissions-From-Natural-Sources.pdf.
  42. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697703.[PubMed]
    [Google Scholar]
  43. Widdel F., Pfennig N. ( 1981 ). Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. . Arch Microbiol 129, 395400. [View Article] [PubMed]
    [Google Scholar]
  44. Yamanaka T., Maeto K., Akashi H., Ishibashi J.-I., Miyoshi Y., Okamura K., Noguchi T., Kuwahara Y., Toki T. et al. ( 2013 ). Shallow submarine hydrothermal activity with significant contribution of magmatic water producing talc chimneys in the Wakamiko Crater of Kagoshima Bay, southern Kyushu, Japan. . J Volcanol Geotherm Res 258, 7484. [View Article]
    [Google Scholar]
  45. Yoshinaga I., Amano T., Yamagishi T., Okada K., Ueda S., Sako Y., Suwa Y. ( 2011 ). Distribution and diversity of anaerobic ammonium oxidation (anammox) bacteria in the sediment of a eutrophic freshwater lake, Lake Kitaura, Japan. . Microbes Environ 26, 189197. [View Article] [PubMed]
    [Google Scholar]
  46. Yoshinari T. ( 1976 ). Nitrous oxide in the sea. . Mar Chem 4, 189202. [View Article]
    [Google Scholar]
  47. Zhang H., Hanada S., Shigematsu T., Shibuya K., Kamagata Y., Kanagawa T., Kurane R. ( 2000 ). Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. . Int J Syst Evol Microbiol 50, 743749. [View Article] [PubMed]
    [Google Scholar]
  48. Zheng H. Y., Liu Y., Gao X. Y., Ai G. M., Miao L. L., Liu Z. P. ( 2012 ). Characterization of a marine origin aerobic nitrifying-denitrifying bacterium. . J Biosci Bioeng 114, 3337. [View Article] [PubMed]
    [Google Scholar]
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